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29 Sep 2023 at 01:46
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Bibliography on: Ecological Informatics


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RJR: Recommended Bibliography 29 Sep 2023 at 01:46 Created: 

Ecological Informatics

Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are the National Science Foundation's Datanet , DataONE and Data Conservancy projects.

Created with PubMed® Query: ( "ecology OR ecological" AND ("data management" OR informatics) NOT "assays for monitoring autophagy" ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2023-09-28

Cai J, Pan R, Lin J, et al (2023)

Improved EfficientNet for corn disease identification.

Frontiers in plant science, 14:1224385.

INTRODUCTION: Corn is one of the world's essential crops, and the presence of corn diseases significantly affects both the yield and quality of corn. Accurate identification of corn diseases in real time is crucial to increasing crop yield and improving farmers' income. However, in real-world environments, the complexity of the background, irregularity of the disease region, large intraclass variation, and small interclass variation make it difficult for most convolutional neural network models to achieve disease recognition under such conditions. Additionally, the low accuracy of existing lightweight models forces farmers to compromise between accuracy and real-time.

METHODS: To address these challenges, we propose FCA-EfficientNet. Building upon EfficientNet, the fully-convolution-based coordinate attention module allows the network to acquire spatial information through convolutional structures. This enhances the network's ability to focus on disease regions while mitigating interference from complex backgrounds. Furthermore, the adaptive fusion module is employed to fuse image information from different scales, reducing interference from the background in disease recognition. Finally, through multiple experiments, we have determined the network structure that achieves optimal performance.

RESULTS: Compared to other widely used deep learning models, this proposed model exhibits outstanding performance in terms of accuracy, precision, recall, and F1 score. Furthermore, the model has a parameter count of 3.44M and Flops of 339.74M, which is lower than most lightweight network models. We designed and implemented a corn disease recognition application and deployed the model on an Android device with an average recognition speed of 92.88ms, which meets the user's needs.

DISCUSSION: Overall, our model can accurately identify corn diseases in realistic environments, contributing to timely and effective disease prevention and control.

RevDate: 2023-09-28

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2022)

The genome sequence of the peacock moth, Macaria notata (Linnaeus, 1758).

Wellcome open research, 7:228.

We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority 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 15.4 kilobases in length.

RevDate: 2023-09-28

Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the Broken-barred Carpet, Electrophaes corylata (Thunberg, 1792).

Wellcome open research, 8:283.

We present a genome assembly from an individual male Electrophaes corylata (the Broken-barred Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 347.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,031 protein coding genes.

RevDate: 2023-09-28

Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the Dark Spectacle, Abrostola triplasia (Linnaeus, 1758).

Wellcome open research, 8:278.

We present a genome assembly from an individual male Abrostola triplasia (the Dark Spectacle; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 362.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,532 protein coding genes.

RevDate: 2023-09-28
CmpDate: 2023-09-28

Aguiar A, Gebremariam MK, Romanenko E, et al (2023)

System dynamics simulation models on overweight and obesity in children and adolescents: A systematic review.

Obesity reviews : an official journal of the International Association for the Study of Obesity, 24 Suppl 2:e13632.

It has increasingly been recognized that developing successful obesity prevention policies and interventions requires understanding of the complex mechanisms driving the obesity pandemic and that models could be useful tools for simulating policies. This paper reviews system dynamics simulation models of mechanisms driving childhood overweight and obesity and/or testing of preventive interventions. A systematic literature search was conducted in six databases from inception to January 2023 using terms related to overweight/obesity, children, and system dynamics. Study descriptives, mechanisms, and where to intervene (the leverage points), as well as quality assessments of the simulation models were extracted by two researchers into a predetermined template and narratively synthesized. Seventeen papers describing 15 models were included. Models describing the mechanisms ranged from only intrapersonal factors to models cutting across multiple levels of the ecological model, but mechanisms across levels were lacking. The majority of interventions tested in the simulation models were changes to existing model parameters with less emphasis on models that alter system structure. In conclusion, existing models included mechanisms driving youth obesity at multiple levels of the ecological model. This is useful for developing an integrated simulation model combining mechanisms at multiple levels and allowing for testing fundamental system changes.

RevDate: 2023-09-27

Bekele D, Aragie S, Alene KA, et al (2023)

Spatiotemporal Distribution of Tuberculosis in the Oromia Region of Ethiopia: A Hotspot Analysis.

Tropical medicine and infectious disease, 8(9): pii:tropicalmed8090437.

Tuberculosis (TB) is a major public health concern in low- and middle-income countries including Ethiopia. This study aimed to assess the spatiotemporal distribution of TB and identify TB risk factors in Ethiopia's Oromia region. Descriptive and spatiotemporal analyses were conducted. Bayesian spatiotemporal modeling was used to identify covariates that accounted for variability in TB and its spatiotemporal distribution. A total of 206,278 new pulmonary TB cases were reported in the Oromia region between 2018 and 2022, with the lowest annual TB case notification (96.93 per 100,000 population) reported in 2020 (i.e., during the COVID-19 pandemic) and the highest TB case notification (106.19 per 100,000 population) reported in 2019. Substantial spatiotemporal variations in the distribution of notified TB case notifications were observed at zonal and district levels with most of the hotspot areas detected in the northern and southern parts of the region. The spatiotemporal distribution of notified TB incidence was positively associated with different ecological variables including temperature (β = 0.142; 95% credible interval (CrI): 0.070, 0.215), wind speed (β = -0.140; 95% CrI: -0.212, -0.068), health service coverage (β = 0.426; 95% CrI: 0.347, 0.505), and population density (β = 0.491; 95% CrI: 0.390, 0.594). The findings of this study indicated that preventive measures considering socio-demographic and health system factors can be targeted to high-risk areas for effective control of TB in the Oromia region. Further studies are needed to develop effective strategies for reducing the burden of TB in hotspot areas.

RevDate: 2023-09-27

Leo P, Onofri S, Zucconi L, et al (2023)

Draft genome sequencing of Naganishia species isolated from the polar environments.

Microbiology resource announcements [Epub ahead of print].

The draft genomes of five Naganishia strains were sequenced using MinION and annotated using Funannotate pipeline. Phylogenetic and genomic analyses were performed to provide their genetic relationships, diversity, and potential functional capabilities. This approach will aid in understanding their potential to survive under microgravity and their resilience to extreme environments.

RevDate: 2023-09-27

Ježová Z, Prokop P, Zvaríková M, et al (2023)

Unraveling the Significance of Draglines: Female Sexual Signalization in the Nursery-Web Spider, Pisaura mirabilis.

Insects, 14(9): pii:insects14090765.

Chemical signals used by animals to attract the opposite sex are well known in insects, but heavily understudied in spiders. We investigated the role of chemical signals in female draglines in a gift-giving spider, Pisaura mirabilis, using combined data from behavioral tests and high-performance liquid chromatography (HPLC). We also investigated whether the quality of sexual signalization is influenced by crucial factors, such as female spider ontogeny, nutritional status, and mating status. We found that draglines of adult (versus subadult) and hungry (versus fed) females stimulated male motivation to produce nuptial gift, and highly sexually excited males invested more silk in gift production than less sexually excited males. Unexpectedly, chemical signals of eggsac-carrying females were similarly sexually attractive to draglines of adult females not carrying eggsac. HPLC identified significant chemical differences in female draglines, but these differences did not always correspond to male behavior. The integration of behavioral and chemical approaches is required to better understand animal behavior in future research.

RevDate: 2023-09-27
CmpDate: 2023-09-27

Riva F, Graco-Roza C, Daskalova GN, et al (2023)

Toward a cohesive understanding of ecological complexity.

Science advances, 9(25):eabq4207.

Ecological systems are quintessentially complex systems. Understanding and being able to predict phenomena typical of complex systems is, therefore, critical to progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity and excessive reliance on conventional scientific approaches hamper conceptual advances and synthesis. Ecological complexity may be better understood by following the solid theoretical basis of complex system science (CSS). We review features of ecological systems described within CSS and conduct bibliometric and text mining analyses to characterize articles that refer to ecological complexity. Our analyses demonstrate that the study of complexity in ecology is a highly heterogeneous, global endeavor that is only weakly related to CSS. Current research trends are typically organized around basic theory, scaling, and macroecology. We leverage our review and the generalities identified in our analyses to suggest a more coherent and cohesive way forward in the study of complexity in ecology.

RevDate: 2023-09-25

Smith SK, Frazel PW, Khodadadi-Jamayran A, et al (2023)

De novo assembly and annotation of the singing mouse genome.

BMC genomics, 24(1):569.

BACKGROUND: Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston's singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions.

RESULTS: Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.

CONCLUSIONS: These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.

RevDate: 2023-09-25

Stenseth NC, Schlatte R, Liu X, et al (2023)

Reply to Ekström and Ottersen: Real-time access to data during outbreaks is a key to avoid a local epidemic becoming a global pandemic.

Proceedings of the National Academy of Sciences of the United States of America, 120(40):e2312649120.

RevDate: 2023-09-25
CmpDate: 2023-09-25

Miletić S, Beloica J, Perović V, et al (2023)

Environmental sensitivity assessment and land degradation in southeastern Serbia: application of modified MEDALUS model.

Environmental monitoring and assessment, 195(10):1241.

This paper aims to improve the methodology and results accuracy of MEDALUS model for assessing land degradation sensitivity through the application of different data detail levels and by introducing the application of Ellenberg indices in metrics related to vegetation drought sensitivity assessment. For that purpose, the MEDALUS model was applied at 2 levels of detail. Level I (municipality level) implied the use of available large-scale databases and level II (watershed) contains more detailed information about vegetation used in the calculation of the VQI and MQI factors (Fig. S6). The comparison was made using data based on CORINE Land Cover (2012) and forest inventory data, complemented with object-based classification. Results showed that data based on forest inventory data with the application of Ellenberg's indices and object-based classification have one class more, critical (C1 and C2) and that the percentage distribution of classes is different in both quantitative (area size of class sensitivity) and qualitative (aggregation and dispersion of sensitivity classes). The use of data from Forest Management Plans and the application of Ellenberg's indices affect the quality of the results and find its application in the model, especially if these results are used for monitoring and land area management on fine scales. Remote sensed data images (Sentinel-2B) were introduced into the methodology as a very important environmental monitoring tool and model results validation.

RevDate: 2023-09-25
CmpDate: 2023-09-25

Isoyama K, Matsuura M, Hayasaka M, et al (2023)

Nationwide trends in and regional factors associated with minimally invasive hysterectomy for benign indications in Japan.

European journal of obstetrics, gynecology, and reproductive biology, 289:129-135.

OBJECTIVE: To examine the prevalence trends of minimally invasive hysterectomy for benign indications in Japan and investigate regional disparities.

STUDY DESIGN: A retrospective cohort and ecological study using "The National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open Data".

SETTING: Nationwide Japan.

PATIENTS: Individuals who underwent hysterectomy for benign indications from 2014 to 2020.

INTERVENTIONS: Trend analysis of minimally invasive surgery (MIS) rates through laparoscopic hysterectomies (LH) and robotic-assisted laparoscopic hysterectomies (RA-LH) at the national and prefecture levels. Examination of regional factors contributing to the disparity in MIS implementation rates by second medical service area (SMSA).

RESULTS: The number of LH has increased from 16,016 in 2014 to 27,755 in 2020. The nationwide MIS hysterectomy rate increased from 29% in 2014 to 55% in 2020 (p less than 0.001). More than 50% of hysterectomies have been performed as MIS since 2019. There was an increasing trend in MIS rates in all age groups. All prefectures except one showed a significant upward trend (p less than 0.05) in the MIS rates, but MIS rates varied widely (23-84%). In a multivariable model, the MIS was more likely to be performed in the SMSAs in western Japan (p = 0.011), in the SMSAs where the number of laparoscopy-qualified gynecologists is 5-10 (p = 0.013), and 11 or higher (p less than 0.001).

CONCLUSIONS: This study reveals a shift towards minimally invasive surgery (MIS) in total hysterectomy procedures in Japan. However, significant disparities in the prevalence of MIS hysterectomy exist, potentially influenced by the number of laparoscopy-qualified gynecologists.

RevDate: 2023-09-25

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2022)

The genome sequence of the dun-bar pinion, Cosmia trapezina (Linnaeus, 1758).

Wellcome open research, 7:189.

We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules with the Z chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

RevDate: 2023-09-25

Otto EC, Held BW, Gould TJ, et al (2021)

Fungal Diversity in Multiple Post-harvest Aged Red Pine Stumps and Their Potential Influence on Heterobasidion Root Rot in Managed Stands Across Minnesota.

Frontiers in fungal biology, 2:782181.

