@article {pmid37262156, year = {2023}, author = {Gao, H and Hamp, T and Ede, J and Schraiber, JG and McRae, J and Singer-Berk, M and Yang, Y and Dietrich, ASD and Fiziev, PP and Kuderna, LFK and Sundaram, L and Wu, Y and Adhikari, A and Field, Y and Chen, C and Batzoglou, S and Aguet, F and Lemire, G and Reimers, R and Balick, D and Janiak, MC and Kuhlwilm, M and Orkin, JD and Manu, S and Valenzuela, A and Bergman, J and Rousselle, M and Silva, FE and Agueda, L and Blanc, J and Gut, M and de Vries, D and Goodhead, I and Harris, RA and Raveendran, M and Jensen, A and Chuma, IS and Horvath, JE and Hvilsom, C and Juan, D and Frandsen, P and de Melo, FR and Bertuol, F and Byrne, H and Sampaio, I and Farias, I and do Amaral, JV and Messias, M and da Silva, MNF and Trivedi, M and Rossi, R and Hrbek, T and Andriaholinirina, N and Rabarivola, CJ and Zaramody, A and Jolly, CJ and Phillips-Conroy, J and Wilkerson, G and Abee, C and Simmons, JH and Fernandez-Duque, E and Kanthaswamy, S and Shiferaw, F and Wu, D and Zhou, L and Shao, Y and Zhang, G and Keyyu, JD and Knauf, S and Le, MD and Lizano, E and Merker, S and Navarro, A and Bataillon, T and Nadler, T and Khor, CC and Lee, J and Tan, P and Lim, WK and Kitchener, AC and Zinner, D and Gut, I and Melin, A and Guschanski, K and Schierup, MH and Beck, RMD and Umapathy, G and Roos, C and Boubli, JP and Lek, M and Sunyaev, S and O'Donnell-Luria, A and Rehm, HL and Xu, J and Rogers, J and Marques-Bonet, T and Farh, KK}, title = {The landscape of tolerated genetic variation in humans and primates.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6648}, pages = {eabn8153}, doi = {10.1126/science.abn8197}, pmid = {37262156}, issn = {1095-9203}, abstract = {Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.}, } @article {pmid37258861, year = {2023}, author = {Abdelsalam, NA and Elshora, H and El-Hadidi, M}, title = {Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {133-174}, pmid = {37258861}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Ecology ; Computational Biology/methods ; Data Analysis ; }, abstract = {Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers' main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.}, } @article {pmid37258857, year = {2023}, author = {Wang, D}, title = {Metagenomics Databases for Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {55-67}, pmid = {37258857}, issn = {1940-6029}, mesh = {Phylogeny ; *Metagenomics ; Bacteria/genetics ; Databases, Genetic ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).}, } @article {pmid37255989, year = {2023}, author = {Pauley, E and Drake, TM and Griffith, DM and Sigfrid, L and Lone, NI and Harrison, EM and Baillie, JK and Scott, JT and Walsh, TS and Semple, MG and Docherty, AB and , }, title = {Recovery from Covid-19 critical illness: A secondary analysis of the ISARIC4C CCP-UK cohort study and the RECOVER trial.}, journal = {Journal of the Intensive Care Society}, volume = {24}, number = {2}, pages = {162-169}, pmid = {37255989}, issn = {1751-1437}, abstract = {BACKGROUND: We aimed to compare the prevalence and severity of fatigue in survivors of Covid-19 versus non-Covid-19 critical illness, and to explore potential associations between baseline characteristics and worse recovery.

METHODS: We conducted a secondary analysis of two prospectively collected datasets. The population included was 92 patients who received invasive mechanical ventilation (IMV) with Covid-19, and 240 patients who received IMV with non-Covid-19 illness before the pandemic. Follow-up data were collected post-hospital discharge using self-reported questionnaires. The main outcome measures were self-reported fatigue severity and the prevalence of severe fatigue (severity >7/10) 3 and 12-months post-hospital discharge.

RESULTS: Covid-19 IMV-patients were significantly younger with less prior comorbidity, and more males, than pre-pandemic IMV-patients. At 3-months, the prevalence (38.9% [7/18] vs. 27.1% [51/188]) and severity (median 5.5/10 vs 5.0/10) of fatigue were similar between the Covid-19 and pre-pandemic populations, respectively. At 6-months, the prevalence (10.3% [3/29] vs. 32.5% [54/166]) and severity (median 2.0/10 vs. 5.7/10) of fatigue were less in the Covid-19 cohort. In the total sample of IMV-patients included (i.e. all Covid-19 and pre-pandemic patients), having Covid-19 was significantly associated with less severe fatigue (severity <7/10) after adjusting for age, sex and prior comorbidity (adjusted OR 0.35 (95%CI 0.15-0.76, p=0.01).

CONCLUSION: Fatigue may be less severe after Covid-19 than after other critical illness.}, } @article {pmid37253577, year = {2023}, author = {Lee, K and McMorris, BJ and Chi, CL and Looman, WS and Burns, MK and Delaney, CW}, title = {Using data-driven analytics and ecological systems theory to identify risk and protective factors for school absenteeism among secondary students.}, journal = {Journal of school psychology}, volume = {98}, number = {}, pages = {148-180}, doi = {10.1016/j.jsp.2023.03.002}, pmid = {37253577}, issn = {1873-3506}, mesh = {Adolescent ; Humans ; Protective Factors ; *Absenteeism ; *Students ; Schools ; Forecasting ; }, abstract = {Chronic absenteeism is an administrative term defining extreme failure for students to be present at school, which can have devastating long-term impacts on students. Although numerous prior studies have investigated associated variables and interventions, there are few studies that utilize both theory-driven and data-informed approaches to investigate absenteeism. The current study applied data-driven machine learning techniques, grounded in "The Kids and Teens at School" (KiTeS) theoretical framework, to student-level data (N = 121,005) to identify risk and protective variables that are highly associated with school absences. A total of 18 risk and protective variables were identified; all 18 variables were characteristics of the microsystem or mesosystem, emphasizing school absences' proximity to variables within inner ecological systems rather than the exosystem or macrosystem. Implications for future studies and health infrastructure are discussed.}, } @article {pmid37253238, year = {2023}, author = {Borg, JM and Buskell, A and Kapitany, R and Powers, ST and Reindl, E and Tennie, C}, title = {Evolved Open-Endedness in Cultural Evolution: A New Dimension in Open-Ended Evolution Research.}, journal = {Artificial life}, volume = {}, number = {}, pages = {1-22}, doi = {10.1162/artl_a_00406}, pmid = {37253238}, issn = {1530-9185}, abstract = {The goal of Artificial Life research, as articulated by Chris Langton, is "to contribute to theoretical biology by locating life-as-we-know-it within the larger picture of life-as-it-could-be." The study and pursuit of open-ended evolution in artificial evolutionary systems exemplify this goal. However, open-ended evolution research is hampered by two fundamental issues: the struggle to replicate open-endedness in an artificial evolutionary system and our assumption that we only have one system (genetic evolution) from which to draw inspiration. We argue not only that cultural evolution should be seen as another real-world example of an open-ended evolutionary system but that the unique qualities seen in cultural evolution provide us with a new perspective from which we can assess the fundamental properties of, and ask new questions about, open-ended evolutionary systems, especially with regard to evolved open-endedness and transitions from bounded to unbounded evolution. Here we provide an overview of culture as an evolutionary system, highlight the interesting case of human cultural evolution as an open-ended evolutionary system, and contextualize cultural evolution by developing a new framework of (evolved) open-ended evolution. We go on to provide a set of new questions that can be asked once we consider cultural evolution within the framework of open-ended evolution and introduce new insights that we may be able to gain about evolved open-endedness as a result of asking these questions.}, } @article {pmid37252922, year = {2023}, author = {Hassard, F and Vu, M and Rahimzadeh, S and Castro-Gutierrez, V and Stanton, I and Burczynska, B and Wildeboer, D and Baio, G and Brown, MR and Garelick, H and Hofman, J and Kasprzyk-Hordern, B and Majeed, A and Priest, S and Denise, H and Khalifa, M and Bassano, I and Wade, MJ and Grimsley, J and Lundy, L and Singer, AC and Di Cesare, M}, title = {Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286259}, pmid = {37252922}, issn = {1932-6203}, abstract = {BACKGROUND: Schools are high-risk settings for infectious disease transmission. Wastewater monitoring for infectious diseases has been used to identify and mitigate outbreaks in many near-source settings during the COVID-19 pandemic, including universities and hospitals but less is known about the technology when applied for school health protection. This study aimed to implement a wastewater surveillance system to detect SARS-CoV-2 and other public health markers from wastewater in schools in England.

METHODS: A total of 855 wastewater samples were collected from 16 schools (10 primary, 5 secondary and 1 post-16 and further education) over 10 months of school term time. Wastewater was analysed for SARS-CoV-2 genomic copies of N1 and E genes by RT-qPCR. A subset of wastewater samples was sent for genomic sequencing, enabling determination of the presence of SARS-CoV-2 and emergence of variant(s) contributing to COVID-19 infections within schools. In total, >280 microbial pathogens and >1200 AMR genes were screened using RT-qPCR and metagenomics to consider the utility of these additional targets to further inform on health threats within the schools.

RESULTS: We report on wastewater-based surveillance for COVID-19 within English primary, secondary and further education schools over a full academic year (October 2020 to July 2021). The highest positivity rate (80.4%) was observed in the week commencing 30th November 2020 during the emergence of the Alpha variant, indicating most schools contained people who were shedding the virus. There was high SARS-CoV-2 amplicon concentration (up to 9.2x106 GC/L) detected over the summer term (8th June - 6th July 2021) during Delta variant prevalence. The summer increase of SARS-CoV-2 in school wastewater was reflected in age-specific clinical COVID-19 cases. Alpha variant and Delta variant were identified in the wastewater by sequencing of samples collected from December to March and June to July, respectively. Lead/lag analysis between SARS-CoV-2 concentrations in school and WWTP data sets show a maximum correlation between the two-time series when school data are lagged by two weeks. Furthermore, wastewater sample enrichment coupled with metagenomic sequencing and rapid informatics enabled the detection of other clinically relevant viral and bacterial pathogens and AMR.

CONCLUSIONS: Passive wastewater monitoring surveillance in schools can identify cases of COVID-19. Samples can be sequenced to monitor for emerging and current variants of concern at the resolution of school catchments. Wastewater based monitoring for SARS-CoV-2 is a useful tool for SARS-CoV-2 passive surveillance and could be applied for case identification and containment, and mitigation in schools and other congregate settings with high risks of transmission. Wastewater monitoring enables public health authorities to develop targeted prevention and education programmes for hygiene measures within undertested communities across a broad range of use cases.}, } @article {pmid37247155, year = {2023}, author = {Wang, Y and Lin, C and Wang, H and Wang, W and Wang, S and Zheng, R}, title = {Implementation of pollution source assessment and treatment strategy for plateau railway construction in China: an AHP-cloud model approach.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {6}, pages = {749}, pmid = {37247155}, issn = {1573-2959}, mesh = {*Analytic Hierarchy Process ; *Sewage ; Environmental Monitoring ; Environmental Pollution ; China ; }, abstract = {During the construction process of railways in the plateau region, various types of pollution sources can have serious or even irreversible impacts on the plateau ecology. To address pollution source treatment during the construction process, protect the ecological environment along the railway, and maintain the ecological balance, we collected geological and environmental data and analyzed the influencing factors of pollution sources. Taking sewage as the main research subject, we propose a new method based on the Analytic Hierarchy Process (AHP)-cloud model to classify the pollution source treatment level, establish an index system, and select the ecological environment level, sewage rate, and pollutant characteristics as the three main influencing factors. Finally, we divide the pollution source treatment level into I, II, and III, corresponding to V1 = {I-level} = {high impact}, V2 = {II-level} = {moderate impact}, and V3 = {III-level} = {low impact} . Based on the comprehensive factor weight analysis and the field engineering conditions of the studied railway in the western plateau of China, we classify the pollution source treatment level of six tunnels and propose treatment suggestions for each level. To advance the efficient implementation of environmental protection during the construction of the plateau railway, we propose three policy recommendations that can positively contribute to environmental protection and green development. This work provides theoretical and technical guidance for the treatment of pollution sources in the construction of the plateau railway, which also serves as a significant reference for other similar projects.}, } @article {pmid37251658, year = {2023}, author = {Boyes, D and , and , and , and , and , and Lees, D and , }, title = {The genome sequence of the long-horned flat-body, Carcina quercana (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {16}, pmid = {37251658}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Carcina quercana (the long-horned flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 409 megabases in span. Most of the assembly (99.96%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,108 protein coding genes.}, } @article {pmid37251651, year = {2023}, author = {Dhellemmes, F and Aspillaga, E and Monk, CT}, title = {ATfiltR: A solution for managing and filtering detections from passive acoustic telemetry data.}, journal = {MethodsX}, volume = {10}, number = {}, pages = {102222}, pmid = {37251651}, issn = {2215-0161}, abstract = {Acoustic telemetry is a popular and cost-efficient method for tracking the movements of animals in the aquatic ecosystem. But data acquired via acoustic telemetry often contains spurious detections that must be identified and excluded by researchers to ensure valid results. Such data management is difficult as the amount of data collected often surpasses the capabilities of simple spreadsheet applications. ATfiltR is an open-source package programmed in R that allows users to integrate all telemetry data collected into a single file, to conditionally attribute animal data and location data to detections and to filter spurious detections based on customizable rules. Such tool will likely be useful to new researchers in acoustic telemetry and enhance results reproducibility.•ATfiltR compiles telemetry files and identifies and stores all data that was collected outside of your study period (e.g. when your receivers were on land for servicing) elsewhere.•As spurious detections are unlikely to appear sequentially in the data, ATfiltR finds all detections that occurred only once (per receiver or in the whole array) within a user-designated time period and stores them elsewhere.•ATfiltR identifies detections that are impossible given the animals' swimming speeds and the receivers detection range and stores them elsewhere.}, } @article {pmid37244965, year = {2023}, author = {Mattalia, G and Svanberg, I and Ståhlberg, S and Kuznetsova, N and Prūse, B and Kolosova, V and Aziz, MA and Kalle, R and Sõukand, R}, title = {Outdoor activities foster local plant knowledge in Karelia, NE Europe.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8627}, pmid = {37244965}, issn = {2045-2322}, support = {714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; }, mesh = {Humans ; Adult ; Child ; Europe ; Finland/epidemiology ; *Plants, Edible ; *Allergens ; Food ; }, abstract = {Wild edible plants, particularly berries, are relevant nutritional elements in the Nordic countries. In contrast to decreasing global trends, approximately 60% of the Finnish population is actively involved in (berry) foraging. We conducted 67 interviews with Finns and Karelians living in Finnish Karelia to: (a) detect the use of wild edible plants, (b) compare those results with the published data about neighbouring Russian Karelians, and (c) document the sources of local plant knowledge. The results revealed three main findings. First, we observed a similarity in wild food plant knowledge among Karelians and Finns from Karelia. Second, we detected divergences in wild food plant knowledge among Karelians living on both sides of the Finnish-Russian border. Third, the sources of local plant knowledge include vertical transmission, acquisition through literary sources, acquisition from "green" nature shops promoting healthy lifestyles, childhood foraging activities performed during the famine period following WWII, and outdoor recreational activities. We argue that the last two types of activities in particular may have influenced knowledge and connectedness with the surrounding environment and its resources at a stage of life that is crucial for shaping adult environmental behaviours. Future research should address the role of outdoor activities in maintaining (and possibly enhancing) local ecological knowledge in the Nordic countries.}, } @article {pmid37243228, year = {2023}, author = {Tokito, T and Kido, T and Muramatsu, K and Tokutsu, K and Okuno, D and Yura, H and Takemoto, S and Ishimoto, H and Takazono, T and Sakamoto, N and Obase, Y and Ishimatsu, Y and Fujino, Y and Yatera, K and Fushimi, K and Matsuda, S and Mukae, H}, title = {Impact of Administering Intravenous Azithromycin within 7 Days of Hospitalization for Influenza Virus Pneumonia: A Propensity Score Analysis Using a Nationwide Administrative Database.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243228}, issn = {1999-4915}, mesh = {Humans ; Azithromycin/therapeutic use ; *Influenza, Human/drug therapy ; Propensity Score ; Retrospective Studies ; *Pneumonia/drug therapy ; Hospitalization ; *Respiratory Insufficiency ; *Orthomyxoviridae ; }, abstract = {The potential antimicrobial and anti-inflammatory effectiveness of azithromycin against severe influenza is yet unclear. We retrospectively investigated the effect of intravenous azithromycin administration within 7 days of hospitalization in patients with influenza virus pneumonia and respiratory failure. Using Japan's national administrative database, we enrolled and classified 5066 patients with influenza virus pneumonia into severe, moderate, and mild groups based on their respiratory status within 7 days of hospitalization. The primary endpoints were total, 30-day, and 90-day mortality rates. The secondary endpoints were the duration of intensive-care unit management, invasive mechanical ventilation, and hospital stay. The inverse probability of the treatment weighting method with estimated propensity scores was used to minimize data collection bias. Use of intravenous azithromycin was proportional to the severity of respiratory failure (mild: 1.0%, moderate: 3.1%, severe: 14.8%). In the severe group, the 30-day mortality rate was significantly lower with azithromycin (26.49% vs. 36.65%, p = 0.038). In the moderate group, the mean duration of invasive mechanical ventilation after day 8 was shorter with azithromycin; there were no significant differences in other endpoints between the severe and moderate groups. These results suggest that intravenous azithromycin has favorable effects in patients with influenza virus pneumonia using mechanical ventilation or oxygen.}, } @article {pmid37240180, year = {2023}, author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP}, title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, pmid = {37240180}, issn = {1422-0067}, mesh = {Humans ; Multiomics ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; U937 Cells ; *Periodontitis/microbiology ; *Microbiota/genetics ; Bacteria/metabolism ; Cytokines/metabolism ; RNA-Binding Proteins ; }, abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.}, } @article {pmid37172351, year = {2023}, author = {Zerouali, B and Santos, CAG and do Nascimento, TVM and Silva, RMD}, title = {A cloud-integrated GIS for forest cover loss and land use change monitoring using statistical methods and geospatial technology over northern Algeria.}, journal = {Journal of environmental management}, volume = {341}, number = {}, pages = {118029}, doi = {10.1016/j.jenvman.2023.118029}, pmid = {37172351}, issn = {1095-8630}, mesh = {Humans ; *Geographic Information Systems ; *Conservation of Natural Resources/methods ; Algeria ; Agriculture ; Environmental Monitoring/methods ; Technology ; }, abstract = {Over the last two decades, forest cover has experienced significant impacts from fires and deforestation worldwide due to direct human activities and climate change. This paper assesses trends in forest cover loss and land use and land cover changes in northern Algeria between 2000 and 2020 using datasets extracted from Google Earth Engine (GEE), such as the Hanssen Global Forest Change and MODIS Land Cover Type products (MCD12Q1). Classification was performed using the pixel-based supervised machine-learning algorithm called Random Forest (RF). Trends were analyzed using methods such as Mann-Kendall and Sen. The study area comprises 17 basins with high rainfall variability. The results indicated that the forest area decreased by 64.96%, from 3718 to 1266 km[2], during the 2000-2020 period, while the barren area increased by 40%, from 134,777 to 188,748 km[2]. The findings revealed that the Constantinois-Seybousse-Mellegue hydrographic basin was the most affected by deforestation and cover loss, exceeding 50% (with an area of 1018 km[2]), while the Seybouse River basin experienced the highest percentage of cover loss at 40%. Nonparametric tests showed that seven river basins (41%) had significantly increasing trends of forest cover loss. According to the obtained results, the forest loss situation in Algeria, especially in the northeastern part, is very alarming and requires an exceptional and urgent plan to protect forests and the ecological system against wildfires and climate change. The study provides a diagnosis that should encourage better protection and management of forest cover in Algeria.}, } @article {pmid37232406, year = {2023}, author = {Watson, SJ and Aguirre, BA and Wright, AJ}, title = {Soil versus atmospheric drought: A test case of plant functional trait responses.}, journal = {Ecology}, volume = {}, number = {}, pages = {e4109}, doi = {10.1002/ecy.4109}, pmid = {37232406}, issn = {1939-9170}, abstract = {Climate change alters mean global surface temperatures, precipitation regimes, and atmospheric moisture. Resultant drought affects the composition and diversity of terrestrial ecosystems worldwide. To date, there are no assessments of the combined impacts of reduced precipitation and atmospheric drying on functional trait distributions of any species in an outdoor experiment. Here, we examined whether soil and atmospheric drought affect the functional traits of a focal grass species (Poa secunda) growing in monoculture and 8-species grass communities in outdoor mesocosms. We focused on specific leaf area (SLA), leaf area, stomatal density, root:shoot ratio, and fine root:coarse root ratio responses. Leaf area and overall growth were reduced with soil drying. Root:shoot ratio only increased for P. secunda growing in monoculture under combined atmospheric and soil drought. Plant energy allocation strategy (measured using principal components) differed when P. secunda was grown in combined soil and atmospheric drought conditions compared with soil drought alone. Given a lack of outdoor manipulations of this kind, our results emphasize the importance of atmospheric drying on functional trait responses more broadly. We suggest that drought methods focused purely on soil water inputs may be imprecisely predicting drought effects on other terrestrial organisms as well (other plants, arthropods, and higher trophic levels). This article is protected by copyright. All rights reserved.}, } @article {pmid37226845, year = {2023}, author = {Bizzotto, E and Bonetto, A and Marcomini, A and Vighi, M}, title = {Environmental exposure and ecotoxicological properties of a new generation fluorosurfactant (cC6O4): A comparison with selected legacy perfluoroalkyl acids (PFAA).}, journal = {Integrated environmental assessment and management}, volume = {}, number = {}, pages = {}, doi = {10.1002/ieam.4794}, pmid = {37226845}, issn = {1551-3793}, abstract = {Cyclic C6O4 (cC6O4, CAS number 1190931-27-1) is a new generation polyfluorinated alkyl substance (PFAS) used as polymerisation aid in the synthesis of fluoropolymers, produced in Italy since 2011. A review of the properties of cC6O4, focused on environmental distribution and ecotoxicology, was conducted. EQC model was applied, using default environmental scenarios, to estimate environmental distribution and fate. In a situation of static thermodynamic equilibrium in a closed system (level I) cC6O4 distributes mainly to water (97.6%) and in a minor amount to soil (2.3%). In a more realistic scenario (level III), with dynamic condition in an open system, with advection in air and water and with equal emissions in air and water, the major amount of the compound is transported through water advection. Monitoring data, mainly referred to surface and groundwater, are available for water bodies close to the production sites (maximum measured concentration 52 μg/L) as well as for a wider area in the river Po watershed with concentrations generally lower than 1 μg/L. Few values are also available for concentration in biota. Effect data indicate low toxicity on all tested organisms with NOEC values always higher than the maximum concentrations tested (100 mg/L for acute tests). Bioaccumulation potential is also very low. A comparison with selected widely used PFAS with five to eight C atoms indicate that cC6O4 is substantially less dangerous to aquatic organisms. At the time being, an ecological risk for the aquatic ecosystem may be excluded even in directly exposed ecosystems. However, for a complete assessment of the suitability of cC6O4 as substitute of other PFAS (namely PFOA), more comprehensive chronic experiments are necessary, to produce realistic NOECs, as well as higher tier experiments (e.g., mesocosms) capable to provide ecologically relevant endpoints. Moreover, a more accurate evaluation of the environmental persistence would be necessary.}, } @article {pmid37226152, year = {2023}, author = {Bakó, C and Balázs, VL and Kerekes, E and Kocsis, B and Nagy, DU and Szabó, P and Micalizzi, G and Mondello, L and Krisch, J and Pethő, D and Horváth, G}, title = {Flowering phenophases influence the antibacterial and anti-biofilm effects of Thymus vulgaris L. essential oil.}, journal = {BMC complementary medicine and therapies}, volume = {23}, number = {1}, pages = {168}, pmid = {37226152}, issn = {2662-7671}, mesh = {*Oils, Volatile/pharmacology ; *Thymus Plant ; Gas Chromatography-Mass Spectrometry ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Essential oils are becoming increasingly popular in medicinal applications because of their antimicrobial effect. Thymus vulgaris L. (Lamiaceae) is a well-known and widely cultivated medicinal plant, which is used as a remedy for cold, cough and gastrointestinal symptoms. Essential oil content of thyme is responsible for its antimicrobial activity, however, it has been reported that the chemical composition of essential oils influences its biological activity. In order to explore flowering phenophases influence on the chemical composition of thyme essential oil and its antibacterial and anti-biofilm activity, plant materials were collected at the beginning of flowering, in full bloom and at the end of flowering periods in 2019.

METHODS: Essential oils from fresh and dried plant materials were distilled and analyzed with gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detection (GC-FID). The antibacterial activity was performed by broth microdilution and thin layer chromatography-direct bioautography (TLC-DB) assays and the anti-biofilm effect by crystal violet assay, respectively. Scanning electron microscopy was applied to illustrate the cellular changes of bacterial cells after essential oil treatment.

RESULTS: Thymol (52.33-62.46%) was the main component in the thyme essential oils. Thyme oil distilled from fresh plant material and collected at the beginning of flowering period exerted the highest antibacterial and anti-biofilm activity against Haemophilus influenzae, H. parainfluenzae and Pseudomonas aeruginosa.

CONCLUSION: The different flowering periods of Thymus vulgaris influence the antibacterial and anti-biofilm activity of its essential oils, therefore, the collection time has to be taken into consideration and not only the full bloom, but the beginning of flowering period may provide biological active thyme essential oil.}, } @article {pmid37225998, year = {2023}, author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Microbial carbon use efficiency promotes global soil carbon storage.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37225998}, issn = {1476-4687}, abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.}, } @article {pmid37225767, year = {2023}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F}, title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {314}, pmid = {37225767}, issn = {2052-4463}, mesh = {Adaptation, Physiological ; *Arabidopsis/genetics ; Biological Evolution ; Databases, Factual ; Plant Leaves ; }, abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.}, } @article {pmid37224178, year = {2023}, author = {Passmore, S and Barth, W and Greenhill, SJ and Quinn, K and Sheard, C and Argyriou, P and Birchall, J and Bowern, C and Calladine, J and Deb, A and Diederen, A and Metsäranta, NP and Araujo, LH and Schembri, R and Hickey-Hall, J and Honkola, T and Mitchell, A and Poole, L and Rácz, PM and Roberts, SG and Ross, RM and Thomas-Colquhoun, E and Evans, N and Jordan, FM}, title = {Kinbank: A global database of kinship terminology.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0283218}, pmid = {37224178}, issn = {1932-6203}, mesh = {Humans ; Female ; Male ; *Sexism ; *Anthropology ; Databases, Factual ; Family ; Interdisciplinary Studies ; }, abstract = {For a single species, human kinship organization is both remarkably diverse and strikingly organized. Kinship terminology is the structured vocabulary used to classify, refer to, and address relatives and family. Diversity in kinship terminology has been analyzed by anthropologists for over 150 years, although recurrent patterning across cultures remains incompletely explained. Despite the wealth of kinship data in the anthropological record, comparative studies of kinship terminology are hindered by data accessibility. Here we present Kinbank, a new database of 210,903 kinterms from a global sample of 1,229 spoken languages. Using open-access and transparent data provenance, Kinbank offers an extensible resource for kinship terminology, enabling researchers to explore the rich diversity of human family organization and to test longstanding hypotheses about the origins and drivers of recurrent patterns. We illustrate our contribution with two examples. We demonstrate strong gender bias in the phonological structure of parent terms across 1,022 languages, and we show that there is no evidence for a coevolutionary relationship between cross-cousin marriage and bifurcate-merging terminology in Bantu languages. Analysing kinship data is notoriously challenging; Kinbank aims to eliminate data accessibility issues from that challenge and provide a platform to build an interdisciplinary understanding of kinship.}, } @article {pmid37224319, year = {2022}, author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and , and , and , and Wahlberg, N and , }, title = {The genome sequence of the high brown fritillary, Fabriciana adippe (Dennis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {298}, pmid = {37224319}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Fabriciana adippe (the high brown fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 485 megabases in span. Most of the assembly (99.98%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.1 kilobases in length. Gene annotation of this assembly in Ensembl identified 13,536 protein coding genes.}, } @article {pmid37221042, year = {2023}, author = {Chaudhary, S and Wu, Y and Strongman, D and Wang, Y}, title = {CIGAF-a database and interactive platform for insect-associated trichomycete fungi.}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, doi = {10.1093/database/baad038}, pmid = {37221042}, issn = {1758-0463}, mesh = {Animals ; *Insecta ; Databases, Factual ; *Fungi ; Metadata ; Software ; }, abstract = {Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.}, } @article {pmid37209314, year = {2023}, author = {Jiang, WJ and Wang, MT and Du, ZY and Li, JH and Shi, Y and Wang, X and Wu, LY and Chen, J and Zhong, M and Yang, J and Hu, BH and Huang, J}, title = {Bioinformatic and functional analysis of OsDHN2 under cadmium stress.}, journal = {Functional & integrative genomics}, volume = {23}, number = {2}, pages = {170}, pmid = {37209314}, issn = {1438-7948}, mesh = {*Cadmium/toxicity/metabolism ; Saccharomyces cerevisiae/metabolism ; Plant Proteins/genetics/metabolism ; *Oryza/genetics/metabolism ; Computational Biology ; Gene Expression Regulation, Plant ; }, abstract = {As a toxic heavy metal, cadmium (Cd) is one of the principal pollutants influencing rice productivity and food security. Despite several studies, the underlying mechanism of Cd response in plants remains largely unclear. Dehydrins are part of the late embryogenesis abundant (LEA) family which protect plants against abiotic stresses. In this study, a Cd-responsive LEA gene, OsDHN2, was functionally characterized. The chromosome localization results indicated that OsDHN2 was located on chromosome 2 of rice. Meanwhile, cis-acting elements, such as MBS (MYB binding site involved in drought-inducibility), ARE (anaerobic induction), and ABRE (abscisic acid), were present in the OsDHN2 promoter region. Expression pattern analysis also showed that OsDHN2 expression was induced in both roots and shoots under Cd stress. Overexpression of OsDHN2 improved Cd tolerance and reduced Cd concentration in yeast. Moreover, increased expression levels of SOD1, CTA1, GSH1, or CTT1 were found in transgenic yeast under Cd stress, suggesting the increased antioxidant enzymatic activities. These results suggested that OsDHN2 is a Cd-responsive gene that has the potential to improve resistance to Cd in rice.}, } @article {pmid37207732, year = {2023}, author = {Girardi, P and Lupo, A and Mastromatteo, LY and Scrimin, S}, title = {Behavioral outcomes and exposure to perfluoroalkyl substances among children aged 6-13 years: The TEDDY child study.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116049}, doi = {10.1016/j.envres.2023.116049}, pmid = {37207732}, issn = {1096-0953}, abstract = {BACKGROUND: Although some studies report that exposure to per- and polyfluoroalkyl substances (PFAS) during pregnancy and early life stages of a child could adversely impact neurodevelopment, literature shows mixed evidence.

OBJECTIVES: Using an ecological framework for human development, we assessed the association of risk factors for environmental PFAS exposure and childhood PFAS concentrations with behavioral difficulties among school-age children exposed to PFAS from birth, while also controlling for the important influence of the parenting and familial environment.

METHODS: The study participants included 331 school-age children (6-13 years) born in a PFAS-contaminated area in the Veneto Region (Italy). We study the associations between environmental risk factors of maternal PFAS exposure (residential time, consumption of tap water, residence in Red zone A or B), and breastfeeding duration with parent assessments of children's behavioral problems (using the Strengths and Difficulties Questionnaire [SDQ]), adjusting for socio-demographic, parenting and familial variables. The direct relationships between serum blood PFAS concentrations and SDQ scores was evaluated in a subset of children (n = 79), both with single PFAS and weighted quantile sum (WQS) regressions.

RESULTS: Poisson regression models reported positive associations between high consumption of tap water and externalizing SDQ scores (Incidence Rate Ratio [IRR]: 1.18; 95% confidence interval [CI]: 1.04-1.32) and total difficulty scores (IRR: 1.14; 95% CI: 1.02-1.26). Childhood perfluorooctane sulfonate (PFOS) and perfluorohexane sulfonate (PFHxS) were associated with higher internalizing SDQ scores (4th vs. 1st quartile, PFOS IRR: 1.54, 95% CI: 1.06-2.25), externalizing scores (4th vs. 1st quartile, PFHxS IRR: 1.59, 95% CI: 1.09-2.32), and total difficulty scores (4th vs. 1st quartile, PFOS IRR: 1.37, 95% CI: 1.05-1.71; PFHxS IRR: 1.54, 95% CI: 1.09-1.90). The WQS regressions confirmed the associations reported by single-PFAS analyses.

CONCLUSIONS: We observed cross-sectional associations of tap water consumption and childhood PFOS, and PFHxS concentrations with greater behavioral difficulties.}, } @article {pmid37207684, year = {2023}, author = {Cocker, D and Chidziwisano, K and Mphasa, M and Mwapasa, T and Lewis, JM and Rowlingson, B and Sammarro, M and Bakali, W and Salifu, C and Zuza, A and Charles, M and Mandula, T and Maiden, V and Amos, S and Jacob, ST and Kajumbula, H and Mugisha, L and Musoke, D and Byrne, R and Edwards, T and Lester, R and Elviss, N and Roberts, AP and Singer, AC and Jewell, C and Morse, T and Feasey, NA}, title = {Investigating One Health risks for human colonisation with extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Malawian households: a longitudinal cohort study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00062-9}, pmid = {37207684}, issn = {2666-5247}, abstract = {BACKGROUND: Low-income countries have high morbidity and mortality from drug-resistant infections, especially from enteric bacteria such as Escherichia coli. In these settings, sanitation infrastructure is of variable and often inadequate quality, creating risks of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales transmission. We aimed to describe the prevalence, distribution, and risks of ESBL-producing Enterobacterales colonisation in sub-Saharan Africa using a One Health approach.

METHODS: Between April 29, 2019, and Dec 3, 2020, we recruited 300 households in Malawi for this longitudinal cohort study: 100 each in urban, peri-urban, and rural settings. All households underwent a baseline visit and 195 were selected for longitudinal follow-up, comprising up to three additional visits over a 6 month period. Data on human health, antibiotic usage, health-seeking behaviours, structural and behavioural environmental health practices, and animal husbandry were captured alongside human, animal, and environmental samples. Microbiological processing determined the presence of ESBL-producing E coli and Klebsiella pneumoniae, and hierarchical logistic regression was performed to evaluate the risks of human ESBL-producing Enterobacterales colonisation.

FINDINGS: A paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites. A total of 11 975 samples were cultured, and ESBL-producing Enterobacterales were isolated from 1190 (41·8%) of 2845 samples of human stool, 290 (29·8%) of 973 samples of animal stool, 339 (66·2%) of 512 samples of river water, and 138 (46·0%) of 300 samples of drain water. Multivariable models illustrated that human ESBL-producing E coli colonisation was associated with the wet season (adjusted odds ratio 1·66, 95% credible interval 1·38-2·00), living in urban areas (2·01, 1·26-3·24), advanced age (1·14, 1·05-1·25), and living in households where animals were observed interacting with food (1·62, 1·17-2·28) or kept inside (1·58, 1·00-2·43). Human ESBL-producing K pneumoniae colonisation was associated with the wet season (2·12, 1·63-2·76).

INTERPRETATION: There are extremely high levels of ESBL-producing Enterobacterales colonisation in humans and animals and extensive contamination of the wider environment in southern Malawi. Urbanisation and seasonality are key risks for ESBL-producing Enterobacterales colonisation, probably reflecting environmental drivers. Without adequate efforts to improve environmental health, ESBL-producing Enterobacterales transmission is likely to persist in this setting.

FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.

TRANSLATION: For the Chichewa translation of the abstract see Supplementary Materials section.}, } @article {pmid36880704, year = {2023}, author = {Amato, S and Benson, JS and Stewart, B and Sarathy, A and Osler, T and Hosmer, D and An, G and Cook, A and Winchell, RJ and Malhotra, AK}, title = {Current patterns of trauma center proliferation have not led to proportionate improvements in access to care or mortality after injury: An ecologic study.}, journal = {The journal of trauma and acute care surgery}, volume = {94}, number = {6}, pages = {755-764}, pmid = {36880704}, issn = {2163-0763}, mesh = {Humans ; United States/epidemiology ; *Trauma Centers ; Income ; Geographic Information Systems ; Health Services Accessibility ; Cell Proliferation ; *Wounds and Injuries/therapy ; }, abstract = {BACKGROUND: Timely access to high-level (I/II) trauma centers (HLTCs) is essential to minimize mortality after injury. Over the last 15 years, there has been a proliferation of HLTC nationally. The current study evaluates the impact of additional HLTC on population access and injury mortality.

METHODS: A geocoded list of HLTC, with year designated, was obtained from the American Trauma Society, and 60-minute travel time polygons were created using OpenStreetMap data. Census block group population centroids, county population centroids, and American Communities Survey data from 2005 and 2020 were integrated. Age-adjusted nonoverdose injury mortality was obtained from CDC Wide-ranging Online Data for Epidemiologic Research and the Robert Wood Johnson Foundation. Geographically weighted regression models were used to identify independent predictors of HLTC access and injury mortality.

RESULTS: Over the 15-year (2005-2020) study period, the number of HLTC increased by 31.0% (445 to 583), while population access to HLTC increased by 6.9% (77.5-84.4%). Despite this increase, access was unchanged in 83.1% of counties, with a median change in access of 0.0% (interquartile range, 0.0-1.1%). Population-level age-adjusted injury mortality rates increased by 5.39 per 100,000 population during this time (60.72 to 66.11 per 100,000). Geographically weighted regression controlling for population demography and health indicators found higher median income and higher population density to be positively associated with majority (≥50%) HLTC population coverage and negatively associated with county-level nonoverdose mortality.

CONCLUSION: Over the past 15 years, the number of HLTC increased 31%, while population access to HLTC increased only 6.9%. High-level (I/II) trauma center designation is likely driven by factors other than population need. To optimize efficiency and decrease potential oversupply, the designation process should include population level metrics. Geographic information system methodology can be an effective tool to assess optimal placement.

LEVEL OF EVIDENCE: Prognostic and Epidemiological; Level IV.}, } @article {pmid36747723, year = {2023}, author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R}, title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {36747723}, abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi , affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.

OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.

DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.

RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.

CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.

AUTHOR SUMMARY: Chagas disease, caused by the parasite Trypanosoma cruzi , is transmitted via triatomine insect vectors. In Latin America, dogs are a common feeding source for triatomine vectors and subsequently an important reservoir of T. cruzi . One proposed intervention to reduce T. cruzi transmission is xenointoxication: treating dogs with oral insecticide to kill triatomine vectors in order to decrease overall T. cruzi transmission. Fluralaner, commonly administered to prevent ectoparasites such as fleas and ticks, is effective under laboratory conditions against the triatomine vectors. One concern with fluralaner treatment is that rapid death of the insect vectors may make the insects more available to oral ingestion by dogs; a more effective transmission pathway than stercorarian, the usual route for T. cruzi transmission. Using a mathematical model, we explored 3 different epidemiologic scenarios: high prevalence endemic disease within a domestic T. cruzi cycle, low prevalence endemic disease within a domestic T. cruzi cycle, and low prevalence endemic disease within a semi-sylvatic T. cruzi cycle. We found a range of beneficial to detrimental effects of fluralaner xenointoxication depending on the epidemiologic scenario. Our results suggest that careful field trials should be designed and carried out before wide scale implementation of fluralaner xenointoxication to reduce T. cruzi transmission.}, } @article {pmid37198478, year = {2023}, author = {Pairo-Castineira, E and Rawlik, K and Bretherick, AD and Qi, T and Wu, Y and Nassiri, I and McConkey, GA and Zechner, M and Klaric, L and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Richmond, A and Millar, J and Russell, CD and Malinauskas, T and Thwaites, R and Morrice, K and Keating, S and Maslove, D and Nichol, A and Semple, MG and Knight, J and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Begg, C and Walsh, T and Tenesa, A and Flores, C and Riancho, JA and Rojas-Martinez, A and Lapunzina, P and , and , and , and , and Yang, J and Ponting, CP and Wilson, JF and Vitart, V and Abedalthagafi, M and Luchessi, AD and Parra, EJ and Cruz, R and Carracedo, A and Fawkes, A and Murphy, L and Rowan, K and Pereira, AC and Law, A and Fairfax, B and Hendry, SC and Baillie, JK}, title = {GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37198478}, issn = {1476-4687}, abstract = {Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown[1] to be highly efficient for discovery of genetic associations[2]. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group[3]. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).}, } @article {pmid37104570, year = {2023}, author = {Osmanski, AB and Paulat, NS and Korstian, J and Grimshaw, JR and Halsey, M and Sullivan, KAM and Moreno-Santillán, DD and Crookshanks, C and Roberts, J and Garcia, C and Johnson, MG and Densmore, LD and Stevens, RD and , and Rosen, J and Storer, JM and Hubley, R and Smit, AFA and Dávalos, LM and Karlsson, EK and Lindblad-Toh, K and Ray, DA}, title = {Insights into mammalian TE diversity through the curation of 248 genome assemblies.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6643}, pages = {eabn1430}, doi = {10.1126/science.abn1430}, pmid = {37104570}, issn = {1095-9203}, support = {R01 HG002939/HG/NHGRI NIH HHS/United States ; U24 HG010136/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Female ; Pregnancy ; *DNA Transposable Elements ; *Evolution, Molecular ; Long Interspersed Nucleotide Elements ; *Eutheria/genetics ; Datasets as Topic ; Feeding Behavior ; *Genetic Variation ; }, abstract = {We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.}, } @article {pmid37196545, year = {2023}, author = {Yang, P and Yang, W and Wei, Z and Li, Y and Yang, Y and Wang, J}, title = {Novel targets for gastric cancer: The tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis and cuproptosis.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {163}, number = {}, pages = {114883}, doi = {10.1016/j.biopha.2023.114883}, pmid = {37196545}, issn = {1950-6007}, abstract = {Gastric cancer (GC) is a fatal illness, and its mortality rate is very high all over the world. At present, it is a serious health problem for any country. It is a multifactorial disease due to the rising drug resistance and the increasing global cancer burden, the treatment of GC still faces many obstacles and problems. In recent years, research on GC is being carried out continuously, and we hope to address the new targets of GC treatment through this review. At the same time, we also hope to discover new ways to fight GC and create more gospel for clinical patients. First, we discuss the descriptive tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis, and cuproptosis. Finally, we expounded on the new or potential targets of GC treatment.}, } @article {pmid37193271, year = {2023}, author = {Mollicone, DJ and Kan, K and Coats, S and Mott, C and van Wollen, M and Hatch, A and Gallagher, J and Williams, S and Motzkin, D}, title = {Use of the psychomotor vigilance test to aid in the selection of risk controls in an air medical transport operation.}, journal = {Sleep advances : a journal of the Sleep Research Society}, volume = {4}, number = {1}, pages = {zpad003}, pmid = {37193271}, issn = {2632-5012}, abstract = {STUDY OBJECTIVES: This study evaluated the utility and ecological validity of the 3-minute psychomotor vigilance test (PVT) completed by safety-critical personnel in an air medical transport operation as part of a fatigue risk management program.

METHODS: Crewmembers in an air medical transport operation self-administered an alertness assessment incorporating a 3-minute PVT at different time points during their duty schedule. The prevalence of alertness deficits was evaluated based on a failure threshold of 12 errors considering both lapses and false starts. To evaluate the ecological validity of the PVT, the relative frequency of failed assessments was evaluated relative to crewmember position, timing of the assessment within the duty schedule, time of day, and sleep quantity in the last 24 h.

RESULTS: 2.1% of assessments were associated with a failing PVT score. Crewmember position, timing of assessment within the duty shift, time of day, and sleep quantity in the last 24 h were found to affect the relative frequency of failed assessments. Obtaining less than 7-9 h of sleep was associated with systematic increases in the failure rate (F[1, 54 612] = 168.1, p < .001). Obtaining less than 4 h of sleep was associated with a frequency of a failed assessment 2.99 times higher than the frequency of a failed assessment when obtaining 7-9 h of sleep.

CONCLUSIONS: Results provide evidence for the utility and ecological validity of the PVT as well as the suitability of the PVT failure threshold to support fatigue risk management in safety-critical operations.}, } @article {pmid37148803, year = {2023}, author = {Tang, Y and Hardy, TJ and Yoon, JY}, title = {Receptor-based detection of microplastics and nanoplastics: Current and future.}, journal = {Biosensors & bioelectronics}, volume = {234}, number = {}, pages = {115361}, doi = {10.1016/j.bios.2023.115361}, pmid = {37148803}, issn = {1873-4235}, mesh = {Microplastics ; Plastics ; *Biosensing Techniques ; Biological Assay ; Databases, Factual ; *Water Pollutants, Chemical ; }, abstract = {Plastic pollution is an emerging environmental concern, gaining significant attention worldwide. They are classified into microplastics (MP; defined from 1 μm to 5 mm) and smaller nanoplastics (NP; <1 μm). NPs may pose higher ecological risks than MPs. Various microscopic and spectroscopic techniques have been used to detect MPs, and the same methods have occasionally been used for NPs. However, they are not based on receptors, which provide high specificity in most biosensing applications. Receptor-based micro/nanoplastics (MNP) detection can provide high specificity, distinguishing MNPs from the environmental samples and, more importantly, identifying the plastic types. It can also offer a low limit of detection (LOD) required for environmental screening. Such receptors are expected to detect NPs specifically at the molecular level. This review categorizes the receptors into cells, proteins, peptides, fluorescent dyes, polymers, and micro/nanostructures. Detection techniques used with these receptors are also summarized and categorized. There is plenty of room for future research to test for broader classes of environmental samples and many plastic types, to lower the LOD, and to apply the current techniques for NPs. Portable and handheld MNP detection should also be demonstrated for field use since the current demonstrations primarily utilized laboratory instruments. Detection on microfluidic platforms will also be crucial in miniaturizing and automating the assay and, eventually, collecting an extensive database to support machine learning-based classification of MNP types.}, } @article {pmid37165242, year = {2023}, author = {Liao, WW and Asri, M and Ebler, J and Doerr, D and Haukness, M and Hickey, G and Lu, S and Lucas, JK and Monlong, J and Abel, HJ and Buonaiuto, S and Chang, XH and Cheng, H and Chu, J and Colonna, V and Eizenga, JM and Feng, X and Fischer, C and Fulton, RS and Garg, S and Groza, C and Guarracino, A and Harvey, WT and Heumos, S and Howe, K and Jain, M and Lu, TY and Markello, C and Martin, FJ and Mitchell, MW and Munson, KM and Mwaniki, MN and Novak, AM and Olsen, HE and Pesout, T and Porubsky, D and Prins, P and Sibbesen, JA and Sirén, J and Tomlinson, C and Villani, F and Vollger, MR and Antonacci-Fulton, LL and Baid, G and Baker, CA and Belyaeva, A and Billis, K and Carroll, A and Chang, PC and Cody, S and Cook, DE and Cook-Deegan, RM and Cornejo, OE and Diekhans, M and Ebert, P and Fairley, S and Fedrigo, O and Felsenfeld, AL and Formenti, G and Frankish, A and Gao, Y and Garrison, NA and Giron, CG and Green, RE and Haggerty, L and Hoekzema, K and Hourlier, T and Ji, HP and Kenny, EE and Koenig, BA and Kolesnikov, A and Korbel, JO and Kordosky, J and Koren, S and Lee, H and Lewis, AP and Magalhães, H and Marco-Sola, S and Marijon, P and McCartney, A and McDaniel, J and Mountcastle, J and Nattestad, M and Nurk, S and Olson, ND and Popejoy, AB and Puiu, D and Rautiainen, M and Regier, AA and Rhie, A and Sacco, S and Sanders, AD and Schneider, VA and Schultz, BI and Shafin, K and Smith, MW and Sofia, HJ and Abou Tayoun, AN and Thibaud-Nissen, F and Tricomi, FF and Wagner, J and Walenz, B and Wood, JMD and Zimin, AV and Bourque, G and Chaisson, MJP and Flicek, P and Phillippy, AM and Zook, JM and Eichler, EE and Haussler, D and Wang, T and Jarvis, ED and Miga, KH and Garrison, E and Marschall, T and Hall, IM and Li, H and Paten, B}, title = {A draft human pangenome reference.}, journal = {Nature}, volume = {617}, number = {7960}, pages = {312-324}, pmid = {37165242}, issn = {1476-4687}, support = {R01 HG002385/HG/NHGRI NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; Sequence Analysis, DNA ; *Genomics/standards ; Reference Standards ; Cohort Studies ; Alleles ; Genetic Variation ; }, abstract = {Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals[1]. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.}, } @article {pmid37162089, year = {2023}, author = {Santana, BEF and Andrade, ACS and Muraro, AP}, title = {Trend of incompleteness of maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System, 2012-2020.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {1}, pages = {e2022725}, pmid = {37162089}, issn = {2237-9622}, mesh = {Female ; Humans ; Pregnancy ; Brazil ; *Educational Status ; *Live Birth ; Pregnancy, Multiple ; Skin Pigmentation ; Databases, Factual/standards/statistics & numerical data ; Health Information Systems ; Racial Groups ; }, abstract = {OBJECTIVE: to analyze the trend of incompleteness of the maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System (SINASC) between 2012 and 2020.

METHODS: this was an ecological time series study of the incompleteness of maternal schooling and race/skin color data for Brazil, its regions and Federative Units, by means of joinpoint regression and calculation of annual percentage change (APC) and average annual percentage change.

RESULTS: a total of 26,112,301 births were registered in Brazil in the period; incompleteness of maternal schooling data decreased for Brazil (APC = -8.1%) and the Southeast (APC = -19.5%) and Midwest (APC = -17.6%) regions; as for race/skin color, there was a downward trend for Brazil (APC = -8.2%) and all regions, except the Northeast region, while nine Federative Units and the Federal District showed a stationary trend.

CONCLUSION: there was an improvement in filling out these variables on the SINASC, but with regional disparities, mainly for race/skin color.}, } @article {pmid37093376, year = {2023}, author = {Alam, N and Saha, S and Gupta, S and Chatterjee, A}, title = {Settlement suitability analysis of a riverine floodplain in the perspective of GIS-based multicriteria decision analysis.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {24}, pages = {66002-66020}, pmid = {37093376}, issn = {1614-7499}, mesh = {Humans ; *Geographic Information Systems ; *Decision Support Techniques ; Spatial Analysis ; Sustainable Development ; Climate ; }, abstract = {Riverine floodplains are highly dynamic and the most vulnerable space on Earth particularly in flat alluvial plains of major river systems. Suitable site selection for sustainable human settlements in active floodplain areas is a critical task for decision-makers in terms of quality of lithology, ecologically fragile landmass, climate-induced hazards, immense population pressure, and environmental conservation issues. This research introduces a methodology for settlement suitability zone (SSZ) that employs GIS-based multi-criteria decision-making (MCDM) techniques. As a case study, an altered hydrological regime of the lower Ganga riparian zone was chosen to identify the SSZ as these areas are the most susceptible to riverine hazards. Twelve significant variables reflecting on topography, climate, landscape, and environment have been selected in the multi-criteria evaluation platform. The CRiteria Importance Through Intercriteria Correlation (CRITIC) method is adopted to specify the weights of the criteria and utilize an inverse distance-weighted (IDW) spatial interpolation technique to generate an SSZ map in a GIS environment. The study zone is spatially quantified into five categories, from unsuitable to high-suitable with a natural breaks (Jenks) classification method. Subsequently, the final results are validated through a receiver operating characteristics (ROC) curve using randomly selected 56 hazard-exposed location points. The outcome revealed that 8.45% of the riparian area falls under unsuitable, 21.87% under low-suitable, and 33.27% under moderate-suitable for locating human settlements. The generally suitable and high-suitable categories account for 36.40% of the total study zone. A spatial sensitivity analysis is also applied to gauge the influence of each parameter on the MCDM outcomes. The SSZ mapping results from this study can help local authorities to plan for sustainable settlement development in environmentally fragile areas.}, } @article {pmid37161334, year = {2023}, author = {Kortz, AR and Moyes, F and Pivello, VR and Pyšek, P and Dornelas, M and Visconti, P and Magurran, AE}, title = {Elevated compositional change in plant assemblages linked to invasion.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1998}, pages = {20222450}, pmid = {37161334}, issn = {1471-2954}, mesh = {*Tracheophyta ; Biodiversity ; Databases, Factual ; Introduced Species ; }, abstract = {Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about.}, } @article {pmid37076624, year = {2023}, author = {Klein, B and Ogbunugafor, CB and Schafer, BJ and Bhadricha, Z and Kori, P and Sheldon, J and Kaza, N and Sharma, A and Wang, EA and Eliassi-Rad, T and Scarpino, SV and Hinton, E}, title = {COVID-19 amplified racial disparities in the US criminal legal system.}, journal = {Nature}, volume = {617}, number = {7960}, pages = {344-350}, pmid = {37076624}, issn = {1476-4687}, mesh = {Humans ; Black or African American/legislation & jurisprudence/statistics & numerical data ; *COVID-19/epidemiology ; *Criminals/legislation & jurisprudence/statistics & numerical data ; *Prisoners/legislation & jurisprudence/statistics & numerical data ; United States/epidemiology ; White/legislation & jurisprudence/statistics & numerical data ; Datasets as Topic ; Hispanic or Latino/legislation & jurisprudence/statistics & numerical data ; *Racial Groups/legislation & jurisprudence/statistics & numerical data ; }, abstract = {The criminal legal system in the USA drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features[1-3]. During the first year of the coronavirus disease 2019 (COVID-19) pandemic, the number of incarcerated people in the USA decreased by at least 17%-the largest, fastest reduction in prison population in American history[4]. Here we ask how this reduction influenced the racial composition of US prisons and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the US prison population and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decade-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people[5]. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacerbated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration. To advance opportunities for data-driven social science, we publicly released the data associated with this study at Zenodo[6].}, } @article {pmid37155680, year = {2023}, author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R}, title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.}, journal = {PLoS computational biology}, volume = {19}, number = {5}, pages = {e1011115}, doi = {10.1371/journal.pcbi.1011115}, pmid = {37155680}, issn = {1553-7358}, abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi, affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.

OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.

DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.

RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.

CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.}, } @article {pmid37155231, year = {2023}, author = {Ondrikova, N and Harris, JP and Douglas, A and Hughes, HE and Iturriza-Gomara, M and Vivancos, R and Elliot, AJ and Cunliffe, NA and Clough, HE}, title = {Predicting Norovirus in England Using Existing and Emerging Syndromic Data: Infodemiology Study.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e37540}, doi = {10.2196/37540}, pmid = {37155231}, issn = {1438-8871}, mesh = {Humans ; Infodemiology ; *Norovirus ; England/epidemiology ; *Gastroenteritis/epidemiology ; *Caliciviridae Infections/epidemiology ; }, abstract = {BACKGROUND: Norovirus is associated with approximately 18% of the global burden of gastroenteritis and affects all age groups. There is currently no licensed vaccine or available antiviral treatment. However, well-designed early warning systems and forecasting can guide nonpharmaceutical approaches to norovirus infection prevention and control.

OBJECTIVE: This study evaluates the predictive power of existing syndromic surveillance data and emerging data sources, such as internet searches and Wikipedia page views, to predict norovirus activity across a range of age groups across England.

METHODS: We used existing syndromic surveillance and emerging syndromic data to predict laboratory data indicating norovirus activity. Two methods are used to evaluate the predictive potential of syndromic variables. First, the Granger causality framework was used to assess whether individual variables precede changes in norovirus laboratory reports in a given region or an age group. Then, we used random forest modeling to estimate the importance of each variable in the context of others with two methods: (1) change in the mean square error and (2) node purity. Finally, these results were combined into a visualization indicating the most influential predictors for norovirus laboratory reports in a specific age group and region.

RESULTS: Our results suggest that syndromic surveillance data include valuable predictors for norovirus laboratory reports in England. However, Wikipedia page views are less likely to provide prediction improvements on top of Google Trends and Existing Syndromic Data. Predictors displayed varying relevance across age groups and regions. For example, the random forest modeling based on selected existing and emerging syndromic variables explained 60% variance in the ≥65 years age group, 42% in the East of England, but only 13% in the South West region. Emerging data sets highlighted relative search volumes, including "flu symptoms," "norovirus in pregnancy," and norovirus activity in specific years, such as "norovirus 2016." Symptoms of vomiting and gastroenteritis in multiple age groups were identified as important predictors within existing data sources.

CONCLUSIONS: Existing and emerging data sources can help predict norovirus activity in England in some age groups and geographic regions, particularly, predictors concerning vomiting, gastroenteritis, and norovirus in the vulnerable populations and historical terms such as stomach flu. However, syndromic predictors were less relevant in some age groups and regions likely due to contrasting public health practices between regions and health information-seeking behavior between age groups. Additionally, predictors relevant to one norovirus season may not contribute to other seasons. Data biases, such as low spatial granularity in Google Trends and especially in Wikipedia data, also play a role in the results. Moreover, internet searches can provide insight into mental models, that is, an individual's conceptual understanding of norovirus infection and transmission, which could be used in public health communication strategies.}, } @article {pmid36758962, year = {2023}, author = {Lee, HE and Kim, YG and Jeong, JY and Kim, DH}, title = {Data resource profile: the Korean Community Health Status Indicators (K-CHSI) database.}, journal = {Epidemiology and health}, volume = {45}, number = {}, pages = {e2023016}, doi = {10.4178/epih.e2023016}, pmid = {36758962}, issn = {2092-7193}, mesh = {Humans ; *Health Status Indicators ; Health Surveys ; Databases, Factual ; *Environment ; Republic of Korea/epidemiology ; }, abstract = {Korean Community Health Status Indicators (K-CHSI) is a model-based database containing annual data on health outcomes and determinants at the municipal level (si/gun/gu-level regions, including mid-sized cities, counties, and districts). K-CHSI's health outcomes include overall mortality, disease incidence, prevalence rates, and self-reported health. Health determinants were measured in 5 domains: socio-demographic factors, health behaviors, social environment, physical environment, and the healthcare system. The data sources are 71 public databases, including Causes of Death Statistics, Cancer Registration Statistics, Community Health Survey, Population Census, and Census on Establishments and Statistics of Urban Plans. This dataset covers Korea's 17 metropolitan cities and provinces, with data from approximately 250 municipal regions (si/gun/gu). The current version of the database (DB version 1.3) was built using 12 years of data from 2008 to 2019. All data included in K-CHSI may be downloaded via the Korea Community Health Survey site, with no login requirement (https://chs.kdca.go.kr/chs/recsRoom/dataBaseMain.do). K-CHSI covers extensive health outcomes and health determinants at the municipal level over a period of more than 10 years, which enables ecological and time-series analyses of the relationships among various health outcomes and related factors.}, } @article {pmid37155109, year = {2023}, author = {Chen, D and Zhang, Y and Feng, Q}, title = {Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37155109}, issn = {1614-7499}, abstract = {Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.}, } @article {pmid37154236, year = {2023}, author = {Lin, F and Kennelly, EJ and Linington, RG and Long, C}, title = {Comprehensive Metabolite Profiling of Two Edible Garcinia Species Based on UPLC-ESI-QTOF-MS[E] Coupled with Bioactivity Assays.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.2c08372}, pmid = {37154236}, issn = {1520-5118}, abstract = {In China, the endemic species Garcinia yunnanensis and native Garcinia xanthochymus are known as edible and medicinal plants. However, a systematic metabolomic and bioactivity evaluation of different plant parts from both species is lacking. In this study, comprehensive investigations of 11 plant parts of G. yunnanensis and 10 of G. xanthochymus employing UPLC-ESI-QTOF-MS[E]-based metabolomic analysis in conjunction with three bioactivity assays were undertaken. A customized chemotaxonomic-based in-house library containing 6456 compounds was constructed and coupled to the Progenesis QI informatic platform for metabolite annotations. From these two species, a total of 235 constituents were characterized using multiple criteria. Differences in metabolite profiles between the plant parts within each species were uncovered using multivariate analysis. Based on orthogonal partial least-squares discriminant analysis (OPLS-DA), 23 markers were identified as highly differential metabolites from G. xanthochymus and 20 from G. yunnanensis. Comparative assessment of the biological assays revealed the activity variations among different plant parts. The seeds of both species and G. yunnanensis latex exhibited excellent cytotoxic and antibacterial activities, while G. xanthochymus roots and G. yunnanensis arils showed strong anti-inflammatory effects. S-plot analysis identified 26 potential biomarkers for the observed activities, including the known cytotoxic agent cycloxanthochymol and the anti-inflammatory compound garcimultiflorone B, which likely explains some of the potent observed bioactivity.}, } @article {pmid37152782, year = {2023}, author = {Mori, Y and Okawara, M and Shibao, K and Kohi, S and Tamura, T and Sato, N and Fujino, Y and Fushimi, K and Matsuda, S and Hirata, K}, title = {Changes in operative trends and short-term outcomes of surgery for congenital biliary dilatation in adults using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.}, journal = {Annals of gastroenterological surgery}, volume = {7}, number = {3}, pages = {471-478}, pmid = {37152782}, issn = {2475-0328}, abstract = {AIM: We aimed to evaluate the operative trends and compare the short-term outcomes between open and laparoscopic surgery for congenital biliary dilatation (CBD) in adults using real-world data from Japan.

METHODS: Data from the Japanese Diagnosis Procedure Combination database on 941 patients undergoing surgery for CBD at 357 hospitals from April 1, 2016, to March 31, 2021, were analyzed. The patients were divided into two groups: open surgery (n = 764) and laparoscopic surgery (n = 177). We performed a retrospective analysis via a multilevel analysis of the short-term surgical outcomes and costs between open and laparoscopic surgery.

RESULTS: The rate of laparoscopic surgery has been increasing annually and had almost doubled to 25% by 2021. There were no significant differences in the in-hospital mortality rate or postoperative morbidity between the two groups. The length of anesthesia was significantly longer in the laparoscopic than open surgery group (8.80 vs 6.16 hours, p < .001). The time to removal of the abdominal drain and length of hospital stay were significantly shorter in the laparoscopic than open surgery group (6.12 vs 8.35 days, p = .001 and 13.57 vs 15.79 days, p < .001, respectively). The coefficient for cost was 463 235 yen (95% confidence interval, 289 679-636 792) higher in laparoscopic than open surgery (p < .001).

CONCLUSION: The short-term results were comparable between laparoscopic and open surgery for CBD. Further investigation is needed to validate our findings and long-term outcomes.}, } @article {pmid37150648, year = {2023}, author = {Wieczorek, P and Pruc, M and Krajsman, M and Wieczorek, W and Cander, B and Szarpak, L and Navolokina, A and Matuszewski, M and Bragazzi, NL and Chirico, F and Smereka, J}, title = {Comparison of the bébé VieScope™ and direct laryngoscope for pediatric tongue oedema scenario: A simulation study.}, journal = {The American journal of emergency medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajem.2023.04.039}, pmid = {37150648}, issn = {1532-8171}, } @article {pmid37134212, year = {2023}, author = {Schuler, T and King, C and Matsveru, T and Back, M and Clark, K and Chin, D and Lilian, R and Gallego, B and Coiera, E and Currow, DC}, title = {Wearable-Triggered Ecological Momentary Assessments Are Feasible in People With Advanced Cancer and Their Family Caregivers: Feasibility Study from an Outpatient Palliative Care Clinic at a Cancer Center.}, journal = {Journal of palliative medicine}, volume = {}, number = {}, pages = {}, doi = {10.1089/jpm.2022.0535}, pmid = {37134212}, issn = {1557-7740}, abstract = {Background: Emerging digital health approaches could play a role in better personalized palliative care. Aim: We conducted a feasibility study testing wearable sensor (WS)-triggered ecological momentary assessments (EMAs) and electronic patient-reported outcomes in community palliative care with patient-caregiver dyads. Design: All wore consumer-grade WS for five weeks. Sensor-detected "stress" (heart rate variability algorithm) that passed individualized thresholds triggered a short smartphone survey. Daily sleep surveys, weekly symptom surveys (Integrated Palliative care Outcome Scale), and a poststudy experience survey were conducted. Setting/Participants: Fifteen dyads (n = 30) were recruited from an outpatient palliative care clinic for people with cancer. Results: Daytime sensor wear-time had 73% adherence. Participants perceived value in this support. Quantity and severity of "stress" events were higher in patients. Sleep disturbance was similar but for different reasons: patients (physical symptoms) and caregivers (worrying about the patient). Conclusions: EMAs are feasible and valued in community palliative care.}, } @article {pmid37117267, year = {2023}, author = {Minhas, BF and Beck, EA and Cheng, CC and Catchen, J}, title = {Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6939}, pmid = {37117267}, issn = {2045-2322}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Temperature ; Heteroplasmy ; Fishes/genetics ; *Perciformes/physiology ; Antarctic Regions ; }, abstract = {Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.}, } @article {pmid37110442, year = {2023}, author = {Maimone, G and Azzaro, M and Placenti, F and Paranhos, R and Cabral, AS and Decembrini, F and Zaccone, R and Cosenza, A and Rappazzo, AC and Patti, B and Basilone, G and Cuttitta, A and Ferreri, R and Aronica, S and Ferla, R}, title = {A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110442}, issn = {2076-2607}, abstract = {A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.}, } @article {pmid36746772, year = {2023}, author = {Wu, Z and Jiang, Z and Li, Z and Jiao, P and Zhai, J and Liu, S and Han, X and Zhang, S and Sun, J and Gai, Z and Qiu, C and Xu, J and Liu, H and Qin, R and Lu, R}, title = {Multi-omics analysis reveals spatiotemporal regulation and function of heteromorphic leaves in Populus.}, journal = {Plant physiology}, volume = {192}, number = {1}, pages = {188-204}, pmid = {36746772}, issn = {1532-2548}, mesh = {*Populus/physiology ; Multiomics ; Plant Leaves/metabolism ; Transcriptome/genetics ; Chromatin/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {Despite the high economic and ecological importance of forests, our knowledge of the adaptive evolution of leaf traits remains very limited. Euphrates poplar (Populus euphratica), which has high tolerance to arid environment, has evolved four heteromorphic leaf forms, including narrow (linear and lanceolate) and broad (ovate and broad-ovate) leaves on different crowns. Here, we revealed the significant functional divergence of four P. euphratica heteromorphic leaves at physiological and cytological levels. Through global analysis of transcriptome and DNA methylation across tree and leaf developmental stages, we revealed that gene expression and DNA epigenetics differentially regulated key processes involving development and functional adaptation of heteromorphic leaves, such as hormone signaling pathways, cell division, and photosynthesis. Combined analysis of gene expression, methylation, ATAC-seq, and Hi-C-seq revealed longer interaction of 3D genome, hypomethylation, and open chromatin state upregulates IAA-related genes (such as PIN-FORMED1 and ANGUSTIFOLIA3) and promotes the occurrence of broad leaves while narrow leaves were associated with highly concentrated heterochromatin, hypermethylation, and upregulated abscisic acid pathway genes (such as Pyrabactin Resistance1-like10). Therefore, development of P. euphratica heteromorphic leaves along with functional divergence was regulated by differentially expressed genes, DNA methylation, chromatin accessibility, and 3D genome remodeling to adapt to the arid desert. This study advances our understanding of differential regulation on development and functional divergence of heteromorphic leaves in P. euphratica at the multi-omics level and provides a valuable resource for investigating the adaptive evolution of heteromorphic leaves in Populus.}, } @article {pmid37107825, year = {2023}, author = {Schütt, EM and Hundsdörfer, MAJ and von Hoyningen-Huene, AJE and Lange, X and Koschmider, A and Oppelt, N}, title = {First Steps towards a near Real-Time Modelling System of Vibrio vulnificus in the Baltic Sea.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {8}, pages = {}, pmid = {37107825}, issn = {1660-4601}, mesh = {Humans ; *Vibrio vulnificus ; *Vibrio Infections ; Water ; Baltic States ; Oxygen ; }, abstract = {Over the last two decades, Vibrio vulnificus infections have emerged as an increasingly serious public health threat along the German Baltic coast. To manage related risks, near real-time (NRT) modelling of V. vulnificus quantities has often been proposed. Such models require spatially explicit input data, for example, from remote sensing or numerical model products. We tested if data from a hydrodynamic, a meteorological, and a biogeochemical model are suitable as input for an NRT model system by coupling it with field samples and assessing the models' ability to capture known ecological parameters of V. vulnificus. We also identify the most important predictors for V. vulnificus in the Baltic Sea by leveraging the St. Nicolas House Analysis. Using a 27-year time series of sea surface temperature, we have investigated trends of V. vulnificus season length, which pinpoint hotspots mainly in the east of our study region. Our results underline the importance of water temperature and salinity on V. vulnificus abundance but also highlight the potential of air temperature, oxygen, and precipitation to serve as predictors in a statistical model, albeit their relationship with V. vulnificus may not be causal. The evaluated models cannot be used in an NRT model system due to data availability constraints, but promising alternatives are presented. The results provide a valuable basis for a future NRT model for V. vulnificus in the Baltic Sea.}, } @article {pmid37107056, year = {2023}, author = {Olivieri, R and Vannini, P and Corzani, A and Bianco, MT and Franchi, F and Cusi, MG and Scolletta, S and Arena, F and Basagni, C and Gusinu, R and Tumbarello, M}, title = {Rapid Decrease in Fluoroquinolones Consumption following Implementation of a Simple Antimicrobial Stewardship Bundled Intervention in a University Hospital during the COVID-19 Pandemic.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {37107056}, issn = {2079-6382}, abstract = {Fluoroquinolones (FQs) represent an class of antibiotics of medical importance, but their use has been restricted due to their ecologic impact and associated side effects. The reduction of FQs use is an important goal of antimicrobial stewardship programs (ASP). This work describes an ASP focused on overall antibiotics and FQs consumption reduction. From January 2021, an ASP was implemented in a 700-bed teaching hospital. The ASP was based on: (i) antibiotics consumption monitoring system (DDD/100 bed days); (ii) mandatory antibiotic prescription-motivation (using a dedicated informatic format) with the goal of >75% of motivated prescriptions; and (iii) data feedback and training on FQs use indications. We evaluated the impact of the intervention on overall systemic antibiotics and FQs consumption according to the objectives posed by Italian PNCAR (National Action Plan on Antimicrobial Resistance). A decrease of 6.6% in antibiotic use was observed (2019 vs. 2021). Notably, the FQs consumption fell by 48.3% from 7.1 DDD/100 bd in 2019 to 3.7 DDD/100 bd in 2021 (p < 0.001). After six months of mandatory antibiotic prescription-indication, all units achieved the target set. The study suggests that a simple, bundled ASP intervention can be rapidly effective obtaining the objectives of PNCAR on the reduction of overall antibiotics and FQs consumption.}, } @article {pmid37106771, year = {2023}, author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R}, title = {Boundaries Are Blurred: Wild Food Plant Knowledge Circulation across the Polish-Lithuanian-Belarusian Borderland.}, journal = {Biology}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/biology12040571}, pmid = {37106771}, issn = {2079-7737}, support = {714874/ERC_/European Research Council/International ; }, abstract = {The circulation of local ecological knowledge (LEK) is a promising avenue of research for wild plant studies. To encourage the acceptance, celebration, and appreciation of biocultural diversity, which is rapidly disappearing nowadays, we need to estimate and assess multifaceted local ecological knowledge. It has direct application for local communities in informing effective policies for improving food security and building community-specific responses to environmental and social transitions. The present study draws on data collected among two ethnic groups-Lithuanians and Poles-via 200 semi-structured in-depth interviews and participant observation conducted in 2018 and 2019 in Podlasie Voivodeship (Poland), the Vilnius Region (Lithuania), and the Hrodna Region (Belarus). We aimed to observe LEK circulation in the border area through cross-ethnic and cross-country comparisons. A total of 2812 detailed use reports of wild plants were recorded. In total, 72 wild plant taxa belonging to 33 plant families were used across the food domain. Our findings show that cross-country differences were minimal, while there was some variation between the ethnic groups selected as case studies. We emphasize the need, in future studies, to combine quantitative research with qualitative approaches in order to more thoroughly identify peculiarities of cross-border circulation as a reservoir for community food resilience and biocultural diversity.}, } @article {pmid37102710, year = {2023}, author = {Green, SJ and Torok, T and Allen, JE and Eloe-Fadrosh, E and Jackson, SA and Jiang, SC and Levine, SS and Levy, S and Schriml, LM and Thomas, WK and Wood, JM and Tighe, SW}, title = {Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1089/ast.2022.0044}, pmid = {37102710}, issn = {1557-8070}, abstract = {Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.}, } @article {pmid37101136, year = {2023}, author = {Mosquera, KD and Martínez Villegas, LE and Rocha Fernandes, G and Rocha David, M and Maciel-de-Freitas, R and A Moreira, L and Lorenzo, MG}, title = {Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {97}, pmid = {37101136}, issn = {1741-7007}, mesh = {Animals ; Humans ; Female ; *Aedes ; Mosquito Vectors ; Water ; Bacteria/genetics ; Oviposition ; Larva ; }, abstract = {BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.

RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.

CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.}, } @article {pmid37100861, year = {2023}, author = {Stocco, A and Pranovi, F}, title = {The paradoxical need for human intervention in the conservation of natural environments in Venice lagoon.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6798}, pmid = {37100861}, issn = {2045-2322}, mesh = {Humans ; *Ecosystem ; *Environment ; Aquaculture ; Climate ; Geography ; Conservation of Natural Resources/methods ; }, abstract = {The Venice lagoon-the largest Mediterranean coastal lagoon-is characterized by the presence at its edges of 31 "valli da pesca", types of artificial ecosystems that mime the ecological processes of a transitional aquatic ecosystem. Constituted by a series of regulated lakes bounded by artificial embankments, the valli da pesca were established centuries ago to maximize provisioning Ecosystem Services (ESs), such as fishing and hunting. As time passed, the valli da pesca underwent an intentional isolation process leading to private management. Nonetheless, the valli da pesca are still exchanging energy and matter with the "open' lagoon and today represent an essential element within the context of lagoon conservation. This study aimed to analyze the possible effects of artificial management on both ESs supply and landscape arrangements by assessing 9 ESs (climate regulation, water purification, lifecycle support, aquaculture, waterfowl hunting, wild food, tourism, information for cognitive development, and birdwatching), along with eight landscape indicators. Obtained results suggested that the valli da pesca are today ruled under five different management strategies, according to the maximized ES. Management conditions influence the landscape pattern and achieve a series of "side effects" on the other ESs. The comparison between the managed and abandoned valli da pesca highlights the importance of anthropogenic interventions for conserving these ecosystems, as the abandoned valli da pesca show a loss of ecological gradients, landscape heterogeneity, and provisioning ESs. Nevertheless, the persistence of intrinsic geographical and morphological characteristics still prevails regardless of intentional landscape molding. The result is that the provisioning ESs capacity per unit area is higher in the abandoned valli da pesca than in the open lagoon, emphasizing the importance of these confined areas of the lagoon ecosystem. Considering the spatial distribution of multiple ESs, the provisioning ESs flow that does not occur in the abandoned valli da pesca seems to be replaced by the flow of cultural ESs. Thus, the ESs spatial pattern highlights a balancing effect between different ESs categories. The results are discussed considering the trade-offs generated by private land conservation, anthropogenic interventions, and their relevance for the ecosystem-based management of Venice lagoon.}, } @article {pmid37099856, year = {2023}, author = {Sutton, C and Prowse, J and McVey, L and Elshehaly, M and Neagu, D and Montague, J and Alvarado, N and Tissiman, C and O'Connell, K and Eyers, E and Faisal, M and Randell, R}, title = {Strategic workforce planning in health and social care - an international perspective: A scoping review.}, journal = {Health policy (Amsterdam, Netherlands)}, volume = {132}, number = {}, pages = {104827}, doi = {10.1016/j.healthpol.2023.104827}, pmid = {37099856}, issn = {1872-6054}, abstract = {Effective strategic workforce planning for integrated and co-ordinated health and social care is essential if future services are to be resourced such that skill mix, clinical practice and productivity meet population health and social care needs in timely, safe and accessible ways globally. This review presents international literature to illustrate how strategic workforce planning in health and social care has been undertaken around the world with examples of planning frameworks, models and modelling approaches. The databases Business Source Premier, CINAHL, Embase, Health Management Information Consortium, Medline and Scopus were searched for full texts, from 2005 to 2022, detailing empirical research, models or methodologies to explain how strategic workforce planning (with at least a one-year horizon) in health and/or social care has been undertaken, yielding ultimately 101 included references. The supply/demand of a differentiated medical workforce was discussed in 25 references. Nursing and midwifery were characterised as undifferentiated labour, requiring urgent growth to meet demand. Unregistered workers were poorly represented as was the social care workforce. One reference considered planning for health and social care workers. Workforce modelling was illustrated in 66 references with predilection for quantifiable projections. Increasingly needs-based approaches were called for to better consider demography and epidemiological impacts. This review's findings advocate for whole-system needs-based approaches that consider the ecology of a co-produced health and social care workforce.}, } @article {pmid37098064, year = {2023}, author = {Shea, K and Borchering, RK and Probert, WJM and Howerton, E and Bogich, TL and Li, SL and van Panhuis, WG and Viboud, C and Aguás, R and Belov, AA and Bhargava, SH and Cavany, SM and Chang, JC and Chen, C and Chen, J and Chen, S and Chen, Y and Childs, LM and Chow, CC and Crooker, I and Del Valle, SY and España, G and Fairchild, G and Gerkin, RC and Germann, TC and Gu, Q and Guan, X and Guo, L and Hart, GR and Hladish, TJ and Hupert, N and Janies, D and Kerr, CC and Klein, DJ and Klein, EY and Lin, G and Manore, C and Meyers, LA and Mittler, JE and Mu, K and Núñez, RC and Oidtman, RJ and Pasco, R and Pastore Y Piontti, A and Paul, R and Pearson, CAB and Perdomo, DR and Perkins, TA and Pierce, K and Pillai, AN and Rael, RC and Rosenfeld, K and Ross, CW and Spencer, JA and Stoltzfus, AB and Toh, KB and Vattikuti, S and Vespignani, A and Wang, L and White, LJ and Xu, P and Yang, Y and Yogurtcu, ON and Zhang, W and Zhao, Y and Zou, D and Ferrari, MJ and Pannell, D and Tildesley, MJ and Seifarth, J and Johnson, E and Biggerstaff, M and Johansson, MA and Slayton, RB and Levander, JD and Stazer, J and Kerr, J and Runge, MC}, title = {Multiple models for outbreak decision support in the face of uncertainty.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {18}, pages = {e2207537120}, doi = {10.1073/pnas.2207537120}, pmid = {37098064}, issn = {1091-6490}, abstract = {Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020.}, } @article {pmid37097029, year = {2023}, author = {Carrol, ED and Ranjit, S and Menon, K and Bennett, TD and Sanchez-Pinto, LN and Zimmerman, JJ and Souza, DC and Sorce, LR and Randolph, AG and Ishimine, P and Flauzino de Oliveira, C and Lodha, R and Harmon, L and Watson, RS and Schlapbach, LJ and Kissoon, N and Argent, AC and , }, title = {Operationalizing Appropriate Sepsis Definitions in Children Worldwide: Considerations for the Pediatric Sepsis Definition Taskforce.}, journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies}, volume = {}, number = {}, pages = {}, doi = {10.1097/PCC.0000000000003263}, pmid = {37097029}, issn = {1529-7535}, abstract = {Sepsis is a leading cause of global mortality in children, yet definitions for pediatric sepsis are outdated and lack global applicability and validity. In adults, the Sepsis-3 Definition Taskforce queried databases from high-income countries to develop and validate the criteria. The merit of this definition has been widely acknowledged; however, important considerations about less-resourced and more diverse settings pose challenges to its use globally. To improve applicability and relevance globally, the Pediatric Sepsis Definition Taskforce sought to develop a conceptual framework and rationale of the critical aspects and context-specific factors that must be considered for the optimal operationalization of future pediatric sepsis definitions. It is important to address challenges in developing a set of pediatric sepsis criteria which capture manifestations of illnesses with vastly different etiologies and underlying mechanisms. Ideal criteria need to be unambiguous, and capable of adapting to the different contexts in which children with suspected infections are present around the globe. Additionally, criteria need to facilitate early recognition and timely escalation of treatment to prevent progression and limit life-threatening organ dysfunction. To address these challenges, locally adaptable solutions are required, which permit individualized care based on available resources and the pretest probability of sepsis. This should facilitate affordable diagnostics which support risk stratification and prediction of likely treatment responses, and solutions for locally relevant outcome measures. For this purpose, global collaborative databases need to be established, using minimum variable datasets from routinely collected data. In summary, a "Think globally, act locally" approach is required.}, } @article {pmid37095444, year = {2023}, author = {Demidova, EV and Serebriiskii, IG and Vlasenkova, R and Kelow, S and Andrake, MD and Hartman, TR and Kent, T and Virtucio, J and Rosen, GL and Pomerantz, RT and Dunbrack, RL and Golemis, EA and Hall, MJ and Chen, DYT and Daly, MB and Arora, S}, title = {Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {212}, pmid = {37095444}, issn = {1471-2164}, support = {P30 CA006927/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; 1R01GM130889/GF/NIH HHS/United States ; R35 GM122517/GF/NIH HHS/United States ; R01 DK108195/GF/NIH HHS/United States ; U01 CA164920/GF/NIH HHS/United States ; 1UH2CA271230-01/GF/NIH HHS/United States ; }, mesh = {Humans ; *Carcinoma, Renal Cell ; Genetic Predisposition to Disease ; DNA Replication ; Germ-Line Mutation ; *Kidney Neoplasms ; Germ Cells ; }, abstract = {BACKGROUND: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.

METHODS: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.

RESULTS: Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol δ and Pol η polymerases revealed defective enzymatic activities.

CONCLUSIONS: Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.}, } @article {pmid37094905, year = {2023}, author = {Girón, JC and Tarasov, S and González Montaña, LA and Matentzoglu, N and Smith, AD and Koch, M and Boudinot, BE and Bouchard, P and Burks, R and Vogt, L and Yoder, M and Osumi-Sutherland, D and Friedrich, F and Beutel, R and Mikó, I}, title = {Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syad025}, pmid = {37094905}, issn = {1076-836X}, abstract = {The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multi-species anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to (1) use controlled vocabularies and create semi-automated computer-parsable insect morphological descriptions; (2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and (3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.}, } @article {pmid37082718, year = {2023}, author = {Boyes, D and , and , and , and , and , and Mulley, JF and , }, title = {The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {66}, pmid = {37082718}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,717 protein coding genes.}, } @article {pmid36899120, year = {2023}, author = {Yilanci, V and Candan, G and Shah, MI}, title = {Identifying the roles of energy and economic factors on environmental degradation in MINT economies: a hesitant fuzzy analytic hierarchy process.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {19}, pages = {55768-55781}, pmid = {36899120}, issn = {1614-7499}, mesh = {Cross-Sectional Studies ; *Analytic Hierarchy Process ; Economic Development ; Carbon Dioxide ; Investments ; Economic Factors ; *Mentha ; Renewable Energy ; }, abstract = {Globally, research communities have been studying the different determinants of environmental degradation or pollution using different contexts and methods. In this study, we identify several energy and economic factors, such as energy consumption (EC), gross domestic product (GDP), energy production (EP), urbanization (URB), and foreign direct investment (FDI) as the most effective factors of environmental degradation by obtaining several environmental researchers' opinions and using the hesitant fuzzy analytic hierarchy process. In the later stage of the analysis, we use these variables as regressors of the ecological footprint (EF) as a proxy for environmental degradation. Since we find evidence of cross-sectional dependence among the members of the variables, we use second-generational panel tests. First, we test the stationarity of the variables using the cross-sectionally augmented IPS (CIPS) panel unit test. The results show that the regressors have different orders of integration. So, we employ the Durbin-Hausman panel cointegration test to test the existence of a long-run relationship between the variables. Having found a long-run relationship, we estimate the long-run coefficients using the common correlated effects mean group estimator, which reveals that energy consumption has an increasing effect on the EF in Indonesia and Turkey, while energy production has a negative impact in Mexico and Turkey. While GDP has an increasing effect in all countries, FDI has a similar effect in only Indonesia. Moreover, URB decreases the ecological footprint in Nigeria, while it increases in Turkey. Our approach to the evaluation of environmental degradation can be generalized to other regions as well as where there is a significant need to understand the roles of different drivers on environmental degradation or pollution.}, } @article {pmid37078321, year = {2023}, author = {Shu, CB and Shen, YL and Liu, G and Zhang, Q and Xu, JH and Guo, Z}, title = {Impacts of Eucalyptus plantation on soil and water losses in a typical small watershed in mountainous area of southern China.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {4}, pages = {1015-1023}, doi = {10.13287/j.1001-9332.202304.021}, pmid = {37078321}, issn = {1001-9332}, mesh = {*Soil ; *Eucalyptus ; Geographic Information Systems ; Forests ; China ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; }, abstract = {Unreasonable exploitation of artificial forest causes severe soil erosion in the mountainous areas of sou-thern China. The spatial-temporal variations of soil erosion in typical small watershed with artificial forest has signifi-cant implications for artificial forest exploitation and sustainable development of mountainous ecological environment. In this study, we used revised universal soil loss equation (RUSLE) and geographic information system (GIS) to evaluate the spatial and temporal variations of soil erosion and its key drivers of Dadingshan watershed in mountainous area of western Guangdong. The results showed that the erosion modulus was 1948.1 t·km[-2]·a[-1] (belonging to light erosion) in the Dadingshan watershed. However, the spatial variation of soil erosion was substantial, with variation coefficient of 5.12. The maximal soil erosion modulus was 191127 t·km[-2]·a[-1]. Slight erosion (<500 t·km[-2]·a[-1]) accounted for 80.6% of the total watershed area. The moderate erosion and above (>2500 t·km[-2]·a[-1]) were mainly distributed in young Eucalyptus forest area with less than 30% of the vegetation coverage, which contributed nearly 75.7% of total soil erosion. During 2014-2019, the interannual variations of mean erosion of Dadingshan catchment was modest, but the spatial variation of soil erosion was large. Vegetation cover, slope, and rainfall were key drivers of such variation. The destruction of natural vegetation resulted by plantation exploitation was the primary cause of soil erosion in afforestation areas. Soil erosion significantly increased with the increases of slope gradient in the young forest area, which was aggravated by extreme rainfall. However, soil erosion gradually decreased with the increases of the age of Eucalypt plantation. Therefore, the hot spot of soil erosion was young forest areas of Eucalypt plantation with slope >25°, and the key period for soil erosion control was the first 2-3 years after Eucalyptus planting. We suggested that reasonable afforestation measures should be used in area with >25° slopes, and that the destruction of natural vegetation should be avoided on hillslope with >35° slope gradient. The road construction standards and forest management should be further improved to address the challenge of extreme rainfalls.}, } @article {pmid37076812, year = {2023}, author = {De Wolfe, TJ and Wright, ES}, title = {Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {107}, pmid = {37076812}, issn = {1471-2180}, support = {T15 LM007059/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.

RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).

CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.}, } @article {pmid35737561, year = {2023}, author = {Swerdlow, BA and Sandel, DB and Johnson, SL}, title = {Shame on me for needing you: A multistudy examination of links between receiving interpersonal emotion regulation and experiencing shame.}, journal = {Emotion (Washington, D.C.)}, volume = {23}, number = {3}, pages = {737-752}, doi = {10.1037/emo0001109}, pmid = {35737561}, issn = {1931-1516}, support = {/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Emotions/physiology ; *Emotional Regulation ; Shame ; Hostility ; Data Management ; }, abstract = {Recent theory and research have drawn attention to interpersonal dimensions of emotion regulation. Yet, few empirical investigations of the outcomes of interpersonal emotion regulation have been conducted. We propose that one negative affective outcome of received interpersonal emotion regulation of conceptual and practical interest is shame. In the present series of studies, participants from six disparate samples reported on experiences of receiving interpersonal emotion regulation using autobiographical recall and ecological sampling paradigms (total analyzed n = 1,868; total analyzed k = 2,515 instances of receiving interpersonal emotion regulation). We sought to quantify the frequency and distinctiveness of shame as an outcome of receiving interpersonal emotion regulation. We used an exploratory-confirmatory approach to identify robust and generalizable correlates of shame. We considered individual (e.g., trait external shame-proneness), situational (e.g., desire for regulation), relational (e.g., perceived closeness with the provider), and interaction-specific (e.g., perceptions of provider hostility) variables. Our results indicate that it is not uncommon for people to experience receiving interpersonal emotion regulation as shame-inducing, and these perceptions are distinct from their evaluations of the overall helpfulness of the interaction. An internal mini meta-analysis showed that the strongest correlates of shame across studies and samples were individual differences in nonacceptance of negative emotions and expressive suppression and interaction-specific ratings of provider responsiveness and hostility. We discuss the conceptual, methodological, and practical implications of these findings for studying interpersonal emotion regulation and shame. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid37075104, year = {2023}, author = {Skirgård, H and Haynie, HJ and Blasi, DE and Hammarström, H and Collins, J and Latarche, JJ and Lesage, J and Weber, T and Witzlack-Makarevich, A and Passmore, S and Chira, A and Maurits, L and Dinnage, R and Dunn, M and Reesink, G and Singer, R and Bowern, C and Epps, P and Hill, J and Vesakoski, O and Robbeets, M and Abbas, NK and Auer, D and Bakker, NA and Barbos, G and Borges, RD and Danielsen, S and Dorenbusch, L and Dorn, E and Elliott, J and Falcone, G and Fischer, J and Ghanggo Ate, Y and Gibson, H and Göbel, HP and Goodall, JA and Gruner, V and Harvey, A and Hayes, R and Heer, L and Herrera Miranda, RE and Hübler, N and Huntington-Rainey, B and Ivani, JK and Johns, M and Just, E and Kashima, E and Kipf, C and Klingenberg, JV and König, N and Koti, A and Kowalik, RGA and Krasnoukhova, O and Lindvall, NLM and Lorenzen, M and Lutzenberger, H and Martins, TRA and Mata German, C and van der Meer, S and Montoya Samamé, J and Müller, M and Muradoglu, S and Neely, K and Nickel, J and Norvik, M and Oluoch, CA and Peacock, J and Pearey, IOC and Peck, N and Petit, S and Pieper, S and Poblete, M and Prestipino, D and Raabe, L and Raja, A and Reimringer, J and Rey, SC and Rizaew, J and Ruppert, E and Salmon, KK and Sammet, J and Schembri, R and Schlabbach, L and Schmidt, FWP and Skilton, A and Smith, WD and de Sousa, H and Sverredal, K and Valle, D and Vera, J and Voß, J and Witte, T and Wu, H and Yam, S and Ye, J and Yong, M and Yuditha, T and Zariquiey, R and Forkel, R and Evans, N and Levinson, SC and Haspelmath, M and Greenhill, SJ and Atkinson, QD and Gray, RD}, title = {Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss.}, journal = {Science advances}, volume = {9}, number = {16}, pages = {eadg6175}, pmid = {37075104}, issn = {2375-2548}, mesh = {Humans ; *Language ; *Linguistics ; Cognition ; Databases, Factual ; }, abstract = {While global patterns of human genetic diversity are increasingly well characterized, the diversity of human languages remains less systematically described. Here, we outline the Grambank database. With over 400,000 data points and 2400 languages, Grambank is the largest comparative grammatical database available. The comprehensiveness of Grambank allows us to quantify the relative effects of genealogical inheritance and geographic proximity on the structural diversity of the world's languages, evaluate constraints on linguistic diversity, and identify the world's most unusual languages. An analysis of the consequences of language loss reveals that the reduction in diversity will be strikingly uneven across the major linguistic regions of the world. Without sustained efforts to document and revitalize endangered languages, our linguistic window into human history, cognition, and culture will be seriously fragmented.}, } @article {pmid37072018, year = {2023}, author = {Jackson, C and Stewart, ID and Plekhanova, T and Cunningham, PS and Hazel, AL and Al-Sheklly, B and Aul, R and Bolton, CE and Chalder, T and Chalmers, JD and Chaudhuri, N and Docherty, AB and Donaldson, G and Edwardson, CL and Elneima, O and Greening, NJ and Hanley, NA and Harris, VC and Harrison, EM and Ho, LP and Houchen-Wolloff, L and Howard, LS and Jolley, CJ and Jones, MG and Leavy, OC and Lewis, KE and Lone, NI and Marks, M and McAuley, HJC and McNarry, MA and Patel, BV and Piper-Hanley, K and Poinasamy, K and Raman, B and Richardson, M and Rivera-Ortega, P and Rowland-Jones, SL and Rowlands, AV and Saunders, RM and Scott, JT and Sereno, M and Shah, AM and Shikotra, A and Singapuri, A and Stanel, SC and Thorpe, M and Wootton, DG and Yates, T and Gisli Jenkins, R and Singh, SJ and Man, WD and Brightling, CE and Wain, LV and Porter, JC and Thompson, AAR and Horsley, A and Molyneaux, PL and Evans, RA and Jones, SE and Rutter, MK and Blaikley, JF and , }, title = {Effects of sleep disturbance on dyspnoea and impaired lung function following hospital admission due to COVID-19 in the UK: a prospective multicentre cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(23)00124-8}, pmid = {37072018}, issn = {2213-2619}, abstract = {BACKGROUND: Sleep disturbance is common following hospital admission both for COVID-19 and other causes. The clinical associations of this for recovery after hospital admission are poorly understood despite sleep disturbance contributing to morbidity in other scenarios. We aimed to investigate the prevalence and nature of sleep disturbance after discharge following hospital admission for COVID-19 and to assess whether this was associated with dyspnoea.

METHODS: CircCOVID was a prospective multicentre cohort substudy designed to investigate the effects of circadian disruption and sleep disturbance on recovery after COVID-19 in a cohort of participants aged 18 years or older, admitted to hospital for COVID-19 in the UK, and discharged between March, 2020, and October, 2021. Participants were recruited from the Post-hospitalisation COVID-19 study (PHOSP-COVID). Follow-up data were collected at two timepoints: an early time point 2-7 months after hospital discharge and a later time point 10-14 months after hospital discharge. Sleep quality was assessed subjectively using the Pittsburgh Sleep Quality Index questionnaire and a numerical rating scale. Sleep quality was also assessed with an accelerometer worn on the wrist (actigraphy) for 14 days. Participants were also clinically phenotyped, including assessment of symptoms (ie, anxiety [Generalised Anxiety Disorder 7-item scale questionnaire], muscle function [SARC-F questionnaire], dyspnoea [Dyspnoea-12 questionnaire] and measurement of lung function), at the early timepoint after discharge. Actigraphy results were also compared to a matched UK Biobank cohort (non-hospitalised individuals and recently hospitalised individuals). Multivariable linear regression was used to define associations of sleep disturbance with the primary outcome of breathlessness and the other clinical symptoms. PHOSP-COVID is registered on the ISRCTN Registry (ISRCTN10980107).

FINDINGS: 2320 of 2468 participants in the PHOSP-COVID study attended an early timepoint research visit a median of 5 months (IQR 4-6) following discharge from 83 hospitals in the UK. Data for sleep quality were assessed by subjective measures (the Pittsburgh Sleep Quality Index questionnaire and the numerical rating scale) for 638 participants at the early time point. Sleep quality was also assessed using device-based measures (actigraphy) a median of 7 months (IQR 5-8 months) after discharge from hospital for 729 participants. After discharge from hospital, the majority (396 [62%] of 638) of participants who had been admitted to hospital for COVID-19 reported poor sleep quality in response to the Pittsburgh Sleep Quality Index questionnaire. A comparable proportion (338 [53%] of 638) of participants felt their sleep quality had deteriorated following discharge after COVID-19 admission, as assessed by the numerical rating scale. Device-based measurements were compared to an age-matched, sex-matched, BMI-matched, and time from discharge-matched UK Biobank cohort who had recently been admitted to hospital. Compared to the recently hospitalised matched UK Biobank cohort, participants in our study slept on average 65 min (95% CI 59 to 71) longer, had a lower sleep regularity index (-19%; 95% CI -20 to -16), and a lower sleep efficiency (3·83 percentage points; 95% CI 3·40 to 4·26). Similar results were obtained when comparisons were made with the non-hospitalised UK Biobank cohort. Overall sleep quality (unadjusted effect estimate 3·94; 95% CI 2·78 to 5·10), deterioration in sleep quality following hospital admission (3·00; 1·82 to 4·28), and sleep regularity (4·38; 2·10 to 6·65) were associated with higher dyspnoea scores. Poor sleep quality, deterioration in sleep quality, and sleep regularity were also associated with impaired lung function, as assessed by forced vital capacity. Depending on the sleep metric, anxiety mediated 18-39% of the effect of sleep disturbance on dyspnoea, while muscle weakness mediated 27-41% of this effect.

INTERPRETATION: Sleep disturbance following hospital admission for COVID-19 is associated with dyspnoea, anxiety, and muscle weakness. Due to the association with multiple symptoms, targeting sleep disturbance might be beneficial in treating the post-COVID-19 condition.

FUNDING: UK Research and Innovation, National Institute for Health Research, and Engineering and Physical Sciences Research Council.}, } @article {pmid37069545, year = {2023}, author = {Cai, P and Liu, S and Zhang, D and Xing, H and Han, M and Liu, D and Gong, L and Hu, QN}, title = {SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {152}, pmid = {37069545}, issn = {1471-2105}, mesh = {*Synthetic Biology ; *Computational Biology/methods ; Registries ; Databases, Factual ; Software ; }, abstract = {BACKGROUND: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology.

RESULTS: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system.

CONCLUSIONS: SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.}, } @article {pmid37069271, year = {2023}, author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H}, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {37069271}, issn = {1548-7105}, support = {R01 EB028159/EB/NIBIB NIH HHS/United States ; RF1 MH128693/MH/NIMH NIH HHS/United States ; }, abstract = {BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.}, } @article {pmid37049742, year = {2023}, author = {Biswas, P and Bibi, S and Yousafi, Q and Mehmood, A and Saleem, S and Ihsan, A and Dey, D and Hasan Zilani, MN and Hasan, MN and Saleem, R and Awaji, AA and Fahmy, UA and Abdel-Daim, MM}, title = {Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {7}, pages = {}, pmid = {37049742}, issn = {1420-3049}, mesh = {Humans ; Tumor Suppressor Protein p53/metabolism ; Molecular Docking Simulation ; Proto-Oncogene Proteins c-mdm2/metabolism ; DNA Copy Number Variations ; Prognosis ; *Brain Neoplasms/drug therapy/genetics/metabolism ; *Glioma/drug therapy/genetics/metabolism ; Biomarkers ; Drug Development ; Brain/metabolism ; }, abstract = {An evaluation of the expression and predictive significance of the MDM2 gene in brain lower-grade glioma (LGG) cancer was carried out using onco-informatics pipelines. Several transcriptome servers were used to measure the differential expression of the targeted MDM2 gene and search mutations and copy number variations. GENT2, Gene Expression Profiling Interactive Analysis, Onco-Lnc, and PrognoScan were used to figure out the survival rate of LGG cancer patients. The protein-protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. Identified bioactive phytochemicals were evaluated through molecular docking using Schrödinger Suite Software, with the MDM2 (PDB ID: 1RV1) target. Protein-ligand interactions were observed with key residues of the macromolecular target. A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. Phytochemicals targeting MDM2 protein, such as Taxifolin and (-)-Epicatechin, have been shown with more highly stable results as compared to the control drug, and hence, concluded that phytochemicals with bioactive potential might be alternative therapeutic options for the management of LGG patients. Our once informatics-based designed pipeline has indicated that the MDM2 gene may have been a predictive biomarker for LGG cancer and selected phytochemicals possessed outstanding interaction results within the macromolecular target's active site after utilizing in silico approaches. In vitro and in vivo experiments are recommended to confirm these outcomes.}, } @article {pmid36736631, year = {2023}, author = {LaVigne, AW and DeWeese, TL and Wright, JL and Deville, C and Yegnasubramanian, S and Alcorn, SR}, title = {Radiotherapy Deserts: The Impact of Race, Poverty, and the Rural-Urban Continuum on Density of Providers and the Use of Radiation Therapy in the US.}, journal = {International journal of radiation oncology, biology, physics}, volume = {116}, number = {1}, pages = {17-27}, doi = {10.1016/j.ijrobp.2023.01.046}, pmid = {36736631}, issn = {1879-355X}, mesh = {Aged ; Humans ; Male ; Medicare/statistics & numerical data ; *Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Poverty/statistics & numerical data ; Rural Population/statistics & numerical data ; Social Class ; United States/epidemiology ; Urban Population/statistics & numerical data ; *Radiotherapy/economics/standards/statistics & numerical data ; Resource-Limited Settings/statistics & numerical data ; Race Factors/statistics & numerical data ; Health Personnel/statistics & numerical data ; Health Services Accessibility/statistics & numerical data ; Health Services Needs and Demand/statistics & numerical data ; Prostatic Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Breast Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Female ; Databases, Factual/statistics & numerical data ; Patient-Centered Care/statistics & numerical data ; *Healthcare Disparities/economics/ethnology/statistics & numerical data ; }, abstract = {PURPOSE: Prior efforts to characterize disparities in radiation therapy access and receipt have not comprehensively investigated interplay between race, socioeconomic status, and geography relative to oncologic outcomes. This study sought to define these complex relationships at the US county level for prostate cancer (PC) and invasive breast (BC) cancer to build a tool that facilitates identification of "radiotherapy deserts"-regions with mismatch between radiation therapy resources and oncologic need.

METHODS AND MATERIALS: An ecologic study model was constructed using national databases to evaluate 3,141 US counties. Radiation therapy resources and use densities were operationalized as physicians to persons at risk (PPR) and use to persons at risk (UPR): the number of attending radiation oncologists and Medicare beneficiaries per 100,000 persons at risk, respectively. Oncologic need was defined by "hot zone" counties with ≥2 standard deviations (SDs) above mean incidence and death rates. Univariable and multivariable logistic regressions examined links between PPR and UPR densities, epidemiologic variables, and hot zones for oncologic outcomes. Statistics are reported at a significance level of P < .05.

RESULTS: The mean (SD) PPR and UPR densities were 2.1 (5.9) and 192.6 (557.6) for PC and 1.9 (5.3) and 174.4 (501.0) for BC, respectively. Counties with high PPR and UPR densities were predominately metropolitan (odds ratio [OR], 2.9-4.4), generally with a higher percentage of Black non-Hispanic constituents (OR, 1.5-2.3). Incidence and death rate hot zones were largely nonmetropolitan (OR, 0.3-0.6), generally with a higher percentage of Black non-Hispanic constituents (OR, 3.2-6.3). Lower PPR density was associated with death rate hot zones for both types of cancer (OR, 0.8-0.9); UPR density was generally not linked to oncologic outcomes on multivariable analysis.

CONCLUSIONS: The study found that mismatch between oncologic need with PPR and UPR disproportionately affects nonmetropolitan communities with a higher percentage of Black non-Hispanic constituents. An interactive web platform (bit.ly/densitymaps) was developed to visualize "radiotherapy deserts" and drive targeted investigation of underlying barriers to care in areas of highest need, with the goal of reducing health inequities in this context.}, } @article {pmid37047894, year = {2023}, author = {Roberts, M and Colley, K and Currie, M and Eastwood, A and Li, KH and Avery, LM and Beevers, LC and Braithwaite, I and Dallimer, M and Davies, ZG and Fisher, HL and Gidlow, CJ and Memon, A and Mudway, IS and Naylor, LA and Reis, S and Smith, P and Stansfeld, SA and Wilkie, S and Irvine, KN}, title = {The Contribution of Environmental Science to Mental Health Research: A Scoping Review.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {7}, pages = {}, pmid = {37047894}, issn = {1660-4601}, mesh = {Humans ; Mental Health ; *COVID-19 ; Pandemics ; *Environmental Science ; Environmental Exposure ; }, abstract = {Mental health is influenced by multiple complex and interacting genetic, psychological, social, and environmental factors. As such, developing state-of-the-art mental health knowledge requires collaboration across academic disciplines, including environmental science. To assess the current contribution of environmental science to this field, a scoping review of the literature on environmental influences on mental health (including conditions of cognitive development and decline) was conducted. The review protocol was developed in consultation with experts working across mental health and environmental science. The scoping review included 202 English-language papers, published between 2010 and 2020 (prior to the COVID-19 pandemic), on environmental themes that had not already been the subject of recent systematic reviews; 26 reviews on climate change, flooding, air pollution, and urban green space were additionally considered. Studies largely focused on populations in the USA, China, or Europe and involved limited environmental science input. Environmental science research methods are primarily focused on quantitative approaches utilising secondary datasets or field data. Mental health measurement was dominated by the use of self-report psychometric scales. Measures of environmental states or exposures were often lacking in specificity (e.g., limited to the presence or absence of an environmental state). Based on the scoping review findings and our synthesis of the recent reviews, a research agenda for environmental science's future contribution to mental health scholarship is set out. This includes recommendations to expand the geographical scope and broaden the representation of different environmental science areas, improve measurement of environmental exposure, prioritise experimental and longitudinal research designs, and giving greater consideration to variation between and within communities and the mediating pathways by which environment influences mental health. There is also considerable opportunity to increase interdisciplinarity within the field via the integration of conceptual models, the inclusion of mixed methods and qualitative approaches, as well as further consideration of the socio-political context and the environmental states that can help support good mental health. The findings were used to propose a conceptual model to parse contributions and connections between environmental science and mental health to inform future studies.}, } @article {pmid37046168, year = {2023}, author = {Chen, D and Feng, Q and Zhang, Y}, title = {Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-023-26775-y}, pmid = {37046168}, issn = {1614-7499}, abstract = {In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.}, } @article {pmid36947137, year = {2023}, author = {James, JE and Nelson, PG and Masel, J}, title = {Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.}, journal = {Molecular biology and evolution}, volume = {40}, number = {4}, pages = {}, pmid = {36947137}, issn = {1537-1719}, mesh = {Animals ; *Proteome ; Protein Domains ; Probability ; Hydrophobic and Hydrophilic Interactions ; Databases, Protein ; }, abstract = {Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.}, } @article {pmid34021761, year = {2021}, author = {Halder, S and Ghosh, S and Chattopadhyay, J and Chatterjee, S}, title = {Bistability in cell signalling and its significance in identifying potential drug-targets.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {22}, pages = {4156-4163}, doi = {10.1093/bioinformatics/btab395}, pmid = {34021761}, issn = {1367-4811}, mesh = {*Signal Transduction ; *Protein Interaction Domains and Motifs ; Computational Biology ; }, abstract = {MOTIVATION: Bistability is one of the salient dynamical features in various all-or-none kinds of decision-making processes. The presence of bistability in a cell signalling network plays a key role in input-output (I/O) relation. Our study is aiming to capture and emphasize the role of motif structure influencing the I/O relation between two nodes in the context of bistability. Here, a model-based analysis is made to investigate the critical conditions responsible for the emergence of different bistable protein-protein interaction (PPI) motifs and their possible applications to find the potential drug-targets.

RESULTS: The global sensitivity analysis is used to identify sensitive parameters and their role in maintaining the bistability. Additionally, the bistable switching through hysteresis is explored to develop an understanding of the underlying mechanisms involved in the cell signalling processes, when significant motifs exhibiting bistability have emerged. Further, we elaborate the application of the results by the implication of the emerged PPI motifs to identify potential drug-targets in three cancer networks, which is validated with existing databases. The influence of stochastic perturbations that could hinder desired functionality of any signalling networks is also described here.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid37043542, year = {2023}, author = {Labbé, F and Abdeladhim, M and Abrudan, J and Araki, AS and Araujo, RN and Arensburger, P and Benoit, JB and Brazil, RP and Bruno, RV and Bueno da Silva Rivas, G and Carvalho de Abreu, V and Charamis, J and Coutinho-Abreu, IV and da Costa-Latgé, SG and Darby, A and Dillon, VM and Emrich, SJ and Fernandez-Medina, D and Figueiredo Gontijo, N and Flanley, CM and Gatherer, D and Genta, FA and Gesing, S and Giraldo-Calderón, GI and Gomes, B and Aguiar, ERGR and Hamilton, JGC and Hamarsheh, O and Hawksworth, M and Hendershot, JM and Hickner, PV and Imler, JL and Ioannidis, P and Jennings, EC and Kamhawi, S and Karageorgiou, C and Kennedy, RC and Krueger, A and Latorre-Estivalis, JM and Ligoxygakis, P and Meireles-Filho, ACA and Minx, P and Miranda, JC and Montague, MJ and Nowling, RJ and Oliveira, F and Ortigão-Farias, J and Pavan, MG and Horacio Pereira, M and Nobrega Pitaluga, A and Proveti Olmo, R and Ramalho-Ortigao, M and Ribeiro, JMC and Rosendale, AJ and Sant'Anna, MRV and Scherer, SE and Secundino, NFC and Shoue, DA and da Silva Moraes, C and Gesto, JSM and Souza, NA and Syed, Z and Tadros, S and Teles-de-Freitas, R and Telleria, EL and Tomlinson, C and Traub-Csekö, YM and Marques, JT and Tu, Z and Unger, MF and Valenzuela, J and Ferreira, FV and de Oliveira, KPV and Vigoder, FM and Vontas, J and Wang, L and Weedall, GD and Zhioua, E and Richards, S and Warren, WC and Waterhouse, RM and Dillon, RJ and McDowell, MA}, title = {Genomic analysis of two phlebotomine sand fly vectors of leishmania from the new and old World.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {4}, pages = {e0010862}, doi = {10.1371/journal.pntd.0010862}, pmid = {37043542}, issn = {1935-2735}, abstract = {Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.}, } @article {pmid37040629, year = {2023}, author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE}, title = {Correction: The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e47896}, doi = {10.2196/47896}, pmid = {37040629}, issn = {1438-8871}, abstract = {[This corrects the article DOI: 10.2196/43623.].}, } @article {pmid34469515, year = {2021}, author = {Sundell, D and Öhrman, C and Svensson, D and Karlsson, E and Brindefalk, B and Myrtennäs, K and Ahlinder, J and Antwerpen, MH and Walter, MC and Forsman, M and Stenberg, P and Sjödin, A}, title = {FlexTaxD: flexible modification of taxonomy databases for improved sequence classification.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {21}, pages = {3932-3933}, doi = {10.1093/bioinformatics/btab621}, pmid = {34469515}, issn = {1367-4811}, mesh = {*Software ; Databases, Factual ; }, abstract = {SUMMARY: The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.

Source code is freely available at https://github.com/FOI-Bioinformatics/flextaxd and installable through Bioconda.}, } @article {pmid37025368, year = {2022}, author = {Lohse, K and Höök, L and Näsvall, K and Backström, N and , and , and , and , }, title = {The genome sequence of the wood white butterfly, Leptidea sinapis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {254}, pmid = {37025368}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Leptidea sinapis (the wood white; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 686 megabases in span. The majority (99.99%) of the assembly is scaffolded into 48 chromosomal pseudomolecules, with three Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 14,800 protein coding genes.}, } @article {pmid37022698, year = {2023}, author = {Nartker, M and Zhou, Z and Firestone, C}, title = {When will AI misclassify? Intuiting failures on natural images.}, journal = {Journal of vision}, volume = {23}, number = {4}, pages = {4}, pmid = {37022698}, issn = {1534-7362}, mesh = {Humans ; *Artificial Intelligence ; *Image Interpretation, Computer-Assisted ; }, abstract = {Machine recognition systems now rival humans in their ability to classify natural images. However, their success is accompanied by a striking failure: a tendency to commit bizarre misclassifications on inputs specifically selected to fool them. What do ordinary people know about the nature and prevalence of such classification errors? Here, five experiments exploit the recent discovery of "natural adversarial examples" to ask whether naive observers can predict when and how machines will misclassify natural images. Whereas classical adversarial examples are inputs that have been minimally perturbed to induce misclassifications, natural adversarial examples are simply unmodified natural photographs that consistently fool a wide variety of machine recognition systems. For example, a bird casting a shadow might be misclassified as a sundial, or a beach umbrella made of straw might be misclassified as a broom. In Experiment 1, subjects accurately predicted which natural images machines would misclassify and which they would not. Experiments 2 through 4 extended this ability to how the images would be misclassified, showing that anticipating machine misclassifications goes beyond merely identifying an image as nonprototypical. Finally, Experiment 5 replicated these findings under more ecologically valid conditions, demonstrating that subjects can anticipate misclassifications not only under two-alternative forced-choice conditions (as in Experiments 1-4), but also when the images appear one at a time in a continuous stream-a skill that may be of value to human-machine teams. We suggest that ordinary people can intuit how easy or hard a natural image is to classify, and we discuss the implications of these results for practical and theoretical issues at the interface of biological and artificial vision.}, } @article {pmid36725822, year = {2023}, author = {Pernet, C and Svarer, C and Blair, R and Van Horn, JD and Poldrack, RA}, title = {On the Long-term Archiving of Research Data.}, journal = {Neuroinformatics}, volume = {21}, number = {2}, pages = {243-246}, pmid = {36725822}, issn = {1559-0089}, mesh = {*Information Dissemination ; *Information Storage and Retrieval ; }, abstract = {Accessing research data at any time is what FAIR (Findable Accessible Interoperable Reusable) data sharing aims to achieve at scale. Yet, we argue that it is not sustainable to keep accumulating and maintaining all datasets for rapid access, considering the monetary and ecological cost of maintaining repositories. Here, we address the issue of cold data storage: when to dispose of data for offline storage, how can this be done while maintaining FAIR principles and who should be responsible for cold archiving and long-term preservation.}, } @article {pmid37022232, year = {2023}, author = {Zimmerman, S and Tierney, BT and Patel, CJ and Kostic, AD}, title = {Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0011823}, doi = {10.1128/msystems.00118-23}, pmid = {37022232}, issn = {2379-5077}, abstract = {Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.}, } @article {pmid36948010, year = {2023}, author = {Hao, N and Sun, P and Zhao, W and Li, X}, title = {Application of a developed triple-classification machine learning model for carcinogenic prediction of hazardous organic chemicals to the US, EU, and WHO based on Chinese database.}, journal = {Ecotoxicology and environmental safety}, volume = {255}, number = {}, pages = {114806}, doi = {10.1016/j.ecoenv.2023.114806}, pmid = {36948010}, issn = {1090-2414}, mesh = {Bayes Theorem ; Carcinogenesis ; *Carcinogens/toxicity/chemistry ; *Hazardous Substances/chemistry/toxicity ; *Machine Learning ; *Organic Chemicals/toxicity/chemistry ; Support Vector Machine ; World Health Organization ; Algorithms ; United States ; European Union ; China ; Databases, Factual ; }, abstract = {Cancer, the second largest human disease, has become a major public health problem. The prediction of chemicals' carcinogenicity before their synthesis is crucial. In this paper, seven machine learning algorithms (i.e., Random Forest (RF), Logistic Regression (LR), Support Vector Machines (SVM), Complement Naive Bayes (CNB), K-Nearest Neighbor (KNN), XGBoost, and Multilayer Perceptron (MLP)) were used to construct the carcinogenicity triple classification prediction (TCP) model (i.e., 1A, 1B, Category 2). A total of 1444 descriptors of 118 hazardous organic chemicals were calculated by Discovery Studio 2020, Sybyl X-2.0 and PaDEL-Descriptor software. The constructed carcinogenicity TCP model was evaluated through five model evaluation indicators (i.e., Accuracy, Precision, Recall, F1 Score and AUC). The model evaluation results show that Accuracy, Precision, Recall, F1 Score and AUC evaluation indicators meet requirements (greater than 0.6). The accuracy of RF, LR, XGBoost, and MLP models for predicting carcinogenicity of Category 2 is 91.67%, 79.17%, 100%, and 100%, respectively. In addition, the constructed machine learning model in this study has potential for error correction. Taking XGBoost model as an example, the predicted carcinogenicity level of 1,2,3-Trichloropropane (96-18-4) is Category 2, but the actual carcinogenicity level is 1B. But the difference between Category 2 and 1B is only 0.004, indicating that the XGBoost is one optimum model of the seven constructed machine learning models. Besides, results showed that functional groups like chlorine and benzene ring might influence the prediction of carcinogenic classification. Therefore, considering functional group characteristics of chemicals before constructing the carcinogenicity prediction model of organic chemicals is recommended. The predicted carcinogenicity of the organic chemicals using the optimum machine leaning model (i.e., XGBoost) was also evaluated and verified by the toxicokinetics. The RF and XGBoost TCP models constructed in this paper can be used for carcinogenicity detection before synthesizing new organic substances. It also provides technical support for the subsequent management of organic chemicals.}, } @article {pmid37021064, year = {2023}, author = {Keller, R and Spanu, A and Puhan, MA and Flahault, A and Lovis, C and Mütsch, M and Beau-Lejdstrom, R}, title = {Social media and internet search data to inform drug utilization: A systematic scoping review.}, journal = {Frontiers in digital health}, volume = {5}, number = {}, pages = {1074961}, pmid = {37021064}, issn = {2673-253X}, abstract = {INTRODUCTION: Drug utilization is currently assessed through traditional data sources such as big electronic medical records (EMRs) databases, surveys, and medication sales. Social media and internet data have been reported to provide more accessible and more timely access to medications' utilization.

OBJECTIVE: This review aims at providing evidence comparing web data on drug utilization to other sources before the COVID-19 pandemic.

METHODS: We searched Medline, EMBASE, Web of Science, and Scopus until November 25th, 2019, using a predefined search strategy. Two independent reviewers conducted screening and data extraction.

RESULTS: Of 6,563 (64%) deduplicated publications retrieved, 14 (0.2%) were included. All studies showed positive associations between drug utilization information from web and comparison data using very different methods. A total of nine (64%) studies found positive linear correlations in drug utilization between web and comparison data. Five studies reported association using other methods: One study reported similar drug popularity rankings using both data sources. Two studies developed prediction models for future drug consumption, including both web and comparison data, and two studies conducted ecological analyses but did not quantitatively compare data sources. According to the STROBE, RECORD, and RECORD-PE checklists, overall reporting quality was mediocre. Many items were left blank as they were out of scope for the type of study investigated.

CONCLUSION: Our results demonstrate the potential of web data for assessing drug utilization, although the field is still in a nascent period of investigation. Ultimately, social media and internet search data could be used to get a quick preliminary quantification of drug use in real time. Additional studies on the topic should use more standardized methodologies on different sets of drugs in order to confirm these findings. In addition, currently available checklists for study quality of reporting would need to be adapted to these new sources of scientific information.}, } @article {pmid37018807, year = {2023}, author = {Xavier, JMA and Firmino, RT and Pereira, IF and Xavier, MA and Costa, MCFD and Soares, RSC and Ribeiro, AIAM}, title = {The impact of the COVID-19 pandemic in Brazil: a study in tertiary dental care.}, journal = {Brazilian oral research}, volume = {37}, number = {}, pages = {025}, doi = {10.1590/1807-3107bor-2023.vol37.0025}, pmid = {37018807}, issn = {1807-3107}, mesh = {Humans ; *COVID-19 ; Pandemics ; Tertiary Healthcare ; Brazil ; Dental Care ; }, abstract = {The pandemic caused by coronavirus has resonated throughout different levels of health care in Brazil and, in this context, the present research aimed to evaluate this impact on tertiary dental care provided by the Unified Health System (SUS). Therefore, an ecological study was conducted with data obtained from the Hospital Information System processed by the Portal of the Department of Informatics of SUS. The sample consisted of patients of all sexes and age groups, whose Hospital Admission Authorizations (AIHs) were approved for dental tertiary care procedures from January 2015 to December 2020. Descriptive analyses and the ANOVA test with a significance level set at p < 0.05 were used. When the annual mean numbers of AIHs approved were evaluated, findings showed that on an average, the Southeast region authorized a higher number of procedures (p-value < 0.001), however, in the pandemic year (2020), a reduction of approximately 24.5% of these hospitalizations occurred throughout Brazil, with the Midwest being the region most affected (32.12%). A percentage increase occurred in the Surgical Treatment of Oral sinus/Oral nasal Fistula (16.1%), in addition to a significant decrease in performing procedures for Resection of Mouth Lesion (33.4%). In the pandemic year, there was a reduction of 14% in expenditures related to hospital services and 23.26% related to professional services. It was concluded that the data presented demonstrated a significant reduction in AIHs for tertiary dental care in the pandemic year.}, } @article {pmid37016902, year = {2023}, author = {Pandit, AA and Mahashabde, RV and Brown, CC and Acharya, M and Shoults, CC and Eswaran, H and Hayes, CJ}, title = {Association between broadband capacity and telehealth utilization among Medicare Fee-for-service beneficiaries during the COVID-19 pandemic.}, journal = {Journal of telemedicine and telecare}, volume = {}, number = {}, pages = {1357633X231166026}, doi = {10.1177/1357633X231166026}, pmid = {37016902}, issn = {1758-1109}, abstract = {BACKGROUND: Telehealth is a rapidly growing modality for expanding healthcare access, especially in the post-COVID-19 era. However, telehealth requires high-quality broadband, thus making broadband a social determinant of health. The objective of this study was to evaluate the association between broadband access and telehealth utilization across the United States during the COVID-19 pandemic.

METHODS: Using a cross-sectional, ecological study design, we merged county-level data on broadband capacity (Microsoft's Rural Broadband Initiative), telehealth utilization among Medicare Fee-for-Service beneficiaries from January through September 2020 (CareJourney), and county-level socioeconomic characteristics (Area Health Resources Files). Multivariable linear regression was used to estimate the association between broadband capacity, county-level characteristics, and telehealth utilization.

RESULTS: Among the 3107 counties, those with the greatest broadband availability (quintile 5) had 47% higher telehealth utilization compared to counties with the least broadband availability (quintile 1). In the adjusted model, a 1 standard deviation (SD) increase in broadband access was associated with a 1.54 percentage point (pp) increase in telehealth utilization (P < 0.001). Rural county designation (-1.96 pp; P < 0.001) and 1 SD increases in average Medicare beneficiary age (-1.34 pp; P = 0.001), number of nursing home beds per 1000 individuals (-0.38 pp; P = 0.002), and proportion of Native Americans/Pacific Islanders (-0.59 pp; P < 0.001) were associated with decreased telehealth utilization.

CONCLUSION: The association between broadband access and telehealth utilization and the decreased telehealth utilization in rural areas highlight the importance of broadband access for healthcare access and the need to continue investing in broadband infrastructure to promote equitable healthcare access across populations.}, } @article {pmid37011221, year = {2023}, author = {Still, CJ and Page, GFM and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, DA and Goulden, M and Pau, S and Detto, M and Helliker, BR and Richardson, AD}, title = {Reply to Garen et al.: Within-canopy temperature data also do not support limited homeothermy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2302515120}, doi = {10.1073/pnas.2302515120}, pmid = {37011221}, issn = {1091-6490}, mesh = {Temperature ; *Body Temperature Regulation ; }, } @article {pmid36478393, year = {2023}, author = {Keck, F and Couton, M and Altermatt, F}, title = {Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {742-755}, doi = {10.1111/1755-0998.13746}, pmid = {36478393}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic ; Biodiversity ; Ecology ; Databases, Nucleic Acid ; *DNA, Environmental ; }, abstract = {Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the nondetection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate inferences of taxonomic assignment. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually nonexclusive list of seven classes of challenges when it comes to selecting, developing and using a reference database for taxonomic assignment. These are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as GenBank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users' awareness of the limitations of metabarcoding data and DNA reference databases will adequate interpretations of these data be achieved.}, } @article {pmid37008251, year = {2022}, author = {Boyes, D and Wright, C and , and , and , and , and , and , }, title = {The genome sequence of the peppered moth, Biston betularia Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {97}, pmid = {37008251}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Biston betularia (the peppered moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 405 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.Gene annotation of this assembly on Ensembl has identified 12,251 protein coding genes.}, } @article {pmid37006240, year = {2023}, author = {Yang, W and Wei, C and Cheng, J and Ding, R and Li, Y and Wang, Y and Yang, Y and Wang, J}, title = {BTG2 and SerpinB5, a novel gene pair to evaluate the prognosis of lung adenocarcinoma.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1098700}, pmid = {37006240}, issn = {1664-3224}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; Molecular Docking Simulation ; *Lung Neoplasms/genetics ; *Adenocarcinoma of Lung/genetics ; Prognosis ; Tumor Microenvironment ; *Immediate-Early Proteins/genetics ; Tumor Suppressor Proteins/genetics ; }, abstract = {INTRODUCTION: Lung adenocarcinoma (LUAD), as the most frequent pathological subtype of non-small cell lung cancer, is often characterized by poor prognosis and low 5-year survival rate. Exploriton of new biomarkers and accurate molecular mechanisms for effectively predicting the prognosis of LUAD patients is still necessary. Presently, BTG2 and SerpinB5, which play important roles in tumors, are studied as a gene pair for the first time with the aim of exploring whether they can be used as potential prognostic markers.

METHODS: Using the bioinformatics method to explore whether BTG2 and SerpinB5 can become independent prognostic factors, and explore their clinical application value and whether they can be used as immunotherapeutic markers. In addition, we also verify the conclusions obtained from external datasets, molecular docking, and SqRT-PCR.

RESULTS: The results show that compared with normal lung tissue, BTG2 expression level was down-regulated and SerpinB5 was up-regulated in LUAD. Additionally, Kaplan-Meier survival analysis demonstrate that the prognosis of low expression level of BTG2 was poor, and that of high expression level of SerpinB5 was poor, suggesting that both of them can be used as independent prognostic factors. Moreover, the prognosis models of the two genes were constructed respectively in this study, and their prediction effect was verified by external data. Besides, ESTIMATE algorithm reveals the relationship between this gene pair and the immune microenvironment. Furthermore, patients with a high expression level of BTG2 and a low expression level of SerpinB5 have higher immunophenoscore for CTLA-4 and PD-1 inhibitors than patients with a low expression level of BTG2 and a high expression level of SerpinB5, indicating that such patients have a more obvious effect of immunotherapy.

DISCUSSION: Collectively, all the results demonstrate that BTG2 and SerpinB5 might serve as potential prognostic biomarkers and novel therapeutic targets for LUAD.}, } @article {pmid37004043, year = {2023}, author = {Khan, AH and Adil, M and Aziz, MA and Sõukand, R and Pieroni, A}, title = {Traditional foraging for ecological transition? Wild food ethnobotany among three ethnic groups in the highlands of the eastern Hindukush, North Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {9}, pmid = {37004043}, issn = {1746-4269}, abstract = {BACKGROUND: The Patrak Valley is home to communities, which have been inextricably linked with nature for generations, and local plant knowledge (LPK) represents an important part of their local cultural diversity. In general, globalization has come at the expense of local plant knowledge among several mountain societies, and therefore the current investigation has been undertaken to record the (possibly) last remaining wild food plant/mushroom foraging practices among Pathans, Kohistanis, and Gujjars living in the highlands of the Hindukush, North Pakistan.

METHODS: Data on the uses of wild food plants and mushrooms (WFPs) were collected through 120 semi-structured interviews. The data were cross-culturally compared among the three linguistic groups. Venn diagrams were used to visualize the comparative analysis. To determine the patterns of similarities in plant use among the different ethnic groups, we used the Jaccard similarity index (JI). The recorded data were also compared with the existing Pakistani food ethnobotanical literature.

RESULTS: A total of 68 WFPs were recorded, the majority of which were used as raw snacks and as cooked vegetables. Fruit was the most frequently reported plant part among the three researched groups. Cross-cultural comparison revealed that 37% of the used plants were commonly shared by the three studied groups. Pathans have retained rich knowledge on WFPs, and they show a comparatively closer affinity with Kohistanis is the use of WFPs compared to Gujjars. While we observed some idiosyncrasies for each of the researched groups, the distinctive plant uses among Gujjars provide insight into their food ecology, their particular human-ecological system centered on mobile pastoralism and their limited exchanges of local food/ecological knowledge due to endogamic patterns. A literature survey revealed some novel or little-known ingredients within Pakistani food ethnobotany/ethnomycology, such as Aesculus indica, Agaricus campestris, Apteranthes tuberculata, Duchesnea indica, Equisetum arvense, Eremurus himalaicus, Isodon rugosus, Morella esculenta, Sophora mollis, and Drimia indica.

CONCLUSION: The researched communities have retained important plant knowledge which could be implemented through future development programs considering that most of these traditional foraging practices fulfill environmental and social sustainability standards. Further field studies are required to thoroughly investigate the patterns of foraging among highland pastoral societies in other parts of the Hindukush region and especially their potential for the ongoing ecological transition.}, } @article {pmid37003550, year = {2023}, author = {Romero Starke, K and Schubert, M and Kaboth, P and Gerlach, J and Hegewald, J and Reusche, M and Friedemann, D and Zülke, A and Riedel-Heller, SG and Zeeb, H and Seidler, A}, title = {Traffic noise annoyance in the LIFE-adult study in Germany: Exposure-response relationships and a comparison to the WHO curves.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115815}, doi = {10.1016/j.envres.2023.115815}, pmid = {37003550}, issn = {1096-0953}, abstract = {BACKGROUND: Noise annoyance is the second-highest cause of lost disability-adjusted life-years due to environmental noise in Europe. Evidence on exposure-response relationships (ERRs) for traffic noise annoyance with more accurate exposure values is still needed.

OBJECTIVES: In an analysis of the population-based LIFE-Adult study in Leipzig, Germany, we aimed to investigate the effect of road, railway (train and tram), and aircraft noise on high annoyance (HA).

METHODS: Traffic exposure data was taken for 2012 and data on noise annoyance was evaluated between 2018 and 2021. HA was defined according to international standardized norms. We calculated risk estimates using logistic regression, controlling for age, sex, and socioeconomic status, and compared our ERRs with those from the last WHO review on this topic.

RESULTS: Aircraft noise had the highest relative risk for noise-related HA (OR = 12.7, 95% CI: 9.37-17.10 per 10 dB Lden increase). The road and railway traffic risk estimates were similar to each other (road: OR = 3.55, 95% CI: 2.78-4.54; railway: OR = 3.31, 95% CI: 2.77-3.97 per 10 dB Lden increase). Compared to the WHO curves, the proportion of highly annoyed individuals was somewhat lower for road and rail traffic noise, but higher for aircraft noise.

DISCUSSION: Aircraft noise is particularly annoying. There were differences between our study's ERRs and those in the WHO review, especially for aircraft noise. These differences may be partly explained by the improved accuracy of the exposure values, as we considered secondary road networks and tram noise, and by a lack of a nighttime flight ban at the Leipzig airport. Geographical, regional and climatic variations, inconsistency in HA cut-offs, as well as temporal developments in the annoyance experience may also explain the differences. Since ERRs serve as a basis for decision making in public policies, regular updates of the curves based on new evidence is recommended.}, } @article {pmid36998243, year = {2022}, author = {Boyes, D and , and , and , and , and , and Boyes, C and , }, title = {The genome sequence of the pale mottled willow, Caradrina clavipalpis (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {225}, pmid = {36998243}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.}, } @article {pmid36992446, year = {2023}, author = {Howison, M and Gillani, FS and Novitsky, V and Steingrimsson, JA and Fulton, J and Bertrand, T and Howe, K and Civitarese, A and Bhattarai, L and MacAskill, M and Ronquillo, G and Hague, J and Dunn, CW and Bandy, U and Hogan, JW and Kantor, R}, title = {An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992446}, issn = {1999-4915}, support = {R01 AI136058, K24 AI134359, P30 AI042853/NH/NIH HHS/United States ; }, mesh = {Humans ; *HIV Infections/diagnosis/epidemiology ; Public Health ; Phylogeny ; Prospective Studies ; *HIV-1/genetics ; *HIV Seropositivity ; }, abstract = {Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.}, } @article {pmid36989356, year = {2023}, author = {Bird, N and Ormond, L and Awah, P and Caldwell, EF and Connell, B and Elamin, M and Fadlelmola, FM and Matthew Fomine, FL and López, S and MacEachern, S and Moñino, Y and Morris, S and Näsänen-Gilmore, P and Nketsia V, NK and Veeramah, K and Weale, ME and Zeitlyn, D and Thomas, MG and Bradman, N and Hellenthal, G}, title = {Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture.}, journal = {Science advances}, volume = {9}, number = {13}, pages = {eabq2616}, pmid = {36989356}, issn = {2375-2548}, mesh = {Humans ; *Ethnicity/genetics ; Nigeria ; *Chromosomes ; Ghana ; Language ; Genetic Variation ; Genetics, Population ; }, abstract = {Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria, and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example, correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relate to the expansions of Bantu language-speaking peoples.}, } @article {pmid36981964, year = {2023}, author = {Sui, J and Zhang, G and Lin, T and Hamm, NAS and Li, C and Wu, X and Hu, K}, title = {Quantitative Evaluation of Spatial Accessibility of Various Urban Medical Services Based on Big Data of Outpatient Appointments.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {6}, pages = {}, pmid = {36981964}, issn = {1660-4601}, mesh = {Child ; Humans ; *Big Data ; *Outpatients ; Health Services Accessibility ; Cities ; Catchment Area, Health ; }, abstract = {Equity of urban medical services affects human health and well-being in cities and is important in building 'just' cities. We carried out a quantitative analysis of the spatial accessibility of medical services considering the diverse demands of people of different ages, using outpatient appointment big data and refining the two-step floating catchment area (2SFCA) method. We used the traditional 2SFCA method to evaluate the overall spatial accessibility of medical services of 504 communities in Xiamen city, considering the total population and the supply of medical resources. Approximately half the communities had good access to medical services. The communities with high accessibility were mainly on Xiamen Island, and those with low accessibility were further from the central city. The refined 2SFCA method showed a more diverse and complex spatial distribution of accessibility to medical services. Overall, 209 communities had high accessibility to internal medicine services, 133 to surgery services, 50 to gynecology and obstetrics services, and 18 to pediatric services. The traditional method may over-evaluate or under-evaluate the accessibility of different types of medical services for most communities compared with the refined evaluation method. Our study can provide more precise information on urban medical service spatial accessibility to support just city development and design.}, } @article {pmid36979124, year = {2023}, author = {Schalli, M and Platzer, S and Schmutz, R and Ofner-Kopeinig, P and Reinthaler, FF and Haas, D}, title = {Dissolved Carbon Dioxide: The Lifespan of Staphylococcus aureus and Enterococcus faecalis in Bottled Carbonated Mineral Water.}, journal = {Biology}, volume = {12}, number = {3}, pages = {}, pmid = {36979124}, issn = {2079-7737}, abstract = {During the process of mineral water production, many possible contamination settings can influence the quality of bottled water. Microbial contamination can originate from different sources, for example, the ambient air, the bottles, the caps, and from the bottling machine itself. The aim of this study was to investigate the influence of three different carbon dioxide (CO2) concentrations (3.0 g/L, 5.5 g/L, and 7.0 g/L; 20 bottles each) in bottled mineral water on the bacterial growth of Staphylococcus aureus (S. aureus) and Enterococcus faecalis (Ent. faecalis). The examined mineral water was artificially contaminated before capping the bottles inside the factory. After a specific number of days, water samples were taken from freshly opened bottles and after filtration (100 mL), filters were placed on Columbia Agar with 5% Sheep blood to cultivate S. aureus and Slanetz and Bartley Agar to cultivate Ent. faecalis. The respective colony-forming units (CFU) were counted after incubation times ranging from 24 to 120 h. Colony-forming units of S. aureus were not detectable after the 16th and 27th day, whereas Ent. faecalis was not cultivable after the 5th and 13th day when stored inside the bottles. The investigation of the bottles that were stored open for a certain amount of time with CO2 bubbling out showed only single colonies for S. aureus after the 5th day and no CFUs for Ent. faecalis after the 17th day. A reduction in the two investigated bacterial strains during storage in carbonated mineral water bottles means that a proper standardized disinfection and cleaning procedure, according to valid hygiene standards of industrial bottling machines, cannot be replaced by carbonation.}, } @article {pmid36978281, year = {2023}, author = {Stanic, B and Milošević, N and Sukur, N and Samardzija Nenadov, D and Fa Nedeljkovic, S and Škrbić, S and Andric, N}, title = {An in silico toxicogenomic approach in constructing the aflatoxin B1-mediated regulatory network of hub genes in hepatocellular carcinoma.}, journal = {Toxicology mechanisms and methods}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/15376516.2023.2196686}, pmid = {36978281}, issn = {1537-6524}, abstract = {Aflatoxin B1 (AFB1) can cause hepatocellular carcinoma (HCC) through a mutagenic mode of action but can also lead to global changes in gene expression; however, the AFB1 network of molecular pathways involved in HCC is not known. Here, we used toxicogenomic data from human liver cells exposed to AFB1 to infer the network of AFB1-responsive molecular pathways involved in HCC. The following computational tools: STRING, MCODE, cytoHubba, iRegulon, kinase enrichment tool KEA3, and DAVID were used to identify protein-protein interaction network, hub genes, transcription factors (TFs), upstream kinases, and biological processes (BPs). Predicted molecular events were validated with an external dataset, whereas the hub genes in HCC were validated using the UALCAN database. The results revealed an association between AFB1 and the hub genes involved in cell cycle. We identified TFs that regulate the hub genes and linked them with upstream kinases including cyclin-dependent kinases, mitogen-activated protein kinase 1, and AKT. This approach enabled the construction of the AFB1-mediated regulatory network consisting of upstream kinases, TFs, hub genes, and BPs, thus revealing the signaling hierarchy and information flow that may contribute to AFB1-induced HCC. This could be a useful tool in predicting the molecular mechanisms involved in chemical-induced diseases when available toxicogenomic data exist.}, } @article {pmid36976384, year = {2023}, author = {Huang, F and Chen, C}, title = {GIS-based approach and multivariate statistical analysis for identifying sources of heavy metals in marine sediments from the coast of Hong Kong.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {4}, pages = {518}, pmid = {36976384}, issn = {1573-2959}, mesh = {Hong Kong ; Geographic Information Systems ; Cadmium ; Lead ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury ; Geologic Sediments/chemistry ; Risk Assessment ; China ; *Water Pollutants, Chemical/analysis ; }, abstract = {Hong Kong is an urbanized coastal city which experiences substantially different metal loads from anthropogenic activities. This study was aimed at analyzing the spatial distribution and pollution evaluation of ten selected heavy metals (As, Cd, Cr, Cu, Pb, Hg, Ni, Zn, Fe, V) in the coastal sediments of Hong Kong. The distribution of heavy metal pollution in sediments has been analyzed using the geographic information system (GIS) technique, and their pollution degrees, corresponding potential ecological risks and source identifications, have been studied by applying the enrichment factor (EF) analysis, contamination factor (CF) analysis, potential ecological risk index (PEI), and integrated multivariate statistical methods, respectively. Firstly, the GIS technique was used to access the spatial distribution of the heavy metals; the result revealed that pollution trend of these metals was decreased from the inner to the outer coast sites of the studied area. Secondly, combining the EF analysis and CF analysis, we found that the pollution degree of heavy metals followed the order of Cu > Cr > Cd > Zn > Pb > Hg > Ni > Fe > As > V. Thirdly, the PERI calculations showed that Cd, Hg, and Cu were the most potential ecological risk factors compared to other metals. Finally, cluster analysis combined with principal component analysis showed that Cr, Cu, Hg, and Ni might originate from the industrial discharges and shipping activities. V, As, and Fe were mainly derived from the natural origin, whereas Cd, Pb, and Zn were identified from the municipal discharges and industrial wastewater. In conclusion, this work should be helpful in the establishment of strategies for contamination control and optimization of industrial structures in Hong Kong.}, } @article {pmid36976982, year = {2023}, author = {Yang, D and Zhu, H and Liu, J and Zhang, Y and Wu, S and Xiong, J and Wang, F}, title = {Risk Assessment of Heavy Metals in Soils from Four Different Industrial Plants in a Medium-Sized City in North China.}, journal = {Toxics}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/toxics11030217}, pmid = {36976982}, issn = {2305-6304}, abstract = {Laboratory experiments were carried out to analyze 39 soil samples collected from four industrial areas in Xuzhou City using inductively coupled plasma mass spectrometry and atomic fluorescence spectrometry. The descriptive statistics of heavy metals (HMs) in the soil profiles showed that the HM content at three depths was highly variable, and most coefficients of variation (CVs) showed moderate variability. The enrichment of Cd at all depths exceeded the risk screening value, and Cd pollution occurred in four plants. The enrichment of the other HMs at three depths was mainly concentrated in the pharmaceutical plant A and chemical plant C. It was found that the different HMs had different vertical distribution characteristics. For the different industrial plants, the raw materials and products not only made the spatial distribution characteristics of the HMs different, but also caused the HM types and contents to differ. The average single pollution indices of Cd in plant A, iron-steel plant B, and plant C indicated a slight pollution level. The other seven HMs in A, B, and C and all HMs in chemical plant D belonged to the safe category. The mean values of the Nemerow pollution index in the four industrial plants belonged to the warning category. The analysis showed that none of the HMs posed potential noncarcinogenic health risks, and only the carcinogenic health risks of Cr in plants A and C were unacceptable. The carcinogenic effect of Cr through the inhalation intake of resuspended soil particulates and that of Cd, Ni, and As via direct oral ingestion were the main exposure pathways.}, } @article {pmid36972774, year = {2023}, author = {Cecchetto, M and Peruzza, L and Giubilato, E and Bernardini, I and Rovere, GD and Marcomini, A and Regoli, F and Bargelloni, L and Patarnello, T and Semenzin, E and Milan, M}, title = {An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115745}, doi = {10.1016/j.envres.2023.115745}, pmid = {36972774}, issn = {1096-0953}, abstract = {The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.}, } @article {pmid36972109, year = {2023}, author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE}, title = {The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e43623}, doi = {10.2196/43623}, pmid = {36972109}, issn = {1438-8871}, mesh = {Adult ; Humans ; United States/epidemiology ; *Social Media ; Cross-Sectional Studies ; Depression/epidemiology ; Income ; Mental Health ; }, abstract = {BACKGROUND: Social connectedness decreases human mortality, improves cancer survival, cardiovascular health, and body mass, results in better-controlled glucose levels, and strengthens mental health. However, few public health studies have leveraged large social media data sets to classify user network structure and geographic reach rather than the sole use of social media platforms.

OBJECTIVE: The objective of this study was to determine the association between population-level digital social connectedness and reach and depression in the population across geographies of the United States.

METHODS: Our study used an ecological assessment of aggregated, cross-sectional population measures of social connectedness, and self-reported depression across all counties in the United States. This study included all 3142 counties in the contiguous United States. We used measures obtained between 2018 and 2020 for adult residents in the study area. The study's main exposure of interest is the Social Connectedness Index (SCI), a pair-wise composite index describing the "strength of connectedness between 2 geographic areas as represented by Facebook friendship ties." This measure describes the density and geographical reach of average county residents' social network using Facebook friendships and can differentiate between local and long-distance Facebook connections. The study's outcome of interest is self-reported depressive disorder as published by the Centers for Disease Control and Prevention.

RESULTS: On average, 21% (21/100) of all adult residents in the United States reported a depressive disorder. Depression frequency was the lowest for counties in the Northeast (18.6%) and was highest for southern counties (22.4%). Social networks in northeastern counties involved moderately local connections (SCI 5-10 the 20th percentile for n=70, 36% of counties), whereas social networks in Midwest, southern, and western counties contained mostly local connections (SCI 1-2 the 20th percentile for n=598, 56.7%, n=401, 28.2%, and n=159, 38.4%, respectively). As the quantity and distance that social connections span (ie, SCI) increased, the prevalence of depressive disorders decreased by 0.3% (SE 0.1%) per rank.

CONCLUSIONS: Social connectedness and depression showed, after adjusting for confounding factors such as income, education, cohabitation, natural resources, employment categories, accessibility, and urbanicity, that a greater social connectedness score is associated with a decreased prevalence of depression.}, } @article {pmid36966822, year = {2023}, author = {Song, W and Song, W}, title = {Cropland fallow reduces agricultural water consumption by 303 million tons annually in Gansu Province, China.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163013}, doi = {10.1016/j.scitotenv.2023.163013}, pmid = {36966822}, issn = {1879-1026}, abstract = {The high-intensity utilization of global cropland causes water shortage and food crisis, which seriously affects the realization of SDG 2 (zero hunger), SDG 6 (clean water and sanitation) and SDG 15 (life on land), and threatens the sustainable social, economic and ecological development. Cropland fallow can not only improve the quality of cropland and maintain ecosystem balance, but also have a significant water-saving effect. However, in most developing countries, such as China, cropland fallow has not yet been widely promoted, and there are few reliable fallow cropland fallow identification methods, making it even more challenging to assess the water-saving effect. To remedy this deficit, we propose a framework for mapping cropland fallow and evaluating its water savings. First, we used the Landsat series of data to interpret the annual land use/cover changes in Gansu Province, China from 1991 to 2020. Subsequently, the spatial-temporal variation of cropland fallow in Gansu province (giving up farming for one to two years) was mapped. Finally, we evaluated the water-saving effect of cropland fallow using evapotranspiration, precipitation, irrigation maps, and crop-related data, instead of actual water consumption. The results showed that the mapping accuracy of fallow land in Gansu Province was 79.50 %, which was higher than that of most known fallow mapping studies. From 1993 to 2018, the average annual fallow rate in Gansu Province, China, was 10.86 %, which was at a low level in arid/semi-arid regions worldwide. More importantly, from 2003 to 2018, cropland fallow reduces annual water consumption of 303.26 million tons in Gansu Province, accounting for 3.44 % of agricultural water use in Gansu Province and equivalent to the annual water demand of 655,000 people in Gansu Province. Based on our research, we speculate that the increasing pilot projects of cropland fallow in China can bring significant water-saving effects and help achieve China's Sustainable Development Goals.}, } @article {pmid36868153, year = {2023}, author = {Jin, H and Zhihong, P and Jiaqing, Z and Chuxuan, L and Lu, T and Jun, J and Xinghua, L and Wenyan, G and Junkang, G and Binbin, S and Shengguo, X}, title = {Source apportionment and quantitative risk assessment of heavy metals at an abandoned zinc smelting site based on GIS and PMF models.}, journal = {Journal of environmental management}, volume = {336}, number = {}, pages = {117565}, doi = {10.1016/j.jenvman.2023.117565}, pmid = {36868153}, issn = {1095-8630}, mesh = {Humans ; Zinc/analysis ; Geographic Information Systems ; Lead ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil ; China ; Risk Assessment ; Cadmium ; }, abstract = {The abandoned smelters have caused serious hazards to the surrounding environment and residents. Taking an abandoned zinc smelter in southern China as an example, a total of 245 soil samples were collected to study spatial heterogeneity, source apportionment, and source-derived risk assessment of heavy metal(loid)s (HMs) in the region. The results showed that the mean values of all HMs concentrations were higher than the local background values, with Zn, Cd, Pb, and As contamination being the most serious and their plume penetrating to the bottom layer. Four sources were identified by principal component analysis and positive matrix factorization, with their contributions to the HMs contents ranked as: surface runoff (F2, 63.2%) > surface solid waste (F1, 22.2%) > atmospheric deposition (F3, 8.5%) > parent material (F4, 6.1%). Among these, F1 was a determinant source of human health risk with a contribution rate of 60%. Therefore, F1 was considered to be the priority control factor, but it only accounted for 22.2% of HMs contents contribution. Hg dominated the ecological risk with a contribution of 91.1%. Pb (25.7%) and As (32.9%) accounted for the non-carcinogenic risk, while As (95%) dominated the carcinogenic effect. The spatial characteristics of human health risk values derived from F1 indicated that high-risk areas were mainly distributed in the casting finished products area, electrolysis area, leaching-concentration area, and fluidization roasting area. The findings highlight the significance of priority control factors (including HMs, pollution sources and functional areas) for consideration in the integrated management of this region, thus saving costs for effective soil remediation.}, } @article {pmid36648611, year = {2023}, author = {Hu, Y and Wang, X and Xu, Y and Yang, H and Tong, Z and Tian, R and Xu, S and Yu, L and Guo, Y and Shi, P and Huang, S and Yang, G and Shi, S and Wei, F}, title = {Molecular mechanisms of adaptive evolution in wild animals and plants.}, journal = {Science China. Life sciences}, volume = {66}, number = {3}, pages = {453-495}, pmid = {36648611}, issn = {1869-1889}, mesh = {*Biological Evolution ; *Adaptation, Physiological/genetics ; *Genome, Plant/genetics ; *Animals, Wild/genetics ; Biological Coevolution/genetics ; Phenotype ; Aquatic Organisms/genetics ; Ecology/methods/trends ; Computational Biology/methods ; }, abstract = {Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.}, } @article {pmid36964402, year = {2023}, author = {Dec, E and Clement, J and Cheng, K and Church, GM and Fossel, MB and Rehkopf, DH and Rosero-Bixby, L and Kobor, MS and Lin, DT and Lu, AT and Fei, Z and Guo, W and Chew, YC and Yang, X and Putra, SED and Reiner, AP and Correa, A and Vilalta, A and Pirazzini, C and Passarino, G and Monti, D and Arosio, B and Garagnani, P and Franceschi, C and Horvath, S}, title = {Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {36964402}, issn = {2509-2723}, support = {U01AG060908/AG/NIA NIH HHS/United States ; }, abstract = {Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.}, } @article {pmid36962744, year = {2023}, author = {Asaaga, FA and Purse, BV and Rahman, M and Srinivas, PN and Kalegowda, SD and Seshadri, T and Young, JC and Oommen, MA}, title = {The role of social vulnerability in improving interventions for neglected zoonotic diseases: The example of Kyasanur Forest Disease in India.}, journal = {PLOS global public health}, volume = {3}, number = {2}, pages = {e0000758}, pmid = {36962744}, issn = {2767-3375}, abstract = {Forest-based communities manage many risks to health and socio-economic welfare including the increasing threat of emerging zoonoses that are expected to disproportionately affect poor and marginalised groups, and further impair their precarious livelihoods, particularly in Low-and-Middle Income (LMIC) settings. Yet, there is a relative dearth of empirical research on the vulnerability and adaptation pathways of poor and marginalised groups facing emerging zoonoses. Drawing on a survey of 229 households and a series of key-informant interviews in the Western Ghats, we examine the factors affecting vulnerability of smallholder and tribal households to Kyasanur Forest Disease (KFD), an often-fatal tick-borne viral haemorrhagic fever endemic in south India. Specifically, we investigate how different socio-demographic and institutional factors interact to shape KFD vulnerability and the strategies employed by households to adapt to disease consequences. Although surveyed households generally perceived KFD as an important health issue in the study region, there was variability in concern about contracting the disease. Overall results showed that poor access to land (AOR = 0.373, 95% CI: 0.152-0.916), being at or below the poverty line (AOR = 0.253, 95% CI: 0.094-0.685) and being headed by an older person (AOR = 1.038, 95% CI: 1.006-1.071) were all significant determinants of perceived KFD vulnerability. Furthermore, KFD vulnerability is also modulated by important extra-household factors including proximity to private hospitals (AOR = 3.281, 95% CI: 1.220-8.820), main roads (AOR = 2.144, 95% CI: 1.215-3.783) and study location (AOR = 0.226, 95% CI: 0.690-0.743). Our findings highlight how homogenous characterisation of smallholder and tribal communities and the 'techno-oriented' approach of existing interventions may further marginalise the most vulnerable and exacerbate existing inequalities. These findings are important for designing context-specific and appropriate health interventions (including the prioritisation of awareness raising, knowledge networks, livelihood diversification) that enhances the resilience of at-risk social groups within the KFD context. More broadly, our findings highlight how a focus on social vulnerability can help national and international health planners improve health interventions and prioritise among diseases with respect to neglected endemic zoonoses.}, } @article {pmid36962522, year = {2022}, author = {Sawires, R and Pearce, C and Fahey, M and Clothier, H and Gardner, K and Buttery, J}, title = {Snotwatch COVID-toes: An ecological study of chilblains and COVID-19 diagnoses in Victoria, Australia.}, journal = {PLOS global public health}, volume = {2}, number = {10}, pages = {e0000488}, pmid = {36962522}, issn = {2767-3375}, abstract = {The COVID-19 pandemic has caused widespread illness with varying clinical manifestations. One less-commonly-reported presentation of COVID-19 infection is chilblain-like lesions. We conducted an ecological analysis of chilblain presentations in comparison with confirmed and suspected COVID-19 infections in a primary care setting to establish that a relationship exists between the two. Our study collated data from three Primary Health Networks across Victoria, Australia, from 2017-2021, to understand patterns of chilblain presentations prior to and throughout the pandemic. Using a zero-inflated negative binomial regression analysis, we estimated the relationship between local minimum temperature, COVID-19 infections and the frequency of chilblain presentations. We found a 5.72 risk ratio of chilblain incidence in relation to COVID-19 infections and a 3.23 risk ratio associated with suspected COVID-19 infections. COVID-19 infections were also more strongly associated with chilblain presentations in 0-16-year-olds throughout the pandemic in Victoria. Our study statistically suggests that chilblains are significantly associated with COVID-19 infections in a primary care setting. This has major implications for clinicians aiming to diagnose COVID-19 infections or determine the cause of a presentation of chilblains. Additionally, we demonstrate the utility of large-scale primary care data in identifying an uncommon manifestation of COVID-19 infections, which will be significantly beneficial to treating physicians.}, } @article {pmid36962247, year = {2022}, author = {Asaaga, FA and Young, JC and Srinivas, PN and Seshadri, T and Oommen, MA and Rahman, M and Kiran, SK and Kasabi, GS and Narayanaswamy, D and Schäfer, SM and Burthe, SJ and August, T and Logie, M and Chanda, MM and Hoti, SL and Vanak, AT and Purse, BV}, title = {Co-production of knowledge as part of a OneHealth approach to better control zoonotic diseases.}, journal = {PLOS global public health}, volume = {2}, number = {3}, pages = {e0000075}, pmid = {36962247}, issn = {2767-3375}, abstract = {There is increased global and national attention on the need for effective strategies to control zoonotic diseases. Quick, effective action is, however, hampered by poor evidence-bases and limited coordination between stakeholders from relevant sectors such as public and animal health, wildlife and forestry sectors at different scales, who may not usually work together. The OneHealth approach recognises the value of cross-sectoral evaluation of human, animal and environmental health questions in an integrated, holistic and transdisciplinary manner to reduce disease impacts and/or mitigate risks. Co-production of knowledge is also widely advocated to improve the quality and acceptability of decision-making across sectors and may be particularly important when it comes to zoonoses. This paper brings together OneHealth and knowledge co-production and reflects on lessons learned for future OneHealth co-production processes by describing a process implemented to understand spill-over and identify disease control and mitigation strategies for a zoonotic disease in Southern India (Kyasanur Forest Disease). The co-production process aimed to develop a joint decision-support tool with stakeholders, and we complemented our approach with a simple retrospective theory of change on researcher expectations of the system-level outcomes of the co-production process. Our results highlight that while co-production in OneHealth is a difficult and resource intensive process, requiring regular iterative adjustments and flexibility, the beneficial outcomes justify its adoption. A key future aim should be to improve and evaluate the degree of inter-sectoral collaboration required to achieve the aims of OneHealth. We conclude by providing guidelines based on our experience to help funders and decision-makers support future co-production processes.}, } @article {pmid36958663, year = {2023}, author = {Lima, GDS and Menegario, AA and Suarez, CA and Kamazuka, SH and Gemeiner, H and Sánchez-Sarmiento, AM and Ferioli, RB and Barreto, AS}, title = {Pelagic and estuarine birds as sentinels of metal(loid)s in the South Atlantic Ocean: Ecological niches as main factors acting on bioaccumulation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121452}, doi = {10.1016/j.envpol.2023.121452}, pmid = {36958663}, issn = {1873-6424}, abstract = {Activities related to the offshore exploration and production of oil and natural gas provide economic development and an essential energy source. However, besides the risk of petroleum hydrocarbon contamination, these activities can also be sources of metals and metalloids for marine organism contamination. In this research, we evaluated the potential use of two pelagic (black-browed albatross Thalassarche melanophris and yellow-nosed albatross T. chlororhynchos) and one estuarine bird species (neotropical cormorant Nannopterum brasilianus) as sentinels of contamination of As, Cd, Cr, Cu, Pb, Mn, Mo, Zn, Ni, Ba, V, and Hg in an area under influence of oil and gas activities. The analyses were carried out in samples collected from 2015 to 2022 from 97 individuals. A factor alert; an adaptation from the contamination factor is proposed to identify individuals with high concentrations that possibly suffered contamination by anthropogenic origin. Grouping all species, the metal(loid)s with the highest concentrations were in decreasing order: Zn > Cu > Mn > Hg > As > Cd > Mo > V > Cr > Ba > Ni > Pb. Similar concentrations were observed for V, Mn, Cr and Pb among the three species. Pelagic birds showed higher levels of concentrations for Hg, As and Cd. Based on the correlations and multivariate analysis performed, the results indicate that the ecological niche factor has greater relevance in the bioaccumulation of these elements compared to the habitat. Although some individuals showed high concentrations in part of the trace elements, suggesting exposure to anthropic sources, the direct influence of oil production and exploration activities was not observed, suggesting that activities on the continent are the primary contamination source. The results of this work highlight the role of seabirds as sentinels for metal(loid)s, contributing to the knowledge of the occurrence of contaminants in the South Atlantic Ocean.}, } @article {pmid36947115, year = {2023}, author = {Bautista, J and Schueller, SM}, title = {Understanding the Adoption and Use of Digital Mental Health Apps Among College Students: Secondary Analysis of a National Survey.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e43942}, doi = {10.2196/43942}, pmid = {36947115}, issn = {2368-7959}, abstract = {BACKGROUND: Increasing rates of mental health diagnoses in college students signal the need for new opportunities to support the mental health of this population. With many mental health apps being efficacious, they may be a promising resource for college campuses to provide support to their students. However, it is important to understand why (or why not) students might want to use apps and their desired features.

OBJECTIVE: Information on students' interest in mental health apps may inform which apps are to be provided and how campuses can support their use. This study aimed to understand the interest and hesitation in app use and the relationship between mental health needs, as defined by depression, anxiety, and positive mental health, and app use.

METHODS: The web-based Healthy Minds Study collected information on mental health needs, perceptions, and service use across colleges and universities. We used a sample of 989 participants who completed the survey between 2018 and 2020 and an elective module on digital mental health. We analyzed the elective module responses using a mixed methods approach, including both descriptive and inferential statistics, along with thematic coding for open text responses.

RESULTS: The Results from this study revealed that anxiety (b=-0.07; P<.001), but not depression (b=0.03; P=.12) and positive mental health (b=-0.02; P=.17), was a significant predictor of app adoption. Prominent qualitative findings indicated that the most desired app features included tips and advice, access to resources and information, and on-demand support that involves interaction throughout the day. The participants also suggested an overall desire for human interaction to be integrated into an app. As predicted, hesitancy was encountered, and the qualitative results suggested that there was a lack of interest in the adoption of mental health app and preference.

CONCLUSIONS: The findings from this study underscore that simply providing digital mental health apps as tools may be insufficient to support their use in college campuses. Although many students were open to using a mental health app, hesitation and uncertainty were common in the participant responses. Working with colleges and universities to increase digital literacy and provide resources that allow students to gauge when app use is appropriate may be helpful when implementing mental health apps as resources in college campuses.}, } @article {pmid36946676, year = {2023}, author = {Oliveira, HC and Seabra, AB and Kondak, S and Adedokun, OP and Kolbert, Z}, title = {Multilevel approach of plant-nanomaterial relationship: from cells to living ecosystems.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erad107}, pmid = {36946676}, issn = {1460-2431}, abstract = {Due to their unique properties, nanomaterials (NMs) behave peculiarly in biosystems. Regarding plants, the interactions of NMs can be interpreted on a spatial scale: from local interactions in cells to systemic effects on whole plants and on ecosystems. Interpreted on a time scale, the effects of NMs on plants may be immediate or subsequent. At the cellular level, the composition and structure of the cell wall and membranes are modified by NMs, promoting internalization. The effects of NMs on germination and seedling physiology and on the primary and secondary metabolisms in the shoot are realized at organ and organism levels. Nanomaterials interact with the beneficial ecological partners of plants. The effects of NMs on plant growth-promoting rhizobacteria and legume-rhizobia symbiosis can be stimulating or inhibitory, depending on the concentration and type of NM. Nanomaterials exert a negative effect on arbuscular mycorrhiza, and vice versa. Pollinators are exposed to NMs, which may affect plant reproduction. The substances released by the roots influence the availability of NMs in the rhizosphere and components of plant cells trigger internalization, translocation, and transformation of NMs. Understanding of the multilevel and bidirectional relationship between plants and NMs is of great relevance in practice.}, } @article {pmid36939939, year = {2023}, author = {Forootan, E}, title = {GIS-based slope-adjusted curve number methods for runoff estimation.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {4}, pages = {489}, pmid = {36939939}, issn = {1573-2959}, mesh = {*Water Movements ; *Geographic Information Systems ; Environmental Monitoring/methods ; Soil ; Hydrology ; Rain ; }, abstract = {Accurate estimation of surface runoff and determination of susceptible lands to runoff generation in ungauged watersheds were the problems for hydrologic engineering which could be predicted through a simple model such as Soil Conservation Service Curve Number (SCS-CN). Due to the slope effects on this method, slope adjustment for curve number was developed to improve its precision. So, the main objectives of this study were to apply GIS-based slope SCS-CN approaches for surface runoff estimation and compare the accuracy of three slope-adjusted models including: (a) model with three empirical parameters, (b) model with two parameters slope function, and (c) model with one parameter in the region located in the central part of Iran. For this purpose, soil texture, hydrologic soil group, land use, slope, and daily rainfall volume maps were utilized. In order to provide the curve number map of the study area, land use and hydrologic soil group layers built in Arc-GIS were intersected and the curve number was determined. Then, three slope adjustment equations were used to modify curve numbers of AMC-II by employing slope map. Finally, recorded runoff data of the hydrometric station were applied to assess the performance of the models through four statistical indicators of the root mean square error (RMSE), the Nash-Sutcliffe efficiency (E), the coefficient of determination [Formula: see text], and percent bias (PB). Land use map analysis showed that rangeland was the dominant land use, whereas the soil texture map specified the greatest and smallest area belonging to loam and sandy loam textures, respectively. Although the runoff results showed the overestimation of large rainfall values and underestimation for rainfall with less than 40 mm volume in both models, the values of E (0.78), RMSE (2), PB (16), and [Formula: see text] (0.88) revealed that eq. (a) with three empirical parameters was the most accurate equation. The maximum percent of runoff generated by rainfall for eqs. (a), (b), and (c) were 68.43, 67.28, and 51.57% which showed that bareland located in south part with the slope of more than 5% was susceptible to runoff generation and should be paid attention to watershed management.}, } @article {pmid36821658, year = {2023}, author = {D'Emic, MD and O'Connor, PM and Sombathy, RS and Cerda, I and Pascucci, TR and Varricchio, D and Pol, D and Dave, A and Coria, RA and Curry Rogers, KA}, title = {Developmental strategies underlying gigantism and miniaturization in non-avialan theropod dinosaurs.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6634}, pages = {811-814}, doi = {10.1126/science.adc8714}, pmid = {36821658}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; *Dinosaurs/anatomy & histology/classification/growth & development ; Fossils ; Phylogeny ; *Body Size ; Datasets as Topic ; }, abstract = {In amniotes, the predominant developmental strategy underlying body size evolution is thought to be adjustments to the rate of growth rather than its duration. However, most theoretical and experimental studies supporting this axiom focus on pairwise comparisons and/or lack an explicit phylogenetic framework. We present the first large-scale phylogenetic comparative analysis examining developmental strategies underlying the evolution of body size, focusing on non-avialan theropod dinosaurs. We reconstruct ancestral states of growth rate and body mass in a taxonomically rich dataset, finding that contrary to expectations, changes in the rate and duration of growth played nearly equal roles in the evolution of the vast body size disparity present in non-avialan theropods-and perhaps that of amniotes in general.}, } @article {pmid36937826, year = {2022}, author = {Wabnitz, K and Schwienhorst-Stich, EM and Asbeck, F and Fellmann, CS and Gepp, S and Leberl, J and Mezger, NCS and Eichinger, M}, title = {National Planetary Health learning objectives for Germany: A steppingstone for medical education to promote transformative change.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1093720}, pmid = {36937826}, issn = {2296-2565}, mesh = {Humans ; *Education, Medical ; Curriculum ; Health Education ; Delivery of Health Care ; Germany ; }, abstract = {Physicians play an important role in adapting to and mitigating the adverse health effects of the unfolding climate and ecological crises. To fully harness this potential, future physicians need to acquire knowledge, values, skills, and leadership attributes to care for patients presenting with environmental change-related conditions and to initiate and propel transformative change in healthcare and other sectors of society including, but not limited to, the decarbonization of healthcare systems, the transition to renewable energies and the transformation of transport and food systems. Despite the potential of Planetary Health Education (PHE) to support medical students in becoming agents of change, best-practice examples of mainstreaming PHE in medical curricula remain scarce both in Germany and internationally. The process of revising and updating the Medical Licensing Regulations and the National Competency-based Catalog of Learning Objectives for Medical Education in Germany provided a window of opportunity to address this implementation challenge. In this article, we describe the development and content of national Planetary Health learning objectives for Germany. We anticipate that the learning objectives will stimulate the development and implementation of innovative Planetary Health teaching, learning and exam formats in medical schools and inform similar initiatives in other health professions. The availability of Planetary Health learning objectives in other countries will provide opportunities for cross-country and interdisciplinary exchange of experiences and validation of content, thus supporting the consolidation of Planetary Health learning objectives and the improvement of PHE for all health professionals globally.}, } @article {pmid36934309, year = {2023}, author = {Newbury, JB and Arseneault, L and Moffitt, TE and Odgers, CL and Howe, LD and Bakolis, I and Reuben, A and Danese, A and Sugden, K and Williams, B and Rasmussen, LJH and Trotta, A and Ambler, AP and Fisher, HL}, title = {Socioenvironmental Adversity and Adolescent Psychotic Experiences: Exploring Potential Mechanisms in a UK Longitudinal Cohort.}, journal = {Schizophrenia bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1093/schbul/sbad017}, pmid = {36934309}, issn = {1745-1701}, support = {G1002190/MRC_/Medical Research Council/United Kingdom ; 218632/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; F31ES029358/ES/NIEHS NIH HHS/United States ; MR/M020894/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND AND HYPOTHESIS: Children exposed to socioenvironmental adversities (eg, urbanicity, pollution, neighborhood deprivation, crime, and family disadvantage) are more likely to subsequently develop subclinical psychotic experiences during adolescence (eg, hearing voices, paranoia). However, the pathways through which this occurs have not been previously investigated. We hypothesized that cognitive ability and inflammation would partly explain this association.

STUDY DESIGN: Data were utilized from the Environmental-Risk Longitudinal Twin Study, a cohort of 2232 children born in 1994-1995 in England and Wales and followed to age 18. Socioenvironmental adversities were measured from birth to age 10 and classified into physical risk (defined by high urbanicity and air pollution) and socioeconomic risk (defined by high neighborhood deprivation, neighborhood disorder, and family disadvantage). Cognitive abilities (overall, crystallized, fluid, and working memory) were assessed at age 12; and inflammatory markers (C-reactive protein, interleukin-6, soluble urokinase plasminogen activator receptor) were measured at age 18 from blood samples. Participants were interviewed at age 18 regarding psychotic experiences.

STUDY RESULTS: Higher physical risk and socioeconomic risk were associated with increased odds of psychotic experiences in adolescence. The largest mediation pathways were from socioeconomic risk via overall cognitive ability and crystallized ability, which accounted for ~11% and ~19% of the association with psychotic experiences, respectively. No statistically significant pathways were found via inflammatory markers in exploratory (partially cross-sectional) analyses.

CONCLUSIONS: Cognitive ability, especially crystallized ability, may partly explain the association between childhood socioenvironmental adversity and adolescent psychotic experiences. Interventions to support cognitive development among children living in disadvantaged settings could buffer them against developing subclinical psychotic phenomena.}, } @article {pmid36932341, year = {2023}, author = {Kasmi, Y and Eschbach, E and Hanel, R}, title = {Mare-MAGE curated reference database of fish mitochondrial genes.}, journal = {BMC genomic data}, volume = {24}, number = {1}, pages = {18}, pmid = {36932341}, issn = {2730-6844}, mesh = {Animals ; Horses/genetics ; Female ; *Ecosystem ; *Genes, Mitochondrial ; Angiotensin Receptor Antagonists ; DNA Barcoding, Taxonomic ; Angiotensin-Converting Enzyme Inhibitors ; Fishes/genetics ; Databases, Nucleic Acid ; }, abstract = {Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.}, } @article {pmid36931511, year = {2023}, author = {Zhang, B and Zheng, T and Zheng, X and Jiang, S and Cao, M and Walther, M and Lu, C}, title = {Dynamics of upstream saltwater intrusion driven by tidal river in coastal aquifers.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162857}, doi = {10.1016/j.scitotenv.2023.162857}, pmid = {36931511}, issn = {1879-1026}, abstract = {For the coastal aquifers, recent research have shown that the tidal has a significant effect on saltwater intrusion in the near-shore aquifer. However, it is currently unclear how the tidal river contributes to the groundwater flow and salinity distribution in the upstream aquifer of the estuary. This study examined the effects of a tidal river on the dynamic characteristics of groundwater flow and salt transport in a tidal river-coastal aquifer system using field monitoring data and numerical simulations. It was found that changes in tidal-river level led to the reversal of groundwater flow. For a tidal cycle, the maximum area of seawater intrusion is about 41.16 km[2] at the end of the high tide stage. Then the area gradually decreased to 39.02 km[2] at the end of the low tide stage. More than 2 km[2] area variation can be observed in a tidal cycle. Compared to the low tide stage, the area of SWI increased by 5 % at high tide stage. The SWI region was also spreading landward from the tidal river. In addition, we quantified the water exchange and salt flux between the tidal river and aquifer. When the tidal fell below the level of the riverbed, the water exchange rate was stabilized at about -1.6 m/h. The negative value indicated that the river was recharged by the groundwater. With the increasing of tidal water level, the water exchange rate gradually changes from negative to positive and reached the maximum value of 3.2 m/h at the beginning of the falling tide stage. The presence of a physical river dam can amplify the difference in water level between high and low tides, thereby enhancing the influence of a tidal river on water exchange and salt flux. The findings lay the foundation for gaining a comprehensive understanding of the tidal river on groundwater flow and salt transport in upstream aquifers.}, } @article {pmid36926380, year = {2022}, author = {Boyes, D and , and , and , and , and , and Parkerson, L and , }, title = {The genome sequence of the garden grass-veneer, Chrysoteuchia culmella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {248}, pmid = {36926380}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Chrysoteuchia culmella (the garden grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 645 megabases in span. The majority of the assembly (99.81%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 21,251 protein coding genes.}, } @article {pmid36921166, year = {2023}, author = {Morais, LS and Pimentel, SVT and Kawa, H and Fonseca, SC}, title = {Temporal trend of congenital syphilis in the most populous municipality of metropolitan region II of Rio de Janeiro state.}, journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo}, volume = {41}, number = {}, pages = {e2021337}, pmid = {36921166}, issn = {1984-0462}, mesh = {Pregnancy ; Adolescent ; Humans ; Female ; *Syphilis, Congenital/epidemiology ; Brazil/epidemiology ; Prenatal Care ; Incidence ; Databases, Factual ; }, abstract = {OBJECTIVE: This study aimed to explore the temporal trend in congenital syphilis, according to sociodemographic and prenatal care in the city of São Gonçalo - Rio de Janeiro, from 2007 to 2018.

METHODS: Ecological time series study, with data from SINAN (Information System for Notifiable Diseases) and SINASC (Information System on Live Births databases). We calculated annual incidence (per 1,000 live births) according to sociodemographic and prenatal variables. For the same variables, we calculated trends by logarithmic regression (Joinpoint Regression), estimating the annual percentage change.

RESULTS: A total of 2,420 cases were reported from 2007 to 2018, with an increasing trend: 64.9% per year (2010-2013) and 24.9% (2013-2018). In 2018, the highest rates were in adolescents (90.6/1,000 live births), black women (87.6/1,000 live births), low-educated women (122.8/1,000 live births), and those without prenatal care (677.4/1,000 live births). The annual percentage change of these categories was, respectively, 37.3% (2010-2018), 33.5% (2012-2018), 39.9% (2014-2018), and 85.0% (2011-2015), but all categories showed a crescent trend.