Thinning operations that occur in managed red pine (Pinus resinosa) stands, create tree stumps that can serve as a habitat for fungi, especially Heterobasidion irregulare, the cause of a serious root disease. Different fungi can colonize stumps early and the community of fungi can change over time as initial fungal species become replaced. Samples were collected from both the native and non-native range of red pine from stumps that were cut at different time periods. Stumps that were harvested at 0-1, 2-3, 5-6, and 10-12 years before sampling were used to provide data on the diversity of fungi that colonize tree stumps and how these communities can change over time as well as how they influence colonization of H. irregulare. Traditional culturing methods and Illumina MiSeq sequencing were used to identify the fungi in the samples. Of particular interest was Phlebiopsis gigantea, which can colonize cut stumps and prevent H. irregulare from becoming established. Overall, P. gigantea was the most abundant fungus isolated and sequenced via Illumina MiSeq. Results show that Phlebiopsis gigantea was isolated from 90% of all stumps sampled for sites harvested within 3 years of sampling in the native range of red pine compared to 33% in the non-native range. For Illumina MiSeq, 5,940 total amplicon sequence variants (ASVs) were detected. P. gigantea represented 14% of the total reads and composed 19% of the reads in the native range and 8% in non-native range of red pine. Furthermore, P. gigantea represented 38% of the reads for stumps that were harvested within 3 years of sampling in the native range of red pine compared to 14% in the non-native range. These results help demonstrate that a higher amount of P. gigantea is present in the native range of red pine and could be acting as a native biological control agent. Additional fungi, including Resinicium bicolor, Hypochnicium cremicolor, Leptographium spp., and others identified at different cutting times are also discussed. Finally, different diversity indices revealed similar, but slightly higher diversity for southern sites via Shannon and Simpson Diversity indices. Beta diversity demonstrated a similar species composition in stumps harvested at different times with these stumps being grouped together based on harvesting years.

RevDate: 2023-09-23

Chen H, Zhang X, Ji C, et al (2023)

Physicochemical properties of environmental media can affect the adsorption of arsenic (As) by microplastics.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(23)01594-4 [Epub ahead of print].

Microplastics are emerging pollutants that can adsorb heavy metals and threaten human health through food chain. Recently, there has been increasing interest in understanding the adsorption behavior of heavy metals by microplastics in farmland soil. In particular, arsenic (As), as a carcinogen, has the potential to be adsorbed by soil microplastics. However, the mechanisms and controlling factors of As adsorption by microplastics in farmland soil under natural conditions are still unknown. Here, microplastics and As were respectively added to farmland soils with different physicochemical properties from twelve provinces of China for adsorption experiment. We performed surface analysis of microplastics, quantified As accumulation through quasi-first-order kinetic equation and developed regression models to screen the factors controlling As adsorption. The results showed that the adsorption of As by soil microplastics was a chemical process accompanied by the loss of electrons from oxygen-containing functional groups. Soil cation exchange capacity (CEC) was the main factor controlling the adsorption rate, while soil organic matter (SOM), total nitrogen (TN) and CEC mainly influenced the equilibrium adsorption capacity. This is the first report on microplastic-As adsorption in natural soil, which allows deeper insights into risk assessment, prediction and control of microplastic-As pollution in agricultural soil.

RevDate: 2023-09-22

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2023)

The genome sequence of the Rustic Shoulder-knot, Apamea sordens (Hufnagel, 1766).

Wellcome open research, 8:51.

We present a genome assembly from an individual male Apamea sordens (the Rustic Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 614 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length.

RevDate: 2023-09-22
CmpDate: 2023-09-22

Kazemi A, Racil G, Ahmadi Hekmatikar AH, et al (2023)

Improved physical performance of elite soccer players based on GPS results after 4 days of carbohydrate loading followed by 3 days of low carbohydrate diet.

Journal of the International Society of Sports Nutrition, 20(1):2258837.

BACKGROUND: Carbohydrate loading is an established sports nutrition strategy for endur- 16 ance exercise performance. We tested if carbohydrate loading could improve the performance of 17 elite soccer players under ecologically valid circumstances using Global Positioning System (GPS) data.

METHODS: Twenty-two adult Iran Premier league soccer players were divided into a carbohydrate-loading group (CLG) and Control group (CG). The carbohydrate loading group restricted carbohydrate intake for three days to 1.5 g/kg/d while increasing exercise intensity. From days four to seven, exercise intensity was decreased and carbohydrate intake was considerably increased up to 7.5 g/kg/d on the day of the match, during which performance was analyzed using GPS data. The control group performed the same exercise training but maintained their habitual carbohydrate intake of 5-6 g/kg/d. The data were analyzed using a univariate ANCOVA with baseline data from a pre-intervention match as the control variable.

RESULTS: The carbohydrate loading team scored significantly higher on running distance, maximum speed and the number of top and repeated sprints; the carbohydrate loading group scored significantly lower on player load, metabolic power and running imbalance compared to the control team during their match.

CONCLUSIONS: Our findings suggest carbohydrate loading enabled elite soccer players to achieve greater running outputs with greater metabolic efficiency and lower fatigue compared to their habitual diets.

RevDate: 2023-09-22
CmpDate: 2023-09-22

Roma P, Giromini L, Sellbom M, et al (2023)

The ecological validity of the IOP-29: A follow-up study using the MMPI-2-RF and the SIMS as criterion variables.

Psychological assessment, 35(10):868-879.

Current guidelines for conducting symptom validity assessments require that professionals administer multiple symptom validity tests (SVTs) and that the SVTs selected for their evaluations provide nonredundant information. However, not many SVTs are currently available, and most of them rely on the same, (in)frequency-based, feigning detection strategy. In this context, the Inventory of Problems (IOP-29) could be a valuable addition to the assessor's toolbox because of its brevity (29 items) and its different approach to assessing the credibility of presented symptoms. As its ecological validity has been poorly investigated, the present study used a criterion groups design to examine the classification accuracy of the IOP-29 in a data set of 174 court-ordered psychological evaluations focused on psychological injury. The validity scales of the Minnesota Multiphasic Personality Inventory-2 Restructured Form and the total score of the Structured Inventory of Malingered Symptoms were used as criterion variables. Overall, the results of this study confirm that the IOP-29 is an effective measure (1.70 ≤ d ≤ 2.67) that provides valuable information when added to the multimethod assessment of symptom validity in civil forensic contexts. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

RevDate: 2023-09-21

Engloner AI, Vargha M, Kós P, et al (2023)

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts.

PloS one, 18(9):e0292057 pii:PONE-D-23-01359.

In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.

RevDate: 2023-09-21

Ohashi K, Osanai T, Fujiwara K, et al (2023)

Access to mechanical thrombectomy and ischemic stroke mortality in Japan: a spatial ecological study.

Frontiers in neurology, 14:1209446.

BACKGROUND: Advances in stroke treatment have greatly improved outcomes; however, disparities in access to treatment might increase. Achieving equitable access to stroke treatment is a health policy challenge, as rapid treatment is essential for positive outcomes. This ecological cross-sectional study aimed to determine the relationship between the disparities in spatial accessibility to mechanical thrombectomy (SAMT) and stroke mortality rates in Japan, hypothesizing that disparities in SAMT may increase the differences in stroke mortality between regions.

METHODS: We used the average number of ischemic stroke (IS) deaths between 2020 and 2021 as the response variable; and SAMT, medical resources, and socioeconomic characteristics of each municipality as explanatory variables. A conditional autoregressive model was used to examine the association between the risk of stroke mortality and SAMT. The standardized mortality ratio (SMR) was mapped to understand the nationwide disparities in stroke mortality risk.

RESULTS: The median number of IS deaths was 17.5 persons per year in the municipalities (2020 to 2021). The study also found that municipalities with low SAMT were located in the northern part of Japan. The non-spatial regression model results indicated that poor accessibility, a small proportion of bachelor's degrees or higher, and a high proportion of workers in secondary industries were related to high IS mortality. Three models were evaluated using spatial analysis; Model 1 with accessibility indicators alone, Model 2 with medical resources added to Model 1, and Model 3 with socioeconomic characteristics added to Model 2. In Models 1 and 2, the population-weighted spatial accessibility index (PWSAI) showed a significant negative relationship with stroke mortality. However, this was not evident in Model 3. Mapping using Model 3 showed that the high-risk areas were predominantly located in northern Japan, excluding Hokkaido.

CONCLUSION: Access to mechanical thrombectomy was estimated, and regional differences were observed. The relationship between accessibility and IS mortality is unknown; however, regardless of accessibility, municipalities with a high proportion of workers in secondary industries and a small proportion with bachelor's degrees or above are at risk of death from stroke.

RevDate: 2023-09-21

Molina MA, Melchers WJG, Andralojc KM, et al (2023)

Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection.

Computational and structural biotechnology journal, 21:4424-4431.

The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease.

RevDate: 2023-09-20
CmpDate: 2023-09-20

Jia H, Zhao Y, Deng H, et al (2023)

Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters.

Journal of hazardous materials, 460:132422.

At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.

RevDate: 2023-09-20
CmpDate: 2023-09-20

Mumme S, Middleton AD, Ciucci P, et al (2023)

Wherever I may roam-Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents.

Global change biology, 29(20):5788-5801.

Human activity and associated landscape modifications alter the movements of animals with consequences for populations and ecosystems worldwide. Species performing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement expression, using the standardized metric Intensity of Use, reflecting both the directionality and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topography, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strongest driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric-based movement expression across widely distributed populations of a deer genus, contributing to the understanding and prediction of animals' responses to human activity.

RevDate: 2023-09-19

Liao PJ, Lee CH, Wang SL, et al (2023)

Low-to-Moderate Arsenic Exposure and Urothelial Tract Cancers with a Long Latent Period of Follow-Up in an Arseniasis Area.

Journal of epidemiology and global health [Epub ahead of print].

BACKGROUND: Arsenic exposure can cause adverse health effects. The effects of long-term low-to-moderate exposure and methylations remain unclear.

OBJECTIVE: This study aims to examine the association between low-to-moderate arsenic exposure and urothelial tract cancers while considering the effects of methylation capacity.

METHODS: In this study, 5,811 participants were recruited from an arseniasis area in Taiwan for inorganic arsenic metabolite analysis. This follow-up study was conducted between August 1995 and December 2017. We identified 85 urothelial tract cancers in these participants, including 49 bladder and 36 upper urothelial tract cancer cases. A Cox proportional hazards model was employed.

RESULTS: The analyses revealed a significant association between concentrations of inorganic arsenic in water > 100 ug/L and bladder cancer occurrence, with a hazard ratio (HR) of 4.88 (95% CI 1.35-17.61). A monotonic trend was observed between concentrations of inorganic arsenic in water (from 0 to > 100 ug/L) and the incidence of urothelial tract cancer, including bladder cancer (p < 0.05) and upper urothelial tract cancers (p < 0.05). Participants with a lower primary methylation index or higher secondary methylation index had a prominent effect.

CONCLUSIONS: Rigorous regulations and active interventions should be considered for populations with susceptible characteristics.

RevDate: 2023-09-19
CmpDate: 2023-09-19

Lu YR, Fang CC, SP He (2023)

cnfishbase: A cyber Chinese fish database.

Zoological research, 44(5):950-953.

RevDate: 2023-09-19
CmpDate: 2023-09-19

Hoyer D, Bennett JS, Reddish J, et al (2023)

Navigating polycrisis: long-run socio-cultural factors shape response to changing climate.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 378(1889):20220402.

Climate variability and natural hazards like floods and earthquakes can act as environmental shocks or socioecological stressors leading to instability and suffering throughout human history. Yet, societies experience a wide range of outcomes when facing such challenges: some suffer from social unrest, civil violence or complete collapse; others prove more resilient and maintain key social functions. We currently lack a clear, generally agreed-upon conceptual framework and evidentiary base to explore what causes these divergent outcomes. Here, we discuss efforts to develop such a framework through the Crisis Database (CrisisDB) programme. We illustrate that the impact of environmental stressors is mediated through extant cultural, political and economic structures that evolve over extended timescales (decades to centuries). These structures can generate high resilience to major shocks, facilitate positive adaptation, or, alternatively, undermine collective action and lead to unrest, violence and even societal collapse. By exposing the ways that different societies have reacted to crises over their lifetime, this framework can help identify the factors and complex social-ecological interactions that either bolster or undermine resilience to contemporary climate shocks. This article is part of the theme issue 'Climate change adaptation needs a science of culture'.

RevDate: 2023-09-18
CmpDate: 2023-09-18

Cosentino F, Castiello G, L Maiorano (2023)

A dataset on African bats' functional traits.

Scientific data, 10(1):623.

Trait-based approaches are becoming extremely common in ecological modeling and the availability of traits databases is increasing. However, data availability is often biased towards particular regions and taxa, with many taxa (e.g., bats) often under-represented. Here, we present the AfroBaT dataset, a compilation of trait data on 320 African bat species containing 76,914 values for 86 traits focusing on morphology, reproduction, life-history, trophic ecology, and species distributions. All data were gathered from published literature following the ecological trait-data standard procedure. Missing data for both numerical and categorical traits were imputed with a machine learning approach including species phylogeny. Trophic ecology traits showed the highest coverage in the literature (72% of the species averaged over all traits), while reproductive traits the lowest. Our data imputation improved the coverage of AfroBaT especially for reproductive traits, going from 27% to 58% of the species covered. AfroBaT has a range of potential applications in macroecology and community ecology, and the availability of open-access data on African bats will enable collaboration and data-sharing among researchers.