CONCLUSIONS: We identified high congenital syphilis incidences and crescent trends, especially in more vulnerable groups, pointing to social and healthcare inequalities. Prenatal care needs to be more comprehensive and qualified, primarily for young, low-educated, and black women.}, } @article {pmid36868417, year = {2023}, author = {Zhang, X and Shao, W and Huo, Y and Kong, Y and Zhang, W and Li, S and Zhou, W and Wu, X and Qin, F and Hu, X}, title = {The effects of short-term dietary exposure to SiO2 nanoparticle on the domesticated lepidopteran insect model silkworm (Bombyx mori): Evidence from the perspective of multi-omics.}, journal = {Chemosphere}, volume = {323}, number = {}, pages = {138257}, doi = {10.1016/j.chemosphere.2023.138257}, pmid = {36868417}, issn = {1879-1298}, mesh = {Animals ; *Bombyx/metabolism ; Silicon Dioxide/metabolism ; Multiomics ; Dietary Exposure ; *Nanoparticles/toxicity ; }, abstract = {Silicon dioxide nanoparticles (nSiO2) are one of the widely utilized nanoparticle (NPSs) materials, and exposure to nSiO2 is ubiquitous. With the increasing commercialization of nSiO2, the potential risk of nSiO2 release to the health and the ecological environment have been attracted more attention. In this study, the domesticated lepidopteran insect model silkworm (Bombyx mori) was utilized to evaluate the biological effects of dietary exposure to nSiO2. Histological investigations showed that nSiO2 exposure resulted in midgut tissue injury in a dose-dependent manner. Larval body mass and cocoon production were reduced by nSiO2 exposure. ROS burst was not triggered, and the activities of antioxidant enzymes were induced in the midgut of silkworm exposure to nSiO2. RNA-sequencing revealed that the differentially expressed genes induced by nSiO2 exposure were predominantly enriched into xenobiotics biodegradation and metabolism, lipid, and amino acid metabolism pathways. 16 S rDNA sequencing revealed that nSiO2 exposure altered the microbial diversity in the gut of the silkworm. Metabolomics analysis showed that the combined uni- and multivariate analysis identified 28 significant differential metabolites from the OPLS-DA model. These significant differential metabolites were predominantly enriched into the metabolic pathways, including purine metabolism and tyrosine metabolism and so. Spearman correlation analysis and the Sankey diagram established the relationship between microbe and metabolites, and some genera may play crucial and pleiotropic functions in the interaction between microbiome and host. These findings indicated that nSiO2 exposure could impact the dysregulation of genes related to xenobiotics metabolism, gut dysbiosis, and metabolic pathways and provided a valuable reference for assessing nSiO2 toxicity from a multi-dimensional perspective.}, } @article {pmid36735127, year = {2023}, author = {Jiang, X and Sun, Y and Qu, Y and Zeng, H and Yang, J and Zhang, K and Liu, L}, title = {The development and future frontiers of global ecological restoration projects in the twenty-first century: a systematic review based on scientometrics.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {12}, pages = {32230-32245}, pmid = {36735127}, issn = {1614-7499}, mesh = {Humans ; *Publications ; *Bibliometrics ; Databases, Factual ; China ; }, abstract = {Ecological restoration projects are becoming a mainstream of research, and their studies are widely followed by scholars worldwide, yet there is no comprehensive review of this research. Nowadays, bibliometrics has attracted much attention from the scientific community, and its methodological approach allows quantitative and qualitative analysis of research performance in journals or subject areas. This paper provides a systematic and comprehensive description of the progress and hotspots of ecological restoration projects from a bibliometric perspective, based on 1173 articles in the Web of Science Core Collection (WOSCC) database. Research on ecological restoration projects has shown a positive growth trend since the twenty-first century. China and the USA are the most active countries in terms of the number of relevant articles published, and more than half of the top 10 active institutions are from China, but there is less collaboration between different countries/institutions. Research in ecological restoration projects is summarized into three main research areas: the main ecological damage problems, the impact of human beings on ecological damage, and the main methods of ecological restoration. Finally, some challenges and outlooks conducive to the rapid and balanced development of ecological restoration projects are presented, which provide valuable references and help for future researchers.}, } @article {pmid36925815, year = {2022}, author = {Viner, AC and Malata, MP and Mtende, M and Membe-Gadama, G and Masamba, M and Makwakwa, E and Bamuya, C and Lissauer, D and Stock, SJ and Norman, JE and Reynolds, RM and Magowan, B and Freyne, B and Gadama, L and Cunningham-Burley, S and Nyondo-Mipando, L and Chipeta, E}, title = {Implementation of a novel ultrasound training programme for midwives in Malawi: A mixed methods evaluation using the RE-AIM framework.}, journal = {Frontiers in health services}, volume = {2}, number = {}, pages = {953677}, pmid = {36925815}, issn = {2813-0146}, abstract = {INTRODUCTION: Despite recommendation that all women receive an ultrasound in pregnancy prior to 24 weeks', this remains unavailable to many women in low-income countries where trained practitioners are scarce. Although many programmes have demonstrated efficacy, few have achieved longterm sustainability, with a lack of information about how best to implement such programmes. This mixed-methods study aimed to evaluate the implementation of a novel education package to teach ultrasound-naive midwives in Malawi basic obstetric ultrasound, assessing its impact in the context of the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework.

METHODS: The study ran across six sites in Malawi between October 2020 and June 2021, encompassing three phases; pre-implementation, implementation and post-implementation. Twenty nine midwives underwent a bespoke education package with matched pre and post course surveys assessed their knowledge, attitudes and confidence and "hands on" assessments evaluating practical skills. Training evaluation forms and in-depth interviews explored their satisfaction with the package, with repeat assessment and remote image review evaluating maintenance of skills.

RESULTS: 28/29 midwives completed the training, with significant increases in knowledge, confidence and practical skills. Adherence to the education package varied, however many changes to the proposed methodology were adaptive and appeared to facilitate the efficacy of the programme. Unfortunately, despite reporting approval regarding the training itself, satisfaction regarding supervision and follow up was mixed, reflecting the difficulties encountered with providing ongoing in-person and remote support.

CONCLUSION: This programme was successful in improving trainees' knowledge, confidence and skill in performing basic obstetric ultrasound, largely on account of an adaptive approach to implementation. The maintenance of ongoing support was challenging, reflected by trainee dissatisfaction. By evaluating the success of this education package based on its implementation and not just its efficacy, we have generated new insights into the barriers to sustainable upscale, specifically those surrounding maintenance.}, } @article {pmid36921339, year = {2023}, author = {Zhang, H and Wang, X and Song, R and Ding, W and Li, F and Ji, L}, title = {Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational-Experimental Synergy Study on Emerging Pollutants.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c00071}, pmid = {36921339}, issn = {1520-5851}, abstract = {Metabolism, especially by CYP450 enzymes, is the main reason for mediating the toxification and detoxification of xenobiotics in humans, while some uncommon metabolic pathways, especially for emerging pollutants, probably causing idiosyncratic toxicity are easily overlooked. The pollution of sulfonamide antibiotics in aqueous system has attracted increasing public attention. Hydroxylation of the central amine group can trigger a series of metabolic processes of sulfonamide antibiotics in humans; however, this work parallelly reported the coupling and fragmenting initiated by amino H-abstraction of sulfamethoxazole (SMX) catalyzed by human CYP450 enzymes. Elucidation of the emerging metabolic profiles was mapped via a multistep synergy between computations and experiments, involving preliminary DFT computations and in vitro and in vivo assays, profiling adverse effects, and rationalizing the fundamental factors via targeted computations. Especially, the confirmed SMX dimer was shown to potentially act as a metabolism disruptor in humans, while spin aromatic delocalization resulting in the low electron donor ability of amino radicals was revealed as the fundamental factor to enable coupling of sulfonamide antibiotics by CYP450 through the nonconventional nonrebound pathway. This work may further strengthen the synergistic use of computations prior to experiments to avoid wasteful experimental screening efforts in environmental chemistry and toxicology.}, } @article {pmid36920898, year = {2023}, author = {Helmer, EH and Kay, S and Marcano-Vega, H and Powers, JS and Wood, TE and Zhu, X and Gwenzi, D and Ruzycki, TS}, title = {Multiscale predictors of small tree survival across a heterogeneous tropical landscape.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0280322}, doi = {10.1371/journal.pone.0280322}, pmid = {36920898}, issn = {1932-6203}, abstract = {Uncertainties about controls on tree mortality make forest responses to land-use and climate change difficult to predict. We tracked biomass of tree functional groups in tropical forest inventories across Puerto Rico and the U.S. Virgin Islands, and with random forests we ranked 86 potential predictors of small tree survival (young or mature stems 2.5-12.6 cm diameter at breast height). Forests span dry to cloud forests, range in age, geology and past land use and experienced severe drought and storms. When excluding species as a predictor, top predictors are tree crown ratio and height, two to three species traits and stand to regional factors reflecting local disturbance and the system state (widespread recovery, drought, hurricanes). Native species, and species with denser wood, taller maximum height, or medium typical height survive longer, but short trees and species survive hurricanes better. Trees survive longer in older stands and with less disturbed canopies, harsher geoclimates (dry, edaphically dry, e.g., serpentine substrates, and highest-elevation cloud forest), or in intervals removed from hurricanes. Satellite image phenology and bands, even from past decades, are top predictors, being sensitive to vegetation type and disturbance. Covariation between stand-level species traits and geoclimate, disturbance and neighboring species types may explain why most neighbor variables, including introduced vs. native species, had low or no importance, despite univariate correlations with survival. As forests recovered from a hurricane in 1998 and earlier deforestation, small trees of introduced species, which on average have lighter wood, died at twice the rate of natives. After hurricanes in 2017, the total biomass of trees ≥12.7 cm dbh of the introduced species Spathodea campanulata spiked, suggesting that more frequent hurricanes might perpetuate this light-wooded species commonness. If hurricane recovery favors light-wooded species while drought favors others, climate change influences on forest composition and ecosystem services may depend on the frequency and severity of extreme climate events.}, } @article {pmid36918541, year = {2023}, author = {Young, WJ and Haessler, J and Benjamins, JW and Repetto, L and Yao, J and Isaacs, A and Harper, AR and Ramirez, J and Garnier, S and van Duijvenboden, S and Baldassari, AR and Concas, MP and Duong, T and Foco, L and Isaksen, JL and Mei, H and Noordam, R and Nursyifa, C and Richmond, A and Santolalla, ML and Sitlani, CM and Soroush, N and Thériault, S and Trompet, S and Aeschbacher, S and Ahmadizar, F and Alonso, A and Brody, JA and Campbell, A and Correa, A and Darbar, D and De Luca, A and Deleuze, JF and Ellervik, C and Fuchsberger, C and Goel, A and Grace, C and Guo, X and Hansen, T and Heckbert, SR and Jackson, RD and Kors, JA and Lima-Costa, MF and Linneberg, A and Macfarlane, PW and Morrison, AC and Navarro, P and Porteous, DJ and Pramstaller, PP and Reiner, AP and Risch, L and Schotten, U and Shen, X and Sinagra, G and Soliman, EZ and Stoll, M and Tarazona-Santos, E and Tinker, A and Trajanoska, K and Villard, E and Warren, HR and Whitsel, EA and Wiggins, KL and Arking, DE and Avery, CL and Conen, D and Girotto, G and Grarup, N and Hayward, C and Jukema, JW and Mook-Kanamori, DO and Olesen, MS and Padmanabhan, S and Psaty, BM and Pattaro, C and Ribeiro, ALP and Rotter, JI and Stricker, BH and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JG and Orini, M and Charron, P and Watkins, H and Kooperberg, C and Lin, HJ and Wilson, JF and Kanters, JK and Sotoodehnia, N and Mifsud, B and Lambiase, PD and Tereshchenko, LG and Munroe, PB}, title = {Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1411}, pmid = {36918541}, issn = {2041-1723}, support = {R01 HL118277/HL/NHLBI NIH HHS/United States ; R56 HL118277/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Cardiovascular Diseases/genetics ; *Atrioventricular Block ; Genome-Wide Association Study ; Risk Factors ; Arrhythmias, Cardiac/genetics ; Electrocardiography/methods ; Biomarkers ; }, abstract = {The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.}, } @article {pmid36859581, year = {2023}, author = {Tucker, C and Brandt, M and Hiernaux, P and Kariryaa, A and Rasmussen, K and Small, J and Igel, C and Reiner, F and Melocik, K and Meyer, J and Sinno, S and Romero, E and Glennie, E and Fitts, Y and Morin, A and Pinzon, J and McClain, D and Morin, P and Porter, C and Loeffler, S and Kergoat, L and Issoufou, BA and Savadogo, P and Wigneron, JP and Poulter, B and Ciais, P and Kaufmann, R and Myneni, R and Saatchi, S and Fensholt, R}, title = {Sub-continental-scale carbon stocks of individual trees in African drylands.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {80-86}, pmid = {36859581}, issn = {1476-4687}, mesh = {*Carbon/analysis/metabolism ; *Ecosystem ; *Trees/anatomy & histology/chemistry/metabolism ; *Desert Climate ; Desiccation ; Satellite Imagery ; Africa South of the Sahara ; Machine Learning ; Wood/analysis ; Plant Roots ; Agriculture ; Environmental Restoration and Remediation ; Databases, Factual ; Biomass ; Computers ; }, abstract = {The distribution of dryland trees and their density, cover, size, mass and carbon content are not well known at sub-continental to continental scales[1-14]. This information is important for ecological protection, carbon accounting, climate mitigation and restoration efforts of dryland ecosystems[15-18]. We assessed more than 9.9 billion trees derived from more than 300,000 satellite images, covering semi-arid sub-Saharan Africa north of the Equator. We attributed wood, foliage and root carbon to every tree in the 0-1,000 mm year[-1] rainfall zone by coupling field data[19], machine learning[20-22], satellite data and high-performance computing. Average carbon stocks of individual trees ranged from 0.54 Mg C ha[-1] and 63 kg C tree[-1] in the arid zone to 3.7 Mg C ha[-1] and 98 kg tree[-1] in the sub-humid zone. Overall, we estimated the total carbon for our study area to be 0.84 (±19.8%) Pg C. Comparisons with 14 previous TRENDY numerical simulation studies[23] for our area found that the density and carbon stocks of scattered trees have been underestimated by three models and overestimated by 11 models, respectively. This benchmarking can help understand the carbon cycle and address concerns about land degradation[24-29]. We make available a linked database of wood mass, foliage mass, root mass and carbon stock of each tree for scientists, policymakers, dryland-restoration practitioners and farmers, who can use it to estimate farmland tree carbon stocks from tablets or laptops.}, } @article {pmid36813959, year = {2023}, author = {Cai, S and Zhao, X and Pittelkow, CM and Fan, M and Zhang, X and Yan, X}, title = {Optimal nitrogen rate strategy for sustainable rice production in China.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {73-79}, pmid = {36813959}, issn = {1476-4687}, mesh = {*Agriculture/economics/methods ; China ; Fertilizers/analysis/economics ; *Nitrogen/analysis/economics/metabolism ; *Oryza/metabolism ; Soil/chemistry ; *Sustainable Development ; *Crops, Agricultural/economics/metabolism/supply & distribution ; Ecology ; Farmers ; Datasets as Topic ; Food Supply ; *Environmentalism ; }, abstract = {Avoiding excessive agricultural nitrogen (N) use without compromising yields has long been a priority for both research and government policy in China[1,2]. Although numerous rice-related strategies have been proposed[3-5], few studies have assessed their impacts on national food self-sufficiency and environmental sustainability and fewer still have considered economic risks faced by millions of smallholders. Here we established an optimal N rate strategy based on maximizing either economic (ON) or ecological (EON) performance using new subregion-specific models. Using an extensive on-farm dataset, we then assessed the risk of yield losses among smallholder farmers and the challenges of implementing the optimal N rate strategy. We find that meeting national rice production targets in 2030 is possible while concurrently reducing nationwide N consumption by 10% (6-16%) and 27% (22-32%), mitigating reactive N (Nr) losses by 7% (3-13%) and 24% (19-28%) and increasing N-use efficiency by 30% (3-57%) and 36% (8-64%) for ON and EON, respectively. This study identifies and targets subregions with disproportionate environmental impacts and proposes N rate strategies to limit national Nr pollution below proposed environmental thresholds, without compromising soil N stocks or economic benefits for smallholders. Thereafter, the preferable N strategy is allocated to each region based on the trade-off between economic risk and environmental benefit. To facilitate the adoption of the annually revised subregional N rate strategy, several recommendations were provided, including a monitoring network, fertilization quotas and smallholder subsidies.}, } @article {pmid36914632, year = {2023}, author = {Kohyama, TI and Sheil, D and Sun, IF and Niiyama, K and Suzuki, E and Hiura, T and Nishimura, N and Hoshizaki, K and Wu, SH and Chao, WC and Nur Hajar, ZS and Rahajoe, JS and Kohyama, TS}, title = {Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1113}, pmid = {36914632}, issn = {2041-1723}, mesh = {Humans ; *Trees ; *Forests ; Biomass ; Wood ; Asia, Eastern ; Tropical Climate ; }, abstract = {Despite their fundamental importance the links between forest productivity, diversity and climate remain contentious. We consider whether variation in productivity across climates reflects adjustment among tree species and individuals, or changes in tree community structure. We analysed data from 60 plots of humid old-growth forests spanning mean annual temperatures (MAT) from 2.0 to 26.6 °C. Comparing forests at equivalent aboveground biomass (160 Mg C ha[-1]), tropical forests ≥24 °C MAT averaged more than double the aboveground woody productivity of forests <12 °C (3.7 ± 0.3 versus 1.6 ± 0.1 Mg C ha[-1] yr[-1]). Nonetheless, species with similar standing biomass and maximum stature had similar productivity across plots regardless of temperature. We find that differences in the relative contribution of smaller- and larger-biomass species explained 86% of the observed productivity differences. Species-rich tropical forests are more productive than other forests due to the high relative productivity of many short-stature, small-biomass species.}, } @article {pmid36911337, year = {2023}, author = {Lim, T and Lee, K and Kim, RH and Ryu, J and Cha, KH and Park, SY and Koo, SY and Hwang, KT}, title = {Effects of black raspberry extract on gut microbiota, microbial metabolites, and expressions of the genes involved in cholesterol and bile acid metabolisms in rats fed excessive choline with a high-fat diet.}, journal = {Food science and biotechnology}, volume = {32}, number = {4}, pages = {577-587}, pmid = {36911337}, issn = {2092-6456}, abstract = {UNLABELLED: In our previous study, black raspberry (BR) reduced the serum levels of trimethylamine-N-oxide and cholesterol in rats fed excessive choline with a high-fat diet (HFC). We hypothesized that gut microbiota could play a crucial role in the production of trimethylamine and microbial metabolites, and BR could influence gut microbial composition. This study aimed to elucidate the role of BR on changes in gut microbiota and microbial metabolites in the rats. The phylogenetic diversity of gut microbiota was reduced in the rats fed HFC, while that in the BR-fed group was restored. The BR supplementation enriched Bifidobacterium and reduced Clostridium cluster XIVa. In the BR-fed group, most cecal bile acids and hippuric acid increased, while serum lithocholic acid was reduced. The BR supplementation upregulated Cyp7a1 and downregulated Srebf2. These results suggest that BR extract may change gut bacterial community, modulate bile acids, and regulate gene expression toward reducing cholesterol.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01267-4.}, } @article {pmid36911308, year = {2023}, author = {Martinez, ND}, title = {Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology.}, journal = {Ecology and evolution}, volume = {13}, number = {3}, pages = {e9872}, pmid = {36911308}, issn = {2045-7758}, abstract = {Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.}, } @article {pmid36901248, year = {2023}, author = {Zeng, L and Liu, C}, title = {Exploring Factors Affecting Urban Park Use from a Geospatial Perspective: A Big Data Study in Fuzhou, China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {5}, pages = {}, pmid = {36901248}, issn = {1660-4601}, mesh = {Humans ; Urban Population ; *Parks, Recreational ; *Big Data ; Cities ; China ; }, abstract = {Promoting research on urban park use is important for developing the ecological and environmental health benefits of parks. This study proposes uniquely integrated methods combined with big data to measure urban park use. It combines comprehensive geographic detectors and multiscale geographically weighted regression from a geospatial perspective to quantify the individual and interactive effects of the parks' characteristics, accessibility, and surrounding environment features on weekday and weekend park use. The study also explores the degree of influence of spatial changes. The results indicate that the park-surrounding facilities and services factor contributed most to use, while its interaction effect with park service capacity had the greatest impact on park use. The interaction effects showed binary or nonlinear enhancement. This suggests that park use should be promoted within multiple dimensions. Many influencing factors had significant changes in the geographic space, suggesting that city-level park zoning construction should be adopted. Finally, park use was found to be affected by users' subjective preference on weekends and convenience factors on weekdays. These findings provide a theoretical basis for the influencing mechanisms of urban park use, which can help urban planners and policymakers formulate more specific policies to successfully manage and plan urban parks.}, } @article {pmid36900138, year = {2023}, author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Burgkart, R and Obermeier, A and Mayr, U and Ringelhan, M and Rasch, S and Lahmer, T and Geisler, F and Turner, PE and Chan, BK and Spinner, CD and Schneider, J}, title = {Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {36900138}, issn = {2075-4418}, abstract = {Ascitic fluid infection is a serious complication of liver cirrhosis. The distinction between the more common spontaneous bacterial peritonitis (SBP) and the less common secondary peritonitis in patients with liver cirrhosis is crucial due to the varying treatment approaches. This retrospective multicentre study was conducted in three German hospitals and analysed 532 SBP episodes and 37 secondary peritonitis episodes. Overall, >30 clinical, microbiological, and laboratory parameters were evaluated to identify key differentiation criteria. Microbiological characteristics in ascites followed by severity of illness and clinicopathological parameters in ascites were the most important predictors identified by a random forest model to distinguish between SBP and secondary peritonitis. To establish a point-score model, a least absolute shrinkage and selection operator (LASSO) regression model selected the ten most promising discriminatory features. By aiming at a sensitivity of 95% either to rule out or rule in SBP episodes, two cut-off scores were defined, dividing patients with infected ascites into a low-risk (score ≥ 45) and high-risk group (score < 25) for secondary peritonitis. Overall, the discrimination of secondary peritonitis from SBP remains challenging. Our univariable analyses, random forest model, and LASSO point score may help clinicians with the crucial differentiation between SBP and secondary peritonitis.}, } @article {pmid36642073, year = {2023}, author = {Paixão, TM and Siqueira, CEG and Tristan-Cheever, E and Fischer, FM and Martinez, MC and Christoffolete, MA and Meisinger, K and Teixeira, LR}, title = {Overweight and Obesity in Brazilian Immigrants in Massachusetts, USA: A Time Series Analysis (2009-2020).}, journal = {Obesity facts}, volume = {16}, number = {2}, pages = {109-118}, doi = {10.1159/000527286}, pmid = {36642073}, issn = {1662-4033}, abstract = {INTRODUCTION: Obesity is considered a growing public health problem by the Brazilian Ministry of Health and a global epidemic by the World Health Organization (WHO). In 2020, the Centers for Disease Control and Prevention (CDC) estimated the prevalence of adult obesity at 31.9% in the USA. The USA is one of the main destinations for Brazilian immigrants in search of better living conditions, and Massachusetts is one of the states with the highest presence of Brazilians. Changes in lifestyle and eating habits are often associated with increases in overweight and obesity in immigrants in the USA, especially Hispanics, an official classification that does not, however, include Brazilians. The aim of this study was to describe the temporal trend of overweight and obesity in Brazilian immigrants assisted by the Cambridge Health Alliance (CHA) healthcare network in Massachusetts.

METHODS: This was an ecological time series study of 128,206 records of Brazilians aged between 18 and 60 years based on hospital data from 2009 to 2020.

RESULTS: Mean age was 38.9 (SD = 10.6), and 61% of the sample were women. The prevalence of overweight and obesity was 38.4% and 25.4%, respectively. Obesity exhibited an increasing trend, while eutrophy and overweight decreased during the study period.

CONCLUSION: As little is known about the health of Brazilian immigrants in the USA, this study contributes to the literature on the subject. The observed increasing trends agree with the worldwide increase in obesity and indicate the need for future research exploring individual factors associated with immigrant acculturation.}, } @article {pmid36899307, year = {2023}, author = {Chan, YO and Dietz, N and Zeng, S and Wang, J and Flint-Garcia, S and Salazar-Vidal, MN and Škrabišová, M and Bilyeu, K and Joshi, T}, title = {The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {107}, pmid = {36899307}, issn = {1471-2164}, abstract = {BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize.

RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes.

CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website (https://soykb.org/SoybeanAlleleCatalogTool/), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website (https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana). Researchers can use this tool to connect variant alleles of genes with meta-information of species.}, } @article {pmid36894986, year = {2023}, author = {de Nies, L and Galata, V and Martin-Gallausiaux, C and Despotovic, M and Busi, SB and Snoeck, CJ and Delacour, L and Budagavi, DP and Laczny, CC and Habier, J and Lupu, PC and Halder, R and Fritz, JV and Marques, T and Sandt, E and O'Sullivan, MP and Ghosh, S and Satagopam, V and , and Krüger, R and Fagherazzi, G and Ollert, M and Hefeng, FQ and May, P and Wilmes, P}, title = {Altered infective competence of the human gut microbiome in COVID-19.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {46}, pmid = {36894986}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; SARS-CoV-2/genetics ; *Microbiota ; Multiomics ; }, abstract = {BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.

CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.}, } @article {pmid36893162, year = {2023}, author = {Rubenstein, DR and Solomon, J}, title = {Target-enriched enzymatic methyl sequencing: Flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282672}, pmid = {36893162}, issn = {1932-6203}, mesh = {*DNA Methylation ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; Nucleic Acid Hybridization ; *Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; CpG Islands/genetics ; }, abstract = {The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling (Lamprotornis superbus), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.}, } @article {pmid36895518, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lees, D and , }, title = {The genome sequence of the yellow-legged clearwing, Synanthedon vespiformis (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {233}, pmid = {36895518}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length.}, } @article {pmid36893405, year = {2023}, author = {Mallinson, DC and Elwert, F and Ehrenthal, DB}, title = {Spillover Effects of Prenatal Care Coordination on Older Siblings Beyond the Mother-Infant Dyad.}, journal = {Medical care}, volume = {61}, number = {4}, pages = {206-215}, doi = {10.1097/MLR.0000000000001822}, pmid = {36893405}, issn = {1537-1948}, abstract = {BACKGROUND: Pregnancy care coordination increases preventive care receipt for mothers and infants. Whether such services affect other family members' health care is unknown.

OBJECTIVE: To estimate the spillover effect of maternal exposure to Wisconsin Medicaid's Prenatal Care Coordination (PNCC) program during pregnancy with a younger sibling on the preventive care receipt for an older child.

RESEARCH DESIGN: Gain-score regressions-a sibling fixed effects strategy-estimated spillover effects while controlling for unobserved family-level confounders.

SUBJECTS: Data came from a longitudinal cohort of linked Wisconsin birth records and Medicaid claims. We sampled 21,332 sibling pairs (one older; one younger) who were born during 2008-2015, who were <4 years apart in age, and whose births were Medicaid-covered. In all, 4773 (22.4%) mothers received PNCC during pregnancy with the younger sibling.

MEASURES: The exposure was maternal PNCC receipt during pregnancy with the younger sibling (none; any). The outcome was the older sibling's number of preventive care visits or preventive care services in the younger sibling's first year of life.

RESULTS: Overall, maternal exposure to PNCC during pregnancy with the younger sibling did not affect older siblings' preventive care. However, among siblings who were 3 to <4 years apart in age, there was a positive spillover on the older sibling's receipt of care by 0.26 visits (95% CI: 0.11, 0.40 visits) and by 0.34 services (95% CI: 0.12, 0.55 services).

CONCLUSION: PNCC may only have spillover effects on siblings' preventive care in selected subpopulations but not in the broader population of Wisconsin families.}, } @article {pmid36882531, year = {2023}, author = {Wei, Z and Jian, Z and Sun, Y and Pan, F and Han, H and Liu, Q and Mei, Y}, title = {Ecological sustainability and high-quality development of the Yellow River Delta in China based on the improved ecological footprint model.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3821}, pmid = {36882531}, issn = {2045-2322}, abstract = {Aiming at the traditional ecological footprint model, the improved ecological footprint of the carbon footprint effectively makes up for the singularity of the ecological footprint's consideration of carbon emissions, and plays an important role in promoting high-quality development and ecological sustainability. This paper selects 2015, 2018 and 2020 as important time points for the study, corrects the ecological footprint parameter factors based on net primary productivity (NPP), measures the ecological footprint after the improvement of the carbon footprint, studies the spatial and temporal variation in the ecological footprint at the 100-m grid scale with the support of IPCC greenhouse gas inventory analysis, and analyzes the current ecological conservation status of the Yellow River Delta. Additionally, in the context of a low carbon economy, the decoupling index of carbon emissions and GDP is extended to the evaluation and analysis of high-quality development. The study showed that (1) the ecological footprint of the Yellow River Delta has increased year by year, from 0.721 hm[2]·person[- 1] to 0.758 hm[2]·person[- 1], an average annual increase of 2.9%; the ecological carrying capacity has decreased from 0.40 hm[2]·person[- 1] to 0.31 hm[2]·person[- 1], an overall decrease of 28.59%. (2) The overall ecological deficit of the Yellow River Delta grid is lightly overloaded, with most of the ecological surplus occurring in the northern and eastern parts of the study area and a few moderate and heavy overloads in the center of the core area where there is a lot of built-up land and the area is small and easy to gather. (3) Based on the low-carbon economy analysis, 2015, 2017 and 2020 reach absolute decoupling and are in the ideal scenario. However, in the rest of the years, carbon emissions and economic development are still in a large contradiction, and decoupling has fluctuated and varied greatly in the last six years. The effective combination of ecological footprint and low carbon economy analysis provides an important theoretical basis for improving ecological conservation and achieving high-quality development.}, } @article {pmid36522346, year = {2022}, author = {Wang, H and Harrison, SP and Li, M and Prentice, IC and Qiao, S and Wang, R and Xu, H and Mengoli, G and Peng, Y and Yang, Y}, title = {The China plant trait database version 2.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {769}, pmid = {36522346}, issn = {2052-4463}, mesh = {China ; Ecology ; *Ecosystem ; *Plants ; Databases, Factual ; }, abstract = {Plant functional traits represent adaptive strategies to the environment, linked to biophysical and biogeochemical processes and ecosystem functioning. Compilations of trait data facilitate research in multiple fields from plant ecology through to land-surface modelling. Here we present version 2 of the China Plant Trait Database, which contains information on morphometric, physical, chemical, photosynthetic and hydraulic traits from 1529 unique species in 140 sites spanning a diversity of vegetation types. Version 2 has five improvements compared to the previous version: (1) new data from a 4-km elevation transect on the edge of Tibetan Plateau, including alpine vegetation types not sampled previously; (2) inclusion of traits related to hydraulic processes, including specific sapwood conductance, the area ratio of sapwood to leaf, wood density and turgor loss point; (3) inclusion of information on soil properties to complement the existing data on climate and vegetation (4) assessments and flagging the reliability of individual trait measurements; and (5) inclusion of standardized templates for systematical field sampling and measurements.}, } @article {pmid36879919, year = {2022}, author = {Boyes, D and , and , and , and , and , and Parker, B and Plotkin, D and Kawahara, AY and , }, title = {The genome sequence of the sallow kitten, Furcula furcula (Clerck, 1759).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {229}, pmid = {36879919}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.}, } @article {pmid35363913, year = {2023}, author = {Zhu, M and Wang, Z and Yang, Y and Wang, Z and Mu, W and Liu, J}, title = {Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau.}, journal = {Molecular ecology}, volume = {32}, number = {6}, pages = {1411-1424}, doi = {10.1111/mec.16449}, pmid = {35363913}, issn = {1365-294X}, mesh = {Tibet ; *Multiomics ; *Plants/genetics ; Transcriptome/genetics ; Flowers/genetics ; }, abstract = {Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. Numerous genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.}, } @article {pmid36752771, year = {2023}, author = {Lippi, CA and Rund, SSC and Ryan, SJ}, title = {Characterizing the Vector Data Ecosystem.}, journal = {Journal of medical entomology}, volume = {60}, number = {2}, pages = {247-254}, pmid = {36752771}, issn = {1938-2928}, mesh = {Animals ; *Ecosystem ; *Vector Borne Diseases ; Databases, Factual ; }, abstract = {A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct control and mitigation efforts. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and serving approaches, means that it is distributed across many formats and data types. Data ranges from collections records to molecular characterization, geospatial data to interactions of vectors and traits, infection experiments to field trials. New initiatives arise, often spanning the effort traditionally siloed in specific research disciplines, and other efforts wane, perhaps in response to funding declines, different research directions, or lack of sustained interest. Thusly, the world of vector data - the Vector Data Ecosystem - can become unclear in scope, and the flows of data through these various efforts can become stymied by obsolescence, or simply by gaps in access and interoperability. As increasing attention is paid to creating FAIR (Findable Accessible Interoperable, and Reusable) data, simply characterizing what is 'out there', and how these existing data aggregation and collection efforts interact, or interoperate with each other, is a useful exercise. This study presents a snapshot of current vector data efforts, reporting on level of accessibility, and commenting on interoperability using an illustration to track a specimen through the data ecosystem to understand where it occurs for the database efforts anticipated to describe it (or parts of its extended specimen data).}, } @article {pmid36876314, year = {2023}, author = {Zhang, J and Qian, H}, title = {U.Taxonstand: An R package for standardizing scientific names of plants and animals.}, journal = {Plant diversity}, volume = {45}, number = {1}, pages = {1-5}, pmid = {36876314}, issn = {2468-2659}, abstract = {The scientific names of organisms are key identifiers of plants and animals. Correctly treating scientific names is a prerequisite for biodiversity research and documentation. Here, we present an R package, 'U.Taxonstand', which can standardize and harmonize scientific names in plant and animal species lists at a fast speed and at a high rate of matching success. Unlike most of other similar R packages each of which works with only one taxonomic database, U.Taxonstand can work with all taxonomic databases, as long as they are properly formatted. Multiple databases for plants and animals that can be directly used by U.Taxonstand, which include bryophytes, vascular plants, amphibians, birds, fishes, mammals, and reptiles, are available online. U.Taxonstand can be a very useful tool for botanists, zoologists, ecologists and biogeographers to standardize and harmonize scientific names of organisms.}, } @article {pmid36874580, year = {2022}, author = {Hayward, A and Lohse, K and Laetsch, DR and Vila, R and , and , and , and Taluy, E and , }, title = {The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {315}, pmid = {36874580}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Plebejus argus (silver-studded blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 382 megabases in span. The entire assembly (100%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 27.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,693 protein coding genes.}, } @article {pmid36706978, year = {2023}, author = {Nosenko, T and Zimmer, I and Ghirardo, A and Köllner, TG and Weber, B and Polle, A and Rosenkranz, M and Schnitzler, JP}, title = {Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis.}, journal = {Fungal genetics and biology : FG & B}, volume = {165}, number = {}, pages = {103779}, doi = {10.1016/j.fgb.2023.103779}, pmid = {36706978}, issn = {1096-0937}, mesh = {Multiomics ; *Sesquiterpenes/metabolism ; Genes, Fungal ; *Mycorrhizae/genetics ; Gene Expression Profiling ; }, abstract = {Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.}, } @article {pmid36874578, year = {2022}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Seraphim, Lobophora halterata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {313}, pmid = {36874578}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Lobophora halterata (the Seraphim; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 315 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules with the Z and W sex chromosomes assembled. The mitochondrial genome has also been assembled and is 15.7 kilobases in length.}, } @article {pmid36874577, year = {2022}, author = {Hawkes, W and Wotton, K and , and , and , and , and , and , }, title = {The genome sequence of the dumpy grass hoverfly, Melanostoma mellinum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {59}, pmid = {36874577}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Melanostoma mellinum (the dumpy grass hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 731 megabases in span. The majority of the assembly (99.67%) is scaffolded into five chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 16.1 kilobases in length.}, } @article {pmid36874564, year = {2022}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the large yellow underwing, Noctua pronuba (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {119}, pmid = {36874564}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Noctua pronuba (the large yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 529 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.}, } @article {pmid36872222, year = {2023}, author = {Zhang, GZ and Chen, SL and Dong, LL}, title = {[Traditional Chinese medicine microbiomics and its research strategies].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {48}, number = {3}, pages = {596-607}, doi = {10.19540/j.cnki.cjcmm.20221101.101}, pmid = {36872222}, issn = {1001-5302}, abstract = {The tight relationships between microbiome and traditional Chinese medicine(TCM)have been widely recognized. New technologies, results, and theories are emerging in the field of microbiomics in recent years with the advances in high-throughput sequencing and multi-omics technologies. Based on the previous research, the present study has proposed the concept of TCM microbiomics(TCMM), which is an interdisciplinary subject aiming at elucidating the functions and applications of microbiome in the areas of herb resources, herb processing, herb storage, and clinical effects by using modern technology of biology, ecology, and informatics. This subject essentially contains the structures, functions, interactions, molecular mechanisms, and application strategies of the microbiome associated with the quality, safety, and efficacy of TCM. Firstly, the development of the TCMM concept was summarized, with the profound understanding of TCMM on the complexity and entirety of microbiome being emphasized. Then, the research contents and applications of TCMM in promoting the sustainable development of herb resources, improving the standardization and diversification of herb fermentation, strengthening the safety of herb storage, and resolving the scientific connotation of theories and clinical efficacy of TCM are reviewed. Finally, the research strategies and methods of TCM microbiomics were elaborated from basic research, application research, and system research. TCMM is expected to promote the integrative development of TCM with frontier science and technology, thereby expanding the depth and scope of TCM study and facilitating TCM modernization.}, } @article {pmid36866381, year = {2023}, author = {Lin, J and Yu, D and Pan, R and Cai, J and Liu, J and Zhang, L and Wen, X and Peng, X and Cernava, T and Oufensou, S and Migheli, Q and Chen, X and Zhang, X}, title = {Improved YOLOX-Tiny network for detection of tobacco brown spot disease.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1135105}, pmid = {36866381}, issn = {1664-462X}, abstract = {INTRODUCTION: Tobacco brown spot disease caused by Alternaria fungal species is a major threat to tobacco growth and yield. Thus, accurate and rapid detection of tobacco brown spot disease is vital for disease prevention and chemical pesticide inputs.

METHODS: Here, we propose an improved YOLOX-Tiny network, named YOLO-Tobacco, for the detection of tobacco brown spot disease under open-field scenarios. Aiming to excavate valuable disease features and enhance the integration of different levels of features, thereby improving the ability to detect dense disease spots at different scales, we introduced hierarchical mixed-scale units (HMUs) in the neck network for information interaction and feature refinement between channels. Furthermore, in order to enhance the detection of small disease spots and the robustness of the network, we also introduced convolutional block attention modules (CBAMs) into the neck network.

RESULTS: As a result, the YOLO-Tobacco network achieved an average precision (AP) of 80.56% on the test set. The AP was 3.22%, 8.99%, and 12.03% higher than that obtained by the classic lightweight detection networks YOLOX-Tiny network, YOLOv5-S network, and YOLOv4-Tiny network, respectively. In addition, the YOLO-Tobacco network also had a fast detection speed of 69 frames per second (FPS).

DISCUSSION: Therefore, the YOLO-Tobacco network satisfies both the advantages of high detection accuracy and fast detection speed. It will likely have a positive impact on early monitoring, disease control, and quality assessment in diseased tobacco plants.}, } @article {pmid36862660, year = {2023}, author = {Nanjala, R and Nyasimi, F and Masiga, D and Kibet, CK}, title = {A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya.}, journal = {PLoS computational biology}, volume = {19}, number = {3}, pages = {e1010904}, pmid = {36862660}, issn = {1553-7358}, support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; U2R TW010677/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; Kenya ; *Mentors ; *Computational Biology ; Genomics ; Students ; }, abstract = {The demand for well-trained bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialization in bioinformatics. Graduates are often unaware of the career opportunities in bioinformatics, and those who are may lack mentors to help them choose a specialization. The Bioinformatics Mentorship and Incubation Program seeks to bridge the gap by laying the foundation for a bioinformatics training pipeline using project-based learning. The program selects six participants through an intensive open recruitment exercise for highly competitive students to join the program for four months. The six interns undergo intensive training within the first one and a half months before being assigned to mini-projects. We track the progress of the interns weekly through code review sessions and a final presentation at the end of the four months. We have trained five cohorts, most of whom have secured master's scholarships within and outside the country and job opportunities. We demonstrate the benefit of structured mentorship using project-based learning in filling the training gap after undergraduate programs to generate well-trained bioinformaticians who are competitive in graduate programs and bioinformatics jobs.}, } @article {pmid36873713, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the swallow prominent, Pheosia tremula (Clerck, 1759).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {335}, pmid = {36873713}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Pheosia tremula (the swallow prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 290 megabases in span. The majority of the assembly, 99.94%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid36873714, year = {2021}, author = {Hawkes, W and Wotton, K and , and , and , and , and , and , }, title = {The genome sequence of the tapered dronefly, Eristalis pertinax (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {292}, pmid = {36873714}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eristalis tenax (the tapered dronefly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 487 megabases in span. The majority of the assembly (95.23%) is scaffolded into seven chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.}, } @article {pmid36866282, year = {2021}, author = {Hawkes, W and Wotton, K and Smith, M and , and , and , and , and , and , and , }, title = {The genome sequence of the two-banded wasp hoverfly, Chrysotoxum bicinctum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {321}, pmid = {36866282}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Chrysotoxum bicinctum (the two-banded wasp hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 913 megabases in span. The majority of the assembly (98.81%) is scaffolded into five chromosomal pseudomolecules, with the X sex chromosome assembled.}, } @article {pmid36865376, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lees, D and , }, title = {The genome sequence of the merveille du jour, Griposia aprilina (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {247}, pmid = {36865376}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Griposia aprilina (the merveille du jour; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 720 megabases in span. The majority of the assembly (99.89%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.}, } @article {pmid36865367, year = {2022}, author = {Broad, GR and Boyes, D and , and , and , and , and , and , and , }, title = {The genome sequence of the setaceous Hebrew character, Xestia c-nigrum, (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {295}, pmid = {36865367}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Xestia c-nigrum (the setaceous Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 760 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, } @article {pmid36864462, year = {2023}, author = {Keuschnig, C and Vogel, TM and Barbaro, E and Spolaor, A and Koziol, K and Björkman, MP and Zdanowicz, C and Gallet, JC and Luks, B and Layton, R and Larose, C}, title = {Selection processes of Arctic seasonal glacier snowpack bacterial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {35}, pmid = {36864462}, issn = {2049-2618}, abstract = {BACKGROUND: Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.

METHODS: We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.

RESULTS: While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.

CONCLUSIONS: These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.}, } @article {pmid36863150, year = {2023}, author = {Liu, X and Wang, Y and Meng, X and Zhang, C and Chen, Z}, title = {Improved method for benthic ecosystem health assessment by integrating chemical indexes into multiple biological indicator species-A case study of the Baiyangdian Lake, China.}, journal = {Journal of environmental management}, volume = {335}, number = {}, pages = {117530}, doi = {10.1016/j.jenvman.2023.117530}, pmid = {36863150}, issn = {1095-8630}, abstract = {A comprehensive and scientific assessment of benthic ecosystem health is key to the rational selection of endogenous pollution reduction technologies for lakes. However, current assessments are mainly limited to biological indicators and ignore the actual benthic ecosystem situations, such as the impact of eutrophication and heavy metal pollution, which may lead to the one-sidedness of the evaluation results. In this study, taking Baiyangdian Lake, the largest shallow mesotrophic-eutrophic lake in the North China Plain, as an example, the chemical assessment index and biological integrity index were first combined to estimate the biological conditions, nutritional status and heavy metal pollution of lakes. The indicator system incorporated three biological assessments (benthic index of biotic integrity (B-IBI), submerged aquatic vegetation index of biological integrity (SAV-IBI) and microbial index of biological integrity (M-IBI)) and three chemical assessments (dissolved oxygen (DO), comprehensive trophic level index (TLI) and index of geoaccumulation (Igeo)). Twenty-three attributes of B-IBI, fourteen attributes of SAV-IBI and twelve attributes of M-IBI were screened by range, responsiveness, and redundancy tests to keep the core metrics that were significantly correlated with disturbance gradients or showed strong discriminatory power between reference and impaired sites. The assessment results of B-IBI, SAV-IBI, and M-IBI showed significant differences in the response to anthropogenic activities and seasonal change, among which the submerged plants showed more significant seasonal differences. It is difficult to reach a comprehensive conclusion regarding the benthic ecosystem health status based on a single biological community. In comparison with biological indicators, the score of chemical indicators is relatively low. DO, TLI and Igeo provide an essential supplement for the benthic ecosystem health assessment of lakes with eutrophication and heavy metal pollution problems. Using the new integrated assessment method, the benthic ecosystem health of Baiyangdian Lake was rated as fair, especially the northern parts of the lake adjacent to the inflow mouth of the Fu River, which were in poor condition, indicating that the lake has experienced anthropogenic disturbance, resulting in eutrophication, heavy metal pollution and biological community degradation. Whether it's spring or summer, the integrated assessment method provides a more plausible and comprehensive view of benthic ecosystem health under the pressure of increasing human activities and changing habitat and hydrological conditions, overcoming the narrow perspective and uncertainties of the single-index method. Thus, it can assist lake managers in providing technical support for ecological indication and restoration.}, } @article {pmid36866281, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the snout, Hypena proboscidalis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {236}, pmid = {36866281}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Hypena proboscidalis (the snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 637 megabases in span. The majority of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid36859647, year = {2023}, author = {Nocci, M and Villa, G and Ragazzoni, L and Tofani, L and Romagnoli, S and Baldini, G and Bertini, P and Hubloue, I and Scolletta, S and Mechi, MT and Della Corte, F}, title = {Relationship between intensive care surge capacity and hospital factors: an extensive experience.}, journal = {Internal and emergency medicine}, volume = {}, number = {}, pages = {1-12}, pmid = {36859647}, issn = {1970-9366}, abstract = {As a prolonged surge scenario, the COVID-19 pandemic has offered an unparalleled opportunity to improve hospital surge capacity (SC) understanding and the ability to manage it. In this study, the authors report the experience of a large hospital network and evaluate potential relationships between Intensive Care Units SC (ICU-SC) and some hospital-related variables: bed occupancy, emergency department admissions, ward admission from ED, and elective surgery procedures. Pearson's partial correlation coefficient (r) has been used to define the relationship between SC and the daily values of the above variables, collected through a dedicated digital platform that also ensured a regular quality check of the data. The observation has concerned several levels of analysis, namely two different types of SC calculation (SC base-SCb and SC actual-SCa), hospital category level and multi-hospital level, and two consecutive pandemic waves. Among the 16 hospitals observed, the correlation was shown to be moderate-positive with non-ICU bed occupancy (r/ = 0.62, r/ = 0.54), strong/moderate with ICU bed occupancy (r/ = 0.72, r/ = 0.54), and moderate with ward admissions from ED (r/ = 0.50, r/ = 0.51) On the contrary, the correlation proved to be moderate-negative with ED admissions (r/ = - 0.69, r/ = - 0.62) and low with the number of elective surgery procedures (r/ = - 0.10, r/ = - 0.16). This study identified a positive correlation between SC and three variables monitored: ICU bed occupancy, non-ICU bed occupancy, and ward admissions from ED. On the contrary, the correlation was negative for ED admission and the number of elective surgery procedures. The results have been confirmed across all levels of analysis adopted.}, } @article {pmid36859503, year = {2023}, author = {Jones, DL and Rhymes, JM and Green, E and Rimmer, C and Kevill, JL and Malham, SK and Weightman, AJ and Farkas, K}, title = {Poor air passenger knowledge of COVID-19 symptoms and behaviour undermines strategies aimed at preventing the import of SARS-CoV-2 into the UK.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3494}, pmid = {36859503}, issn = {2045-2322}, abstract = {Air travel mediates transboundary movement of SARS-CoV-2. To prepare for future pandemics, we sought to understand air passenger behaviour and perceived risk during the COVID-19 pandemic. This study of UK adults (n = 2103) quantified knowledge of COVID-19 symptoms, perceived health risk of contracting COVID-19, likelihood of returning to the UK with COVID-19 symptoms, likelihood to obey self-quarantining guidelines, how safe air travellers felt when flying during the pandemic (n = 305), and perceptions towards face covering effectiveness.Overall knowledge of COVID-19 symptoms was poor. Men and younger age groups (18-44) were less informed than women and older age groups (44 +). A significant proportion (21%) of the population would likely travel back to the UK whilst displaying COVID-19 symptoms with many expressing that they would not fully comply with self-isolation guidelines. Overall, males and younger age groups had a reduced perceived personal risk from contracting COVID-19, posing a higher risk of transporting SARS-CoV-2 back to the UK. Poor passenger knowledge and behaviour undermines government guidelines and policies aimed at preventing SARS-CoV-2 entry into the UK. This supports the need for stricter, clearer and more targeted guidelines with point-of-departure viral testing and stricter quarantining upon arrival.}, } @article {pmid36858189, year = {2023}, author = {Kushwaha, B and Nagpure, NS and Srivastava, S and Pandey, M and Kumar, R and Raizada, S and Agarwal, S and Singh, M and Basheer, VS and Kumar, RG and Das, P and Das, SP and Patnaik, S and Bit, A and Kumar Srivastava, S and Vishwakarma, AL and Joshi, CG and Kumar, D and Jena, JK}, title = {Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes.}, journal = {Gene}, volume = {}, number = {}, pages = {147294}, doi = {10.1016/j.gene.2023.147294}, pmid = {36858189}, issn = {1879-0038}, abstract = {Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (28 commercially important, 10 vulnerable and 14 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.}, } @article {pmid36852195, year = {2023}, author = {Streng, K and de Best, PA and Timen, A and Koopmans, MPG and van der Poel, WHM and Sikkema, RS}, title = {Rapid response screening for emerging zoonotic pathogens, barriers and opportunities: A study for enhanced preparedness of the Netherlands.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100507}, pmid = {36852195}, issn = {2352-7714}, abstract = {BACKGROUND: Outbreaks of zoonotic emerging infectious diseases (EIDs) require rapid identification of potential reservoir hosts and mapping disease spread in these hosts to inform risk assessment and adequate control measures. Animals are often understudied when a novel EID is detected in humans and acquisition of animal samples is hampered by practical, ethical, and legal barriers, of which there is currently no clear overview. Therefore, the three aims of this study are (1) to map potentially available collections of animal samples, (2) to assess possibilities and barriers for reuse of these samples and (3) to assess possibilities and barriers for active animal and environmental sampling in the Netherlands.

METHODS: A literature search was performed to identify ongoing sampling activities and opportunities for reuse or active sampling. Semi-structured interviews with stakeholder organizations were conducted to gain further insight into the three research questions.

RESULTS: Various sample collections of surveillance, diagnostic and research activities exist in the Netherlands. Sample size, coverage, storage methods and type of samples collected differs per animal species which influences reuse suitability. Organizations are more likely to share samples, for reuse in outbreak investigations, when they have a pre-existing relationship with the requesting institute. Identified barriers for sharing were, among others, unfamiliarity with legislation and unsuitable data management systems. Active sampling of animals or the environment is possible through several routes. Related barriers are acquiring approval from animal- or property owners, conflicts with anonymization, and time needed to acquire ethical approval.

CONCLUSION: The animal sample collections identified would be very valuable for use in outbreak investigations. Barriers for sharing may be overcome by increasing familiarity with legislation, building (international) sharing networks and agreements before crises occur and developing systems for sample registration and biobanking. Proactive setting up of ethical approvals will allow for rapid animal sample collection to identify EID hosts and potential spillovers.}, } @article {pmid36850776, year = {2023}, author = {Di Paolo, S and Nijmeijer, EM and Bragonzoni, L and Gokeler, A and Benjaminse, A}, title = {Definition of High-Risk Motion Patterns for Female ACL Injury Based on Football-Specific Field Data: A Wearable Sensors Plus Data Mining Approach.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {4}, pages = {}, pmid = {36850776}, issn = {1424-8220}, mesh = {Female ; Humans ; *Anterior Cruciate Ligament Injuries ; *Football ; Rotation ; Data Mining ; *Wearable Electronic Devices ; }, abstract = {The aim of the present study was to investigate if the presence of anterior cruciate ligament (ACL) injury risk factors depicted in the laboratory would reflect at-risk patterns in football-specific field data. Twenty-four female footballers (14.9 ± 0.9 year) performed unanticipated cutting maneuvers in a laboratory setting and on the football pitch during football-specific exercises (F-EX) and games (F-GAME). Knee joint moments were collected in the laboratory and grouped using hierarchical agglomerative clustering. The clusters were used to investigate the kinematics collected on field through wearable sensors. Three clusters emerged: Cluster 1 presented the lowest knee moments; Cluster 2 presented high knee extension but low knee abduction and rotation moments; Cluster 3 presented the highest knee abduction, extension, and external rotation moments. In F-EX, greater knee abduction angles were found in Cluster 2 and 3 compared to Cluster 1 (p = 0.007). Cluster 2 showed the lowest knee and hip flexion angles (p < 0.013). Cluster 3 showed the greatest hip external rotation angles (p = 0.006). In F-GAME, Cluster 3 presented the greatest knee external rotation and lowest knee flexion angles (p = 0.003). Clinically relevant differences towards ACL injury identified in the laboratory reflected at-risk patterns only in part when cutting on the field: in the field, low-risk players exhibited similar kinematic patterns as the high-risk players. Therefore, in-lab injury risk screening may lack ecological validity.}, } @article {pmid36848570, year = {2023}, author = {Stenseth, NC and Schlatte, R and Liu, X and Pielke, R and Li, R and Chen, B and Bjørnstad, ON and Kusnezov, D and Gao, GF and Fraser, C and Whittington, JD and Bai, Y and Deng, K and Gong, P and Guan, D and Xiao, Y and Xu, B and Johnsen, EB}, title = {How to avoid a local epidemic becoming a global pandemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {10}, pages = {e2220080120}, doi = {10.1073/pnas.2220080120}, pmid = {36848570}, issn = {1091-6490}, mesh = {Humans ; Pandemics/prevention & control ; *COVID-19/epidemiology/prevention & control ; SARS-CoV-2 ; Disease Outbreaks ; *Air Travel ; }, abstract = {Here, we combine international air travel passenger data with a standard epidemiological model of the initial 3 mo of the COVID-19 pandemic (January through March 2020; toward the end of which the entire world locked down). Using the information available during this initial phase of the pandemic, our model accurately describes the main features of the actual global development of the pandemic demonstrated by the high degree of coherence between the model and global data. The validated model allows for an exploration of alternative policy efficacies (reducing air travel and/or introducing different degrees of compulsory immigration quarantine upon arrival to a country) in delaying the global spread of SARS-CoV-2 and thus is suggestive of similar efficacy in anticipating the spread of future global disease outbreaks. We show that a lesson from the recent pandemic is that reducing air travel globally is more effective in reducing the global spread than adopting immigration quarantine. Reducing air travel out of a source country has the most important effect regarding the spreading of the disease to the rest of the world. Based upon our results, we propose a digital twin as a further developed tool to inform future pandemic decision-making to inform measures intended to control the spread of disease agents of potential future pandemics. We discuss the design criteria for such a digital twin model as well as the feasibility of obtaining access to the necessary online data on international air travel.}, } @article {pmid36840322, year = {2023}, author = {Hou, H and Liu, H and Xiong, J and Wang, C and Zhang, S and Ding, Z}, title = {Comparison of Soil Bacterial Communities under Canopies of Pinus tabulaeformis and Populus euramericana in a Reclaimed Waste Dump.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840322}, issn = {2223-7747}, abstract = {To compare the effects of different remediation tree species on soil bacterial communities and provide a theoretical basis for the selection of ecosystem function promotion strategies after vegetation restoration, the characteristic changes in soil bacterial communities after Pinus tabulaeformis and Populus euramericana reclamation were explored using high-throughput sequencing and molecular ecological network methods. The results showed that: (1) With the increase in reclamation years, the reclaimed soil properties were close to the control group, and the soil properties of Pinus tabulaeformis were closer to the control group than those of P. euramericana. (2) The dominant bacteria under the canopies of P. tabulaeformis and P. euramericana was the same. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Bacteroidetes, and Cyanobacteria were the dominant bacteria in the restored soil, accounting for more than 95% of the total abundance. The average values of the Shannon diversity index, Simpson diversity index, Chao 1 richness estimator, and abundance-based coverage estimator of the bacterial community in the P. euramericana reclaimed soil were higher than those in the P. tabulaeformis reclaimed soil. The influence of reclamation years on the bacterial community of samples is greater than that of species types. (3) The results of ecological network construction showed that the total number of nodes, total number of connections, and average connectivity of the soil bacterial network under P. euramericana reclamation were greater than those under P. tabulaeformis reclamation. The bacterial molecular ecological network under P. euramericana was more abundant. (4) Among the dominant bacteria, the relative abundance of Actinobacteria was negatively correlated with soil pH, soil total nitrogen content, and the activities of urease, invertase, and alkaline phosphatase, while the relative abundance of Proteobacteria and Bacteroidetes was positively correlated with these environmental factors. The relationship between the soil bacterial community of P. tabulaeformis and P. euramericana and the environmental factors is not completely the same, and even the interaction between some environmental factors and bacteria is opposite.}, } @article {pmid36840309, year = {2023}, author = {Jocienė, L and Krokaitė, E and Rekašius, T and Vilčinskas, R and Judžentienė, A and Marozas, V and Kupčinskienė, E}, title = {Ionomic Parameters of Populations of Common Juniper (Juniperus communis L.) Depending on the Habitat Type.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840309}, issn = {2223-7747}, abstract = {For the study of the ionomic parameters of Juniperus communis needles, fourteen sites covering most of the territory of Lithuania and belonging to distinct habitats (coastal brown dunes covered with natural Scots pine forests (G), Juniperus communis scrubs (F), transition mires and quaking bogs (D), subcontinental moss Scots pine forests (G), and xero-thermophile fringes) were selected. Concentrations of macro-, micro-, and non-essential elements were analyzed in current-year needles, sampled in September. According to the concentrations of elements in J. communis needles, the differences between the most contrasting populations were as follows: up to 2-fold for Mg, N, K, Ca, and Zn; 2- to 7-fold for P, Na, Fe, Cu, Al, Cr, Ni, and Pb; and 26- to 31-fold for Mn and Cd. The concentrations of Cd, Cr, and Ni in needles of J. communis did not reach levels harmful for conifers. When compared to all other habitats (B, F, G, and E), the populations from transition mires and quaking bogs (D) had significantly lower concentrations of main nutritional elements N (12176 µg/g d. m.), P (1054 µg/g d. m.), and K (2916 µg/g d. m.). In Juniperus communis scrubs (F), a habitat protected by EUNIS, the concentration of K in the needles was highest, while Zn and Cu concentrations were the lowest. Principal component (PC) analyses using concentrations of 15 elements as variables for the discrimination of populations or habitats allowed authors to distinguish F and B habitats from the E habitat (PC1) and F and D habitats from the G habitat (PC2). Discriminating between populations, the most important variables were concentrations of P, N, Mg, Ca, Cu, and K. Discriminating between habitats, the important variables were concentrations of N and P.}, } @article {pmid36816807, year = {2022}, author = {Ben Aribi, H and Ding, M and Kiran, A}, title = {Gene expression data visualization tool on the o[2]S[2]PARC platform.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {1267}, pmid = {36816807}, issn = {2046-1402}, mesh = {*Gene Expression Profiling ; *Computational Biology ; Data Visualization ; Gene Ontology ; Gene Expression ; }, abstract = {Background: The identification of differentially expressed genes and their associated biological processes, molecular function, and cellular components are essential for genetic disease studies because they present potential biomarkers and therapeutic targets. Methods: In this study, we developed an o[2]S[2]PARC template to instantiate an interactive pipeline for gene expression data visualization, ontological mapping, and statistical evaluation. To demonstrate the tool's usefulness, we performed a case study on a publicly available dataset. Results: The tool enables users to identify the differentially expressed genes (DEGs) and visualize them in a volcano plot format. Ontologies associated with the DEGs are assigned and visualized in barplots. Conclusions: The "Expression data visualization" template is publicly available on the o[2]S[2]PARC platform.}, } @article {pmid36820086, year = {2023}, author = {Huo, J and Hu, X and Bai, J and Lv, A}, title = {Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1098455}, pmid = {36820086}, issn = {1664-3224}, mesh = {Animals ; *Goldfish ; Aeromonas hydrophila ; Gills ; Zebrafish/genetics ; Multiomics ; NF-kappa B/genetics ; Phylogeny ; Immunity, Innate/genetics ; *MicroRNAs/genetics ; }, abstract = {The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.}, } @article {pmid35549363, year = {2023}, author = {Wylie, MS and Colasante, T and De France, K and Lin, L and Hollenstein, T}, title = {Momentary emotion regulation strategy use and success: Testing the influences of emotion intensity and habitual strategy use.}, journal = {Emotion (Washington, D.C.)}, volume = {23}, number = {2}, pages = {375-386}, doi = {10.1037/emo0001074}, pmid = {35549363}, issn = {1931-1516}, mesh = {Humans ; Female ; Young Adult ; Adult ; Male ; *Emotional Regulation/physiology ; Emotions/physiology ; Ecological Momentary Assessment ; Data Management ; }, abstract = {Successful emotion regulation (ER) is important for a wide range of psychosocial outcomes. Specific ER strategies have been identified as being more or less likely to be successful. However, recent evidence suggests significant individual differences in the association between strategy implementation and ER success. Indeed, 2 key factors may play an important role in moderating the link between ER strategy use and ER success in the moment: (a) the intensity of the specific emotional experience, and (b) the relative frequency in using a given ER strategy. Experience-sampling across 14-days (N = 304, Mage = 19.14, % female = 87.5) was used to assess whether emotion intensity and trait ER strategy use were differentially associated with perceived regulatory success depending on which ER strategy was used. Multilevel modeling revealed that more intense emotions were associated with lower perceived success for all strategies. Additionally, habitual reappraisal predicted greater success and habitual rumination predicted lower success. We discuss the possibility that results reflected intensity-based ER strategy choices and add to the growing call to abandon the reductive labeling of ER strategies as either "adaptive" or "maladaptive." (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid36840203, year = {2023}, author = {Visztra, GV and Frei, K and Hábenczyus, AA and Soóky, A and Bátori, Z and Laborczi, A and Csikós, N and Szatmári, G and Szilassi, P}, title = {Applicability of Point- and Polygon-Based Vegetation Monitoring Data to Identify Soil, Hydrological and Climatic Driving Forces of Biological Invasions-A Case Study of Ailanthus altissima, Elaeagnus angustifolia and Robinia pseudoacacia.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/plants12040855}, pmid = {36840203}, issn = {2223-7747}, abstract = {Invasive tree species are a significant threat to native flora. They modify the environment with their allelopathic substances and inhibit the growth of native species by shading, thus reducing diversity. The most effective way to control invasive plants is to prevent their spread which requires identifying the environmental parameters promoting it. Since there are several types of invasive plant databases available, determining which database type is the most relevant for investigating the occurrence of alien plants is of great importance. In this study, we compared the efficiency and reliability of point-based (EUROSTAT Land Use and Coverage Area Frame Survey (LUCAS)) and polygon-based (National Forestry Database (NFD)) databases using geostatistical methods in ArcGIS software. We also investigated the occurrence of three invasive tree species (Ailanthus altissima, Elaeagnus angustifolia, and Robinia pseudoacacia) and their relationships with soil, hydrological, and climatic parameters such as soil organic matter content, pH, calcium carbonate content, rooting depth, water-holding capacity, distance from the nearest surface water, groundwater depth, mean annual temperature, and mean annual precipitation with generalized linear models in R-studio software. Our results show that the invasion levels of the tree species under study are generally over-represented in the LUCAS point-based vegetation maps, and the point-based database requires a dataset with a larger number of samples to be reliable. Regarding the polygon-based database, we found that the occurrence of the invasive species is generally related to the investigated soil and hydrological and climatic factors.}, } @article {pmid36836247, year = {2023}, author = {Wang, J and Qin, S and Fan, R and Peng, Q and Hu, X and Yang, L and Liu, Z and Baccelli, I and Migheli, Q and Berg, G and Chen, X and Cernava, T}, title = {Plant Growth Promotion and Biocontrol of Leaf Blight Caused by Nigrospora sphaerica on Passion Fruit by Endophytic Bacillus subtilis Strain GUCC4.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/jof9020132}, pmid = {36836247}, issn = {2309-608X}, abstract = {Passion fruit (Passiflora edulis Sims) is widely cultivated in tropic and sub-tropic regions for the production of fruit, flowers, cosmetics, and for pharmacological applications. Its high economic, nutritional, and medical values elicit the market demand, and the growing areas are rapidly increasing. Leaf blight caused by Nigrospora sphaerica is a new and emerging disease of passion fruit in Guizhou, in southwest China, where the unique karst mountainous landscape and climate conditions are considered potential areas of expansion for passion fruit production. Bacillus species are the most common biocontrol and plant-growth-promotion bacteria (PGPB) resources in agricultural systems. However, little is known about the endophytic existence of Bacillus spp. in the passion fruit phyllosphere as well as their potential as biocontrol agents and PGPB. In this study, 44 endophytic strains were isolated from 15 healthy passion fruit leaves, obtained from Guangxi province, China. Through purification and molecular identification, 42 of the isolates were ascribed to Bacillus species. Their inhibitory activity against N. sphaerica was tested in vitro. Eleven endophytic Bacillus spp. strains inhibited the pathogen by >65%. All of them produced biocontrol- and plant-growth-promotion-related metabolites, including indole-3-acetic acid (IAA), protease, cellulase, phosphatase, and solubilized phosphate. Furthermore, the plant growth promotion traits of the above 11 endophytic Bacillus strains were tested on passion fruit seedlings. One isolate, coded B. subtilis GUCC4, significantly increased passion fruit stem diameter, plant height, leaf length, leaf surface, fresh weight, and dry weight. In addition, B. subtilis GUCC4 reduced the proline content, which indicated its potential to positively regulate passion fruit biochemical properties and resulted in plant growth promotion effects. Finally, the biocontrol efficiencies of B. subtilis GUCC4 against N. sphaerica were determined in vivo under greenhouse conditions. Similarly to the fungicide mancozeb and to a commercial B. subtilis-based biofungicide, B. subtilis GUCC4 significantly reduced disease severity. These results suggest that B. subtilis GUCC4 has great potential as a biological control agent and as PGPB on passion fruit.}, } @article {pmid36835681, year = {2023}, author = {Srygley, RB and Dudley, R and Hernandez, EJ and Kainz, F and Riveros, AJ and Ellington, CP}, title = {Quantifying the Aerodynamic Power Required for Flight and Testing for Adaptive Wind Drift in Passion-Vine Butterflies Heliconius sara (Lepidoptera: Nymphalidae).}, journal = {Insects}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/insects14020112}, pmid = {36835681}, issn = {2075-4450}, abstract = {Although theoretical work on optimal migration has been largely restricted to birds, relevant free-flight data are now becoming available for migratory insects. Here we report, for the first time in passion-vine butterflies, that Heliconius sara migrates directionally. To test optimal migration models for insects, we quantified the aerodynamic power curve for free-flying H. sara as they migrated across the Panama Canal. Using synchronized stereo-images from high-speed video cameras, we reconstructed three-dimensional flight kinematics of H. sara migrating naturally across the Panama Canal. We also reconstructed flight kinematics from a single-camera view of butterflies flying through a flight tunnel. We calculated the power requirements for flight for H. sara over a range of flight velocities. The relationship between aerodynamic power and velocity was "J"-shaped across the measured velocities with a minimum power velocity of 0.9 m/s and a maximum range velocity of 2.25 m/s. Migrating H. sara did not compensate for crosswind drift. Changes in airspeed with tailwind drift were consistent with the null hypothesis that H. sara did not compensate for tailwind drift, but they were also not significantly different from those predicted to maximize the migratory range of the insects.}, } @article {pmid36834418, year = {2023}, author = {Liu, J and Chen, J and Yang, Y and You, H and Han, X}, title = {Construction and Optimization of an Ecological Network in the Yellow River Source Region Based on MSPA and MCR Modelling.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, doi = {10.3390/ijerph20043724}, pmid = {36834418}, issn = {1660-4601}, abstract = {The source region of the Yellow River (SRYR) is an important water conservation and farming area in China. Under the dual influence of the natural environment and external pressure, ecological patches in the region are becoming increasingly fragmented, and landscape connectivity is continuously declining, which directly affect the landscape patch pattern and SRYR sustainable development. In the SRYR, morphological spatial pattern analysis (MSPA) and landscape index methods were used to extract ecologically important sources. Based on the minimum cumulative resistance model (MCR), Linkage Mapper was used to generate a potential corridor, and then potential stepped stone patches were identified and extracted by the gravity model and betweenness centrality to build an optimal SRYR ecological network. The distribution of patches in the core area of the SRYR was fragmented, accounting for 80.53% of the total grassland area. The 10 ecological sources based on the landscape connectivity index and 15 important corridors identified based on the MCR model were mainly distributed in the central and eastern regions of the SRYR. Through betweenness centrality, 10 stepped stone patches were added, and 45 planned ecological corridors were obtained to optimize the SRYR ecological network and enhance east and west connectivity. Our research results can provide an important reference for the protection of the SRYR ecosystem, and have important guiding significance and practical value for ecological network construction in ecologically fragmented areas.}, } @article {pmid36834206, year = {2023}, author = {Li, Y and Liu, H and Su, L and Chen, S and Zhu, X and Zhang, P}, title = {Developmental Features, Influencing Factors, and Formation Mechanism of Underground Mining-Induced Ground Fissure Disasters in China: A Review.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, doi = {10.3390/ijerph20043511}, pmid = {36834206}, issn = {1660-4601}, abstract = {Mining-induced ground fissures are one of the major geological disasters affecting coal mines. In recent years, many effective monitoring methods have been developed to explore the developmental characteristics and nature of mining-induced ground fissures for being treated scientifically. This paper is mainly on the development law and mechanism of mining ground fissure research results which have been comprehensively combed, highlighting the development trend, including the formation condition, development features, influencing factors, and mechanical mechanism of mining-induced ground fissures. Outstanding issues are discussed and future research hot spots and trends are pointed out. The major conclusions include: (1) under the shallow coal mining condition, because the rock layer fault zone directly reaches the surface, the ground fissure usually develops seriously; (2) mining-induced ground fissures are generally divided into four types: tensile fissures, compression fissures, collapsed fissures, and sliding fissures; (3) mining-induced ground fissures are affected by the coupling effect of underground mining and surface topography. The main factors are geological mining conditions, surface deformation, and surface topography, including rock and soil structure, rock and soil mechanical properties, surface horizontal deformation, surface slope, and so on; and (4) to ensure the safety of underground mining, temporary ground fissures formed during the process of coal mining must be treated when ground fissures and rock ground fissures are connected. The results of this article make up for the deficiencies of the relevant research, provide the basis and direction for future research, and have universal applicability and scientific guiding significance.}, } @article {pmid36827177, year = {2023}, author = {Martínez-Pernía, D and Olavarría, L and Fernández-Manjón, B and Cabello, V and Henríquez, F and Robert, P and Alvarado, L and Barría, S and Antivilo, A and Velasquez, J and Cerda, M and Farías, G and Torralva, T and Ibáñez, A and Parra, MA and Gilbert, S and Slachevsky, A}, title = {The limitations and challenges in the assessment of executive dysfunction associated with real-world functioning: The opportunity of serious games.}, journal = {Applied neuropsychology. Adult}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/23279095.2023.2174438}, pmid = {36827177}, issn = {2327-9109}, abstract = {Nowadays, there is a broad range of methods for detecting and evaluating executive dysfunction ranging from clinical interview to neuropsychological evaluation. Nevertheless, a critical issue of these assessments is the lack of correspondence of the neuropsychological test's results with real-world functioning. This paper proposes serious games as a new framework to improve the neuropsychological assessment of real-world functioning. We briefly discuss the contribution and limitations of current methods of evaluation of executive dysfunction (paper-and-pencil tests, naturalistic observation methods, and Information and Communications Technologies) to inform on daily life functioning. Then, we analyze what are the limitations of these methods to predict real-world performance: (1) A lack of appropriate instruments to investigate the complexity of real-world functioning, (2) the vast majority of neuropsychological tests assess well-structured tasks, and (3) measurement of behaviors are based on simplistic data collection and statistical analysis. This work shows how serious games offer an opportunity to develop more efficient tools to detect executive dysfunction in everyday life contexts. Serious games provide meaningful narrative stories and virtual or real environments that immerse the user in natural and social environments with social interactions. In those highly interactive game environments, the player needs to adapt his/her behavioral performance to novel and ill-structured tasks which are suited for collecting user interaction evidence. Serious games offer a novel opportunity to develop better tools to improve diagnosis of the executive dysfunction in everyday life contexts. However, more research is still needed to implement serious games in everyday clinical practice.}, } @article {pmid36826765, year = {2023}, author = {Wei, T and Guo, G and Li, H and Wang, L and Jiang, Q and Jiang, C}, title = {A novel probability integral method segmental modified model for subsidence prediction applicable to thick loose layer mining areas.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36826765}, issn = {1614-7499}, abstract = {In response to the problem that the actual extent of coal mining impacts on the surface in thick loose layer mines significantly exceeds the theoretical predictions, based on the literature study, the form of influence of thick loose layer on the predicted parameters of the probability integral method is summarized and analyzed; taking into account the influence of the subsidence coefficient, the sine modification formula of the major influence radius and the logistic modification formula of the subsidence coefficient are established, respectively, and based on the characteristics of the major influence radius, a new subsidence basin demarcation point is proposed and a novel probability integral method segmental parameter modified prediction model is constructed. The simulated experiment and real data experiment results prove that the constructed probability integral method segmented parameter modified model can both reduce the convergence of surface subsidence basin edge better and take into account the predicted accuracy inside the subsidence basin. The research achievements provide scientific data support for disaster warning, pollution management, ecological restoration, and coordination between coal mining and surface city construction in thick loose layer mining areas.}, } @article {pmid36792824, year = {2023}, author = {Woodhouse, A and Swain, A and Fagan, WF and Fraass, AJ and Lowery, CM}, title = {Late Cenozoic cooling restructured global marine plankton communities.}, journal = {Nature}, volume = {614}, number = {7949}, pages = {713-718}, pmid = {36792824}, issn = {1476-4687}, mesh = {Animals ; *Aquatic Organisms/classification/isolation & purification ; *Biodiversity ; *Cold Temperature ; Datasets as Topic ; *Foraminifera/classification/isolation & purification ; Fossils ; *Geographic Mapping ; History, Ancient ; Phylogeny ; *Phylogeography ; *Plankton/classification/isolation & purification ; *Spatio-Temporal Analysis ; Time Factors ; Hydrobiology ; }, abstract = {The geographic ranges of marine organisms, including planktonic foraminifera[1], diatoms, dinoflagellates[2], copepods[3] and fish[4], are shifting polewards owing to anthropogenic climate change[5]. However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear[6]. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences[7]. The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms[1,2,8] in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios.}, } @article {pmid36815186, year = {2023}, author = {Zhou, T and Li, W}, title = {Analysis on Logistics Efficiency Measurement of New Western Land-Sea Corridor under the Background of "Double Carbon" and Ecological Environment Protection.}, journal = {Journal of environmental and public health}, volume = {2023}, number = {}, pages = {8642841}, pmid = {36815186}, issn = {1687-9813}, mesh = {*Carbon ; *Environment ; Efficiency ; Industry ; China ; Economic Development ; }, abstract = {Under the research background of ecological environment protection and "double carbon" goal, this paper applies panel data on the logistics industry from 2010 to 2019 in 12 provinces of China's new western land-sea corridor to statically measure the logistics industry's technical efficiency after taking into account the impact of different environmental elements and to analyze the dynamics trends of total factor productivity in the logistics sector. It is measured by using the three-stage SBM model and the Malmquist-Luenberger productivity index, which considers undesirable output. The findings indicate the following: (1) In the context of "double carbon," the overall technical efficiency of the logistics sector in the new western land-sea corridor seems to be relatively low; however, the average technical efficiency of the logistics sector in the southern portion of the new western land-sea corridor does seem to be higher than that of the northern part. (2) The logistics industry's technical efficiency varies greatly by region, with locations near central China having much higher technical efficiency than remote inland areas. (3) The fundamental reason for the improvement of technical efficiency in the logistics industry is pure technical efficiency, and the driving force behind the increase in total factor productivity is technological advancement. (4) Economic development, informatization development, industrial market scale, and import and export all have a substantial influence on the logistics industry's technical efficiency. Finally, depending on the findings, policy recommendations are offered.}, } @article {pmid36806940, year = {2023}, author = {Rivera-Colón, AG and Rayamajhi, N and Fazal Minhas, B and Madrigal, G and Bilyk, KT and Yoon, V and Hüne, M and Gregory, S and Cheng, CC and Catchen, JM}, title = {Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad029}, pmid = {36806940}, issn = {1537-1719}, abstract = {White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.}, } @article {pmid36334202, year = {2023}, author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y}, title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {9}, pages = {24284-24298}, pmid = {36334202}, issn = {1614-7499}, mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; }, abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.}, } @article {pmid36803728, year = {2023}, author = {Niu, L and Zhagn, L and Xi, F and Wang, J}, title = {[Influencing factors and scenario forecasting of carbon emissions in Liaoning Province, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {2}, pages = {499-509}, doi = {10.13287/j.1001-9332.202302.001}, pmid = {36803728}, issn = {1001-9332}, mesh = {*Carbon/analysis ; *Carbon Dioxide/analysis ; Economic Development ; China ; Forecasting ; }, abstract = {Liaoning is a province with large energy consumption and carbon emissions. Management of carbon emissions in Liaoning Province is crucial to realizing China's carbon peaking and carbon neutrality goals. To clarify the driving factors and trends of carbon emissions in Liaoning Province, we analyzed the impacts of six factors on carbon emissions in Liaoning Province through STIRPAT model based on carbon emission data from 1999 to 2019. The impact factors included population, urbanization rate, per-capita GDP, secondary industry ratio, energy consumption per unit GDP, and coal consumption ratio. Nine forecasting scenarios with three economic and population growth models and three emission reduction models were set up, and their carbon emission trends under the above nine forecasting scenarios were predicted. The results showed that the main driving factor of carbon emissions in Liaoning Province was per-capita GDP, and that the main inhibitor was energy consumption per unit GDP. The carbon peak year in Liaoning Province would fluctuate between 2020 and 2055 under the nine forecasting scenarios, with peak values ranging from 544 to 1088 million tons CO2. The medium economic development growth and high carbon emission reduction scenario would be the optimal carbon emission scenario in Liaoning Province. Under this forecasting scenario, Liaoning Province could achieve carbon peak (611 million tons CO2) by 2030 without affec-ting economic development through optimizing energy structure and controlling the intensity of energy consumption. Our results would be helpful for seeking the best path for carbon emission reduction in Liaoning Province and providing a reference for its realization of carbon peaking and carbon neutrality goals.}, } @article {pmid36795572, year = {2023}, author = {Wang, J and Ding, R and Ouyang, T and Gao, H and Kan, H and Li, Y and Hu, Q and Yang, Y}, title = {Systematic investigation of the mechanism of herbal medicines for the treatment of prostate cancer.}, journal = {Aging}, volume = {15}, number = {}, pages = {}, doi = {10.18632/aging.204516}, pmid = {36795572}, issn = {1945-4589}, abstract = {Due to various unpleasant side effects and general ineffectiveness of current treatments for prostate cancer (PCa), more and more people with PCa try to look for complementary and alternative medicine such as herbal medicine. However, since herbal medicine has multi-components, multi-targets and multi-pathways features, its underlying molecular mechanism of action is not yet known and still needs to be systematically explored. Presently, a comprehensive approach consisting of bibliometric analysis, pharmacokinetic assessment, target prediction and network construction is firstly performed to obtain PCa-related herbal medicines and their corresponding candidate compounds and potential targets. Subsequently, a total of 20 overlapping genes between DEGs in PCa patients and the target genes of the PCa-related herbs, as well as five hub genes, i.e., CCNA2, CDK2, CTH, DPP4 and SRC were determined employing bioinformatics analysis. Further, the roles of these hub genes in PCa were also investigated through survival analysis and tumour immunity analysis. Moreover, to validate the reliability of the C-T interactions and to further explore the binding modes between ingredients and their targets, the molecular dynamics (MD) simulations were carried out. Finally, based on the modularization of the biological network, four signaling pathways, i.e., PI3K-Akt, MAPK, p53 and cell cycle were integrated to further analyze the therapeutic mechanism of PCa-related herbal medicine. All the results show the mechanism of action of herbal medicines on treating PCa from the molecular to systematic levels, providing a reference for the treatment of complex diseases using TCM.}, } @article {pmid36792330, year = {2023}, author = {Suzuki, S and Nishikawa, Y and Okada, H and Nakayama, T}, title = {Information-seeking behaviour of community pharmacists during the COVID-19 pandemic: an ecological study.}, journal = {BMJ open}, volume = {13}, number = {2}, pages = {e062465}, pmid = {36792330}, issn = {2044-6055}, mesh = {Humans ; *COVID-19/epidemiology ; Pharmacists ; Pandemics ; Information Seeking Behavior ; *Community Pharmacy Services ; }, abstract = {OBJECTIVE: To evaluate the information-seeking behaviour of pharmacists during the COVID-19 pandemic and its relation to COVID-19 and related infections and deaths within the local prefecture.

DESIGN: Ecological study.

SETTING: Japan-47 prefectures.

METHODS: The number of accesses to a Japanese web page established by the Pharmacy Informatics Group to disseminate information about infection control and the number of infections and deaths in 47 prefectures were investigated from 6 April to 30 September 2020 using the access information on the web page and publicly available information.

RESULTS: During the first 6 months of the COVID-19 pandemic, the total number of accesses was 226 130 (range: 10 984-138 898 per month), the total number of infections was 78 761 (1738-31 857) and the total number of deaths was 1470 (39-436). The correlation between the total number of accesses and that of infections per 100 000 individuals in 47 prefectures was r=0.72 (95% CI 0.55 to 0.83, p<0.001), and between the total number of accesses and deaths per 100 000 individuals in 47 prefectures was r=0.44 (95% CI 0.17 to 0.65, p=0.002).

CONCLUSIONS: The information-seeking behaviour of community pharmacists correlated positively with infection status within the community.}, } @article {pmid36640933, year = {2023}, author = {Gautam, P and Pandey, AK and Dubey, SK}, title = {Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid.}, journal = {Environmental research}, volume = {221}, number = {}, pages = {115271}, doi = {10.1016/j.envres.2023.115271}, pmid = {36640933}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; Molecular Docking Simulation ; Multiomics ; Neonicotinoids/analysis ; *Insecticides/analysis ; Nitro Compounds/analysis/chemistry/metabolism ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Soil ; }, abstract = {The residual imidacloprid, a widely used insecticide is causing serious environmental concerns. Knowledge of its biodegradation will help in assessing its residual mass in soil. In view of this, a soil microcosm-based study was performed to test the biodegradation potential of Agrobacterium sp. InxBP2. It achieved ∼88% degradation in 20 days and followed the pseudo-first-order kinetics (k = 0.0511 day[-1] and t1/2=7 days). Whole genome sequencing of Agrobacterium sp. InxBP2 revealed a genome size of 5.44 Mbp with 5179 genes. Imidacloprid degrading genes at loci K7A42_07110 (ABC transporter substrate-binding protein), K7A42_07270 (amidohydrolase family protein), K7A42_07385 (ABC transporter ATP-binding protein), K7A42_16,845 (nitronate monooxygenase family protein), and K7A42_20,660 (FAD-dependent monooxygenase) having sequence and functional similarity with known counterparts were identified. Molecular docking of proteins encoded by identified genes with their respective degradation pathway intermediates exhibited significant binding energies (-6.56 to -4.14 kcal/mol). Molecular dynamic simulation discovered consistent interactions and binding depicting high stability of docked complexes. Proteome analysis revealed differential protein expression in imidacloprid treated versus untreated samples which corroborated with the in-silico findings. Further, the detection of metabolites proved the bacterial degradation of imidacloprid. Thus, results provided a mechanistic link between imidacloprid and associated degradative genes/enzymes of Agrobacterium sp. InxBP2. These findings will be of immense significance in carrying out the lifecycle analysis and formulating strategies for the bioremediation of soils contaminated with insecticides like imidacloprid.}, } @article {pmid36527232, year = {2023}, author = {Petrén, H and Köllner, TG and Junker, RR}, title = {Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv.}, journal = {The New phytologist}, volume = {237}, number = {6}, pages = {2478-2492}, doi = {10.1111/nph.18685}, pmid = {36527232}, issn = {1469-8137}, mesh = {*Phytochemicals ; *Plants ; Ecology ; Phenotype ; Databases, Factual ; }, abstract = {Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and - most importantly - structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.}, } @article {pmid36264457, year = {2023}, author = {Nasiruddin, M and Islam, ARMT and Siddique, MAB and Hasanuzaman, M and Hassan, MM and Akbor, MA and Hasan, M and Islam, MS and Khan, R and Al Amin, M and Pal, SC and Idris, AM and Kumar, S}, title = {Distribution, sources, and pollution levels of toxic metal(loid)s in an urban river (Ichamati), Bangladesh using SOM and PMF modeling with GIS tool.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {8}, pages = {20934-20958}, pmid = {36264457}, issn = {1614-7499}, mesh = {Humans ; *Metals, Heavy/analysis ; Environmental Monitoring ; Geographic Information Systems ; Rivers ; Bangladesh ; Cadmium/analysis ; Lead/analysis ; Geologic Sediments/analysis ; *Water Pollutants, Chemical/analysis ; Water Quality ; Risk Assessment ; China ; }, abstract = {Indexical assessment coupled with a self-organizing map (SOM) and positive matrix factorization (PMF) modeling of toxic metal(loid)s in sediment and water of the aquatic environment provides valuable information from the environmental management perspective. However, in northwest Bangladesh, indexical and modeling assessments of toxic metal(loid)s in surface water and sediment are still rare. Toxic metal(loid)s were measured in sediment and surface water from an urban polluted river (Ichamati) in northwest Bangladesh using an atomic absorption spectrophotometer to assess distribution, pollution levels, sources, and potential environmental risks to the aquatic environment. The mean concentrations (mg/kg) of metal(loid)s in water are as follows: Fe (871) > Mn (382) > Cr (72.4) > Zn (34.2) > Co (20.8) > Pb (17.6) > Ni (16.7) > Ag (14.9) > As (9.0) > Cu (5.63) > Cd (2.65), while in sediment, the concentration follows the order, Fe (18,725) > Mn (551) > Zn (213) > Cu (47.6) > Cr (30.2) > Ni (24.2) > Pb (23.8) > Co (9.61) > As (8.23) > Cd (0.80) > Ag (0.60). All metal concentrations were within standard guideline values except for Cr and Pb for water and Cd, Zn, Cu, Pb, and As for sediment. The outcomes of eco-environmental indices, including contamination and enrichment factors and geo-accumulation index, differed spatially, indicating that most of the sediment sites were moderately to highly polluted by Cd, Zn, and As. Cd and Zn content can trigger ecological risks. The positive matrix factorization (PMF) model recognized three probable sources of sediment, i.e., natural source (49.39%), industrial pollution (19.72%), and agricultural source (30.92%), and three possible sources of water, i.e., geogenic source (45.41%), industrial pollution (22.88%), and industrial point source (31.72%), respectively. SOM analysis identified four spatial patterns, e.g., Fe-Mn-Ag, Cd-Cu, Cr-Pb-As-Ni, and Zn-Co in water and three patterns, e.g., Mn-Co-Ni-Cr, Cd-Cu-Pb-Zn, and As-Fe-Ag in sediment. The spatial distribution of entropy water quality index values shows that the southwestern area possesses "poor" quality water. Overall, the levels of metal(loid) pollution in the investigated river surpassed a critical threshold, which might have serious consequences for the river's aquatic biota and human health in the long run.}, } @article {pmid36788337, year = {2023}, author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41375-023-01839-7}, pmid = {36788337}, issn = {1476-5551}, } @article {pmid36194325, year = {2023}, author = {Zhou, Y and Hu, Z and Geng, Q and Ma, J and Liu, J and Wang, M and Wang, Y}, title = {Monitoring and analysis of desertification surrounding Qinghai Lake (China) using remote sensing big data.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {7}, pages = {17420-17436}, pmid = {36194325}, issn = {1614-7499}, mesh = {Humans ; *Remote Sensing Technology ; *Conservation of Natural Resources/methods ; Lakes ; Big Data ; Environmental Monitoring/methods ; China ; }, abstract = {Desertification is one of the most serious ecological environmental problems in the world. Monitoring the spatiotemporal dynamics of desertification is crucial for its control. The region around Qinghai Lake, in the northeastern part of the Qinghai-Tibet Plateau in China, is a special ecological function area and a climate change sensitive area, making its environmental conditions a great concern. Using cloud computing via Google Earth Engine (GEE), we collected Landsat 5 TM, Landsat 8 OLI/TIRS, and MODIS Albedo images from 2000 to 2020 in the region around Qinghai Lake, acquired land surface albedo (Albedo), and normalized vegetation index (NDVI) to build a remote sensing monitoring model of desertification. Our results showed that the desertification difference index based on the Albedo-NDVI feature space could reflect the degree of desertification in the region around Qinghai Lake. GEE offers significant advantages, such as massive data processing and long-term dynamic monitoring. The desertification land area fluctuated downward in the study area from 2000 to 2020, and the overall desertification status improved. Natural factors, such as climate change from warm-dry to warm-wet and decreased wind speed, and human factors improved the desertification situation. The findings indicate that desertification in the region around Qinghai Lake has been effectively controlled, and the overall desertification trend is improving.}, } @article {pmid36787802, year = {2023}, author = {Dennis, A and Cuthbertson, DJ and Wootton, D and Crooks, M and Gabbay, M and Eichert, N and Mouchti, S and Pansini, M and Roca-Fernandez, A and Thomaides-Brears, H and Kelly, M and Robson, M and Hishmeh, L and Attree, E and Heightman, M and Banerjee, R and Banerjee, A}, title = {Multi-organ impairment and long COVID: a 1-year prospective, longitudinal cohort study.}, journal = {Journal of the Royal Society of Medicine}, volume = {}, number = {}, pages = {1410768231154703}, doi = {10.1177/01410768231154703}, pmid = {36787802}, issn = {1758-1095}, abstract = {OBJECTIVES: To determine the prevalence of organ impairment in long COVID patients at 6 and 12 months after initial symptoms and to explore links to clinical presentation.

DESIGN: Prospective cohort study.

PARTICIPANTS: Individuals.

METHODS: In individuals recovered from acute COVID-19, we assessed symptoms, health status, and multi-organ tissue characterisation and function.

SETTING: Two non-acute healthcare settings (Oxford and London). Physiological and biochemical investigations were performed at baseline on all individuals, and those with organ impairment were reassessed.

MAIN OUTCOME MEASURES: Primary outcome was prevalence of single- and multi-organ impairment at 6 and 12 months post COVID-19.

RESULTS: A total of 536 individuals (mean age 45 years, 73% female, 89% white, 32% healthcare workers, 13% acute COVID-19 hospitalisation) completed baseline assessment (median: 6 months post COVID-19); 331 (62%) with organ impairment or incidental findings had follow-up, with reduced symptom burden from baseline (median number of symptoms 10 and 3, at 6 and 12 months, respectively). Extreme breathlessness (38% and 30%), cognitive dysfunction (48% and 38%) and poor health-related quality of life (EQ-5D-5L < 0.7; 57% and 45%) were common at 6 and 12 months, and associated with female gender, younger age and single-organ impairment. Single- and multi-organ impairment were present in 69% and 23% at baseline, persisting in 59% and 27% at follow-up, respectively.

CONCLUSIONS: Organ impairment persisted in 59% of 331 individuals followed up at 1 year post COVID-19, with implications for symptoms, quality of life and longer-term health, signalling the need for prevention and integrated care of long COVID.Trial Registration: ClinicalTrials.gov Identifier: NCT04369807.}, } @article {pmid36782205, year = {2023}, author = {Amin, M and Aziz, MA and Pieroni, A and Nazir, A and Al-Ghamdi, AA and Kangal, A and Ahmad, K and Abbasi, AM}, title = {Edible wild plant species used by different linguistic groups of Kohistan Upper Khyber Pakhtunkhwa (KP), Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {6}, pmid = {36782205}, issn = {1746-4269}, abstract = {BACKGROUND: The mountainous territory of Kohistan shelters diverse food plant species and is considered one of the important hotspots of local plant knowledge. In the era of globalization and food commodification, wild food plants (WFPs) play an important role in supporting local food systems and related local knowledge is one of the important pillars of food sustainability across the region. Since the area is populated by different cultural groups and each culture has retained particular knowledge on the local plant species, therefore, to make a cross-culturally comparison, the study was planned to record and compare the local plants knowledge among three linguistic groups viz Gujjar, Kohistani and Shina in order to not only protect the local knowledge but to determine the food cultural adaptations among these groups looking through the lens of their food ethnobotanies.

METHODS: Field ethnobotanical survey was carried out in 2020-2021 to gather the data on wild food plants. We used semi-structured interviews. Use reports were counted, and the results were visualized through Venn diagrams.

RESULTS: In total, 64 plant species belonging to 45 botanical families were documented. Among these Ajuga integrifolia, Barbarea verna, Clematis grata, Impatiens edgeworthii, Ranunculus laetus (vegetables), Parrotiopsis jacquemontiana (fruit), Indigofera tinctoria (flower), Juniperus excelsa, Primula elliptica, P. macrophylla (flavoring agent), Leontopodium himalayanum (Chewing gum), and Juniperus excelsa (snuff) were reported for the first time. The highest use reports (≥ 90) were recorded for Mentha longifolia, Amaranthus hybridus, Quercus semecarpifolia, Solanum miniatum, Oxalis corniculata, Ficus palmata, and Urtica dioica. Maximum number of wild food plant species (WFPs) were reported by Kohistani, followed by Shinaki and Gujjari linguistic groups. The percentage overlap of traditional knowledge on WFPs was highest among Kohistani and Shinaki (56.0%), followed by Shinaki and Gujjars (17.0%), and Kohistani and Gujjars (15.0%). Kohistani and Shinaki groups exhibited maximum homogeneity in traditional knowledge. However, Gujjars had more knowledge on WFPs compared to Kohistani and Shinaki. In addition, some dairy products viz. Bhorus, Bagora, Bak, Cholam, Kacha, Gurloo and Poyeen were reported also reported that are consumed orally and used in traditional cuisines.

CONCLUSIONS: The study indicates that Kohistan is one of the important spots of biocultural diversity and could be recognized as biocultural refugia. WFPs have been an integral part of the traditional food systems among the studied groups, particularly the Gujjars have reported more distinct plant uses which could be referred to their distinctive ecological experiences among others. However, social change is one of the challenges that might lead to the erosion of local plant knowledge. Moreover, intercultural negotiations among the studied groups are also a matter of concern which could homogenize the local knowledge among them. Therefore, we suggest solid policy measures to protect the local knowledge and celebrate diversity across this mountain territory.}, } @article {pmid36781356, year = {2023}, author = {Mayne, SL and DiFiore, G and Hannan, C and Nwokeji, U and Tam, V and Filograna, C and Martin, T and South, E and Mitchell, JA and Glanz, K and Fiks, AG}, title = {Feasibility and acceptability of mobile methods to assess home and neighborhood environments related to adolescent sleep.}, journal = {Sleep health}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.sleh.2023.01.014}, pmid = {36781356}, issn = {2352-7226}, abstract = {OBJECTIVE: A growing evidence base suggests home and neighborhood environmental exposures may influence adolescent sleep, but few studies have assessed these relationships using methods that account for time-varying, location-specific exposures, or multiple neighborhood contexts. This study aimed to assess the feasibility and acceptability of using smartphone global positioning system (GPS) tracking and ecological momentary assessment (EMA) to assess time-varying home and neighborhood environmental exposures hypothesized to be associated with adolescent sleep.

METHODS: Adolescents aged 15-17 years in Philadelphia completed 7 days of continuous smartphone GPS tracking, which was used to identify daily levels of exposure to geocoded neighborhood factors (eg, crime, green space). Four daily EMA surveys assessed home sleep environment (eg, noise, light), stress, health behaviors, and neighborhood perceptions. Feasibility and acceptability of GPS tracking and EMA were assessed, and distributions of daily environmental exposures were examined.

RESULTS: Among 25 teens (mean age 16, 56% male), there was a high level of GPS location data captured (median daily follow-up: 24 hours). Seventy-eight percent of EMA surveys were completed overall. Most participants (96%) reported no privacy concerns related to GPS tracking and minimal burden from EMA surveys. Exposures differed between participants' home neighborhoods and locations visited outside the home neighborhood (eg, higher crime away from home). Sleep environment disruptions were present on 29% of nights (most common: uncomfortable temperature) and were reported by 52% of adolescents.

CONCLUSIONS: Results demonstrate the feasibility and acceptability of mobile methods for assessing time-varying home and neighborhood exposures relevant to adolescent sleep for up to 1 week.}, } @article {pmid36775641, year = {2023}, author = {Liu, L and Zhang, WQ and Hu, FC and Pang, K and Guo, YL and Zhang, T and Li, M}, title = {[Evaluation and Optimization of Rural Sewage Treatment Technologies in the Middle Reaches of the Yangtze River Based on Group Decision Making and Analytic Hierarchy Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {2}, pages = {1191-1200}, doi = {10.13227/j.hjkx.202203043}, pmid = {36775641}, issn = {0250-3301}, mesh = {*Sewage ; *Rivers ; Analytic Hierarchy Process ; Nitrogen ; Decision Making ; China ; }, abstract = {Rural sewage treatment in the Yangtze River basin is an important link to achieve the great protection of the Yangtze River, but the existing treatment technologies are difficult to choose and have various techniques and a lack of evaluation. Therefore, this study researched and collected the case information of rural sewage treatment projects in the middle reaches of the Yangtze River, analyzed the application of each treatment technology under different collection modes and discharge standards, constructed the evaluation index system of rural sewage treatment technologies, and then conducted a classification evaluation of processing technologies for each application scenario based on group decision making and the Analytic Hierarchy Process. The results showed that:the collection modes of rural sewage in the middle reaches of the Yangtze River were mainly single village or small-scale joint village, the treatment scale was mainly concentrated below 200 m[3]·d[-1], the treatment technology was most applied by the anaerobic+ecological process (28.05%), and the application of integrated equipment was also more widely used (22.47%). The technical performance in the criterion layer had the largest weight (0.5039) in the evaluation index system, followed by those of economic benefits (0.2474), operation and management (0.1559), and environmental impact (0.0928), respectively; the four indicators of TP removal rate, ton water operation cost, ammonia nitrogen removal rate, and maintenance difficulty had higher weights. The evaluation and optimization results showed that the enhanced ecological and anaerobic+ecological treatment technologies were suitable for promotion and application in the rural areas of the middle reaches of the Yangtze River. The results of this study can provide scientific basis and reference for the selection of rural sewage treatment technologies in the middle reaches of the Yangtze River.}, } @article {pmid36767964, year = {2023}, author = {Cao, H and Ou, H and Ju, W and Pan, M and Xue, H and Zhu, F}, title = {Visual Analysis of International Environmental Security Management Research (1997-2021) Based on VOSviewer and CiteSpace.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, pmid = {36767964}, issn = {1660-4601}, mesh = {Bayes Theorem ; *Agriculture ; Australia ; *Big Data ; China ; }, abstract = {To investigate the international development status and hot trends in the field of environmental security management in recent years, the published the environmental security management literature from 1997 to 2021, which was retrieved from Web of Science, with VOSviewer as the main and CiteSpace as the auxiliary, through the cooperation network of authors, scientific research institutions, and countries. The keywords were visualized by clustering, time zone analysis, and burst analysis. A total of 7596 articles were retrieved, forming six main clustering labels, including 28,144 authors. The research hotspots are from the fields of personal health, society, agriculture, ecological environment, energy, and sustainable development, as well as the development of internet environmental safety management, such as big data, Bayesian networks, and conceptual frameworks. Through cluster analysis, the cooperation of major research teams and scientific research institutions and the cooperation and development between countries were analyzed. The cooperation between scientific research institutions in various countries is relatively close. The United States currently occupies a dominant and authoritative position in this field. China has cooperated more closely with the United States, Britain, Australia, and India.}, } @article {pmid36777713, year = {2021}, author = {Dussex, N and van der Valk, T and Morales, HE and Wheat, CW and Díez-Del-Molino, D and von Seth, J and Foster, Y and Kutschera, VE and Guschanski, K and Rhie, A and Phillippy, AM and Korlach, J and Howe, K and Chow, W and Pelan, S and Mendes Damas, JD and Lewin, HA and Hastie, AR and Formenti, G and Fedrigo, O and Guhlin, J and Harrop, TWR and Le Lec, MF and Dearden, PK and Haggerty, L and Martin, FJ and Kodali, V and Thibaud-Nissen, F and Iorns, D and Knapp, M and Gemmell, NJ and Robertson, F and Moorhouse, R and Digby, A and Eason, D and Vercoe, D and Howard, J and Jarvis, ED and Robertson, BC and Dalén, L}, title = {Population genomics of the critically endangered kākāpō.}, journal = {Cell genomics}, volume = {1}, number = {1}, pages = {100002}, pmid = {36777713}, issn = {2666-979X}, abstract = {The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.}, } @article {pmid36777319, year = {2022}, author = {Glasgow, L and Lewis, R and Charles, S}, title = {The cancer epidemic in the Caribbean region: Further opportunities to reverse the disease trend.}, journal = {Lancet regional health. Americas}, volume = {13}, number = {}, pages = {100295}, pmid = {36777319}, issn = {2667-193X}, abstract = {Cancer incidence has been rising in the Caribbean and is expected to have significant adverse implications for the health of people in the region and health systems in this decade. While developed countries, for the most part, enjoy the benefits of advanced technologies and adaptive systems in cancer control and management, a different experience confronts a large segment of the Caribbean population. The region has experienced some success in enhancing cancer services, however, there is a need to address gaps in several areas through nationally and regionally tailored initiatives. This Review complements previous publications on the challenges, actions, and progress towards cancer prevention and care in Caribbean countries but also further outlines potential positive impacts that can be derived from addressing gaps pertaining to cancer education, data management, screening and risk assessment, navigation services, gender factors, and resource development. The proposed approaches encapsulate concepts of health theories that are applicable across the ecological domains. When implemented in combination, the proposals may effectively contribute to reducing the cancer burden in the region.}, } @article {pmid36771658, year = {2023}, author = {Shah, AA and Badshah, L and Khalid, N and Shah, MA and Manduzai, AK and Faiz, A and De Chiara, M and Mattalia, G and Sõukand, R and Pieroni, A}, title = {Disadvantaged Economic Conditions and Stricter Border Rules Shape Afghan Refugees' Ethnobotany: Insights from Kohat District, NW Pakistan.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36771658}, issn = {2223-7747}, abstract = {The study of migrants' ethnobotany can help to address the diverse socio-ecological factors affecting temporal and spatial changes in local ecological knowledge (LEK). Through semi-structured and in-depth conversations with ninety interviewees among local Pathans and Afghan refugees in Kohat District, NW Pakistan, one hundred and forty-five wild plant and mushroom folk taxa were recorded. The plants quoted by Afghan refugees living inside and outside the camps tend to converge, while the Afghan data showed significant differences with those collected by local Pakistani Pathans. Interviewees mentioned two main driving factors potentially eroding folk plant knowledge: (a) recent stricter border policies have made it more difficult for refugees to visit their home regions in Afghanistan and therefore to also procure plants in their native country; (b) their disadvantaged economic conditions have forced them to engage more and more in urban activities in the host country, leaving little time for farming and foraging practices. Stakeholders should foster the exposure that refugee communities have to their plant resources, try to increase their socio-economic status, and facilitate both their settling outside the camps and their transnational movement for enhancing their use of wild plants, ultimately leading to improvements in their food security and health status.}, } @article {pmid36768056, year = {2023}, author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, JM and Radak, Đ and Maksimović, J and Vujčić, I and Prijović, N and Vlajinac, H}, title = {Body Mass Index and Late Adverse Outcomes after a Carotid Endarterectomy.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, pmid = {36768056}, issn = {1660-4601}, abstract = {A cohort study was conducted to examine the association of an increased body mass index (BMI) with late adverse outcomes after a carotid endarterectomy (CEA). It comprised 1597 CEAs, performed in 1533 patients at the Vascular Surgery Clinic in Belgrade, from 1 January 2012 to 31 December 2017. The follow-up lasted four years after CEA. Data for late myocardial infarction and stroke were available for 1223 CEAs, data for death for 1305 CEAs, and data for restenosis for 1162 CEAs. Logistic and Cox regressions were used in the analysis. The CEAs in patients who were overweight and obese were separately compared with the CEAs in patients with a normal weight. Out of 1223 CEAs, 413 (33.8%) were performed in patients with a normal weight, 583 (47.7%) in patients who were overweight, and 220 (18.0%) in patients who were obese. According to the logistic regression analysis, the compared groups did not significantly differ in the frequency of myocardial infarction, stroke, and death, as late major adverse outcomes (MAOs), or in the frequency of restenosis. According to the Cox and logistic regression analyses, BMI was neither a predictor for late MAOs, analyzed separately or all together, nor for restenosis. In conclusion, being overweight and being obese were not related to the occurrence of late adverse outcomes after a carotid endarterectomy.}, } @article {pmid36767252, year = {2023}, author = {Liu, Q and Guo, R and Huang, Z and He, B and Li, X}, title = {The Nonlinear Impact of Mobile Human Activities on Vegetation Change in the Guangdong-Hong Kong-Macao Greater Bay Area.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, doi = {10.3390/ijerph20031874}, pmid = {36767252}, issn = {1660-4601}, abstract = {Vegetation is essential for ecosystem function and sustainable urban development. In the context of urbanization, the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), as the typical urban-dominated region, has experienced a remarkable increase in social and economic activities. Their impact on vegetation is of great significance but unclear, as interannual flow data and linear methods have limitations. Therefore, in this study, we used human and vehicle flow data to build and simulate the indices of mobile human activity. In addition, we used partial least squares regression (PLSR), random forest (RF), and geographical detector (GD) models to analyze the impact of mobile human activities on vegetation change. The results showed that indices of mobile human and vehicle flow increased by 1.43 and 7.68 times from 2000 to 2019 in the GBA, respectively. Simultaneously, vegetation increased by approximately 64%, whereas vegetation decreased mainly in the urban areas of the GBA. Vegetation change had no significant linear correlation with mobile human activities, exhibiting a regression coefficient below 0.1 and a weight of coefficients of PLSR less than 40 between vegetation change and all the factors of human activities. However, a more significant nonlinear relationship between vegetation change and driving factors were obtained. In the RF regression model, vegetation decrease was significantly affected by mobile human activity of vehicle flow, with an importance score of 108.11. From the GD method, vegetation decrease was found to mainly interact with indices of mobile human and vehicle inflow, and the highest interaction force was 0.82. These results may support the attainment of sustainable social-ecological systems and global environmental change.}, } @article {pmid36750720, year = {2023}, author = {Mechenich, MF and Žliobaitė, I}, title = {Eco-ISEA3H, a machine learning ready spatial database for ecometric and species distribution modeling.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {77}, pmid = {36750720}, issn = {2052-4463}, mesh = {Animals ; Humans ; Climate Change ; *Databases, Factual ; *Ecosystem ; Geography ; Machine Learning ; Mammals ; }, abstract = {We present the Eco-ISEA3H database, a compilation of global spatial data characterizing climate, geology, land cover, physical and human geography, and the geographic ranges of nearly 900 large mammalian species. The data are tailored for machine learning (ML)-based ecological modeling, and are intended primarily for continental- to global-scale ecometric and species distribution modeling. Such models are trained on present-day data and applied to the geologic past, or to future scenarios of climatic and environmental change. Model training requires integrated global datasets, describing species' occurrence and environment via consistent observational units. The Eco-ISEA3H database incorporates data from 17 sources, and includes 3,033 variables. The database is built on the Icosahedral Snyder Equal Area (ISEA) aperture 3 hexagonal (3H) discrete global grid system (DGGS), which partitions the Earth's surface into equal-area hexagonal cells. Source data were incorporated at six nested ISEA3H resolutions, using scripts developed and made available here. We demonstrate the utility of the database in a case study analyzing the bioclimatic envelopes of ten large, widely distributed mammalian species.}, } @article {pmid36748522, year = {2022}, author = {Cunningham-Oakes, E and Pointon, T and Murphy, B and Campbell-Lee, S and Connor, TR and Mahenthiralingam, E}, title = {Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36748522}, issn = {2057-5858}, mesh = {Retrospective Studies ; *Bacteria/genetics ; *Metagenome ; Metagenomics/methods ; Workflow ; }, abstract = {The home and personal care (HPC) industry generally relies on initial cultivation and subsequent biochemical testing for the identification of microorganisms in contaminated products. This process is slow (several days for growth), labour intensive, and misses organisms which fail to revive from the harsh environment of preserved consumer products. Since manufacturing within the HPC industry is high-throughput, the process of identification of microbial contamination could benefit from the multiple cultivation-independent methodologies that have developed for the detection and analysis of microbes. We describe a novel workflow starting with automated DNA extraction directly from a HPC product, and subsequently applying metagenomic methodologies for species and strain-level identification of bacteria. The workflow was validated by application to a historic microbial contamination of a general-purpose cleaner (GPC). A single strain of Pseudomonas oleovorans was detected metagenomically within the product. The metagenome mirrored that of a contaminant isolated in parallel by a traditional cultivation-based approach. Using a dilution series of the incident sample, we also provide evidence to show that the workflow enables detection of contaminant organisms down to 100 CFU/ml of product. To our knowledge, this is the first validated example of metagenomics analysis providing confirmatory evidence of a traditionally isolated contaminant organism, in a HPC product.}, } @article {pmid36637211, year = {2023}, author = {Feldner-Busztin, D and Firbas Nisantzis, P and Edmunds, SJ and Boza, G and Racimo, F and Gopalakrishnan, S and Limborg, MT and Lahti, L and de Polavieja, GG}, title = {Dealing with dimensionality: the application of machine learning to multi-omics data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36637211}, issn = {1367-4811}, mesh = {Humans ; *Multiomics ; *Neoplasms/genetics ; Machine Learning ; Genome ; }, abstract = {MOTIVATION: Machine learning (ML) methods are motivated by the need to automate information extraction from large datasets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.

RESULTS: Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas dataset, which is accessible and contains many diverse experiments.

All data and processing scripts are available at this GitLab repository: https://gitlab.com/polavieja_lab/ml_multi-omics_review/ or in Zenodo: https://doi.org/10.5281/zenodo.7361807.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36171318, year = {2023}, author = {Wen, C and Zhen, Z and Zhang, L and Yan, C}, title = {A bibliometric analysis of river health based on publications in the last three decades.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {6}, pages = {15400-15413}, pmid = {36171318}, issn = {1614-7499}, mesh = {Humans ; *Rivers ; *Bibliometrics ; Australia ; China ; Databases, Factual ; Publications ; }, abstract = {Rivers are a vital part of the earth's environment and the basis for human survival. River health has been widely concerned by scholars and practitioners, and the number of studies in this area is increasing. In order to examine the evolution of river health research and identify the research frontiers, a total of 675 articles were retrieved from the Web of Science Core Collection database, and CiteSpace was used for bibliometrics. The results revealed that the research on river health is multidisciplinary. Freshwater Biology and Ecological Indicators were two of the most influential journals. Researchers and institutions from America, Australia, and China were the core research forces, and a certain gap was observed between developed and developing countries in river health. The most productive institution was Michigan State University, followed by Griffith University and Hohai University. There are three development trends in river health: (1) Research scale is expanding; (2) Research methods are diversified and interdisciplinary; and (3) Evaluation index is more comprehensive and systematic. The frontier of river health had been expanded from the connotation of river health to the evaluation methods, evaluation indexes, and comprehensive river ecological research. Overall, research on river health is a well-developed and promising research field. This study provides a framework in the river health field for new researchers and helps scholars to identify further potential perspectives on collaborators, research frontiers, hotspots, and research trends.}, } @article {pmid36744611, year = {2023}, author = {Smail, EJ and Alpert, JM and Mardini, MT and Kaufmann, CN and Bai, C and Gill, TM and Fillingim, RB and Cenko, E and Zapata, R and Karnati, Y and Marsiske, M and Ranka, S and Manini, TM}, title = {Feasibility of A Smartwatch Platform to Assess Ecological Mobility: Real-time Online Assessment and Mobility Monitor (ROAMM).}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glad046}, pmid = {36744611}, issn = {1758-535X}, abstract = {BACKGROUND: Early detection of mobility decline is critical to prevent subsequent reductions in quality of life, disability, and mortality. However, traditional approaches to mobility assessment are limited in their ability to capture daily fluctuations that align with sporadic health events. We aim to describe findings from a pilot study of our Real-time Online Assessment and Mobility Monitor (ROAMM) smartwatch application, which uniquely captures multiple streams of data in real-time in ecological settings.

METHODS: Data come from a sample of 31 participants (Mage=74.7, 51.6% female) who used ROAMM for approximately two weeks. We describe the usability and feasibility of ROAMM, summarize prompt data using descriptive metrics, and compare prompt data with traditional survey-based questionnaires or other established measures.

RESULTS: Participants were satisfied with ROAMM's function (87.1%) and ranked the usability as "above average." Most were highly engaged (average adjusted compliance = 70.7%) and the majority reported being "likely" to enroll in a two-year study (77.4%). Some smartwatch features were correlated with their respective traditional measurements (e.g., certain GPS-derived life-space mobility features (r=0.50-0.51, p<0.05) and ecologically-measured pain (r=0.72, p=0.01)), but others were not (e.g., ecologically-measured fatigue).

CONCLUSION: ROAMM was usable, acceptable, and effective at measuring mobility and risk factors for mobility decline in our pilot sample. Additional work with a larger and more diverse sample is necessary to confirm associations between smartwatch-measured features and traditional measures. By monitoring multiple data streams simultaneously in ecological settings, this technology could uniquely contribute to the evolution of mobility measurement and risk factors for mobility loss.}, } @article {pmid36727564, year = {2023}, author = {Kinkar, L and Korhonen, PK and Saarma, U and Wang, T and Zhu, XQ and Harliwong, I and Yang, B and Fink, JL and Wang, D and Chang, BCH and Chelomina, GN and Koehler, AV and Young, ND and Gasser, RB}, title = {Genome-wide exploration reveals distinctive northern and southern variants of Clonorchis sinensis in the Far East.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13760}, pmid = {36727564}, issn = {1755-0998}, abstract = {Clonorchis sinensis is a carcinogenic liver fluke that causes clonorchiasis - a neglected tropical disease (NTD) affecting ~ 35 million people worldwide. No vaccine is available, and chemotherapy relies on one anthelmintic, praziquantel. This parasite has a complex life history and is known to infect a range of species of intermediate (freshwater snails and fish) and definitive (piscivorous) hosts. Despite this biological complexity and the impact of this biocarcinogenic pathogen, there has been no previous study of molecular variation in this parasite on a genome-wide scale. Here, we conducted the first extensive nuclear genomic exploration of C. sinensis individuals (n = 152) representing five distinct populations from mainland China, and one from Far East Russia, and revealed marked genetic variation within this species between 'northern' and 'southern' geographic regions. The discovery of this variation indicates the existence of biologically distinct variants within C. sinensis, which may have distinct epidemiology, pathogenicity and/or chemotherapic responsiveness. The detection of high heterozygosity within C. sinensis specimens suggests that this parasite has developed mechanisms to readily adapt to changing environments and/or host species during its life history/evolution. From an applied perspective, the identification of invariable genes could assist in finding new intervention targets in this parasite, given the major clinical relevance of clonorchiasis. From a technical perspective, the genomic-informatic workflow established herein will be readily applicable to a wide range of other parasites that cause NTDs.}, } @article {pmid36495963, year = {2023}, author = {Tong, H and Warren, JL and Kang, J and Li, M}, title = {Using multi-sourced big data to correlate sleep deprivation and road traffic noise: A US county-level ecological study.}, journal = {Environmental research}, volume = {220}, number = {}, pages = {115029}, doi = {10.1016/j.envres.2022.115029}, pmid = {36495963}, issn = {1096-0953}, mesh = {Humans ; *Sleep Deprivation/epidemiology ; *Noise, Transportation/adverse effects ; Bayes Theorem ; Big Data ; Sleep ; Environmental Exposure ; }, abstract = {BACKGROUND: Road traffic noise is a serious public health problem globally as it has adverse psychological and physiologic effects (i.e., sleep). Since previous studies mainly focused on individual levels, we aim to examine associations between road traffic noise and sleep deprivation on a large scale; namely, the US at county level.

METHODS: Information from a large-scale sleep survey and national traffic noise map, both obtained from government's open data, were utilized and processed with Geographic Information System (GIS) techniques. To examine the associations between traffic noise and sleep deprivation, we used a hierarchical Bayesian spatial modelling framework to simultaneously adjust for multiple socioeconomic factors while accounting for spatial correlation.

FINDINGS: With 62.90% of people not getting enough sleep, a 10 dBA increase in average sound-pressure level (SPL) or Ls10 (SPL of the relatively noisy area) in a county, was associated with a 49% (OR: 1.49; 95% CrIs:1.19-1.86) or 8% (1.08; 1.00-1.16) increase in the odds of a person in a particular county not getting enough sleep. No significant association was observed for Ls90 (SPL of the relatively quiet area). A 10% increase in noise exposure area or population ratio was associated with a 3% (1.03; 1.01-1.06) or 4% (1.04; 1.02-1.06) increase in the odds of a person within a county not getting enough sleep.

INTERPRETATION: Traffic noise can contribute to variations in sleep deprivation among counties. This study suggests that policymakers could set up different noise-management strategies for relatively quiet and noisy areas and incorporate geospatial noise indicators, such as exposure population or area ratio. Furthermore, urban planners should consider urban sprawl patterns differently in terms of noise-induced sleep problems.}, } @article {pmid36085224, year = {2023}, author = {Gul, S and Bibi, T and Rahim, S and Gul, Y and Niaz, A and Mumtaz, S and Shedayi, AA}, title = {Spatio-temporal change detection of land use and land cover in Malakand Division Khyber Pakhtunkhwa, Pakistan, using remote sensing and geographic information system.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {4}, pages = {10982-10994}, pmid = {36085224}, issn = {1614-7499}, mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; Pakistan ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Agriculture ; }, abstract = {The land use land cover (LULC) change due to the rapidly growing population is a common feature of the urban area. The rapidly growing population in Malakand Division is a greater threat to the LULC of the area due to its negative impact on environment and ecology. This research aims to detect the variations in LULC from 1991 to 2017 in the Malakand Division, Khyber Pakhtunkhwa (KP) province of Pakistan. The study relies on secondary dataset downloaded from the US Geological Survey (1991, 2001, 2011, and 2017 imageries) and the United Nations Office for the Coordination of Humanitarian Affairs (UN OCHA) website. Maximum likelihood technique under supervised image classification was opted to analyze the LULC changes in between 1991 and 2017. The results were based on six major land use classes including agriculture built-up area, vegetation cover, water bodies, snow cover, and barren land. The results from 1991 to 2017 show a substantial reduction in snow cover and barren land which is consequence of climate change. A known change has been recorded in built-up area which shows an increase from 1.02 to 6.2% with a change of 5.18% of the total land. The vegetation cover water bodies were also showing increase in area. The vegetation cover increased from 28.89 to 44.67% while barren land decreased from 45.68 to 40.29% of the total area. Furthermore, the built-up area increased from 1.02 to 6.2%, whereas water covers increased from 0.63% (1991) to 0.86% (2017) of the total area. The study concludes that there is an immense need for planning to preserve the natural habitat for sustainable development in the area.}, } @article {pmid35462586, year = {2023}, author = {Zhan, Y and Chang, Y and Tao, Y and Zhang, H and Lin, Y and Deng, J and Ma, T and Ding, G and Wei, Y and Li, J}, title = {Insight into the dynamic microbial community and core bacteria in composting from different sources by advanced bioinformatics methods.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {4}, pages = {8956-8966}, pmid = {35462586}, issn = {1614-7499}, mesh = {Animals ; Sheep ; Soil ; *Composting ; Manure/analysis ; *Refuse Disposal ; Bacteria/genetics ; Computational Biology ; *Microbiota ; Vegetables ; Chickens ; }, abstract = {Microbial communities are important for high composting efficiency and good quality composts. This study was conducted to compare the changes of physicochemical and bacterial characteristics in composting from different raw materials, including chicken manure (CM), duck manure (DM), sheep manure (SM), food waste (FW), and vegetable waste (VW). The role and interactions of core bacteria and their contribution to maturity in diverse composts were analyzed by advanced bioinformatics methods combined sequencing with co-occurrence network and structural equation modeling (SEM). Results indicated that there were obviously different bacterial composition and diversity in composting from diverse sources. FW had a low pH and different physiochemical characteristics compared to other composts but they all achieved similar maturity products. Redundancy analysis suggested total organic carbon, phosphorus, and temperature governed the composition of microbial species but key factors were different in diverse composts. Network analysis showed completely different interactions of core bacterial community from diverse composts but Thermobifida was the ubiquitous core bacteria in composting bacterial network. Sphaerobacter and Lactobacillus as core genus were presented in the starting mesophilic and thermophilic phases of composting from manure (CM, DM, SM) and municipal solid waste (FW, VW), respectively. SEM indicated core bacteria had the positive, direct, and the biggest (> 80%) effects on composting maturity. Therefore, this study presents theoretical basis to identify and enhance the core bacteria for improving full-scale composting efficiency facing more and more organic wastes.}, } @article {pmid33907064, year = {2023}, author = {Ibayashi, K and Fujino, Y and Mimaki, M and Fujimoto, K and Matsuda, S and Goto, YI}, title = {Estimation of the Number of Patients With Mitochondrial Diseases: A Descriptive Study Using a Nationwide Database in Japan.}, journal = {Journal of epidemiology}, volume = {33}, number = {2}, pages = {68-75}, pmid = {33907064}, issn = {1349-9092}, mesh = {Male ; Female ; Humans ; Adult ; Middle Aged ; Japan/epidemiology ; Prevalence ; Databases, Factual ; Tokyo ; *Mitochondrial Diseases/epidemiology ; }, abstract = {BACKGROUND: To provide a better healthcare system for patients with mitochondrial diseases, it is important to understand the basic epidemiology of these conditions, including the number of patients affected. However, little information about them has appeared in Japan to date.

METHODS: To gather data of patients with mitochondrial diseases, we estimated the number of patients with mitochondrial diseases from April 2018 through March 2019 using a national Japanese health care claims database, the National Database (NDB). Further, we calculated the prevalence of patients, and sex ratio, age class, and geographical distribution.

RESULTS: From April 2018 through March 2019, the number of patients with mitochondrial diseases was 3,629, and the prevalence was 2.9 (95% confidence interval [CI], 2.8-3.0) per 100,000 general population. The ratio of females and males was 53 to 47, and the most frequent age class was 40-49 years old. Tokyo had the greatest number of patients with mitochondrial diseases, at 477, whereas Yamanashi had the fewest, at 13. Kagoshima had the highest prevalence of patients with mitochondrial diseases, 8.4 (95% CI, 7.1-10.0) per 100,000 population, whereas Yamanashi had the lowest, 1.6 (95% CI, 0.8-2.7).

CONCLUSION: The number of patients with mitochondrial diseases estimated by this study, 3,269, was more than double that indicated by the Japanese government. This result may imply that about half of all patients are overlooked for reasons such as low severity of illness, suggesting that the Japanese healthcare system needs to provide additional support for these patients.}, } @article {pmid36726097, year = {2023}, author = {Alwafi, H and Naser, AY and Ashoor, DS and Aldhahir, AM and Alqahtani, JS and Minshawi, F and Salawati, E and Samannodi, M and Dairi, MS and Alansari, AK and Ekram, R}, title = {Trends in hospital admissions and prescribing due to chronic obstructive pulmonary disease and asthma in England and Wales between 1999 and 2020: an ecological study.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {49}, pmid = {36726097}, issn = {1471-2466}, mesh = {Humans ; Female ; Wales/epidemiology ; *Pulmonary Disease, Chronic Obstructive/drug therapy/epidemiology ; Hospitalization ; *Asthma/drug therapy/epidemiology ; England/epidemiology ; Hospitals ; Drug Prescriptions ; *Respiratory Tract Infections/drug therapy ; }, abstract = {OBJECTIVE: To investigate the trends in hospital admissions and medication prescriptions related to asthma and chronic obstructive pulmonary disease (COPD) in England and Wales.

METHODS: An ecological study was conducted between April 1999 and April 2020 using data extracted from the hospital episode statistics database in England and the patient episode database for Wales. The Office of National Statistics mid-year population estimates for 1999 through 2020 were collected, and medication prescription data for 2004-2020 were extracted from the prescription cost analysis database.

RESULTS: The total annual number of COPD and asthma hospital admissions for various causes increased by 82.2%, from 210,525 in 1999 to 383,652 in 2020, representing a 59.1% increase in hospital admission rate (from 403.77 in 1999 to 642.42 per 100,000 persons in 2020, p < 0.05). Chronic obstructive pulmonary disease with acute lower respiratory infection accounted for 38.7% of hospital admissions. Around 34.7% of all hospital admissions involved patients aged 75 and older. Around 53.8% of all COPD and asthma hospital admissions were attributable to females. The annual number of prescriptions dispensed for COPD and asthma medications increased by 42.2%.

CONCLUSIONS: Throughout the study period, hospital admissions due to chronic obstructive pulmonary disease and asthma, as well as medication prescriptions, increased dramatically among all age groups. Hospitalization rates were higher for women. Further observational and epidemiological research is required to identify the factors contributing to increased hospitalization rates.}, } @article {pmid35947263, year = {2023}, author = {Liu, S and Zhang, Y and Cai, J}, title = {Operation of high-speed rail and reduction of corporate pollution: evidence from China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {2}, pages = {3562-3575}, pmid = {35947263}, issn = {1614-7499}, mesh = {Humans ; China ; *Asian People ; Databases, Factual ; *Economic Development ; Environmental Pollution ; }, abstract = {As an environmentally friendly means of transport, the high-speed rail (HSR) is conducive to promoting corporate performance. An innovative approach extends the impact of HSR networks on pollution emissions from the regional level to the micro-enterprise level. Based on the quasi-natural experiment of the opening of HSR, a difference-in-difference model is used to investigate the impact of HSR on enterprise pollution emission levels and its action mechanism by using the matched data from the Chinese Enterprise Pollution Emission Database, the Chinese Industrial Enterprise Database, and the Chinese City Statistical Yearbook from 2000 to 2010. The results show that opening HSR significantly reduces the enterprises' pollution emission level, while reducing the number of polluting enterprises and transportation costs as well as improving the innovation capacity of enterprises are the corresponding action mechanisms. The impact of HSR on the enterprises' pollution emission varies with industry intensity, population size, and regional economic development level. The conclusions not only provide important insights to increase the ecological quality of China's environment through transportation infrastructure upgrades but also bring some guidance to more developing countries to improve their air environment.}, } @article {pmid36722081, year = {2023}, author = {Ehlman, SM and Scherer, U and Bierbach, D and Francisco, F and Laskowski, KL and Krause, J and Wolf, M}, title = {Leveraging big data to uncover the eco-evolutionary factors shaping behavioural development.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1992}, pages = {20222115}, doi = {10.1098/rspb.2022.2115}, pmid = {36722081}, issn = {1471-2954}, mesh = {Animals ; *Big Data ; *Biological Evolution ; }, abstract = {Mapping the eco-evolutionary factors shaping the development of animals' behavioural phenotypes remains a great challenge. Recent advances in 'big behavioural data' research-the high-resolution tracking of individuals and the harnessing of that data with powerful analytical tools-have vastly improved our ability to measure and model developing behavioural phenotypes. Applied to the study of behavioural ontogeny, the unfolding of whole behavioural repertoires can be mapped in unprecedented detail with relative ease. This overcomes long-standing experimental bottlenecks and heralds a surge of studies that more finely define and explore behavioural-experiential trajectories across development. In this review, we first provide a brief guide to state-of-the-art approaches that allow the collection and analysis of high-resolution behavioural data across development. We then outline how such approaches can be used to address key issues regarding the ecological and evolutionary factors shaping behavioural development: developmental feedbacks between behaviour and underlying states, early life effects and behavioural transitions, and information integration across development.}, } @article {pmid36719907, year = {2023}, author = {Turtle, L and Thorpe, M and Drake, TM and Swets, M and Palmieri, C and Russell, CD and Ho, A and Aston, S and Wootton, DG and Richter, A and de Silva, TI and Hardwick, HE and Leeming, G and Law, A and Openshaw, PJM and Harrison, EM and , and Baillie, JK and Semple, MG and Docherty, AB}, title = {Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study.}, journal = {PLoS medicine}, volume = {20}, number = {1}, pages = {e1004086}, doi = {10.1371/journal.pmed.1004086}, pmid = {36719907}, issn = {1549-1676}, abstract = {BACKGROUND: Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic.

METHODS AND FINDINGS: We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. Approximately 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent.

CONCLUSIONS: Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group.

TRIAL REGISTRATION: ISRCTN 66726260.}, } @article {pmid36718952, year = {2023}, author = {Freedman, AH and Harrigan, RJ and Zhen, Y and Hamilton, AM and Smith, TB}, title = {Evidence for Ecotone Speciation Across an African Rainforest-Savanna Gradient.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16867}, pmid = {36718952}, issn = {1365-294X}, abstract = {Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly likely driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.}, } @article {pmid36308510, year = {2023}, author = {Sun, Y and Chang, J and Fang, J}, title = {Above- and belowground net-primary productivity: A field-based global database of grasslands.}, journal = {Ecology}, volume = {104}, number = {2}, pages = {e3904}, doi = {10.1002/ecy.3904}, pmid = {36308510}, issn = {1939-9170}, mesh = {*Ecosystem ; *Grassland ; Temperature ; Databases, Factual ; Carbon ; }, abstract = {Net primary productivity (NPP) over global grasslands is crucial for understanding the terrestrial carbon cycling and for the assessments of wild herbivores food security. During the past few decades, numerous field investigations have been conducted to estimate grassland NPP since the measuring criterion released by the International Biological Program. However, a comprehensive NPP database, particularly for belowground NPP (BNPP), in global grasslands is rare to date. Here, field NPP measurements from 438 publications (1957-2018) in global grasslands were collected, critically filtered, and incorporated in a comprehensive global database with observations for aboveground NPP (ANPP), BNPP, total NPP (TNPP), and BNPP fraction (fBNPP). Associated information on geographical locations, climatic records, grassland types, land use patterns, manipulations subjected to manipulative experiments, sampling year of study sites, as well as NPP measurement methods are also documented. This database included 2985 entries from 1785 study sites. Among them, 806 entries contained paired data of ANPP and BNPP, resulting in the 806 fBNPP data. The study sites encompassed global grasslands with latitudinal range of 54.5° S~78.9° N, longitudinal range of 157.4° W~175.8° E, and altitudes from 0 to 5168 m above sea level, covering broad climatic gradients (-17.6 to 28.8°C in mean annual temperature and 63-2052 mm in mean annual precipitation). This global database is the world's largest paired data of ANPP and BNPP field measurements in grasslands. It can be used to study the spatio-temporal patterns of NPP and its allocation, evaluate the responses of above- and below-ground carbon components to future global changes, and validate the NPP estimation by empirical or process-based models in global grasslands. The database can be freely used for noncommercial applications. We kindly request users cite this data paper when using the database, respecting all the hard work during data compilation.}, } @article {pmid36714536, year = {2023}, author = {Astorga, F and Groom, Q and Shimabukuro, PHF and Manguin, S and Noesgaard, D and Orrell, T and Sinka, M and Hirsch, T and Schigel, D}, title = {Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100484}, pmid = {36714536}, issn = {2352-7714}, abstract = {The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.}, } @article {pmid36705582, year = {2023}, author = {Bettisworth, B and Smith, SA and Stamatakis, A}, title = {Lagrange-NG: The next generation of Lagrange.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syad002}, pmid = {36705582}, issn = {1076-836X}, abstract = {Computing ancestral ranges via the Dispersion Extinction and Cladogensis (DEC) model of biogeography is characterized by an exponential number of states relative to the number of regions considered. This is because the DEC model requires computing a large matrix exponential, which typically accounts for up to 80% of overall runtime. Therefore, the kinds of biogeographical analyses that can be conducted under the DEC model are limited by the number of regions under consideration. In this work, we present a completely redesigned efficient version of the popular tool Lagrange which is up to 49 times faster with multi-threading enabled, and is also 26 times faster when using only one thread. We call this new version Lagrange-NG (Lagrange-Next Generation). The increased computational efficiency allows Lagrange-NG to analyze datasets with a large number of regions in a reasonable amount of time, up to 12 regions in approximately 18 minutes. We achieve these speedups using a relatively new method of computing the matrix exponential based on Krylov subspaces. In order to validate the correctness of Lagrange-NG, we also introduce a novel metric on range distributions for trees so that researchers can assess the difference between any two range inferences. Finally, Lagrange-NG exhibits substantially higher adherence to coding quality standards. It improves a respective software quality indicator as implemented in the SoftWipe tool from average (5.5; Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available under GPL2.}, } @article {pmid36621304, year = {2023}, author = {Liu, X and Han, Y and Luo, L and Pan, H and Cheng, T and Zhang, Q}, title = {Multiomics analysis reveals the mechanisms underlying the different floral colors and fragrances of Rosa hybrida cultivars.}, journal = {Plant physiology and biochemistry : PPB}, volume = {195}, number = {}, pages = {101-113}, doi = {10.1016/j.plaphy.2022.12.028}, pmid = {36621304}, issn = {1873-2690}, mesh = {*Rosa/genetics/metabolism ; Odorants ; Multiomics ; Color ; Plant Breeding ; Flowers/genetics/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {The color and fragrance of rose flowers affect their commercial value. However, several rose varieties with new floral colors developed by the bud mutation method lost their fragrance during the breeding process, raising the question: Is there a relationship between floral color and aroma traits? Rose cultivar 'Yellow Island' (YI) with intensely aroma and yellow petals, while its bud mutant 'Past Feeling' (PF) with light aroma and pink petals mixing some yellow, two cultivars were used to explore this question using multiomics approaches. We investigated the genomic polymorphisms between PF and YI by whole-genome resequencing. 71 differentially abundant metabolites and 155 related differentially expressed genes identified in petals between PF and YI. From this, we constructed a model of metabolic changes affecting floral color and fragrance integrating shikimate, terpenoid, carotenoid, and green leaf volatile metabolites and predicted the associated key genes and transcription factors. This study provides a reference for understanding the molecular mechanism of variation in rose floral color and aroma traits.}, } @article {pmid36704891, year = {2023}, author = {Crandall, ED and Toczydlowski, RH and Liggins, L and Holmes, AE and Ghoojaei, M and Gaither, MR and Wham, BE and Pritt, AL and Noble, C and Anderson, TJ and Barton, RL and Berg, JT and Beskid, SG and Delgado, A and Farrell, E and Himmelsbach, N and Queeno, SR and Trinh, T and Weyand, C and Bentley, A and Deck, J and Riginos, C and Bradburd, GS and Toonen, RJ}, title = {The importance of timely metadata curation to the global surveillance of genetic diversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cobi.14061}, pmid = {36704891}, issn = {1523-1739}, abstract = {Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and from direct communication with authors. Starting with 848 candidate genomic datasets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 datasets (N = 440 datasets comprising 45,105 individuals from 762 species in 17 phyla). Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declined significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever. This article is protected by copyright. All rights reserved.}, } @article {pmid36699674, year = {2022}, author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X}, title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {1112278}, pmid = {36699674}, issn = {1664-042X}, abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.}, } @article {pmid36699126, year = {2023}, author = {Wortel, MT and Agashe, D and Bailey, SF and Bank, C and Bisschop, K and Blankers, T and Cairns, J and Colizzi, ES and Cusseddu, D and Desai, MM and van Dijk, B and Egas, M and Ellers, J and Groot, AT and Heckel, DG and Johnson, ML and Kraaijeveld, K and Krug, J and Laan, L and Lässig, M and Lind, PA and Meijer, J and Noble, LM and Okasha, S and Rainey, PB and Rozen, DE and Shitut, S and Tans, SJ and Tenaillon, O and Teotónio, H and de Visser, JAGM and Visser, ME and Vroomans, RMA and Werner, GDA and Wertheim, B and Pennings, PS}, title = {Towards evolutionary predictions: Current promises and challenges.}, journal = {Evolutionary applications}, volume = {16}, number = {1}, pages = {3-21}, pmid = {36699126}, issn = {1752-4571}, abstract = {Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.}, } @article {pmid36696549, year = {2023}, author = {Menon, K and Sorce, LR and Argent, A and Bennett, TD and Carrol, ED and Kissoon, N and Sanchez-Pinto, LN and Schlapbach, LJ and de Souza, DC and Watson, RS and Wynn, JL and Zimmerman, JJ and Ranjit, S and , and , }, title = {Reporting of Social Determinants of Health in Pediatric Sepsis Studies.}, journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies}, volume = {}, number = {}, pages = {}, doi = {10.1097/PCC.0000000000003184}, pmid = {36696549}, issn = {1529-7535}, abstract = {OBJECTIVE: Standardized, consistent reporting of social determinants of health (SDOH) in studies on children with sepsis would allow for: 1) understanding the association of SDOH with illness severity and outcomes, 2) comparing populations and extrapolating study results, and 3) identification of potentially modifiable socioeconomic factors for policy makers. We, therefore, sought to determine how frequently data on SDOH were reported, which factors were collected and how these factors were defined in studies of sepsis in children.

DATA SOURCES AND SELECTION: We reviewed 106 articles (published between 2005 and 2020) utilized in a recent systematic review on physiologic criteria for pediatric sepsis.

DATA EXTRACTION: Data were extracted by two reviewers on variables that fell within the World Health Organization's SDOH categories.

DATA SYNTHESIS: SDOH were not the primary outcome in any of the included studies. Seventeen percent of articles (18/106) did not report on any SDOH, and a further 36.8% (39/106) only reported on gender/sex. Of the remaining 46.2% of articles, the most reported SDOH categories were preadmission nutritional status (35.8%, 38/106) and race/ethnicity (18.9%, 20/106). However, no two studies used the same definition of the variables reported within each of these categories. Six studies reported on socioeconomic status (3.8%, 6/106), including two from upper-middle-income and four from lower middle-income countries. Only three studies reported on parental education levels (2.8%, 3/106). No study reported on parental job security or structural conflict.

CONCLUSIONS: We found overall low reporting of SDOH and marked variability in categorizations and definitions of SDOH variables. Consistent and standardized reporting of SDOH in pediatric sepsis studies is needed to understand the role these factors play in the development and severity of sepsis, to compare and extrapolate study results between settings and to implement policies aimed at improving socioeconomic conditions related to sepsis.}, } @article {pmid36692937, year = {2023}, author = {de Angel, V and Adeleye, F and Zhang, Y and Cummins, N and Munir, S and Lewis, S and Laporta Puyal, E and Matcham, F and Sun, S and Folarin, AA and Ranjan, Y and Conde, P and Rashid, Z and Dobson, R and Hotopf, M}, title = {The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e42866}, doi = {10.2196/42866}, pmid = {36692937}, issn = {2368-7959}, abstract = {BACKGROUND: Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.

OBJECTIVE: A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.

METHODS: A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.

RESULTS: The overall retention rate was 60%. Higher-intensity treatment (χ[2]1=4.6; P=.03) and higher baseline anxiety (t56.28=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t50.4=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.

CONCLUSIONS: Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.}, } @article {pmid36690591, year = {2023}, author = {Sambo, B and Bonato, M and Sperotto, A and Torresan, S and Furlan, E and Lambert, JH and Linkov, I and Critto, A}, title = {Framework for multirisk climate scenarios across system receptors with application to the Metropolitan City of Venice.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {}, number = {}, pages = {}, doi = {10.1111/risa.14097}, pmid = {36690591}, issn = {1539-6924}, abstract = {Climate change influences the frequency of extreme events that affect both human and natural systems. It requires systemic climate change adaptation to address the complexity of risks across multiple domains and tackle the uncertainties of future scenarios. This paper introduces a multirisk analysis of climate hazard, exposure, vulnerability, and risk severity, specifically designed to hotspot geographic locations and prioritize system receptors that are affected by climate-related extremes. The analysis is demonstrated for the Metropolitan City of Venice. Representative scenarios (RCP4.5 and RCP8.5) of climate threats (i.e., storm surges, pluvial flood, heat waves, and drought) are selected and represented by projections of Regional Climate Models for a 30-year period (2021-2050). A sample of results is as follows. First, an increase in the risk is largely due to drought, pluvial flood, and storm surge, depending on the areas of interest, with the overall situation worsening under the RCP8.5 scenario. Second, particular locations have colocated vulnerable receptors at higher risk, concentrated in the urban centers (e.g., housing, railways, roads) and along the coast (e.g., beaches, wetlands, primary sector). Third, risk communication of potential environmental and socio-economic losses via the multirisk maps is useful to stakeholders and public administration. Fourth, the multirisk maps recommend priorities for future investigation and risk management, such as collection of sensor data, elaboration of mitigations, and adaptation plans at hotspot locations.}, } @article {pmid36689893, year = {2023}, author = {Werneck, RA and Meinberg, MF and Passos, MZ and Brandão, WC and de Moraes, EN and da Silva-Filho, AL}, title = {Quality of information regarding abnormal uterine bleeding available online.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {282}, number = {}, pages = {83-88}, doi = {10.1016/j.ejogrb.2023.01.020}, pmid = {36689893}, issn = {1872-7654}, abstract = {INTRODUCTION: The Internet and electronic devices with Internet access allow for a greater fluidity of information and speed of communication, especially in the field of health. Abnormal uterine bleeding (AUB) affects approximately 3-30% of women and can negatively impact their health and quality of life. Information regarding AUB that is available on the Internet may not be clear or accurate, rendering it difficult to understand and likely to result in delayed medical evaluation, which subsequently leads to worsening of the AUB.

OBJECTIVE: To evaluate the quality of the information regarding AUB currently available on the Internet, including information regarding treatments.

METHODS: The Google Trends website was searched for the most widely used English terms related to AUB. The identified descriptors were searched individually on the Google, Yahoo!, and Bing search engines. The first 10 results of each search were pre-selected and evaluated for inclusion in this study. Selected websites were categorically divided into two groups (news/magazine and academic) and individually analyzed by three experts using the DISCERN quality criteria (reliability, general quality, and quality of information) and the presence or absence of the Health on the Net Foundation Code of Conduct (HONcode®) seal.

RESULTS: Of the 168 websites included in this study, 60.1% were allocated to the news/magazine group and 39.9% were allocated to the academic group. Over half of the websites (54.2%) did not have the HONcode® quality seal. Websites in the academic group were more likely to include accurate information regarding AUB with greater reliability than websites in the news/magazine group. There were no statistical differences regarding the general quality of the websites. Most websites were rated as either moderate quality (70.8%) or low quality (28.6%). The HONcode® criterion was found to be a confounding factor of the analyses, as the grouping and quality results of websites without this seal were significantly associated. In addition, websites in the news/magazines group were 6.7 times more likely to provide low quality information than websites in the academic group (odds ratio: 6.7; 95% confidence interval: 2.1-21.4).

CONCLUSION: The information regarding AUB that is available on the Internet is of low to moderate quality. Academic websites present more reliable information of greater quality. The presence of the HONcode® seal is considered important to determine the quality of the content of a website, especially for news/magazine websites, and may help Internet users identify websites that contain more reliable information. Algorithms and applications that categorize the quality of information and the reliability of health content may be useful tools that can help patients clarify their symptoms for several conditions including AUB.}, } @article {pmid36669842, year = {2023}, author = {Guan, Y and Qi, Y and Zheng, L and Yang, J and Zhang, M and Zhang, Q and Ji, L}, title = {Data mining techniques for detecting signals of adverse drug reaction of cardiac therapy drugs based on Jinan adverse event reporting system database: a retrospective study.}, journal = {BMJ open}, volume = {13}, number = {1}, pages = {e068127}, doi = {10.1136/bmjopen-2022-068127}, pmid = {36669842}, issn = {2044-6055}, mesh = {Humans ; United States ; Retrospective Studies ; Bayes Theorem ; *Adverse Drug Reaction Reporting Systems ; *Drug-Related Side Effects and Adverse Reactions/diagnosis/epidemiology ; Data Mining ; Databases, Factual ; United States Food and Drug Administration ; }, abstract = {OBJECTIVE: Cardiac therapy drugs are widely used in the treatment of heart disease. However, the concern regarding adverse events (AEs) of cardiac therapy drugs have been rising. This study aimed to analyse cardiac therapy drug-related AEs using the Jinan adverse event reporting system (JAERS) database mining and conduct a comprehensive evaluation to provide safe medication information for patients.

DESIGN: Retrospective observational study.

SETTING: In this study, cardiac therapy drug-related AEs were detected using the JAERS database from January 2000 to March 2022.

METHODS: Reports of cardiac therapy drug-related AEs were extracted from JAERS database, and the basic information of patients, reports and common AEs were analysed. Four disproportionality analysis methods, proportional reporting ratio (PRR), reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN), Medicines and Healthcare products Regulatory Agency (MHRA), were used to detect cardiac therapy drug-related signals. We further checked whether the detected signals exist on drug labels in China and two developed countries, the USA and Japan.

RESULTS: In total, 168 314 AEs were reported, of which 4788 were associated with cardiac therapy drugs. Using the PRR, ROR, MHRA and BCPNN method, we detected 52 signals, 52 signals, 33 signals and 43 signals, respectively. Among the 52 signals, 14 were not included on the drug labels of China. One (isosorbide mononitrate-head bilges) was not included on the drug labels of the three countries.

CONCLUSION: We identified 14 new cardiac therapy drug signals that did not appear on drug labels in China and 1 new signal that did not appear on drug labels in 3 counties. A causal link between cardiac therapy drugs and AEs should be evaluated in further studies.}, } @article {pmid36685700, year = {2022}, author = {Jazayeri, SM and Pooralinaghi, M and Torres-Navarrete, Y and Oviedo-Bayas, B and Guerra, ÍE and Jácome, DH and Morán, CQ and Macias, CS and Escobar, KM and Ghafoor, SMHAS and Veiskarami, G and Jandaghi, P and Torres, ROV}, title = {Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses.}, journal = {Biotechnologia}, volume = {103}, number = {4}, pages = {355-384}, pmid = {36685700}, issn = {2353-9461}, abstract = {Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.}, } @article {pmid36684825, year = {2023}, author = {Liew, CY and Labadin, J and Kok, WC and Eze, MO}, title = {A methodology framework for bipartite network modeling.}, journal = {Applied network science}, volume = {8}, number = {1}, pages = {6}, pmid = {36684825}, issn = {2364-8228}, abstract = {The graph-theoretic based studies employing bipartite network approach mostly focus on surveying the statistical properties of the structure and behavior of the network systems under the domain of complex network analysis. They aim to provide the big-picture-view insights of a networked system by looking into the dynamic interaction and relationship among the vertices. Nonetheless, incorporating the features of individual vertex and capturing the dynamic interaction of the heterogeneous local rules governing each of them in the studies is lacking. The methodology in achieving this could hardly be found. Consequently, this study intends to propose a methodology framework that considers the influence of heterogeneous features of each node to the overall network behavior in modeling real-world bipartite network system. The proposed framework consists of three main stages with principal processes detailed in each stage, and three libraries of techniques to guide the modeling activities. It is iterative and process-oriented in nature and allows future network expansion. Two case studies from the domain of communicable disease in epidemiology and habitat suitability in ecology employing this framework are also presented. The results obtained suggest that the methodology could serve as a generic framework in advancing the current state of the art of bipartite network approach.}, } @article {pmid36682374, year = {2023}, author = {Traore, T and Shanks, S and Haider, N and Ahmed, K and Jain, V and Rüegg, SR and Razavi, A and Kock, R and Erondu, N and Rahman-Shepherd, A and Yavlinsky, A and Mboera, L and Asogun, D and McHugh, TD and Elton, L and Oyebanji, O and Okunromade, O and Ansumana, R and Djingarey, MH and Ali Ahmed, Y and Diallo, AB and Balde, T and Talisuna, A and Ntoumi, F and Zumla, A and Heymann, D and Socé Fall, I and Dar, O}, title = {How prepared is the world? Identifying weaknesses in existing assessment frameworks for global health security through a One Health approach.}, journal = {Lancet (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1016/S0140-6736(22)01589-6}, pmid = {36682374}, issn = {1474-547X}, abstract = {The COVID-19 pandemic has exposed faults in the way we assess preparedness and response capacities for public health emergencies. Existing frameworks are limited in scope, and do not sufficiently consider complex social, economic, political, regulatory, and ecological factors. One Health, through its focus on the links among humans, animals, and ecosystems, is a valuable approach through which existing assessment frameworks can be analysed and new ways forward proposed. Although in the past few years advances have been made in assessment tools such as the International Health Regulations Joint External Evaluation, a rapid and radical increase in ambition is required. To sufficiently account for the range of complex systems in which health emergencies occur, assessments should consider how problems are defined across stakeholders and the wider sociopolitical environments in which structures and institutions operate. Current frameworks do little to consider anthropogenic factors in disease emergence or address the full array of health security hazards across the social-ecological system. A complex and interdependent set of challenges threaten human, animal, and ecosystem health, and we cannot afford to overlook important contextual factors, or the determinants of these shared threats. Health security assessment frameworks should therefore ensure that the process undertaken to prioritise and build capacity adheres to core One Health principles and that interventions and outcomes are assessed in terms of added value, trade-offs, and cobenefits across human, animal, and environmental health systems.}, } @article {pmid36659170, year = {2020}, author = {Gong, P and Chen, B and Li, X and Liu, H and Wang, J and Bai, Y and Chen, J and Chen, X and Fang, L and Feng, S and Feng, Y and Gong, Y and Gu, H and Huang, H and Huang, X and Jiao, H and Kang, Y and Lei, G and Li, A and Li, X and Li, X and Li, Y and Li, Z and Li, Z and Liu, C and Liu, C and Liu, M and Liu, S and Mao, W and Miao, C and Ni, H and Pan, Q and Qi, S and Ren, Z and Shan, Z and Shen, S and Shi, M and Song, Y and Su, M and Ping Suen, H and Sun, B and Sun, F and Sun, J and Sun, L and Sun, W and Tian, T and Tong, X and Tseng, Y and Tu, Y and Wang, H and Wang, L and Wang, X and Wang, Z and Wu, T and Xie, Y and Yang, J and Yang, J and Yuan, M and Yue, W and Zeng, H and Zhang, K and Zhang, N and Zhang, T and Zhang, Y and Zhao, F and Zheng, Y and Zhou, Q and Clinton, N and Zhu, Z and Xu, B}, title = {Mapping essential urban land use categories in China (EULUC-China): preliminary results for 2018.}, journal = {Science bulletin}, volume = {65}, number = {3}, pages = {182-187}, doi = {10.1016/j.scib.2019.12.007}, pmid = {36659170}, issn = {2095-9281}, } @article {pmid36656265, year = {2023}, author = {Yu, Y and Yu, X and Zhang, D and Jin, L and Huang, J and Zhu, X and Sun, J and Yu, M and Zhu, L}, title = {Biotransformation of Organophosphate Esters by Rice and Rhizosphere Microbiome: Multiple Metabolic Pathways, Mechanism, and Toxicity Assessment.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c07796}, pmid = {36656265}, issn = {1520-5851}, abstract = {The biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.}, } @article {pmid36654087, year = {2022}, author = {Yang, L and Zou, K and Gao, K and Jiang, Z}, title = {A fuzzy DRBFNN-based information security risk assessment method in improving the efficiency of urban development.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {19}, number = {12}, pages = {14232-14250}, doi = {10.3934/mbe.2022662}, pmid = {36654087}, issn = {1551-0018}, abstract = {The rapid development of urban informatization is an important way for cities to achieve a higher pattern, but the accompanying information security problem become a major challenge restricting the efficiency of urban development. Therefore, effective identification and assessment of information security risks has become a key factor to improve the efficiency of urban development. In this paper, an information security risk assessment method based on fuzzy theory and neural network technology is proposed to help identify and solve the information security problem in the development of urban informatization. Combined with the theory of information ecology, this method establishes an improved fuzzy neural network model from four aspects by using fuzzy theory, neural network model and DEMATEL method, and then constructs the information security risk assessment system of smart city. According to this method, this paper analyzed 25 smart cities in China, and provided suggestions and guidance for information security control in the process of urban informatization construction.}, } @article {pmid36653564, year = {2023}, author = {Battin, TJ and Lauerwald, R and Bernhardt, ES and Bertuzzo, E and Gener, LG and Hall, RO and Hotchkiss, ER and Maavara, T and Pavelsky, TM and Ran, L and Raymond, P and Rosentreter, JA and Regnier, P}, title = {River ecosystem metabolism and carbon biogeochemistry in a changing world.}, journal = {Nature}, volume = {613}, number = {7944}, pages = {449-459}, pmid = {36653564}, issn = {1476-4687}, abstract = {River networks represent the largest biogeochemical nexus between the continents, ocean and atmosphere. Our current understanding of the role of rivers in the global carbon cycle remains limited, which makes it difficult to predict how global change may alter the timing and spatial distribution of riverine carbon sequestration and greenhouse gas emissions. Here we review the state of river ecosystem metabolism research and synthesize the current best available estimates of river ecosystem metabolism. We quantify the organic and inorganic carbon flux from land to global rivers and show that their net ecosystem production and carbon dioxide emissions shift the organic to inorganic carbon balance en route from land to the coastal ocean. Furthermore, we discuss how global change may affect river ecosystem metabolism and related carbon fluxes and identify research directions that can help to develop better predictions of the effects of global change on riverine ecosystem processes. We argue that a global river observing system will play a key role in understanding river networks and their future evolution in the context of the global carbon budget.}, } @article {pmid36648719, year = {2023}, author = {Zhu, F and Su, T and Lei, B and Liang, Q and Zhou, Y and Liu, X and Wang, X and Zhang, D}, title = {Considerations on the impact of "source-sink" landscape pattern changes on urban thermal environment and cooling efficiency: a case study of Nanjing, China.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36648719}, issn = {1614-7499}, abstract = {The urban heat island effect caused by rapid urbanization has had a great impact on human health and ecological environment. The evolution of landscape patterns often affects regional thermal characteristics at the local scale. How to rationally allocate land cover types from the perspective of urban planning is a huge challenge. This paper takes Nanjing, a typical "stove city" in China, as an example to study the impact of landscape pattern changes on the urban thermal environment. Firstly, based on the "source" landscape "/sink" landscape identified by the "source-sink" landscape index, on this basis, the contributions of the "source-sink" landscape and its effects are calculated, and the temporal and spatial evolution laws are analyzed. Second, we study the cooling effect of different characteristic landscapes. The results show that the change of landscape pattern is closely related to the urban thermal environment, and the expansion of built-up areas is the main reason for the urban thermal environment. With the development of urbanization, the "source-sink" landscape structure in most districts and counties has aggravated the heat island effect, and the ratios of "sink" and "source" landscape contribution ratios with strong levels are concentrated in the suburban areas. The results of cooling efficiency research show that the cooling range of forest land is larger than that of water bodies. At the same time, we found that the cooling efficiency of the sink landscape is the highest when the area of the sink landscape is 0.18-0.9 hm[2] and the shape index is between 1 and 4. The research results can provide feasible and practical scientific suggestions for the planning and ecological construction of Nanjing.}, } @article {pmid36400569, year = {2023}, author = {Wu, L and Yan, B and Han, J and Li, R and Xiao, J and He, S and Bo, X}, title = {TOXRIC: a comprehensive database of toxicological data and benchmarks.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1432-D1445}, pmid = {36400569}, issn = {1362-4962}, mesh = {Humans ; Benchmarking ; *Databases, Factual ; *Toxicology/methods ; Software ; }, abstract = {The toxic effects of compounds on environment, humans, and other organisms have been a major focus of many research areas, including drug discovery and ecological research. Identifying the potential toxicity in the early stage of compound/drug discovery is critical. The rapid development of computational methods for evaluating various toxicity categories has increased the need for comprehensive and system-level collection of toxicological data, associated attributes, and benchmarks. To contribute toward this goal, we proposed TOXRIC (https://toxric.bioinforai.tech/), a database with comprehensive toxicological data, standardized attribute data, practical benchmarks, informative visualization of molecular representations, and an intuitive function interface. The data stored in TOXRIC contains 113 372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering in vivo/in vitro endpoints and 39 feature types, covering structural, target, transcriptome, metabolic data, and other descriptors. All the curated datasets of endpoints and features can be retrieved, downloaded and directly used as output or input to Machine Learning (ML)-based prediction models. In addition to serving as a data repository, TOXRIC also provides visualization of benchmarks and molecular representations for all endpoint datasets. Based on these results, researchers can better understand and select optimal feature types, molecular representations, and baseline algorithms for each endpoint prediction task. We believe that the rich information on compound toxicology, ML-ready datasets, benchmarks and molecular representation distribution can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery and the development of computational methods.}, } @article {pmid35999848, year = {2022}, author = {Kopperud, BT and Lidgard, S and Liow, LH}, title = {Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13921}, pmid = {35999848}, issn = {2167-8359}, mesh = {Animals ; *Biodiversity ; *Bryozoa ; Information Storage and Retrieval ; }, abstract = {We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.}, } @article {pmid36647630, year = {2023}, author = {Watts, JD and Farina, M and Kimball, JS and Schiferl, LD and Liu, Z and Arndt, KA and Zona, D and Ballantyne, A and Euskirchen, ES and Parmentier, FW and Helbig, M and Sonnentag, O and Tagesson, T and Rinne, J and Ikawa, H and Ueyama, M and Kobayashi, H and Sachs, T and Nadeau, DF and Kochendorfer, J and Jackowicz-Korczynski, M and Virkkala, A and Aurela, M and Commane, R and Byrne, B and Birch, L and Johnson, MS and Madani, N and Rogers, B and Du, J and Endsley, A and Savage, K and Poulter, B and Zhang, Z and Bruhwiler, LM and Miller, CE and Goetz, S and Oechel, WC}, title = {Carbon uptake in Eurasian boreal forests dominates the high-latitude net ecosystem carbon budget.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16553}, pmid = {36647630}, issn = {1365-2486}, support = {80NM0018D004/NASA/NASA/United States ; 80NSSC18K0770/NASA/NASA/United States ; 19-EARTH20-0105/NASA/NASA/United States ; NNX15AT74A/NASA/NASA/United States ; 80NSSC19M0113/NASA/NASA/United States ; }, abstract = {Arctic-boreal landscapes are experiencing profound warming, along with changes in ecosystem moisture status and disturbance from fire. This region is of global importance in terms of carbon feedbacks to climate, yet the sign (sink or source) and magnitude of the Arctic-boreal carbon budget within recent years remains highly uncertain. Here, we provide new estimates of recent (2003-2015) vegetation gross primary productivity (GPP), ecosystem respiration (Reco), net ecosystem CO2 exchange (NEE; Reco - GPP), and terrestrial methane (CH4) emissions for the Arctic-boreal zone using a satellite data-driven process-model for northern ecosystems (TCFM-Arctic), calibrated and evaluated using measurements from >60 tower eddy covariance (EC) sites. We used TCFM-Arctic to obtain daily 1-km[2] flux estimates and annual carbon budgets for the pan-Arctic-boreal region. Across the domain, the model indicated an overall average NEE sink of -850 Tg CO2 -C year[-1] . Eurasian boreal zones, especially those in Siberia, contributed to a majority of the net sink. In contrast, the tundra biome was relatively carbon neutral (ranging from small sink to source). Regional CH4 emissions from tundra and boreal wetlands (not accounting for aquatic CH4) were estimated at 35 Tg CH4 -C year[-1] . Accounting for additional emissions from open water aquatic bodies and from fire, using available estimates from the literature, reduced the total regional NEE sink by 21% and shifted many far northern tundra landscapes, and some boreal forests, to a net carbon source. This assessment, based on in situ observations and models, improves our understanding of the high-latitude carbon status and also indicates a continued need for integrated site-to-regional assessments to monitor the vulnerability of these ecosystems to climate change.}, } @article {pmid36643652, year = {2023}, author = {Mugnai, F and Costantini, F and Chenuil, A and Leduc, M and Gutiérrez Ortega, JM and Meglécz, E}, title = {Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14616}, pmid = {36643652}, issn = {2167-8359}, mesh = {Humans ; *DNA Barcoding, Taxonomic ; Databases, Factual ; Mediterranean Sea ; }, abstract = {BACKGROUND: In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.

METHODS: We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.

RESULTS: The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).}, } @article {pmid36462728, year = {2023}, author = {Sosa, CC and Clavijo-Buriticá, DC and García-Merchán, VH and López-Rozo, N and Riccio-Rengifo, C and Diaz, MV and Londoño, DA and Quimbaya, MA}, title = {GOCompare: An R package to compare functional enrichment analysis between two species.}, journal = {Genomics}, volume = {115}, number = {1}, pages = {110528}, doi = {10.1016/j.ygeno.2022.110528}, pmid = {36462728}, issn = {1089-8646}, mesh = {*Aluminum ; Genomics/methods ; Computational Biology/methods ; Algorithms ; Gene Ontology ; *Arabidopsis/genetics ; }, abstract = {Functional enrichment analysis is a cornerstone in bioinformatics as it makes possible to identify functional information by using a gene list as source. Different tools are available to compare gene ontology (GO) terms, based on a directed acyclic graph structure or content-based algorithms which are time-consuming and require a priori information of GO terms. Nevertheless, quantitative procedures to compare GO terms among gene lists and species are not available. Here we present a computational procedure, implemented in R, to infer functional information derived from comparative strategies. GOCompare provides a framework for functional comparative genomics starting from comparable lists from GO terms. The program uses functional enrichment analysis (FEA) results and implement graph theory to identify statistically relevant GO terms for both, GO categories and analyzed species. Thus, GOCompare allows finding new functional information complementing current FEA approaches and extending their use to a comparative perspective. To test our approach GO terms were obtained for a list of aluminum tolerance-associated genes in Oryza sativa subsp. japonica and their orthologues in Arabidopsis thaliana. GOCompare was able to detect functional similarities for reactive oxygen species and ion binding capabilities which are common in plants as molecular mechanisms to tolerate aluminum toxicity. Consequently, the R package exhibited a good performance when implemented in complex datasets, allowing to establish hypothesis that might explain a biological process from a functional perspective, and narrowing down the possible landscapes to design wet lab experiments.}, } @article {pmid36318246, year = {2023}, author = {Lei, B and Xu, Y and Lei, Y and Li, C and Zhou, P and Wang, L and Yang, Q and Li, X and Li, F and Liu, C and Cui, C and Chen, T and Ni, W and Hu, S}, title = {CRAMdb: a comprehensive database for composition and roles of microbiome in animals.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D700-D707}, pmid = {36318246}, issn = {1362-4962}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Databases, Factual ; }, abstract = {CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).}, } @article {pmid36645791, year = {2022}, author = {Marwali, EM and Kekalih, A and Yuliarto, S and Wati, DK and Rayhan, M and Valerie, IC and Cho, HJ and Jassat, W and Blumberg, L and Masha, M and Semple, C and Swann, OV and Kohns Vasconcelos, M and Popielska, J and Murthy, S and Fowler, RA and Guerguerian, AM and Streinu-Cercel, A and Pathmanathan, MD and Rojek, A and Kartsonaki, C and Gonçalves, BP and Citarella, BW and Merson, L and Olliaro, PL and Dalton, HJ and , }, title = {Paediatric COVID-19 mortality: a database analysis of the impact of health resource disparity.}, journal = {BMJ paediatrics open}, volume = {6}, number = {1}, pages = {}, doi = {10.1136/bmjpo-2022-001657}, pmid = {36645791}, issn = {2399-9772}, abstract = {BACKGROUND: The impact of the COVID-19 pandemic on paediatric populations varied between high-income countries (HICs) versus low-income to middle-income countries (LMICs). We sought to investigate differences in paediatric clinical outcomes and identify factors contributing to disparity between countries.

METHODS: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database was queried to include children under 19 years of age admitted to hospital from January 2020 to April 2021 with suspected or confirmed COVID-19 diagnosis. Univariate and multivariable analysis of contributing factors for mortality were assessed by country group (HICs vs LMICs) as defined by the World Bank criteria.

RESULTS: A total of 12 860 children (3819 from 21 HICs and 9041 from 15 LMICs) participated in this study. Of these, 8961 were laboratory-confirmed and 3899 suspected COVID-19 cases. About 52% of LMICs children were black, and more than 40% were infants and adolescent. Overall in-hospital mortality rate (95% CI) was 3.3% [=(3.0% to 3.6%), higher in LMICs than HICs (4.0% (3.6% to 4.4%) and 1.7% (1.3% to 2.1%), respectively). There were significant differences between country income groups in intervention profile, with higher use of antibiotics, antivirals, corticosteroids, prone positioning, high flow nasal cannula, non-invasive and invasive mechanical ventilation in HICs. Out of the 439 mechanically ventilated children, mortality occurred in 106 (24.1%) subjects, which was higher in LMICs than HICs (89 (43.6%) vs 17 (7.2%) respectively). Pre-existing infectious comorbidities (tuberculosis and HIV) and some complications (bacterial pneumonia, acute respiratory distress syndrome and myocarditis) were significantly higher in LMICs compared with HICs. On multivariable analysis, LMIC as country income group was associated with increased risk of mortality (adjusted HR 4.73 (3.16 to 7.10)).

CONCLUSION: Mortality and morbidities were higher in LMICs than HICs, and it may be attributable to differences in patient demographics, complications and access to supportive and treatment modalities.}, } @article {pmid36635306, year = {2023}, author = {Siddik, MAB and Dickson, KE and Rising, J and Ruddell, BL and Marston, LT}, title = {Interbasin water transfers in the United States and Canada.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {27}, pmid = {36635306}, issn = {2052-4463}, mesh = {United States ; Humans ; *Ecosystem ; *Water Supply ; Canada ; Hydrology ; Surveys and Questionnaires ; }, abstract = {Interbasin water transfers (IBTs) can have a significant impact on the environment, water availability, and economies within the basins importing and exporting water, as well as basins downstream of these water transfers. The lack of comprehensive data identifying and describing IBTs inhibits understanding of the role IBTs play in supplying water for society, as well as their collective hydrologic impact. We develop three connected datasets inventorying IBTs in the United States and Canada, including their features, geospatial details, and water transfer volumes. We surveyed the academic and gray literature, as well as local, state, and federal water agencies, to collect, process, and verify IBTs in Canada and the United States. Our comprehensive IBT datasets represent all known transfers of untreated water that cross subregion (US) or subdrainage area (CA) boundaries, characterizing a total of 641 IBT projects. The infrastructure-level data made available by these data products can be used to close water budgets, connect water supplies to water use, and better represent human impacts within hydrologic and ecosystem models.}, } @article {pmid36641462, year = {2023}, author = {Filip, T and Michal, Š and Radoslava, J and Ivan, B and Michal, A and Lucia, Z and Gyözö, H}, title = {The impact of the striped field mouse's range expansion on communities of native small mammals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {753}, pmid = {36641462}, issn = {2045-2322}, abstract = {Understanding species expansion as an element of the dispersal process is crucial to gaining a better comprehension of the functioning of the populations and the communities. Populations of the same species that are native in one area could be considered nonindigenous, naturalised or invasive somewhere else. The striped field mouse has been expanding its range in south-western Slovakia since 2010, although the origin of the spread has still not been clarified. In light of the striped field mouse's life history, the recent range expansion is considered to be the expansion of a native species. This study analyses the impact of the striped field mouse's expansion on the native population and small mammal communities and confronts the documented stages of striped field mouse expansion with the stages of invasion biology. Our research replicates the design and compares results from past research of small mammals prior to this expansion at the same three study areas with the same 20 study sites and control sites. Several years after expansion, the striped field mouse has a 100% frequency of occurrence in all study sites and has become the dominant species in two of the study areas. The native community is significantly affected by the striped field mouse's increasing dominance, specifically: (i) we found a re-ordering of the species rank, mainly in areas with higher dominance, and (ii) an initial positive impact on diversity and evenness during low dominance of the striped field mouse turned markedly negative after crossing the 25% dominance threshold. Results suggested that the variation in the striped field mouse's dominance is affected by the northern direction of its spread. Our findings show that establishment in a new area, spread and impact on the native community are stages possibly shared by both invasive and native species during their range expansion.}, } @article {pmid36639402, year = {2023}, author = {Mack, M and Stojan, R and Bock, O and Voelcker-Rehage, C}, title = {The association of executive functions and physical fitness with cognitive-motor multitasking in a street crossing scenario.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {697}, pmid = {36639402}, issn = {2045-2322}, abstract = {Age-related decline in cognitive-motor multitasking performance has been attributed to declines in executive functions and physical fitness (motor coordinative fitness and cardiovascular fitness). It has been suggested that those cognitive and physical resources strongly depend on lifestyle factors such as long-term regular physical activity and cognitive engagement. Although research suggests that there is covariation between components of executive functions and physical fitness, the interdependence between these components for cognitive-motor multitasking performance is not yet clear. The aim of the study was to examine the contribution and interrelationship between executive functions, motor coordinative fitness, and cardiovascular fitness on street crossing while multitasking. We used the more ecologically valid scenario to obtain results that might be directly transferable to daily life situation. Data from 50 healthy older adults (65-75 years, 17 females, recruited in two different cities in Germany) were analyzed. Participants' executive functions (composite score including six tests), motor coordinative fitness (composite score including five tests), and cardiovascular fitness (spiroergometry), as well as their street crossing performance while multitasking were assessed. Street crossing was tested under single-task (crossing a two-line road), and multitask conditions (crossing a two-line road while typing numbers on a keypad as simulation of mobile phone use). Street crossing performance was assessed by use of cognitive outcomes (typing, crossing failures) and motor outcomes (stay time, crossing speed). Linear mixed-effects models showed beneficial main effects of executive functions for typing (p = 0.004) and crossing failures (p = 0.023), and a beneficial main effect of motor coordinative fitness for stay time (p = 0.043). Commonality analysis revealed that the proportion of variance commonly explained by executive functions, motor coordinative fitness, and cardiovascular fitness was small for all street crossing outcomes. For typing and crossing failures (cognitive outcomes), the results further showed a higher relative contribution of executive functions compared to motor coordinative fitness and cardiovascular fitness. For stay time (motor outcome), the results correspondingly revealed a higher relative contribution of motor coordinative fitness compared to executive functions and cardiovascular fitness. The findings suggest that during cognitive-motor multitasking in everyday life, task performance is determined by the components of executive functions and physical fitness related to the specific task demands. Since multitasking in everyday life includes cognitive and motor tasks, it seems to be important to maintain both executive functions and physical fitness for independent living up to old age.}, } @article {pmid36629615, year = {2023}, author = {Brito, MIBDS and Oliveira, ECA and Barbosa, CS and Gomes, ECS}, title = {Factors associated with severe forms and deaths from schistosomiasis and application of probabilistic linkage in databases, state of Pernambuco, Brazil, 2007-2017.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230003}, doi = {10.1590/1980-549720230003.2}, pmid = {36629615}, issn = {1980-5497}, mesh = {Humans ; Brazil/epidemiology ; *Schistosomiasis/epidemiology ; Databases, Factual ; }, abstract = {OBJECTIVE: To verify the agreement of data on severe forms and deaths from schistosomiasis recorded in the Brazilian Notifiable Diseases Information System and the Mortality Information System, sociodemographic variables with the occurrence of severe forms and deaths, and the temporal trend of the disease in the state of Pernambuco, Brazil.

METHODS: This is an ecological, descriptive, time series study with data on severe forms and deaths from schistosomiasis in Pernambuco, from 2007 to 2017. For the linkage between databases, a function was developed in python programming language, using the Soundex method. To identify sociodemographic and health factors that correlated with the dependent variables, Pearson's correlation test was applied. For trend analysis, linear regression was applied.

RESULTS: We identified 9,085 severe cases, 1,956 deaths, and 186 cases in the linkage. The correlation between the average positivity rate with the general water supply and waste collection was 0.22 and 0.26 respectively. We verified a correlation of the average cumulative mortality rate with water supply by well or spring (r=0.27), water supply by the general network (r=0.3), waste collection (r=0.42), and road urbanization (r=0.29). We found 3,153 severe forms in 2007 with a decrease trend and 205 deaths in 2010, without a trend pattern.

CONCLUSION: There is a need for greater investments in disease control and in the quality of information, especially in the record of severe forms, considering that, due to the pathophysiology of the disease, death only occurs when the individual develops the chronic form, and its notification on the Notifiable Diseases Information System is imperative.}, } @article {pmid36629614, year = {2023}, author = {Batista, JFC and Oliveira, MR and Pereira, DLM and Matos, MLSDS and Souza, IT and Menezes, MO}, title = {Spatial distribution and temporal trends of AIDS in Brazil and regions between 2005 and 2020.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230002}, doi = {10.1590/1980-549720230002}, pmid = {36629614}, issn = {1980-5497}, mesh = {Humans ; Adolescent ; Young Adult ; Adult ; Brazil/epidemiology ; *Acquired Immunodeficiency Syndrome/epidemiology ; Bayes Theorem ; Information Systems ; Incidence ; }, abstract = {OBJECTIVE: To analyze the spatial distribution and the temporal trend of the AIDS incidence rate in Brazil from 2005 to 2020.