RevDate: 2023-09-18
CmpDate: 2023-09-18

Đokić M, Manić M, Đorđević M, et al (2023)

Remote sensing and nuclear techniques for high-resolution mapping and quantification of gully erosion in the highly erodible area of the Malčanska River Basin, Eastern Serbia.

Environmental research, 235:116679.

Gully erosion leads to the formation of deep and wide channels that increase the risk of soil loss, flooding, and water pollution. In addition, this process reduces the productivity and viability of agricultural land and natural ecosystems. Preventing gully erosion is critical for maintaining ecological balance and preserving natural resources in certain areas. This paper presents a methodology integrating remote sensing and nuclear techniques to study gully erosion. The morphometric characterization of gullies using 360-degree camera photogrammetry was introduced as a new method in erosion research. This approach aims to investigate the suitability of unmanned aerial vehicle and terrestrial photogrammetry for modeling gullies, to study the variability of erosion processes in gullies at a small scale, and to compare the differences in erosion intensity between nearby gullies. The study's objectives include identifying the effective and economical method for gullies monitoring and providing a starting point for controlling and safeguarding gullies. Mainly erosion process was detected in the studied gullies, while deposition was identified at only 2 out of 39 sampling locations. The results showed an average soil redistribution rate of 16.2 t ha[-1] yr[-1] and coefficients of variation of 32%, 59%, and 91% for three investigated gullies. It was determined that aerial photogrammetry methods were not practical under the conditions prevailing in the study area. Highly detailed 3D models of the gullies were created using 360-degree photogrammetry. It was confirmed that the micro-relief obtained by photogrammetric modeling is an essential contribution to erosion research. The 360-degree camera photogrammetry serves as a reliable tool for analyzing the morphology of gullies and, in perspective, tracking changes in gully systems over time or monitoring the effectiveness of the applied protection measures.

RevDate: 2023-09-18
CmpDate: 2023-09-18

Xing Z, Chen S, Xu F, et al (2023)

Quantitative analysis of TCE biodegradation pathway in landfill cover utilizing continuous monitoring, droplet digital PCR and multi-omics sequencing technology.

Journal of environmental management, 344:118509.

The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 10[4]-6.78 ± 0.09 × 10[6] and 1.17 ± 0.78 × 10[3]-7.82 ± 0.07 × 10[5] copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.

RevDate: 2023-09-18
CmpDate: 2023-09-18

Liu J, Xu X, Zou C, et al (2023)

A Bayesian network-GIS probabilistic model for addressing human disturbance risk to ecological conservation redline areas.

Journal of environmental management, 344:118400.

Population growth and associated ecological space occupation are posing great risks to regional ecological security and social stability. In China, "Ecological Conservation Redline" (ECR) that prohibited urbanization and industrial construction has been proposed as a national policy to resolve spatial mismatches and management contradictions. However, unfriendly human disturbance activities (e.g., cultivation, mining, and infrastructure construction) still exist within the ECR, posing a great threat to ecological stability and safety. In this article, a Bayesian network (BN)-GIS probabilistic model is proposed to spatially and quantitatively address the human disturbance risk to the ECR at the regional scale. The Bayesian models integrate multiple human activities, ecological receptors of the ECR, and their exposure relationships for calculating the human disturbance risk. The case learning method geographic information systems (GIS) is then introduced to train BN models based on the spatial attribute of variables to evaluate the spatial distribution and correlation of risks. This approach was applied to the human disturbance risk assessment for the ECR that was delineated in 2018 in Jiangsu Province, China. The results indicated that most of the ECRs were at a low or medium human disturbance risk level, while some drinking water sources and forest parks in Lianyungang City possessed the highest risk. The sensitivity analysis result showed the ECR vulnerability, especially for cropland, that contributed most to the human disturbance risk. This spatially probabilistic method can not only enhance model's prediction precision, but also help decision-makers to determine how to establish priorities for policy design and conservation interventions. Overall, it presents a foundation for later ECR adjustments as well as for human disturbance risk supervision and management at the regional scale.

RevDate: 2023-09-15

Reid MC, Mittler JE, Murphy JT, et al (2023)

Evolution of HIV virulence in response to disease-modifying vaccines: A modeling study.

Vaccine pii:S0264-410X(23)01027-7 [Epub ahead of print].

Pathogens face a tradeoff with respect to virulence; while more virulent strains often have higher per-contact transmission rates, they are also more likely to kill their hosts earlier. Because virulence is a heritable trait, there is concern that a disease-modifying vaccine, which reduces the disease severity of an infected vaccinee without changing the underlying pathogen genotype, may result in the evolution of higher pathogen virulence. We explored the potential for such virulence evolution with a disease-modifying HIV-1 vaccine in an agent-based stochastic epidemic model of HIV in United States men who have sex with men (MSM). In the model, vaccinated agents received no protection against infection, but experienced lower viral loads and slower disease progression. We compared the genotypic set point viral load (SPVL), a measure of HIV virulence, in populations given vaccines that varied in the degree of SPVL reduction they induce. Sensitivity analyses were conducted under varying vaccine coverage scenarios. With continual vaccination rollout under ideal circumstances of 90 % coverage over thirty years, the genotypic SPVL of vaccinated individuals evolved to become greater than the genotypic SPVL of unvaccinated individuals. This virulence evolution in turn diminished the public health benefit of the vaccine, and in some scenarios resulted in an accelerated epidemic. These findings demonstrate the complexity of viral evolution and have important implications for the design and development of HIV vaccines.

RevDate: 2023-09-15

Faria AL, Latorre J, Silva Cameirão M, et al (2023)

Ecologically valid virtual reality-based technologies for assessment and rehabilitation of acquired brain injury: a systematic review.

Frontiers in psychology, 14:1233346.

PURPOSE: A systematic review was conducted to examine the state of the literature regarding using ecologically valid virtual environments and related technologies to assess and rehabilitate people with Acquired Brain Injury (ABI).

MATERIALS AND METHODS: A literature search was performed following the PRISMA guidelines using PubMed, Web of Science, ACM and IEEE databases. The focus was on assessment and intervention studies using ecologically valid virtual environments (VE). All studies were included if they involved individuals with ABI and simulated environments of the real world or Activities of Daily Living (ADL).

RESULTS: Seventy out of 363 studies were included in this review and grouped and analyzed according to the nature of its simulation, prefacing a total of 12 kitchens, 11 supermarkets, 10 shopping malls, 16 streets, 11 cities, and 10 other everyday life scenarios. These VE were mostly presented on computer screens, HMD's and laptops and patients interacted with them primarily via mouse, keyboard, and joystick. Twenty-five out of 70 studies had a non-experimental design.

CONCLUSION: Evidence about the clinical impact of ecologically valid VE is still modest, and further research with more extensive samples is needed. It is important to standardize neuropsychological and motor outcome measures to strengthen conclusions between studies.

identifier CRD42022301560, https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=301560.

RevDate: 2023-09-15
CmpDate: 2023-09-15

Williams JW, Spanbauer TL, Heintzman PD, et al (2023)

Strengthening global-change science by integrating aeDNA with paleoecoinformatics.

Trends in ecology & evolution, 38(10):946-960.

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

RevDate: 2023-09-15
CmpDate: 2023-09-15

de Koning K, Broekhuijsen J, Kühn I, et al (2023)

Digital twins: dynamic model-data fusion for ecology.

Trends in ecology & evolution, 38(10):916-926.

Digital twins (DTs) are an emerging phenomenon in the public and private sectors as a new tool to monitor and understand systems and processes. DTs have the potential to change the status quo in ecology as part of its digital transformation. However, it is important to avoid misguided developments by managing expectations about DTs. We stress that DTs are not just big models of everything, containing big data and machine learning. Rather, the strength of DTs is in combining data, models, and domain knowledge, and their continuous alignment with the real world. We suggest that researchers and stakeholders exercise caution in DT development, keeping in mind that many of the strengths and challenges of computational modelling in ecology also apply to DTs.

RevDate: 2023-09-14

Mora-Rubio A, Bravo-Ortíz MA, Quiñones Arredondo S, et al (2023)

Classification of Alzheimer's disease stages from magnetic resonance images using deep learning.

PeerJ. Computer science, 9:e1490 pii:cs-1490.

Alzheimer's disease (AD) is a progressive type of dementia characterized by loss of memory and other cognitive abilities, including speech. Since AD is a progressive disease, detection in the early stages is essential for the appropriate care of the patient throughout its development, going from asymptomatic to a stage known as mild cognitive impairment (MCI), and then progressing to dementia and severe dementia; is worth mentioning that everyone suffers from cognitive impairment to some degree as we age, but the relevant task here is to identify which people are most likely to develop AD. Along with cognitive tests, evaluation of the brain morphology is the primary tool for AD diagnosis, where atrophy and loss of volume of the frontotemporal lobe are common features in patients who suffer from the disease. Regarding medical imaging techniques, magnetic resonance imaging (MRI) scans are one of the methods used by specialists to assess brain morphology. Recently, with the rise of deep learning (DL) and its successful implementation in medical imaging applications, it is of growing interest in the research community to develop computer-aided diagnosis systems that can help physicians to detect this disease, especially in the early stages where macroscopic changes are not so easily identified. This article presents a DL-based approach to classifying MRI scans in the different stages of AD, using a curated set of images from Alzheimer's Disease Neuroimaging Initiative and Open Access Series of Imaging Studies databases. Our methodology involves image pre-processing using FreeSurfer, spatial data-augmentation operations, such as rotation, flip, and random zoom during training, and state-of-the-art 3D convolutional neural networks such as EfficientNet, DenseNet, and a custom siamese network, as well as the relatively new approach of vision transformer architecture. With this approach, the best detection percentage among all four architectures was around 89% for AD vs. Control, 80% for Late MCI vs. Control, 66% for MCI vs. Control, and 67% for Early MCI vs. Control.

RevDate: 2023-09-14
CmpDate: 2023-09-14

Sharaf A, Ndiribe CC, Omotoriogun TC, et al (2023)

Bridging the gap in African biodiversity genomics and bioinformatics.

Nature biotechnology, 41(9):1348-1354.

RevDate: 2023-09-13

Paudel S, Mueller K, Ovando-Montejo G, et al (2023)

A dataset cataloging product-specific human appropriation of net primary production (HANPP) in US counties.

Data in brief, 50:109530.

This paper describes the dataset associated with the paper "Product-Specific Human Appropriation of Net Primary Production (HANPP) in US Counties" (Paudel et al., 2023). This dataset comprises human appropriation of net primary production (HANPP) values for 3101 counties in the conterminous US for the years 1997, 2002, 2007, and 2012. For this dataset, HANPP is the carbon content of specific crop, timber, and livestock grazing products appropriated by humans in a county in a year. To calculate HANPP, raw agricultural data were downloaded from public databases such as USDA-National Agricultural Statistics Service Quick Stats and Cropland Data Layer, US Forest Service Timber Product Output, and NPP data from MODIS. These data were processed in Microsoft Excel using stoichiometry derived from established scientific literature. HANPP was partitioned by year, county, product, used and unused and above- and below-ground. This complete dataset is published in Mendeley Data and the methods used to compile them are included to make our research well documented, reproducible, and useful for future studies.

RevDate: 2023-09-13
CmpDate: 2023-09-13

Chen L, Qin L, Zhang Y, et al (2023)

Insights from multi-omics integration into seed germination of Taxus chinensis var mairei.

Communications biology, 6(1):931.

The transition from deep dormancy to seed germination is essential for the life cycle of plants, but how this process occurs in the gymnosperm Chinese yew (Taxus chinensis var mairei), the natural source of the anticancer drug paclitaxel, remains unclear. Herein, we analyse the transcriptome, proteome, spatial metabolome, and spatial lipidome of the Chinese yew and present the multi-omics profiles of dormant and germinating seeds. Our results show that abscisic acid and gibberellic acid 12 homoeostasis is closely associated with gene transcription and protein translation, and the balance between these phytohormones thereby determines if seeds remain dormant or germinate. We find that an energy supply of carbohydrates from glycolysis and the TCA cycle feed into the pentose phosphate pathway during seed germination, and energy supplied from lipids are mainly derived from the lipolysis of triacylglycerols. Using mass spectrometry imaging, we demonstrate that the spatial distribution of plant hormones and phospholipids has a remarkable influence on embryo development. We also provide an atlas of the spatial distribution of paclitaxel C in Chinese yew seeds for the first time. The data from this study enable exploration of the germination mechanism of Chinese yew seeds across several omics levels.

RevDate: 2023-09-12
CmpDate: 2023-09-12

Jiang BY, Zhang YL, Li S, et al (2023)

Spatio-temporal dynamics and sensitive distance of nighttime light environment in Pearl River Delta Protected Areas, China.

Ying yong sheng tai xue bao = The journal of applied ecology, 34(6):1601-1609.

Protected areas (PAs) are important barriers to ensure the ecological security of territory. Light pollution is a threat to PAs, which is particularly obvious in the urban agglomeration environment. We used multi-source big data (satellite remote sensing light data, land cover types and points of interest) to quantitatively analyze the temporal and spatial dynamics of nighttime light in the PAs of the Pearl River Delta (PRD) urban agglomeration from 2000 to 2018, the correlation between the night light environment within the PAs and human activity intensity outside, as well as the sensitive distance of the PAs to artificial light interference. The results showed that the total value of nighttime light data of PAs in the PRD increased from 71107 nanoW·cm[-2]·sr[-1] to 127682 nanoW·cm[-2]·sr[-1] from 2000 to 2018, the mean value per pixel increased from 15.3 nanoW·cm[-2]·sr[-1] to 23.7 nanoW·cm[-2]·sr[-1], and the lighted ratio increased from 73.3% to 86.4%, indicating that the nighttime light environment of PAs in the region were facing cumulative deterioration risks and serious challenges. The nighttime light intensity of the PAs in the core area of the PRD was much higher than that in the peripheral areas such as Zhaoqing and Huizhou, whereas the expansion degree of the PAs in the peripheral areas was higher than that in the core area. The nighttime light environment inside the PAs was positively correlated with the intensity of human activities around it. The most sensitive distance of the PAs to the artificial light interference around it was 10 km, and the interference degree tended to be stable after 30 km. We proposed that 0-10 km area outside the boundary of the PAs should be the light control core zone and 10-20 km area as the control buffer zone.

RevDate: 2023-09-12
CmpDate: 2023-09-12

Tokatlı C, Uğurluoğlu A, S Muhammad (2023)

Ecotoxicological evaluation of organic contamination in the world's two significant gateways to the Black Sea using GIS techniques: Turkish Straits.

Marine pollution bulletin, 194(Pt A):115405.

This study was carried out to determine the spatial-temporal distributions of limnological parameters of Çanakkale Strait (ÇS) and İstanbul Strait (İS), Turkiye. Fluvial (n = 11) and lacustrine (n = 4) habitats water samples were collected in the dry and rainy seasons of 2022-2023. Among limnological parameters, the highest mean electrical conductivity values of 6063 μS/cm were noted in the İS basin during the rainy season and the lowest was 0.04 mg/L for nitrite in the ÇS basin. Generally, the levels of organic contaminants and ecological risk indices were as follows: rivers of İS > rivers of ÇS > Alibey Dam Lake (İS) > Atikhisar Dam Lake (ÇS). The highest non-carcinogenic health risks of 0.88 were noted for children in the ÇS basin during the dry season and the lowest of <0.01 in Atikhisar Dam Lake during the rainy season. Multivariate statistical techniques were applied to data to categorize investigated ecosystems and sources apportionment of contaminants and geospatial distribution.

RevDate: 2023-09-11

Mullowney MW, Duncan KR, Elsayed SS, et al (2023)

Artificial intelligence for natural product drug discovery.

Nature reviews. Drug discovery [Epub ahead of print].

Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.

RevDate: 2023-09-11

Fan R, Liu Y, Bin Y, et al (2023)

Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.

Frontiers in microbiology, 14:1222844.

Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.

RevDate: 2023-09-11
CmpDate: 2023-09-11

Wu X, Zhang X, Chen X, et al (2023)

The effects of polylactic acid bioplastic exposure on midgut microbiota and metabolite profiles in silkworm (Bombyx mori): An integrated multi-omics analysis.

Environmental pollution (Barking, Essex : 1987), 334:122210.

Polylactic acid (PLA) is a highly common biodegradable plastic and a potential threat to health and the environment. However, limited data are available on the effects of PLA exposure in the silkworm (Bombyx mori), a model organism used in toxicity studies. In this study, silkworms with or without PLA exposure (P1: 1 mg/L, P5: 5 mg/L, P25: 25 mg/L, and P0: 0 mg/L) for the entire 5th instar period were used to investigate the impact of PLA exposure on midgut morphology, larvae growth, and survival. Mitochondrial damage was observed in the P5 and P25 groups. The weights of the P25 posterior silk gland (5th day in the 5th instar), mature larvae and pupae were all significantly lower than those of the controls (P < 0.05). Dead worm cocoon rates and larva-pupa to 5th instar larvae ratios showed a positive and negative dose-dependent manner with respect to PLA concentrations, respectively. Additionally, reactive oxygen species levels and superoxide dismutase activity of the P25 midgut were significantly higher and lower when compared with controls, respectively (P < 0.05). The molecular mechanisms underlying the effects of PLA and associated physiological responses were also investigated. In the midgut metabolome, 127 significantly different metabolites (variable importance projection >1 and P < 0.05) were identified between the P0 and P25 groups and were mainly enriched for amino acid metabolism and energy supply pathways. The 16 S rDNA data showed that PLA altered microbial richness and structural composition. Microbiota, classified into 34 genera and 63 species, were significantly altered after 25 mg/L PLA exposure (P < 0.05). Spearman's correlation results showed that Bifidobacterium catenulatum and Schaalia odontolytica played potentially vital roles during exposure, as they demonstrated stronger correlations with the significantly different metabolites than other bacterial species. In sum, PLA induced toxic effects on silkworms, especially on energy- and protein-relevant metabolism, but at high concentrations (25 mg/L). This prospective mechanistic investigation on the effects of PLA on larval toxicity provides novel insight regarding the ecological risks of biodegradable plastics in the environment.

RevDate: 2023-09-09

Milicevic O, Loncar A, Abazovic D, et al (2023)

Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization.

International journal of molecular sciences, 24(17): pii:ijms241713125.

Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly.

RevDate: 2023-09-08

Sukur N, Milošević N, Pogrmic-Majkic K, et al (2023)

Predicting chemicals' toxicity pathway of female reproductive disorders using AOP7 and deep neural networks.

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association pii:S0278-6915(23)00415-5 [Epub ahead of print].

Experimental evidence shows that certain chemicals, particularly endocrine disrupting chemicals, may negatively affect the female reproductive system, thereby lowering women's fertility. However, humans are constantly exposed to a number of different chemicals with limited or no experimental data regarding their effect and the mechanism of action in the female reproductive system. To predict chemical hazards to the female reproductive system, we used a previously defined adverse outcome pathway (AOP) that links activation of the peroxisome proliferator-activated receptor γ to the reproductive toxicity in adult females (AOP7) and the Convolutional Deep Neural Network models that produce meaningful predictions when trained on a significant amount of data. The models trained using CompTox assays with intended molecular and biological targets corresponding to AOP7 achieved high performance (over 90% validation accuracy). The integration of AOP7 and Deep Neural Network identified chemicals that could negatively affect female reproduction through the mechanism described in AOP7. We provide a solution to quickly analyze the data and produce machine learning models to identify potentially active chemicals in the female reproductive system. Although we focused on the female reproductive system, this approach could be valid for a number of other chemicals and AOPs if the right data exist.

RevDate: 2023-09-08

Xie X, Wu TC, Cao BL, et al (2023)

Virtual ecological technology: Concepts, systems, and application perspectives.

Ying yong sheng tai xue bao = The journal of applied ecology, 34(8):2297-2304.

Virtual ecological technology is a new technology that builds the foundation of a digital ecological system, simulates the process of ecological evolution, and establishes a global knowledge analysis system based on a unified spatio-temporal benchmark. It is a new direction for the interdisciplinary integration and development of eco-logy, geographic information science, computer science and other subjects towards modernization, informatization, and intelligence. Research, development, and application of virtual ecological technology is of great significance for the development of ecology as a discipline, ecosystem management, and regional sustainable development. Curren-tly, research on virtual ecological technology is still in its infancy and lacks a complete and clearly defined framework, making it difficult to support systematic iterative development and scientific analysis. In this paper, starting from the main theories and objectives of modern ecology, we summarized the main contents and technical requirements of virtual ecological construction, and proposed a key technical system of virtual ecology that integrated vir-tual geography and digital twin technology. From the perspective of application scenarios, we analyzed the application capabilities of virtual ecological technology in air pollution and energy analysis. Finally, we summarized the deve-lopment potential of virtual ecological technology in the digital construction of the ecological environment, intelligent computing, and realistic expression of different levels of ecological space resources transformation under the background of new generation of information technology, both at the local computing point breakthrough and the global technology point fusion aspects. This would enrich and advance the technical capabilities that support China's ecological space resource transformation.

RevDate: 2023-09-08

Tóth F, Zsuga K, Kerepeczki É, et al (2023)

Discordant spatiotemporal dynamics of functional and phylogenetic diversity of rotiferan communities exposed to aquaculture effluent.

Ecology and evolution, 13(9):e10503 pii:ECE310503.

The growth of the human population brought about the global intensification of aquacultural production, and aquaculture became the fastest growing animal husbandry sector. Effluent from aquaculture is an anthropogenic environmental burden, containing organic matter, nutrients and suspended solids that affect water quality especially in the water bodies of high biodiversity and conservation value. Water quality assessment often relies on bioindicators, analysing changes in taxonomic diversity of various freshwater organismal groups. Stepping beyond taxon diversity, we used functional and phylogenetic diversities of rotifers to identify factors affecting their community organization in response to an aquaculture effluent gradient in the largest oxbow lake in the Carpathian Basin, Hungary. Sampling was carried out three times per season at five points along a 3.5 km section of the oxbow lake, including the point of effluent inflow. We used eight traits to evaluate functional diversity: body size, trophi type, feeding mode, protection type, body wall type, corona type, habitat preference and tolerance level. Functional and phylogenetic distances among the 24 species identified indicated trait conservatism. Rotiferan diversity increased with increasing distance from the point of influx in spring and summer. Among the factors affecting community organization in spring and summer, we find examples of environmental filtering, while in autumn the role of biotic interaction is more frequent. Under nutrient-rich conditions in spring and summer, organisms belonging to the same functional group were dominant, whereas under oligotrophic conditions, more diverse but less abundant groups were present. Considering functional and phylogenetic traits allowed us to identify organising forces of rotifer communities in the largest oxbow lake of the Hungarian Lowland.

RevDate: 2023-09-08

Moran ME, Aparecido LMT, Koepke DF, et al (2023)

Limits of thermal and hydrological tolerance in a foundation tree species (Populus fremontii) in the desert southwestern United States.

The New phytologist [Epub ahead of print].

Populus fremontii is among the most dominant, and ecologically important riparian tree species in the western United States and can thrive in hyper-arid riparian corridors. Yet, P. fremontii forests have rapidly declined over the last decade, particularly in places where temperatures sometimes exceed 50°C. We evaluated high temperature tolerance of leaf metabolism, leaf thermoregulation, and leaf hydraulic function in eight P. fremontii populations spanning a 5.3°C mean annual temperature gradient in a well-watered common garden, and at source locations throughout the lower Colorado River Basin. Two major results emerged. First, despite having an exceptionally high Tcrit (the temperature at which Photosystem II is disrupted) relative to other tree taxa, recent heat waves exceeded Tcrit , requiring evaporative leaf cooling to maintain leaf-to-air thermal safety margins. Second, in midsummer, genotypes from the warmest locations maintained lower midday leaf temperatures, a higher midday stomatal conductance, and maintained turgor pressure at lower water potentials than genotypes from more temperate locations. Taken together, results suggest that under well-watered conditions, P. fremontii can regulate leaf temperature below Tcrit along the warm edge of its distribution. Nevertheless, reduced Colorado River flows threaten to lower water tables below levels needed for evaporative cooling during episodic heat waves.

RevDate: 2023-09-07

Green Ii DA (2023)

Tracking technologies: advances driving new insights into monarch migration.

Current opinion in insect science pii:S2214-5745(23)00108-6 [Epub ahead of print].

Understanding the rules of how monarch butterflies complete their annual North American migration will be clarified by studying them within a movement ecology framework. Insect movement ecology is growing at a rapid pace due to the development of novel monitoring systems that allow ever smaller animals to be tracked at higher spatiotemporal resolution for longer periods of time. New innovations in tracking hardware and associated software, including miniaturization, energy autonomy, data management, and wireless communication, are reducing the size and increasing the capability of next generation tracking technologies, bringing the goal of tracking monarchs over their entire migration closer within reach. These tools are beginning to be leveraged to provide insight into different aspects of monarch biology and ecology, and to contribute to a growing capacity to understand insect movement ecology more broadly and its impact on human life.

RevDate: 2023-09-07

Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the Feathered Gothic, Tholera decimalis (Poda, 1761).

Wellcome open research, 8:200.

We present a genome assembly from an individual female Tholera decimalis (the Feathered Gothic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,334.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,771 protein coding genes.

RevDate: 2023-09-07

Asaaga FA, Sriram A, Chanda MM, et al (2023)

'It doesn't happen how you think, it is very complex!' Reconciling stakeholder priorities, evidence, and processes for zoonoses prioritisation in India.

Frontiers in public health, 11:1228950.