METHODS: This is an ecological, temporal, and spatial study on AIDS cases in Brazil. Data from the Notifiable Diseases Information System were stratified by year of diagnosis, region of the country/municipalities of residence, and age group (over 13 years). Incidence rates were calculated for temporal estimation using the Joinpoint model, as well as Spatial Empirical Bayes (SEB) for spatial distribution, using the Kernel density estimator.

RESULTS: The incidence rate in Brazil, in 2020, was 17.69 cases per 100 thousand inhabitants. The general trend (2005-2020) was decrease in Brazil (Annual Percent Change - APC=-2.0%), in the Southeast (APC=-4.4%) and South (APC=-3.0%) regions. The North (APC=2.3%) showed an increase trend, whereas the Southeast and Midwest regions were stationary (p>0.05). Brazil, Southeast, South, and Midwest regions showed a decrease trend in most age groups. The Northeast and North regions showed an increase in the age groups of 13-29 years and 13-24 years, respectively. The Kernel estimator showed clusters with SEB above 30/10 thousand inhabitants in the states of Paraíba, Sergipe, Alagoas, Pernambuco, São Paulo, Minas Gerais, Pará, Rio Grande do Sul, and Santa Catarina.

CONCLUSION: Brazil, the Southeast, and South regions showed a decrease in the incidence rate, whereas the North region increased and the Northeast and Midwest regions were stationary. The Southeast, South, and Northeast regions presented the largest clusters of SEB.}, } @article {pmid35615290, year = {2022}, author = {Adhikari, JN and Bhattarai, BP and Rokaya, MB and Thapa, TB}, title = {Land use/land cover changes in the central part of the Chitwan Annapurna Landscape, Nepal.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13435}, pmid = {35615290}, issn = {2167-8359}, mesh = {*Conservation of Natural Resources ; Nepal ; *Environmental Monitoring/methods ; Geographic Information Systems ; Remote Sensing Technology ; }, abstract = {BACKGROUND: Land use/land cover assessment and monitoring of the land cover dynamics are essential to know the ecological, physical and anthropogenic processes in the landscape. Previous studies have indicated changes in the landscape of mid-hills of Nepal in the past few decades. But there is a lack of study in the Chitwan Annapurna Landscape; hence, this study was carried out to fill in study gap that existed in the area.

METHODS: This study evaluates land use/land cover dynamics between 2000 to 2020 in the central part of the Chitwan Annapurna Landscape, Nepal by using Landsat images. The Landsat images were classified into eight different classes using remote sensing and geographic information system (GIS). The accuracy assessment of classified images was evaluated by calculating actual accuracy, producer's accuracy, user's accuracy and kappa coefficient based on the ground-truthing points for 2020 and Google Earth and topographic maps for images of 2010 and 2000.

RESULTS: The results of land use/land cover analysis of Landsat image 2020 showed that the study area was composed of grassland (1.73%), barren area (1.76%), riverine forest (1.93%), water body (1.97%), developed area (4.13%), Sal dominated forest (15.4%), cropland (28.13%) and mixed forest (44.95%). The results of land cover change between 2000 to 2020 indicated an overall increase in Sal dominated forest (7.6%), developed area (31.34%), mixed forest (37.46%) and decrease in riverine forest (11.29%), barren area (20.03%), croplands (29.87%) and grasslands (49.71%). The classification of the images of 2000, 2010 and 2020 had 81%, 81.6% and 84.77% overall accuracy, respectively. This finding can be used as a baseline information for the development of a proper management plan to protect wildlife habitats and forecasting possible future changes, if needed.}, } @article {pmid35833012, year = {2022}, author = {Ramirez-Delgado, D and Cicala, F and Gonzalez-Sanchez, RA and Avalos-Tellez, R and Solana-Arellano, E and Licea-Navarro, A}, title = {Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13235}, pmid = {35833012}, issn = {2167-8359}, mesh = {Animals ; *Sea Lions/genetics ; RNA, Ribosomal, 16S/genetics ; Mexico ; Bacteria/genetics ; Computational Biology ; }, abstract = {BACKGROUND: The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.

METHODS: We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.

RESULTS: As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.}, } @article {pmid35791366, year = {2022}, author = {Zheng, C and Yang, X and Liu, Z and Liu, K and Huang, Y}, title = {Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13239}, pmid = {35791366}, issn = {2167-8359}, mesh = {*Soil/chemistry ; *Agriculture ; Geographic Information Systems ; Nutrients ; Phosphorus ; Nitrogen/analysis ; }, abstract = {It is of great significance to promote the quantitative research of soil science and the implementation of precision agriculture. On this basis, taking Xuwen County as the research object, this paper comprehensively analyzed the soil characteristics of cultivated land in Xuwen County and clarify the soil nutrient content and spatial distribution characteristics of cultivated land in Xuwen County, this paper comprehensively applied the methods of geostatistics, geographic information system (GIS) and fuzzy mathematics, and referred to the cultivated land quality grade standard (GB/T 33469-2016), to analyze the soil characteristics and evaluate the soil fertility of this region. The results show that the optimal interpolation model of soil pH and available phosphorus (AP) is a Gaussian model, and the optimal interpolation model of soil organic matter (SOM), available nitrogen (AN) and available potassium (AK) is a J-Bessel model. In addition, the spatial correlation of AK is weak, whereas pH, SOM, AN and AP show moderate spatial correlation. The proportion of excellent, good, average, medium and poor comprehensive fertility index are 26.00%, 32.67%, 19.33%, 19.00% and 3.00%, respectively. The overall level of soil fertility in Xuwen County is above the average, and the fertility quality presents an obvious trend of high in the South and low in the North. Areas that above average fertility are mainly distributed in Maichen Town, Qujie Town, Nanshan Town and Chengbei Town. The results can provide theoretical basis for improving the utilization rate of chemical fertilizer, fine management of cultivated land and ecological environment in this region, which can help in decision-making of precision fertilization.}, } @article {pmid36416261, year = {2023}, author = {Guo, S and Xu, Z and Dong, X and Hu, D and Jiang, Y and Wang, Q and Zhang, J and Zhou, Q and Liu, S and Song, W}, title = {GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D964-D968}, pmid = {36416261}, issn = {1362-4962}, mesh = {Humans ; RNA-Seq/methods ; Cell Line ; *Databases, Genetic ; *Software ; }, abstract = {Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.}, } @article {pmid36399502, year = {2023}, author = {Camargo, AP and Nayfach, S and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Ritter, SJ and Reddy, TBK and Mukherjee, S and Schulz, F and Call, L and Neches, RY and Woyke, T and Ivanova, NN and Eloe-Fadrosh, EA and Kyrpides, NC and Roux, S}, title = {IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D733-D743}, pmid = {36399502}, issn = {1362-4962}, mesh = {*Metadata ; Software ; Databases, Genetic ; Genome, Viral ; Metagenomics ; *Virtual Reality ; }, abstract = {Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.}, } @article {pmid36305818, year = {2023}, author = {Chen, Y and Zhang, X and Peng, X and Jin, Y and Ding, P and Xiao, J and Li, C and Wang, F and Chang, A and Yue, Q and Pu, M and Chen, P and Shen, J and Li, M and Jia, T and Wang, H and Huang, L and Guo, G and Zhang, W and Liu, H and Wang, X and Chen, D}, title = {SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1150-D1159}, pmid = {36305818}, issn = {1362-4962}, mesh = {Databases, Factual ; *Single-Cell Analysis ; }, abstract = {It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http://8.142.154.29 or http://speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The 'Pan' module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the 'Evo', 'Devo', and 'Diz' modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The 'C2C', 'G2G' and 'S2S' modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The 'sSearch', 'sMarker', 'sUp', and 'sDown' modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules ('HOME' and 'HELP') offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.}, } @article {pmid36617091, year = {2023}, author = {Abdallah, M and Joung, BG and Lee, WJ and Mousoulis, C and Raghunathan, N and Shakouri, A and Sutherland, JW and Bagchi, S}, title = {Anomaly Detection and Inter-Sensor Transfer Learning on Smart Manufacturing Datasets.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {1}, pages = {}, pmid = {36617091}, issn = {1424-8220}, mesh = {*Commerce ; Databases, Factual ; Time Factors ; *Machine Learning ; }, abstract = {Smart manufacturing systems are considered the next generation of manufacturing applications. One important goal of the smart manufacturing system is to rapidly detect and anticipate failures to reduce maintenance cost and minimize machine downtime. This often boils down to detecting anomalies within the sensor data acquired from the system which has different characteristics with respect to the operating point of the environment or machines, such as, the RPM of the motor. In this paper, we analyze four datasets from sensors deployed in manufacturing testbeds. We detect the level of defect for each sensor data leveraging deep learning techniques. We also evaluate the performance of several traditional and ML-based forecasting models for predicting the time series of sensor data. We show that careful selection of training data by aggregating multiple predictive RPM values is beneficial. Then, considering the sparse data from one kind of sensor, we perform transfer learning from a high data rate sensor to perform defect type classification. We release our manufacturing database corpus (4 datasets) and codes for anomaly detection and defect type classification for the community to build on it. Taken together, we show that predictive failure classification can be achieved, paving the way for predictive maintenance.}, } @article {pmid36612401, year = {2022}, author = {Liu, F and Sun, D and Zhang, Y and Hong, S and Wang, M and Dong, J and Yan, C and Yang, Q}, title = {Tourist Landscape Preferences in a Historic Block Based on Spatiotemporal Big Data-A Case Study of Fuzhou, China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, pmid = {36612401}, issn = {1660-4601}, mesh = {*Big Data ; Surveys and Questionnaires ; China ; *Sustainable Development ; Hot Temperature ; }, abstract = {Historic blocks are valuable architectural and landscape heritage, and it is important to explore the distribution characteristics of tourists to historic blocks and their landscape preferences to realize the scientific construction and conservation of historic blocks and promote their sustainable development. At present, few studies combine the analysis of tourist distribution characteristics with landscape preferences. This study takes the historic block of Three Lanes and Seven Alleys in Fuzhou as an example, combines field research and questionnaires to construct a landscape preference evaluation indicator system for the historic block, measures the distribution characteristics of tourists in the block through the heat value of tourist flow obtained from the Tencent regional heat map, and analyses the influence of landscape preference indicators on the heat value of tourist flow in the block through stepwise multiple linear regression. The research shows that: (1) the spatial and temporal variation in the heat value of tourist flow tends to be consistent throughout the block, from 7 a.m. to 6 p.m., showing a "rising, slightly fluctuating and then stabilizing" state, both on weekdays and on weekends. (2) The factors influencing the heat value of tourist flow in the different spatial samples are various, with commercial atmosphere, plant landscape, accessibility of the road space, architecture, and the surrounding environment having a significant impact on the heat value of tourist flow. Based on the analysis of the landscape preferences of tourists in the historic block, a landscape optimization strategy is proposed to provide a reference for the management and construction of the block.}, } @article {pmid36384190, year = {2023}, author = {Liu, H and Wu, M and Gao, H and Gao, J and Wang, S}, title = {Application of [15]N tracing and bioinformatics for estimating microbial-mediated nitrogen cycle processes in oil-contaminated soils.}, journal = {Environmental research}, volume = {217}, number = {}, pages = {114799}, doi = {10.1016/j.envres.2022.114799}, pmid = {36384190}, issn = {1096-0953}, mesh = {Nitrogen Cycle ; Nitrogen/analysis ; Soil/chemistry ; *Microbiota ; Soil Microbiology ; Computational Biology ; *Soil Pollutants/analysis ; }, abstract = {Crude oil pollution can profoundly alter the nitrogen (N) cycle in the soil. Here, a 30-day incubation with [15]N tracer approach was performed to assess the impacts of crude oil concentrations (medium: 10,000 mg kg[-1]; heavy: 50,000 mg kg[-1]) on soil N cycling based on a numerical model. Results showed that crude oil pollution significantly increased the gross N-transformation rates, but the rates of oxidation of recalcitrant organic N, the immbolization of NO3[-] and the adsorption of NH4[+] changed differently as a function of hydrocarbon concentrations. There was no significant difference of the oxidation rate of recalcitrant organic N between the medium and heavy oil-contaminated soils (medium: 0.1149 mmol N kg[-1] d[-1]; heavy: 0.1299 mmol N kg[-1] d[-1]), but the rates of NO3[-] immobilization (0.1135 mmol N kg[-1] d[-1]) and NH4[+] adsorption were the highest (0.1148 mmol N kg[-1] d[-1]) in the moderately oil-contaminated soils than those in the heavy polluted soil (0.0849 mmol N kg[-1] d[-1] and 0.0034 mmol N kg[-1] d[-1], respectively). The NO3[-] immobilization rate was 2.5-fold higher than its reduction rate, indicating that NO3[-] immobilization played a more important role during the process of NO3[-] transformation. Microbial community structure analysis indicated that phyla of Actinobacteria and Ascomycota respectively promoted the immobilization of NO3[-] to recalcitrant organic N and the reduction of NO3[-] to NH4[+]. The genus of Aspergillus was related to net NH4[+] production, and the genera of Penicillium and Acremonium were responsible for oxidation of recalcitrant organic N to NO3[-].}, } @article {pmid35186498, year = {2022}, author = {Reijnders, MJMF}, title = {Wei2GO: weighted sequence similarity-based protein function prediction.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12931}, pmid = {35186498}, issn = {2167-8359}, mesh = {*Software ; *Algorithms ; Molecular Sequence Annotation ; Proteins/genetics ; Databases, Protein ; }, abstract = {BACKGROUND: Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.

METHODS: This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.

RESULTS: Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes.

AVAILABILITY: Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.}, } @article {pmid36620398, year = {2023}, author = {Gries, C and Hanson, PC and O'Brien, M and Servilla, M and Vanderbilt, K and Waide, R}, title = {The Environmental Data Initiative: Connecting the past to the future through data reuse.}, journal = {Ecology and evolution}, volume = {13}, number = {1}, pages = {e9592}, pmid = {36620398}, issn = {2045-7758}, abstract = {The Environmental Data Initiative (EDI) is a trustworthy, stable data repository, and data management support organization for the environmental scientist. In a bottom-up community process, EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. Almost ten years since going into production, we analyze metadata to provide a general description of EDI's collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.}, } @article {pmid36618211, year = {2022}, author = {Krishnan, RA and Ravindran, RM and Vincy, VS and Arun, P and Shinu, KS and Jithesh, V and Varma, RP}, title = {Analysis of daily COVID-19 death bulletin data during the first two waves of the COVID-19 pandemic in Thiruvananthapuram district, Kerala, India.}, journal = {Journal of family medicine and primary care}, volume = {11}, number = {10}, pages = {6190-6196}, pmid = {36618211}, issn = {2249-4863}, abstract = {CONTEXT: Coronavirus disease 2019 (COVID-19) mortality trends can help discern the pattern of outbreak evolution and systemic responses.

AIM: This study aimed to explore patterns of COVID-19 deaths in Thiruvananthapuram district from 31 March 2020 to 31 December 2021.

SETTING AND DESIGN: Secondary data analysis of COVID-19 deaths in Thiruvananthapuram district was performed.

MATERIALS AND METHODS: Mortality data were obtained from the district COVID-19 control room, and deaths in the first and second waves of COVID-19 were compared.

STATISTICAL ANALYSIS: We summarised data as proportions and medians with the inter-quartile range (IQR) and performed Chi-square tests to make comparisons wherever applicable.

RESULTS: As on 31 December 2021, 4587 COVID-19 deaths were reported in Thiruvananthapuram district, with a case fatality rate of 0.91%. We observed high mortality among older persons (66.7%) and men (56.6%). The leading cause of death was bronchopneumonia (60.6%). The majority (88.5%) had co-morbidities, commonly diabetes mellitus (54.9%). The median interval from diagnosis to hospitalisation was 4 days (IQR 2-7), and that from hospitalisation to death was 2 days (IQR 0-6). The deaths reported during the second wave were four times higher than those of the first wave with a higher proportion of deaths in the absence of co-morbidities (p < 0.001). The majority of the deceased were unvaccinated. Ecological analysis with vaccine coverage data indicated 5.4 times higher mortality among unvaccinated than those who received two vaccine doses.

CONCLUSIONS: The presence of co-morbidities, an unvaccinated status, and delay in hospitalisation were important reasons for COVID-19 deaths. Primary level health providers can potentially help sustaining vaccination, expeditious referral, and monitoring of COVID-19 patients.}, } @article {pmid36613120, year = {2023}, author = {Qin, J and Ma, M and Shi, J and Ma, S and Wu, B and Su, X}, title = {The Time-Lag Effect of Climate Factors on the Forest Enhanced Vegetation Index for Subtropical Humid Areas in China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010799}, pmid = {36613120}, issn = {1660-4601}, abstract = {Forests represent the greatest carbon reservoir in terrestrial ecosystems. Climate change drives the changes in forest vegetation growth, which in turn influences carbon sequestration capability. Exploring the dynamic response of forest vegetation to climate change is thus one of the most important scientific questions to be addressed in the precise monitoring of forest resources. This paper explores the relationship between climate factors and vegetation growth in typical forest ecosystems in China from 2007 to 2019 based on long-term meteorological monitoring data from six forest field stations in different subtropical ecological zones in China. The time-varying parameter vector autoregressive model (TVP-VAR) was used to analyze the temporal and spatial differences of the time-lag effects of climate factors, and the impact of climate change on vegetation was predicted. The enhanced vegetation index (EVI) was used to measure vegetation growth. Monthly meteorological observations and solar radiation data, including precipitation, air temperature, relative humidity, and photosynthetic effective radiation, were provided by the resource sharing service platform of the national ecological research data center. It was revealed that the time-lag effect of climate factors on the EVI vanished after a half year, and the lag accumulation tended to be steady over time. The TVP-VAR model was found to be more suitable than the vector autoregressive model (VAR). The predicted EVI values using the TVP-VAR model were close to the true values with the root mean squares error (RMSE) < 0.05. On average, each site improved its prediction accuracy by 14.81%. Therefore, the TVP-VAR model can be used to analyze the relationship of climate factors and forest EVI as well as the time-lag effect of climate factors on vegetation growth in subtropical China. The results can be used to improve the predictability of the EVI for forests and to encourage the development of intensive forest management.}, } @article {pmid36612902, year = {2022}, author = {Vlăduțu, DE and Ionescu, M and Mercuț, R and Noveri, L and Lăzărescu, G and Popescu, SM and Scrieciu, M and Manolea, HO and Iacov Crăițoiu, MM and Ionescu, AG and Mercuț, V}, title = {Ecological Momentary Assessment of Masseter Muscle Activity in Patients with Bruxism.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010581}, pmid = {36612902}, issn = {1660-4601}, abstract = {According to the International Bruxism Consensus, bruxism refers to the activity of the masticatory muscles reflecting contraction disorders, regardless of whether it is during sleep (SB) or an awake (AB) state. The objective of the present study was to evaluate the activity of the masseter muscle by surface electromyographic (sEMG) recordings. This study was performed on 20 participants with self-reported "possible bruxism" (study group) and 20 participants with no self-reported bruxism (control group); all participants underwent an evaluation of the masseter muscle activity using the dia-BRUXO device, which provides numerical parameters regarding sEMG (the total duration and the type of bruxism specific events, the effort made by the masticatory muscles during the recording period, and the personal bruxism index of each participant). Participants from the study group presented more clenching events during AB, three times more frequent than the control group (p = 0.002, Mann-Whitney U test); for SB, the frequency of clenching and grinding events was comparable within the study group, being more frequent than for the control group; the mean value of the effort index was higher for AB (1.177%) than SB (0.470%) and the same for the duration index, with a mean value of 2.788% for AB and 1.054% for SB. All participants from the control group presented reduced values for all acquired parameters. Overall, the personal bruxism index in AB was approximately four times higher for the study group (2.251%) compared to the control group (0.585%) (p < 0.005, Mann-Whitney U test). Similar values were obtained for SB. All participants with "possible bruxism" from the study group presented a higher activity of the masseter muscle, which is specific for bruxism, thus being defined as "definite bruxism".}, } @article {pmid36612815, year = {2022}, author = {Yang, X and Lei, S and Shi, Y and Wang, W}, title = {Effects of Ground Subsidence on Vegetation Chlorophyll Content in Semi-Arid Mining Area: From Leaf Scale to Canopy Scale.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010493}, pmid = {36612815}, issn = {1660-4601}, abstract = {Ground subsidence is the main cause of vegetation degradation in mining areas. It is of great significance to study the effects of ground subsidence on vegetation. At present, few studies have analyzed the effects of ground subsidence on vegetation from different scales. However, the conclusions on different scales may differ. In this experiment, chlorophyll content was used as an indicator of vegetation degradation. We conducted a long-term field survey in the Lijiahao coalfield in China. Based on field survey data and remote sensing images, we analyzed the effects of ground subsidence on chlorophyll content from two scales (leaf scale and canopy scale) and summarized the similarities and differences. We found that, regardless of leaf scale or canopy scale, the effects of subsidence on chlorophyll content have the following three characteristics: (1) mining had the least effect on chlorophyll content in the neutral area, followed by the compression area, and the greatest effect on chlorophyll content in the extension area; (2) subsidence had a slight effect on chlorophyll content of Caragana korshins, but a serious effect on chlorophyll content of Stipa baicalensis; (3) chlorophyll content was not immediately affected when the ground sank. It was the cumulative subsidence that affects chlorophyll content. The difference between leaf scale and canopy scale was that the chlorophyll content at canopy scale is more affected by mining. This means that when assessing vegetation degradation, the results obtained by remote sensing were more severe than those measured in the field. We believe that this is because the canopy chlorophyll content obtained by remote sensing is also affected by the plant canopy structure. We recommend that mining and ecological restoration should be carried out concurrently, and that ground fissures should be taken as the focus of ecological restoration. In addition, Caragana korshins ought to be widely planted. Most importantly, managers should assess the effects of ground subsidence on vegetation on different scales. However, managers need to be aware of differences at different scales.}, } @article {pmid36612520, year = {2022}, author = {Zhou, Z and Zhang, Z and Zhang, W and Luo, J and Zhang, K and Cao, Z and Wang, Z}, title = {The Impact of Residences and Roads on Wind Erosion in a Temperate Grassland Ecosystem: A Spatially Oriented Perspective.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010198}, pmid = {36612520}, issn = {1660-4601}, abstract = {The existence of residences and roads is an important way in which human activity affects wind erosion in arid and semiarid environments. Studies assessing the impact of these elements on wind erosion have only focused on limited plots, and their threat of erosion to the surrounding environment has been ignored by many studies. This study was based on spatially overlayed analysis of independent wind erosion distribution simulated by the revised wind erosion equation (RWEQ) and remote-sensing-image-derived residence and road distribution data. Wind erosion at different distances from residences and roads was quantified at the landscape scale of a typical temperate grassland ecosystem, explicitly demonstrating the crucial impacts of both elements on wind erosion. The results showed that wind erosion weakened as the distance from residences and roads increased due to the priority pathways of human activities, and the wind erosion around the residence was more severe than around the road. Human activities in the buffer zones 0-200 m from the residences most frequently caused severe wind erosion, with a wind soil loss of 25 t ha[-1] yr[-1] and a wind soil loss of approximately 5.25 t ha[-1] yr[-1] for 0-60 m from the roads. The characteristics of wind erosion variation in the buffer zones were also affected by residence size and the environments in which the residences were located. The variation in wind erosion was closely related to the road levels. Human activities intensified wind erosion mainly by affecting the soil and vegetation around residences and roads. Ecological management should not be limited to residences and roads but should also protect the surrounding environments. The findings of this study are aimed towards a spatial perspective that can help implement rational and effective environmental management measures for the sustainability of wind-eroded ecosystems.}, } @article {pmid36607160, year = {2023}, author = {Van Sundert, K and Leuzinger, S and Bader, MK and Chang, SX and De Kauwe, MG and Dukes, JS and Langley, JA and Ma, Z and Mariën, B and Reynaert, S and Ru, J and Song, J and Stocker, B and Terrer, C and Thoresen, J and Vanuytrecht, E and Wan, S and Yue, K and Vicca, S}, title = {When things get MESI: the Manipulation Experiments Synthesis Initiative - a coordinated effort to synthesize terrestrial global change experiments.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16585}, pmid = {36607160}, issn = {1365-2486}, abstract = {Responses of the terrestrial biosphere to rapidly changing environmental conditions are a major source of uncertainty in climate projections. In an effort to reduce this uncertainty, a wide range of global change experiments have been conducted that mimic future conditions in terrestrial ecosystems, manipulating CO2 , temperature, nutrient and water availability. Syntheses of results across experiments provide a more general sense of ecosystem responses to global change, and help to discern the influence of background conditions such as climate and vegetation type in determining global change responses. Several independent syntheses of published data have yielded distinct databases for specific objectives. Such parallel, uncoordinated initiatives carry the risk of producing redundant data collection efforts and have led to contrasting outcomes without clarifying the underlying reason for divergence. These problems could be avoided by creating a publicly available, updatable, curated database. Here, we report on a global effort to collect and curate 57,089 treatment responses across 3,644 manipulation experiments at 1,145 sites, simulating elevated CO2 , warming, nutrient addition and precipitation changes. In the resulting Manipulation Experiments Synthesis Initiative (MESI) database, effects of experimental global change drivers on carbon and nutrient cycles are included, as well as ancillary data such as background climate, vegetation type, treatment magnitude, duration, and, unique to our database, measured soil properties. Our analysis of the database indicates that most experiments are short-term (one or few growing seasons), conducted in the USA, Europe or China, and that the most abundantly reported variable is aboveground biomass. We provide the most comprehensive multifactor global change database to date, enabling the research community to tackle open research questions, vital to global policymaking. The MESI database, freely accessible at doi.org/10.5281/zenodo.7153253, opens new avenues for model evaluation and synthesis-based understanding of how global change affects terrestrial biomes. We welcome contributions to the database on GitHub.}, } @article {pmid35900623, year = {2023}, author = {Sharma, N and Kaushal, A and Yousuf, A and Sood, A and Kaur, S and Sharda, R}, title = {Geospatial technology for assessment of soil erosion and prioritization of watersheds using RUSLE model for lower Sutlej sub-basin of Punjab, India.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {1}, pages = {515-531}, pmid = {35900623}, issn = {1614-7499}, mesh = {Humans ; *Soil ; *Soil Erosion ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; Geographic Information Systems ; India ; Technology ; }, abstract = {Erosion of soil by water coupled with human activities is considered as one of the most serious agents of land degradation, posing severe threat to agricultural productivity, soil health, water quality, and ecological setup. The assessment of soil erosion and recognition of problematic watersheds are pre-requisite for management of erosion hazards. In the present study, Revised Universal Soil Loss Equation (RUSLE) integrated with remote sensing (RS) and geographic information system (GIS) has been used to assess the soil erosion in lower Sutlej River basin of Punjab, India, and prioritize the watersheds for implementation of land and water conservation measures. The total basin area was about 8577 km[2] which was divided into 14 sub-watersheds with the area ranging from 357.8 to 1354 km[2]. The data on rainfall (IMD gridded data), soil characteristics (FAO soil map), topography (ALOS PALSAR DEM) and land use (ESRI land use and land cover map) were prepared in the form of raster layers and overlaid together to determine the average annual soil loss. The results revealed that the average annual soil loss varied from 1.26 to 25 t ha[-1], whereas total soil loss was estimated to be 2,441,639 tonnes. The spatial distribution map of soil erosion showed that about 94.4% and 4.7% of the total area suffered from very slight erosion (0-5 t ha[-1] year[-1]) and slight erosion (5-10 t ha[-1] year[-1]), respectively, whereas 0.11% (9.38 km[2]) experienced very severe soil loss (> 25 t ha[-1] year[-1]). Based on estimated average annual soil loss of sub-watersheds, WS8 was assigned the highest priority for implementation of soil and water conservation measures (323.5 t ha[-1] year[-1]), followed by WS9 (303.8 t ha[-1] year[-1]), whereas WS2 was given last priority owing to its lowest value of soil loss (122.02 t ha[-1] year[-1]). The present study urges that conservation strategies should be carried out in accordance with the priority ranking of diverse watersheds. These findings can certainly be used to implement soil conservation plans and management practices in order to diminish soil loss in the river basin.}, } @article {pmid36604610, year = {2023}, author = {Prager, M and Lundin, D and Ronquist, F and Andersson, AF}, title = {ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {6}, pmid = {36604610}, issn = {1471-2105}, abstract = {BACKGROUND: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.

RESULTS: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure.

CONCLUSION: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.}, } @article {pmid36602254, year = {2023}, author = {Koenig, CJ and Vasquez, TS and Peterson, EB and Wollney, EN and Bylund, CL and Ho, EY}, title = {Mapping Uncharted Terrain: A Systematic Review of Complementary and Integrative Health Communication Using Observational Data in Biomedical Settings.}, journal = {Health communication}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/10410236.2022.2140080}, pmid = {36602254}, issn = {1532-7027}, abstract = {Complementary and integrative health (CIH) use is diverse and highly prevalent worldwide. Prior research of CIH communication in biomedical encounters address safety, efficacy, symptom management, and overall wellness. Observational methods are rarely used to study CIH communication and avoid recall bias, preserve ecological validity, and contextualize situated clinical communication. Following PRISMA guidelines, we systematically reviewed studies at the intersection of social scientific observational research and findings about CIH communication between clinicians, patients, and caregivers in biomedical settings. We identified international, peer-reviewed publications from seven databases between January 2010 and December 2020. Titles and abstracts were first screened for inclusion, then full studies were coded using explicit criteria. We used a standard checklist was modified to assess article quality. Ten of 11,793 studies examined CIH communication using observational methods for CIH communication in biomedical settings. Studies used a range of observational techniques, including participant and non-participant observation, which includes digital audio or video recordings. Results generated two broad sets of findings, one focused on methodological insights and another on CIH communication. Despite methodological and topic similarities, included studies addressed CIH communication as a process and as proximal and intermediate health outcomes. We recommend how observational studies of CIH communication can better highlight relationships between communication processes and health outcomes. Current research using observational methods offers an incomplete picture of CIH communication in biomedical settings. Future studies should standardize how observational techniques are reported to enhance consistency and comparability within and across biomedical settings to improve comparability.}, } @article {pmid36601075, year = {2022}, author = {Leal, JSV and Fogal, AS and Meireles, AL and Cardoso, LO and Machado, ÍE and de Menezes, MC}, title = {Health economic impacts associated with the consumption of sugar-sweetened beverages in Brazil.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1088051}, pmid = {36601075}, issn = {2296-861X}, abstract = {INTRODUCTION: The consumption of sugar-sweetened beverages (SSBs) is among the main risk factors for non-communicable diseases (NCDs). This study aimed to estimate the financial costs of hospitalizations and procedures of high and medium complexity for NCDs attributable to the consumption of SSBs in the Brazilian Unified Health System (SUS) in 2019.

METHODS: This ecological study used data from the Global Burden of Disease (GBD) 2019 and the Department of Informatics of the Unified Health System (DATASUS). The attributable costs were estimated from the population-attributable fraction (PAF) and the costs in the treatment of chronic diseases [type 2 diabetes mellitus and ischemic heart disease (IHD)], stratified by sex, age group, level of complexity of treatment, and federative units.

RESULTS: In 2019, in Brazil, US$ 14,116,240.55 were the costs of hospitalizations and procedures of high and medium complexity in the treatment of NCDs attributable to the consumption of SSBs. These values were higher in males (US$ 8,469,265.14) and the southeast and southern regions, mainly in the state of São Paulo. However, when evaluating these results at a rate per 10,000 inhabitants, it was observed that the states of Paraná, Tocantins, and Roraima had higher costs per 10,000 inhabitants. Regarding the age groups, higher costs were observed in the older age groups.

CONCLUSION: This study revealed the high financial impact of the NCDs treatment attributed to the consumption of SSBs in Brazil and the variability among Brazilian macro-regions. The results demonstrate the urgency and need for the expansion of policies to reduce the consumption of SSBs in Brazil with strategies that consider regional particularities.}, } @article {pmid36599936, year = {2023}, author = {Juan, D and Santpere, G and Kelley, JL and Cornejo, OE and Marques-Bonet, T}, title = {Current advances in primate genomics: novel approaches for understanding evolution and disease.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {36599936}, issn = {1471-0064}, abstract = {Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.}, } @article {pmid36107138, year = {2023}, author = {Bassing, SB and DeVivo, M and Ganz, TR and Kertson, BN and Prugh, LR and Roussin, T and Satterfield, L and Windell, RM and Wirsing, AJ and Gardner, B}, title = {Are we telling the same story? Comparing inferences made from camera trap and telemetry data for wildlife monitoring.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {33}, number = {1}, pages = {e2745}, doi = {10.1002/eap.2745}, pmid = {36107138}, issn = {1051-0761}, mesh = {Animals ; *Animals, Wild ; *Ecosystem ; Geographic Information Systems ; Surveys and Questionnaires ; Telemetry ; }, abstract = {Estimating habitat and spatial associations for wildlife is common across ecological studies and it is well known that individual traits can drive population dynamics and vice versa. Thus, it is commonly assumed that individual- and population-level data should represent the same underlying processes, but few studies have directly compared contemporaneous data representing these different perspectives. We evaluated the circumstances under which data collected from Lagrangian (individual-level) and Eulerian (population-level) perspectives could yield comparable inference to understand how scalable information is from the individual to the population. We used Global Positioning System (GPS) collar (Lagrangian) and camera trap (Eulerian) data for seven species collected simultaneously in eastern Washington (2018-2020) to compare inferences made from different survey perspectives. We fit the respective data streams to resource selection functions (RSFs) and occupancy models and compared estimated habitat- and space-use patterns for each species. Although previous studies have considered whether individual- and population-level data generated comparable information, ours is the first to make this comparison for multiple species simultaneously and to specifically ask whether inferences from the two perspectives differed depending on the focal species. We found general agreement between the predicted spatial distributions for most paired analyses, although specific habitat relationships differed. We hypothesize the discrepancies arose due to differences in statistical power associated with camera and GPS-collar sampling, as well as spatial mismatches in the data. Our research suggests data collected from individual-based sampling methods can capture coarse population-wide patterns for a diversity of species, but results differ when interpreting specific wildlife-habitat relationships.}, } @article {pmid36239541, year = {2023}, author = {Keck, F and Altermatt, F}, title = {Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb.}, journal = {Molecular ecology resources}, volume = {23}, number = {2}, pages = {511-518}, doi = {10.1111/1755-0998.13723}, pmid = {36239541}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Biodiversity ; Gene Library ; Databases, Nucleic Acid ; }, abstract = {DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.}, } @article {pmid36595968, year = {2018}, author = {Martínková, N and Pikula, J and Zukal, J and Kovacova, V and Bandouchova, H and Bartonička, T and Botvinkin, AD and Brichta, J and Dundarova, H and Kokurewicz, T and Irwin, NR and Linhart, P and Orlov, OL and Piacek, V and Škrabánek, P and Tiunov, MP and Zahradníková, A}, title = {Hibernation temperature-dependent Pseudogymnoascus destructans infection intensity in Palearctic bats.}, journal = {Virulence}, volume = {9}, number = {1}, pages = {1734-1750}, doi = {10.1080/21505594.2018.1548685}, pmid = {36595968}, issn = {2150-5608}, abstract = {White-nose syndrome (WNS) is a fungal disease caused by Pseudogymnoascus destructans that is devastating to Nearctic bat populations but tolerated by Palearctic bats. Temperature is a factor known to be important for fungal growth and bat choice of hibernation. Here we investigated the effect of temperature on the pathogenic fungal growth in the wild across the Palearctic. We modelled body surface temperature of bats with respect to fungal infection intensity and disease severity and were able to relate this to the mean annual surface temperature at the site. Bats that hibernated at lower temperatures had less fungal growth and fewer skin lesions on their wings. Contrary to expectation derived from laboratory P. destructans culture experiments, natural infection intensity peaked between 5 and 6°C and decreased at warmer hibernating temperature. We made predictive maps based on bat species distributions, temperature and infection intensity and disease severity data to determine not only where P. destructans will be found but also where the infection will be invasive to bats across the Palearctic. Together these data highlight the mechanistic model of the interplay between environmental and biological factors, which determine progression in a wildlife disease.}, } @article {pmid36590525, year = {2022}, author = {Prylutskyy, Y and Nozdrenko, D and Gonchar, O and Prylutska, S and Bogutska, K and Franskevych, D and Hromovyk, B and Scharff, P and Ritter, U}, title = {C60 fullerene attenuates muscle force reduction in a rat during fatigue development.}, journal = {Heliyon}, volume = {8}, number = {12}, pages = {e12449}, pmid = {36590525}, issn = {2405-8440}, abstract = {C60 fullerene (C60) as a nanocarbon particle, compatible with biological structures, capable of penetrating through cell membranes and effectively scavenging free radicals, is widely used in biomedicine. A protective effect of C60 on the biomechanics of fast (m. gastrocnemius) and slow (m. soleus) muscle contraction in rats and the pro- and antioxidant balance of muscle tissue during the development of muscle fatigue was studied compared to the same effect of the known antioxidant N-acetylcysteine (NAC). C60 and NAC were administered intraperitoneally at doses of 1 and 150 mg kg[-1], respectively, daily for 5 days and 1 h before the start of the experiment. The following quantitative markers of muscle fatigue were used: the force of muscle contraction, the level of accumulation of secondary products of lipid peroxidation (TBARS) and the oxygen metabolite H2O2, the activity of first-line antioxidant defense enzymes (superoxide dismutase (SOD) and catalase (CAT)), and the condition of the glutathione system (reduced glutathione (GSH) content and the activity of the glutathione peroxidase (GPx) enzyme). The analysis of the muscle contraction force dynamics in rats against the background of induced muscle fatigue showed, that the effect of C60, 1 h after drug administration, was (15-17)% more effective on fast muscles than on slow muscles. A further slight increase in the effect of C60 was revealed after 2 h of drug injection, (7-9)% in the case of m. gastrocnemius and (5-6)% in the case of m. soleus. An increase in the effect of using C60 occurred within 4 days (the difference between 4 and 5 days did not exceed (3-5)%) and exceeded the effect of NAC by (32-34)%. The analysis of biochemical parameters in rat muscle tissues showed that long-term application of C60 contributed to their decrease by (10-30)% and (5-20)% in fast and slow muscles, respectively, on the 5th day of the experiment. At the same time, the protective effect of C60 was higher compared to NAC by (28-44)%. The obtained results indicate the prospect of using C60 as a potential protective nano agent to improve the efficiency of skeletal muscle function by modifying the reactive oxygen species-dependent mechanisms that play an important role in the processes of muscle fatigue development.}, } @article {pmid36581858, year = {2022}, author = {Huang, Y and Lu, W and Zeng, M and Hu, X and Su, Z and Liu, Y and Liu, Z and Yuan, J and Li, L and Zhang, X and Huang, L and Hu, W and Wang, X and Li, S and Zhang, H}, title = {Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {245}, pmid = {36581858}, issn = {2049-2618}, mesh = {Infant, Newborn ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Inflammation ; Bacteria ; *Heart Defects, Congenital ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD.

METHODS: Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis.

RESULTS: Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD.

CONCLUSIONS: We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.}, } @article {pmid36371952, year = {2023}, author = {Zhao, H and Liu, X and Jiang, T and Cai, C and Gu, K and Liu, Y and He, P}, title = {Activated abscisic acid pathway and C4 pathway, inhibited cell cycle progression, responses of Ulva prolifera to short term high temperature elucidated by multi-omics.}, journal = {Marine environmental research}, volume = {183}, number = {}, pages = {105796}, doi = {10.1016/j.marenvres.2022.105796}, pmid = {36371952}, issn = {1879-0291}, mesh = {*Ulva/metabolism ; Temperature ; Abscisic Acid/metabolism ; Multiomics ; Cell Cycle ; Eutrophication ; China ; }, abstract = {The annual outbreak of green tides since 2007 has destroyed coastal waters' ecological environment and caused substantial economic losses. Ulva prolifera, known as the dominant species of green tides, is influenced by temperatures. Omics-based technology was used to analyze U. prolifera under 12 h of treatment at 30 °C in the work. High temperature has the following advantages, e.g., activating the abscisic acid signaling pathway, improving the heat tolerance of U. prolifera, up-regulating metabolites such as glycolipids, glyceroyl, and glutamic acid to maintain the stability and fluidity of cells, and reducing the stimulatory effect of external stress on cells. The key genes and proteins of the tricarboxylic acid cycle, glycolysis, and pentose phosphorylation pathways were inhibited; however, the key enzyme pyruvate phospho-dikinase of the C4 pathway was up-regulated. The C4 pathway was activated in U. prolifera in response to high-temperature stress and may play a key role in photosynthesis. Besides, U. prolifera metabolizing amino acids was active. High temperature inhibited genes and proteins related to DNA replication and cell cycle in the transcriptome and proteome as well as the growth and reproduction of U. prolifera.}, } @article {pmid36576353, year = {2022}, author = {Liu, C and Economo, EP and Guénard, B}, title = {GABI-I: The global ant biodiversity informatics-island database.}, journal = {Ecology}, volume = {}, number = {}, pages = {e3969}, doi = {10.1002/ecy.3969}, pmid = {36576353}, issn = {1939-9170}, abstract = {Island systems are known to harbor disproportionate amounts of geographically restricted biodiversity, but also for experiencing high rates of species loss, ultimately representing critical systems with significant conservation values. Knowledge of the biodiversity value of insular systems remains, however, highly fragmented and incomplete for many groups of organisms, especially insects. This gap limits our understanding of their global significance for biodiversity and inhibits prioritization for future exploration and conservation efforts. Here, we developed a new database introducing current knowledge of ants on 2678 islands globally, based on nominal species, and providing information on their native or exotic status. In total, this database contains 7,010 ant species (44.6% of the known global ant fauna) that have been recorded on islands globally from 449,232 records. In addition, this database identifies 108 large islands (area > 200km2) that have received no ant sampling efforts globally. This new data set provides the most comprehensive understanding of ant diversity and composition on islands globally, opening new opportunities to address questions on a multitude of research questions and fields related to biogeography, ecology, and evolution. This data set also provides a roadmap for future exploration and conservation actions of ants on islands as well as for overall ant diversity, with updates available as new records and taxonomic updates are published. There are no copyright restrictions on this database and users should cite this data paper in publications when using the data. This article is protected by copyright. All rights reserved.}, } @article {pmid36575453, year = {2022}, author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S}, title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {500}, pmid = {36575453}, issn = {1741-7015}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.

METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.

RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.

CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.}, } @article {pmid36572855, year = {2022}, author = {Schwarz, J and Hemmerling, J and Kabisch, N and Galbusera, L and Heinze, M and von Peter, S and Wolff, J}, title = {Equal access to outreach mental health care? Exploring how the place of residence influences the use of intensive home treatment in a rural catchment area in Germany.}, journal = {BMC psychiatry}, volume = {22}, number = {1}, pages = {826}, pmid = {36572855}, issn = {1471-244X}, mesh = {Humans ; *Mental Health ; Ambulatory Care ; *Community Mental Health Services ; Catchment Area, Health ; Germany ; Health Services Accessibility ; }, abstract = {BACKGROUND: Internationally, intensive psychiatric home treatment has been increasingly implemented as a community-based alternative to inpatient admission. Since 2018, the so-called Inpatient Equivalent Home Treatment (IEHT; German: "Stationsäquivalente Behandlung", short: "StäB") has been introduced as a particularly intensive form of home treatment that provides at least one daily treatment contact in the service users' (SU) home environment. Prior research shows that this can be challenging in rural catchment areas. Our paper investigates to which extent the location of the SU home location within the catchment area as well as the distance between the home and the clinic influence the utilisation of inpatient treatment compared to IEHT.

METHOD: Routine data of one psychiatric hospital in the federal state of Brandenburg in Germany were analysed for the observational period 07/2018-06/2021. Two comparison groups were formed: SU receiving inpatient treatment and SU receiving IEHT. The SU places of residence were respectively anonymised and converted into geo-coordinates. A geographic information system (GIS) was used to visualise the places of residence, and car travel distances as well as travel times to the clinic were determined. Spatial analyses were performed to show the differences between comparison groups. In a more in-depth analysis, the proximity of SU residences to each other was examined as an indicator of possible clustering.

RESULTS: During the observational period, the location of 687 inpatient and 140 IEHT unique SU were mapped using the GIS. SU receiving treatment resided predominantly within the catchment area, and this proportion was slightly higher for SU receiving IEHT than for those treated in inpatient setting (95.3% vs. 84.7%). In the catchment area, the geographical distribution of SU place of residence was similar in the two groups. There was a general higher service provision in the more densely populated communities close to Berlin. SU with residence in peripheral communities were mainly treated within the inpatient setting. The mean travel times and distances to the place of residence only differed minimally between the two groups of SU (p > 0.05). The places of residence of SU treated with IEHT were located in greater proximity to each other than those of SU treated in inpatient setting (p < 0.1).

CONCLUSION: In especially peripheral parts of the examined catchment area, it may be more difficult to have access to IEHT rather than to inpatient services. The results raise questions regarding health equity and the planning of health care services and have important implications for the further development of intensive home treatment. Telehealth interventions such as blended-care approaches and an increase of flexibility in treatment intensity, e.g. eliminating the daily visit requirement, could ease the implementation of intensive home treatment especially in rural areas.}, } @article {pmid36572749, year = {2022}, author = {Kon, T and Fukuta, K and Chen, Z and Kon-Nanjo, K and Suzuki, K and Ishikawa, M and Tanaka, H and Burgess, SM and Noguchi, H and Toyoda, A and Omori, Y}, title = {Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1404}, pmid = {36572749}, issn = {2399-3642}, mesh = {Animals ; *Goldfish/genetics ; *Transcriptome ; Genome ; Evolution, Molecular ; Gene Expression Profiling ; }, abstract = {The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.}, } @article {pmid36566315, year = {2022}, author = {Dualib, PM and Fernandes, G and Taddei, CR and Carvalho, CRS and Sparvoli, LG and Bittencourt, C and Silva, IT and Mattar, R and Ferreira, SRG and Dib, SA and de Almeida-Pititto, B}, title = {The gut microbiome of obese postpartum women with and without previous gestational diabetes mellitus and the gut microbiota of their babies.}, journal = {Diabetology & metabolic syndrome}, volume = {14}, number = {1}, pages = {194}, pmid = {36566315}, issn = {1758-5996}, abstract = {BACKGROUND: The incidence of gestational diabetes mellitus (GDM) is increasing worldwide, and has been associated with some changes in the gut microbiota. Studies have shown that the maternal gut microbiota pattern with hyperglycemia can be transmitted to the offspring. The study aimed to evaluate the gut microbiota of obese postpartum women with and without previous GDM and their offspring.

METHODS: We evaluated a total of 84 puerperal women who had (n = 40) or not GDM (n = 44), and their infants were also included. Stool samples were obtained 2-6 months after delivery. The molecular profile of the fecal microbiota was obtained by sequencing V4 region of 16S rRNA gene (Illumina[®] MiSeq).

RESULTS: We found that the gut microbiota structures of the puerperal women and their infants were similar. Stratifying according to the type of delivery, the relative abundance of Victivallis genus was higher in women who had natural delivery. Exposure to exclusive breastfeeding was associated with a greater abundance of Bacteroides and Staphylococcus. The differential abundance test showed correlations to clinical and laboratory parameters. This work showed no difference in the microbiota of obese puerperal women with and without GDM and their offspring. However, breastfeeding contributed to the ecological succession of the intestinal microbiota of the offspring.

CONCLUSION: This work can contribute to understanding the potential effects of GDM and early life events on the gut microbiome of mothers and their offspring and its possible role in metabolism later in life.}, } @article {pmid36557752, year = {2022}, author = {Schalli, M and Inwinkl, SM and Platzer, S and Baumert, R and Reinthaler, FF and Ofner-Kopeinig, P and Haas, D}, title = {Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557752}, issn = {2076-2607}, abstract = {Background microorganism growth on Chromogenic Coliform Agar (CCA) can be challenging. For this reason, a new alternative method with a Cefsulodin/Vancomycin (CV)-supplemented CCA should be developed in this study. CCA supplemented with CV was validated according to ÖNORM EN ISO 16140-4:2021 using water from natural sources in Styria, Austria. Results show that the alternative method using the supplemented CCA has similar values in relation to sensitivity (82.2%), specificity (98.6%) and higher selectivity (59%) compared to the reference method. Repeatability and reproducibility were acceptable for the alternative method and showed similar results with the reference method. The alternative method shows a very low false positive rate and a low false negative rate paired with good performance regarding the inclusion study. The exclusion study shows the advantage of our method by suppressing background microorganisms and facilitating the process of enumeration of Escherichia coli and other coliform bacteria on CCA plates. Aeromonas hydrophila and Pseudomonas aeruginosa growth was inhibited using the supplement. To conclude, the coliform CV selective supplement combined with CCA is an appropriate tool for coliform bacteria detection in water samples.}, } @article {pmid36554991, year = {2022}, author = {Xue, Y and Lin, C and Wang, Y and Liu, W and Wan, F and Zhang, Y and Ji, L}, title = {Predicting Climate Change Effects on the Potential Distribution of Two Invasive Cryptic Species of the Bemisia tabaci Species Complex in China.}, journal = {Insects}, volume = {13}, number = {12}, pages = {}, pmid = {36554991}, issn = {2075-4450}, abstract = {Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) are two invasive cryptic species of the Bemisia tabaci species complex (Hemiptera: Aleyrodidae) that cause serious damage to agricultural and horticultural crops worldwide. To explore the possible impact of climate change on their distribution, the maximum entropy (MaxEnt) model was used to predict the potential distribution ranges of MEAM1 and MED in China under current and four future climate scenarios, using shared socioeconomic pathways (SSPs), namely SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5, over four time periods (2021-2040, 2041-2060, 2061-2080, and 2081-2100). The distribution ranges of MEAM1 and MED were extensive and similar in China under current climatic conditions, while their moderately and highly suitable habitat ranges differed. Under future climate scenarios, the areas of suitable habitat of different levels for MEAM1 and MED were predicted to increase to different degrees. However, the predicted expansion of suitable habitats varied between them, suggesting that these invasive cryptic species respond differently to climate change. Our results illustrate the difference in the effects of climate change on the geographical distribution of different cryptic species of B. tabaci and provide insightful information for further forecasting and managing the two invasive cryptic species in China.}, } @article {pmid36554882, year = {2022}, author = {Deng, F and Yang, Y and Zhao, E and Xu, N and Li, Z and Zheng, P and Han, Y and Gong, J}, title = {Urban Heat Island Intensity Changes in Guangdong-Hong Kong-Macao Greater Bay Area of China Revealed by Downscaling MODIS LST with Deep Learning.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554882}, issn = {1660-4601}, mesh = {Humans ; Macau ; Hong Kong ; Cities ; *Hot Temperature ; Temperature ; *Deep Learning ; China ; Environmental Monitoring/methods ; }, abstract = {The urban heat island (UHI) effect caused by urbanization negatively impacts the ecological environment and human health. It is crucial for urban planning and social development to monitor the urban heat island effect and study its mechanism. Due to spatial and temporal resolution limitations, existing land surface temperature (LST) data obtained from remote sensing data is challenging to meet the long-term fine-scale surface temperature mapping requirement. Given the above situation, this paper introduced the ResNet-based surface temperature downscaling method to make up for the data deficiency and applied it to the study of thermal environment change in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 2000 to 2020. The results showed (1) the ResNet-based surface temperature downscaling method achieves high accuracy (R[2] above 0.85) and is suitable for generating 30 m-resolution surface temperature data from 1 km data; (2) the area of severe heat islands in the GBA continued to increase, increasing by 7.13 times within 20 years; and (3) except for Hong Kong and Macau, the heat island intensity of most cities showed an apparent upward trend, especially the cities with rapid urban expansion such as Guangzhou, Zhongshan, and Foshan. In general, the evolution of the heat island in the GBA diverges from the central urban area to the surrounding areas, with a phenomenon of local aggregation and the area of the intense heat island in the Guangzhou-Foshan metropolitan area is the largest. This study can enrich the downscaling research methods of surface temperature products in complex areas with surface heterogeneity and provide a reference for urban spatial planning in the GBA.}, } @article {pmid36554755, year = {2022}, author = {Chen, D and Xiong, K and Zhang, J}, title = {Progress on the Integrity Protection in the Natural World Heritage Site and Agroforestry Development in the Buffer Zone: An Implications for the World Heritage Karst.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554755}, issn = {1660-4601}, mesh = {*Conservation of Natural Resources ; China ; Databases, Factual ; *Knowledge ; }, abstract = {In the face of increasing development pressure, how to fulfill the obligations under the World Cultural and Natural Heritage Convention and maintain the integrity of the Natural World Heritage Site (NWHS) is a major problem to be solved at present. Agroforestry (AF) development in the buffer zone maintains the integrity of NWHS and promotes sustainable ecological and economic development in the buffer zone. Still, few studies on the knowledge system of integrity protection of NWHS and AF development in the buffer zone research have been conducted. To fill this gap, this study conducts a systematic literature review based on 128 related articles retrieved from the Web of Science (WoS) database and the China National Knowledge Infrastructure (CNKI) database. Firstly, quantitative studies were conducted to analyze the annual numbers, content and study regions of the published literature. Secondly, the main research progress and achievements of integrity protection of WNHS and AF development in the buffer zone are classified and summarized. On this basis, this paper proposed key scientific issues that remain to be addressed in future, as well as exploring the implications for the World Heritage (WH) karst. This study is a scientific reference for the balanced development of NWHS integrity protection and AF in the buffer zone.}, } @article {pmid36554469, year = {2022}, author = {Zhou, T and Zhu, Y and Sun, K and Chen, J and Wang, S and Zhu, H and Wang, X}, title = {Variance Analysis in China's Coal Mine Accident Studies Based on Data Mining.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554469}, issn = {1660-4601}, mesh = {*Accidents, Occupational/prevention & control ; *Coal Mining ; Analysis of Variance ; China ; Coal ; }, abstract = {The risk of coal mine accidents rises significantly with mining depth, making it urgent for accident prevention to be supported by both scientific analysis and advanced technologies. Hence, a comprehensive grasp of the research progress and differences in hotspots of coal mine accidents in China serves as a guide to find the shortcomings of studies in the field, promote the effectiveness of coal mine disaster management, and enhance the prevention and control ability of coal mine accidents. This paper analyzes Chinese and foreign literature based on data mining algorithms (LSI + Apriori), and the findings indicate that: (1) 99% of the available achievements are published in Chinese or English-language journals, with the research history conforming to the stage of Chinese coal industry development, which is characterized by "statistical description, risk evaluation, mechanism research, and intelligent reasoning". (2) Chinese authors are the primary contributors that lead and contribute to the continued development of coal mine accident research in China globally. Over 81% of the authors and over 60% of the new authors annually are from China. (3) The emphasis of the Chinese and English studies is different. Specifically, the Chinese studies focus on the analysis of accident patterns and causes at the macroscale, while the English studies concentrate on the occupational injuries of miners at the small-scale and the mechanism of typical coal mine disasters (gas and coal spontaneous combustion). (4) The research process in Chinese is generally later than that in English due to the joint influence of the target audience, industrial policy, and scientific research evaluation system. After 2018, the Chinese studies focus significantly on AI technology in deep mining regarding accident rules, regional variation analysis, risk monitoring and early warning, as well as knowledge intelligence services, while the hotspots of English studies remain unchanged. Furthermore, both Chinese and English studies around 2019 focus on "public opinion", with Chinese ones focusing on serving the government to guide the correct direction of public opinion while English studies focus on critical research of news authenticity and China's safety strategy.}, } @article {pmid36554342, year = {2022}, author = {Dantas, JDC and Marinho, CDSR and Pinheiro, YT and Silva, RARD}, title = {Temporal Trend of Gestational Syphilis between 2008 and 2018 in Brazil: Association with Socioeconomic and Health Care Factors.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554342}, issn = {1660-4601}, mesh = {Pregnancy ; Female ; Humans ; *Syphilis/epidemiology ; *Pregnancy Complications, Infectious/epidemiology ; *Syphilis, Congenital/epidemiology/prevention & control ; Brazil/epidemiology ; Literacy ; Delivery of Health Care ; Socioeconomic Factors ; }, abstract = {The increased number of cases in recent years has turned syphilis into a global public health problem. In 2020, 115,371 cases of acquired syphilis were reported (detection rate of 54.5 cases/100,000 inhabitants) in Brazil. In that same period, the country notified 61,441 cases of gestational syphilis (detection rate of 21.6 per 1000 live births). The number of syphilis cases points to the need to reinforce surveillance, prevention, and infection control actions, which is a worrying scenario for government organizations. This study aims to describe the temporal trend of gestational syphilis from 2008 to 2018 in Brazilian regions and to associate its detection rate with socioeconomic and health care indicators. We conducted an ecological study of temporal trends using secondary data from the Department of Informatics of the Unified Health System. The temporal trend was analyzed using the Joinpoint Regression program. The annual percent change (APC) and 95% confidence intervals (95%CI) were estimated and tested; statistical significance was assessed using the Monte Carlo permutation test. Correlations were assessed using Pearson's correlation coefficient, and statistical significance was calculated using Pearson's product-moment correlation. The gestational syphilis detection rate increased between 2008 and 2018. The South region showed the greatest trend, whereas the Midwest region presented the lowest trend. The following variables were significantly correlated with the gestational syphilis detection rate: Municipal Human Development Index, illiteracy rate, percentage of primary health care coverage, and proportion of doctors, nurses, and basic health units per inhabitant. Health policies are needed to mitigate social vulnerabilities and strengthen primary health care.}, } @article {pmid36552295, year = {2022}, author = {Sokhansanj, BA and Zhao, Z and Rosen, GL}, title = {Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity.}, journal = {Biology}, volume = {11}, number = {12}, pages = {}, pmid = {36552295}, issn = {2079-7737}, abstract = {Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect COVID-19 disease severity is critical in planning public health responses as the virus continues to evolve. This paper presents a novel computational framework to complement conventional lineage classification and applies it to predict the severe disease potential of viral genetic variation. The transformer-based neural network model architecture has additional layers that provide sample embeddings and sequence-wide attention for interpretation and visualization. First, training a model to predict SARS-CoV-2 taxonomy validates the architecture's interpretability. Second, an interpretable predictive model of disease severity is trained on spike protein sequence and patient metadata from GISAID. Confounding effects of changing patient demographics, increasing vaccination rates, and improving treatment over time are addressed by including demographics and case date as independent input to the neural network model. The resulting model can be interpreted to identify potentially significant virus mutations and proves to be a robust predctive tool. Although trained on sequence data obtained entirely before the availability of empirical data for Omicron, the model can predict the Omicron's reduced risk of severe disease, in accord with epidemiological and experimental data.}, } @article {pmid36547621, year = {2022}, author = {Jamal, QMS and Ahmad, V}, title = {Lysinibacilli: A Biological Factories Intended for Bio-Insecticidal, Bio-Control, and Bioremediation Activities.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {12}, pages = {}, pmid = {36547621}, issn = {2309-608X}, abstract = {Microbes are ubiquitous in the biosphere, and their therapeutic and ecological potential is not much more explored and still needs to be explored more. The bacilli are a heterogeneous group of Gram-negative and Gram-positive bacteria. Lysinibacillus are dominantly found as motile, spore-forming, Gram-positive bacilli belonging to phylum Firmicutes and the family Bacillaceae. Lysinibacillus species initially came into light due to their insecticidal and larvicidal properties. Bacillus thuringiensis, a well-known insecticidal Lysinibacillus, can control many insect vectors, including a malarial vector and another, a Plasmodium vector that transmits infectious microbes in humans. Now its potential in the environment as a piece of green machinery for remediation of heavy metal is used. Moreover, some species of Lysinibacillus have antimicrobial potential due to the bacteriocin, peptide antibiotics, and other therapeutic molecules. Thus, this review will explore the biological disease control abilities, food preservative, therapeutic, plant growth-promoting, bioremediation, and entomopathogenic potentials of the genus Lysinibacillus.}, } @article {pmid36545372, year = {2022}, author = {Ruttoh, RC and Obiero, JPO and Omuto, CT and Tanui, L}, title = {Assessment of Land Cover and Land Use Change Dynamics in Kibwezi Watershed, Kenya.}, journal = {TheScientificWorldJournal}, volume = {2022}, number = {}, pages = {3944810}, pmid = {36545372}, issn = {1537-744X}, mesh = {Kenya ; *Geographic Information Systems ; *Forests ; Soil ; Trees ; Environmental Monitoring/methods ; Conservation of Natural Resources ; }, abstract = {Land use and land cover (LULC) parameters influence the hydrological and ecological processes taking place in a watershed. Understanding the changes in LULC is essential in the planning and development of management strategies for water resources. The purpose of the study was to detect changes in LULC in the Kibwezi watershed in Kenya, using geospatial approaches. Supervised and unsupervised classification techniques using remote sensing (RS) and geographical information system (GIS) were used to process Landsat imagery for 1999, 2009, and 2019 while ERDAS IMAGINE™ 14 and MS Excel software were used to derive change detection, and the Soil and Water Assessment Tool (SWAT) model was used to delineate the watershed using an in-built watershed delineation tool. The watershed was classified into ten major LULC classes, namely cropland (rainfed), cropland (irrigated), cropland (perennial), crop and shrubs/trees, closed shrublands, open shrubland, shrub grasslands, wooded shrublands, riverine woodlands, and built-up land. The results showed that LULC under shrub grassland, urban areas, and crops and shrubs increased drastically by 552.5%, 366.2%, and 357.1% respectively between 1999 and 2019 with an annual increase of 35.55%, 35.38%, and 33.86% per annum. The area under open shrubland and closed shrubland declined by73.7%, and 30.4% annually. These LULC transformations pose a negative impact on the watershed resources. There is therefore a need for proper management of the watershed for sustainable socio-economic development of the Kibwezi area.}, } @article {pmid36543718, year = {2022}, author = {Liew, F and Talwar, S and Cross, A and Willett, BJ and Scott, S and Logan, N and Siggins, MK and Swieboda, D and Sidhu, JK and Efstathiou, C and Moore, SC and Davis, C and Mohamed, N and Nunag, J and King, C and Thompson, AAR and Rowland-Jones, SL and Docherty, AB and Chalmers, JD and Ho, LP and Horsley, A and Raman, B and Poinasamy, K and Marks, M and Kon, OM and Howard, L and Wootton, DG and Dunachie, S and Quint, JK and Evans, RA and Wain, LV and Fontanella, S and de Silva, TI and Ho, A and Harrison, E and Baillie, JK and Semple, MG and Brightling, C and Thwaites, RS and Turtle, L and Openshaw, PJM and , and , }, title = {SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination.}, journal = {EBioMedicine}, volume = {}, number = {}, pages = {104402}, pmid = {36543718}, issn = {2352-3964}, abstract = {BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced.

METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data.

FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination.

INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity.

FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript.}, } @article {pmid36538553, year = {2022}, author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, J and Gajin, P and Ilijevski, N and Vasiljević, N and Radak, Đ and Vlajinac, H}, title = {Body mass index and early outcomes after carotid endarterectomy.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0278298}, pmid = {36538553}, issn = {1932-6203}, mesh = {Male ; Humans ; *Endarterectomy, Carotid/adverse effects ; Body Mass Index ; Cohort Studies ; Overweight/complications ; Treatment Outcome ; Risk Factors ; Retrospective Studies ; *Stroke/complications ; Hemorrhage/etiology ; Obesity/complications ; *Diabetes Mellitus, Type 2/complications ; *Carotid Stenosis/surgery ; Risk Assessment ; }, abstract = {As the existing data on the correlation of adiposity with adverse outcomes of carotid endarterectomy (CEA) are inconsistent, the aim of the present study is to examine the correlation of an increased body mass index with 30-day complications after carotid endarterectomy. The cohort study comprises 1586 CEAs, performed at the Clinic for Vascular Surgery in Belgrade, from 2012-2017. Out of them, 550 CEAs were performed in patients with normal body mass index (18.5-24.9), 750 in overweight (25.0-29.9), and 286 in obese (≥30) patients. The association of overweight and obesity with early outcomes of carotid endarterectomy was assessed using univariate and multivariate logistic regression analysis. Overweight patients, in whom CEAs were performed, were significantly more frequently males, compared to normal weight patients-Odds Ratio (OR) 1.51 (95% confidence interval- 1.19-1.89). Moreover, overweight patients significantly more frequently had non-insulin-dependent diabetes mellitus-OR 1.44 (1.09-1.90), and more frequently used ACEI in hospital discharge therapy-OR 1.41 (1.07-1.84) than normal weight patients. Additionally, the CEAs in them were less frequently followed by bleedings-OR 0.37 (0.16-0.83). Compared to normal weight patients, obese patients were significantly younger-OR 0.98 (0.96-0.99), and with insulin-dependent and non-insulin-dependent diabetes mellitus-OR 1.83 (1.09-3.06) and OR 2.13 (1.50-3.01) respectively. They also more frequently had increased triglyceride levels-OR 1.36 (1.01-1.83), and more frequently used oral anticoagulants in therapy before the surgery-OR 2.16 (1.11-4.19). According to the results obtained, overweight and obesity were not associated with an increased death rate, transient ischemic attack (TIA), stroke, myocardial infarction, or with minor complications, and the need for reoperation after carotid endarterectomy. The only exception was bleeding, which was significantly less frequent after CEA in overweight compared to normal weight patients.}, } @article {pmid36529723, year = {2022}, author = {Liu, X and Lu, X and Yang, S and Liu, Y and Wang, W and Wei, X and Ji, H and Zhang, B and Xin, W and Wen, J and Wang, J and Chen, Q}, title = {Role of exogenous abscisic acid in freezing tolerance of mangrove Kandelia obovata under natural frost condition at near 32[°]N.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {593}, pmid = {36529723}, issn = {1471-2229}, mesh = {*Rhizophoraceae ; Abscisic Acid/metabolism ; Antioxidants/metabolism ; Freezing ; Proline/metabolism ; Starch/metabolism ; Sucrose/metabolism ; }, abstract = {BACKGROUND: Mangroves possess substantial ecological, social, and economic functions in tropical and subtropical coastal wetlands. Kandelia obovata is the most cold-resistance species among mangrove plants, with a widespread distribution in China that ranges from Sanya (18° 12' N) to Wenzhou (28° 20' N). Here, we explored the temporal variations in physiological status and transcriptome profiling of K. obovata under natural frost conditions at ~ 32[o]N, as well as the positive role of exogenous abscisic acid (ABA) in cold resistance.

RESULTS: The soluble sugar (SS) and proline (Pro) functioned under freezing stress, of which SS was more important for K. obovata. Consistently, up-regulated DEGs responding to low temperature were significantly annotated to glycometabolism, such as starch and sucrose metabolism and amino sugar and nucleotide sugar metabolism. Notably, the top 2 pathways of KEGG enrichment were phenylpropanoid biosynthesis and flavonoid biosynthesis. For the antioxidant system, POD in conjunction with CAT removed hydrogen peroxide, and CAT appeared to be more important. The up-regulated DEGs responding to low temperature and ABA were also found to be enriched in arginine and proline metabolism, starch and sucrose metabolism, and peroxisome. Moreover, ABA triggered the expression of P5CS and P5CR, but inhibited the ProDH expression, which might contribute to Pro accumulation. Interestingly, there was no significant change in malondialdehyde (MDA) content during the cold event (P > 0.05), suggesting foliar application of ABA effectively alleviated the adverse effects of freezing stress on K. obovata by activating the antioxidant enzyme activity and increasing osmolytes accumulation, such as Pro, and the outcome was proportional to ABA concentration.

CONCLUSIONS: This study deepened our understanding of the physiological characters and molecular mechanisms underlying the response of K. obovata to natural frost conditions and exogenous ABA at the field level, which could provide a sound theoretical foundation for expanding mangroves plantations in higher latitudes, as well as the development coastal landscape.}, } @article {pmid36528093, year = {2022}, author = {Milan, M and Bernardini, I and Bertolini, C and Dalla Rovere, G and Manuzzi, A and Pastres, R and Peruzza, L and Smits, M and Fabrello, J and Breggion, C and Sambo, A and Boffo, L and Gallocchio, L and Carrer, C and Sorrentino, F and Bettiol, C and Lodigiulia, C and Semenzin, E and Varagnolo, M and Matozzo, V and Bargelloni, L and Patarnello, T}, title = {Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions.}, journal = {The Science of the total environment}, volume = {863}, number = {}, pages = {160796}, doi = {10.1016/j.scitotenv.2022.160796}, pmid = {36528093}, issn = {1879-1026}, abstract = {In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.}, } @article {pmid36527397, year = {2022}, author = {Viner, A and Membe-Gadama, G and Whyte, S and Kayambo, D and Masamba, M and Martin, CJH and Magowan, B and Reynolds, RM and Stock, SJ and Freyne, B and Gadama, L}, title = {Midwife-Led Ultrasound Scanning to Date Pregnancy in Malawi: Development of a Novel Training Program.}, journal = {Journal of midwifery & women's health}, volume = {67}, number = {6}, pages = {728-734}, doi = {10.1111/jmwh.13442}, pmid = {36527397}, issn = {1542-2011}, mesh = {Female ; Pregnancy ; Humans ; *Midwifery/education ; *Nurse Midwives/education ; Malawi ; }, abstract = {The use of ultrasound to determine gestational age is fundamental to the optimum management of pregnancy and is recommended for all women by the World Health Organization. However, this modality remains unavailable to many women in low-income countries where trained practitioners are scarce. Although previous initiatives have demonstrated efficacy in training midwives and technicians to perform antenatal ultrasound, these programs have often been too long and too complex to be realistic within the specific constraints of this context, highlighting the need for a novel and pragmatic approach. We describe the development and piloting of a bespoke course to teach midwives 3 fundamental components of early antenatal ultrasound scanning: (1) to identify the number of fetuses, (2) to confirm fetal viability, and (3) to determine gestational age. Having established that 5 days is insufficient, we propose that the minimum duration required to train ultrasound-naive midwives to competency is 10 days. Our completed program therefore consists of one and one-half days of didactic teaching, followed by 8 and one-half days of supervised hands-on practical training in which trainees are assessed on their skills. This package has subsequently been successfully implemented across 6 sites in Malawi, where 28 midwives have achieved competency. By describing the processes involved in our cross-continental collaboration, we explain how unexpected challenges helped shape and improve our program, demonstrating the value of preimplementation piloting and a pragmatic and adaptive approach.}, } @article {pmid36526212, year = {2022}, author = {Zhang, Z and Fan, Y and Jiao, Z}, title = {Wetland ecological index and assessment of spatial-temporal changes of wetland ecological integrity.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {160741}, doi = {10.1016/j.scitotenv.2022.160741}, pmid = {36526212}, issn = {1879-1026}, abstract = {Long-term, quantitative, and dynamic monitoring of regional ecological integrity using remote sensing can provide powerful decision-making support for sustainable regional development. However, existing methods are unable to accurately evaluate the quality of the surface ecological integrity because they do not consider vegetation saturation and salinization of wetlands. In addition, the ecological fragility of wetlands is characterized by a high frequency of changes in ecological conditions over time, leading to a lack of directionality in the analysis of ecological changes over long time series. To accurately assess the surface ecological integrity, this study integrates environmental salinity (Baseline-based Soil Salinity Index, BSSI) and a new vegetation element (Improved Hyperspectral Image-based Vegetation Index, IHSVI), and proposes the wetland ecological index (WEI) for the ecological integrity assessment system. Combined with the annual ecological integrity assessment using the WEI, the Mann-Kendall test was used to obtain the nodes of long-term changes. The WEI-Mann Kendall (WEI-MK) framework indicates the direction of analysis and realizes clear long-term series change monitoring. In this study, we analyzed the spatial and temporal changes in ecological integrity in the Yellow River Delta from 1991 to 2020 based on the WEI-MK framework. The results showed that: 1) Compared with Remote Sensing-based Ecological Index (RSEI), the WEI improved the accuracy of wetland integrity evaluation to 89 %. The WEI also improved accuracy of assessments in other typical regions by approximately 10 %. 2) The selection of nodes based on the WEI-MK framework clarified the direction of environmental change analysis. The results show that although the quality of the terrestrial ecological environment has improved over the past 30 years in the Yellow River Delta, that of the marine ecological environment has gradually declined. In particular, the state of the marine ecological environment after 2016 should be of concern.}, } @article {pmid36522390, year = {2022}, author = {Acerbi, A and Snyder, WD and Tennie, C}, title = {The method of exclusion (still) cannot identify specific mechanisms of cultural inheritance.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21680}, pmid = {36522390}, issn = {2045-2322}, support = {714658//European Research Council/International ; 714658//European Research Council/International ; }, mesh = {Animals ; Social Behavior ; *Social Learning ; Databases, Genetic ; *Hominidae ; *Cultural Evolution ; }, abstract = {The method of exclusion identifies patterns of distributions of behaviours and/or artefact forms among different groups, where these patterns are deemed unlikely to arise from purely genetic and/or ecological factors. The presence of such patterns is often used to establish whether a species is cultural or not-i.e. whether a species uses social learning or not. Researchers using or describing this method have often pointed out that the method cannot pinpoint which specific type(s) of social learning resulted in the observed patterns. However, the literature continues to contain such inferences. In a new attempt to warn against these logically unwarranted conclusions, we illustrate this error using a novel approach. We use an individual-based model, focused on wild ape cultural patterns-as these patterns are the best-known cases of animal culture and as they also contain the most frequent usage of the unwarranted inference for specific social learning mechanisms. We built a model that contained agents unable to copy specifics of behavioural or artefact forms beyond their individual reach (which we define as "copying"). We did so, as some of the previous inference claims related to social learning mechanisms revolve around copying defined in this way. The results of our model however show that non-copying social learning can already reproduce the defining-even iconic-features of observed ape cultural patterns detected by the method of exclusion. This shows, using a novel model approach, that copying processes are not necessary to produce the cultural patterns that are sometimes still used in an attempt to identify copying processes. Additionally, our model could fully control for both environmental and genetic factors (impossible in real life) and thus offers a new validity check for the method of exclusion as related to general cultural claims-a check that the method passed. Our model also led to new and additional findings, which we likewise discuss.}, } @article {pmid36520387, year = {2023}, author = {Melayah, D and Bontemps, Z and Bruto, M and Nguyen, A and Oger, P and Hugoni, M}, title = {Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {17-35}, pmid = {36520387}, issn = {1940-6029}, mesh = {*Ecosystem ; *Archaea/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Biodiversity ; }, abstract = {High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.}, } @article {pmid36519374, year = {2023}, author = {Seidu, S and Gillies, C and Zaccardi, F and Reeves, K and Gallier, S and Khunti, K}, title = {Temporal trends in admissions for atrial fibrillation and severe bleeding in England: an 18-year longitudinal analysis.}, journal = {Scandinavian cardiovascular journal : SCJ}, volume = {57}, number = {1}, pages = {40-47}, doi = {10.1080/14017431.2022.2156597}, pmid = {36519374}, issn = {1651-2006}, mesh = {Humans ; *Atrial Fibrillation/diagnosis/epidemiology/therapy ; Anticoagulants/therapeutic use ; Administration, Oral ; Risk Factors ; Treatment Outcome ; Time Factors ; Hemorrhage/diagnosis/epidemiology ; *Stroke ; }, abstract = {Objective. Temporal trends in admissions for atrial fibrillation (AF) and severe bleeding associated with AF vary worldwide. We aimed to explore their temporal trends in England and their relation to the introduction of DOACs in 2014 in the UK. Design. This longitudinal ecological study utilised aggregated data that was extracted from the Hospital Episode Statistics database, which captured annual admissions for AF and severe bleeding associated with AF between 2001 and 2018. Trends in admissions over the study period and across age groups, gender and regions in England were assessed. Results. In total, there were 11,292,177 admissions for AF and 324,851 admissions for severe bleeding associated with AF. There was a steady rise in admissions for AF from 2001 to 2017 (204,808 to 1,109,295; p for trend<.001). A similar trend was observed for severe bleeding (4940 to 30,169; p for trend <.001), but the increase dropped slightly between 2013 and 2014 and continued thereafter. Conclusions. There was a rise in admissions for AF and severe bleeding in England between 2001 and 2018. There is little evidence that the slight drop in admissions for severe bleeding between 2013 and 2014 may have been caused by the introduction of DOACs in 2014. Contributors to these trends need urgent exploration.}, } @article {pmid36517756, year = {2022}, author = {Zhang, H and Yao, G and He, M}, title = {Transcriptome analysis of gene expression profiling from the deep sea in situ to the laboratory for the cold seep mussel Gigantidas haimaensis.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {828}, pmid = {36517756}, issn = {1471-2164}, mesh = {Animals ; *Ecosystem ; *Mytilidae/genetics ; Gene Expression Profiling ; Transcriptome ; Gene Ontology ; }, abstract = {BACKGROUND: The deep-sea mussel Gigantidas haimaensis is a representative species from the Haima cold seep ecosystem in the South China Sea that establishes endosymbiosis with chemotrophic bacteria. During long-term evolution, G. haimaensis has adapted well to the local environment of cold seeps. Until now, adaptive mechanisms responding to environmental stresses have remained poorly understood.

RESULTS: In this study, transcriptomic analysis was performed for muscle tissue of G. haimaensis in the in situ environment (MH) and laboratory environment for 0 h (M0), 3 h (M3) and 9 h (M9), and 187,368 transcript sequences and 22,924 annotated differentially expressed genes (DEGs) were generated. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DEGs were enriched with a broad spectrum of biological processes and pathways, including those associated with antioxidants, apoptosis, chaperones, immunity and metabolism. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum and metabolism were the most affected metabolic pathways. These results may imply that G. haimaensis struggles to support the life response to environmental change by changing gene expression profiles.

CONCLUSION: The present study provides a better understanding of the biological responses and survival strategies of the mussel G. haimaensis from deep sea in situ to the laboratory environment.}, } @article {pmid36512954, year = {2022}, author = {Kim, B and Barrington, WE and Dobra, A and Rosenberg, D and Hurvitz, P and Belza, B}, title = {Mediating role of walking between perceived and objective walkability and cognitive function in older adults.}, journal = {Health & place}, volume = {79}, number = {}, pages = {102943}, doi = {10.1016/j.healthplace.2022.102943}, pmid = {36512954}, issn = {1873-2054}, abstract = {The aim of this study was to examine the role of walking in explaining associations between perceived and objective measures of walkability and cognitive function among older adults. The study employed a cross-sectional design analyzing existing data. Data were obtained from the Adult Changes in Thought Activity Monitor study. Cognitive function and perceived walkability were measured by a survey. Objective walkability was measured using geographic information systems (GIS). Walking was measured using an accelerometer. We tested the mediating relationship based on 1,000 bootstrapped samples. Perceived walkability was associated with a 0.04 point higher cognitive function score through walking (p = 0.006). The mediating relationship accounted for 34% of the total relationship between perceived walkability and cognitive function. Walking did not have a significant indirect relationship on the association between objective walkability and cognitive function. Perceived walkability may be more relevant to walking behavior than objective walkability among older adults. Greater levels of perceived walkability may encourage older adults to undertake more walking, and more walking may in turn improve cognitive function in older adults.}, } @article {pmid36512230, year = {2023}, author = {Barlow, LD and Maciejowski, W and More, K and Terry, K and Vargová, R and Záhonová, K and Dacks, JB}, title = {Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2557}, number = {}, pages = {431-452}, pmid = {36512230}, issn = {1940-6029}, mesh = {*Amoeba/genetics ; Reproducibility of Results ; Genomics/methods ; Biological Evolution ; Golgi Apparatus/metabolism ; Computational Biology/methods ; }, abstract = {Taking an evolutionary approach to cell biology can yield important new information about how the cell works and how it evolved to do so. This is true of the Golgi apparatus, as it is of all systems within the cell. Comparative genomics is one of the crucial first steps to this line of research, but comes with technical challenges that must be overcome for rigor and robustness. We here introduce AMOEBAE, a workflow for mid-range scale comparative genomic analyses. It allows for customization of parameters, queries, and taxonomic sampling of genomic and transcriptomics data. This protocol article covers the rationale for an evolutionary approach to cell biological study (i.e., when would AMOEBAE be useful), how to use AMOEBAE, and discussion of limitations. It also provides an example dataset, which demonstrates that the Golgi protein AP4 Epsilon is present as the sole retained subunit of the AP4 complex in basidiomycete fungi. AMOEBAE can facilitate comparative genomic studies by balancing reproducibility and speed with user-input and interpretation. It is hoped that AMOEBAE or similar tools will encourage cell biologists to incorporate an evolutionary context into their research.}, } @article {pmid36504957, year = {2022}, author = {Zhang, Y and Liu, S and Wang, Y and Wang, Y}, title = {Causal relationship between particulate matter 2.5 and hypothyroidism: A two-sample Mendelian randomization study.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1000103}, pmid = {36504957}, issn = {2296-2565}, mesh = {*Particulate Matter/adverse effects ; *Genome-Wide Association Study ; Analysis of Variance ; Databases, Factual ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Epidemiological surveys have found that particulate matter 2.5 (PM2.5) plays an important role in hypothyroidism. However, due to the methodological limitations of traditional observational studies, it is difficult to make causal inferences. In the present study, we assessed the causal association between PM2.5 concentrations and risk of hypothyroidism using two-sample Mendelian randomization (TSMR).

METHODS: We performed TSMR by using aggregated data from genome-wide association studies (GWAS) on the IEU Open GWAS database. We identified seven single nucleotide polymorphisms (SNPs) associated with PM2.5 concentrations as instrumental variables (IVs). We used inverse-variance weighting (IVW) as the main analytical method, and we selected MR-Egger, weighted median, simple model, and weighted model methods for quality control.

RESULTS: MR analysis showed that PM2.5 has a positive effect on the risk of hypothyroidism: An increase of 1 standard deviation (SD) in PM2.5 concentrations increases the risk of hypothyroidism by ~10.0% (odds ratio 1.10, 95% confidence interval 1.06-1.13, P = 2.93E-08, by IVW analysis); there was no heterogeneity or pleiotropy in the results.

CONCLUSION: In conclusion, increased PM2.5 concentrations are associated with an increased risk of hypothyroidism. This study provides evidence of a causal relationship between PM2.5 and the risk of hypothyroidism, so air pollution control may have important implications for the prevention of hypothyroidism.}, } @article {pmid36503572, year = {2022}, author = {Yan, X and Si, H and Zhu, Y and Li, S and Han, Y and Liu, H and Du, R and Pope, PB and Qiu, Q and Li, Z}, title = {Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {222}, pmid = {36503572}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Multiomics ; *Deer/microbiology ; Rumen/microbiology ; Fatty Acids, Volatile ; }, abstract = {BACKGROUND: The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that occur across the host-microbiome axis remains elusive, particularly during the critical development stages at early life. Here, we present an integrative multi-omics approach that simultaneously resolved the taxonomic and functional attributes of microbiota from five GIT regions as well as the metabolic features of the liver, muscle, urine, and serum in sika deer (Cervus nippon) across three key early life stages.

RESULTS: Within the host, analysis of metabolites over time in serum, urine, and muscle (longissimus lumborum) showed that changes in the fatty acid profile were concurrent with gains in body weight. Additional host transcriptomic and metabolomic analysis revealed that fatty acid β-oxidation and metabolism of tryptophan and branched chain amino acids play important roles in regulating hepatic metabolism. Across the varying regions of the GIT, we demonstrated that a complex and variable community of bacteria, viruses, and archaea colonized the GIT soon after birth, whereas microbial succession was driven by the cooperative networks of hub populations. Furthermore, GIT volatile fatty acid concentrations were marked by increased microbial metabolic pathway abundances linked to mannose (rumen) and amino acids (colon) metabolism. Significant functional shifts were also revealed across varying GIT tissues, which were dominated by host fatty acid metabolism associated with reactive oxygen species in the rumen epithelium, and the intensive immune response in both small and large intestine. Finally, we reveal a possible contributing role of necroptosis and apoptosis in enhancing ileum and colon epithelium development, respectively.

CONCLUSIONS: Our findings provide a comprehensive view for the involved mechanisms in the context of GIT microbiome and ruminant metabolic growth at early life. Video Abstract.}, } @article {pmid36498115, year = {2022}, author = {Li, W and Liu, R and Sun, L and Guo, Z and Gao, J}, title = {An Investigation of Employees' Intention to Comply with Information Security System-A Mixed Approach Based on Regression Analysis and fsQCA.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {23}, pages = {}, pmid = {36498115}, issn = {1660-4601}, mesh = {Humans ; *Intention ; *Information Systems ; Self Efficacy ; Motivation ; Regression Analysis ; }, abstract = {Employee security compliance behavior has become an important safeguard to protect the security of corporate information assets. Focusing on human factors, this paper discusses how to regulate and guide employees' compliance with information security systems through effective methods. Based on protection motivation theory (PMT), a model of employees' intention to comply with the information security system was constructed. A questionnaire survey was adopted to obtain 224 valid data points, and SPSS 26.0 was applied to verify the hypotheses underlying the research model. Then, based on the results of a regression analysis, fuzzy set qualitative comparative analysis (fsQCA) was used to explore the conditional configurations that affect employees' intention to comply with the information security system from a holistic perspective. The empirical results demonstrated that perceived severity, perceived vulnerability, response efficacy, and self-efficacy all positively influenced the employees' intention to comply with the information security system; while rewards and response costs had a negative effect. Threat appraisal had a greater effect on employees' intention to comply with the information security system compared to response appraisal. The fsQCA results showed that individual antecedent conditions are not necessary to influence employees' intention to comply with an information security system. Seven pathways exist that influence an employees' intention to comply with an information security system, with reward, self-efficacy, and response cost being the core conditions having the highest probability of occurring in each configuration of pathways, and with perceived severity and self-efficacy appearing in the core conditions of configurations with an original coverage greater than 40%. Theoretically, this study discusses the influence of the elements of PMT on employees' intention to comply with an information security system, reveals the mechanism of influence of the combination of the influencing factors on the outcome variables, and identifies the core factors and auxiliary factors in the condition configurations, providing a new broader perspective for the study of information security compliance behavior and providing some theoretical support for strengthening enterprise security management. Practically, targeted suggestions are proposed based on the research results, to increase the intention of enterprise employees to comply with information security systems, thereby improving the effectiveness of enterprise information security management and the degree of information security in enterprises.}, } @article {pmid36497480, year = {2022}, author = {Islam, MM and Poly, TN and Walther, BA and Yeh, CY and Seyed-Abdul, S and Li, YJ and Lin, MC}, title = {Deep Learning for the Diagnosis of Esophageal Cancer in Endoscopic Images: A Systematic Review and Meta-Analysis.}, journal = {Cancers}, volume = {14}, number = {23}, pages = {}, pmid = {36497480}, issn = {2072-6694}, abstract = {Esophageal cancer, one of the most common cancers with a poor prognosis, is the sixth leading cause of cancer-related mortality worldwide. Early and accurate diagnosis of esophageal cancer, thus, plays a vital role in choosing the appropriate treatment plan for patients and increasing their survival rate. However, an accurate diagnosis of esophageal cancer requires substantial expertise and experience. Nowadays, the deep learning (DL) model for the diagnosis of esophageal cancer has shown promising performance. Therefore, we conducted an updated meta-analysis to determine the diagnostic accuracy of the DL model for the diagnosis of esophageal cancer. A search of PubMed, EMBASE, Scopus, and Web of Science, between 1 January 2012 and 1 August 2022, was conducted to identify potential studies evaluating the diagnostic performance of the DL model for esophageal cancer using endoscopic images. The study was performed in accordance with PRISMA guidelines. Two reviewers independently assessed potential studies for inclusion and extracted data from retrieved studies. Methodological quality was assessed by using the QUADAS-2 guidelines. The pooled accuracy, sensitivity, specificity, positive and negative predictive value, and the area under the receiver operating curve (AUROC) were calculated using a random effect model. A total of 28 potential studies involving a total of 703,006 images were included. The pooled accuracy, sensitivity, specificity, and positive and negative predictive value of DL for the diagnosis of esophageal cancer were 92.90%, 93.80%, 91.73%, 93.62%, and 91.97%, respectively. The pooled AUROC of DL for the diagnosis of esophageal cancer was 0.96. Furthermore, there was no publication bias among the studies. The findings of our study show that the DL model has great potential to accurately and quickly diagnose esophageal cancer. However, most studies developed their model using endoscopic data from the Asian population. Therefore, we recommend further validation through studies of other populations as well.}, } @article {pmid36493775, year = {2022}, author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, ÖD and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, Ö and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, Ç and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M}, title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2022.11.034}, pmid = {36493775}, issn = {1879-0445}, abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.}, } @article {pmid36478264, year = {2022}, author = {Mairal, M and García-Verdugo, C and Le Roux, JJ and Chau, JH and van Vuuren, BJ and Hui, C and Münzbergová, Z and Chown, SL and Shaw, JD}, title = {Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16809}, pmid = {36478264}, issn = {1365-294X}, abstract = {Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.}, } @article {pmid36477523, year = {2022}, author = {Takemura, LS and Barbosa, ÁRG and Amaral, BS and Bosco, AAD and Lourenço, DB and Apezzato, M and Barbosa, JABA and Faria, EF and Bianco, B and Lemos, GC and Carneiro, A}, title = {Radical prostatectomies for treatment of prostate cancer: trends in a ten-year period in public health services in the city of São Paulo, Brazil.}, journal = {Einstein (Sao Paulo, Brazil)}, volume = {20}, number = {}, pages = {eAO0049}, pmid = {36477523}, issn = {2317-6385}, mesh = {United States ; Humans ; Male ; Brazil/epidemiology ; *Prostatic Neoplasms/surgery ; Health Services ; }, abstract = {OBJECTIVE: To analyze the characteristics of public health services related to radical prostatectomy, according to hospital volume of surgeries and stratified as academic and non-academic centers.

METHODS: An ecological study was conducted using a database available in TabNet platform of the Unified Health System Department of Informatics. Number of surgeries, length of hospital stay, length of stay in intensive care unit, in-hospital mortality rate, and cost of hospitalization were evaluated. The hospitals were divided into three subgroups according to surgery volume (tercile), and results were compared. The same comparisons were made among academic and non-academic centers. We considered academic centers those providing Urology residency program.

RESULTS: A total of 11,259 radical prostatectomies were performed in the city of São Paulo between 2008 and 2018. We observed a significant trend of increase in radical prostatectomies for treating prostate cancer over the years (p=0.007). The length of stay in intensive care unit, and number of deaths were not statistically different among centers with diverse surgery volume, nor between academic and non-academic centers. However, length of hospital stay was significantly shorter in academic centers (p=0.043), while cost of hospitalization was significantly higher in high-volume center compared to low- (p<0.001) and intermediate-volume centers (p<0.001).

CONCLUSION: Length of hospital stay for radical prostatectomies performed in public services in the city of São Paulo was shorter in academic centers, whereas hospitals with a high volume of surgeries showed greater cost of hospitalization.}, } @article {pmid36475098, year = {2022}, author = {Karaarslan, F and Yılmaz, H and Akkurt, HE and Kaya, FM and Şafak Yılmaz, E}, title = {Comparison of the efficacy of mud-pack and hot-pack treatments in chronic non-specific neck pain: A single-blind, randomized-controlled study.}, journal = {Turkish journal of physical medicine and rehabilitation}, volume = {68}, number = {3}, pages = {381-390}, pmid = {36475098}, issn = {2587-1250}, abstract = {OBJECTIVES: This study aims to compare the short-term efficacy of mud-pack (MP) and hot-pack (HP) treatments with the same temperature and duration on sleep, function, depression, and quality of life for chronic non-specific neck pain (CNNP) patients.

PATIENTS AND METHODS: Between December 2018 and September 2019, a total of 70 patients with CNNP diagnosis (12 males, 58 females; mean age: 50.2±9.4 years; range, 24 to 65 years) were included. The patients were divided into two groups. The MP group (n=35) had a total of 15 sessions of MP for 20 min + transcutaneous electrical nerve stimulation (TENS) for 20 min + home exercise (HE) on five days per week for three weeks. The HP group (n=35) had 15 similar sessions of HP for 20 min + TENS for 20 min + HE. The patients were assessed with the Visual Analog Scale (VAS-pain), VAS physician's and patient's global assessments, modified Neck Disability Index (mNDI), Beck Depression Inventory (BDI), Pittsburgh Sleep Quality Index (PSQI), and Short Form-36 (SF-36) measures before treatment, at the end of post-treatment third week and one month later.

RESULTS: In the MP group, there were statistically significant improvements in all parameters at the end of treatment three-week and one-month follow-up (p<0.05), apart from SF-36 Vitality/Energy (SF-36V/E) at the end of treatment and SF-36 General Health (SF-36GH) at one month. In the HP group, there were statistically significant improvements observed for all parameters (p<0.05), apart from the SF-36 Physical Role and SF-36GH at the end of treatment third week and SF-36V/E at the first-month assessment. The VAS-pain(p<0.001), mNDI (p=0.019), BDI (p=0.002), SF-36GH (p<0.001), SF-36V/E (p<0.001) and SF-36 mental health (p<0.001) showed statistically significantly superior improvements in the MP group (p<0.05).

CONCLUSION: In CNNP patients, both MP and HP treatments are effective. However, MP therapy has more positive effects on pain, function, depression, and quality of life parameters. The MP treatment may be used in addition to TENS treatment for CNNP patients.}, } @article {pmid36473660, year = {2022}, author = {Simeoni, C and Furlan, E and Pham, HV and Critto, A and de Juan, S and Trégarot, E and Cornet, CC and Meesters, E and Fonseca, C and Botelho, AZ and Krause, T and N'Guetta, A and Cordova, FE and Failler, P and Marcomini, A}, title = {Evaluating the combined effect of climate and anthropogenic stressors on marine coastal ecosystems: Insights from a systematic review of cumulative impact assessment approaches.}, journal = {The Science of the total environment}, volume = {861}, number = {}, pages = {160687}, doi = {10.1016/j.scitotenv.2022.160687}, pmid = {36473660}, issn = {1879-1026}, abstract = {Cumulative impacts increasingly threaten marine and coastal ecosystems. To address this issue, the research community has invested efforts on designing and testing different methodological approaches and tools that apply cumulative impact appraisal schemes for a sound evaluation of the complex interactions and dynamics among multiple pressures affecting marine and coastal ecosystems. Through an iterative scientometric and systematic literature review, this paper provides the state of the art of cumulative impact assessment approaches and applications. It gives a specific attention to cutting-edge approaches that explore and model inter-relations among climatic and anthropogenic pressures, vulnerability and resilience of marine and coastal ecosystems to these pressures, and the resulting changes in ecosystem services flow. Despite recent advances in computer sciences and the rising availability of big data for environmental monitoring and management, this literature review evidenced that the implementation of advanced complex system methods for cumulative risk assessment remains limited. Moreover, experts have only recently started integrating ecosystem services flow into cumulative impact appraisal frameworks, but more as a general assessment endpoint within the overall evaluation process (e.g. changes in the bundle of ecosystem services against cumulative impacts). The review also highlights a lack of integrated approaches and complex tools able to frame, explain, and model spatio-temporal dynamics of marine and coastal ecosystems' response to multiple pressures, as required under relevant EU legislation (e.g., Water Framework and Marine Strategy Framework Directives). Progress in understanding cumulative impacts, exploiting the functionalities of more sophisticated machine learning-based approaches (e.g., big data integration), will support decision-makers in the achievement of environmental and sustainability objectives.}, } @article {pmid36469956, year = {2022}, author = {Marcusson-Clavertz, D and Persson, SD and Davidson, P and Kim, J and Cardeña, E and Kuehner, C}, title = {Mind wandering and sleep in daily life: A combined actigraphy and experience sampling study.}, journal = {Consciousness and cognition}, volume = {107}, number = {}, pages = {103447}, doi = {10.1016/j.concog.2022.103447}, pmid = {36469956}, issn = {1090-2376}, abstract = {Individuals who sleep poorly report spending more time mind wandering during the day. However, past research has relied on self-report measures of sleep or measured mind wandering during laboratory tasks, which prevents generalization to everyday contexts. We used ambulatory assessments to examine the relations between several features of sleep (duration, fragmentation, and disturbances) and mind wandering (task-unrelated, stimulus-independent, and unguided thoughts). Participants wore a wristband device that collected actigraphy and experience-sampling data across 7 days and 8 nights. Contrary to our expectations, task-unrelated and stimulus-independent thoughts were not associated with sleep either within- or between-persons (n = 164). Instead, individual differences in unguided thoughts were associated with sleep disturbances and duration, suggesting that individuals who more often experience unguided train-of-thoughts have greater sleep disturbances and sleep longer. These results highlight the need to consider the context and features of mind wandering when relating it to sleep.}, } @article {pmid36469554, year = {2022}, author = {Zhao, C and Goldman, M and Smith, BJ and Pollard, KS}, title = {Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.}, journal = {Current protocols}, volume = {2}, number = {12}, pages = {e604}, doi = {10.1002/cpz1.604}, pmid = {36469554}, issn = {2691-1299}, mesh = {*Metagenome/genetics ; Genotype ; Alleles ; *Microbiota/genetics ; Nucleotides ; }, abstract = {The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants and gene copy number variants in metagenomes using comprehensive reference databases built from public microbial genome collections (metagenotyping). MIDAS2 is the first metagenotyping tool with functionality to control metagenomic read mapping filters and to customize the reference database to the microbial community, features that improve the precision and recall of detected variants. In this article we present four basic protocols for the most common use cases of MIDAS2, along with supporting protocols for installation and use. In addition, we provide in-depth guidance on adjusting command line parameters, editing the reference database, optimizing hardware utilization, and understanding the metagenotyping results. All the steps of metagenotyping, from raw sequencing reads to population genetic analysis, are demonstrated with example data in two downloadable sequencing libraries of single-end metagenomic reads representing a mixture of multiple bacterial species. This set of protocols empowers users to accurately genotype hundreds of species in thousands of samples, providing rich genetic data for studying the evolution and strain-level ecology of microbial communities. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Species prescreening Basic Protocol 2: Download MIDAS reference database Basic Protocol 3: Population single nucleotide variant calling Basic Protocol 4: Pan-genome copy number variant calling Support Protocol 1: Installing MIDAS2 Support Protocol 2: Command line inputs Support Protocol 3: Metagenotyping with a custom collection of genomes Support Protocol 4: Metagenotyping with advanced parameters.}, } @article {pmid36458815, year = {2022}, author = {Yang, B and García-Carreras, B and Lessler, J and Read, JM and Zhu, H and Metcalf, CJE and Hay, JA and Kwok, KO and Shen, R and Jiang, CQ and Guan, Y and Riley, S and Cummings, DA}, title = {Long term intrinsic cycling in human life course antibody responses to influenza A(H3N2): an observational and modeling study.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36458815}, issn = {2050-084X}, support = {200861/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 200187/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; R56 AG048075/AG/NIA NIH HHS/United States ; R01 AI114703/AI/NIAID NIH HHS/United States ; R01 TW008246/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Influenza, Human ; Influenza A Virus, H3N2 Subtype ; *Influenza Vaccines ; Antibody Formation ; Life Change Events ; Antibodies, Viral ; }, abstract = {BACKGROUND: Over a life course, human adaptive immunity to antigenically mutable pathogens exhibits competitive and facilitative interactions. We hypothesize that such interactions may lead to cyclic dynamics in immune responses over a lifetime.

METHODS: To investigate the cyclic behavior, we analyzed hemagglutination inhibition titers against 21 historical influenza A(H3N2) strains spanning 47 years from a cohort in Guangzhou, China, and applied Fourier spectrum analysis. To investigate possible biological mechanisms, we simulated individual antibody profiles encompassing known feedbacks and interactions due to generally recognized immunological mechanisms.

RESULTS: We demonstrated a long-term periodicity (about 24 years) in individual antibody responses. The reported cycles were robust to analytic and sampling approaches. Simulations suggested that individual-level cross-reaction between antigenically similar strains likely explains the reported cycle. We showed that the reported cycles are predictable at both individual and birth cohort level and that cohorts show a diversity of phases of these cycles. Phase of cycle was associated with the risk of seroconversion to circulating strains, after accounting for age and pre-existing titers of the circulating strains.

CONCLUSIONS: Our findings reveal the existence of long-term periodicities in individual antibody responses to A(H3N2). We hypothesize that these cycles are driven by preexisting antibody responses blunting responses to antigenically similar pathogens (by preventing infection and/or robust antibody responses upon infection), leading to reductions in antigen-specific responses over time until individual's increasing risk leads to an infection with an antigenically distant enough virus to generate a robust immune response. These findings could help disentangle cohort effects from individual-level exposure histories, improve our understanding of observed heterogeneous antibody responses to immunizations, and inform targeted vaccine strategy.

FUNDING: This study was supported by grants from the NIH R56AG048075 (DATC, JL), NIH R01AI114703 (DATC, BY), the Wellcome Trust 200861/Z/16/Z (SR), and 200187/Z/15/Z (SR). This work was also supported by research grants from Guangdong Government HZQB-KCZYZ-2021014 and 2019B121205009 (YG and HZ). DATC, JMR and SR acknowledge support from the National Institutes of Health Fogarty Institute (R01TW0008246). JMR acknowledges support from the Medical Research Council (MR/S004793/1) and the Engineering and Physical Sciences Research Council (EP/N014499/1). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.}, } @article {pmid36456926, year = {2022}, author = {Li, Y and Wei, CM and Li, XY and Meng, DC and Gu, ZJ and Qu, SP and Huang, MJ and Huang, HQ}, title = {De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {553}, pmid = {36456926}, issn = {1471-2229}, mesh = {*Impatiens ; Transcriptome ; Exome Sequencing ; Cell Cycle ; Databases, Protein ; }, abstract = {BACKGROUND: Spur, a structure capable of producing and storing nectar, not only plays a vital role in the pollination process but also promotes the rapid diversification of some plant lineages, which is considered a key innovation in plants. Spur is the focus of many studies, such as evolution and ecological hypothesis, but the current understanding of spur development is limited. High-throughput sequencing of Impatiens uliginosa was carried out to study the molecular mechanism of its spur development, which is believed to provide some insights into the spur development of Impatiens.

RESULTS: Transcriptomic sequencing and analysis were performed on spurs and limbs of I. uliginosa at three developmental stages. A total of 47.83 Gb of clean data were obtained, and 49,716 unigene genes were assembled. After comparison with NR, Swiss-Prot, Pfam, COG, GO and KEGG databases, a total of 27,686 genes were annotated successfully. Through comparative analysis, 19,356 differentially expressed genes were found and enriched into 208 GO terms and 146 KEGG pathways, among which plant hormone signal transduction was the most significantly enriched pathway. One thousand thirty-two transcription factors were identified, which belonged to 33 TF families such as MYB, bHLH and TCP. Twenty candidate genes that may be involved in spur development were screened and verified by qPCR, such as SBP, IAA and ABP.

CONCLUSIONS: Transcriptome data of different developmental stages of spurs were obtained, and a series of candidate genes related to spur development were identified. The importance of genes related to cell cycle, cell division, cell elongation and hormones in spur development was clarified. This study provided valuable information and resources for understanding the molecular mechanism of spur development in Impatiens.}, } @article {pmid36455989, year = {2022}, author = {Van Bortel, W and Mariën, J and Jacobs, BKM and Sinzinkayo, D and Sinarinzi, P and Lampaert, E and D'hondt, R and Mafuko, JM and De Weggheleire, A and Vogt, F and Alexander, N and Wint, W and Maes, P and Vanlerberghe, V and Leclair, C}, title = {Long-lasting insecticidal nets provide protection against malaria for only a single year in Burundi, an African highland setting with marked malaria seasonality.}, journal = {BMJ global health}, volume = {7}, number = {12}, pages = {}, pmid = {36455989}, issn = {2059-7908}, mesh = {Humans ; *Insecticides ; Burundi/epidemiology ; *Malaria/epidemiology/prevention & control ; *Health Information Systems ; Time Factors ; }, abstract = {BACKGROUND: Long-lasting insecticidal nets (LLINs) are one of the key interventions in the global fight against malaria. Since 2014, mass distribution campaigns of LLINs aim for universal access by all citizens of Burundi. In this context, we assess the impact of LLINs mass distribution campaigns on malaria incidence, focusing on the endemic highland health districts. We also explored the possible correlation between observed trends in malaria incidence with any variations in climate conditions.

METHODS: Malaria cases for 2011-2019 were obtained from the National Health Information System. We developed a generalised additive model based on a time series of routinely collected data with malaria incidence as the response variable and timing of LLIN distribution as an explanatory variable to investigate the duration and magnitude of the LLIN effect on malaria incidence. We added a seasonal and continuous-time component as further explanatory variables, and health district as a random effect to account for random natural variation in malaria cases between districts.

RESULTS: Malaria transmission in Burundian highlands was clearly seasonal and increased non-linearly over the study period. Further, a fast and steep decline of malaria incidence was noted during the first year after mass LLIN distribution (p<0.0001). In years 2 and 3 after distribution, malaria cases started to rise again to levels higher than before the control intervention.

CONCLUSION: This study highlights that LLINs did reduce the incidence in the first year after a mass distribution campaign, but in the context of Burundi, LLINs lost their impact after only 1 year.}, } @article {pmid36454025, year = {2022}, author = {Velasco, VME and Ferreira, A and Zaman, S and Noordermeer, D and Ensminger, I and Wegrzyn, JL}, title = {A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir).}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkac304}, pmid = {36454025}, issn = {2160-1836}, abstract = {Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber trees. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under non-stress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used two computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long non-coding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.}, } @article {pmid36451580, year = {2022}, author = {Danneels, B and Blignaut, M and Marti, G and Sieber, S and Vandamme, P and Meyer, M and Carlier, A}, title = {Cyclitol metabolism is a central feature of Burkholderia leaf symbionts.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16292}, pmid = {36451580}, issn = {1462-2920}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.}, } @article {pmid36449461, year = {2022}, author = {van der Feltz-Cornelis, CM and Sweetman, J and Allsopp, G and Attree, E and Crooks, MG and Cuthbertson, DJ and Forshaw, D and Gabbay, M and Green, A and Heightman, M and Hillman, T and Hishmeh, L and Khunti, K and Lip, GYH and Lorgelly, P and Montgomery, H and Strain, WD and Wall, E and Watkins, C and Williams, N and Wootton, DG and Banerjee, A and , }, title = {STIMULATE-ICP-Delphi (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways Delphi): Study protocol.}, journal = {PloS one}, volume = {17}, number = {11}, pages = {e0277936}, pmid = {36449461}, issn = {1932-6203}, mesh = {Humans ; *COVID-19/epidemiology ; Critical Pathways ; Mental Health ; *Delivery of Health Care, Integrated ; Post-Acute COVID-19 Syndrome ; }, abstract = {INTRODUCTION: As mortality rates from COVID-19 disease fall, the high prevalence of long-term sequelae (Long COVID) is becoming increasingly widespread, challenging healthcare systems globally. Traditional pathways of care for Long Term Conditions (LTCs) have tended to be managed by disease-specific specialties, an approach that has been ineffective in delivering care for patients with multi-morbidity. The multi-system nature of Long COVID and its impact on physical and psychological health demands a more effective model of holistic, integrated care. The evolution of integrated care systems (ICSs) in the UK presents an important opportunity to explore areas of mutual benefit to LTC, multi-morbidity and Long COVID care. There may be benefits in comparing and contrasting ICPs for Long COVID with ICPs for other LTCs.

METHODS AND ANALYSIS: This study aims to evaluate health services requirements for ICPs for Long COVID and their applicability to other LTCs including multi-morbidity and the overlap with medically not yet explained symptoms (MNYES). The study will follow a Delphi design and involve an expert panel of stakeholders including people with lived experience, as well as clinicians with expertise in Long COVID and other LTCs. Study processes will include expert panel and moderator panel meetings, surveys, and interviews. The Delphi process is part of the overall STIMULATE-ICP programme, aimed at improving integrated care for people with Long COVID.

ETHICS AND DISSEMINATION: Ethical approval for this Delphi study has been obtained (Research Governance Board of the University of York) as have approvals for the other STIMULATE-ICP studies. Study outcomes are likely to inform policy for ICPs across LTCs. Results will be disseminated through scientific publication, conference presentation and communications with patients and stakeholders involved in care of other LTCs and Long COVID.

REGISTRATION: Researchregistry: https://www.researchregistry.com/browse-the-registry#home/registrationdetails/6246bfeeeaaed6001f08dadc/.}, } @article {pmid36447758, year = {2022}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the square-spot rustic, Xestia xanthographa (Schiffermuller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {37}, pmid = {36447758}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Xestia xanthographa (the square-spot rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 934 megabases in span. The majority of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid36437091, year = {2022}, author = {Zhang, KK and He, J and Zhong, YX and Wei, QQ and Chen, F}, title = {[Identification of Soil Heavy Metal Sources Around a Copper-silver Mining Area in Ningxia Based on GIS].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {11}, pages = {5192-5204}, doi = {10.13227/j.hjkx.202201113}, pmid = {36437091}, issn = {0250-3301}, mesh = {Humans ; Soil ; Copper ; Silver ; *Soil Pollutants/analysis ; Geographic Information Systems ; Cadmium/analysis ; Lead/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury/analysis ; }, abstract = {This study area was based on the catchment area of the Yaoxianzi ditch located in the arid region of western China. A total of 194 topsoil samples of 0-20 cm depth were collected using the mesh distribution method. The contents of nine heavy metals (Ni, Cu, Zn, As, Ag, Cr, Cd, Hg, and Pb) were determined using ICP-MS. The source and spatial distribution of heavy metals were analyzed using PMF and IDW. Spatial autocorrelation and clustering and outlier analysis were performed using the Spatial Statistical Analysis tool of ArcGIS. The main sources and distribution areas of heavy metals in the soil were obtained through comprehensive analysis. In the study area, the average values of Hg, Ag, Cd, and Pb were 20.48, 3.13, 2.23, and 1.12 times the background values, and the maximum values of Cd, Cu, Pb, and As were 10.92, 5.52, 2.03, and 1.39 times the filter values, respectively. The coefficients of variation of Cu, Cd, Pb, and Hg were ordered as Cu(283.23%)>Cd(224.77%)>Pb(144.40%)>Hg(67.12%) and were closely affected by human activities. The heavy metals in the soil around mining areas came from four main sources:natural parent material (32%), the mixed source of mining activities and transportation (17.1%), the mixed source of industrial activities and atmospheric sedimentation (40.3%), and the mixed source of agricultural activity and putting sandy gravel in farmland (10.6%). Cr and Ni, As and Cu, Hg, and Cd could represent these four sources of heavy metal pollution, respectively. The main sources of soil heavy metal pollution were mining activities and agricultural activities. The heavily contaminated areas were distributed in the mining areas in the south of the study area and in the planting areas in the eastern, central, and northwestern parts of the study area.}, } @article {pmid36435969, year = {2022}, author = {Kafkas, S and Ma, X and Zhang, X and Topçu, H and Navajas-Pérez, R and Wai, CM and Tang, H and Xu, X and Khodaeiaminjan, M and Güney, M and Paizila, A and Karcı, H and Zhang, X and Lin, J and Lin, H and Herrán, R and Rejón, CR and García-Zea, JA and Robles, F and Muñoz, CDV and Hotz-Wagenblatt, A and Min, XJ and Özkan, H and Motalebipour, EZ and Gozel, H and Çoban, N and Kafkas, NE and Kilian, A and Huang, H and Lv, X and Liu, K and Hu, Q and Jacygrad, E and Palmer, W and Michelmore, R and Ming, R}, title = {Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution.}, journal = {Plant communications}, volume = {}, number = {}, pages = {100497}, doi = {10.1016/j.xplc.2022.100497}, pmid = {36435969}, issn = {2590-3462}, abstract = {Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.}, } @article {pmid36429843, year = {2022}, author = {Zhang, T and Wang, B and Ge, Y and Li, C}, title = {Research on Green Space Service Space Based on Crowd Aggregation and Activity Characteristics under Big Data-Take Tacheng City as an Example.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {22}, pages = {}, pmid = {36429843}, issn = {1660-4601}, mesh = {Humans ; *Parks, Recreational ; *Big Data ; Cities ; Personal Satisfaction ; }, abstract = {People-oriented planning has become the mainstream of urban space design. As an important research object of urban space, the accessibility and service level of accessibility and service level of green space as important indicators to evaluate the level of urban livability cannot be truly fed back to people's daily life. Therefore, based on big data and from the perspective of crowd activities and aggregation characteristics, this study analyzes the shortage of green space service space in Tacheng City and puts forward suggestions for improvement. The main conclusions are as follows: (1) The satisfaction of green space based on service scope covers up the imbalance of green space resources enjoyed by actual crowd activities and aggregation. (2) Although the accessibility of green space obtained by population density meets the needs in space, it cannot take care of the potential needs generated by daily crowd activities and aggregation, which leads to the overall spatial imbalance of accessibility. (3) The comprehensive analysis shows that the northeast and southwest regions are the focus of the later planning and construction. The southwest region echoes with the old urban area and attracts people's daily activities. The woodland in the northeast region, as the main green space supply, meets the potential needs of the daily population activities and aggregation of the new development urban area and the old urban area, and also serves as a place for rest and entertainment to meet the needs of the activities and aggregation of the accidental behavior of the people in the new and old urban areas after the opening up.}, } @article {pmid36421254, year = {2022}, author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Triebelhorn, J and Burgkart, R and Obermeier, A and Mayr, U and Heller, S and Rasch, S and Lahmer, T and Geisler, F and Chan, B and Turner, PE and Rothe, K and Spinner, CD and Schneider, J}, title = {A Novel Machine Learning-Based Point-Score Model as a Non-Invasive Decision-Making Tool for Identifying Infected Ascites in Patients with Hydropic Decompensated Liver Cirrhosis: A Retrospective Multicentre Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36421254}, issn = {2079-6382}, abstract = {This study is aimed at assessing the distinctive features of patients with infected ascites and liver cirrhosis and developing a scoring system to allow for the accurate identification of patients not requiring abdominocentesis to rule out infected ascites. A total of 700 episodes of patients with decompensated liver cirrhosis undergoing abdominocentesis between 2006 and 2020 were included. Overall, 34 clinical, drug, and laboratory features were evaluated using machine learning to identify key differentiation criteria and integrate them into a point-score model. In total, 11 discriminatory features were selected using a Lasso regression model to establish a point-score model. Considering pre-test probabilities for infected ascites of 10%, 15%, and 25%, the negative and positive predictive values of the point-score model for infected ascites were 98.1%, 97.0%, 94.6% and 14.9%, 21.8%, and 34.5%, respectively. Besides the main model, a simplified model was generated, containing only features that are fast to collect, which revealed similar predictive values. Our point-score model appears to be a promising non-invasive approach to rule out infected ascites in clinical routine with high negative predictive values in patients with hydropic decompensated liver cirrhosis, but further external validation in a prospective study is needed.}, } @article {pmid36419146, year = {2022}, author = {Atkins, S and Heimo, L and Carter, DJ and Ribas Closa, M and Vanleeuw, L and Chenciner, L and Wambi, P and Sidney-Annerstedt, K and Egere, U and Verkuijl, S and Brands, A and Masini, T and Viney, K and Wingfield, T and Lönnroth, K and Boccia, D}, title = {The socioeconomic impact of tuberculosis on children and adolescents: a scoping review and conceptual framework.}, journal = {BMC public health}, volume = {22}, number = {1}, pages = {2153}, pmid = {36419146}, issn = {1471-2458}, support = {001/WHO_/World Health Organization/International ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Child ; Humans ; Adolescent ; *Tuberculosis/epidemiology ; Social Stigma ; Databases, Factual ; Educational Status ; Knowledge ; }, abstract = {BACKGROUND: Tuberculosis (TB) has been repeatedly shown to have socioeconomic impacts in both individual-level and ecological studies; however, much less is known about this effect among children and adolescents and the extent to which being affected by TB during childhood and adolescence can have life-course implications. This paper describes the results of the development of a conceptual framework and scoping review to review the evidence on the short- and long-term socioeconomic impact of tuberculosis on children and adolescents.

OBJECTIVES: To increase knowledge of the socioeconomic impact of TB on children and adolescents.

METHODS: We developed a conceptual framework of the socioeconomic impact of TB on children and adolescents, and used scoping review methods to search for evidence supporting or disproving it. We searched four academic databases from 1 January 1990 to 6 April 2021 and conducted targeted searches of grey literature. We extracted data using a standard form and analysed data thematically.

RESULTS: Thirty-six studies (29 qualitative, five quantitative and two mixed methods studies) were included in the review. Overall, the evidence supported the conceptual framework, suggesting a severe socioeconomic impact of TB on children and adolescents through all the postulated pathways. Effects ranged from impoverishment, stigma, and family separation, to effects on nutrition and missed education opportunities. TB did not seem to exert a different socioeconomic impact when directly or indirectly affecting children/adolescents, suggesting that TB can affect this group even when they are not affected by the disease. No study provided sufficient follow-up to observe the long-term socioeconomic effect of TB in this age group.

CONCLUSION: The evidence gathered in this review reinforces our understanding of the impact of TB on children and adolescents and highlights the importance of considering effects during the entire life course. Both ad-hoc and sustainable social protection measures and strategies are essential to mitigate the socioeconomic consequences of TB among children and adolescents.}, } @article {pmid36418120, year = {2022}, author = {Kumpik, DP and Santos-Rodriguez, R and Selwood, J and Coulthard, E and Twomey, N and Craddock, I and Ben-Shlomo, Y}, title = {A longitudinal observational study of home-based conversations for detecting early dementia: protocol for the CUBOId TV task.}, journal = {BMJ open}, volume = {12}, number = {11}, pages = {e065033}, pmid = {36418120}, issn = {2044-6055}, mesh = {Humans ; Pregnancy ; Female ; *Cognitive Dysfunction/diagnosis/psychology ; Neuropsychological Tests ; Longitudinal Studies ; Biomarkers ; *Dementia/diagnosis/psychology ; Observational Studies as Topic ; }, abstract = {INTRODUCTION: Limitations in effective dementia therapies mean that early diagnosis and monitoring are critical for disease management, but current clinical tools are impractical and/or unreliable, and disregard short-term symptom variability. Behavioural biomarkers of cognitive decline, such as speech, sleep and activity patterns, can manifest prodromal pathological changes. They can be continuously measured at home with smart sensing technologies, and permit leveraging of interpersonal interactions for optimising diagnostic and prognostic performance. Here we describe the ContinUous behavioural Biomarkers Of cognitive Impairment (CUBOId) study, which explores the feasibility of multimodal data fusion for in-home monitoring of mild cognitive impairment (MCI) and early Alzheimer's disease (AD). The report focuses on a subset of CUBOId participants who perform a novel speech task, the 'TV task', designed to track changes in ecologically valid conversations with disease progression.

METHODS AND ANALYSIS: CUBOId is a longitudinal observational study. Participants have diagnoses of MCI or AD, and controls are their live-in partners with no such diagnosis. Multimodal activity data were passively acquired from wearables and in-home fixed sensors over timespans of 8-25 months. At two time points participants completed the TV task over 5 days by recording audio of their conversations as they watched a favourite TV programme, with further testing to be completed after removal of the sensor installations. Behavioural testing is supported by neuropsychological assessment for deriving ground truths on cognitive status. Deep learning will be used to generate fused multimodal activity-speech embeddings for optimisation of diagnostic and predictive performance from speech alone.

ETHICS AND DISSEMINATION: CUBOId was approved by an NHS Research Ethics Committee (Wales REC; ref: 18/WA/0158) and is sponsored by University of Bristol. It is supported by the National Institute for Health Research Clinical Research Network West of England. Results will be reported at conferences and in peer-reviewed scientific journals.}, } @article {pmid36414269, year = {2022}, author = {Nguyen, PY and Kanukula, R and McKenzie, JE and Alqaidoom, Z and Brennan, SE and Haddaway, NR and Hamilton, DG and Karunananthan, S and McDonald, S and Moher, D and Nakagawa, S and Nunan, D and Tugwell, P and Welch, VA and Page, MJ}, title = {Changing patterns in reporting and sharing of review data in systematic reviews with meta-analysis of the effects of interventions: cross sectional meta-research study.}, journal = {BMJ (Clinical research ed.)}, volume = {379}, number = {}, pages = {e072428}, pmid = {36414269}, issn = {1756-1833}, mesh = {Humans ; Cross-Sectional Studies ; PubMed ; *Research Design ; Systematic Reviews as Topic ; *Information Dissemination ; }, abstract = {OBJECTIVES: To examine changes in completeness of reporting and frequency of sharing data, analytical code, and other review materials in systematic reviews over time; and factors associated with these changes.

DESIGN: Cross sectional meta-research study.

POPULATION: Random sample of 300 systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioural, or educational intervention. Reviews were indexed in PubMed, Science Citation Index, Social Sciences Citation Index, Scopus, and Education Collection in November 2020.

MAIN OUTCOME MEASURES: The extent of complete reporting and the frequency of sharing review materials in the systematic reviews indexed in 2020 were compared with 110 systematic reviews indexed in February 2014. Associations between completeness of reporting and various factors (eg, self-reported use of reporting guidelines, journal policies on data sharing) were examined by calculating risk ratios and 95% confidence intervals.

RESULTS: Several items were reported suboptimally among 300 systematic reviews from 2020, such as a registration record for the review (n=113; 38%), a full search strategy for at least one database (n=214; 71%), methods used to assess risk of bias (n=185; 62%), methods used to prepare data for meta-analysis (n=101; 34%), and source of funding for the review (n=215; 72%). Only a few items not already reported at a high frequency in 2014 were reported more frequently in 2020. No evidence indicated that reviews using a reporting guideline were more completely reported than reviews not using a guideline. Reviews published in 2020 in journals that mandated either data sharing or inclusion of data availability statements were more likely to share their review materials (eg, data, code files) than reviews in journals without such mandates (16/87 (18%) v 4/213 (2%)).

CONCLUSION: Incomplete reporting of several recommended items for systematic reviews persists, even in reviews that claim to have followed a reporting guideline. Journal policies on data sharing might encourage sharing of review materials.}, } @article {pmid36412269, year = {2022}, author = {Ebenezer, TE and Low, RS and O'Neill, EC and Huang, I and DeSimone, A and Farrow, SC and Field, RA and Ginger, ML and Guerrero, SA and Hammond, M and Hampl, V and Horst, G and Ishikawa, T and Karnkowska, A and Linton, EW and Myler, P and Nakazawa, M and Cardol, P and Sánchez-Thomas, R and Saville, BJ and Shah, MR and Simpson, AGB and Sur, A and Suzuki, K and Tyler, KM and Zimba, PV and Hall, N and Field, MC}, title = {Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world.}, journal = {Biology open}, volume = {11}, number = {11}, pages = {}, doi = {10.1242/bio.059561}, pmid = {36412269}, issn = {2046-6390}, mesh = {*Euglena/physiology ; Biotechnology ; Symbiosis ; }, abstract = {Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.}, } @article {pmid36408293, year = {2022}, author = {Ebdon, S and Bisschop, G and Lohse, K and Saccheri, I and Davies, J and , and , and , and , }, title = {The genome sequence of the orange-tip butterfly, Anthocharis cardamines (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {260}, pmid = {36408293}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.}, } @article {pmid36407110, year = {2022}, author = {Michel, L and Palma, K and Cerda, M and Lagadec, R and Mayeur, H and Fuentès, M and Besseau, L and Martin, P and Magnanou, E and Blader, P and Concha, ML and Mazan, S}, title = {Diversification of habenular organization and asymmetries in teleosts: Insights from the Atlantic salmon and European eel.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {1015074}, pmid = {36407110}, issn = {2296-634X}, abstract = {Habenulae asymmetries are widespread across vertebrates and analyses in zebrafish, the reference model organism for this process, have provided insight into their molecular nature, their mechanisms of formation and their important roles in the integration of environmental and internal cues with a variety of organismal adaptive responses. However, the generality of the characteristics identified in this species remains an open question, even on a relatively short evolutionary scale, in teleosts. To address this question, we have characterized the broad organization of habenulae in the Atlantic salmon and quantified the asymmetries in each of the identified subdomains. Our results show that a highly conserved partitioning into a dorsal and a ventral component is retained in the Atlantic salmon and that asymmetries are mainly observed in the former as in zebrafish. A remarkable difference is that a prominent left-restricted pax6 positive nucleus is observed in the Atlantic salmon, but undetectable in zebrafish. This nucleus is not observed outside teleosts, and harbors a complex presence/absence pattern in this group, retaining its location and cytoarchitectonic organization in an elopomorph, the European eel. These findings suggest an ancient origin and high evolvability of this trait in the taxon. Taken together, our data raise novel questions about the variability of asymmetries across teleosts and their biological significance depending on ecological contexts.}, } @article {pmid36405737, year = {2022}, author = {Yousaf, M and Ismail, S and Ullah, A and Bibi, S}, title = {Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1035924}, pmid = {36405737}, issn = {1664-3224}, mesh = {Humans ; *Monkeypox virus ; Molecular Docking Simulation ; Membrane Proteins ; *Monkeypox ; Vaccines, Subunit ; Epitopes, T-Lymphocyte ; }, abstract = {Monkeypox is a viral etiological agent with hallmarks analogous to those observed in smallpox cases in the past. The ongoing outbreak of Monkeypox viral infection is becoming a global health problem. Multi-valent peptide based next generation vaccines provides us a promising solution to combat these emerging infectious diseases by eliciting cell-mediated and humoral immune response. Considering the success rate of subtractive proteomics pipeline and reverse vaccinology approach, in this study, we have developed a novel, next-generation, multi-valent, in silico peptide based vaccine construct by employing cell surface binding protein. After analyzing physiochemical and biological properties of the selected target, the protein was subjected to B cell derived T cell epitope mapping. Iterative scrutinization lead to the identification of two highly antigenic, virulent, non-allergic, non-toxic, water soluble, and Interferon-gamma inducer epitopes i.e. HYITENYRN and TTSPVRENY. We estimated that the shortlisted epitopes for vaccine construction, roughly correspond to 99.74% of the world's population. UK, Finland and Sweden had the highest overall population coverage at 100% which is followed by Austria (99.99%), Germany (99.99%), France (99.98%), Poland (99.96), Croatia (99.93), Czech Republic (99.87%), Belgium (99.87), Italy (99.86%), China (97.83%), India (97.35%) and Pakistan (97.13%). The designed vaccine construct comprises of 150 amino acids with a molecular weight of 16.97242 kDa. Molecular docking studies of the modelled MEMPV (Multi-epitope Monkeypox Vaccine) with MHC I (PDB ID: 1I1Y), MHC II (PDB ID: 1KG0), and other immune mediators i.e. toll like receptors TLR3 (PDB ID: 2A0Z), and TLR4 (PDB ID: 4G8A) revealed strong binding affinity with immune receptors. Host immune simulation results predicted that the designed vaccine has strong potency to induce immune responses against target pathogen in the form of cellular and antibody-dependent immunity. Our findings suggest that the hypothesized vaccine candidate can be utilized as a potential therapeutic against Monkeypox however experimental study is required to validate the results and safe immunogenicity.}, } @article {pmid36399496, year = {2022}, author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac1049}, pmid = {36399496}, issn = {1362-4962}, support = {GM134688/NH/NIH HHS/United States ; BBSRC/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid36394851, year = {2022}, author = {Zhang, L and Gong, R and Shi, L and Wen, M and Sun, X and Yabroff, KR and Han, X}, title = {Association of Residential Racial and Economic Segregation With Cancer Mortality in the US.}, journal = {JAMA oncology}, volume = {}, number = {}, pages = {}, pmid = {36394851}, issn = {2374-2445}, abstract = {IMPORTANCE: Residential segregation is a structural risk factor for poor cancer outcomes. Previous research examining the association of residential segregation with cancer outcomes was limited by older data, restricted geographic areas, and few cancer sites. To guide targeted interventions, a comprehensive evaluation of the association between segregation and cancer outcomes is needed.

OBJECTIVE: To examine the association of residential racial and economic segregation with cancer mortality at the US county level for all cancers combined and for the 13 cancer types that represent the top 10 causes of cancer deaths in males or females.

This ecological study used county-level sociodemographic data from the 2015-2019 American Community Survey linked with 2015-2019 county-level mortality data. Data analysis was performed from September 2021 to April 2022.

EXPOSURES: Residential racial and economic segregation measured by the Index of Concentration at the Extremes (ICE) and categorized into quintiles 1 (most deprived) through 5 (most privileged).

MAIN OUTCOMES AND MEASURES: Age-adjusted cancer mortality was the outcome. Multilevel linear mixed modeling was used to calculate the adjusted mortality rate ratio (aRR).

RESULTS: A total of 3110 counties were included. The age-adjusted mortality rates of all cancers combined were 179.8, 177.3, 167.6, 159.6, and 146.1 per 100 000 population (P < .001 for trend) for the 5 ICE categories (most deprived to least deprived), respectively. Compared with the least deprived counties, aRRs for all cancers combined were 1.22 (95% CI, 1.20-1.24) for the most deprived counties, followed by 1.17 (95% CI, 1.15-1.19), 1.10 (95% CI, 1.09-1.12), and 1.06 (95% CI, 1.04-1.08) for the other 3 quintiles, respectively (P < .001 for trend). Segregation was associated with increased mortality from 12 of 13 selected cancer sites, in which aRRs ranged from 1.06 (95% CI, 1.02-1.09) for brain and other nervous system cancer to 1.49 (95% CI, 1.43-1.54) for lung and bronchus cancer.

CONCLUSIONS AND RELEVANCE: The findings of this ecological study suggest that residential racial and economic segregation is associated with higher cancer mortality at the county level, highlighting opportunities for geographically targeted cancer prevention and control efforts.}, } @article {pmid36383289, year = {2022}, author = {McGuinness, KN and Klau, GW and Morrison, SM and Moore, EK and Seipp, J and Falkowski, PG and Nanda, V}, title = {Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {52}, number = {4}, pages = {263-275}, pmid = {36383289}, issn = {1573-0875}, support = {K12GM093854/NH/NIH HHS/United States ; K12GM093854/NH/NIH HHS/United States ; }, mesh = {*Metalloproteins ; Minerals ; *Iron-Sulfur Proteins/chemistry/metabolism ; Sulfur/chemistry/metabolism ; Iron/chemistry ; }, abstract = {Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfide minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infinite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are finite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a finite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere.}, } @article {pmid36378489, year = {2022}, author = {Gupta, VK and Bakshi, U and Chang, D and Lee, AR and Davis, JM and Chandrasekaran, S and Jin, YS and Freeman, MF and Sung, J}, title = {TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0092522}, pmid = {36378489}, issn = {2379-5077}, mesh = {Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Multigene Family/genetics ; }, abstract = {Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.}, } @article {pmid36378100, year = {2022}, author = {Oh, AY and Rising, CJ and Gaysynsky, A and Tsakraklides, S and Huang, GC and Chou, WS and Blake, KD and Vanderpool, RC}, title = {Advancing multi-level health communication research: A Delphi study on barriers and opportunities.}, journal = {Translational behavioral medicine}, volume = {12}, number = {12}, pages = {1133-1145}, doi = {10.1093/tbm/ibac068}, pmid = {36378100}, issn = {1613-9860}, support = {HHSN261201800002B/CA/NCI NIH HHS/United States ; HHSN261201800002B/CA/NCI NIH HHS/United States ; }, abstract = {Adopting a multi-level perspective that considers the many interrelated contexts influencing health could make health communication interventions more effective and equitable. However, despite increasing interest in the use of multi-level approaches, multi-level health communication (MLHC) interventions are infrequently utilized. We therefore sought to conduct a modified Delphi study to better understand how researchers conceptualize MLHC interventions and identify opportunities for advancing MLHC work. Communication and health behavior experts were invited to complete two rounds of surveys about the characteristics, benefits, pitfalls, best practices, barriers, and facilitators of MLHC interventions; the role of technology in facilitating MLHC interventions; and ways to advance MLHC intervention research (46 experts completed the first survey, 44 completed both surveys). Survey data were analyzed using a mixed-methods approach. Panelists reached consensus on two components of the proposed definition of MLHC interventions and also put forward a set of best practices for these interventions. Panelists felt that most health intervention research could benefit from a multi-level approach, and generally agreed that MLHC approaches offered certain advantages over single-level approaches. However, they also expressed concern related to the time, cost, and complexity of MLHC interventions. Although panelists felt that technology could potentially support MLHC interventions, they also recognized the potential for technology to exacerbate disparities. Finally, panelists prioritized a set of methodological advances and practical supports that would be needed to facilitate future MLHC intervention research. The results of this study point to several future directions for the field, including advancing how interactions between levels are assessed, increasing the empirical evidence base demonstrating the advantages of MLHC interventions, and identifying best practices for the use of technology. The findings also suggest that researchers may need additional support to overcome the perceived practical challenges of conducting MLHC interventions.}, } @article {pmid36374834, year = {2022}, author = {Boyle, BL and Maitner, BS and Barbosa, GGC and Sajja, RK and Feng, X and Merow, C and Newman, EA and Park, DS and Roehrdanz, PR and Enquist, BJ}, title = {Geographic name resolution service: A tool for the standardization and indexing of world political division names, with applications to species distribution modeling.}, journal = {PloS one}, volume = {17}, number = {11}, pages = {e0268162}, pmid = {36374834}, issn = {1932-6203}, mesh = {Databases, Factual ; *Biodiversity ; *Names ; Reference Standards ; }, abstract = {Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This otherwise simple validation is complicated by the difficulty of matching political division names to the correct geospatial object. Spelling errors, abbreviations, alternative codes, and synonyms in multiple languages present daunting name disambiguation challenges. The inability to resolve political division names reduces usable data, and analysis of erroneous observations can lead to flawed results. Here, we present the Geographic Name Resolution Service (GNRS), an application for correcting, standardizing, and indexing world political division names. The GNRS resolves political division names against a reference database that combines names and codes from GeoNames with geospatial object identifiers from the Global Administrative Areas Database (GADM). In a trial resolution of political division names extracted from >270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In assessing geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled the detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a significant data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and is accessible via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows.}, } @article {pmid36365380, year = {2022}, author = {Ganie, IB and Ahmad, Z and Shahzad, A and Zaushintsena, A and Neverova, O and Ivanova, S and Wasi, A and Tahseen, S}, title = {Biotechnological Intervention and Secondary Metabolite Production in Centella asiatica L.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36365380}, issn = {2223-7747}, abstract = {Centella asiatica L., commonly known as Gotu kola, Indian pennywort, and Asiatic pennyworts, is an herbaceous perennial plant that belongs to the family Apiaceae and has long been used in the traditional medicine system. The plant is known to produce a wide range of active metabolites such as triterpenoids including asiatic acid, asiaticoside, brahmoside, and madecassic acid along with other constituents including centellose, centelloside, and madecassoside, etc., which show immense pharmacological activity. Due to its beneficial role in neuroprotection activity, the plant has been considered as a brain tonic. However, limited cultivation, poor seed viability with low germination rate, and overexploitation for decades have led to severe depletion and threatened its wild stocks. The present review aimed to provide up-to-date information on biotechnological tools applied to this endangered medicinal plant for its in vitro propagation, direct or indirect regeneration, synthetic seed production, strategies for secondary metabolite productions including different elicitors. In addition, a proposed mechanism for the biosynthesis of triterpenoids is also discussed.}, } @article {pmid36362326, year = {2022}, author = {Decewicz, P and Kitowicz, M and Radlinska, M}, title = {Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36362326}, issn = {1422-0067}, mesh = {*Bacteriophages ; Prophages/genetics ; Sequence Analysis, DNA ; Computational Biology ; Genomics ; Genome, Viral ; }, abstract = {Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages.}, } @article {pmid36357425, year = {2022}, author = {Oliveira-Rodrigues, C and Correia, AM and Valente, R and Gil, Á and Gandra, M and Liberal, M and Rosso, M and Pierce, G and Sousa-Pinto, I}, title = {Assessing data bias in visual surveys from a cetacean monitoring programme.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {682}, pmid = {36357425}, issn = {2052-4463}, mesh = {Animals ; *Cetacea/physiology ; Data Collection ; Datasets as Topic ; Bias ; }, abstract = {Long-term monitoring datasets are fundamental to understand physical and ecological responses to environmental changes, supporting management and conservation. The data should be reliable, with the sources of bias identified and quantified. CETUS Project is a cetacean monitoring programme in the Eastern North Atlantic, based on visual methods of data collection. This study aims to assess data quality and bias in the CETUS dataset, by 1) applying validation methods, through photographic confirmation of species identification; 2) creating data quality criteria to evaluate the observer's experience; and 3) assessing bias to the number of sightings collected and to the success in species identification. Through photographic validation, the species identification of 10 sightings was corrected and a new species was added to the CETUS dataset. The number of sightings collected was biased by external factors, mostly by sampling effort but also by weather conditions. Ultimately, results highlight the importance of identifying and quantifying data bias, while also yielding guidelines for data collection and processing, relevant for species monitoring programmes based on visual methods.}, } @article {pmid36352171, year = {2022}, author = {Mohsen, A and Zeidan, B and Elshemy, M}, title = {Water quality assessment of Lake Burullus, Egypt, utilizing statistical and GIS modeling as environmental hydrology applications.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {93}, pmid = {36352171}, issn = {1573-2959}, mesh = {*Water Quality ; *Lakes ; Hydrology ; Geographic Information Systems ; Egypt ; Environmental Monitoring/methods ; }, abstract = {GIS is a very powerful tool for analyzing huge amount of data and connecting them with the geography; moreover, recently, there is great advancement in the field. The main objective of this study is to assess the water quality (WQ) and trophic status (TS) conditions of Lake Burullus, Egypt, using statistical modeling (PCA/FA and CA), WQ index (L-WQI), and trophic status index (Carlson TSI and TRIX) approaches, in addition to using GIS tools for building models able to automatically calculate the various indices and producing color coded maps for the lake. The results indicated that PCA/FA grouped the twenty-four WQ parameters into nine principal components explaining 72.6% of the total variance, domestic, and agriculture pollution were dominant. CA divided the twelve sampling stations into most and least polluted groups. The lake WQ was classified as a "Very Poor," according to L-WQI. Moreover, the results of the Carlson TSI and TRIX indices were coincided and classified the eutrophication levels in the lake as "Hyper-Eutrophic" and "Elevated Trophic," respectively. Based on the results of this study, Lake Burullus needs urgent plans for recovering its WQ. Pre-treatment for its drains' effluents and implementing of a periodical WQ monitoring program are highly recommended.}, } @article {pmid36350456, year = {2022}, author = {Zhang, X and Dong, X and Liu, F and Lv, T and Wu, Z and Ranagalage, M}, title = {Spatiotemporal dynamics of ecological security in a typical conservation region of southern China based on catastrophe theory and GIS.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {90}, pmid = {36350456}, issn = {1573-2959}, mesh = {*Ecology/methods ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Environmental Monitoring ; Ecosystem ; China ; }, abstract = {Ecological security assessment can effectively reflect the ecological status of a region and reveal its level of sustainable development. In this paper, an ecological security-oriented evaluation system was constructed, and the ecological security level of the Dongjiangyuan region from 2000 to 2020 was evaluated based on catastrophe theory and GIS. The results were as follows: (1) As shown in the land use and cover maps, by 2020, the forestland area had decreased the most, and the artificial surface area had increased the most. (2) The ecological security index of the Dongjiangyuan region showed a low trend in the artificial surface area and its surrounding areas. The quite low values of the ecological security index in 2000 and 2010 were improved in 2020 due to the increase in ecological services capacity. The increased vegetation cover from 2000 to 2020 promoted the improved ecological service capacity. (3) The rapid urbanization process in the Dongjiangyuan region resulted in a lower ecological sensitivity index value. Notably, the ecological sensitivity index of the study area had a slightly decreasing trend. (4) The spatial autocorrelation showed that the proportion of hot and cold spots from 2000 to 2020 decreased by 2.96% and 6.91%, respectively. This study can provide a scientific basis and decision-making guidance for ecological management in the Dongjiangyuan region in the future.}, } @article {pmid36348471, year = {2022}, author = {Baaijens, JA and Zulli, A and Ott, IM and Nika, I and van der Lugt, MJ and Petrone, ME and Alpert, T and Fauver, JR and Kalinich, CC and Vogels, CBF and Breban, MI and Duvallet, C and McElroy, KA and Ghaeli, N and Imakaev, M and Mckenzie-Bennett, MF and Robison, K and Plocik, A and Schilling, R and Pierson, M and Littlefield, R and Spencer, ML and Simen, BB and , and Hanage, WP and Grubaugh, ND and Peccia, J and Baym, M}, title = {Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {236}, pmid = {36348471}, issn = {1474-760X}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; TL1 TR001864/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *SARS-CoV-2/genetics ; Wastewater ; RNA, Viral/genetics ; Transcriptome ; *COVID-19 ; }, abstract = {Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.}, } @article {pmid36344967, year = {2022}, author = {Toh, H and Yang, C and Formenti, G and Raja, K and Yan, L and Tracey, A and Chow, W and Howe, K and Bergeron, LA and Zhang, G and Haase, B and Mountcastle, J and Fedrigo, O and Fogg, J and Kirilenko, B and Munegowda, C and Hiller, M and Jain, A and Kihara, D and Rhie, A and Phillippy, AM and Swanson, SA and Jiang, P and Clegg, DO and Jarvis, ED and Thomson, JA and Stewart, R and Chaisson, MJP and Bukhman, YV}, title = {A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {245}, pmid = {36344967}, issn = {1741-7007}, mesh = {Humans ; Animals ; Haplotypes ; *Diabetes Mellitus, Type 2/genetics ; Murinae ; Genome ; Genomics ; }, abstract = {BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.

RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.

CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.}, } @article {pmid36333350, year = {2022}, author = {Zhang, X and Zhang, B and Li, J and Yao, Y and Wang, J and Liu, J and Yu, F}, title = {A database of seed plants on taxonomy, geography and ecology in the Qinling-Daba Mountains and adjacent areas.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {672}, pmid = {36333350}, issn = {2052-4463}, mesh = {Humans ; *Biodiversity ; China ; Ecology ; Ecosystem ; Geography ; Plants ; *Seeds ; Databases, Factual ; }, abstract = {The Qinling-Daba Mountains span subtropical and warm temperate zones and are one of the most remarkable biodiversity hotspots in China. Establishing a complete checklist of seed plants organized by nature reserves in the Qinling-Daba Mountains and adjacent areas is an important basis for managing and utilizing plant resources. First, we collected seed plant species data from published checklists representing 58 nature reserves in the Qinling-Daba Mountains and adjacent areas; second, we comprehensively and systematically sorted and integrated these data; third, we proofread and revised the data with the help of the R language and Flora of China dataset; and finally, we set up a seed plant database containing 96148 records, including the name, order, family, genus, life form, and endemism of each species for the entirety of the Qinling-Daba Mountains. The database contains 9491 species of seed plants belonging to 1729 genera, 211 families, and 59 orders, accounting for 39% of China's seed plants.}, } @article {pmid36329351, year = {2022}, author = {Pillay, R and Watson, JEM and Hansen, AJ and Jantz, PA and Aragon-Osejo, J and Armenteras, D and Atkinson, SC and Burns, P and Ervin, J and Goetz, SJ and González-Del-Pliego, P and Robinson, NP and Supples, C and Virnig, ALS and Williams, BA and Venter, O}, title = {Humid tropical vertebrates are at lower risk of extinction and population decline in forests with higher structural integrity.}, journal = {Nature ecology & evolution}, volume = {6}, number = {12}, pages = {1840-1849}, pmid = {36329351}, issn = {2397-334X}, mesh = {Animals ; Humans ; *Tropical Climate ; *Conservation of Natural Resources ; Forests ; Biodiversity ; Vertebrates ; }, abstract = {Reducing deforestation underpins global biodiversity conservation efforts. However, this focus on retaining forest cover overlooks the multitude of anthropogenic pressures that can degrade forest quality and imperil biodiversity. We use remotely sensed indices of tropical rainforest structural condition and associated human pressures to quantify the relative importance of forest cover, structural condition and integrity (the cumulative effect of condition and pressures) on vertebrate species extinction risk and population trends across the global humid tropics. We found that tropical rainforests of high integrity (structurally intact and under low pressures) were associated with lower likelihood of species being threatened and having declining populations, compared with forest cover alone (without consideration of condition and pressures). Further, species were more likely to be threatened or have declining populations if their geographic ranges contained high proportions of degraded forest than if their ranges contained lower proportions of forest cover but of high quality. Our work suggests that biodiversity conservation policies to preserve forest integrity are now urgently required alongside ongoing efforts to halt deforestation in the hyperdiverse humid tropics.}, } @article {pmid36324785, year = {2022}, author = {Gao, Y and Gong, L and Liu, H and Kong, Y and Wu, X and Guo, Y and Hu, D}, title = {Research on the influencing factors of users' information processing in online health communities based on heuristic-systematic model.}, journal = {Frontiers in psychology}, volume = {13}, number = {}, pages = {966033}, pmid = {36324785}, issn = {1664-1078}, abstract = {With the rapid development of the Internet and the normalization of COVID-19 epidemic prevention and control, Online health communities (OHCs) have gradually become one of the important ways for people to obtain health information, and users have to go through a series of information processing when facing the massive amount of data. Understanding the factors influencing user information processing is necessary to promote users' health literacy, health knowledge popularization and health behavior shaping. Based on the Heuristic-Systematic Model (HSM), Information Ecology Theory, Privacy Trade-Off and Self-Efficacy Theory, we constructed a model of factors influencing user information processing in online health communities. We found that information quality and emotional support had indirect effects on heuristic and systematic information processing, and these effects were mediated by privacy concerns and self-efficacy. In our research model, systematic information processing was most positively influenced directly by self-efficacy. Privacy concerns had a direct negative correlation with both dual information processing pathways. Therefore, OHCs managers should develop relevant regulations to ensure the information quality in OHCs and improve privacy protection services to promote user information processing by improving users' self-efficacy and reducing their privacy concerns. Providing a user-friendly and interactive environment for users is also recommended to create more emotional support, thus facilitating more systematic information processing.}, } @article {pmid36324701, year = {2022}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the angle shades moth, Phlogophora meticulosa (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {89}, pmid = {36324701}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Phlogophora meticulosa (the angle shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 539 megabases in span. The majority of the assembly, 95.17%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Some unassigned scaffolds are identified as belonging to the W chromosome based on half-depth coverage and comparison to other Noctuidae W chromosomes. The mitochondrial genome was also assembled and is 15.4 kilobases in length.}, } @article {pmid36323316, year = {2022}, author = {Vatanen, T and Ang, QY and Siegwald, L and Sarker, SA and Le Roy, CI and Duboux, S and Delannoy-Bruno, O and Ngom-Bru, C and Boulangé, CL and Stražar, M and Avila-Pacheco, J and Deik, A and Pierce, K and Bullock, K and Dennis, C and Sultana, S and Sayed, S and Rahman, M and Ahmed, T and Modesto, M and Mattarelli, P and Clish, CB and Vlamakis, H and Plichta, DR and Sakwinska, O and Xavier, RJ}, title = {A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning.}, journal = {Cell}, volume = {185}, number = {23}, pages = {4280-4297.e12}, doi = {10.1016/j.cell.2022.10.011}, pmid = {36323316}, issn = {1097-4172}, mesh = {Infant ; Child ; Female ; Humans ; Child, Preschool ; *Bifidobacterium longum/metabolism ; Bifidobacterium/metabolism ; Weaning ; Oligosaccharides/metabolism ; Bangladesh ; Milk, Human ; Feces/microbiology ; }, abstract = {The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis, indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development.}, } @article {pmid36322519, year = {2022}, author = {Wood, ALC and Kirby, KR and Ember, CR and Silbert, S and Passmore, S and Daikoku, H and McBride, J and Paulay, F and Flory, MJ and Szinger, J and D'Arcangelo, G and Bradley, KK and Guarino, M and Atayeva, M and Rifkin, J and Baron, V and El Hajli, M and Szinger, M and Savage, PE}, title = {The Global Jukebox: A public database of performing arts and culture.}, journal = {PloS one}, volume = {17}, number = {11}, pages = {e0275469}, pmid = {36322519}, issn = {1932-6203}, mesh = {Humans ; Reproducibility of Results ; *Music ; Cross-Cultural Comparison ; Language ; Databases, Factual ; Culture ; }, abstract = {Standardized cross-cultural databases of the arts are critical to a balanced scientific understanding of the performing arts, and their role in other domains of human society. This paper introduces the Global Jukebox as a resource for comparative and cross-cultural study of the performing arts and culture. The Global Jukebox adds an extensive and detailed global database of the performing arts that enlarges our understanding of human cultural diversity. Initially prototyped by Alan Lomax in the 1980s, its core is the Cantometrics dataset, encompassing standardized codings on 37 aspects of musical style for 5,776 traditional songs from 1,026 societies. The Cantometrics dataset has been cleaned and checked for reliability and accuracy, and includes a full coding guide with audio training examples (https://theglobaljukebox.org/?songsofearth). Also being released are seven additional datasets coding and describing instrumentation, conversation, popular music, vowel and consonant placement, breath management, social factors, and societies. For the first time, all digitized Global Jukebox data are being made available in open-access, downloadable format (https://github.com/theglobaljukebox), linked with streaming audio recordings (theglobaljukebox.org) to the maximum extent allowed while respecting copyright and the wishes of culture-bearers. The data are cross-indexed with the Database of Peoples, Languages, and Cultures (D-PLACE) to allow researchers to test hypotheses about worldwide coevolution of aesthetic patterns and traditions. As an example, we analyze the global relationship between song style and societal complexity, showing that they are robustly related, in contrast to previous critiques claiming that these proposed relationships were an artifact of autocorrelation (though causal mechanisms remain unresolved).}, } @article {pmid36316770, year = {2022}, author = {Ohashi, K and Osanai, T and Fujiwara, K and Tanikawa, T and Tani, Y and Takamiya, S and Sato, H and Morii, Y and Bando, K and Ogasawara, K}, title = {Spatial-temporal analysis of cerebral infarction mortality in Hokkaido, Japan: an ecological study using a conditional autoregressive model.}, journal = {International journal of health geographics}, volume = {21}, number = {1}, pages = {16}, pmid = {36316770}, issn = {1476-072X}, mesh = {Humans ; Bayes Theorem ; Japan/epidemiology ; *Stroke ; Socioeconomic Factors ; Cerebral Infarction/diagnosis/epidemiology/therapy ; }, abstract = {BACKGROUND: Accessibility to stroke treatments is a challenge that depends on the place of residence. However, recent advances in medical technology have improved health outcomes. Nevertheless, the geographic heterogeneity of medical resources may increase regional disparities. Therefore, evaluating spatial and temporal influences of the medical system on regional outcomes and advanced treatment of cerebral infarction are important from a health policy perspective. This spatial and temporal study aims to identify factors associated with mortality and to clarify regional disparities in cerebral infarction mortality at municipality level.

METHODS: This ecological study used public data between 2010 and 2020 from municipalities in Hokkaido, Japan. We applied spatial and temporal condition autoregression analysis in a Bayesian setting, with inference based on the Markov chain Monte Carlo simulation. The response variable was the number of deaths due to cerebral infarction (ICD-10 code: I63). The explanatory variables were healthcare accessibility and socioeconomic status.

RESULTS: The large number of emergency hospitals per 10,000 people (relative risk (RR) = 0.906, credible interval (Cr) = 0.861 to 0.954) was associated with low mortality. On the other hand, the large number of general hospitals per 10,000 people (RR = 1.123, Cr = 1.068 to 1.178) and longer distance to primary stroke centers (RR = 1.064, Cr = 1.014 to 1.110) were associated with high mortality. The standardized mortality ratio decreased from 2010 to 2020 in Hokkaido by approximately 44%. Regional disparity in mortality remained at the same level from 2010 to 2015, after which it narrowed by approximately 5% to 2020. After mapping, we identified municipalities with high mortality rates that emerged in Hokkaido's central and northeastern parts.

CONCLUSION: Cerebral infarction mortality rates and the disparity in Hokkaido improved during the study period (2010-2020). This study emphasized that healthcare accessibility through places such as emergency hospitals and primary stroke centers was important in determining cerebral infarction mortality at the municipality level. In addition, this study identified municipalities with high mortality rates that require healthcare policy changes. The impact of socioeconomic factors on stroke is a global challenge, and improving access to healthcare may reduce disparities in outcomes.}, } @article {pmid36316345, year = {2022}, author = {Yfantidou, S and Karagianni, C and Efstathiou, S and Vakali, A and Palotti, J and Giakatos, DP and Marchioro, T and Kazlouski, A and Ferrari, E and Girdzijauskas, Š}, title = {LifeSnaps, a 4-month multi-modal dataset capturing unobtrusive snapshots of our lives in the wild.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {663}, pmid = {36316345}, issn = {2052-4463}, mesh = {Humans ; *Ecological Momentary Assessment ; Exercise ; *Mental Health ; Sleep ; Surveys and Questionnaires ; }, abstract = {Ubiquitous self-tracking technologies have penetrated various aspects of our lives, from physical and mental health monitoring to fitness and entertainment. Yet, limited data exist on the association between in the wild large-scale physical activity patterns, sleep, stress, and overall health, and behavioral and psychological patterns due to challenges in collecting and releasing such datasets, including waning user engagement or privacy considerations. In this paper, we present the LifeSnaps dataset, a multi-modal, longitudinal, and geographically-distributed dataset containing a plethora of anthropological data, collected unobtrusively for the total course of more than 4 months by n = 71 participants. LifeSnaps contains more than 35 different data types from second to daily granularity, totaling more than 71 M rows of data. The participants contributed their data through validated surveys, ecological momentary assessments, and a Fitbit Sense smartwatch and consented to make these data available to empower future research. We envision that releasing this large-scale dataset of multi-modal real-world data will open novel research opportunities and potential applications in multiple disciplines.}, } @article {pmid36311410, year = {2022}, author = {Nicotra, AB and Geange, SR and Bahar, NHA and Carle, H and Catling, A and Garcia, A and Harris, RJ and Head, ML and Jin, M and Whitehead, MR and Zurcher, H and Beckmann, EA}, title = {An innovative approach to using an intensive field course to build scientific and professional skills.}, journal = {Ecology and evolution}, volume = {12}, number = {10}, pages = {e9446}, pmid = {36311410}, issn = {2045-7758}, abstract = {This paper reports on the design and evaluation of Field Studies in Functional Ecology (FSFE), a two-week intensive residential field course that enables students to master core content in functional ecology alongside skills that facilitate their transition from "student" to "scientist." We provide an overview of the course structure, showing how the constituent elements have been designed and refined over successive iterations of the course. We detail how FSFE students: (1) Work closely with discipline specialists to develop a small group project that tests an hypothesis to answer a genuine scientific question in the field; (2) Learn critical skills of data management and communication; and (3) Analyze, interpret, and present their results in the format of a scientific symposium. This process is repeated in an iterative "cognitive apprenticeship" model, supported by a series of workshops that name and explicitly instruct the students in "hard" and "soft" skills (e.g., statistics and teamwork, respectively) critically relevant for research and other careers. FSFE students develop a coherent and nuanced understanding of how to approach and execute ecological studies. The sophisticated knowledge and ecological research skills that they develop during the course is demonstrated through high-quality presentations and peer-reviewed publications in an open-access, student-led journal. We outline our course structure and evaluate its efficacy to show how this novel combination of field course elements allows students to gain maximum value from their educational journey, and to develop cognitive, affective, and reflective tools to help apply their skills as scientists.}, } @article {pmid36302928, year = {2022}, author = {Hammoud, R and Tognin, S and Burgess, L and Bergou, N and Smythe, M and Gibbons, J and Davidson, N and Afifi, A and Bakolis, I and Mechelli, A}, title = {Smartphone-based ecological momentary assessment reveals mental health benefits of birdlife.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17589}, pmid = {36302928}, issn = {2045-2322}, mesh = {Humans ; *Ecological Momentary Assessment ; Smartphone ; Mental Health ; Retrospective Studies ; *Mobile Applications ; }, abstract = {The mental health benefits of everyday encounters with birdlife for mental health are poorly understood. Previous studies have typically relied on retrospective questionnaires or artificial set-ups with little ecological validity. In the present study, we used the Urban Mind smartphone application to examine the impact of seeing or hearing birds on self-reported mental wellbeing in real-life contexts. A sample of 1292 participants completed a total of 26,856 ecological momentary assessments between April 2018 and October 2021. Everyday encounters with birdlife were associated with time-lasting improvements in mental wellbeing. These improvements were evident not only in healthy people but also in those with a diagnosis of depression, the most common mental illness across the world. These findings have potential implications for both environmental and wildlife protection and mental healthcare policies. Specific measures, aimed at preserving and increasing everyday encounters with birdlife in urban areas, should be implemented.}, } @article {pmid36300397, year = {2022}, author = {Kulikowski, CA}, title = {50 Years of Achievements and Persistent Challenges for Biomedical and Health Informatics and John Mantas' Educational and Nursing Informatics Contributions.}, journal = {Studies in health technology and informatics}, volume = {300}, number = {}, pages = {1-11}, doi = {10.3233/SHTI220936}, pmid = {36300397}, issn = {1879-8365}, mesh = {*Nursing Informatics ; *Medical Informatics ; Cybernetics ; Expert Systems ; }, abstract = {Biomedical and Health Informatics (BMHI) have been essential catalysts for achievements in medical research and healthcare applications over the past 50 years. These include increasingly sophisticated information systems and data bases for documentation and processing, standardization of biomedical data, nomenclatures, and vocabularies to assist with large scale literature indexing and text analysis for information retrieval, and methods for computationally modeling and analyzing research and clinical data. Statistical and AI techniques for decision support, instrumentation integration, and workflow aids with improved data/information management tools are critical for scientific discoveries in the - omics revolutions with their related drug and vaccine breakthroughs and their translation to clinical and preventive healthcare. Early work on biomedical image and pattern recognition, knowledge-based expert systems, innovative database, software and simulation techniques, natural language processing and computational ontologies have all been invaluable for basic research and education. However, these methods are still in their infancy and many fundamental open scientific problems abound. Scientifically this is due to persistent limitations in understanding biological processes within complex living environments and ecologies. In clinical practice the modeling of fluid practitioner roles and methods as they adjust to novel cybernetic technologies present great opportunities but also the potential of unintended e-iatrogenic harms which must be constrained in order to adhere to ethical Hippocratic norms of responsible behavior. Balancing the art, science, and technologies of BMHI has been a hallmark of debates about the field's historical evolution. The present article reviews selected milestones, achievements, and challenges in BMHI education mainly, from a historical perspective, including some commentaries from leaders and pioneers in the field, a selection of which have been published online recently by the International Medical Informatics Association (IMIA) as the first volume of an IMIA History WG eBook. The focus of this chapter is primarily on the development of BMHI in terms of those of its educational activities which have been most significant during the first half century of IMIA, and it concentrates mainly on the leadership and contributions of John Mantas who is being honored on his retirement by the Symposia in Athens for which this chapter has been written.}, } @article {pmid36297864, year = {2022}, author = {Macchia, A and Biribicchi, C and Zaratti, C and Testa Chiari, K and D'Ambrosio, M and Toscano, D and Izzo, FC and La Russa, MF}, title = {Mattel's Barbie: Investigation of a Symbol-Analysis of Polymeric Matrices and Degradation Phenomena for Sixteen Dolls from 1959 to 1976.}, journal = {Polymers}, volume = {14}, number = {20}, pages = {}, pmid = {36297864}, issn = {2073-4360}, abstract = {Mattel's Barbie dolls are the most famous and iconic dolls since 1959. Today, they are being collected by individuals and often conserved in museum environments due to their cultural and historical significance reflecting everyday life and historical events. However, just like most museum objects made of plastics, both historical and more recent Barbies show evident degradation phenomena. Firstly, Barbies were made of plasticized polyvinyl chloride (PVC), affected by the migration of additives-mostly the plasticizers-from the bulk phase to the outermost layer, appearing as a tacky and glossy exudate. Over the years, Barbies' polymeric constituents were replaced with more stable ones, whose additives migration is limited compared to PVC, even though still occurring. Multispectral photography in visible (VIS) and ultraviolet (UV) light, microscopical observations in VIS and UV light, and Fourier Transform Infrared spectroscopy in the Attenuated Total Reflectance mode (FT-IR ATR) were performed to characterize the constituent materials of 15 Barbies produced between 1959 and 1976, bridging the information gap on their processing over the years. The micro-invasive multi-analytical approach also allowed for the characterization of the degradation products, permitting the reference of the exudated compound to the specific bulk polymer.}, } @article {pmid36297101, year = {2022}, author = {Maugeri, A and Magnano San Lio, R and Favara, G and La Rosa, MC and La Mastra, C and Riela, PM and Guarnera, L and Battiato, S and Barchitta, M and Agodi, A}, title = {Impact of Eating Context on Dietary Choices of College Students: Evidence from the HEALTHY-UNICT Project.}, journal = {Nutrients}, volume = {14}, number = {20}, pages = {}, pmid = {36297101}, issn = {2072-6643}, mesh = {Humans ; *Diet ; *Vegetables ; Feeding Behavior ; Meals ; Students ; }, abstract = {While personal characteristics have been evaluated as determinants of dietary choices over the years, only recently studies have looked at the impact of eating context. Examining eating context, however, can be challenging. Here, we propose the use of a web-app for the Ecological Momentary Assessment of dietary habits among 138 college students from Catania (Italy) and therefore for examining the impact of eating context on dietary choices. Eating away from home was associated with lower odds of consuming vegetables, fruits, and legumes and higher odds of consuming processed meat, salty snacks, and alcoholic drinks compared with eating at home. Eating in the company of other people was associated with higher odds of consuming vegetables, red meat, fish, legumes, milk, and sugar-sweetened beverages and lower odds of consuming nuts than eating alone. This study proposed a new way to capture and assess how eating environment might affect dietary habits. Based on our results, meal location and social context have significant effects on the dietary choices of college students, pointing to the need to incorporate these aspects into further epidemiological studies.}, } @article {pmid36296237, year = {2022}, author = {Trego, A and Keating, C and Nzeteu, C and Graham, A and O'Flaherty, V and Ijaz, UZ}, title = {Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296237}, issn = {2076-2607}, support = {14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 16/RC/3889/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.}, } @article {pmid36295335, year = {2022}, author = {Cherevko, AG and Krygin, AS and Ivanov, AI and Soots, RA and Antonova, IV}, title = {Benefits of Printed Graphene with Variable Resistance for Flexible and Ecological 5G Band Antennas.}, journal = {Materials (Basel, Switzerland)}, volume = {15}, number = {20}, pages = {}, pmid = {36295335}, issn = {1996-1944}, abstract = {The possibility of creating antennas of the 5G standard (5.2-5.9 GHz) with specified electrodynamic characteristics by printing layers of variable thickness using a graphene suspension has been substantiated experimentally and by computer simulation. A graphene suspension for screen printing on photographic paper and other flexible substrates was prepared by means of exfoliation from graphite. The relation between the graphene layer thickness and its sheet resistance was studied with the aim of determining the required thickness of the antenna conductive layer. To create a two-sided dipole, a technology has been developed for the double-sided deposition of graphene layers on photographic paper. The electrodynamic characteristics of graphene and copper antennas of identical design are compared. The antenna design corresponds to the operating frequency of 2.4 GHz. It was found that the use of graphene as a conductive layer made it possible to suppress the fundamental (first) harmonic (2.45 GHz) and to observe radiation at the second harmonic (5.75 GHz). This effect is assumed to observe in the case when the thickness of graphene is lower than that of the skin depth. The result indicates the possibility of changing the antenna electrodynamic characteristics by adjusting the graphene layer thickness.}, } @article {pmid36293641, year = {2022}, author = {Zou, H and Liu, Y and Li, B and Luo, W}, title = {Sustainable Development Efficiency of Cultural Landscape Heritage in Urban Fringe Based on GIS-DEA-MI, a Case Study of Wuhan, China.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {20}, pages = {}, pmid = {36293641}, issn = {1660-4601}, mesh = {Humans ; Cities ; *Conservation of Natural Resources/methods ; *Sustainable Development ; Geographic Information Systems ; Urbanization ; China ; }, abstract = {Cultural landscape heritage refers to the rare and irreplaceable cultural landscapes recognized by UNESCO and the World Heritage Committee. It is recognized as a "common works of nature and human beings" of outstanding significance and universal value, and is a type of world heritage. Dueto construction, land isincreasingly limited in urban and rural areasin the process of urbanization, and cultural landscape heritage faces a huge threat, especially larger culturallandscapeheritagelocated at the edgesof cities. However, most of the existing studies have mainly focused on the material protection of heritage but have not paid enough attention to the non-material aspects of heritage sites, failing to reveal the inseparable nature of heritage and land. Therefore, this study takes sustainable development efficiency as its analysis tool, examines two pieces of cultural landscape heritage (the Panlongcheng site and the Tomb of the King of the Ming Dynasty) in the urban edge area of Wuhan, China as examples, innovates and establishes a multidimensional evaluation method based on the GIS-DEA-Ml model, and compares the dynamic changes of the spatial development efficiency and non-spatial development efficiency of the above two cultural landscape heritage cases. The results show that: both the spatial development efficiency and non-spatial development efficiency of Panlongcheng from 2010 to 2019 are significantly higher than that of the Tomb. This method makes up for the deficiency of traditional subjective qualitative analysis. It can be used to study the development efficiency of cultural landscape heritage more objectively and comprehensively, and promote the overall sustainable development of material and intangible cultural heritage. It can provide the basis for early decision-making and post-implementation evaluation for the preservation and utilization of cultural landscape heritage under the background of urban renewal.}, } @article {pmid36293613, year = {2022}, author = {Aleni, C and Rinaldi, C and Bettio, V and Mazzucco, E and Antona, A and Meini, C and Loria, E and Bonvicini, P and Cracas, SV and Caristia, S and Rimedio, A and Faggiano, F and Ferrante, D and Capello, D}, title = {Public Attitude towards Biobanking: An Italian University Survey.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {20}, pages = {}, pmid = {36293613}, issn = {1660-4601}, mesh = {Humans ; *Biological Specimen Banks ; Universities ; Attitude ; Public Opinion ; Surveys and Questionnaires ; *Biomedical Research ; }, abstract = {Biobanks have established a critical role in biomedical research by collecting, preserving, organizing, and disseminating biospecimens and related health data, contributing to precision medicine development. Participation in biobanks is influenced by several factors, such as trust in institutions and scientists, knowledge about biobanking, and the consideration of benefit sharing. Understanding public attitudes, fears, and concerns toward biobanking is fundamental to designing targeted interventions to increase trust towards biobanks. The aim of our study was to investigate the level of knowledge and perception of biobanks in students and personnel of the University of Piemonte Orientale. An online questionnaire was designed and administered via e-mail. A total of 17,758 UPO personnel and students were invited to participate in the survey, and 1521 (9.3%) subjects completed the survey. The results showed that 65.0% of the participants were aware of the term "biobank" and knew what the activity of a biobank was, and 76.3% of subjects were willing to provide biospecimens to a research biobank, whereas 67.3% of the respondents were willing to contribute, in addition to biospecimens, their health and lifestyle data. Concerns were raised about the confidentiality of the information (25.6%) and the commercial use of the samples (25.0%). In conclusion, participants were aware of the role that biobanks play in research and were eager to participate for the sake of furthering scientific research. Still, several concerns need to be addressed regarding the confidentiality of the data along with the commercial use of the samples and associated data.}, } @article {pmid36289166, year = {2022}, author = {Navidi, MN and Chatrenour, M and Seyedmohammadi, J and Khaki, BD and Moradi-Majd, N and Mirzaei, S}, title = {Ecological potential assessment and land use area estimation of agricultural lands based on multi-time images of Sentinel-2 using ANP-WLC and GIS in Bastam, Iran.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {36}, pmid = {36289166}, issn = {1573-2959}, mesh = {Agriculture ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; *Geographic Information Systems ; Iran ; Soil ; }, abstract = {The use of land-based ecological potential is a key management factor in achieving sustainable development and conserving soil and water resources. The purpose of this study is to use multi-time images of Sentinel-2 to determine the area of agricultural lands and evaluate their ecological potential in Bastam, Semnan Province, Iran. Therefore, in the first step, the most common agricultural lands (including apricot and grape orchards), field crops (including wheat and forage maize), and their phenological period were determined. Then, the information was classified using, namely support vector machine, maximum likelihood, and minimum distance. In the next step, soil, topography, and climate data were extracted according to expert opinions and the analysis of the basin's natural potential. The ecological evaluation models of the region were applied to homogeneous units, and after calculating the ecological potential index by the integrated ANP-WLC model, the ecological potential map was generated. The results of the land use classification showed that the support vector machine model and the minimum distance, respectively, had the best and worst performance with kappa coefficient of 0.82 and 0.61. The highest area of cultivated lands (3423 hectares) was estimated for wheat and the lowest (738 hectares) for forage maize. Moreover, the results of the ecological potential evaluation showed that 60% of apricot orchards, and 40.19% of the wheat fields, were in the class of good ecological potential. Overall, 2290 hectares were in the poor class, and 4030 hectares in the excellent class in terms of ecological potential.}, } @article {pmid36287517, year = {2022}, author = {Gonçalves, ICM and Freitas, RF and Aquino, EC and Carneiro, JA and Lessa, ADC}, title = {Mortality trend from falls in Brazilian older adults from 2000 to 2019.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {}, pages = {e220031}, doi = {10.1590/1980-549720220031.2}, pmid = {36287517}, issn = {1980-5497}, mesh = {Male ; Humans ; Female ; Aged ; *Accidental Falls ; Brazil/epidemiology ; *Quality of Life ; Retrospective Studies ; Information Systems ; Mortality ; }, abstract = {OBJECTIVE: To analyze the trend of mortality from falls among older adults in Brazil from 2000 to 2019.

METHODS: This is an epidemiological, analytical study with an ecological time-series design. A retrospective analysis was performed using secondary health data extracted from the Brazilian Mortality Information System in the specific period. Standardized rates of general and sex- and age-specific mortality were calculated. To observe the mortality trend, the Prais-Winsten model and the Annual Increase Rate (AIR) were used.

RESULTS: We identified 135,209 deaths resulting from falls in older adults in the period from 2000 to 2019. Mortality from falls in general, during the study period, had an upward trend (β=0.023; p<0.001; AIR=5.45%). We observed that both men (β=0.022; p<0.001; AIR=5.19%) and women (β=0.024; p<0.001; AIR=5.72%) had an upward trend. Regarding age group, the results also pointed to an upward mortality trend in all age strata, although higher in older people aged ≥80 years (β=0.027; p<0.001; AIR=6.38%).