BACKGROUND: Why do some zoonotic diseases receive priority from health policy decision-makers and planners whereas others receive little attention? By leveraging Shiffman and Smith's political prioritisation framework, our paper advances a political economy of disease prioritisation focusing on four key components: the strength of the actors involved in the prioritisation, the power of the ideas they use to portray the issue, the political contexts in which they operate, and the characteristics of the issue itself (e.g., overall burdens, severity, cost-effective interventions). These components afford a nuanced characterisation of how zoonotic diseases are prioritised for intervention and highlight the associated knowledge gaps affecting prioritisation outcomes. We apply this framework to the case of zoonoses management in India, specifically to identify the factors that shape disease prioritisation decision-making and outcomes.

METHODS: We conducted 26 semi-structured interviews with national, state and district level health policymakers, disease managers and technical experts involved in disease surveillance and control in India.

RESULTS: Our results show pluralistic interpretation of risks, exemplified by a disconnect between state and district level actors on priority diseases. The main factors identified as shaping prioritisation outcomes were related to the nature of the zoonoses problem (the complexity of the zoonotic disease, insufficient awareness and lack of evidence on disease burdens and impacts) as well as political, social, cultural and institutional environments (isolated departmental priorities, limited institutional authority, opaque funding mechanisms), and challenges in organisation leadership for cross-sectoral engagement.

CONCLUSION: The findings highlight a compartmentalised regulatory system for zoonoses where political, social, cultural, and media factors can influence disease management and prioritisation. A major policy window is the institutionalisation of One Health to increase the political priority for strengthening cross-sectoral engagement to address several challenges, including the creation of effective institutions to reconcile stakeholder priorities and prioritisation processes.

RevDate: 2023-09-07
CmpDate: 2023-09-07

Zhylkybekova A, Turlayev A, Grjibovski AM, et al (2023)

Measures to support informal care for the older adults in Kazakhstan: a review of the current status.

Frontiers in public health, 11:1247684.

The demand for informal caregivers to support the older adults has grown worldwide in recent decades. However, informal caregivers themselves require support. This article aims to examine existing support measures for caregivers of the older adults in the Republic of Kazakhstan. Relevant articles and grey literature were identified through manual searches on Google and Google Scholar, as well as electronic searches using indexed databases like PubMed, Web of Science, and Scopus. Moreover, the reference lists of identified sources and government ministry websites were meticulously scrutinized. This review highlights the scarcity of research on caregiver support measures in Kazakhstan, supported by the lack of peer-reviewed articles on this subject. A comprehensive analysis of the literature shows that in Kazakhstan's legislative framework, "caregivers" exclusively refers to individuals providing care for a first-degree disability. The responsibility of caring for older adults parents lies with able-bodied children. However, there is a lack of registration and assessment procedures to evaluate the burden and quality of life of caregivers. As a result, the medical and social support provided to caregivers is standardized, failing to adequately address their unique needs and requirements. The analysis of current support measures for informal caregivers highlights the need to develop support mechanisms and recognize individuals providing informal care as key figures in the long-term care system.

RevDate: 2023-09-06

Lu AT, Fei Z, Haghani A, et al (2023)

Author Correction: Universal DNA methylation age across mammalian tissues.

RevDate: 2023-09-06

Pinho-Gomes AC, Roaf E, Fuller G, et al (2023)

Air pollution and climate change.

The Lancet. Planetary health, 7(9):e727-e728.

RevDate: 2023-09-06
CmpDate: 2023-09-06

Li Y, Niu Z, Zhu M, et al (2023)

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.

Communications biology, 6(1):906.

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

RevDate: 2023-09-04

Bayer JM, Scully RA, Dlabola EK, et al (2023)

Sharing FAIR monitoring program data improves discoverability and reuse.

Environmental monitoring and assessment, 195(10):1141.

Data resulting from environmental monitoring programs are valuable assets for natural resource managers, decision-makers, and researchers. These data are often collected to inform specific reporting needs or decisions with a specific timeframe. While program-oriented data and related publications are effective for meeting program goals, sharing well-documented data and metadata allows users to research aspects outside initial program intentions. As part of an effort to integrate data from four long-term large-scale US aquatic monitoring programs, we evaluated the original datasets against the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and offer recommendations and lessons learned. Differences in data governance across these programs resulted in considerable effort to access and reuse the original datasets. Requirements, guidance, and resources available to support data publishing and documentation are inconsistent across agencies and monitoring programs, resulting in various data formats and storage locations that are not easily found, accessed, or reused. Making monitoring data FAIR will reduce barriers to data discovery and reuse. Programs are continuously striving to improve data management, data products, and metadata; however, provision of related tools, consistent guidelines and standards, and more resources to do this work is needed. Given the value of these data and the significant effort required to access and reuse them, actions and steps intended on improving data documentation and accessibility are described.

RevDate: 2023-09-04

Boyes D, Sims I, Holland PWH, et al (2023)

The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804).

Wellcome open research, 8:298.

We present a genome assembly from an individual female Thumatha senex (the Round-winged Muslin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 810.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.

RevDate: 2023-09-04

Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the Light Brocade, Lacanobia w-latinum (Hufnagel, 1766).

Wellcome open research, 8:299.

We present a genome assembly from an individual male Lacanobia w-latinum (the Light Brocade; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 903.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,592 protein coding genes.

RevDate: 2023-09-04

Günther F, Wong D, Elison-Davies S, et al (2023)

Identifying factors associated with user retention and outcomes of a digital intervention for substance use disorder: a retrospective analysis of real-world data.

JAMIA open, 6(3):ooad072.

OBJECTIVES: Successful delivery of digital health interventions is affected by multiple real-world factors. These factors may be identified in routinely collected, ecologically valid data from these interventions. We propose ideas for exploring these data, focusing on interventions targeting complex, comorbid conditions.

MATERIALS AND METHODS: This study retrospectively explores pre-post data collected between 2016 and 2019 from users of digital cognitive behavioral therapy (CBT)-containing psychoeducation and practical exercises-for substance use disorder (SUD) at UK addiction services. To identify factors associated with heterogenous user responses to the technology, we employed multivariable and multivariate regressions and random forest models of user-reported questionnaire data.

RESULTS: The dataset contained information from 14 078 individuals of which 12 529 reported complete data at baseline and 2925 did so again after engagement with the CBT. Ninety-three percent screened positive for dependence on 1 of 43 substances at baseline, and 73% screened positive for anxiety or depression. Despite pre-post improvements independent of user sociodemographics, women reported more frequent and persistent symptoms of SUD, anxiety, and depression. Retention-minimum 2 use events recorded-was associated more with deployment environment than user characteristics. Prediction accuracy of post-engagement outcomes was acceptable (Area Under Curve [AUC]: 0.74-0.79), depending non-trivially on user characteristics.

DISCUSSION: Traditionally, performance of digital health interventions is determined in controlled trials. Our analysis showcases multivariate models with which real-world data from these interventions can be explored and sources of user heterogeneity in retention and symptom reduction uncovered.

CONCLUSION: Real-world data from digital health interventions contain information on natural user-technology interactions which could enrich results from controlled trials.

RevDate: 2023-09-04
CmpDate: 2023-09-04

Bezerra ALL, de Almeida PRB, Reis RK, et al (2023)

Human immunodeficiency virus epidemic scenery among brazilian women: a spatial analysis study.

BMC women's health, 23(1):463.

BACKGROUND: Approximately 37.7 million people worldwide are infected with human immunodeficiency virus (HIV). Although HIV detection among women, they still representing 53% of population living with the virus. Spatial analysis techniques are powerful tools for combating HIV allowing the association of the phenomenon with socioeconomic and political factors. Therefore, the main goal of this study was to spatially analyze HIV prevalence among Brazilian women from 2007 to 2020.

METHODS: ecological study was conducted using secondary databases of the Notifiable Diseases Information System (SINAN) for HIV and Acquired Immunodeficiency Syndrom (AIDS) in Brazilian women 15 years old and over. Age-adjusted HIV/AIDS incidence rates were analyzed using spatial distribution, autocorrelation, and spatiotemporal risk analysis techniques.

RESULTS: During the study period, 119,890 cases of HIV/AIDS were reported among Brazilian women. The southeastern region had a higher age-adjusted HIV/AIDS incidence than other Brazilian regions. Hotspot HIV/AIDS incidence rates decreased in all Brazil. Piauí, Paraná, and Minas Gerais were the only states with an increased number of cold spots. Previous spatiotemporal risk zones were observed in the states of São Paulo, Rio Grande do Sul, and Rio de Janeiro. Belém was a risk zone with a later spatiotemporal risk.

CONCLUSIONS: The efficiency of public policies fighting HIV has not been uniform among municipalities, although HIV/AIDS cases have decreased among Brazilian women. The social determinants of health in each municipality should be considered when local health authorities implement policies. Women empowerment should be promoted, and access to preventive, diagnostic, and treatment healthcare places should be expanded and guaranteed.

RevDate: 2023-09-02

Schulz G, van Beusekom JEE, Jacob J, et al (2023)

Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.

The Science of the total environment pii:S0048-9697(23)05365-2 [Epub ahead of print].

Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.

RevDate: 2023-09-01

LeBaron V, Homdee N, Ogunjirin E, et al (2023)

Describing and visualizing the patient and caregiver experience of cancer pain in the home context using ecological momentary assessments.

Digital health, 9:20552076231194936.

BACKGROUND: Pain continues to be a difficult and pervasive problem for patients with cancer, and those who care for them. Remote health monitoring systems (RHMS), such as the Behavioral and Environmental Sensing and Intervention for Cancer (BESI-C), can utilize Ecological Momentary Assessments (EMAs) to provide a more holistic understanding of the patient and family experience of cancer pain within the home context.

METHODS: Participants used the BESI-C system for 2-weeks which collected data via EMAs deployed on wearable devices (smartwatches) worn by both patients with cancer and their primary family caregiver. We developed three unique EMA schemas that allowed patients and caregivers to describe patient pain events and perceived impact on quality of life from their own perspective. EMA data were analyzed to provide a descriptive summary of pain events and explore different types of data visualizations.

RESULTS: Data were collected from five (n = 5) patient-caregiver dyads (total 10 individual participants, 5 patients, 5 caregivers). A total of 283 user-initiated pain event EMAs were recorded (198 by patients; 85 by caregivers) over all 5 deployments with an average severity score of 5.4/10 for patients and 4.6/10 for caregivers' assessments of patient pain. Average self-reported overall distress and pain interference levels (1 = least distress; 4 = most distress) were higher for caregivers (x¯ 3.02, x¯2.60,respectively) compared to patients (x¯ 2.82, x¯ 2.25, respectively) while perceived burden of partner distress was higher for patients (i.e., patients perceived caregivers to be more distressed, x¯ 3.21, than caregivers perceived patients to be distressed, x¯2.55). Data visualizations were created using time wheels, bubble charts, box plots and line graphs to graphically represent EMA findings.

CONCLUSION: Collecting data via EMAs is a viable RHMS strategy to capture longitudinal cancer pain event data from patients and caregivers that can inform personalized pain management and distress-alleviating interventions.

RevDate: 2023-09-01

Papadopoulos NG, Akdis C, Akdis M, et al (2023)

Addressing adverse synergies between chemical and biological pollutants at schools-The 'SynAir-G' hypothesis.

Allergy [Epub ahead of print].

While the number and types of indoor air pollutants is rising, much is suspected but little is known about the impact of their potentially synergistic interactions, upon human health. Gases, particulate matter, organic compounds but also allergens and viruses, fall within the 'pollutant' definition. Distinct populations, such as children and allergy and asthma sufferers are highly susceptible, while a low socioeconomic background is a further susceptibility factor; however, no specific guidance is available. We spend most of our time indoors; for children, the school environment is of paramount importance and potentially amenable to intervention. The interactions between some pollutant classes have been studied. However, a lot is missing with respect to understanding interactions between specific pollutants of different classes in terms of concentrations, timing and sequence, to improve targeting and upgrade standards. SynAir-G is a European Commission-funded project aiming to reveal and quantify synergistic interactions between different pollutants affecting health, from mechanisms to real life, focusing on the school setting. It will develop a comprehensive and responsive multipollutant monitoring system, advance environmentally friendly interventions, and disseminate the generated knowledge to relevant stakeholders in accessible and actionable formats. The aim of this article it to put forward the SynAir-G hypothesis, and describe its background and objectives.

RevDate: 2023-08-31

Fang R, Chen T, Han Z, et al (2023)

From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems.

Journal of hazardous materials, 460:132407 pii:S0304-3894(23)01690-4 [Epub ahead of print].

Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, β = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (10[4] ∼ 10[8] copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.

RevDate: 2023-08-31
CmpDate: 2023-08-31

Bosch M, López-Pujol J, Blanché C, et al (2023)

DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae): Structure, Exploitation, and Recent Development.

Methods in molecular biology (Clifton, N.J.), 2703:173-192.