CONCLUSION: There was an upward trend in mortality rates in Brazil during the time series studied. These findings suggest the importance of defining a line of care for this age group, focusing on promoting health in older adults and preventing the risk of falls, aiming at a reduction in the number of deaths from this cause and favoring the quality of life of this population.}, } @article {pmid36287142, year = {2022}, author = {Miller-Ter Kuile, A and Apigo, A and Bui, A and Butner, K and Childress, JN and Copeland, S and DiFiore, BP and Forbes, ES and Klope, M and Motta, CI and Orr, D and Plummer, KA and Preston, DL and Young, HS}, title = {Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts.}, journal = {Biology letters}, volume = {18}, number = {10}, pages = {20220364}, pmid = {36287142}, issn = {1744-957X}, mesh = {Animals ; *Food Chain ; *Ecosystem ; Predatory Behavior/physiology ; Invertebrates ; Diet ; }, abstract = {Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ[15]N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator-prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.}, } @article {pmid36284162, year = {2022}, author = {Geneva, AJ and Park, S and Bock, DG and de Mello, PLH and Sarigol, F and Tollis, M and Donihue, CM and Reynolds, RG and Feiner, N and Rasys, AM and Lauderdale, JD and Minchey, SG and Alcala, AJ and Infante, CR and Kolbe, JJ and Schluter, D and Menke, DB and Losos, JB}, title = {Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1126}, pmid = {36284162}, issn = {2399-3642}, mesh = {Animals ; *Lizards/genetics ; Genome ; Sex Chromosomes ; Genomics ; X Chromosome ; }, abstract = {Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei - a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei.}, } @article {pmid36270368, year = {2023}, author = {Derx, J and Kılıç, HS and Linke, R and Cervero-Aragó, S and Frick, C and Schijven, J and Kirschner, AKT and Lindner, G and Walochnik, J and Stalder, G and Sommer, R and Saracevic, E and Zessner, M and Blaschke, AP and Farnleitner, AH}, title = {Probabilistic fecal pollution source profiling and microbial source tracking for an urban river catchment.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159533}, doi = {10.1016/j.scitotenv.2022.159533}, pmid = {36270368}, issn = {1879-1026}, mesh = {Animals ; Humans ; Rivers ; Water Pollution/analysis ; Water Microbiology ; *Cryptosporidiosis ; Escherichia coli ; Environmental Monitoring/methods ; *Cryptosporidium ; Feces/chemistry ; Giardia ; Water/analysis ; }, abstract = {We developed an innovative approach to estimate the occurrence and extent of fecal pollution sources for urban river catchments. The methodology consists of 1) catchment surveys complemented by literature data where needed for probabilistic estimates of daily produced fecal indicator (FIBs, E. coli, enterococci) and zoonotic reference pathogen numbers (Campylobacter, Cryptosporidium and Giardia) excreted by human and animal sources in a river catchment, 2) generating a hypothesis about the dominant sources of fecal pollution and selecting a source targeted monitoring design, and 3) verifying the results by comparing measured concentrations of the informed choice of parameters (i.e. chemical tracers, C. perfringensspores, and host-associated genetic microbial source tracking (MST) markers) in the river, and by multi-parametric correlation analysis. We tested the approach at a study area in Vienna, Austria. The daily produced microbial particle numbers according to the probabilistic estimates indicated that, for the dry weather scenario, the discharge of treated wastewater (WWTP) was the primary contributor to fecal pollution. For the wet weather scenario, 80-99 % of the daily produced FIBs and pathogens resulted from combined sewer overflows (CSOs) according to the probabilistic estimates. When testing our hypothesis in the river, the measured concentrations of the human genetic fecal marker were log10 4 higher than for selected animal genetic fecal markers. Our analyses showed for the first-time statistical relationships between C. perfringens spores (used as conservative microbial tracer for communal sewage) and a human genetic fecal marker (i.e. HF183/BacR287) with the reference pathogen Giardia in river water (Spearman rank correlation: 0.78-0.83, p < 0.05. The developed approach facilitates urban water safety management and provides a robust basis for microbial fate and transport models and microbial infection risk assessment.}, } @article {pmid36263952, year = {2023}, author = {Jensen, MA and Blatz, DJ and LaLone, CA}, title = {Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death.}, journal = {Environmental toxicology and chemistry}, volume = {42}, number = {1}, pages = {71-87}, doi = {10.1002/etc.5501}, pmid = {36263952}, issn = {1552-8618}, mesh = {Animals ; Bees ; *Adverse Outcome Pathways ; *Receptors, Nicotinic/genetics ; Ecotoxicology/methods ; Databases, Factual ; Amino Acid Sequence ; Risk Assessment ; }, abstract = {For the majority of developed adverse outcome pathways (AOPs), the taxonomic domain of applicability (tDOA) is typically narrowly defined with a single or a handful of species. Defining the tDOA of an AOP is critical for use in regulatory decision-making, particularly when considering protection of untested species. Structural and functional conservation are two elements that can be considered when defining the tDOA. Publicly accessible bioinformatics approaches, such as the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool, take advantage of existing and growing databases of protein sequence and structural information to provide lines of evidence toward structural conservation of key events (KEs) and KE relationships (KERs) of an AOP. It is anticipated that SeqAPASS results could readily be combined with data derived from empirical toxicity studies to provide evidence of both structural and functional conservation, to define the tDOA for KEs, KERs, and AOPs. Such data could be incorporated in the AOP-Wiki as lines of evidence toward biological plausibility for the tDOA. We present a case study describing the process of using bioinformatics to define the tDOA of an AOP using an AOP linking the activation of the nicotinic acetylcholine receptor to colony death/failure in Apis mellifera. Although the AOP was developed to gain a particular biological understanding relative to A. mellifera health, applicability to other Apis bees, as well as non-Apis bees, has yet to be defined. The present study demonstrates how bioinformatics can be utilized to rapidly take advantage of existing protein sequence and structural knowledge to enhance and inform the tDOA of KEs, KERs, and AOPs, focusing on providing evidence of structural conservation across species. Environ Toxicol Chem 2023;42:71-87. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.}, } @article {pmid36261521, year = {2022}, author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB}, title = {Evolution of immune genes is associated with the Black Death.}, journal = {Nature}, volume = {611}, number = {7935}, pages = {312-319}, pmid = {36261521}, issn = {1476-4687}, support = {F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Aminopeptidases/genetics/immunology ; *DNA, Ancient ; *Plague/genetics/immunology/microbiology/mortality ; *Yersinia pestis/immunology/pathogenicity ; *Selection, Genetic/immunology ; Europe/epidemiology/ethnology ; *Immunity/genetics ; Datasets as Topic ; *Genetic Predisposition to Disease ; London/epidemiology ; Denmark/epidemiology ; }, abstract = {Infectious diseases are among the strongest selective pressures driving human evolution[1,2]. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis[3]. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population[4]. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.}, } @article {pmid36261519, year = {2022}, author = {Jandt, U and Bruelheide, H and Jansen, F and Bonn, A and Grescho, V and Klenke, RA and Sabatini, FM and Bernhardt-Römermann, M and Blüml, V and Dengler, J and Diekmann, M and Doerfler, I and Döring, U and Dullinger, S and Haider, S and Heinken, T and Horchler, P and Kuhn, G and Lindner, M and Metze, K and Müller, N and Naaf, T and Peppler-Lisbach, C and Poschlod, P and Roscher, C and Rosenthal, G and Rumpf, SB and Schmidt, W and Schrautzer, J and Schwabe, A and Schwartze, P and Sperle, T and Stanik, N and Storm, C and Voigt, W and Wegener, U and Wesche, K and Wittig, B and Wulf, M}, title = {More losses than gains during one century of plant biodiversity change in Germany.}, journal = {Nature}, volume = {611}, number = {7936}, pages = {512-518}, pmid = {36261519}, issn = {1476-4687}, mesh = {*Biodiversity ; Germany ; *Plants/classification ; Species Specificity ; Time Factors ; Datasets as Topic ; }, abstract = {Long-term analyses of biodiversity data highlight a 'biodiversity conservation paradox': biological communities show substantial species turnover over the past century[1,2], but changes in species richness are marginal[1,3-5]. Most studies, however, have focused only on the incidence of species, and have not considered changes in local abundance. Here we asked whether analysing changes in the cover of plant species could reveal previously unrecognized patterns of biodiversity change and provide insights into the underlying mechanisms. We compiled and analysed a dataset of 7,738 permanent and semi-permanent vegetation plots from Germany that were surveyed between 2 and 54 times from 1927 to 2020, in total comprising 1,794 species of vascular plants. We found that decrements in cover, averaged across all species and plots, occurred more often than increments; that the number of species that decreased in cover was higher than the number of species that increased; and that decrements were more equally distributed among losers than were gains among winners. Null model simulations confirmed that these trends do not emerge by chance, but are the consequence of species-specific negative effects of environmental changes. In the long run, these trends might result in substantial losses of species at both local and regional scales. Summarizing the changes by decade shows that the inequality in the mean change in species cover of losers and winners diverged as early as the 1960s. We conclude that changes in species cover in communities represent an important but understudied dimension of biodiversity change that should more routinely be considered in time-series analyses.}, } @article {pmid36261518, year = {2022}, author = {Jarvis, ED and Formenti, G and Rhie, A and Guarracino, A and Yang, C and Wood, J and Tracey, A and Thibaud-Nissen, F and Vollger, MR and Porubsky, D and Cheng, H and Asri, M and Logsdon, GA and Carnevali, P and Chaisson, MJP and Chin, CS and Cody, S and Collins, J and Ebert, P and Escalona, M and Fedrigo, O and Fulton, RS and Fulton, LL and Garg, S and Gerton, JL and Ghurye, J and Granat, A and Green, RE and Harvey, W and Hasenfeld, P and Hastie, A and Haukness, M and Jaeger, EB and Jain, M and Kirsche, M and Kolmogorov, M and Korbel, JO and Koren, S and Korlach, J and Lee, J and Li, D and Lindsay, T and Lucas, J and Luo, F and Marschall, T and Mitchell, MW and McDaniel, J and Nie, F and Olsen, HE and Olson, ND and Pesout, T and Potapova, T and Puiu, D and Regier, A and Ruan, J and Salzberg, SL and Sanders, AD and Schatz, MC and Schmitt, A and Schneider, VA and Selvaraj, S and Shafin, K and Shumate, A and Stitziel, NO and Stober, C and Torrance, J and Wagner, J and Wang, J and Wenger, A and Xiao, C and Zimin, AV and Zhang, G and Wang, T and Li, H and Garrison, E and Haussler, D and Hall, I and Zook, JM and Eichler, EE and Phillippy, AM and Paten, B and Howe, K and Miga, KH and , }, title = {Semi-automated assembly of high-quality diploid human reference genomes.}, journal = {Nature}, volume = {611}, number = {7936}, pages = {519-531}, pmid = {36261518}, issn = {1476-4687}, support = {U01 HG010961/HG/NHGRI NIH HHS/United States ; R01 HG010040/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Chromosome Mapping/standards ; *Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing/methods/standards ; Sequence Analysis, DNA/methods/standards ; Reference Standards ; *Genomics/methods/standards ; Chromosomes, Human/genetics ; Genetic Variation/genetics ; }, abstract = {The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society[1,2]. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals[3,4]. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome[5]. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity[6]. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.}, } @article {pmid36257775, year = {2022}, author = {Peltier, DMP and Anderegg, WRL and Guo, JS and Ogle, K}, title = {Contemporary tree growth shows altered climate memory.}, journal = {Ecology letters}, volume = {25}, number = {12}, pages = {2663-2674}, doi = {10.1111/ele.14130}, pmid = {36257775}, issn = {1461-0248}, mesh = {*Trees ; *Climate Change ; Droughts ; Temperature ; }, abstract = {Trees are long-lived organisms, exhibiting temporally complex growth arising from strong climatic "memory." But conditions are becoming increasingly arid in the western USA. Using a century-long tree-ring network, we find altered climate memory across the entire range of a widespread western US conifer: growth is supported by precipitation falling further into the past (+15 months), while increasingly impacted by more recent temperature conditions (-8 months). Tree-ring datasets can be biased, so we confirm altered climate memory in a second, ecologically-sampled tree-ring network. Predicted drought responses show trees may have also become more sensitive to repeat drought. Finally, plots near sites with relatively longer precipitation memory and shorter temperature memory had significantly lower recent mortality rates (R[2] = 0.61). We argue that increased drought frequency has altered climate memory, demonstrate how non-stationarity may arise from failure to account for memory, and suggest memory length may be predictive of future tree mortality.}, } @article {pmid36255408, year = {2022}, author = {Sorokina, M and Ukubayev, T and Koichubekov, B}, title = {Tuberculosis incidence and its socioeconomic determinants: developing a parsimonious model.}, journal = {Annali di igiene : medicina preventiva e di comunita}, volume = {}, number = {}, pages = {}, doi = {10.7416/ai.2022.2549}, pmid = {36255408}, issn = {1120-9135}, abstract = {BACKGROUND: Tuberculosis is a widespread communicable disease, which is one of the top 10 causes of demise globally. Several regression models have been built, and then utilized for the Tuberculosis incidence projections. However, when fitting a multiple linear regression model, an analysis must account for multicollinearity aspects. The present study aimed to develop a parsimonious model that produces unbiased results based on socioeconomic variables as predictors of Tuberculosis incidence.

STUDY DESIGN: Ecological study.

METHODS: Data were collected from the Karaganda Regional Center of Phthisio-pulmonology and Bureau of National Statistics. By multiple linear regression model, we investigated associations between Tuberculosis incidence rate and socioeconomic determinants in Karaganda region, Kazakhstan, during 2001-2019. A Principal components analysis was performed on the socioeconomic variables with oblique rotation. Furthermore, associations of Tuberculosis incidence with the principal components derived from the Principal components analysis were assessed.

RESULTS: The incidence of Tuberculosis in Karaganda region decreased over the period of 2001-2019. Economic development and healthcare capacity were negatively correlated with Tuberculosis incidence. A multiple linear regression equation on Tuberculosis incidence (y) was developed with economic development (x1) and healthcare capacity (x2) clustering two components (utilizing Principal components analysis) to eliminate collinearity: y = 1442 - 454.3x1 - 211.4x2. The incidence of Tuberculosis decreased with the increase of economic development and healthcare capacity.

CONCLUSIONS: In conclusion, the study indicated that economic development and healthcare capacity are closely associated with the incidence of Tuberculosis. The findings support the implementation of optimal preventive measures for Tuberculosis control, including improving the level of economic status, increasing social protection, health expenditure, and strengthening health sector capacity, which are key determinants of the incidence of Tuberculosis.

AUTHORS’ CONTRIBUTION: M. Sorokina supervised the study, Ukubayev T. collected the data, performed statistical analysis, and drafted the manuscript; M. Sorokina and B. Koichubekov, reviewed and edited the manuscript. All authors discussed and contributed to the final manuscript.}, } @article {pmid36254310, year = {2022}, author = {Cui, J and Khomkrich, K}, title = {Ethnic Music Inheritance and Environmental Monitoring Using Big Data Analysis from the Cultural Perspective.}, journal = {Journal of environmental and public health}, volume = {2022}, number = {}, pages = {2485596}, pmid = {36254310}, issn = {1687-9813}, mesh = {Big Data ; China ; Data Analysis ; Environmental Monitoring ; Ethnicity/genetics ; Humans ; *Music ; }, abstract = {Ethnic music has too many expectations due to its significance to the national culture. It serves as a mirror, reflecting all the true characteristics of many geographical areas and ethnic groupings. Instilling national self-confidence and fostering national unity are essential outcomes of this. The optimal design plan for Xinjiang folk music inheritance and environmental monitoring based on big data technology is presented in this study from the standpoint of cultural ecology. Big data technology can categorize users who are interested in Xinjiang ethnic music, and after that, through customized recommendation filtering, consumers may be presented with Xinjiang ethnic music that meets their interests. Last but not least, a simulation test and analysis are performed. The algorithm's accuracy is 7.86% higher than that of the conventional algorithm, according to the simulation data. By studying and calculating the user's behavioral traits and interests, this result demonstrates in detail how the recommender system can display the user's content efficiently. However, there are numerous possibilities and varied contexts for the use of clustering techniques in recommender systems. It is crucially vital for directing the protection of ethnic music and fostering the inheritance and development of ethnic culture to conduct design study on the Xinjiang region's ethnic music heritage and development with cultural ecology as the central guiding principle. This article is from "A comprehensive study of Uygur Muqam music art with Chinese characteristics," which aims to improve the data reserve of the world and Southeast Asia on the research of Chinese Uighur Muqam art. Improve the inheritance and development of music in Xinjiang, China, and provide more detailed data to more scholars. This study adopts qualitative research methods and field survey data. The author proposes to focus on the perspective of cultural ecology, based on the use of big data technology, to improve the inheritance and development of Xinjiang national music.}, } @article {pmid36249208, year = {2022}, author = {Qamar, AI and Gronwald, L and Timmesfeld, N and Diebner, HH}, title = {Local socio-structural predictors of COVID-19 incidence in Germany.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {970092}, pmid = {36249208}, issn = {2296-2565}, mesh = {*COVID-19/epidemiology ; Germany/epidemiology ; Humans ; Incidence ; Risk Factors ; Socioeconomic Factors ; }, abstract = {Socio-economic conditions and social attitudes are known to represent epidemiological determinants. Credible knowledge on socio-economic driving factors of the COVID-19 epidemic is still incomplete. Based on linear random effects regression, an ecological model is derived to estimate COVID-19 incidence in German rural/urban districts from local socio-economic factors and popularity of political parties in terms of their share of vote. Thereby, records provided by Germany's public health institute (Robert Koch Institute) of weekly notified 7-day incidences per 100,000 inhabitants per district from the outset of the epidemic in 2020 up to December 1, 2021, are used to construct the dependent variable. Local socio-economic conditions including share of votes, retrieved from the Federal Statistical Office of Germany, have been used as potential risk factors. Socio-economic parameters like per capita income, proportions of protection seekers and social benefit claimants, and educational level have negligible impact on incidence. To the contrary, incidence significantly increases with population density and we observe a strong association with vote shares. Popularity of the right-wing party Alternative for Germany (AfD) bears a considerable risk of increasing COVID-19 incidence both in terms of predicting the maximum incidences during three epidemic periods (alternatively, cumulative incidences over the periods are used to quantify the dependent variable) and in a time-continuous sense. Thus, districts with high AfD popularity rank on top in the time-average regarding COVID-19 incidence. The impact of the popularity of the Free Democrats (FDP) is markedly intermittent in the course of time showing two pronounced peaks in incidence but also occasional drops. A moderate risk emanates from popularities of the Green Party (GRÜNE) and the Christian Democratic Union (CDU/CSU) compared to the other parties with lowest risk level. In order to effectively combat the COVID-19 epidemic, public health policymakers are well-advised to account for social attitudes and behavioral patterns reflected in local popularities of political parties, which are conceived as proper surrogates for these attitudes. Whilst causal relations between social attitudes and the presence of parties remain obscure, the political landscape in terms of share of votes constitutes at least viable predictive "markers" relevant for public health policy making.}, } @article {pmid36248684, year = {2022}, author = {Laroche, J and Tomassini, A and Volpe, G and Camurri, A and Fadiga, L and D'Ausilio, A}, title = {Interpersonal sensorimotor communication shapes intrapersonal coordination in a musical ensemble.}, journal = {Frontiers in human neuroscience}, volume = {16}, number = {}, pages = {899676}, pmid = {36248684}, issn = {1662-5161}, abstract = {Social behaviors rely on the coordination of multiple effectors within one's own body as well as between the interacting bodies. However, little is known about how coupling at the interpersonal level impacts coordination among body parts at the intrapersonal level, especially in ecological, complex, situations. Here, we perturbed interpersonal sensorimotor communication in violin players of an orchestra and investigated how this impacted musicians' intrapersonal movements coordination. More precisely, first section violinists were asked to turn their back to the conductor and to face the second section of violinists, who still faced the conductor. Motion capture of head and bow kinematics showed that altering the usual interpersonal coupling scheme increased intrapersonal coordination. Our perturbation also induced smaller yet more complex head movements, which spanned multiple, faster timescales that closely matched the metrical levels of the musical score. Importantly, perturbation differentially increased intrapersonal coordination across these timescales. We interpret this behavioral shift as a sensorimotor strategy that exploits periodical movements to effectively tune sensory processing in time and allows coping with the disruption in the interpersonal coupling scheme. As such, head movements, which are usually deemed to fulfill communicative functions, may possibly be adapted to help regulate own performance in time.}, } @article {pmid36247175, year = {2022}, author = {Sukma, P and Srinok, K and Papong, S and Supakata, N}, title = {Chula model for sustainable municipal solid waste management in university canteens.}, journal = {Heliyon}, volume = {8}, number = {10}, pages = {e10975}, pmid = {36247175}, issn = {2405-8440}, abstract = {Managing the large amount and variety of waste produced by university canteens is challenging. This study used life cycle assessment (LCA) to investigate sustainable municipal solid waste (MSW) management solutions for Chulalongkorn University (CU) canteens. This study assessed three scenarios for MSW management in CU canteens: the past scenario (prior to the Chula Zero Waste Project in 2016; S1); the current scenario (2017-2021, when the Chula Zero Waste Project's MSW management system was used; S2); and the future scenario (after 2021 with the new MSW management option for CU canteens under Chula Zero Waste; S3). The obtained results were characterized by eight impact categories: climate change, ozone depletion, terrestrial acidification, freshwater eutrophication, human toxicity, photochemical oxidant formation, particulate matter formation, and fossil depletion. The LCA results show that the future scenario (S3) under the Chula Zero Waste Project is sustainable for MSW management. The most environmentally sustainable MSW plan for CU canteens is to reduce, separate it at the source, and reuse materials instead of landfilling mixed waste.}, } @article {pmid36228685, year = {2023}, author = {Seyed Hashtroudi, M and Aghadadashi, V and Mehdinia, A and Sheijooni Fumani, N}, title = {Combining theoretical concepts and Geographic Information System (GIS) to highlight source, risk, and hotspots of sedimentary PAHs: A case study of Chabahar Bay.}, journal = {Environmental research}, volume = {216}, number = {Pt 1}, pages = {114540}, doi = {10.1016/j.envres.2022.114540}, pmid = {36228685}, issn = {1096-0953}, mesh = {Geographic Information Systems ; Geologic Sediments/analysis ; Bays ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Vehicle Emissions/analysis ; China ; }, abstract = {Sedimentary PAHs are regionalized variables and their levels, source, and ecological hazards must be discussed in relation to their spatial locations. Our research targeted GIS and Chabahar Bay-Iran to trace spatial variability of PAHs, improve the diagnostic ratios and receptor models in source identification, and determine hotspot of PAH-originated hazards. The entropy Voronoi map distinguished an "entropy strip" in which ∑22PAHs levels increased sharply. Different molecular signatures were individually interpolated and the indicative ratios of distinctive sources were extracted and summed by GIS. The resulting code map reduced potential disagreement among molecular signatures and highlighted the areas where petroleum inputs are prevalent. PCA-MLR analysis extracted three potential sources including fossil fuel combustion (54.36%), petrogenic inputs (29.03%), and vehicle exhaust emissions (16.61%). Interpolated risk layers were re-arranged and overlaid via Fuzzy Membership Functions. The obtained ''Fuzzy AND" map showed the hotspot of the study area in the vicinity of a seasonal estuary.}, } @article {pmid36226159, year = {2022}, author = {Boyes, D and , and , and , and , and , and Phillips, D and , }, title = {The genome sequence of the brimstone moth, Opisthograptis luteolata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {227}, pmid = {36226159}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Opisthograptis luteolata (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.}, } @article {pmid36225383, year = {2022}, author = {Richardson, AD and Kong, GV and Taylor, KM and Le Moine, JM and Bowker, MA and Barber, JJ and Basler, D and Carbone, MS and Hayer, M and Koch, GW and Salvatore, MR and Sonnemaker, AW and Trilling, DE}, title = {Soil-atmosphere fluxes of CO2, CH4, and N2O across an experimentally-grown, successional gradient of biocrust community types.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {979825}, pmid = {36225383}, issn = {1664-302X}, abstract = {Biological soil crusts (biocrusts) are critical components of dryland and other ecosystems worldwide, and are increasingly recognized as novel model ecosystems from which more general principles of ecology can be elucidated. Biocrusts are often diverse communities, comprised of both eukaryotic and prokaryotic organisms with a range of metabolic lifestyles that enable the fixation of atmospheric carbon and nitrogen. However, how the function of these biocrust communities varies with succession is incompletely characterized, especially in comparison to more familiar terrestrial ecosystem types such as forests. We conducted a greenhouse experiment to investigate how community composition and soil-atmosphere trace gas fluxes of CO2, CH4, and N2O varied from early-successional light cyanobacterial biocrusts to mid-successional dark cyanobacteria biocrusts and late-successional moss-lichen biocrusts and as biocrusts of each successional stage matured. Cover type richness increased as biocrusts developed, and richness was generally highest in the late-successional moss-lichen biocrusts. Microbial community composition varied in relation to successional stage, but microbial diversity did not differ significantly among stages. Net photosynthetic uptake of CO2 by each biocrust type also increased as biocrusts developed but tended to be moderately greater (by up to ≈25%) for the mid-successional dark cyanobacteria biocrusts than the light cyanobacterial biocrusts or the moss-lichen biocrusts. Rates of soil C accumulation were highest for the dark cyanobacteria biocrusts and light cyanobacteria biocrusts, and lowest for the moss-lichen biocrusts and bare soil controls. Biocrust CH4 and N2O fluxes were not consistently distinguishable from the same fluxes measured from bare soil controls; the measured rates were also substantially lower than have been reported in previous biocrust studies. Our experiment, which uniquely used greenhouse-grown biocrusts to manipulate community composition and accelerate biocrust development, shows how biocrust function varies along a dynamic gradient of biocrust successional stages.}, } @article {pmid36224329, year = {2022}, author = {Bayer, N and Hausman, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {36}, number = {11}, pages = {2705-2714}, pmid = {36224329}, issn = {1476-5551}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; *Gastrointestinal Microbiome ; Immunity ; }, abstract = {The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45[+] leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.}, } @article {pmid36224130, year = {2022}, author = {Zhao, CH and Shen, HY and Wang, ZH and Liang, YP and Zhao, Y and Xie, H and Tang, CL}, title = {[Hydrochemical and Isotopic Characteristics in the Surface Water of the Fenhe River Basin and Influence Factors].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {10}, pages = {4440-4448}, doi = {10.13227/j.hjkx.202201103}, pmid = {36224130}, issn = {0250-3301}, mesh = {Calcium Sulfate ; Carbonates ; Environmental Monitoring/methods ; *Groundwater/chemistry ; Hydrogen ; Minerals ; Oxygen Isotopes ; Sulfides ; *Water Pollutants, Chemical/analysis ; Water Quality ; }, abstract = {The Fenhe River Basin is the mother river of Shanxi Province. Due to the over-exploitation of water resources and the impact of social and economic development, the ecological environment has deteriorated. After a series of treatment and protection measures, the water quality has since been improved. Mathematical statistics, Piper diagrams, Gibbs model, hydrogen and oxygen isotopes, and other methods were used to analyze the characteristics and sources of hydrochemistry in the surface water of the Fenhe River basin, which revealed the evolution process of surface water quality of the Fenhe River basin. The results showed that the content of the main hydrochemical components in the main stream surface water of Fenhe River basin increased gradually along the runoff path. The hydrochemical types of surface water of Fenhe River basin were mainly HCO3·SO4·Cl-Ca·Na·Mg and SO4·HCO3·Cl-Ca·Na·Mg. There were great differences in hydrochemical components of tributaries and karst water in the basin. There were also great differences in hydrochemical components of tributaries in the basin. The hydrochemical types of surface water of karst water were mainly SO4·HCO3-Ca·Mg. The hydrochemical composition of surface water in Fenhe River basin was mainly affected by rock weathering and evaporation crystallization, whereas rainfall had little effect. Na[+] and K[+] mainly came from the dissolution of evaporated salt rocks with Na in the surrounding loess. Ca[2+], Mg[2+], and HCO3[-] mainly came from the dissolution of carbonate rocks. SO4[2-] may have also come from the dissolution of sulfide minerals in the loess layer around Fenhe River in addition to the dissolution of gypsum. The values of δD and δ[18]O of Fenhe River surface water were gradually enriched from upstream to downstream. The characteristics of hydrogen and oxygen isotopes further showed that the surface water was mainly affected by evaporation. The results of this study can provide evidence for ecological restoration and protection and ecological civilization construction in the Fenhe River basin.}, } @article {pmid36215495, year = {2022}, author = {Zhao, J and Jin, L and Wu, D and Xie, JW and Li, J and Fu, XW and Cong, ZY and Fu, PQ and Zhang, Y and Luo, XS and Feng, XB and Zhang, G and Tiedje, JM and Li, XD}, title = {Global airborne bacterial community-interactions with Earth's microbiomes and anthropogenic activities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {42}, pages = {e2204465119}, pmid = {36215495}, issn = {1091-6490}, mesh = {*Air Microbiology ; Anthropogenic Effects ; Bacteria/genetics ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Airborne bacteria are an influential component of the Earth's microbiomes, but their community structure and biogeographic distribution patterns have yet to be understood. We analyzed the bacterial communities of 370 air particulate samples collected from 63 sites around the world and constructed an airborne bacterial reference catalog with more than 27 million nonredundant 16S ribosomal RNA (rRNA) gene sequences. We present their biogeographic pattern and decipher the interlacing of the microbiome co-occurrence network with surface environments of the Earth. While the total abundance of global airborne bacteria in the troposphere (1.72 × 10[24] cells) is 1 to 3 orders of magnitude lower than that of other habitats, the number of bacterial taxa (i.e., richness) in the atmosphere (4.71 × 10[8] to 3.08 × 10[9]) is comparable to that in the hydrosphere, and its maximum occurs in midlatitude regions, as is also observed in other ecosystems. The airborne bacterial community harbors a unique set of dominant taxa (24 species); however, its structure appears to be more easily perturbed, due to the more prominent role of stochastic processes in shaping community assembly. This is corroborated by the major contribution of surface microbiomes to airborne bacteria (averaging 46.3%), while atmospheric conditions such as meteorological factors and air quality also play a role. Particularly in urban areas, human impacts weaken the relative importance of plant sources of airborne bacteria and elevate the occurrence of potential pathogens from anthropogenic sources. These findings serve as a key reference for predicting planetary microbiome responses and the health impacts of inhalable microbiomes with future changes in the environment.}, } @article {pmid36215030, year = {2022}, author = {Yang, Z and Wang, J and Huang, Y and Wang, S and Wei, L and Liu, D and Weng, Y and Xiang, J and Zhu, Q and Yang, Z and Nie, X and Yu, Y and Yang, Z and Yang, QY}, title = {CottonMD: a multi-omics database for cotton biological study.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac863}, pmid = {36215030}, issn = {1362-4962}, abstract = {Cotton is an important economic crop, and many loci for important traits have been identified, but it remains challenging and time-consuming to identify candidate or causal genes/variants and clarify their roles in phenotype formation and regulation. Here, we first collected and integrated the multi-omics datasets including 25 genomes, transcriptomes in 76 tissue samples, epigenome data of five species and metabolome data of 768 metabolites from four tissues, and genetic variation, trait and transcriptome datasets from 4180 cotton accessions. Then, a cotton multi-omics database (CottonMD, http://yanglab.hzau.edu.cn/CottonMD/) was constructed. In CottonMD, multiple statistical methods were applied to identify the associations between variations and phenotypes, and many easy-to-use analysis tools were provided to help researchers quickly acquire the related omics information and perform multi-omics data analysis. Two case studies demonstrated the power of CottonMD for identifying and analyzing the candidate genes, as well as the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.}, } @article {pmid36213026, year = {2022}, author = {Wen, Y}, title = {Analysis of Regional Economy Development on Local Environmental Protection and Natural Resources Utilization from the Perspective of Big Data.}, journal = {Journal of environmental and public health}, volume = {2022}, number = {}, pages = {9461377}, pmid = {36213026}, issn = {1687-9813}, mesh = {Big Data ; China ; Cities ; *Conservation of Natural Resources ; *Economic Development ; Natural Resources ; Rivers ; }, abstract = {The ecological restoration and civilization construction is one of the key tasks in China. The economic development of different regions has different effects on the resource protection and utilization. In the face of complex natural conditions and resource-rich areas, how to carry out the ecological environment promotion work is put forward. The urbanization level of the Yangtze River region increases from 17.9% to 60.6%, showing the characteristics of rapid expansion. In the face of urban diseases such as unreasonable industrial layout, it is urgent to improve regional economy and promote green urban development from the perspective of big data. Adhering to the concept of ecological priority, the development of digital technology drove the development of local economy in 2019, accounting for 43% of the national population. While promoting the economic development, it is of great significance to ensure the efficiency of resource utilization and promote the high-quality development of common economy.}, } @article {pmid36212380, year = {2022}, author = {Shao, P and Peng, Y and Wu, Y and Wang, J and Pan, Z and Yang, Y and Aini, N and Guo, C and Shui, G and Chao, L and Tian, X and An, Q and Yang, Q and You, C and Lu, L and Zhang, X and Wang, M and Nie, X}, title = {Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {988647}, pmid = {36212380}, issn = {1664-462X}, abstract = {Fruit branch angle (FBA), a pivotal component of cotton plant architecture, is vital for field and mechanical harvesting. However, the molecular mechanism of FBA formation is poorly understood in cotton. To uncover the genetic basis for FBA formation in cotton, we performed a genome-wide association study (GWAS) of 163 cotton accessions with re-sequencing data. A total of 55 SNPs and 18 candidate genes were significantly associated with FBA trait. By combining GWAS and transcriptome analysis, four genes underlying FBA were identified. An FBA-associated candidate gene Ghi_A09G08736, which is homologous to SAUR46 in Arabidopsis thaliana, was detected in our study. In addition, transcriptomic evidence was provided to show that gravity and light were implicated in the FBA formation. This study provides new insights into the genetic architecture of FBA that informs architecture breeding in cotton.}, } @article {pmid36210994, year = {2022}, author = {Ju, X}, title = {Application of Big Data Technology to Promote Agricultural Structure Adjustment and High-Quality Development of Modern Agriculture.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {5222760}, pmid = {36210994}, issn = {1687-5273}, mesh = {*Agriculture ; *Big Data ; China ; Conservation of Natural Resources ; Remote Sensing Technology ; Technology ; }, abstract = {The implementation of the strategy of rural revitalization is a major ministerial work made by the Nineteenth National Congress of the Communist Party of China and is the general grasp of contemporary agriculture, peasants, and rural work. In recent years, with the rapid development of remote sensing technology and deep learning technology, the demand for the technology for the classification of crops on satellite remote sensing images based on deep learning technology has increased in agricultural insurance and land survey. Therefore, this paper trains one, which is 85.9%-92.8%, the accuracy of corn classification is 77%-93%, and the accuracy of forest classification is 77%-87.6%. Subsequently, the overall accuracy of classifying all directories through the multi-temporal validation data set between May 2017 and October 2017 reached 92.6%. Such a multi-time combination method can be used for monthly, timely, and efficient iteration of agricultural insurance and crop yield estimation, which will be more accurate each time. These methods can also be further applied to the growth and change monitoring of large agricultural planting areas, adding bricks and tiles to China's agricultural remote sensing. If the countryside is to be revitalized, agriculture must develop rapidly at the same time, industries must flourish, ecology must be livable, rural customs must be civilized, and life must be prosperous. Modern agriculture is a comprehensive circulation system with high yield, high quality, low consumption, ecology, environmental protection, and high efficiency. The development of modern agriculture is inseparable from the industrialization of agriculture, the globalization of agriculture, the digitization of agriculture, the integration of agriculture, the adjustment of agricultural structure, and agricultural innovation. Only the continuous development of modern agriculture can make rural revitalization enter a new journey.}, } @article {pmid36209915, year = {2022}, author = {Chetty, M and Hallinan, J and Ruz, GA and Wipat, A}, title = {Computational intelligence and machine learning in bioinformatics and computational biology.}, journal = {Bio Systems}, volume = {222}, number = {}, pages = {104792}, doi = {10.1016/j.biosystems.2022.104792}, pmid = {36209915}, issn = {1872-8324}, mesh = {*Computational Biology ; *Artificial Intelligence ; Machine Learning ; }, } @article {pmid36207680, year = {2022}, author = {Asghari-Jafarabadi, M and Gholipour, K and Khodayari-Zarnaq, R and Azmin, M and Alizadeh, G}, title = {Estimation of myocardial infarction death in Iran: artificial neural network.}, journal = {BMC cardiovascular disorders}, volume = {22}, number = {1}, pages = {438}, pmid = {36207680}, issn = {1471-2261}, mesh = {Humans ; *Hypercholesterolemia/diagnosis/epidemiology ; Iran/epidemiology ; Male ; *Myocardial Infarction/diagnosis/epidemiology ; Neural Networks, Computer ; Obesity/diagnosis/epidemiology ; Overweight ; Risk Factors ; }, abstract = {BACKGROUND: Examining past trends and predicting the future helps policymakers to design effective interventions to deal with myocardial infarction (MI) with a clear understanding of the current and future situation. The aim of this study was to estimate the death rate due to MI in Iran by artificial neural network (ANN).

METHODS: In this ecological study, the prevalence of diabetes, hypercholesterolemia over 200, hypertension, overweight and obesity were estimated for the years 2017-2025. ANN and Linear regression model were used. Also, Specialists were also asked to predict the death rate due to MI by considering the conditions of 3 conditions (optimistic, pessimistic, and probable), and the predicted process was compared with the modeling process.

RESULTS: Death rate due to MI in Iran is expected to decrease on average, while there will be a significant decrease in the prevalence of hypercholesterolemia 1.031 (- 24.81, 26.88). Also, the trend of diabetes 10.48 (111.45, - 132.42), blood pressure - 110.48 (- 174.04, - 46.91) and obesity and overweight - 35.84 (- 18.66, - 5.02) are slowly increasing. MI death rate in Iran is higher in men but is decreasing on average. Experts' forecasts are different and have predicted a completely upward trend.

CONCLUSION: The trend predicted by the modeling shows that the death rate due to MI will decrease in the future with a low slope. Improving the infrastructure for providing preventive services to reduce the risk factors for cardiovascular disease in the community is one of the priority measures in the current situation.}, } @article {pmid36202356, year = {2023}, author = {Jones, DL and Rhymes, JM and Wade, MJ and Kevill, JL and Malham, SK and Grimsley, JMS and Rimmer, C and Weightman, AJ and Farkas, K}, title = {Suitability of aircraft wastewater for pathogen detection and public health surveillance.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159162}, pmid = {36202356}, issn = {1879-1026}, mesh = {Adult ; Male ; Humans ; *Wastewater ; Public Health Surveillance ; SARS-CoV-2 ; *COVID-19/epidemiology ; Aircraft ; }, abstract = {International air travel is now widely recognised as one of the primary mechanisms responsible for the transnational movement and global spread of SARS-CoV-2. Monitoring the viral load and novel lineages within human-derived wastewater collected from aircraft and at air transport hubs has been proposed as an effective way to monitor the importation frequency of viral pathogens. The success of this approach, however, is highly dependent on the bathroom and defecation habits of air passengers during their journey. In this study of UK adults (n = 2103), we quantified the likelihood of defecation prior to departure, on the aircraft and upon arrival on both short- and long-haul flights. The results were then used to assess the likelihood of capturing the signal from infected individuals at UK travel hubs. To obtain a representative cross-section of the population, the survey was stratified by geographical region, gender, age, parenting status, and social class. We found that an individual's likelihood to defecate on short-haul flights (< 6 h in duration) was low (< 13 % of the total), but was higher on long-haul flights (< 36 %; > 6 h in duration). This behaviour pattern was higher among males and younger age groups. The maximum likelihood of defecation was prior to departure (< 39 %). Based on known SARS-CoV-2 faecal shedding rates (30-60 %) and an equal probability of infected individuals being on short- (71 % of inbound flights) and long-haul flights (29 %), we estimate that aircraft wastewater is likely to capture ca. 8-14 % of SARS-CoV-2 cases entering the UK. Monte Carlo simulations predicted that SARS-CoV-2 would be present in wastewater on 14 % of short-haul flights and 62 % of long-haul flights under current pandemic conditions. We conclude that aircraft wastewater alone is insufficient to effectively monitor all the transboundary entries of faecal-borne pathogens but can form part of a wider strategy for public heath surveillance at national borders.}, } @article {pmid36198068, year = {2022}, author = {Wanchai, V and Jenjaroenpun, P and Leangapichart, T and Arrey, G and Burnham, CM and Tümmler, MC and Delgado-Calle, J and Regenberg, B and Nookaew, I}, title = {CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, doi = {10.1093/bib/bbac422}, pmid = {36198068}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R37 CA251763/CA/NCI NIH HHS/United States ; T32 GM106999/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA, Circular/genetics ; *Genome ; DNA/genetics ; Eukaryotic Cells ; }, abstract = {Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.}, } @article {pmid36197407, year = {2022}, author = {Cunha, APD and Cruz, MMD}, title = {Analysis of trend in mortality due to HIV/AIDS-defining and non-HIV/AIDS defining illnesses according to sociodemographic characteristics, by Federative Unit and Brazil, 2000-2018.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {31}, number = {2}, pages = {e2022093}, doi = {10.1590/S2237-96222022000200021}, pmid = {36197407}, issn = {2237-9622}, mesh = {*Acquired Immunodeficiency Syndrome/epidemiology ; Brazil/epidemiology ; Humans ; Information Systems ; Time Factors ; }, abstract = {OBJECTIVE: To analyze the temporal trend of mortality rate due to HIV/AIDS defining and non-HIV/AIDS defining illnesses in Brazil between 2000 and 2018.

METHODS: This was an ecological time series study, using data from the Mortality Information System, in Brazil and the Federative Units. Trend analysis was performed by means of Prais-Winsten regression model, according to overall mortality rate, sex, age group, marital status and race/skin color.

RESULTS: A total of 237,435 deaths were recorded in the period. In the country, defining illnesses showed higher rates (7.4 to 4.4 deaths/100,000 inhabitants in the period) than those observed among non-defining diseases (0.4 to 0.8 death/100,000 inhabitants in the period). It could be seen a decrease in overall mortality due to defining diseases (-6.3%; 95%CI -8.8;-3.8); while it increased due to non-defining diseases (11.0%; 95%CI 6.5;15.7).

CONCLUSION: There was a change in HIV/AIDS mortality profile over the years, with a decrease in deaths due to HIV/AIDS-defining diseases.}, } @article {pmid36197074, year = {2022}, author = {Gonçalves, BP and Hall, M and Jassat, W and Balan, V and Murthy, S and Kartsonaki, C and Semple, MG and Rojek, A and Baruch, J and Reyes, LF and Dasgupta, A and Dunning, J and Citarella, BW and Pritchard, M and Martín-Quiros, A and Sili, U and Baillie, JK and Aryal, D and Arabi, Y and Rashan, A and Angheben, A and Caoili, J and Carrier, FM and Harrison, EM and Gómez-Junyent, J and Figueiredo-Mello, C and Douglas, JJ and Mat Nor, MB and Chow, YP and Wong, XC and Bertagnolio, S and Thwin, SS and Streinu-Cercel, A and Salazar, L and Rishu, A and Rangappa, R and Ong, DSY and Hashmi, M and Carson, G and Diaz, J and Fowler, R and Kraemer, MUG and Wils, EJ and Horby, P and Merson, L and Olliaro, PL and , }, title = {An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36197074}, issn = {2050-084X}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 200927/WT_/Wellcome Trust/United Kingdom ; OV2170359//CIHR/Canada ; 222410/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; 225288/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; 222048/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*COVID-19/epidemiology/virology ; Humans ; *SARS-CoV-2/genetics ; }, abstract = {BACKGROUND: Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.

METHODS: Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.

RESULTS: Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61-0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.

CONCLUSIONS: Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.

FUNDING: Bronner P. Gonçalves, Peter Horby, Gail Carson, Piero L. Olliaro, Valeria Balan, Barbara Wanjiru Citarella, and research costs were supported by the UK Foreign, Commonwealth and Development Office (FCDO) and Wellcome [215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z]; and Janice Caoili and Madiha Hashmi were supported by the UK FCDO and Wellcome [222048/Z/20/Z]. Peter Horby, Gail Carson, Piero L. Olliaro, Kalynn Kennon and Joaquin Baruch were supported by the Bill & Melinda Gates Foundation [OPP1209135]; Laura Merson was supported by University of Oxford's COVID-19 Research Response Fund - with thanks to its donors for their philanthropic support. Matthew Hall was supported by a Li Ka Shing Foundation award to Christophe Fraser. Moritz U.G. Kraemer was supported by the Branco Weiss Fellowship, Google.org, the Oxford Martin School, the Rockefeller Foundation, and the European Union Horizon 2020 project MOOD (#874850). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Contributions from Srinivas Murthy, Asgar Rishu, Rob Fowler, James Joshua Douglas, François Martin Carrier were supported by CIHR Coronavirus Rapid Research Funding Opportunity OV2170359 and coordinated out of Sunnybrook Research Institute. Contributions from Evert-Jan Wils and David S.Y. Ong were supported by a grant from foundation Bevordering Onderzoek Franciscus; and Andrea Angheben by the Italian Ministry of Health "Fondi Ricerca corrente-L1P6" to IRCCS Ospedale Sacro Cuore-Don Calabria. The data contributions of J.Kenneth Baillie, Malcolm G. Semple, and Ewen M. Harrison were supported by grants from the National Institute for Health Research (NIHR; award CO-CIN-01), the Medical Research Council (MRC; grant MC_PC_19059), and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. All funders of the ISARIC Clinical Characterisation Group are listed in the appendix.}, } @article {pmid36195605, year = {2022}, author = {Peters, K and König-Ries, B}, title = {Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {598}, pmid = {36195605}, issn = {2052-4463}, mesh = {Biodiversity ; *Bryophyta ; Computational Biology/methods ; *Hepatophyta ; Image Processing, Computer-Assisted/methods ; }, abstract = {Macro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic characters of the species belonging to the liverwort family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable metadata using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.}, } @article {pmid36195601, year = {2022}, author = {Pottier, P and Lin, HY and Oh, RRY and Pollo, P and Rivera-Villanueva, AN and Valdebenito, JO and Yang, Y and Amano, T and Burke, S and Drobniak, SM and Nakagawa, S}, title = {A comprehensive database of amphibian heat tolerance.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {600}, pmid = {36195601}, issn = {2052-4463}, mesh = {*Amphibians ; Animals ; Databases, Factual ; Hot Temperature ; Temperature ; *Thermotolerance ; }, abstract = {Rising temperatures represent a significant threat to the survival of ectothermic animals. As such, upper thermal limits represent an important trait to assess the vulnerability of ectotherms to changing temperatures. For instance, one may use upper thermal limits to estimate current and future thermal safety margins (i.e., the proximity of upper thermal limits to experienced temperatures), use this trait together with other physiological traits in species distribution models, or investigate the plasticity and evolvability of these limits for buffering the impacts of changing temperatures. While datasets on thermal tolerance limits have been previously compiled, they sometimes report single estimates for a given species, do not present measures of data dispersion, and are biased towards certain parts of the globe. To overcome these limitations, we systematically searched the literature in seven languages to produce the most comprehensive dataset to date on amphibian upper thermal limits, spanning 3,095 estimates across 616 species. This resource will represent a useful tool to evaluate the vulnerability of amphibians, and ectotherms more generally, to changing temperatures.}, } @article {pmid36191222, year = {2022}, author = {Yang, L and Constantino, SM and Grenfell, BT and Weber, EU and Levin, SA and Vasconcelos, VV}, title = {Sociocultural determinants of global mask-wearing behavior.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {41}, pages = {e2213525119}, pmid = {36191222}, issn = {1091-6490}, mesh = {*COVID-19/epidemiology/prevention & control ; Humans ; *Masks ; *Pandemics/prevention & control ; Public Policy ; Risk ; SARS-CoV-2 ; Social Conditions ; }, abstract = {Behavioral responses influence the trajectories of epidemics. During the COVID-19 pandemic, nonpharmaceutical interventions (NPIs) reduced pathogen transmission and mortality worldwide. However, despite the global pandemic threat, there was substantial cross-country variation in the adoption of protective behaviors that is not explained by disease prevalence alone. In particular, many countries show a pattern of slow initial mask adoption followed by sharp transitions to high acceptance rates. These patterns are characteristic of behaviors that depend on social norms or peer influence. We develop a game-theoretic model of mask wearing where the utility of wearing a mask depends on the perceived risk of infection, social norms, and mandates from formal institutions. In this model, increasing pathogen transmission or policy stringency can trigger social tipping points in collective mask wearing. We show that complex social dynamics can emerge from simple individual interactions and that sociocultural variables and local policies are important for recovering cross-country variation in the speed and breadth of mask adoption. These results have implications for public health policy and data collection.}, } @article {pmid36188695, year = {2022}, author = {Zhang, W}, title = {Design of Urban Garden Landscape Visualization System Based on GIS and Remote Sensing Technology.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {9592376}, pmid = {36188695}, issn = {1687-5273}, mesh = {Cities ; Environmental Monitoring/methods ; Gardens ; *Geographic Information Systems ; Hot Temperature ; *Remote Sensing Technology ; }, abstract = {Urban green ecological space is an important manifestation of the environmental characteristics of a green city. The research results show that the urban green ecological space has obvious cooling and humidity effects, which are very important for reducing the urban heat island effect. Remote sensing technology describes the slow-release effects of urban green parks in different seasons from the two perspectives of thermal slow-release intensity and thermal slow-release distance. In this paper, UAV remote sensing is used to extract the internal and external factors of the urban green environment characteristics and to identify the main factors that affect the slow-release heat effect and seasonal changes of the urban green environment. In addition, it analyzes the factors that affect the urban environmental temperature within the environmental temperature slow-release range of urban green space, establishes a model to predict the environmental temperature within the thermal slow-release range outside the park, and realizes the largest thermal slow release in the urban greening ecological space. These are new technologies created in the context of digitization, which include image understanding and synthesis, which involve the use of computer graphics and image processing technology to convert data into graphics or images displayed on the screen to achieve an interactive process.}, } @article {pmid36187697, year = {2022}, author = {Ekpenyong, N and Heitz Tokpa, K and Nwankwo, O and O'Donnell, D and Rodriguez Franco, D and Berté, S and Amani Kouassi, S and Eteng, G and Undelikwo, V and Auer, C and Guessan Bi, GB and Oyo-Ita, A and Bosch-Capblanch, X}, title = {Using and improving the PHISICC paper-based tools in the health facility laboratories: Examples of Human Centered Design taking systems thinking into practice, in Côte d'Ivoire and Nigeria.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {916397}, pmid = {36187697}, issn = {2296-2565}, mesh = {Cote d'Ivoire ; Health Facilities ; Humans ; *Laboratories ; Nigeria ; Systems Analysis ; *Universal Design ; }, abstract = {BACKGROUND: Health workers in low- and middle-income countries are increasingly demanded to collect more and more data to report them to higher levels of the health information system (HIS), in detriment of useful data for clinical and public health decision-making, potentially compromising the quality of their health care provison. In order to support health workers' decision-making, we engaged with partners in Côte d'Ivoire, Mozambique and Nigeria in a research project to conceive, design, produce, implement and test paper-based health information tools: the PHISICC tools. Our aim was to understand the use of PHISICC tools by health workers and to improve them based on their feedback.

METHODS: The design Health Facility Laboratories (HF Labs) in Côte d'Ivoire and in Nigeria were set up after months of use of PHISICC tools. Activities were structured in three phases or 'sprints' of co-creative research. We used a transdisciplinary approach, including anthropology and Human Centered Design (HCD), observations, shadowing, structured interviews and co-creation.

RESULTS: Health workers appreciated the standardization of the tools across different health care areas, with a common visual language that optimized use. Several design issues were raised, in terms of formats and contents. They strongly appreciated how the PHISICC registers guided their clinical decision-making and how it facilitated tallying and counting for monthly reporting. However, adherence to new procedures was not universal. The co-creation sessions resulted in modifications to the PHISICC tools of out-patient care and postnatal care.

DISCUSSION: Although health systems and systemic thinking allowed the teams to embrace complexity, it was the HCD approach that actually produced a shift in researchers' mind-set: from HIS as data management tools to HIS as quality of care instruments. HCD allowed navigating the complexity of health systems interventions due to its capacity to operate change: it not only allowed us to understand how the PHISICC tools were used but also how to further improve them. In the absence of (or even with) an analytical health systems framework, HCD approaches can work in real-life situations for the ideation, testing and implementation of interventions to improve health systems and health status outcomes.}, } @article {pmid36179444, year = {2022}, author = {Chin, JM and Growns, B and Sebastian, J and Page, MJ and Nakagawa, S}, title = {The transparency and reproducibility of systematic reviews in forensic science.}, journal = {Forensic science international}, volume = {340}, number = {}, pages = {111472}, doi = {10.1016/j.forsciint.2022.111472}, pmid = {36179444}, issn = {1872-6283}, mesh = {*Benchmarking ; Databases, Factual ; *Forensic Sciences ; Reproducibility of Results ; Systematic Reviews as Topic ; }, abstract = {Systematic reviews are indispensable tools for both reliably informing decision-makers about the state of the field and for identifying areas that need further study. Their value, however, depends on their transparency and reproducibility. Readers should be able to determine what was searched for and when, where the authors searched, and whether that search was predetermined or evolved based on what was found. In this article, we measured the transparency and reproducibility of systematic reviews in forensic science, a field where courts, policymakers, and legislators count on systematic reviews to make informed decisions. In a sample of 100 systematic reviews published between 2018 and 2021, we found that completeness of reporting varied markedly. For instance, 50 % of reviews claimed to follow a reporting guideline and such statements were only modestly related to compliance with that reporting guideline. As to specific reporting items, 82 % reported all of the databases searched, 22 % reported the review's full Boolean search logic, and just 7 % reported the review was registered. Among meta-analyses (n = 23), only one stated data was available and none stated the analytic code was available. After considering the results, we end with recommendations for improved regulation of reporting practices, especially among journals. Our results may serve as a useful benchmark as the field evolves.}, } @article {pmid36175492, year = {2022}, author = {Leonardi, M and Boschin, F and Boscato, P and Manica, A}, title = {Following the niche: the differential impact of the last glacial maximum on four European ungulates.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1038}, pmid = {36175492}, issn = {2399-3642}, mesh = {Animals ; Archaeology ; Databases, Factual ; *Deer ; Ecosystem ; Horses ; Species Specificity ; Sus scrofa ; Swine ; }, abstract = {Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.}, } @article {pmid36174014, year = {2022}, author = {Porter, TM and Hajibabaei, M}, title = {MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0274260}, pmid = {36174014}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Biomarkers ; *Computational Biology ; Ecology ; Eukaryota ; }, abstract = {Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as for molecular ecology and biomonitoring applications in different sectors from academic research to regulatory agencies and industry. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are often used to process animal metabarcode markers from the same study. MetaWorks provides a harmonized processing environment, pipeline, and taxonomic assignment approach for demultiplexed Illumina reads for all biota using a wide range of metabarcoding markers such as 16S, ITS, and COI. A Conda environment is provided to quickly gather most of the programs and dependencies for the pipeline. Several workflows are provided such as: taxonomically assigning exact sequence variants, provides an option to generate operational taxonomic units, and facilitates single-read processing. Pipelines are automated using Snakemake to minimize user intervention and facilitate scalability. All pipelines use the RDP classifier to provide taxonomic assignments with confidence measures. We extend the functionality of the RDP classifier for taxonomically assigning 16S (bacteria), ITS (fungi), and 28S (fungi), to also support COI (eukaryotes), rbcL (eukaryotes, land plants, diatoms), 12S (fish, vertebrates), 18S (eukaryotes, diatoms) and ITS (fungi, plants). MetaWorks properly handles ITS by trimming flanking conserved rRNA gene regions as well as protein coding genes by providing two options for removing obvious pseudogenes. MetaWorks can be downloaded from https://github.com/terrimporter/MetaWorks and quickstart instructions, pipeline details, and a tutorial for new users can be found at https://terrimporter.github.io/MetaWorksSite.}, } @article {pmid36172318, year = {2022}, author = {Yin, G and Liu, J}, title = {Research on Movement Analysis and Guidance in Dance Learning Based on Data Mining.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {9327442}, pmid = {36172318}, issn = {1687-5273}, mesh = {Data Mining ; Humans ; *Learning ; *Movement ; Students ; }, abstract = {In dance, we must understand the essential meaning of dance movements from the inside and express them on the basis of dance. Therefore, in the process of developing new dance teaching methods, it is necessary to improve the basic education of dance students, so that they can express the emotions conveyed by dance through body language and movements, and improve dance expression ability. In this context, we made the research and reached the following conclusions: (1) the number of frames of different dance types is also different, and the number of frames to be learned is also increasing. The dance with the highest number of frames is Latin2, which has 3635 frames, and the dance with the highest number of frames that need to be learned is also Latin2, which requires 2519 frames to learn. (2) The data mining method is still the highest among the three methods, and the accuracy of the complete teaching method is 82%, which is the lowest among the three methods, and the accuracy of the decentralized teaching method is 87%. No matter in the test set or the mixed test set, the curve values of deep mining are very stable. First of all, human movements emphasize that in dance, the essential meaning of dance movements needs to be understood from the inside and expressed through the foundation of dance. Therefore, when developing new dance teaching methods, it is necessary to strengthen the basic dance training of students so that students can express the emotions conveyed by dance through body language and movements and improve their dance expression ability. We conduct research in this ecological environment. Different types of dance learning process using different frames, different types of dance in the algorithm transport have different recognition methods, using better and different algorithms can achieve the best performance. Both groups in the Hip Hop dance had a shorter average learning time than both groups in the Latin dance.}, } @article {pmid36169445, year = {2022}, author = {Martins, ACM and Giordani, F and Gonçalves, MC and Guaraldo, L and Rozenfeld, S}, title = {[Deaths from adverse drug events in Brazil: Mortality Information System as a source of information].}, journal = {Cadernos de saude publica}, volume = {38}, number = {8}, pages = {e00291221}, doi = {10.1590/0102-311XPT291221}, pmid = {36169445}, issn = {1678-4464}, mesh = {Aged ; Brazil/epidemiology ; Child ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; Information Systems ; Middle Aged ; Psychotropic Drugs/adverse effects ; Retrospective Studies ; }, abstract = {Adverse drug events (ADEs) are harmful events caused by medication, and some of which can lead to death. Death records are an important source of information when using codes from the 10th revision of the International Classification of Diseases (ICD-10) suggestive of ADE. This study aimed to identify the ADEs registered in Brazililian Mortality Information System (SIM), analyzing data distribution by year, age group, and type of event. This is an ecological study with retrospective data collection, identifying ADEs in the SIM, using the ICD-10 codes. The study included deaths that occurred in Brazil from 2008 to 2016. An increase in the number of deaths associated with ADE was observed from 2008 to 2016, with a mortality rate per 1 million inhabitants ranging from 8.70 to 14.40 in the period. Most events corresponded to mental and behavioral disorders due to the use of psychotropic drugs. Most deaths (12,311) related to ADE codes were identified in several chapters of the ICD-10. Chapter XX, about adverse events, allowed the identification of a smaller number of deaths (4,893). Higher event rates were observed among individuals aged 60 years and over (39.8/1 million) and children younger than one year (22.0/1 million). The identification of ADE-related deaths on the SIM is an important strategy for addressing undesirable drug-related events. Deaths related to the use of psychotropic drugs were the most frequent ADE-related deaths and the elderly were the age group most affected by ADEs.}, } @article {pmid36167554, year = {2022}, author = {Kim, J and Lee, C and Ko, BJ and Yoo, DA and Won, S and Phillippy, AM and Fedrigo, O and Zhang, G and Howe, K and Wood, J and Durbin, R and Formenti, G and Brown, S and Cantin, L and Mello, CV and Cho, S and Rhie, A and Kim, H and Jarvis, ED}, title = {False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {204}, pmid = {36167554}, issn = {1474-760X}, support = {WT206194/WT_/Wellcome Trust/United Kingdom ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; R03 NS115145/NS/NINDS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Base Composition/genetics ; Chromosomes ; *Genome/genetics ; Sequence Analysis, DNA ; *Vertebrates/genetics ; }, abstract = {BACKGROUND: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements.

RESULTS: Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna's hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5'-proximal promoters and 5' exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies.

CONCLUSIONS: Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.}, } @article {pmid36167140, year = {2023}, author = {Tölgyesi, C and Hábenczyus, AA and Kelemen, A and Török, P and Valkó, O and Deák, B and Erdős, L and Tóth, B and Csikós, N and Bátori, Z}, title = {How to not trade water for carbon with tree planting in water-limited temperate biomes?.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {158960}, doi = {10.1016/j.scitotenv.2022.158960}, pmid = {36167140}, issn = {1879-1026}, mesh = {*Ecosystem ; *Carbon ; Water ; Sand ; Forests ; Soil ; }, abstract = {The most widespread nature-based solution for mitigating climate change is tree planting. When realized as forest restoration in historically forested biomes, it can efficiently contribute to the sequestration of atmospheric carbon and can also entail significant biodiversity and ecosystem service benefits. Conversely, tree planting in naturally open biomes can have adverse effects, of which water shortage due to increased evapotranspiration is among the most alarming ones. Here we assessed how soil texture affects the strength of the trade-off between tree cover and water balance in the forest-steppe biome, where the global pressure for afforestation is threatening with increasing tree cover above historical levels. Here we monitored vertical soil moisture dynamics in four stands in each of the most common forest types of lowland Hungary on well-drained, sandy (natural poplar groves, and Robinia and pine plantations) and on poorly drained, silty-clayey soils (natural oak stands and Robinia plantations), and neighboring grasslands. We found that forests on sand retain moisture in the topsoil (approx. 20 cm) throughout the year, but a thick dry layer develops below that during the vegetation period, significantly impeding groundwater recharge. Neighboring sandy grasslands showed an opposite pattern, with often dry topsoil but intact moisture reserves below, allowing deep percolation. In contrast, forests on silty-clayey soils did not desiccate lower soil layers compared neighboring grasslands, which in turn showed moisture patterns similar to sandy grasslands. We conclude that, in water-limited temperate biomes where landscape-wide water regime depends on deep percolation, soil texture should drive the spatial allocation of tree-based climate mitigation efforts. On sand, the establishment of new forests should be kept to a minimum and grassland restoration should be preferred. The trade-off between water and carbon is less pronounced on silty-clayey soils, making forest patches and wooded rangelands viable targets for both climate mitigation and ecosystem restoration.}, } @article {pmid36166925, year = {2023}, author = {Koo, SY and Hwang, KT and Hwang, S and Choi, KY and Park, YJ and Choi, JH and Truong, TQ and Kim, SM}, title = {Nanoencapsulation enhances the bioavailability of fucoxanthin in microalga Phaeodactylum tricornutum extract.}, journal = {Food chemistry}, volume = {403}, number = {}, pages = {134348}, doi = {10.1016/j.foodchem.2022.134348}, pmid = {36166925}, issn = {1873-7072}, mesh = {Humans ; Mice ; Animals ; Biological Availability ; *Microalgae/metabolism ; Caco-2 Cells ; Xanthophylls/metabolism ; }, abstract = {The marine carotenoid fucoxanthin (FX) has various health benefits but suffers from poor bioavailability. We hypothesize that the bioavailability of FX in microalga Phaeodactylum tricornutum extract (PE) could be improved through nanoencapsulation. Here, we developed two types of nanoparticles: one consisting of alginate and casein (A-C-PE, 246 nm diameter, 79.6% encapsulation efficiency) and the other A-C-PE coated with chitosan (CS-A-C-PE, 258 nm, 78.1%). Both types of nanoparticles incorporating PE showed controlled FX release during simulated gastrointestinal digestion, as well as 1.8-fold improvement of membrane permeability in Caco-2/TC7 cells compared to non-encapsulated PE. Pharmacokinetic behavior of two FX metabolites (fucoxanthinol and amarouciaxanthin A) in mouse plasma was monitored after oral administration. The results showed that 31.8-332.1% more FX metabolites from the nanoparticles were absorbed into plasma than those from PE. In conclusion, encapsulation of PE in both types of nanoparticles significantly promoted the bioavailability of FX.}, } @article {pmid36157711, year = {2022}, author = {Mihaljevic, JR and Borkovec, S and Ratnavale, S and Hocking, TD and Banister, KE and Eppinger, JE and Hepp, C and Doerry, E}, title = {SPARSEMODr: Rapidly simulate spatially explicit and stochastic models of COVID-19 and other infectious diseases.}, journal = {Biology methods & protocols}, volume = {7}, number = {1}, pages = {bpac022}, pmid = {36157711}, issn = {2396-8923}, abstract = {Building realistically complex models of infectious disease transmission that are relevant for informing public health is conceptually challenging and requires knowledge of coding architecture that can implement key modeling conventions. For example, many of the models built to understand COVID-19 dynamics have included stochasticity, transmission dynamics that change throughout the epidemic due to changes in host behavior or public health interventions, and spatial structures that account for important spatio-temporal heterogeneities. Here we introduce an R package, SPARSEMODr, that allows users to simulate disease models that are stochastic and spatially explicit, including a model for COVID-19 that was useful in the early phases of the epidemic. SPARSEMOD stands for SPAtial Resolution-SEnsitive Models of Outbreak Dynamics, and our goal is to demonstrate particular conventions for rapidly simulating the dynamics of more complex, spatial models of infectious disease. In this report, we outline the features and workflows of our software package that allow for user-customized simulations. We believe the example models provided in our package will be useful in educational settings, as the coding conventions are adaptable, and will help new modelers to better understand important assumptions that were built into sophisticated COVID-19 models.}, } @article {pmid36155927, year = {2022}, author = {Russo, A and Blettner, M and Merzenich, H and Wollschlaeger, D and Erdmann, F and Gianicolo, E}, title = {Incidence of childhood leukemia before and after shut down of nuclear power plants in Germany in 2011: A population-based register study during 2004 to 2019.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.34303}, pmid = {36155927}, issn = {1097-0215}, abstract = {The association between leukemia and proximity to nuclear-power-plants (NPPs) has been assessed in several countries with inconsistent results. A case-control study from Germany had shown an increased risk for childhood leukemia (diagnoses 1980-2003) near NPPs. Germany began shutting down nuclear reactors in 2011, following the Fukushima disaster. We tested whether the previously observed association between leukemia and proximity to NPP persisted despite the shutdown. We used an ecological study design to investigate the incidence of leukemia during 2004 to 2019 in children aged 0 to 14 years living near NPPs where at least one reactor was shut down in 2011. We defined study and control areas as municipalities whose surface area was at least 75% within 10 km or between 10 and 50 km of NPPs, respectively. We calculated age-standardized rates and incidence rate ratios (IRR) using control-areas as the reference. We also computed standardized incidence ratios (SIR) separately for each NPP using incidence rates of the German population as a reference. IRR decreased from 1.20 (95% confidence interval: 0.81-1.77) in 2004 to 2011 to 1.12 (0.75-1.68) in 2012 to 2019. Analyses of single plants showed an excess of childhood leukemia during 2004 to 2019 for the Unterweser-NPP, based only on three cases, and the Krümmel-NPP (n = 14; SIR: 1.98, 1.17-3.35). We found slightly decreasing of leukemia incidence rate ratios after the shutdown of nuclear reactors in 2011. Due to the small number of cases, risk estimates have large uncertainty. Further research including a longer follow-up is warranted. The consistent excess of incidence cases around Krümmel may require analytical epidemiological analysis.}, } @article {pmid36149894, year = {2022}, author = {Zhang, L and Chen, L and Yu, XA and Duvallet, C and Isazadeh, S and Dai, C and Park, S and Frois-Moniz, K and Duarte, F and Ratti, C and Alm, EJ and Ling, F}, title = {MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010472}, pmid = {36149894}, issn = {1553-7358}, mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Pandemics ; Population Density ; Sewage ; Wastewater ; }, abstract = {The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. Analyzing the viral fraction of wastewater in the ongoing COVID-19 pandemic has shown the potential of wastewater as aggregated samples for early detection, prevalence monitoring, and variant identification of human diseases in large populations. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we show that taxon abundance and sub-species diversisty in gut-associated microbiomes are new feature space to utilize for human population estimation. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships with respect to human population size. Here and throughout this paper, the human population size is essentially the sample size from the wastewater sample. We present a new algorithm, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxa's relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. New theorems are provided to justify our approach. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.}, } @article {pmid36141528, year = {2022}, author = {Emelyanova, A and Savolainen, A and Oksanen, A and Nieminen, P and Loginova, O and Abass, K and Rautio, A}, title = {Research on Selected Wildlife Infections in the Circumpolar Arctic-A Bibliometric Review.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {18}, pages = {}, pmid = {36141528}, issn = {1660-4601}, mesh = {Alaska/epidemiology ; Animals ; *Animals, Wild ; Arctic Regions ; Bibliometrics ; *Communicable Diseases/epidemiology/veterinary ; Humans ; Mammals ; }, abstract = {One Health, a multidisciplinary approach to public health, which integrates human, animal, and environmental studies, is prudent for circumpolar Arctic health research. The objective of our bibliometric review was to identify and compare research in select infectious diseases in Arctic wildlife species with importance to human health indexed in English language databases (PubMed, Scopus) and the Russian database eLibrary.ru. Included articles (in English and Russian languages) needed to meet the following criteria: (1) data comes from the Arctic, (2) articles report original research or surveillance reports, (3) articles were published between 1990 and 2018, and (4) research relates to naturally occurring infections. Of the included articles (total n = 352), most were from Russia (n = 131, 37%), Norway (n = 58, 16%), Canada (n = 39, 11%), and Alaska (n = 39, 11%). Frequently reported infectious agents among selected mammals were Trichinella spp. (n = 39), Brucella spp. (n = 25), rabies virus (n = 11), Echinococcus spp. (n = 10), and Francisella tularensis (n = 9). There were 25 articles on anthrax in eLibrary.ru, while there were none in the other two databases. We identified future directions where opportunities for further research, collaboration, systematic reviews, or monitoring programs are possible and needed.}, } @article {pmid36138772, year = {2022}, author = {Botella, C and Bonnet, P and Hui, C and Joly, A and Richardson, DM}, title = {Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion.}, journal = {Biology}, volume = {11}, number = {9}, pages = {}, pmid = {36138772}, issn = {2079-7737}, abstract = {Plant invasions generate massive ecological and economic costs worldwide. Predicting their spatial dynamics is crucial to the design of effective management strategies and the prevention of invasions. Earlier studies highlighted the crucial role of long-distance dispersal in explaining the speed of many invasions. In addition, invasion speed depends highly on the duration of its lag phase, which may depend on the scaling of fecundity with age, especially for woody plants, even though empirical proof is still rare. Bayesian dynamic species distribution models enable the fitting of process-based models to partial and heterogeneous observations using a state-space modeling approach, thus offering a tool to test such hypotheses on past invasions over large spatial scales. We use such a model to explore the roles of long-distance dispersal and age-structured fecundity in the transient invasion dynamics of Plectranthus barbatus, a woody plant invader in South Africa. Our lattice-based model accounts for both short and human-mediated long-distance dispersal, as well as age-structured fecundity. We fitted our model on opportunistic occurrences, accounting for the spatio-temporal variations of the sampling effort and the variable detection rates across datasets. The Bayesian framework enables us to integrate a priori knowledge on demographic parameters and control identifiability issues. The model revealed a massive wave of spatial spread driven by human-mediated long-distance dispersal during the first decade and a subsequent drastic population growth, leading to a global equilibrium in the mid-1990s. Without long-distance dispersal, the maximum population would have been equivalent to 30% of the current equilibrium population. We further identified the reproductive maturity at three years old, which contributed to the lag phase before the final wave of population growth. Our results highlighted the importance of the early eradication of weedy horticultural alien plants around urban areas to hamper and delay the invasive spread.}, } @article {pmid36130600, year = {2022}, author = {Bidel, F and Bennett, NC and Wardill, TJ}, title = {Octopus bimaculoides' arm recruitment and use during visually evoked prey capture.}, journal = {Current biology : CB}, volume = {32}, number = {21}, pages = {4727-4733.e3}, doi = {10.1016/j.cub.2022.08.080}, pmid = {36130600}, issn = {1879-0445}, mesh = {Animals ; *Octopodiformes/physiology ; Movement/physiology ; Extremities/physiology ; Adaptation, Physiological ; }, abstract = {Octopus' limb hyper-redundancy complicates traditional motor control system theory due to its extensive sensory inputs, subsequent decision-making, and arm coordination. Octopuses are thought to reduce flexibility control complexity by relying on highly stereotypical motor primitives (e.g., reaching[1][,][2][,][3][,][4] and crawling[5]) and multi-level processes to coordinate movement,[6][,][7] utilizing extensive peripheral nervous system (PNS) processing.[2][,][8][,][9] Division of labor along the anterior-posterior axis[10] and limb specialization of the four anterior arms in T-maze food retrieval[11] further simplify control. However, specific arm recruitment and coordination during visually guided reaching behavior remains poorly understood. Here, we investigated visually evoked Octopus bimaculoides' prey capture capabilities[12][,][13] by eliciting and examining prey-specific arm recruitment. When striking crabs, octopuses preferred synchronous arm recruitment, while sequential arm recruitment with a characteristic swaying movement is employed for shrimp. Such behavioral selection aligns with specific prey escape strategies and the octopus' flexible arm biomechanical constraints. Although side bias existed, we found significant bilateral symmetry, with one side being functionally a mirror of the other rather than anterior arm use being functionally equal and differing to posterior arm use. Among arms, the second limb is unequivocally dominant for goal-directed monocularly driven prey capture. Although the eight arms share gross anatomy and are considered equipotential,[10][,][14] such arm use for specific actions could reflect subtle evolutionary adaptations. Finally, we quantitatively show, corroborating earlier observations,[10][,][15] that octopuses employ a dimension reduction strategy by actively deciding to recruit adjacent arms over other available arms during either sequential or synchronous visually evoked prey attack.}, } @article {pmid36130260, year = {2022}, author = {Sun, D and Ding, S and Cai, P and Zhang, D and Han, M and Hu, QN}, title = {BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {22}, pages = {5137-5138}, doi = {10.1093/bioinformatics/btac640}, pmid = {36130260}, issn = {1367-4811}, mesh = {*Metabolic Engineering/methods ; *Synthetic Biology ; Databases, Factual ; }, abstract = {SUMMARY: Advances in metabolic engineering have boosted the production of bulk chemicals, resulting in tons of production volumes of some bulk chemicals with very low prices. A decrease in the production cost and overproduction of bulk chemicals makes it necessary and desirable to explore the potential to synthesize higher-value products from them. It is also useful and important for society to explore the use of design methods involving synthetic biology to increase the economic value of these bulk chemicals. Therefore, we developed 'BioBulkFoundary', which provides an elaborate analysis of the biosynthetic potential of bulk chemicals based on the state-of-art exploration of pathways to synthesize value-added chemicals, along with associated comprehensive technology and economic database into a user-friendly framework.

Freely available on the web at http://design.rxnfinder.org/biobulkfoundary/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36127081, year = {2022}, author = {Barrigon, ML and Porras-Segovia, A and Courtet, P and Lopez-Castroman, J and Berrouiguet, S and Pérez-Rodríguez, MM and Artes, A and , and Baca-Garcia, E}, title = {Smartphone-based Ecological Momentary Intervention for secondary prevention of suicidal thoughts and behaviour: protocol for the SmartCrisis V.2.0 randomised clinical trial.}, journal = {BMJ open}, volume = {12}, number = {9}, pages = {e051807}, pmid = {36127081}, issn = {2044-6055}, mesh = {Ecological Momentary Assessment ; Humans ; Randomized Controlled Trials as Topic ; Secondary Prevention ; *Smartphone ; Suicidal Ideation ; *Telemedicine ; }, abstract = {INTRODUCTION: Suicide is one of the leading public health issues worldwide. Mobile health can help us to combat suicide through monitoring and treatment. The SmartCrisis V.2.0 randomised clinical trial aims to evaluate the effectiveness of a smartphone-based Ecological Momentary Intervention to prevent suicidal thoughts and behaviour.

METHODS AND ANALYSIS: The SmartCrisis V.2.0 study is a randomised clinical trial with two parallel groups, conducted among patients with a history of suicidal behaviour treated at five sites in France and Spain. The intervention group will be monitored using Ecological Momentary Assessment (EMA) and will receive an Ecological Momentary Intervention called 'SmartSafe' in addition to their treatment as usual (TAU). TAU will consist of mental health follow-up of the patient (scheduled appointments with a psychiatrist) in an outpatient Suicide Prevention programme, with predetermined clinical appointments according to the Brief Intervention Contact recommendations (1, 2, 4, 7 and 11 weeks and 4, 6, 9 and 12 months). The control group would receive TAU and be monitored using EMA.

ETHICS AND DISSEMINATION: This study has been approved by the Ethics Committee of the University Hospital Fundación Jiménez Díaz. It is expected that, in the near future, our mobile health intervention and monitoring system can be implemented in routine clinical practice. Results will be disseminated through peer-reviewed journals and psychiatric congresses. Reference number EC005-21_FJD. Participants gave informed consent to participate in the study before taking part.

TRIAL REGISTRATION NUMBER: NCT04775160.}, } @article {pmid36123315, year = {2022}, author = {Fontana, F and Alessandri, G and Tarracchini, C and Bianchi, MG and Rizzo, SM and Mancabelli, L and Lugli, GA and Argentini, C and Vergna, LM and Anzalone, R and Longhi, G and Viappiani, A and Taurino, G and Chiu, M and Turroni, F and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M}, title = {Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5825-5839}, doi = {10.1111/1462-2920.16205}, pmid = {36123315}, issn = {1462-2920}, support = {SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Humans ; Infant ; *Bifidobacterium/genetics ; *Multiomics ; Reproducibility of Results ; Feces/microbiology ; Metagenomics ; Bacteria ; }, abstract = {The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.}, } @article {pmid36120670, year = {2022}, author = {Liu, X and Wang, J and Rui, X and Zhang, J}, title = {Application of GIS Technology-Supported Cross Media Fusion Method Based on Deep Learning in Landscape Performance Evaluation.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {8339895}, pmid = {36120670}, issn = {1687-5273}, mesh = {Algorithms ; *Deep Learning ; Geographic Information Systems ; Humans ; Neural Networks, Computer ; Technology ; }, abstract = {GIS technology can provide reasonable and sustainable data support for landscape planning and ecological development and make wetland landscape planning consider the spatial layout of landscape and the optimal allocation of resources more. The key technologies of cross media intelligence mainly focus on intelligent information retrieval, analysis and reasoning, knowledge map construction, and intelligent storage. Convolutional neural network (CNN), as one of the representative algorithms of deep learning, plays an important role in retrieving landscape data and extracting image and text features across media. Further retrieval of media data, in-depth text processing, and image feature data extraction are realized by using deep learning technology, and comprehensive in-depth analysis is carried out by combining landscape plane images, three-dimensional images, and vector information in GIS technology. Provide quantitative information for the evaluation system of human landscape, economy, history, and region, so as to formulate a scientific and reasonable performance evaluation system.}, } @article {pmid36114727, year = {2022}, author = {Ma, X and Zhu, X and Xie, Q and Jin, J and Zhou, Y and Luo, Y and Liu, Y and Tian, J and Zhao, Y}, title = {Monitoring nature's calendar from space: Emerging topics in land surface phenology and associated opportunities for science applications.}, journal = {Global change biology}, volume = {28}, number = {24}, pages = {7186-7204}, doi = {10.1111/gcb.16436}, pmid = {36114727}, issn = {1365-2486}, mesh = {*Ecosystem ; Seasons ; *Climate Change ; Carbon ; Water ; }, abstract = {Vegetation phenology has been viewed as the nature's calendar and an integrative indicator of plant-climate interactions. The correct representation of vegetation phenology is important for models to accurately simulate the exchange of carbon, water, and energy between the vegetated land surface and the atmosphere. Remote sensing has advanced the monitoring of vegetation phenology by providing spatially and temporally continuous data that together with conventional ground observations offers a unique contribution to our knowledge about the environmental impact on ecosystems as well as the ecological adaptations and feedback to global climate change. Land surface phenology (LSP) is defined as the use of satellites to monitor seasonal dynamics in vegetated land surfaces and to estimate phenological transition dates. LSP, as an interdisciplinary subject among remote sensing, ecology, and biometeorology, has undergone rapid development over the past few decades. Recent advances in sensor technologies, as well as data fusion techniques, have enabled novel phenology retrieval algorithms that refine phenology details at even higher spatiotemporal resolutions, providing new insights into ecosystem dynamics. As such, here we summarize the recent advances in LSP and the associated opportunities for science applications. We focus on the remaining challenges, promising techniques, and emerging topics that together we believe will truly form the very frontier of the global LSP research field.}, } @article {pmid36112603, year = {2022}, author = {Miller, JC and Satheesh Babu, AK and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Anandh Babu, PV}, title = {Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.}, journal = {Molecular nutrition & food research}, volume = {66}, number = {22}, pages = {e2200112}, pmid = {36112603}, issn = {1613-4133}, support = {R01 HL141540/HL/NHLBI NIH HHS/United States ; R03AGO52848/HL/NHLBI NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; }, mesh = {Male ; Mice ; Animals ; *Fragaria/chemistry ; *Metabolic Syndrome/etiology/drug therapy ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Inflammation ; }, abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. This study investigates whether strawberry consumption reduces vascular complications in an animal model of MetS and identifies whether this effect is associated with changes in the composition of gut microbes.

METHODS AND RESULTS: Seven-week-old male mice consume diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups are fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to ≈160 g of strawberry. After 12 weeks treatment, vascular inflammation is enhanced in HF versus C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppresses vascular inflammation in HF+SB versus HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe is decreased in HF+SB. Importantly, circulating chemokines are positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).

CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS.}, } @article {pmid36111781, year = {2022}, author = {Eyre, MT and Souza, FN and Carvalho-Pereira, TSA and Nery, N and de Oliveira, D and Cruz, JS and Sacramento, GA and Khalil, H and Wunder, EA and Hacker, KP and Hagan, JE and Childs, JE and Reis, MG and Begon, M and Diggle, PJ and Ko, AI and Giorgi, E and Costa, F}, title = {Linking rattiness, geography and environmental degradation to spillover Leptospira infections in marginalised urban settings: An eco-epidemiological community-based cohort study in Brazil.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36111781}, issn = {2050-084X}, support = {F31 AI114245/NH/NIH HHS/United States ; R25 TW009338/NH/NIH HHS/United States ; 102330/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; U01 AI088752/NH/NIH HHS/United States ; R01 AI052473/NH/NIH HHS/United States ; R01 TW009504/NH/NIH HHS/United States ; 001/WHO_/World Health Organization/International ; 964635/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Animals ; Brazil/epidemiology ; Cohort Studies ; Epidemiologic Studies ; Geography ; Humans ; *Leptospirosis/epidemiology ; Male ; *Poverty Areas ; Rats ; Zoonoses/epidemiology ; }, abstract = {BACKGROUND: Zoonotic spillover from animal reservoirs is responsible for a significant global public health burden, but the processes that promote spillover events are poorly understood in complex urban settings. Endemic transmission of Leptospira, the agent of leptospirosis, in marginalised urban communities occurs through human exposure to an environment contaminated by bacteria shed in the urine of the rat reservoir. However, it is unclear to what extent transmission is driven by variation in the distribution of rats or by the dispersal of bacteria in rainwater runoff and overflow from open sewer systems.

METHODS: We conducted an eco-epidemiological study in a high-risk community in Salvador, Brazil, by prospectively following a cohort of 1401 residents to ascertain serological evidence for leptospiral infections. A concurrent rat ecology study was used to collect information on the fine-scale spatial distribution of 'rattiness', our proxy for rat abundance and exposure of interest. We developed and applied a novel geostatistical framework for joint spatial modelling of multiple indices of disease reservoir abundance and human infection risk.

RESULTS: The estimated infection rate was 51.4 (95%CI 40.4, 64.2) infections per 1000 follow-up events. Infection risk increased with age until 30 years of age and was associated with male gender. Rattiness was positively associated with infection risk for residents across the entire study area, but this effect was stronger in higher elevation areas (OR 3.27 95% CI 1.68, 19.07) than in lower elevation areas (OR 1.14 95% CI 1.05, 1.53).

CONCLUSIONS: These findings suggest that, while frequent flooding events may disperse bacteria in regions of low elevation, environmental risk in higher elevation areas is more localised and directly driven by the distribution of local rat populations. The modelling framework developed may have broad applications in delineating complex animal-environment-human interactions during zoonotic spillover and identifying opportunities for public health intervention.

FUNDING: This work was supported by the Oswaldo Cruz Foundation and Secretariat of Health Surveillance, Brazilian Ministry of Health, the National Institutes of Health of the United States (grant numbers F31 AI114245, R01 AI052473, U01 AI088752, R01 TW009504 and R25 TW009338); the Wellcome Trust (102330/Z/13/Z), and by the Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB/JCB0020/2016). MTE was supported by a Medical Research UK doctorate studentship. FBS participated in this study under a FAPESB doctorate scholarship.}, } @article {pmid36109660, year = {2022}, author = {Negesse, A and Woyraw, W and Temesgen, H and Teka, Y and Yismaw, L and Akalu, TY and Deml, YA and Sume, BW and Negesse, Y and Taddege, T and Kidie, WD and Teym, A and Asmare, B and Hune, Y and Damte, D and Getaneh, T and Gebre, T and Tilahun, B and Tenagne, A and Tegegne, E and Birhanu, MY and Mekonen, H and Shiferaw, M and Kassahun, W and Desalegn, BB}, title = {Spatial exploration of non-resilience to food insecurity, its association with COVID-19 and household coping strategies in East Gojjam districts, Northwest Ethiopia, 2020.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15511}, pmid = {36109660}, issn = {2045-2322}, mesh = {Adaptation, Psychological ; *COVID-19/epidemiology ; Cross-Sectional Studies ; Ethiopia/epidemiology ; Family Characteristics ; Food Insecurity ; *Food Supply ; Humans ; Male ; Pandemics ; Socioeconomic Factors ; }, abstract = {The coronavirus disease-2019 (COVID-19) pandemic has posed a significant multifaceted threat to the global community. Ethiopia, as a Sub-Saharan African country, is suffering from chronic food insecurity, and the emergence of such a pandemic will exacerbate the situation. As a result, this study investigated the spatial variation of non-resilience to food insecurity, its relationship with COVID-19, and household coping strategies to become resilient in the long run among households in the East Gojjam Zone of Northwest Ethiopia. From September 22 to December 24, 2020, an agro-ecological-based cross-sectional study of 3532 households was conducted to assess the spatial distribution and associated factors of non-resilience to household food insecurity. The enumeration areas (EAs) and households were chosen using a multistage sampling technique. Data were gathered using a semi-structured questionnaire and checklist using an Android device loaded with an Open Data Kit (ODK) template. Binary logistic regression was used to identify the specific factors associated with household non-resilience to food insecurity. A thematic analysis was conducted to investigate the opportunities and challenges of resilience for household food insecurity. Nearly two-thirds (62.5%) of the households were farmers, 67.9% lived in rural areas, and nearly three-quarters (73.8%) earned less than or equal to ETB 2100 per month. Males headed more than four-fifths of the households (81.7%). We found that nearly two-thirds of the households (60.02%), 95% CI 58.40, 61.64) were food insecure. After bivariate logistic regression, we found that households who were divorced (AOR = 2.54 (1.65, 3.87)), daily laborers (AOR = 2.37 (1.15, 4.87)), government employees (AOR = 2.06 (1.05, 4.05)), residents of highland and hot areas (AOR = 11.5 (5.37, 16.77)) and lowland areas (AOR = 1.35 (1.02, 3.15)) were frustrated by COVID-19 (AOR = 1.23 (1.02, 1.50)) and price inflation (1.89 (AOR = 1.42, 2.56))) were at higher odds of being non-resilient to household food insecurity at a 95% confidence level. Geospatial hot spot analysis revealed that Kurar kebele (the lowest government administrative unit) in Dejen District and Debre Markos town were the red-hotspot areas of household non-resilience to food insecurity. Less than a quarter of the households attempted to cope with food insecurity by adjusting their food consumption, while more than 60% of the households chose none of the coping strategies tested. According to the thematic analysis, the degree of poverty (lack of asset ownership), the COVID-19 pandemic, farm decreased variety, and low crop productivity were identified as challenges to coping with the hardship of resilience to food insecurity. During the COVID-19 pandemic and public emergency, the proportion of households that were unprepared for food insecurity reached its peak. It was recognized that a segment of the population with low economic capacity was more vulnerable to food insecurity and less resilient. Tough developmental gains will be undermined in this case. As a result, each responsible body and stakeholder should develop and implement solid corrective plans for the local context.}, } @article {pmid36109545, year = {2022}, author = {Domma, F and Condino, F and Franceschi, S and De Luca, DL and Biondi, D}, title = {On the extreme hydrologic events determinants by means of Beta-Singh-Maddala reparameterization.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15537}, pmid = {36109545}, issn = {2045-2322}, mesh = {*Hydrology ; }, abstract = {In previous studies, beta-k distribution and distribution functions strongly related to that, have played important roles in representing extreme events. Among these distributions, the Beta-Singh-Maddala turned out to be adequate for modelling hydrological extreme events. Starting from this distribution, the aim of the paper is to express the model as a function of indexes of hydrological interest and simultaneously investigate on their dependence with a set of explanatory variables in such a way to explore on possible determinants of extreme hydrologic events. Finally, an application to a real hydrologic dataset is considered in order to show the potentiality of the proposed model in describing data and in understanding effects of covariates on frequently adopted hydrological indicators.}, } @article {pmid36108049, year = {2022}, author = {Tegally, H and San, JE and Cotten, M and Moir, M and Tegomoh, B and Mboowa, G and Martin, DP and Baxter, C and Lambisia, AW and Diallo, A and Amoako, DG and Diagne, MM and Sisay, A and Zekri, AN and Gueye, AS and Sangare, AK and Ouedraogo, AS and Sow, A and Musa, AO and Sesay, AK and Abias, AG and Elzagheid, AI and Lagare, A and Kemi, AS and Abar, AE and Johnson, AA and Fowotade, A and Oluwapelumi, AO and Amuri, AA and Juru, A and Kandeil, A and Mostafa, A and Rebai, A and Sayed, A and Kazeem, A and Balde, A and Christoffels, A and Trotter, AJ and Campbell, A and Keita, AK and Kone, A and Bouzid, A and Souissi, A and Agweyu, A and Naguib, A and Gutierrez, AV and Nkeshimana, A and Page, AJ and Yadouleton, A and Vinze, A and Happi, AN and Chouikha, A and Iranzadeh, A and Maharaj, A and Batchi-Bouyou, AL and Ismail, A and Sylverken, AA and Goba, A and Femi, A and Sijuwola, AE and Marycelin, B and Salako, BL and Oderinde, BS and Bolajoko, B and Diarra, B and Herring, BL and Tsofa, B and Lekana-Douki, B and Mvula, B and Njanpop-Lafourcade, BM and Marondera, BT and Khaireh, BA and Kouriba, B and Adu, B and Pool, B and McInnis, B and Brook, C and Williamson, C and Nduwimana, C and Anscombe, C and Pratt, CB and Scheepers, C and Akoua-Koffi, CG and Agoti, CN and Mapanguy, CM and Loucoubar, C and Onwuamah, CK and Ihekweazu, C and Malaka, CN and Peyrefitte, C and Grace, C and Omoruyi, CE and Rafaï, CD and Morang'a, CM and Erameh, C and Lule, DB and Bridges, DJ and Mukadi-Bamuleka, D and Park, D and Rasmussen, DA and Baker, D and Nokes, DJ and Ssemwanga, D and Tshiabuila, D and Amuzu, DSY and Goedhals, D and Grant, DS and Omuoyo, DO and Maruapula, D and Wanjohi, DW and Foster-Nyarko, E and Lusamaki, EK and Simulundu, E and Ong'era, EM and Ngabana, EN and Abworo, EO and Otieno, E and Shumba, E and Barasa, E and Ahmed, EB and Ahmed, EA and Lokilo, E and Mukantwari, E and Philomena, E and Belarbi, E and Simon-Loriere, E and Anoh, EA and Manuel, E and Leendertz, F and Taweh, FM and Wasfi, F and Abdelmoula, F and Takawira, FT and Derrar, F and Ajogbasile, FV and Treurnicht, F and Onikepe, F and Ntoumi, F and Muyembe, FM and Ragomzingba, FEZ and Dratibi, FA and Iyanu, FA and Mbunsu, GK and Thilliez, G and Kay, GL and Akpede, GO and van Zyl, GU and Awandare, GA and Kpeli, GS and Schubert, G and Maphalala, GP and Ranaivoson, HC and Omunakwe, HE and Onywera, H and Abe, H and Karray, H and Nansumba, H and Triki, H and Kadjo, HAA and Elgahzaly, H and Gumbo, H and Mathieu, H and Kavunga-Membo, H and Smeti, I and Olawoye, IB and Adetifa, IMO and Odia, I and Ben Boubaker, IB and Muhammad, IA and Ssewanyana, I and Wurie, I and Konstantinus, IS and Halatoko, JWA and Ayei, J and Sonoo, J and Makangara, JC and Tamfum, JM and Heraud, JM and Shaffer, JG and Giandhari, J and Musyoki, J and Nkurunziza, J and Uwanibe, JN and Bhiman, JN and Yasuda, J and Morais, J and Kiconco, J and Sandi, JD and Huddleston, J and Odoom, JK and Morobe, JM and Gyapong, JO and Kayiwa, JT and Okolie, JC and Xavier, JS and Gyamfi, J and Wamala, JF and Bonney, JHK and Nyandwi, J and Everatt, J and Nakaseegu, J and Ngoi, JM and Namulondo, J and Oguzie, JU and Andeko, JC and Lutwama, JJ and Mogga, JJH and O'Grady, J and Siddle, KJ and Victoir, K and Adeyemi, KT and Tumedi, KA and Carvalho, KS and Mohammed, KS and Dellagi, K and Musonda, KG and Duedu, KO and Fki-Berrajah, L and Singh, L and Kepler, LM and Biscornet, L and de Oliveira Martins, L and Chabuka, L and Olubayo, L and Ojok, LD and Deng, LL and Ochola-Oyier, LI and Tyers, L and Mine, M and Ramuth, M and Mastouri, M and ElHefnawi, M and Mbanne, M and Matsheka, MI and Kebabonye, M and Diop, M and Momoh, M and Lima Mendonça, MDL and Venter, M and Paye, MF and Faye, M and Nyaga, MM and Mareka, M and Damaris, MM and Mburu, MW and Mpina, MG and Owusu, M and Wiley, MR and Tatfeng, MY and Ayekaba, MO and Abouelhoda, M and Beloufa, MA and Seadawy, MG and Khalifa, MK and Matobo, MM and Kane, M and Salou, M and Mbulawa, MB and Mwenda, M and Allam, M and Phan, MVT and Abid, N and Rujeni, N and Abuzaid, N and Ismael, N and Elguindy, N and Top, NM and Dia, N and Mabunda, N and Hsiao, NY and Silochi, NB and Francisco, NM and Saasa, N and Bbosa, N and Murunga, N and Gumede, N and Wolter, N and Sitharam, N and Ndodo, N and Ajayi, NA and Tordo, N and Mbhele, N and Razanajatovo, NH and Iguosadolo, N and Mba, N and Kingsley, OC and Sylvanus, O and Femi, O and Adewumi, OM and Testimony, O and Ogunsanya, OA and Fakayode, O and Ogah, OE and Oludayo, OE and Faye, O and Smith-Lawrence, P and Ondoa, P and Combe, P and Nabisubi, P and Semanda, P and Oluniyi, PE and Arnaldo, P and Quashie, PK and Okokhere, PO and Bejon, P and Dussart, P and Bester, PA and Mbala, PK and Kaleebu, P and Abechi, P and El-Shesheny, R and Joseph, R and Aziz, RK and Essomba, RG and Ayivor-Djanie, R and Njouom, R and Phillips, RO and Gorman, R and Kingsley, RA and Neto Rodrigues, RMDESA and Audu, RA and Carr, RAA and Gargouri, S and Masmoudi, S and Bootsma, S and Sankhe, S and Mohamed, SI and Femi, S and Mhalla, S and Hosch, S and Kassim, SK and Metha, S and Trabelsi, S and Agwa, SH and Mwangi, SW and Doumbia, S and Makiala-Mandanda, S and Aryeetey, S and Ahmed, SS and Ahmed, SM and Elhamoumi, S and Moyo, S and Lutucuta, S and Gaseitsiwe, S and Jalloh, S and Andriamandimby, SF and Oguntope, S and Grayo, S and Lekana-Douki, S and Prosolek, S and Ouangraoua, S and van Wyk, S and Schaffner, SF and Kanyerezi, S and Ahuka-Mundeke, S and Rudder, S and Pillay, S and Nabadda, S and Behillil, S and Budiaki, SL and van der Werf, S and Mashe, T and Mohale, T and Le-Viet, T and Velavan, TP and Schindler, T and Maponga, TG and Bedford, T and Anyaneji, UJ and Chinedu, U and Ramphal, U and George, UE and Enouf, V and Nene, V and Gorova, V and Roshdy, WH and Karim, WA and Ampofo, WK and Preiser, W and Choga, WT and Ahmed, YA and Ramphal, Y and Bediako, Y and Naidoo, Y and Butera, Y and de Laurent, ZR and , and Ouma, AEO and von Gottberg, A and Githinji, G and Moeti, M and Tomori, O and Sabeti, PC and Sall, AA and Oyola, SO and Tebeje, YK and Tessema, SK and de Oliveira, T and Happi, C and Lessells, R and Nkengasong, J and Wilkinson, E}, title = {The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.}, journal = {Science (New York, N.Y.)}, volume = {378}, number = {6615}, pages = {eabq5358}, pmid = {36108049}, issn = {1095-9203}, support = {U01 HG007480/HG/NHGRI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U19 AI089696/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; U54 TW012041/TW/FIC NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; K24 AI131924/AI/NIAID NIH HHS/United States ; U01 AI151698/AI/NIAID NIH HHS/United States ; U19 AI129387/AI/NIAID NIH HHS/United States ; 001/WHO_/World Health Organization/International ; K24 AI131928/AI/NIAID NIH HHS/United States ; U2R TW010673/TW/FIC NIH HHS/United States ; }, mesh = {Africa/epidemiology ; *COVID-19/epidemiology/virology ; *Epidemiological Monitoring ; Genomics ; Humans ; *Pandemics ; *SARS-CoV-2/genetics ; }, abstract = {Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.}, } @article {pmid36107252, year = {2022}, author = {Lukasová, V and Bičárová, S and Buchholcerová, A and Adamčíková, K}, title = {Low sensitivity of Pinus mugo to surface ozone pollution in the subalpine zone of continental Europe.}, journal = {International journal of biometeorology}, volume = {66}, number = {11}, pages = {2311-2324}, pmid = {36107252}, issn = {1432-1254}, mesh = {Humans ; *Ozone/analysis ; *Air Pollutants/analysis ; *Pinus ; Environmental Monitoring ; Plant Leaves ; Polyesters/analysis/pharmacology ; }, abstract = {High altitudes have been exposed to enhanced levels of surface ozone (O3) concentrations over recent decades compared to the pre-industrial era. The responses of vegetation to this toxic pollutant are species-specific and depend on the climate conditions. In this paper, we explored the reaction of Pinus mugo (P. mugo) to O3-induced stress in the continental climate of an ozone-rich mountain area in the High Tatra Mountains (Western Carpathians). The effects of O3 doses modelled by a deposition model, O3 concentrations and other factors on P. mugo were identified from (a) satellite-based data via NDVI (normalised differenced vegetation index) over 2000-2020 and (b) visible injury on needle samples gathered from P. mugo individuals at ground-truth sites in 2019 and 2020. Analysing the NDVI trend, we observed non-significant changes (p > 0.05) in the greenness of P. mugo despite growing in an environment with the average seasonal O3 concentration around 51.6 ppbv, the maximum hourly concentrations more than 90 ppbv and increasing trend of O3 doses by 0.1 mmol m[-2] PLA (plant leaf area) year[-1]. The visible O3 injury of samples collected at study sites was low (mean injury observed on 1-10% of needles' surface), and the symptoms of injury caused by other biotic and abiotic factors prevailed over those caused by O3. In addition, the correlation analyses between NDVI and the climatic factors indicated a significant (p < 0.05) and positive relationship with photosynthetic active radiation (R = 0.45) in July, and with stomatal conductance (R = 0.52) and temperature factor (R = 0.43) in August. Therefore, we concluded that the positive effect of climate conditions, which support the growth processes of P. mugo, may suppress the negative effect of the mean O3 doses of 17.8 mmol m[-2] PLA accumulated over the growing season.}, } @article {pmid36103465, year = {2022}, author = {Nam, S and Jeon, S and Lee, SJ and Ash, G and Nelson, LE and Granger, DA}, title = {Real-time racial discrimination, affective states, salivary cortisol and alpha-amylase in Black adults.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0273081}, pmid = {36103465}, issn = {1932-6203}, mesh = {Adult ; Cross-Sectional Studies ; Humans ; *Hydrocortisone ; *Racism/psychology ; Retrospective Studies ; Saliva ; Stress, Psychological/psychology ; alpha-Amylases ; }, abstract = {Perceived racial discrimination has been associated with the autonomic nervous system (ANS) and hypothalamic-pituitary-adrenal (HPA) axis activities-two major stress response systems. To date, most studies have used cross-sectional data that captured retrospective measures of the racial discrimination associated with current physiological stress responses. The purpose of this study was to examine the relationship between racial discrimination measured in real-time and physiological stress responses. Twelve healthy Black adults completed baseline surveys and self-collected saliva samples 4x/day for 4 days to measure cortisol and alpha amylase (AA) as a proxy of HPA and ANS systems, respectively. Real-time racial discrimination was measured using ecological momentary assessments (EMA) sent to participants 5x/day for 7 days. Multilevel models were conducted to examine the relationship between racial discrimination and stress responses. In multilevel models, the previous day's racial discrimination was significantly associated with the next day's cortisol level at wakening (β = 0.81, partial r = 0.74, p<0.01) and diurnal slope (β = -0.85, partial r = -0.73, p<0.01). Also, microaggressions were significantly associated with the diurnal cortisol slope in the same day, indicating that on the day when people reported more microaggressions than usual, a flatter diurnal slope of cortisol was observed (β = -0.50, partial r = -0.64, p<0.01). The concurrent use of salivary biomarkers and EMA was feasible methods to examine the temporal relationship between racial discrimination and physiological stress responses. The within-person approach may help us understand the concurrent or lagged effects of racial discrimination on the stress responses. Further studies are needed to confirm the observed findings with a large sample size and to improve stress related health outcomes in racial/ethnic minorities.}, } @article {pmid36102834, year = {2022}, author = {Débarre, F and Lecoeur, E and Guimier, L and Jauffret-Roustide, M and Jannot, AS}, title = {The French Covid-19 vaccination policy did not solve vaccination inequities: a nationwide study on 64.5 million people.}, journal = {European journal of public health}, volume = {32}, number = {5}, pages = {825-830}, pmid = {36102834}, issn = {1464-360X}, mesh = {*COVID-19/epidemiology/prevention & control ; *COVID-19 Vaccines ; Emigration and Immigration ; Humans ; Policy ; Vaccination ; }, abstract = {BACKGROUND: To encourage Covid-19 vaccination, France introduced during the Summer 2021 a 'Sanitary Pass', which morphed into a 'Vaccine Pass' in early 2022. While the sanitary pass led to an increase in Covid-19 vaccination rates, spatial heterogeneities in vaccination rates remained. To identify potential determinants of these heterogeneities and evaluate the French sanitary and vaccine passes' efficacies in reducing them, we used a data-driven approach on exhaustive nationwide data, gathering 141 socio-economic, political and geographic indicators.

METHODS: We considered the association between vaccination rates and each indicator at different time points: before the sanitary pass announcement (week 2021-W27), before the sanitary pass came into force (week 2021-W31) and 1 month after (week 2021-W35) and the equivalent dates for the vaccine pass (weeks 2021-W49, 2022-W03 and 2022-W07).

RESULTS: The indicators most associated with vaccination rates were the share of local income coming from unemployment benefits, overcrowded households rate, immigrants rate and vote for an 'anti-establishment' candidate at the 2017 Presidential election. These associations increase over time. Consequently, living in a district below the median of such indicator decreases the probability to be vaccinated by about 30% at the end of the studied period, and this probability gradually decreases by deciles of these indicators.

CONCLUSIONS: Our analysis reveals that factors related to poverty, immigration and trust in the government are strong determinants of vaccination rate, and that vaccination inequities tended to increase after the introduction of the French sanitary and vaccination passes.}, } @article {pmid36100598, year = {2022}, author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H}, title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {565}, pmid = {36100598}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; }, abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.}, } @article {pmid36095758, year = {2022}, author = {Golovatch, S and Vandenspiegel, D}, title = {Carinobolus gen. nov. and Costabolus gen. nov., two new, remarkably crested, monospecific genera of spirobolidan millipedes from West Africa, with the proposal of a new tribe, Amblybolini tribus nova (Diplopoda, Spirobolida, Pachybolidae).}, journal = {Zootaxa}, volume = {5150}, number = {1}, pages = {97-110}, doi = {10.11646/zootaxa.5150.1.5}, pmid = {36095758}, issn = {1175-5334}, mesh = {Africa, Western ; Animals ; *Arthropods ; }, abstract = {Two new genera, Carinobolus gen. nov. and Costabolus gen. nov., both belonging to the very large, widespread, pantropical family Pachybolidae, are described based on Carinobolus complex sp. nov. and Costabolus baculus sp. nov., respectively. Chiefly based on the posterior gonopod being distinctly articulated at midlength, both new genera seem to be especially similar to Amblybolus Keeton, 1964a (three species in western Africa) and Atlanticobolus Hoffman, 1979 (one species from an island off the Brazilian coast), all of them meriting a separate tribal category, Amblybolini tribus nova. A key is proposed to distinguish all four presently accepted genera of the new tribe. The new genera and species are clearly distinguished in showing unusually strongly crested/ribbed metazonae, a character that is only very seldom observed in Pachybolidae generally, and apparently unique among Afrotropical members. Being rather similar in many respects, both new genera and species differ from each other sufficiently well in gonopodal and leg structure, even though both come from forests in southeastern Nigeria close to the border to Cameroon.}, } @article {pmid36095211, year = {2022}, author = {Still, CJ and Page, G and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, D and Goulden, M and Pau, S and Detto, M and Helliker, B and Richardson, AD}, title = {No evidence of canopy-scale leaf thermoregulation to cool leaves below air temperature across a range of forest ecosystems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {38}, pages = {e2205682119}, pmid = {36095211}, issn = {1091-6490}, mesh = {*Carbon/metabolism ; *Carbon Cycle ; *Forests ; *Plant Leaves/anatomy & histology/metabolism ; Temperature ; }, abstract = {Understanding and predicting the relationship between leaf temperature (Tleaf) and air temperature (Tair) is essential for projecting responses to a warming climate, as studies suggest that many forests are near thermal thresholds for carbon uptake. Based on leaf measurements, the limited leaf homeothermy hypothesis argues that daytime Tleaf is maintained near photosynthetic temperature optima and below damaging temperature thresholds. Specifically, leaves should cool below Tair at higher temperatures (i.e., > ∼25-30°C) leading to slopes <1 in Tleaf/Tair relationships and substantial carbon uptake when leaves are cooler than air. This hypothesis implies that climate warming will be mitigated by a compensatory leaf cooling response. A key uncertainty is understanding whether such thermoregulatory behavior occurs in natural forest canopies. We present an unprecedented set of growing season canopy-level leaf temperature (Tcan) data measured with thermal imaging at multiple well-instrumented forest sites in North and Central America. Our data do not support the limited homeothermy hypothesis: canopy leaves are warmer than air during most of the day and only cool below air in mid to late afternoon, leading to Tcan/Tair slopes >1 and hysteretic behavior. We find that the majority of ecosystem photosynthesis occurs when canopy leaves are warmer than air. Using energy balance and physiological modeling, we show that key leaf traits influence leaf-air coupling and ultimately the Tcan/Tair relationship. Canopy structure also plays an important role in Tcan dynamics. Future climate warming is likely to lead to even greater Tcan, with attendant impacts on forest carbon cycling and mortality risk.}, } @article {pmid36094211, year = {2022}, author = {Njoroge, SM and Madé, LF and von Mentzer, A and Kulohoma, BW and Kamanu, TK and Ouko, TT and Kiiru, J and Ward, MJ and Thomson, NR and Fèvre, EM and Woolhouse, M and Kariuki, S}, title = {Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0041622}, pmid = {36094211}, issn = {2576-098X}, abstract = {Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.}, } @article {pmid36090080, year = {2022}, author = {Chang, Y and Chen, F and Zhu, Y and You, Y and Cheng, Y and Ma, J}, title = {Influence of revegetation on soil microbial community and its assembly process in the open-pit mining area of the Loess Plateau, China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {992816}, pmid = {36090080}, issn = {1664-302X}, abstract = {Vegetation recovery is an important marker of ecosystem health in the mining area. Clarifying the influence of vegetation recovery on the characteristics of soil microbial community and its assembly process can improve our understanding of the ecological resilience and self-maintaining mechanism in the open-pit mining area. For this purpose, we employed MiSeq high-throughput sequencing coupled with null model analysis to determine the composition, molecular ecological network characteristics, key bacterial and fungal clusters, and the assembly mechanism of the soil microbial communities in shrubs (BL), coniferous forest (CF), broad-leaved forests (BF), mixed forest (MF), and the control plot (CK, the poplar plantation nearby that had been continuously grown for over 30 a without disturbance). The results showed that the vegetation restoration model had a significant influence on the α-diversity of the microbial community (p < 0.05). Compared with CK, Sobs and Shannon index of MF and CF have increased by 35.29, 3.50, and 25.18%, 1.05%, respectively, whereas there was no significant difference in the α-diversity of fungal community among different vegetation restoration types, Actinobacteria, Chloroflexi, Proteobacteria, and Acidobacteria were the dominant phyla. The diversity of the first two phyla was significantly higher than those of CK. However, the diversity of the last two phyla was dramatically lower than those of CK (p < 0.05). Ascomycota and Basidiomycota were dominant phyla in the fungal community. The abundance and diversity of Ascomycota were significantly higher than those of CK, while the abundance and diversity of the latter were considerably lower than those of CK (p < 0.05). The stochastic process governed the assembly of the soil microbial community, and the contribution rate to the bacterial community construction of CK, CF, BF, and MF was 100.0%. Except for MF, where the soil fungal community assembly was governed by the deterministic process, all other fungal communities were governed by the stochastic process. Proteobacteria and Acidobacteria are key taxa of the bacterial network, while Mortierellales, Thelebolales, Chaetothyriales, and Hypocreales are the key taxa of the fungal network. All these results might provide the theoretical foundation for restoring the fragile ecosystem in the global mining region.}, } @article {pmid36089013, year = {2022}, author = {Lyu, Y and Wu, Z and Wu, H and Pang, X and Qin, K and Wang, B and Ding, S and Chen, D and Chen, J}, title = {Tracking long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China 2015-2021.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158599}, doi = {10.1016/j.scitotenv.2022.158599}, pmid = {36089013}, issn = {1879-1026}, abstract = {China has experienced severe air pollution in the past decade, especially PM2.5 and emerging ozone pollution recently. In this study, we comprehensively analyzed long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China during 2015-2021 regarding two-stage clean-air actions based on the Ministry of Ecology and the Environment (MEE) air monitoring network. Overall, the ratio of the population living in the regions exceeding the Chinese National Ambient Air Quality Standard (35 μg/m[3]) decreases by 29.9 % for PM2.5 from 2015 to 2021, driven by high proportions in the Middle Plain (MP, 42.3 %) and Lan-Xi (35.0 %) regions. However, this ratio almost remains unchanged for ozone and even increases by 1.5 % in the MP region. As expected, the improved air quality leads to 234.7 × 10[3] avoided premature mortality (ΔMort), mainly ascribed to the reduction in PM2.5 concentration. COVID-19 pandemic may influence the annual variation of PM2.5-related ΔMort as it affects the shape of the population exposure curve to become much steeper. Although all eleven urban agglomerations share stroke (43.6 %) and ischaemic heart disease (IHD, 30.1 %) as the two largest contributors to total ΔMort, cause-specific ΔMort is highly regional heterogeneous, in which ozone-related ΔMort is significantly higher (21 %) in the Tibet region than other urban agglomeration. Despite ozone-related ΔMort being one order of magnitude lower than PM2.5-related ΔMort from 2015 to 2021, ozone-related ΔMort is predicted to increase in major urban agglomerations initially along with a continuous decline for PM2.5-related ΔMort from 2020 to 2060, highlighting the importance of ozone control. Coordinated controls of PM2.5 and O3 are warranted for reducing health burdens in China during achieving carbon neutrality.}, } @article {pmid36088355, year = {2022}, author = {Mull, CG and Pacoureau, N and Pardo, SA and Ruiz, LS and García-Rodríguez, E and Finucci, B and Haack, M and Harry, A and Judah, AB and VanderWright, W and Yin, JS and Kindsvater, HK and Dulvy, NK}, title = {Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {559}, pmid = {36088355}, issn = {2052-4463}, mesh = {Animals ; Conservation of Natural Resources ; Databases, Factual ; Internationality ; *Life History Traits ; *Sharks ; }, abstract = {A curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 274 sources, for 170 species, from 39 families, and 12 orders related to length (n = 9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.}, } @article {pmid36074761, year = {2022}, author = {Cappellato, M and Baruzzo, G and Di Camillo, B}, title = {Investigating differential abundance methods in microbiome data: A benchmark study.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010467}, pmid = {36074761}, issn = {1553-7358}, mesh = {*Benchmarking ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Reproducibility of Results ; }, abstract = {The development of increasingly efficient and cost-effective high throughput DNA sequencing techniques has enhanced the possibility of studying complex microbial systems. Recently, researchers have shown great interest in studying the microorganisms that characterise different ecological niches. Differential abundance analysis aims to find the differences in the abundance of each taxa between two classes of subjects or samples, assigning a significance value to each comparison. Several bioinformatic methods have been specifically developed, taking into account the challenges of microbiome data, such as sparsity, the different sequencing depth constraint between samples and compositionality. Differential abundance analysis has led to important conclusions in different fields, from health to the environment. However, the lack of a known biological truth makes it difficult to validate the results obtained. In this work we exploit metaSPARSim, a microbial sequencing count data simulator, to simulate data with differential abundance features between experimental groups. We perform a complete comparison of recently developed and established methods on a common benchmark with great effort to the reliability of both the simulated scenarios and the evaluation metrics. The performance overview includes the investigation of numerous scenarios, studying the effect on methods' results on the main covariates such as sample size, percentage of differentially abundant features, sequencing depth, feature variability, normalisation approach and ecological niches. Mainly, we find that methods show a good control of the type I error and, generally, also of the false discovery rate at high sample size, while recall seem to depend on the dataset and sample size.}, } @article {pmid36071746, year = {2022}, author = {Prenzel, F and Treudler, R and Lipek, T and Vom Hove, M and Kage, P and Kuhs, S and Kaiser, T and Bastl, M and Bumberger, J and Genuneit, J and Hornick, T and Klotz, S and Zarnowski, J and Boege, M and Zebralla, V and Simon, JC and Dunker, S}, title = {Invasive Growth of Ailanthus altissima Trees is Associated with a High Rate of Sensitization in Atopic Patients.}, journal = {Journal of asthma and allergy}, volume = {15}, number = {}, pages = {1217-1226}, pmid = {36071746}, issn = {1178-6965}, abstract = {PURPOSE: Ailanthus altissima is one of the world's most invasive species with a globally problematic spread. Pollen is dispersed locally and partially airborne. We aimed at investigating if (i) A. altissima pollen can be detected in relevant quantity in the air and if (ii) sensitization to A. altissima can be detected in patients with seasonal exacerbation of atopic diseases.

PATIENTS AND METHODS: We recorded distribution of A. altissima in Leipzig, Germany. In 2019 and 2020, pollen was collected with a Hirst-type pollen trap placed on the roof of the University Hospital. Specific IgE investigations were performed in children and adults with history of atopic diseases with deterioration between May and July. We analysed specific IgE for A. altissima, Alternaria sp., birch, grasses, profilins, polcalcins and crossreacting carbohydrates.

RESULTS: We found abundant growth of A. altissima and pollen was detected from early June to mid-July with a maximum pollen concentration of 31 pollen/m[3]. Out of 138 patients (63 female, 69 children/adolescents), 95 (69%) had seasonal allergic rhinitis, 84 (61%) asthma, and 43 (31%) atopic dermatitis. Sensitization to A. altissima was shown in 59 (42%). There were no significant differences between age groups. In 59% of patients sensitized (35/59), there was no sensitization to possibly cross-reacting structures.

CONCLUSION: Sensitization to A. altissima pollen could be detected in 42% of our patients with atopic diseases, suggesting allergenic potential of this neophyte. In the context of further spread with climate change, eradication strategies and population-based sensitization studies are needed.}, } @article {pmid36071164, year = {2022}, author = {Arostegui, MC and Gaube, P and Woodworth-Jefcoats, PA and Kobayashi, DR and Braun, CD}, title = {Anticyclonic eddies aggregate pelagic predators in a subtropical gyre.}, journal = {Nature}, volume = {609}, number = {7927}, pages = {535-540}, pmid = {36071164}, issn = {1476-4687}, mesh = {Animals ; Cyclonic Storms ; Datasets as Topic ; *Ecosystem ; Fisheries ; Food Chain ; Nutrients/analysis ; Pacific Ocean ; *Predatory Behavior ; Tropical Climate ; *Water ; *Water Movements ; }, abstract = {Ocean eddies are coherent, rotating features that can modulate pelagic ecosystems across many trophic levels. These mesoscale features, which are ubiquitous at mid-latitudes[1], may increase productivity of nutrient-poor regions[2,3], accumulate prey[4] and modulate habitat conditions in the water column[5]. However, in nutrient-poor subtropical gyres-the largest marine biome-the role of eddies in modulating behaviour throughout the pelagic predator community remains unknown despite predictions for these gyres to expand[6] and pelagic predators to become increasingly important for food security[7]. Using a large-scale fishery dataset in the North Pacific Subtropical Gyre, we show a pervasive pattern of increased pelagic predator catch inside anticyclonic eddies relative to cyclones and non-eddy areas. Our results indicate that increased mesopelagic prey abundance in anticyclone cores[4,8] may be attracting diverse predators, forming ecological hotspots where these predators aggregate and exhibit increased abundance. In this energetically quiescent gyre, we expect that isolated mesoscale features (and the habitat conditions in them) exhibit primacy over peripheral submesoscale dynamics in structuring the foraging opportunities of pelagic predators. Our finding that eddies influence coupling of epi- to mesopelagic communities corroborates the growing evidence that deep scattering layer organisms are vital prey for a suite of commercially important predator species[9] and, thus, provide valuable ecosystem services.}, } @article {pmid36071118, year = {2022}, author = {Brown, JM and Bossomaier, T and Barnett, L}, title = {Information flow in first-order potts model phase transition.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15145}, pmid = {36071118}, issn = {2045-2322}, mesh = {Entropy ; *Hot Temperature ; Phase Transition ; Thermodynamics ; }, abstract = {Phase transitions abound in nature and society, and, from species extinction to stock market collapse, their prediction is of widespread importance. In earlier work we showed that Global Transfer Entropy, a general measure of information flow, was found to peaks away from the transition on the disordered side for the Ising model, a canonical second order transition. Here we show that (a) global transfer entropy also peaks on the disordered side of the transition of finite first order transitions, such as ecology dynamics on coral reefs, which have latent heat and no correlation length divergence, and (b) analysis of information flow across state boundaries unifies both transition orders. We obtain the first information-theoretic result for the high-order Potts model and the first demonstration of early warning of a first order transition. The unexpected earlier finding that global transfer entropy peaks on the disordered side of a transition is also found for finite first order systems, albeit not in the thermodynamic limit. By noting that the interface length of clusters in each phase is the dominant region of information flow, we unify the information theoretic behaviour of first and second order transitions.}, } @article {pmid36058075, year = {2022}, author = {Maloney, KO and Buchanan, C and Jepsen, RD and Krause, KP and Cashman, MJ and Gressler, BP and Young, JA and Schmid, M}, title = {Explainable machine learning improves interpretability in the predictive modeling of biological stream conditions in the Chesapeake Bay Watershed, USA.}, journal = {Journal of environmental management}, volume = {322}, number = {}, pages = {116068}, doi = {10.1016/j.jenvman.2022.116068}, pmid = {36058075}, issn = {1095-8630}, mesh = {Agriculture ; *Bays ; Ecosystem ; Environmental Monitoring/methods ; Machine Learning ; *Rivers ; }, abstract = {Anthropogenic alterations have resulted in widespread degradation of stream conditions. To aid in stream restoration and management, baseline estimates of conditions and improved explanation of factors driving their degradation are needed. We used random forests to model biological conditions using a benthic macroinvertebrate index of biotic integrity for small, non-tidal streams (upstream area ≤200 km[2]) in the Chesapeake Bay watershed (CBW) of the mid-Atlantic coast of North America. We utilized several global and local model interpretation tools to improve average and site-specific model inferences, respectively. The model was used to predict condition for 95,867 individual catchments for eight periods (2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019). Predicted conditions were classified as Poor, FairGood, or Uncertain to align with management needs and individual reach lengths and catchment areas were summed by condition class for the CBW for each period. Global permutation and local Shapley importance values indicated percent of forest, development, and agriculture in upstream catchments had strong impacts on predictions. Development and agriculture negatively influenced stream condition for model average (partial dependence [PD] and accumulated local effect [ALE] plots) and local (individual condition expectation and Shapley value plots) levels. Friedman's H-statistic indicated large overall interactions for these three land covers, and bivariate global plots (PD and ALE) supported interactions among agriculture and development. Total stream length and catchment area predicted in FairGood conditions decreased then increased over the 19-years (length/area: 66.6/65.4% in 2001, 66.3/65.2% in 2011, and 66.6/65.4% in 2019). Examination of individual catchment predictions between 2001 and 2019 showed those predicted to have the largest decreases in condition had large increases in development; whereas catchments predicted to exhibit the largest increases in condition showed moderate increases in forest cover. Use of global and local interpretative methods together with watershed-wide and individual catchment predictions support conservation practitioners that need to identify widespread and localized patterns, especially acknowledging that management actions typically take place at individual-reach scales.}, } @article {pmid36053136, year = {2022}, author = {Kelleher, K and McGinnity, P and Howard, BJ and Boyer, P and Vidal, M and Bildstein, OM}, title = {The use of the IAEA MARIS database in determining the variability of sediment distribution coefficients in the marine environment and potential implications for marine dispersion modelling.}, journal = {Journal of radiological protection : official journal of the Society for Radiological Protection}, volume = {42}, number = {3}, pages = {}, doi = {10.1088/1361-6498/ac8a53}, pmid = {36053136}, issn = {1361-6498}, mesh = {Geologic Sediments ; Information Systems ; *Radioactivity ; Seawater ; *Water Pollutants, Radioactive/analysis ; }, abstract = {A prototype tool has been developed for deriving sediment distribution coefficients,Kd, in the marine environment by harvesting simultaneous measurements of activity concentrations of radionuclides in seawater and sediments based on the International Atomic Energy Agency's Marine Radioactivity Information System (MARIS). As a case study, theKdvariability in the Baltic Sea was investigated as this region has been extensively monitored by HELCOM since 1984 resulting in a comprehensive dataset with good spatial and temporal coverage and required ancillary parameters. The prototype tool was used to derive a dataset ofin-situapparentKd(a)values derived from measurements of seawater and sediment in quasi-equilibrium conditions from the Baltic Sea over a period of approximately 35 years. For Cs, a comprehensive analysis of the Baltic SeaKd(a)dataset was undertaken, focusing on the temporal trend ofKd(a)and comparing the results toKdvalues derived elsewhere. For Sr and Pu, for which there were fewer data records available a more rudimentary analysis was carried out. The CsKd(a)median values derived from[137]Cs data in this study were estimated to be 2154 l kg[-1]for seabed sediment and 10 000 l kg[-1]for suspended sediment. The value derived for seabed sediment is in good agreement with the previously recommended ocean margin CsKdvalue of 4000 l kg[-1]. The analysis demonstrated the important distinction in the Baltic Sea betweenKdvalues for seabed sediment and suspended sediments, which differed by an order of magnitude. The analysis also highlighted the dependence ofKdvalues on the variation in both the salinity of seawater and the type of seabed sediment. Such variability can significantly influence outcomes when modelling the behaviour of radionuclides in marine dispersion modelling.}, } @article {pmid36051895, year = {2022}, author = {Boyes, D and , and , and , and , and , and Gibbs, M and , }, title = {The genome sequence of the clay, Mythimna ferrago (Fabricius, 1787).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {177}, pmid = {36051895}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Mythimna ferrago (the clay; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 861 megabases in span. The majority of the assembly (99.98%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,075 protein coding genes.}, } @article {pmid36050321, year = {2022}, author = {Young, WJ and Lahrouchi, N and Isaacs, A and Duong, T and Foco, L and Ahmed, F and Brody, JA and Salman, R and Noordam, R and Benjamins, JW and Haessler, J and Lyytikäinen, LP and Repetto, L and Concas, MP and van den Berg, ME and Weiss, S and Baldassari, AR and Bartz, TM and Cook, JP and Evans, DS and Freudling, R and Hines, O and Isaksen, JL and Lin, H and Mei, H and Moscati, A and Müller-Nurasyid, M and Nursyifa, C and Qian, Y and Richmond, A and Roselli, C and Ryan, KA and Tarazona-Santos, E and Thériault, S and van Duijvenboden, S and Warren, HR and Yao, J and Raza, D and Aeschbacher, S and Ahlberg, G and Alonso, A and Andreasen, L and Bis, JC and Boerwinkle, E and Campbell, A and Catamo, E and Cocca, M and Cutler, MJ and Darbar, D and De Grandi, A and De Luca, A and Ding, J and Ellervik, C and Ellinor, PT and Felix, SB and Froguel, P and Fuchsberger, C and Gögele, M and Graff, C and Graff, M and Guo, X and Hansen, T and Heckbert, SR and Huang, PL and Huikuri, HV and Hutri-Kähönen, N and Ikram, MA and Jackson, RD and Junttila, J and Kavousi, M and Kors, JA and Leal, TP and Lemaitre, RN and Lin, HJ and Lind, L and Linneberg, A and Liu, S and MacFarlane, PW and Mangino, M and Meitinger, T and Mezzavilla, M and Mishra, PP and Mitchell, RN and Mononen, N and Montasser, ME and Morrison, AC and Nauck, M and Nauffal, V and Navarro, P and Nikus, K and Pare, G and Patton, KK and Pelliccione, G and Pittman, A and Porteous, DJ and Pramstaller, PP and Preuss, MH and Raitakari, OT and Reiner, AP and Ribeiro, ALP and Rice, KM and Risch, L and Schlessinger, D and Schotten, U and Schurmann, C and Shen, X and Shoemaker, MB and Sinagra, G and Sinner, MF and Soliman, EZ and Stoll, M and Strauch, K and Tarasov, K and Taylor, KD and Tinker, A and Trompet, S and Uitterlinden, A and Völker, U and Völzke, H and Waldenberger, M and Weng, LC and Whitsel, EA and Wilson, JG and Avery, CL and Conen, D and Correa, A and Cucca, F and Dörr, M and Gharib, SA and Girotto, G and Grarup, N and Hayward, C and Jamshidi, Y and Järvelin, MR and Jukema, JW and Kääb, S and Kähönen, M and Kanters, JK and Kooperberg, C and Lehtimäki, T and Lima-Costa, MF and Liu, Y and Loos, RJF and Lubitz, SA and Mook-Kanamori, DO and Morris, AP and O'Connell, JR and Olesen, MS and Orini, M and Padmanabhan, S and Pattaro, C and Peters, A and Psaty, BM and Rotter, JI and Stricker, B and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JF and Arking, DE and Ramirez, J and Lambiase, PD and Sotoodehnia, N and Mifsud, B and Newton-Cheh, C and Munroe, PB}, title = {Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5144}, pmid = {36050321}, issn = {2041-1723}, support = {R01 HL128914/HL/NHLBI NIH HHS/United States ; MR/N025083/1/MRC_/Medical Research Council/United Kingdom ; R01 HL139731/HL/NHLBI NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; U24 AG051129/AG/NIA NIH HHS/United States ; R01 HL105756/HL/NHLBI NIH HHS/United States ; T32 HL007604/HL/NHLBI NIH HHS/United States ; U01 HG007416/HG/NHGRI NIH HHS/United States ; R01 DK107786/DK/NIDDK NIH HHS/United States ; K23 HL127704/HL/NHLBI NIH HHS/United States ; R01 DK124097/DK/NIDDK NIH HHS/United States ; R01 DK110113/DK/NIDDK NIH HHS/United States ; R01 HL141989/HL/NHLBI NIH HHS/United States ; R01 HL143070/HL/NHLBI NIH HHS/United States ; U54 GM115428/GM/NIGMS NIH HHS/United States ; MR/R017468/1/MRC_/Medical Research Council/United Kingdom ; T32 HL139439/HL/NHLBI NIH HHS/United States ; R01 HL142302/HL/NHLBI NIH HHS/United States ; R01 HL138737/HL/NHLBI NIH HHS/United States ; K24 HL105780/HL/NHLBI NIH HHS/United States ; K24 HL148521/HL/NHLBI NIH HHS/United States ; R01 HL142825/HL/NHLBI NIH HHS/United States ; }, mesh = {*Arrhythmias, Cardiac/genetics ; Death, Sudden, Cardiac ; *Electrocardiography/methods ; Genetic Testing ; Humans ; Male ; }, abstract = {The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.}, } @article {pmid36048827, year = {2022}, author = {Omoru, OB and Pereira, F and Janga, SC and Manzourolajdad, A}, title = {A Putative long-range RNA-RNA interaction between ORF8 and Spike of SARS-CoV-2.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0260331}, pmid = {36048827}, issn = {1932-6203}, support = {R01 GM123314/GM/NIGMS NIH HHS/United States ; }, mesh = {*COVID-19 ; Genome, Viral ; Humans ; RNA, Viral/genetics ; *SARS-CoV-2/genetics ; *Spike Glycoprotein, Coronavirus/genetics ; *Viral Proteins/genetics ; }, abstract = {SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing in-silico fragment-based predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. The patterns of sequence variation using data gathered worldwide further supported the predicted stability of the sub-interacting region (23679-23690 Spike) and (28031-28042 ORF8). Such RNA-RNA interactions can potentially impact viral life cycle including sub-genomic RNA production rates.}, } @article {pmid36044830, year = {2022}, author = {Niestroj, SC and Steden, S and Boecker, M and Brodkin, ES and Konrad, K}, title = {The Development and Validation of the First German Open Scale of Social Information Processing.}, journal = {Psychopathology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1159/000525950}, pmid = {36044830}, issn = {1423-033X}, abstract = {INTRODUCTION: This study introduces the first German Open Scale of Social Information Processing (GOSSIP) and evaluates its psychometric properties. Even though social information processing (SIP) and its important role in developmental psychopathology is a rising field of interest, model-based standardized assessment tools are still scarce.

METHODS: GOSSIP was developed to assess SI processes in boys and girls aged eight to 21 years. First, 61 vignettes (combinations of pictures and short written descriptions of the situation depicted) were evaluated by an expert group and piloted with 48 healthy participants (aged 8-21). The best-rated vignettes were then implemented in a Web-based application. 191 participants completed GOSSIP. Of those, 76 answered additional questionnaires to assess their social skills and psychopathology. Internal consistencies for the emotional and cognitive GOSSIP scales were determined. Latent profile analysis (LPA) was used to identify subgroups of children and adolescents characterized by specific SIP profiles (i.e., patterns of emotional, cognitive, and behavioral responses to the GOSSIP). Furthermore, the external validity of the participants' attribution tendencies in GOSSIP was evaluated in real life by smartphone-based Ecological Momentary Assessments (EMA).

RESULTS: The internal consistencies for the emotional and cognitive scales (angry, ashamed, physical aggression, pro-social response, revenge, and outcome expectancy) were good to excellent. The scales of hostile interpretation, relation aggression, sadness, and exclusion showed borderline/acceptable internal consistency. Correlation analysis confirmed convergent validity with self-reported social skills and external validity with ratings of aggressive and pro-social behaviors. The LPA revealed three profiles as the best fit of the data. The first group is named "aggressors," the second "social-emotional group," and a third named "ashamed-internalizing group." However, no significant association was found between the attribution tendencies derived from GOSSIP and EMA data.

DISCUSSION/CONCLUSION: GOSSIP is the first model-based German Web-based assessment for several SIP mechanisms that showed overall adequate psychometric properties. GOSSIP can be used to classify individuals into SIP profiles that differ in terms of their cognitive and emotional response tendencies and therefore could contribute to the development of targeted interventions. Integrating assessments of emotional responses into GOSSIP revealed an important role of "shame" in SIP and the development of psychopathology. Furthermore, the lack of external validity between GOSSIP and EMA calls into question how attribution tendencies are best assessed in future studies.}, } @article {pmid36041271, year = {2022}, author = {Sokhansanj, BA and Rosen, GL}, title = {Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning.}, journal = {Computers in biology and medicine}, volume = {149}, number = {}, pages = {105969}, pmid = {36041271}, issn = {1879-0534}, mesh = {*COVID-19/epidemiology ; Humans ; Machine Learning ; Mutation ; Phylogeny ; Retrospective Studies ; SARS-CoV-2 ; Severity of Illness Index ; *Spike Glycoprotein, Coronavirus/genetics ; }, abstract = {Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.}, } @article {pmid36039768, year = {2022}, author = {De Calheiros Velozo, J and Habets, J and George, SV and Niemeijer, K and Minaeva, O and Hagemann, N and Herff, C and Kuppens, P and Rintala, A and Vaessen, T and Riese, H and Delespaul, P}, title = {Designing daily-life research combining experience sampling method with parallel data.}, journal = {Psychological medicine}, volume = {}, number = {}, pages = {1-10}, doi = {10.1017/S0033291722002367}, pmid = {36039768}, issn = {1469-8978}, abstract = {BACKGROUND: Ambulatory monitoring is gaining popularity in mental and somatic health care to capture an individual's wellbeing or treatment course in daily-life. Experience sampling method collects subjective time-series data of patients' experiences, behavior, and context. At the same time, digital devices allow for less intrusive collection of more objective time-series data with higher sampling frequencies and for prolonged sampling periods. We refer to these data as parallel data. Combining these two data types holds the promise to revolutionize health care. However, existing ambulatory monitoring guidelines are too specific to each data type, and lack overall directions on how to effectively combine them.

METHODS: Literature and expert opinions were integrated to formulate relevant guiding principles.

RESULTS: Experience sampling and parallel data must be approached as one holistic time series right from the start, at the study design stage. The fluctuation pattern and volatility of the different variables of interest must be well understood to ensure that these data are compatible. Data have to be collected and operationalized in a manner that the minimal common denominator is able to answer the research question with regard to temporal and disease severity resolution. Furthermore, recommendations are provided for device selection, data management, and analysis. Open science practices are also highlighted throughout. Finally, we provide a practical checklist with the delineated considerations and an open-source example demonstrating how to apply it.

CONCLUSIONS: The provided considerations aim to structure and support researchers as they undertake the new challenges presented by this exciting multidisciplinary research field.}, } @article {pmid36039277, year = {2022}, author = {Stokes, J and Bower, P and Guthrie, B and Mercer, SW and Rice, N and Ryan, AM and Sutton, M}, title = {Cuts to local government spending, multimorbidity and health-related quality of life: A longitudinal ecological study in England.}, journal = {The Lancet regional health. Europe}, volume = {19}, number = {}, pages = {100436}, pmid = {36039277}, issn = {2666-7762}, support = {MR/T027517/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Population health has stagnated or is declining in many high-income countries. We analysed whether nationally administered austerity cuts in England were associated with prevalence of multimorbidity (individuals with two or more long-term conditions) and health-related quality of life.

METHODS: We conducted an observational, longitudinal study on 147 local authorities in England. We examined associations of changes in spending over time (2009/10-2017/18), in total and by budget line, with (i) prevalence of multimorbidity, 2+ conditions (2011/12-2017/18), and (ii) health-related quality of life (EQ-5D-5L) score (2012/13-2016/17). We estimated linear, log-log regression models, incorporating local authority fixed-effects, time-varying demographic and socio-economic confounders, and time trends.

FINDINGS: All local authorities experienced real spending cuts, varying from 42% (Barking and Dagenham) to 0·3% (Sefton). A 1% cut in per capita total service expenditure was associated with a 0·10% (95% CI 0·03 to 0·16) increase in prevalence of multimorbidity. We found no association (0·003%; 95% CI -0·01 to 0·01) with health-related quality of life. By budget line, after controlling for other spending, a 1% cut in public health expenditure was associated with a 0·15% (95% CI 0·11 to 0·20) increase in prevalence of multimorbidity, and a 1% cut in adult social care expenditure was associated with a 0·01% (95% CI 0·002 to 0·02) decrease in average health-related quality of life.

INTERPRETATION: Fiscal austerity is associated with worse multimorbidity and health-related quality of life. Policymakers should consider the potential health consequences of local government expenditure cuts and knock-on effects for health systems.

FUNDING: Medical Research Council.}, } @article {pmid36037884, year = {2022}, author = {Luoma, E and Laurila-Pant, M and Altarriba, E and Nevalainen, L and Helle, I and Granhag, L and Lehtiniemi, M and Srėbalienė, G and Olenin, S and Lehikoinen, A}, title = {A multi-criteria decision analysis model for ship biofouling management in the Baltic Sea.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158316}, doi = {10.1016/j.scitotenv.2022.158316}, pmid = {36037884}, issn = {1879-1026}, mesh = {*Biofouling/prevention & control ; Ships ; Carbon Dioxide ; Bayes Theorem ; Water ; Decision Support Techniques ; }, abstract = {Biofouling of ship hulls form a vector for the introduction of non-indigenous organisms worldwide. Through increasing friction, the organisms attached to ships' hulls increase the fuel consumption, leading to both higher fuel costs and air emissions. At the same time, ship biofouling management causes both ecological risks and monetary costs. All these aspects should be considered case-specifically in the search of sustainable management strategies. Applying Bayesian networks, we developed a multi-criteria decision analysis model to compare biofouling management strategies in the Baltic Sea, given the characteristics of a ship, its operating profile and operational environment, considering the comprehensive environmental impact and the monetary costs. The model is demonstrated for three scenarios (SC1-3) and sub-scenarios (A-C), comparing the alternative biofouling management strategies in relation to NIS (non-indigenous species) introduction risk, eco-toxicological risk due to biocidal coating, carbon dioxide emissions and costs related to fuel consumption, in-water cleaning and hull coating. The scenarios demonstrate that by the careful consideration of the hull fouling management strategy, both money and environment can be saved. We suggest biocidal-free coating with a regular in-water cleaning using a capture system is generally the lowest-risk option. The best biocidal-free coating type and the optimal in-water cleaning interval should be evaluated case-specifically, though. In some cases, however, biocidal coating remains a justifiable option.}, } @article {pmid36036236, year = {2022}, author = {Strobl, MR and Vollmann, U and Eckl-Dorna, J and Radakovics, A and Ibl, V and Schnurer, M and Brenner, M and Dermendjiev, G and Weckwerth, W and Neumüller, M and Frommlet, F and Demir, H and Bublin, M and Müller, C and Bohle, B}, title = {Identification of apple cultivars hypoallergenic for birch pollen-allergic individuals by a multidisciplinary in vitro and in vivo approach.}, journal = {Clinical and translational allergy}, volume = {12}, number = {8}, pages = {e12186}, pmid = {36036236}, issn = {2045-7022}, abstract = {BACKGROUND: Birch pollen-related apple allergy is the most frequent IgE-mediated food allergy in Central-Northern Europe with Mal d 1 as major allergen. Its concentration in apples varies with the cultivar and storage time. Year-round appealing, hypoallergenic cultivars still are needed to satisfy the nutritional needs of affected individuals. We characterized three promising cultivars by multidisciplinary in vitro assays including long-term storage and by clinical challenges of allergic individuals before and after the birch pollen season.

METHODS: Proteins were extracted from fruits of 'Santana', 'Golden Delicious' (GD), and three genuine cultivars in November 2018 and April 2019. Mal d 1-levels were analysed by mass spectrometry, SDS-PAGE, immunoblotting, competitive ELISA, and basophil activation tests. Twenty-eight allergic individuals underwent single-blinded open food challenges and skin testing with the cultivars and birch pollen in November 2018 and May 2019. Allergen-specific IgE-levels were determined.

RESULTS: After storage all cultivars except 'Santana' were of appealing appearance and taste. Their Mal d 1 content had increased, also reflected by significantly amplified basophil activation and stronger reactions in clinical challenges. Besides, individuals showed boosted reactivity after pollen exposure indicated by enhanced allergen-specific IgE-levels and skin reactions to birch pollen. Still, all cultivars remained significantly less allergenic than GD and comparable to Santana in November 2018 in all assessments except for skin testing.

CONCLUSIONS: Combined expertise in pomology and allergology identified promising new cultivars for allergic consumers. The evaluation of hypoallergenic apples should incorporate long-term storage and birch pollen exposure. Basophil activation tests may be suitable in the selection of promising cultivars for oral challenges.}, } @article {pmid36035686, year = {2022}, author = {Del Vecchio, S and Sharma, SK and Pavan, M and Acosta, ATR and Bacchetta, G and de Bello, F and Isermann, M and Michalet, R and Buffa, G}, title = {Within-species variation of seed traits of dune engineering species across a European climatic gradient.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {978205}, pmid = {36035686}, issn = {1664-462X}, abstract = {Within-species variation is a key component of biodiversity and linking it to climatic gradients may significantly improve our understanding of ecological processes. High variability can be expected in plant traits, but it is unclear to which extent it varies across populations under different climatic conditions. Here, we investigated seed trait variability and its environmental dependency across a latitudinal gradient of two widely distributed dune-engineering species (Thinopyrum junceum and Calamagrostis arenaria). Seed germination responses against temperature and seed mass were compared within and among six populations exposed to a gradient of temperature and precipitation regimes (Spiekeroog, DE; Bordeaux, FR; Valencia, ES; Cagliari, IT, Rome, IT; Venice, IT). Seed germination showed opposite trends in response to temperature experienced during emergence in both species: with some expectation, in populations exposed to severe winters, seed germination was warm-cued, whereas in populations from warm sites with dry summer, seed germination was cold-cued. In C. arenaria, variability in seed germination responses disappeared once the seed coat was incised. Seed mass from sites with low precipitation was smaller than that from sites with higher precipitation and was better explained by rainfall continentality than by aridity in summer. Within-population variability in seed germination accounted for 5 to 54%, while for seed mass it was lower than 40%. Seed trait variability can be considerable both within- and among-populations even at broad spatial scale. The variability may be hardly predictable since it only partially correlated with the analyzed climatic variables, and with expectation based on the climatic features of the seed site of origin. Considering seed traits variability in the analysis of ecological processes at both within- and among-population levels may help elucidate unclear patterns of species dynamics, thereby contributing to plan adequate measures to counteract biodiversity loss.}, } @article {pmid36033213, year = {2022}, author = {Pho, AT and Mangal, S and Bakken, S}, title = {Human Papillomavirus Vaccination Among Transgender and Gender Diverse People in the United States: An Integrative Review.}, journal = {Transgender health}, volume = {7}, number = {4}, pages = {303-313}, pmid = {36033213}, issn = {2688-4887}, abstract = {OBJECTIVE: This integrative review explores the barriers to and facilitators for human papillomavirus (HPV) vaccination among adult transgender and gender diverse (TGD) people in the United States.

DATA SOURCE: A systematic search of electronic databases included PubMed/MEDLINE, CINAHL, and EMBASE from 1985 to 2020.

Inclusion criteria included studies from the United States that described HPV vaccination barriers or facilitators and included adult TGD participants, both quantitative and qualitative studies. Exclusion criteria were studies that reported only HPV vaccine prevalence, non-English/non-U.S. studies, and studies limited to pediatric populations.

DATA EXTRACTION: Two investigators used Covidence software to screen studies and manage data extraction. Quality of the quantitative studies was appraised using a checklist proposed by the Joanna Briggs Institute (JBI); qualitative studies were appraised using quality criteria informed by the literature.

DATA SYNTHESIS: The Social Ecological Model guided the review to organize barriers to and facilitators for HPV vaccination at the patient-, provider-, and system-levels.

RESULTS: Database searches and hand-searching yielded 843 citations. After screening, eight articles were retained in the review. Seven were cross-sectional studies and one was a qualitative focus-group. All retained quantitative studies met six of the eight JBI quality checklist items.

CONCLUSION: The low proportion of TGD participants in the retained studies highlights a gap in knowledge about HPV vaccination among this population. Future studies of HPV vaccination should recruit TGD people to better represent their perspectives.}, } @article {pmid36032727, year = {2022}, author = {Kenzie, ES and Parks, EL and Carney, N and Wakeland, W}, title = {System dynamics modeling for traumatic brain injury: Mini-review of applications.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {854358}, pmid = {36032727}, issn = {2296-4185}, abstract = {Traumatic brain injury (TBI) is a highly complex phenomenon involving a cascade of disruptions across biomechanical, neurochemical, neurological, cognitive, emotional, and social systems. Researchers and clinicians urgently need a rigorous conceptualization of brain injury that encompasses nonlinear and mutually causal relations among the factors involved, as well as sources of individual variation in recovery trajectories. System dynamics, an approach from systems science, has been used for decades in fields such as management and ecology to model nonlinear feedback dynamics in complex systems. In this mini-review, we summarize some recent uses of this approach to better understand acute injury mechanisms, recovery dynamics, and care delivery for TBI. We conclude that diagram-based approaches like causal-loop diagramming have the potential to support the development of a shared paradigm of TBI that incorporates social support aspects of recovery. When developed using adequate data from large-scale studies, simulation modeling presents opportunities for improving individualized treatment and care delivery.}, } @article {pmid36030325, year = {2022}, author = {Cooney, DB and Rossine, FW and Morris, DH and Levin, SA}, title = {A PDE Model for Protocell Evolution and the Origin of Chromosomes via Multilevel Selection.}, journal = {Bulletin of mathematical biology}, volume = {84}, number = {10}, pages = {109}, doi = {10.1007/s11538-022-01062-y}, pmid = {36030325}, issn = {1522-9602}, mesh = {*Artificial Cells ; Chromosomes ; Genome ; Mathematical Concepts ; Models, Biological ; }, abstract = {The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper, we formulate a minimal model of the evolution of proto-chromosomes within protocells. We model a simple protocell composed of two types of genes: a "fast gene" with an advantage for gene-level self-replication and a "slow gene" that replicates more slowly at the gene level, but which confers an advantage for protocell-level reproduction. Protocell-level replication capacity depends on cellular composition of fast and slow genes. We use a partial differential equation to describe how the composition of genes within protocells evolves over time under within-cell and between-cell competition, considering an infinite population of protocells that each contain infinitely many genes. We find that the gene-level advantage of fast replicators casts a long shadow on the multilevel dynamics of protocell evolution: no level of between-protocell competition can produce coexistence of the fast and slow replicators when the two genes are equally needed for protocell-level reproduction. By introducing a "dimer replicator" consisting of a linked pair of the slow and fast genes, we show analytically that coexistence between the two genes can be promoted in pairwise multilevel competition between fast and dimer replicators, and provide numerical evidence for coexistence in trimorphic competition between fast, slow, and dimer replicators. Our results suggest that dimerization, or the formation of a simple chromosome-like dimer replicator, can help to overcome the shadow of lower-level selection and work in concert with deterministic multilevel selection in protocells featuring high gene copy number to allow for the coexistence of two genes that are complementary at the protocell level but compete at the level of individual gene-level replication. These results for the PDE model complement existing results on the benefits of dimerization in the case of low genetic copy number, for which it has been shown that genetic linkage can help to overcome the stochastic loss of necessary genetic templates.}, } @article {pmid36016080, year = {2022}, author = {Yousaf, M and Ullah, A and Sarosh, N and Abbasi, SW and Ismail, S and Bibi, S and Hasan, MM and Albadrani, GM and Talaat Nouh, NA and Abdulhakim, JA and Abdel-Daim, MM and Bin Emran, T}, title = {Design of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach.}, journal = {Vaccines}, volume = {10}, number = {8}, pages = {}, pmid = {36016080}, issn = {2076-393X}, abstract = {Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E. coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.}, } @article {pmid36016053, year = {2022}, author = {Tropea, M and Fedele, G and De Luca, R and Miriello, D and De Rango, F}, title = {Automatic Stones Classification through a CNN-Based Approach.}, journal = {Sensors (Basel, Switzerland)}, volume = {22}, number = {16}, pages = {}, pmid = {36016053}, issn = {1424-8220}, mesh = {Bayes Theorem ; Cluster Analysis ; Machine Learning ; *Neural Networks, Computer ; *Support Vector Machine ; }, abstract = {This paper presents an automatic recognition system for classifying stones belonging to different Calabrian quarries (Southern Italy). The tool for stone recognition has been developed in the SILPI project (acronym of "Sistema per l'Identificazione di Lapidei Per Immagini"), financed by POR Calabria FESR-FSE 2014-2020. Our study is based on the Convolutional Neural Network (CNNs) that is used in literature for many different tasks such as speech recognition, neural language processing, bioinformatics, image classification and much more. In particular, we propose a two-stage hybrid approach based on the use of a model of Deep Learning (DL), in our case the CNN, in the first stage and a model of Machine Learning (ML) in the second one. In this work, we discuss a possible solution to stones classification which uses a CNN for the feature extraction phase and the Softmax or Multinomial Logistic Regression (MLR), Support Vector Machine (SVM), k-Nearest Neighbors (kNN), Random Forest (RF) and Gaussian Naive Bayes (GNB) ML techniques in order to perform the classification phase basing our study on the approach called Transfer Learning (TL). We show the image acquisition process in order to collect adequate information for creating an opportune database of the stone typologies present in the Calabrian quarries, also performing the identification of quarries in the considered region. Finally, we show a comparison of different DL and ML combinations in our Two-Stage Hybrid Model solution.}, } @article {pmid36007741, year = {2022}, author = {Ali, A and Farhan, SB and Zhang, Y and Nasir, J and Farhan, H and Zamir, UB and Gao, H}, title = {Changes in temporal pattern and spatial distribution of environmental pollutants in 8 Asian countries owing to COVID-19 pandemic.}, journal = {Chemosphere}, volume = {308}, number = {Pt 1}, pages = {136075}, pmid = {36007741}, issn = {1879-1298}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; *COVID-19/epidemiology ; Carbon Monoxide/analysis ; Environmental Monitoring/methods ; *Environmental Pollutants ; Formaldehyde ; Humans ; Nitrogen Dioxide/analysis ; *Ozone/analysis ; Pakistan ; Pandemics ; Particulate Matter/analysis ; Sulfur Dioxide/analysis ; }, abstract = {This study investigated the changes in air pollutant's concentration, spatio-temporal distribution and sensitivity of changes in air pollutant's concentration during pre and post COVID-19 outbreak. We employed Google Earth Engine Platform to access remote sensing datasets of air pollutants across Asian continent. Air pollution and cumulative confirmed-COVID cases data of Asian countries (Afghanistan, Bangladesh, China, India, Iran, Iraq, Pakistan, and Saudi Arabia) have been collected and analyzed for 2019 and 2020. The results indicate that aerosol index (AI) and nitrogen dioxide (NO2) is significantly reduced during COVID outbreak i.e. in year 2020. In addition, we found significantly positive (P < 0.05, 95% confidence interval, two-tailed) correlation between changes in AI and NO2 concentration for net active-COVID case increment in almost each country. For other atmospheric gases i.e. carbon monoxide (CO), formaldehyde (HCHO), ozone (O3), and Sulfur dioxide (SO2), insignificant and/or significant negative correlation is also observed. These results suggest that the atmospheric concentration of AI and NO2 are good indicators of human activities. Furthermore, the changes in O3 shows significantly negative correlation for net active-COVID case increment. In conclusion, we observed significant positive environmental impact of COVID-19 restrictions in Asia. This study would help and assist environmentalist and policy makers in restraining air pollution by implementing efficient restrictions on human activities with minimal economic loss.}, } @article {pmid36007087, year = {2022}, author = {Wang, Y and Cai, G and Yang, L and Zhang, N and Du, M}, title = {Monitoring of urban ecological environment including air quality using satellite imagery.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0266759}, pmid = {36007087}, issn = {1932-6203}, mesh = {*Air Pollution ; China ; Environment ; Environmental Monitoring/methods ; Remote Sensing Technology ; *Satellite Imagery ; }, abstract = {Rapid urbanisation has highlighted problems in the urban ecological environment and stimulated research on the evaluation of urban environments. In previous studies, key factors such as greenness, wetness, and temperature were extracted from satellite images to assess the urban ecological environment. Although air pollution has become increasingly serious as urbanisation proceeds, information on air pollution is not included in existing models. The Sentinel-5P satellite launched by the European Space Agency in 2017 is a reliable data source for monitoring air quality. By making full use of images from Landsat 8, Sentinel-2A, and Sentinel-5P, this work attempts to construct a new remote sensing monitoring index for urban ecology by adding air quality information to the existing remote sensing ecological index. The proposed index was tested in the Beijing metropolitan area using satellite data from 2020. The results obtained using the proposed index differ greatly in the central urban region and near large bodies of water from those obtained using the existing remote sensing monitoring model, indicating that air quality plays a significant role in evaluating the urban ecological environment. Because the model constructed in this study integrates information on vegetation, soil, humidity, heat, and air quality, it can comprehensively and objectively reflect the quality of the urban ecological environment. Consequently, the proposed remote sensing index provides a new approach to effectively monitoring the urban ecological environment.}, } @article {pmid35999898, year = {2021}, author = {Waterhouse, RM and Adam-Blondon, AF and Agosti, D and Baldrian, P and Balech, B and Corre, E and Davey, RP and Lantz, H and Pesole, G and Quast, C and Glöckner, FO and Raes, N and Sandionigi, A and Santamaria, M and Addink, W and Vohradsky, J and Nunes-Jorge, A and Willassen, NP and Lanfear, J}, title = {Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {}, pmid = {35999898}, issn = {2046-1402}, support = {BB/CSP1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016855/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9783/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9814/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; *Biological Science Disciplines ; Computational Biology ; Europe ; }, abstract = {Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.}, } @article {pmid36002452, year = {2022}, author = {Yang, C and Liu, H and Li, Q and Wang, X and Ma, W and Liu, C and Fang, X and Tang, Y and Shi, T and Wang, Q and Xu, Y and Zhang, J and Li, X and Xu, G and Chen, J and Su, M and Wang, S and Wu, J and Huang, L and Li, X and Wu, G}, title = {Human expansion into Asian highlands in the 21st Century and its effects.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4955}, pmid = {36002452}, issn = {2041-1723}, mesh = {Asia ; Asia, Southeastern ; *Asian People ; *Ecosystem ; Humans ; }, abstract = {Most intensive human activities occur in lowlands. However, sporadic reports indicate that human activities are expanding in some Asian highlands. Here we investigate the expansions of human activities in highlands and their effects over Asia from 2000 to 2020 by combining earth observation data and socioeconomic data. We find that ∼23% of human activity expansions occur in Asian highlands and ∼76% of these expansions in highlands comes from ecological lands, reaching 95% in Southeast Asia. The expansions of human activities in highlands intensify habitat fragmentation and result in large ecological costs in low and lower-middle income countries, and they also support Asian developments. We estimate that cultivated land net growth in the Asian highlands contributed approximately 54% in preventing the net loss of the total cultivated land. Moreover, the growth of highland artificial surfaces may provide living and working spaces for ∼40 million people. Our findings suggest that highland developments hold dual effects and provide new insight for regional sustainable developments.}, } @article {pmid36001546, year = {2022}, author = {Diodato, N and Borrelli, P and Panagos, P and Bellocchi, G}, title = {Global assessment of storm disaster-prone areas.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0272161}, pmid = {36001546}, issn = {1932-6203}, mesh = {*Disasters ; Geographic Information Systems ; Humans ; Hydrology ; *Rain ; Soil ; }, abstract = {BACKGROUND: Advances in climate change research contribute to improved forecasts of hydrological extremes with potentially severe impacts on human societies and natural landscapes. Rainfall erosivity density (RED), i.e. rainfall erosivity (MJ mm hm-2 h-1 yr-1) per rainfall unit (mm), is a measure of rainstorm aggressiveness and a proxy indicator of damaging hydrological events.

METHODS AND FINDINGS: Here, using downscaled RED data from 3,625 raingauges worldwide and log-normal ordinary kriging with probability mapping, we identify damaging hydrological hazard-prone areas that exceed warning and alert thresholds (1.5 and 3.0 MJ hm-2 h-1, respectively). Applying exceedance probabilities in a geographical information system shows that, under current climate conditions, hazard-prone areas exceeding a 50% probability cover ~31% and ~19% of the world's land at warning and alert states, respectively.

CONCLUSION: RED is identified as a key driver behind the spatial growth of environmental disruption worldwide (with tropical Latin America, South Africa, India and the Indian Archipelago most affected).}, } @article {pmid36001047, year = {2023}, author = {Shaffer, M and Thurimella, K and Sterrett, JD and Lozupone, CA}, title = {SCNIC: Sparse correlation network investigation for compositional data.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {312-325}, pmid = {36001047}, issn = {1755-0998}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; }, mesh = {*Software ; Algorithms ; *Microbiota ; }, abstract = {Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.}, } @article {pmid36000659, year = {2022}, author = {Santos, JS and Cruz, AJS and Ruas, CM and Pereira Júnior, EA and Mattos, FF and Klevens, M and Abreu, MHNG}, title = {Factors associated with the use of a public information system of dentist-prescribed antibiotics in Minas Gerais, Brazil.}, journal = {Ciencia & saude coletiva}, volume = {27}, number = {9}, pages = {3741-3750}, doi = {10.1590/1413-81232022279.07422022}, pmid = {36000659}, issn = {1678-4561}, mesh = {*Anti-Bacterial Agents ; Brazil ; *Dentists ; Humans ; Information Systems ; Socioeconomic Factors ; }, abstract = {This article aims to investigate the association between socioeconomic factors, health care organizations, and the use of a management and monitoring system for the dispensing of antibiotics prescribed by dentists in public health services in Minas Gerais, Brazil. This is an ecological-epidemiological study that analyzed secondary data from the Integrated Pharmaceutical Care Management System (SIGAF) of the Department of Health of the state of MG, Brazil, in 2017. Thirteen independent variables were analyzed to assess their influence on municipal adherence to SIGAF system considering dental prescriptions of antibiotics. Descriptive statistical analyses were performed, and the Classification and Regression Tree technique was used to identify the municipal variables associated with the outcome. A total of 57,279 antibiotic courses prescribed by dentists and recorded in SIGAF were examined. Socioeconomic factors were not associated with the use of SIGAF to record these prescriptions. Oral healthcare coverage was positively associated with the use of SIGAF for the dispensing of antibiotics prescribed by dentists. Dental Specialties Center were negatively associated with the outcome. Municipalities with high oral healthcare coverage and those without a Dental Specialties Center were more likely to use SIGAF.}, } @article {pmid35990172, year = {2022}, author = {Xiao, H and Xu, Z and Ren, J and Zhou, Y and Lin, R and Bao, S and Zhang, L and Lu, S and Lee, CKM and Liu, J}, title = {Navigating Chinese cities to achieve sustainable development goals by 2030.}, journal = {Innovation (Cambridge (Mass.))}, volume = {3}, number = {5}, pages = {100288}, pmid = {35990172}, issn = {2666-6758}, abstract = {Achieving the 17 United Nations sustainable development goals (SDGs) in China largely depends on the transition of cities toward sustainable development. However, significant knowledge gaps exist in evaluating the SDG index at the city scale and in understanding how to simulate pathways to achieve the 17 SDGs for Chinese cities by 2030. This study aimed to quantify the SDG index of 285 Chinese cities and developed a forecasting model to simulate the performance of each SDG in each city until 2030 using varied scenarios. The results indicated that although the SDG index in Chinese cities increased by 33.97% during 2005-2016, Chinese cities, which continued their past paths, achieved an average of only five SDGs by 2030. To promote the joint achievement of all SDGs, we designed different paths for all SDGs of each of the 285 cities and simulated their SDG index until 2030. Under the scenarios, 216 Chinese cities (75.79%) could achieve 9-13 more SDGs in 2030 and the overall SDG index can improve from 74.57 in 2030 to 97.49 (target score 100) by adopting more intensive path adjustment. We lastly determined a cost-effective path for each SDG of each city to promote joint achievement of all SDGs by 2030. The proposed simulation model and cost-effective path serve as a foundation for other countries to simulate SDG progress and develop pathways for achieving SDGs in the future.}, } @article {pmid35990120, year = {2022}, author = {Zhang, H}, title = {The Impact of Tax Reduction and Fee Reduction Based on Big Data Algorithm on the High-Quality Development of the Real Economy under the Action of Coupling Effect or Substitution Effect.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {2828687}, pmid = {35990120}, issn = {1687-5273}, mesh = {Algorithms ; *Big Data ; China ; Ecology ; *Economic Development ; }, abstract = {The basic idea of the mass of medical growth is to adhere to local market price thinking with a Chinese touch and follow the development policy of "quality first, efficiency first." It insists on properly handling a series of important relationships betwixt socialism and market economy, the first to drive the rich later, the government and the market, equality and efficiency, short-term growth and long-term development, China and the international economy, ecology and growth of the region. Under the guidance of the qualitative thinking theory, it combines the strategic goals of China's economic qualitative development and actively draws on the research results of other countries. It uses big data algorithms to focus on the impact of qualitative development on tax and income reduction in the real economy. It conducts research experiments on the impact of tax reduction and fee reduction based on big data algorithms on the top-notch growth of the real economy. Its experimental data show that: in 2018, the share of primary, tertiary, and primary sector in China's dimensional economy top-notch growth coordination index was 7.2%, 40.7%, and 52.2%, respectively. Its contribution rate to economic growth was 4.2%, 36.1%, and 59.7%, respectively. From these data, it can be concluded that the top-notch growth of the real economy is getting better and better under the influence of tax reduction and fee reduction by big data algorithms.}, } @article {pmid35983321, year = {2022}, author = {Zhu, Y and Ge, X and Wang, L and You, Y and Cheng, Y and Ma, J and Chen, F}, title = {Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {972300}, pmid = {35983321}, issn = {1664-302X}, abstract = {Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.}, } @article {pmid35977400, year = {2022}, author = {IJdema, F and De Smet, J and Crauwels, S and Lievens, B and Van Campenhout, L}, title = {Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {9}, pages = {}, pmid = {35977400}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; *Diptera/microbiology ; Genes, rRNA ; Larva/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.}, } @article {pmid35975694, year = {2022}, author = {Orlando, CG and Possell, M and Price, C and Banks, PB and Mercorelli, L and McArthur, C}, title = {A new conceptual and quantitative approach to exploring and defining potential open-access olfactory information.}, journal = {The New phytologist}, volume = {236}, number = {4}, pages = {1605-1619}, doi = {10.1111/nph.18432}, pmid = {35975694}, issn = {1469-8137}, mesh = {*Odorants ; *Plants/chemistry ; Reproducibility of Results ; Trees/chemistry ; }, abstract = {All organisms emit odour, providing 'open-access' olfactory information for any receiver with the right sensory apparatus. Characterizing open-access information emitted by groups of organisms, such as plant species, provides the means to answer significant questions about ecological interactions and their evolution. We present a new conceptual framework defining information reliability and a practical method to characterize and recover information from amongst olfactory noise. We quantified odour emissions from two tree species, one focal group and one outgroup, to demonstrate our approach using two new R statistical functions. We explore the consequences of relaxing or tightening criteria defining information and, from thousands of odour combinations, we identify and quantify those few likely to be informative. Our method uses core general principles characterizing information while incorporating knowledge of how receivers detect and discriminate odours. We can now map information in consistency-precision reliability space, explore the concept of information, and test information-noise boundaries, and between cues and signals.}, } @article {pmid35974327, year = {2022}, author = {Garza, DR and von Meijenfeldt, FAB and van Dijk, B and Boleij, A and Huynen, MA and Dutilh, BE}, title = {Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {101}, pmid = {35974327}, issn = {2730-7182}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; *Genome, Bacterial/genetics ; Genomics ; Humans ; Phylogeny ; Prokaryotic Cells ; }, abstract = {BACKGROUND: Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism's external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions.

RESULTS: We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency by which reactions are retained in functional networks when stochastic gene loss is simulated in diverse environments allowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of the external environment (constrained by "nutrition") from those that are independent of the environment (constrained by "nature"). By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets.

CONCLUSION: We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics.}, } @article {pmid35972961, year = {2022}, author = {Ramírez-Castañeda, V and Westeen, EP and Frederick, J and Amini, S and Wait, DR and Achmadi, AS and Andayani, N and Arida, E and Arifin, U and Bernal, MA and Bonaccorso, E and Bonachita Sanguila, M and Brown, RM and Che, J and Condori, FP and Hartiningtias, D and Hiller, AE and Iskandar, DT and Jiménez, RA and Khelifa, R and Márquez, R and Martínez-Fonseca, JG and Parra, JL and Peñalba, JV and Pinto-García, L and Razafindratsima, OH and Ron, SR and Souza, S and Supriatna, J and Bowie, RCK and Cicero, C and McGuire, JA and Tarvin, RD}, title = {A set of principles and practical suggestions for equitable fieldwork in biology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {34}, pages = {e2122667119}, pmid = {35972961}, issn = {1091-6490}, mesh = {*Bioethical Issues ; *Biology/ethics ; Humans ; }, abstract = {Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.}, } @article {pmid35972940, year = {2022}, author = {Vimercati, G and Probert, AF and Volery, L and Bernardo-Madrid, R and Bertolino, S and Céspedes, V and Essl, F and Evans, T and Gallardo, B and Gallien, L and González-Moreno, P and Grange, MC and Hui, C and Jeschke, JM and Katsanevakis, S and Kühn, I and Kumschick, S and Pergl, J and Pyšek, P and Rieseberg, L and Robinson, TB and Saul, WC and Sorte, CJB and Vilà, M and Wilson, JRU and Bacher, S}, title = {The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity.}, journal = {PLoS biology}, volume = {20}, number = {8}, pages = {e3001729}, pmid = {35972940}, issn = {1545-7885}, mesh = {*Biodiversity ; Ecosystem ; Human Activities ; Humans ; *Introduced Species ; }, abstract = {Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions.}, } @article {pmid35969597, year = {2022}, author = {Ramasawmy, M and Mu, Y and Clutterbuck, D and Pantelic, M and Lip, GYH and van der Feltz-Cornelis, C and Wootton, D and Williams, NH and Montgomery, H and Mallinson Cookson, R and Attree, E and Gabbay, M and Heightman, M and Alwan, NA and Banerjee, A and Lorgelly, P and , }, title = {STIMULATE-ICP-CAREINEQUAL (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways) study protocol: Defining usual care and examining inequalities in Long Covid support.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271978}, pmid = {35969597}, issn = {1932-6203}, support = {COV-LT2-0043/DH_/Department of Health/United Kingdom ; }, mesh = {*COVID-19/complications/epidemiology/therapy ; Critical Pathways ; *Delivery of Health Care, Integrated ; Humans ; Longitudinal Studies ; Post-Acute COVID-19 Syndrome ; }, abstract = {INTRODUCTION: Individuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor. In a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients' experiences of stigma and discrimination.

METHODS AND ANALYSIS: A mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received.

ETHICS AND DISSEMINATION: Ethical approval was obtained from South Central-Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.}, } @article {pmid35964757, year = {2022}, author = {Loli, M and Kefalas, G and Dafis, S and Mitoulis, SA and Schmidt, F}, title = {Bridge-specific flood risk assessment of transport networks using GIS and remotely sensed data.}, journal = {The Science of the total environment}, volume = {850}, number = {}, pages = {157976}, doi = {10.1016/j.scitotenv.2022.157976}, pmid = {35964757}, issn = {1879-1026}, mesh = {*Floods ; *Geographic Information Systems ; Hydrology ; Reproducibility of Results ; Risk Assessment ; }, abstract = {A novel framework for the expedient assessment of flood risk to transportation networks focused on the response of the most critical and vulnerable infrastructure assets, the bridges, is developed, validated and applied. Building upon the recent French guidelines on scour risk (CEREMA, 2019), this paper delivers a thorough methodology, that incorporates three key, risk parameters: (i) the hydrodynamic loading, a hazard component of equal significance to scour, for the assessment of hazard; (ii) the correlation of select scour indicators with a new index relating to flow velocity, a primary measure of the adverse impacts of flow-structure interaction, enabling a more accurate and automated, assessment of bridge susceptibility to scour; (iii) the use of a new, comprehensive indicator, namely the Indicator of Flood Hazard Intensity (IFHI) which incorporates, in a simple yet efficient way, the key parameters controlling the severity of flood impact on bridges, namely flow velocity, floodwater height, flow obstruction, and sediment type. The framework is implemented for the analysis of flood risk in a case study area, considering an inventory of 117 bridges of diverse construction characteristics, which were affected by a major flood that impacted Greece in September 2020. The reliability of the method is validated against an extensive record of inspected and documented bridge damages. Regional scale analysis is facilitated by the adoption of the Multi-Criteria Decision-Making method for flood hazard indexing, considering geomorphological, meteorological, hydrological, and land use/cover data, based on the processing of remotely sensed imagery and openly available geospatial datasets in GIS.}, } @article {pmid35964726, year = {2022}, author = {Karimian, H and Zou, W and Chen, Y and Xia, J and Wang, Z}, title = {Landscape ecological risk assessment and driving factor analysis in Dongjiang river watershed.}, journal = {Chemosphere}, volume = {307}, number = {Pt 3}, pages = {135835}, doi = {10.1016/j.chemosphere.2022.135835}, pmid = {35964726}, issn = {1879-1298}, mesh = {China ; *Environmental Monitoring/methods ; Factor Analysis, Statistical ; Humans ; Risk Assessment ; *Rivers ; Urbanization ; }, abstract = {The ecological and environmental quality of Dongjiang river watershed has great influence on Guangdong, Hong Kong and Macao. The landscape ecological risk assessment model could effectively monitor and assess environmental quality. In this study, spatial autocorrelation and geographic detector methods were used to explore the spatial characteristics of landscape ecological risk and their driving factors in the Dongjiang river watershed for four decades. The results showed that the ecological risks of Dongjiang River Source Watershed are mainly classified as low and intermediate, which are distributed in the hilly regions and the marginal mountainous regions at the junction of the Xunwu and Dingnan counties. From 1980 to 2018, the area of regions with the low ecological risk increased by 587.01 km [2]. The size of regions with moderate, high and severe ecological risk decreased by 165.6 km [2], 258.82 km[2] and 162.58 km[2], respectively. Moreover, landscape ecological risk values exhibited an apparent spatial dependency, and high-risk areas cluster together. Among influencing factors, population density has the most significant impact on the change of landscape ecological risk in the Dongjiang river watershed, followed by elevation (DEM), human interface, vegetation index (NDVI), and urbanization level. However, the interaction of driving factors has a greater impact on the ecological risk of the Dongjiang river watershed than a single driving factor. The research provides good knowledge for environmental quality management, and the proposed methods can be used for other regions.}, } @article {pmid35960845, year = {2022}, author = {Amend, AS and Swift, SOI and Darcy, JL and Belcaid, M and Nelson, CE and Buchanan, J and Cetraro, N and Fraiola, KMS and Frank, K and Kajihara, K and McDermot, TG and McFall-Ngai, M and Medeiros, M and Mora, C and Nakayama, KK and Nguyen, NH and Rollins, RL and Sadowski, P and Sparagon, W and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA}, title = {A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {33}, pages = {e2204146119}, pmid = {35960845}, issn = {1091-6490}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; }, abstract = {Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.}, } @article {pmid35960769, year = {2022}, author = {Ali, MA and Iqbal, MS and Ahmad, KS and Akbar, M and Mehmood, A and Hussain, SA and Arshad, N and Munir, S and Masood, H and Ahmad, T and Kaloi, GM and Islam, M}, title = {Plant species diversity assessment and monitoring in catchment areas of River Chenab, Punjab, Pakistan.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0272654}, pmid = {35960769}, issn = {1932-6203}, mesh = {Biodiversity ; *Ecosystem ; Humans ; Pakistan ; Plants ; Potassium ; *Rivers ; Soil/chemistry ; Trees ; }, abstract = {BACKGROUND: Biodiversity data is crucial for sustainable development and making decisions regarding natural resources and its conservation. The study goal was to use quantitative ecological approaches to determine the species richness and diversity of wild flora and the ultimate impact of environmental factors on vegetation dynamics.

METHODS: Quadrats having sizes of 1×1 for herbs, 5×5 for shrubs, and 10×10 m2 for trees were used. Various phytosociological characteristics were investigated in association with a wide variety of environmental variables. Soil analysis based on texture, moisture, pH, electrical conductivity (EC), organic matter (OM), available potassium (K), and phosphorus (P) were examined. The existing state of vegetation along the River Chenab was assessed using SWOT analysis and a future conservation strategy was devised.

RESULTS: One hundred twenty different plant speies were divided into 51 families including 92 dicots, 17 monocots, 6 pteridophytes and 1 bryophyte species. Herbs accounted for 89 followed by shrubs (16 species) and trees (15 species). Correlation analysis revealed a highly positive correlation between relative density and relative frequency (0.956**). Shannon and Simpson's diversity indices elaborated that site 3 and 7 with clay loamy soil had non-significant alpha diversity and varies from site to site. Diversity analysis showed that site 10 was most diverse (22.25) in terms of species richness. The principal coordinate analysis expressed that different environmental variables including OM, soil pH, P, K, and EC affect vegetation significantly, therefore, loamy soil showed presence and dispersal of more vegetation as compared to loam, sandy and sandy loam soils. Further, 170 ppm of available potassium had significant affect on plant diversity and distribution.

CONCLUSION: Asteraceae family was found dominant as dicot while poaceae among monocot. Adhatoda vasica was one of the unique species and found in Head Maralla site. For evenness, site 3 had maximum value 0.971. Most of the soil represented loamy soil texture where site 2 and 4 possess high soil moisture content. SWOT analysis revealed strengths as people prefered plants for medicine, food and economic purposes. In weakness, agricultural practices, soil erosion and flooding affected the vegetation. In opportunities, Forest and Irrigation Departments were planting plants for the restoration of ecosystem. Threats include anthropogenic activities overgrazing, urbanization and road infrastructure at Head Maralla, habitat fragmentation at Head Khanki, and extensive fish farming at Head Qadirabad. Future conservation efforts should be concentrated on SWOT analysis outcome in terms of stopping illegal consumption of natural resources, restoration of plant biodiversity through reforestation, designating protected areas and multiplying rare species locally.}, } @article {pmid35959935, year = {2022}, author = {Stahlke, AR and Chang, J and Tembrock, LR and Sim, SB and Chudalayandi, S and Geib, SM and Scheffler, BE and Perera, OP and Gilligan, TM and Childers, AK and Hackett, KJ and Coates, BS}, title = {A chromosome-scale genome assembly of a Helicoverpa zea strain resistant to Bacillus thuringiensis Cry1Ac insecticidal protein.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evac131}, pmid = {35959935}, issn = {1759-6653}, abstract = {Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. H. zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single-copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.}, } @article {pmid35955104, year = {2022}, author = {Zhou, X and Shen, D and Gu, X}, title = {Influences of Land Policy on Urban Ecological Corridors Governance: A Case Study from Shanghai.}, journal = {International journal of environmental research and public