An updated (and now online) version of the former chromosome database of tribe Delphinieae (Ranunculaceae) is presented (http://www.delphinieae.online). This new version is the result of an accurate, exhaustive literature and Internet research, by adding chromosome counts and all related karyological information for the genera Aconitum L., Gymnaconitum (Stapf) Wei Wang & Z. D. Chen, Delphinium L. (including Staphisagria Spach), Consolida (DC.) S. F. Gray and Aconitella Spach, accumulated during the approximately last 25 years and that comprise worldwide published data from 1889 to 2021. The Delphinieae Chromosome Database (DCDB) (last updated 31.12.2021) contains a total number of 3435 reports belonging to 425 species (503 taxa), which represents 48.6% of the total species of the tribe (an increase of c. 213% and 32% compared with the 1097 and 2598 reports gathered in the 1999 and 2016 versions, respectively). This increase is due both to chromosome research progress and to improved information capture system. Moreover, recent taxonomic advances, synonymization, and new phylogenetic criteria have also been considered.The DCDB database provides the most complete currently available information on published chromosome numbers, ploidy-level estimates, and other karyological data of Delphinieae, and it is aimed to be useful for the building of cytotaxonomical databases and for specific research ongoing projects of systematics and evolution of Ranunculaceae. DCDB includes two levels of taxonomic resolution, published name (original and standardized form) and database accepted name (based on either Plants of the World - POWO or expert specialist criteria), as well as the geographic origin of each count (country, locality, geographic coordinates, elevation, or ecological information when reported in the original publication), associated karyological data if originally provided (studied material type, graphic information, chromosome measures and formulas, satellites, B chromosomes, other cytogenetic techniques used, etc.), voucher information and reference (with DOI and other links to access the original document). An effort to check the original sources and to search in grey literature allowed to indicate the counts that appear to be registered twice.

RevDate: 2023-08-31
CmpDate: 2023-08-31

Henniges MC, Johnston E, Pellicer J, et al (2023)

The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data.

Methods in molecular biology (Clifton, N.J.), 2703:111-122.

Genome size is a plant character with far-reaching implications, ranging from impacts on the financial and computing feasibility of sequencing and assembling genomes all the way to influencing the very ecology and evolution of species. The increasing recognition of the role of genome size in plant science has led to a rising demand for comprehensive and easily accessible sources of genome size data. The Plant DNA C-values database has established itself as a trusted and widely used central hub for users needing to access available plant genome size data, complemented with related cytogenetic (ploidy level) and karyological (chromosome number) information where available. Since its inception in 2001, the database has undergone six major updates to incorporate newly available genome size information, leading to the most recent release (Release 7.1), which comprises data for 12,273 species across all the major land plant and some algal lineages. Here we describe how to use the database efficiently, making use of its different query and filtering settings.

RevDate: 2023-08-31
CmpDate: 2023-08-31

Zhao W, Zhang P, Chen D, et al (2023)

Data mining from process monitoring of typical polluting enterprise.

Environmental monitoring and assessment, 195(9):1109.

With the increasing volume of environmental monitoring data, extracting valuable insights from multivariate time series sensor data can facilitate comprehensive information utilization and support informed decision-making in environmental management. However, there is a dearth of comprehensive research on multivariate data analysis for process monitoring in typical polluting enterprises. In this study, an artificial neural network model based on back-propagation algorithm (BP-ANN) was developed to predict the wastewater and exhaust gas emissions using IoT data obtained from process monitoring of a typical polluting enterprise located in Taizhou, Zhejiang Province, China. The results indicate that the model constructed has a high predictive coefficient of determination (R[2]) with values of 0.8510, 0.9565, 0.9561, 0.9677, and 0.9061 for chemical oxygen demand (COD), potential of hydrogen (pH), electrical conductivity (EC), flue gas emission (FGE), and non-methane hydrocarbon concentration (NMHC) respectively. For the first time, the variable importance measure (VIM)-assisted BP-ANN was employed to investigate the internal and external correlations between wastewater and exhaust gas treatment, thereby enhancing the interpretability of mapping features in the BP-ANN model. The predicted errors for pH and FGE have been demonstrated to fall within the range of - 0.62 ~ 0.30 and - 0.21 ~ 0.15 m[3]/s, respectively, with average relative errors of 1.05% and 9.60%, which is advantageous in detecting anomalous data and forecasting pollution indicator values. Our approach successfully addresses the challenge of segregating data analysis for wastewater disposal and exhaust gas disposal in the process monitoring of polluting enterprises, while also unearthing potential variables that significantly contribute to the BP-ANN model, thereby facilitating the selection and extraction of characteristic variables.

RevDate: 2023-08-31
CmpDate: 2023-08-31

Mudge L, JF Bruno (2023)

Disturbance intensification is altering the trait composition of Caribbean reefs, locking them into a low functioning state.

Scientific reports, 13(1):14022.

Anthropogenic climate change is intensifying natural disturbance regimes, which negatively affects some species, while benefiting others. This could alter the trait composition of ecological communities and influence resilience to disturbance. We investigated how the frequency and intensification of the regional storm regime (and likely other disturbances) is altering coral species composition and in turn resistance and recovery. We developed regional databases of coral cover and composition (3144 reef locations from 1970 to 2017) and of the path and strength of cyclonic storms in the region (including 10,058 unique storm-reef intersections). We found that total living coral cover declined steadily through 2017 (the median annual loss rate was ~ 0.25% per year). Our results also indicate that despite the observed increase in the intensity of Atlantic cyclonic storms, their effect on coral cover has decreased markedly. This could be due in part to selection for disturbance-resistant taxa in response to the intensifying disturbance regime. We found that storms accelerated the loss of threatened acroporid corals but had no measurable effect on the cover of more resilient "weedy" corals, thereby increasing their relative cover. Although resistance to disturbance has increased, recovery rates have slowed due to the dominance of small, slow-growing species. This feedback loop is locking coral communities into a low-functioning state dominated by weedy species with limited ecological or societal value.

RevDate: 2023-08-30

Tan M, Bian Z, Dong J, et al (2023)

Comparing the variation and influencing factors of CO2 emission from subsidence waterbodies under different restoration modes in coal mining area.

Environmental research pii:S0013-9351(23)01740-1 [Epub ahead of print].

Subsidence waterbodies play an important role in carbon cycle in coal mining area. However, little effort has been made to explore the carbon dioxide (CO2) release characteristics and influencing factors in subsidence waterbodies, especially under different restoration modes. Here, we measured CO2 release fluxes (F(CO2)) across Anguo wetland (AW), louts pond (LP), fishpond (FP), fishery-floating photovoltaic wetland (FFPV), floating photovoltaic wetland (FPV) in coal mining subsidence area, with unrestored subsidence waterbodies (SW) and unaffected normal Dasha river (DR) as the control area. We sampled each waterbody and tested which physical, chemical, and biological characteristics of water and sediment related to variability in CO2. The results indicated that F(CO2) exhibited the following patterns: FFPV > FPV > FP > SW > DR > LP > AW. Trophic lake index (TLI) and microbial biomass carbon content (MBC) in sediment had a positive impact on F(CO2). The dominant archaea Euryarchaeota and Thaumarchaeota, and dominant bacteria Proteobacteria promoted F(CO2). This study can help more accurately quantify CO2 emissions and guide CO2 future emission reduction and subsidence waterbodies estoration.

RevDate: 2023-08-30

Anegg M, Prakofjewa J, Kalle R, et al (2022)

Local ecological knowledge and folk medicine in historical Estonia, Livonia, Courland and Galicia in Northeastern Europe, 1805-1905.

Open research Europe, 2:30.

Background: Historical ethnobotanical data can provide valuable information about past human-nature relationships as well as serve as a basis for diachronic analysis. This data note aims to present a dataset which documented medicinal plant uses, mentioned in a selection of German-language sources from the 19 [th] century covering the historical regions of Estonia, Livonia, Courland, and Galicia. Methods: Data was mainly entered by systematic manual search in various ethnobotanical historical German-language works focused on the medicinal use of plants. Data about plant and non-plant constituents, their usage, the mode of administration, used plant parts, and their German and local names was extracted and collected into a database in the form of Use Reports.

RevDate: 2023-08-29

Goparaju L, Pillutla RCP, SBK Venkata (2023)

Assessment of forest fire emissions in Uttarakhand State, India, using Open Geospatial data and Google Earth Engine.

Environmental science and pollution research international [Epub ahead of print].

In the recent past, forest fires have increased due to the changing climate pattern. It is necessary to analyse and quantify various gaseous emissions so as to mitigate their harmful effects on air pollution. Satellite remote sensing data provides an opportunity to study the greenhouse gases in the atmosphere. The multispectral sensor of the Tropospheric Monitoring Instrument (Sentinel-5) is capable of recording the reflectance of wavelengths vital for measuring the atmospheric concentrations of methane, formaldehyde, aerosol, carbon monoxide, etc., at a spatial resolution of 0.01°. The present study utilized the Google Earth Engine (GEE) platform to study the emissions caused by forest fires in four districts of Uttarakhand State of India, which witnessed unprecedented fires in April-May 2021. All the datasets were ingested in GEE, which has the capability to analyse large datasets without the need to download them. The pre-fire period chosen was September 2020; the fire period was February-May 2021, and the post-fire period was June 2021. The variables chosen were aerosol absorbing index (AAI), carbon monoxide (CO) and nitrogen dioxide (NO2). The climate parameter temperature (Moderate Resolution Imaging Spectroradiometer Land Surface Temperature) and precipitation (from Climate Hazards Group InfraRed Precipitation (CHIRPS) Pentad) were also studied for the period mentioned. The results indicate a different trend for emissions in each district. For AAI, maximum emissions were noted in district Nainital followed by Almora, Tehri Garhwal and Garhwal. For CO emissions, the most affected district was Almora followed by Nainital, Garhwal and Tehri Garhwal. For NO2 emissions, the most affected district was Garhwal, followed by Nainital, Tehri Garhwal and Almora. Delta Normalized Burn Ratio was computed from Sentinel data (difference of pre-fire and post-fire images) to assess the burnt area severity. The Delta Normalized Burn Ratio values observed that the district with the most burnt area is Garhwal, followed by Nainital, Almora and Tehri Garhwal. The elevated temperatures and scanty rainfall patterns regulated the intensity and duration of forest fire. Monitoring the gaseous emissions as a consequence of forest fire in the GEE platform is much easier and more convenient at a regional level. Such data is much needed for mitigation measures to be implemented in time.

RevDate: 2023-08-28

Wang F, Liu J, Qin G, et al (2023)

Coastal blue carbon in China as a nature-based solution toward carbon neutrality.

Innovation (Cambridge (Mass.)), 4(5):100481.

To achieve the Paris Agreement, China pledged to become "Carbon Neutral" by the 2060s. In addition to massive decarbonization, this would require significant changes in ecosystems toward negative CO2 emissions. The ability of coastal blue carbon ecosystems (BCEs), including mangrove, salt marsh, and seagrass meadows, to sequester large amounts of CO2 makes their conservation and restoration an important "nature-based solution (NbS)" for climate adaptation and mitigation. In this review, we examine how BCEs in China can contribute to climate mitigation. On the national scale, the BCEs in China store up to 118 Tg C across a total area of 1,440,377 ha, including over 75% as unvegetated tidal flats. The annual sedimental C burial of these BCEs reaches up to 2.06 Tg C year[-1], of which most occurs in salt marshes and tidal flats. The lateral C flux of mangroves and salt marshes contributes to 1.17 Tg C year[-1] along the Chinese coastline. Conservation and restoration of BCEs benefit climate change mitigation and provide other ecological services with a value of $32,000 ha[-1] year[-1]. The potential practices and technologies that can be implemented in China to improve BCE C sequestration, including their constraints and feasibility, are also outlined. Future directions are suggested to improve blue carbon estimates on aerial extent, carbon stocks, sequestration, and mitigation potential. Restoring and preserving BCEs would be a cost-effective step to achieve Carbon Neutral by 2060 in China despite various barriers that should be removed.

RevDate: 2023-08-28

Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the Powdered Quaker, Orthosia gracilis (Schiffermüller, 1775).

Wellcome open research, 8:290.

We present a genome assembly from an individual male Orthosia gracilis (the powdered quaker; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 715.5 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.43 kilobases in length.

RevDate: 2023-08-28
CmpDate: 2023-08-28

Kelliher JM, Robinson AJ, Longley R, et al (2023)

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.

Microbiome, 11(1):192.

As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.

RevDate: 2023-08-28
CmpDate: 2023-08-28

Elser D, Pflieger D, Villette C, et al (2023)

Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations.

Science advances, 9(34):eade8984.

Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse ecological niches. Here, we implemented a computational mass spectrometry-based metabolomics approach to exploring SM diversification in tissues of 20 species covering Nicotiana phylogenetics sections. To markedly increase metabolite annotation, we created a large in silico fragmentation database, comprising >1 million structures, and scripts for connecting class prediction to consensus substructures. Together, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case study and in combination with nuclear magnetic resonance and mass spectrometry imaging, we explored the distribution of N-acylnornicotines, alkaloids predicted to be specific to Repandae allopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Together, the data integration approaches provided here should act as a resource for future research in plant SM evolution.

RevDate: 2023-08-28
CmpDate: 2023-08-28

Qiu S, Yang A, H Zeng (2023)

Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.

PLoS computational biology, 19(8):e1011391.

In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.

RevDate: 2023-08-27

Zhou L, Ye T, Zheng S, et al (2023)

Experimental and modeling investigation of dual-source iron release in water-solid-gas interaction of abandoned coal mine drainage.

Environmental geochemistry and health [Epub ahead of print].

After mine closure and flooding, abandoned iron-prone devices and equipment (e.g., steel bolts and ground support meshes) and iron-bearing minerals (e.g., pyrite) form a dual-source iron pollution system in mine groundwater. Dual-source iron contributes to the water-solid-gas interaction in abandoned coal mines and the release of iron at different periods after mine closure, posing environmental risks in groundwater and discharging acid mine drainage, which contains large amounts of iron. In this study, a series of hydrochemical experiments were conducted to simulate the iron release process of the dual-source system, and electrochemical experiments were carried out to reveal the reaction mechanism, characterize the dual-source iron pollution release mode and quantify the release rate ratio. PHREEQC package was used to simulate the long-term hydrogeochemistry reactions of the water-solid-gas interaction to determine the key factors and suitable conditions that inhibit dual-source iron release. The results show that the dual-source system of iron-bearing minerals (pyrite) and steel bolts promote iron release from each other. The resulting calculated annual iron release indicated that the overall iron release rate ratio is: dual-source > bolt > pyrite, indicating that mine water would remain acidic for a long time due to the continuous release of iron from the system. Numerical modeling results show that maintaining the environment temperature below 25 °C and the pH above 3.5 is an effective way to reduce the iron release rate.

RevDate: 2023-08-26

Medo A, Ohte N, Kajitani H, et al (2023)

Striped catfish (Pangasianodon hypophthalmus) exploit food sources across anaerobic decomposition- and primary photosynthetic production-based food chains.

Scientific reports, 13(1):13992.

Dietary information from aquatic organisms is instrumental in predicting biological interactions and understanding ecosystem functionality. In freshwater habitats, generalist fish species can access a diverse array of food sources from multiple food chains. These may include primary photosynthetic production and detritus derived from both oxic and anoxic decomposition. However, the exploitation of anoxic decomposition products by fish remains insufficiently explored. This study examines feeding habits of striped catfish (Pangasianodon hypophthalmus) at both adult and juvenile stages within a tropical reservoir, using stable carbon, nitrogen, and sulfur isotope ratios (δ[13]C, δ[15]N, and δ[34]S, respectively) and fatty acid (FA) analyses. The adult catfish exhibited higher δ[15]N values compared to primary consumers that feed on primary photosynthetic producers, which suggests ingestion of food sources originating from primary photosynthetic production-based food chains. On the other hand, juvenile catfish demonstrated lower δ[15]N values than primary consumers, correlating with low δ[34]S value and large proportions of bacterial FA but contained small proportions of polyunsaturated FA. This implies that juveniles utilize food sources from both anoxic decomposition and primary photosynthetic production-based food chains. Our results indicate that food chains based on anoxic decomposition can indeed contribute to the dietary sources of tropical fish species.

RevDate: 2023-08-26

Shan Y, Zhao W, Hao W, et al (2023)

Five-year changes of social activity and incident long-term care needs among depressed older adults: A 15-year follow up.

Archives of gerontology and geriatrics, 116:105163 pii:S0167-4943(23)00241-8 [Epub ahead of print].

OBJECTIVES: To examine the effects of changes in individual/multiple social activities between 65 and 70 years of age on incident long-term care (LTC) needs between 70 and 80 in older adults with depressive symptoms.

METHODS: Participants were recruited from the New Integrated Suburban Seniority Investigation Project, an ongoing prospective cohort study. A total of 525 older adults with depressive symptoms were included. The validated 15-item Geriatric Depression Scale was used to assess depressive symptoms. A self-report questionnaire was used to measure social activities (social-related, learning, and personal). LTC needs was defined according to Japan's Long-term Care Insurance System. A competing risk model and a Laplace regression model were used to estimate the hazard ratios of LTC needs incidence and the 25th percentile difference in LTC-needs-free survival time and their 95% confidence intervals.

RESULTS: Out of 4314 person-years of mild LTC needs, 108 individuals developed it. Participants who increased their frequency of learning activities have a lower risk of developing mild LTC needs. Increasing the frequency could also prolong LTC-needs-free survival time by approximately 2.61 years. Out of 4535 person-years for severe LTC needs, 54 individuals developed it. Participants with a continuous regular frequency of learning activities had a lower risk of developing severe LTC needs. However, the association between this frequency and LTC-needs-free survival time for severe LTC needs was insignificant in the multivariable models.

CONCLUSIONS: Increased frequency of learning activities reduced the risk of LTC needs among older adults with depressive symptoms and prolonged their LTC-needs-free survival time.

RevDate: 2023-08-26

Meyer R, Davies N, Pitz KJ, et al (2022)

The founding charter of the Omic Biodiversity Observation Network (Omic BON).

GigaScience, 12:.

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

RevDate: 2023-08-26

Koga S, Takazono T, Kido T, et al (2023)

Evaluation of the Effectiveness and Use of Anti-Methicillin-Resistant Staphylococcus aureus Agents for Aspiration Pneumonia in Older Patients Using a Nationwide Japanese Administrative Database.

Microorganisms, 11(8): pii:microorganisms11081905.

Studies indicated potential harm from empirical broad-spectrum therapy. A recent study of hospitalizations for community-acquired pneumonia suggested that empirical anti-methicillin-resistant Staphylococcus aureus (MRSA) therapy was associated with an increased risk of death and other complications. However, limited evidence supports empirical anti-MRSA therapy for older patients with aspiration pneumonia. In a nationwide Japanese database, patients aged ≥65 years on admission with aspiration pneumonia were analyzed. Patients were divided based on presence of respiratory failure and further sub-categorized based on their condition within 3 days of hospital admission, either receiving a combination of anti-MRSA agents and other antibiotics, or not using MRSA agents. An inverse probability weighting method with estimated propensity scores was used. Out of 81,306 eligible patients, 55,098 had respiratory failure, and 26,208 did not. In the group with and without respiratory failure, 0.93% and 0.42% of the patients, respectively, received anti-MRSA agents. In patients with respiratory failure, in-hospital mortality (31.38% vs. 19.03%, p < 0.001), 30-day mortality, and 90-day mortality were significantly higher, and oxygen administration length was significantly longer in the anti-MRSA agent combination group. Anti-MRSA agent combination use did not improve the outcomes in older patients with aspiration pneumonia and respiratory failure, and should be carefully and comprehensively considered.

RevDate: 2023-08-26

Irwin G, Rogatzki MJ, Wiltshire HD, et al (2023)

Sports-Related Concussion Assessment: A New Physiological, Biomechanical, and Cognitive Methodology Incorporating a Randomized Controlled Trial Study Protocol.

Biology, 12(8): pii:biology12081089.

BACKGROUND: Taking part in moderate-to-vigorous exercise in contact sports on a regular basis may be linked to an increase in cerebrovascular injury and head trauma. Validated objective measures are lacking in the initial post-event diagnosis of head injury. The exercise style, duration, and intensity may also confound diagnostic indicators. As a result, we propose that the new Interdisciplinary Group in Movement & Performance from Acute & Chronic Head Trauma (IMPACT) analyze a variety of functional (biomechanical and motor control) tests as well as related biochemistry to see how they are affected by contact in sports and head injury. The study's goal will be to look into the performance and physiological changes in rugby players after a game for head trauma and injury.

METHODS: This one-of-a-kind study will use a randomized controlled trial (RCT) utilizing a sport participation group and a non-participation control group. Forty male rugby 7 s players will be recruited for the study and allocated randomly to the experimental groups. The intervention group will participate in three straight rugby matches during a local 7 s rugby event. At the pre-match baseline, demographic and anthropometric data will be collected. This will be followed by the pre-match baseline collection of biochemical, biomechanical, and cognitive-motor task data. After three consecutive matches, the same measures will be taken. During each match, a notational analysis will be undertaken to obtain contact information. All measurements will be taken again 24, 48, and 72 h after the third match.

DISCUSSION: When the number of games increases owing to weariness and/or stressful circumstances, we expect a decline in body movement, coordination, and cognitive-motor tasks. Changes in blood biochemistry are expected to correspond to changes in biomechanics and cognitive-motor processes. This research proposal will generate considerable, ecologically valid data on the occurrence of head trauma events under game conditions, as well as the influence of these events on the biological systems of the performers. This will lead to a greater understanding of how sports participants react to exercise-induced injuries. This study's scope will have far-reaching ramifications for doctors, coaches, managers, scientists, and sports regulatory bodies concerned with the health and well-being of athletic populations at all levels of competition, including all genders and ages.

RevDate: 2023-08-25

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2023)

The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766).

Wellcome open research, 8:92.

We present a genome assembly from an individual female Spilarctia lutea (the Buff Ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 584.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the assembled Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,304 protein coding genes.

RevDate: 2023-08-25
CmpDate: 2023-08-25

Gavurova B, Kelemen M, Polishchuk V, et al (2023)

A fuzzy decision support model for the evaluation and selection of healthcare projects in the framework of competition.

Frontiers in public health, 11:1222125.

Our research aims to support decision-making regarding the financing of healthcare projects by structural funds with policies targeting reduction of the development gap among different regions and countries of the European Union as well as the achievement of economic and social cohesion. A fuzzy decision support model for the evaluation and selection of healthcare projects should rank the project applications for the selected region, accounting for the investor's wishes in the form of a regional coefficient in order to reduce the development gap between regions. On the one hand, our proposed model evaluates project applications based on selected criteria, which may be structured, weakly structured, or unstructured. On the other hand, it also incorporates information on the level of healthcare development in the region. The obtained ranking increases the degree of validity of the decision regarding the selection of projects for financing by investors, considering the level of development of the region where the project will be implemented. At the expense of European Union (EU) structural funds, a village, city, region, or state can receive funds for modernization and development of the healthcare sector and all related processes. To minimize risks, it is necessary to implement adequate support systems for decision-making in the assessment of project applications, as well as regional policy in the region where the project will be implemented. The primary goal of this study was to develop a complex fuzzy decision support model for the evaluation and selection of projects in the field of healthcare with the aim of reducing the development gap between regions. Based on the above description, we formed the following scientific hypothesis for this research: if the project selected for financing can successfully achieve its stated goals and increase the level of development of its region, it should be evaluated positively. This evaluation can be obtained using a complex fuzzy model constructed to account for the region's level of development in terms of the availability and quality of healthcare services in the region where the project will be implemented.

RevDate: 2023-08-25
CmpDate: 2023-08-25

Sentamu DN, Kungu J, Dione M, et al (2023)

Prevention of human exposure to livestock faecal waste in the household: a scoping study of interventions conducted in sub-Saharan Africa.

BMC public health, 23(1):1613.

BACKGROUND: Poorly managed animal faecal waste can result in detrimental environmental and public health implications. Limiting human exposure to animal waste through Animal inclusive Water Sanitation and Hygiene (A-WASH) strategies is imperative to improve public health in livestock keeping households but has received little attention to date. A small number of A-WASH interventions have previously been identified through a systematic review by another research team, and published in 2017. To inform intervention design with the most up-to-date information, a scoping study was conducted to map the existing evidence for A-WASH in sub-Saharan Africa (SSA) emerging since the previous review.

METHODS: This review followed PRISMA guidelines to identify interventions in SSA published between January 2016 to October 2022. Databases searched included PubMed, PMC Europe, CabDirect and Web of Science. Studies were eligible for inclusion if they were written in English and documented interventions limiting human contact with animal faecal material in the SSA context. Key data extracted included: the intervention itself, its target population, cost, measure of effectiveness, quantification of effect, assessment of success, acceptability and limitations. These data were synthesized into a narrative, structured around the intervention type.

FINDINGS: Eight eligible articles were identified. Interventions to reduce human exposure to animal faecal matter were conducted in combination with 'standard' human-centric WASH practices. Identified interventions included the management of human-animal co-habitation, educational programs and the creation of child-safe spaces. No novel A-WASH interventions were identified in this review, beyond those identified by the review in 2017. Randomised Controlled Trials (RCTs) were used to evaluate six of the eight identified interventions, but as effect was evaluated through various measures, the ability to formally compare efficacy of interventions is lacking.

CONCLUSION: This study indicates that the number of A-WASH studies in SSA is increasing and the use of RCTs suggests a strong desire to create high-quality evidence within this field. There is a need for standardisation of effect measures to enable meta-analyses to be conducted to better understand intervention effectiveness. Evaluation of scalability and sustainability of interventions is still lacking in A - WASH research.

RevDate: 2023-08-25
CmpDate: 2023-08-25

Dethier EN, Silman M, Leiva JD, et al (2023)

A global rise in alluvial mining increases sediment load in tropical rivers.

Nature, 620(7975):787-793.

Increasing gold and mineral mining activity in rivers across the global tropics has degraded ecosystems and threatened human health[1,2]. Such river mineral mining involves intensive excavation and sediment processing in river corridors, altering river form and releasing excess sediment downstream[2]. Increased suspended sediment loads can reduce water clarity and cause siltation to levels that may result in disease and mortality in fish[3,4], poor water quality[5] and damage to human infrastructure[6]. Although river mining has been investigated at local scales, no global synthesis of its physical footprint and impacts on hydrologic systems exists, leaving its full environmental consequences unknown. We assemble and analyse a 37-year satellite database showing pervasive, increasing river mineral mining worldwide. We identify 396 mining districts in 49 countries, concentrated in tropical waterways that are almost universally altered by mining-derived sediment. Of 173 mining-affected rivers, 80% have suspended sediment concentrations (SSCs) more than double pre-mining levels. In 30 countries in which mining affects large (>50 m wide) rivers, 23 ± 19% of large river length is altered by mining-derived sediment, a globe-spanning effect representing 35,000 river kilometres, 6% (±1% s.e.) of all large tropical river reaches. Our findings highlight the ubiquity and intensity of mining-associated degradation in tropical river systems.

RevDate: 2023-08-25
CmpDate: 2023-08-25

Weinstein ES, Cuthbertson JL, Herbert TL, et al (2023)

Advancing the scientific study of prehospital mass casualty response through a Translational Science process: the T1 scoping literature review stage.

European journal of trauma and emergency surgery : official publication of the European Trauma Society, 49(4):1647-1660.

PURPOSE: The European Union Horizon 2020 research and innovation funding program awarded the NIGHTINGALE grant to develop a toolkit to support first responders engaged in prehospital (PH) mass casualty incident (MCI) response. To reach the projects' objectives, the NIGHTINGALE consortium used a Translational Science (TS) process. The present work is the first TS stage (T1) aimed to extract data relevant for the subsequent modified Delphi study (T2) statements.

METHODS: The authors were divided into three work groups (WGs) MCI Triage, PH Life Support and Damage Control (PHLSDC), and PH Processes (PHP). Each WG conducted simultaneous literature searches following the PRISMA extension for scoping reviews. Relevant data were extracted from the included articles and indexed using pre-identified PH MCI response themes and subthemes.

RESULTS: The initial search yielded 925 total references to be considered for title and abstract review (MCI Triage 311, PHLSDC 329, PHP 285), then 483 articles for full reference review (MCI Triage 111, PHLSDC 216, PHP 156), and finally 152 articles for the database extraction process (MCI Triage 27, PHLSDC 37, PHP 88). Most frequent subthemes and novel concepts have been identified as a basis for the elaboration of draft statements for the T2 modified Delphi study.

CONCLUSION: The three simultaneous scoping reviews allowed the extraction of relevant PH MCI subthemes and novel concepts that will enable the NIGHTINGALE consortium to create scientifically anchored statements in the T2 modified Delphi study.

RevDate: 2023-08-24

Gonzalez A, Vihervaara P, Balvanera P, et al (2023)

A global biodiversity observing system to unite monitoring and guide action.

Nature ecology & evolution [Epub ahead of print].

RevDate: 2023-08-24

Boyes D, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the White-shouldered Marble, Apotomis turbidana (Hübner, 1825).

Wellcome open research, 8:127.

We present a genome assembly from an individual male Apotomis turbidana (the White-shouldered Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 720.5 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,646 protein coding genes.

RevDate: 2023-08-23

Sarkar DJ, Das Sarkar S, Santhana Kumar V, et al (2023)

Ameliorative effect of natural floating island as fish aggregating devices on heavy metals distribution in a freshwater wetland.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(23)01430-6 [Epub ahead of print].

Growing human population and climate change are leading reasons for water quality deterioration globally; and ecologically important waterbodies including freshwater wetlands are in a vulnerable state due to increasing concentrations of pollutants like heavy metals. Given the declining health of these valuable resources, the present study was conducted to evaluate the effect of natural floating island in the form of fish aggregating devices (FADs) made of native weed mass on the distribution of heavy metals in the abiotic and bio compartments of a freshwater wetland. Lower concentrations of surface water heavy metals were observed inside the FADs with a reduction of 73.91%, 65.22% and 40.57-49.16% for Cd, Pb and other metals (viz. Co, Cr, Cu, Ni and Zn), respectively as compared to outside FAD. These led to 14.72-55.39% reduction in the heavy metal pollution indices inside the FAD surface water. The fish species inside the FADs were also found less contaminated (24.07-25.07% reduction) with lower health risk indices. The study signifies the valuable contribution of natural floating island as FADs in ameliorating the effect of heavy metals pollution emphasizing the tremendous role of the natural floating islands in sustainable maintenance of freshwater wetlands for better human health and livelihood.

RevDate: 2023-08-23

Brodie JF, Mohd-Azlan J, Chen C, et al (2023)

Landscape-scale benefits of protected areas for tropical biodiversity.

Nature, 620(7975):807-812.

The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines[1]. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear[2-5]. Unregulated hunting can empty PAs of large animals[6], illegal tree felling can degrade habitat quality[7], and parks can simply displace disturbances such as logging and hunting to unprotected areas of the landscape[8] (a phenomenon called leakage). Alternatively, well-functioning PAs could enhance animal diversity within reserves as well as in nearby unprotected sites[9] (an effect called spillover). Here we test whether PAs across mega-diverse Southeast Asia contribute to vertebrate conservation inside and outside their boundaries. Reserves increased all facets of bird diversity. Large reserves were also associated with substantially enhanced mammal diversity in the adjacent unprotected landscape. Rather than PAs generating leakage that deteriorated ecological conditions elsewhere, our results are consistent with PAs inducing spillover that benefits biodiversity in surrounding areas. These findings support the United Nations goal of achieving 30% PA coverage by 2030 by demonstrating that PAs are associated with higher vertebrate diversity both inside their boundaries and in the broader landscape.

RevDate: 2023-08-21

Rocha AFBM, Freitas-Junior R, Soares LR, et al (2023)

Breast cancer screening and diagnosis in older adults women in Brazil: why it is time to reconsider the recommendations.

Frontiers in public health, 11:1232668.

INTRODUCTION: Breast cancer screening in women of 70 years of age or older remains controversial due to a lack of studies that include women of this age.

METHODS: This ecological study evaluated data from the Brazilian National Health Service (SUS) on breast cancer screening and staging in this age group compared to 50-69-year olds, for Brazil as a whole and for its geographical regions, between 2013 and 2019. A secondary database was obtained from the outpatient data system of the SUS's Informatics Department, the Brazil Oncology Panel, the Brazilian Institute of Geography and Statistics, the Supplementary Health Agency and the Online Mortality Atlas.

RESULTS: There was a marked reduction in screening in women ≥70 years of age (annual percent change [APC] -3.5; p < 0.001) compared to those of 50-69 years of age (APC-2.2; p = 0.010). There was a trend towards an increase in clinical staging, with a greater occurrence of stages III and IV in the ≥70 group (44.3%) compared to the women of 50-69 years of age (40.8%; p < 0.001).

CONCLUSION: Considering the increasing age of the Brazilian population and the heterogeneity among older adults women, screening for the over-70s within the SUS merits greater debate insofar as the implementation of public policies is concerned.

RevDate: 2023-08-21

Saccheri IJ, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, et al (2023)

The genome sequence of the Squinting Bush Brown, Bicyclus anynana (Butler, 1879).

Wellcome open research, 8:280.

We present a genome assembly from an individual female Bicyclus anynana (the Squinting Bush Brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 457.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length.

RevDate: 2023-08-21

Lohse K, Hayward A, Vila R, et al (2023)

The genome sequence of the Large Skipper, Ochlodes sylvanus, (Esper, 1777).

Wellcome open research, 8:75.

We present a genome assembly from an individual female Ochlodes sylvanus, the Large Skipper (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 380 megabases in span. Most of the assembly (99.97%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,451 protein coding genes.

RevDate: 2023-08-21

Lees D, Boyes D, Natural History Museum Genome Acquisition Lab, et al (2023)

The genome sequence of the Dotted Border, Agriopis marginaria (Fabricius, 1776).

Wellcome open research, 8:152.

We present a genome assembly from an individual male Agriopis marginaria (the Dotted Border, Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 500.9 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,443 protein coding genes.

RevDate: 2023-08-21
CmpDate: 2023-08-21

Tom M, Lubinevsky H, M Kanari (2023)

Integrative data system for monitoring biota and natural habitats in the Israeli Eastern Mediterranean marine environment.

Environmental monitoring and assessment, 195(9):1068.

An integrative data system for monitoring the biota of the Mediterranean waters of Israel as well as selected records from adjacent Levantine basin regions is presented here, aimed at providing data and research tools for long-term bio-geographic and ecological studies and more important, providing background data for assisting governmental regulators to establish educated habitat-oriented environmental policy. The system relies on the geographic information system (GIS) online map-based platform and contains at present the following components: biotic database of ~ 170,000 recorded sampling events; uniform habitat maps of 63 benthic habitats and 2 pelagic ones, constructed using relevant bathymetric features and biotic community compositions; bathymetric hill-shade map; depth contours; raster depth grid and human interference map. Other informative auxiliary maps are planned to be added (e.g., map of potential pockmark sites, detailed maps of tiny carbonate crust nolls and more). A number of 883 cited documents were listed by us for potential extraction of sampling efforts, most of them are available to us as PDFs and are available also to the users, excluding copyright-protected ones. Forty-three major projects were depicted in addition to a variety of small studies (e.g., university theses). Thirty-five sampling devices were documented and described, and 3187 species-level identifications were already recorded. In addition, the system provides access to description of sampling devices and pictures of species and seascapes. New data is continuously deposited to the system and the system is flexible, allowing future addition of new types of information. The system site is accessible through the link: https://experience.arcgis.com/experience/40e86605ff4d4e5096ed2c901fec2a2f .

RevDate: 2023-08-21
CmpDate: 2023-08-21

Szymura TH, Kassa H, Swacha G, et al (2023)

Spatial patterns of vascular plant species richness in Poland - a data set.

Scientific data, 10(1):542.

Recognition of species richness spatial patterns is important for nature conservation and theoretical studies. Inventorying species richness, especially at a larger spatial extent is challenging, thus different data sources are joined and harmonized to obtain a comprehensive data set. Here we present a new data set showing vascular plant species richness in Poland based on a grid of 10 × 10 km squares. The data set was created using data from two sources: the Atlas of Distribution of Vascular Plants in Poland and the Polish Vegetation Database. Using this data set, we analysed 2,160 species with taxonomical nomenclature according to the Euro + Med PlantBase checklist in 3,283 squares covering the entire territory of Poland (ca. 312,000 km[2]). The species were divided into groups according to their status and frequency of distribution, and the statistics for each square were obtained. For purposes of analysis, sampling bias was assessed. The data set promotes theoretical analysis on species richness and reinforces the planning of nature conservations.

RevDate: 2023-08-19

Nazari Ashani M, Alesheikh AA, Neisani Samani Z, et al (2023)

Socioeconomic and environmental determinants of foot and mouth disease incidence: an ecological, cross-sectional study across Iran using spatial modeling.

Scientific reports, 13(1):13526.

Foot-and-mouth disease (FMD) is a highly contagious animal disease caused by a ribonucleic acid (RNA) virus, with significant economic costs and uneven distribution across Asia, Africa, and South America. While spatial analysis and modeling of FMD are still in their early stages, this research aimed to identify socio-environmental determinants of FMD incidence in Iran at the provincial level by studying 135 outbreaks reported between March 21, 2017, and March 21, 2018. We obtained 46 potential socio-environmental determinants and selected four variables, including percentage of population, precipitation in January, percentage of sheep, and percentage of goats, to be used in spatial regression models to estimate variation in spatial heterogeneity. In our analysis, we employed global models, namely ordinary least squares (OLS), spatial error model (SEM), and spatial lag model (SLM), as well as local models, including geographically weighted regression (GWR) and multiscale geographically weighted regression (MGWR). The MGWR model yielded the highest adjusted [Formula: see text] of 90%, outperforming the other local and global models. Using local models to map the effects of environmental determinants (such as the percentage of sheep and precipitation) on the spatial variability of FMD incidence provides decision-makers with helpful information for targeted interventions. Our findings advocate for multiscale and multidisciplinary policies to reduce FMD incidence.

RevDate: 2023-08-18

Jaron KS, Berg MP, Ellers J, et al (2023)

The genome sequence of the springtail Allacma fusca (Linnaeus, 1758).

Wellcome open research, 8:319.

We present a genome assembly from an individual male Allacma fusca (the springtail; Arthropoda; Collembola; Symphypleona; Sminthuridae). The genome sequence is 392.8 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 14.94 kilobases in length.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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This book introduces readers to ecological informatics as an emerging discipline that takes into account the data-intensive nature of ecology, the valuable information to be found in ecological data, and the need to communicate results and inform decisions, including those related to research, conservation and resource management. At its core, ecological informatics combines developments in information technology and ecological theory with applications that facilitate ecological research and the dissemination of results to scientists and the public. Its conceptual framework links ecological entities (genomes, organisms, populations, communities, ecosystems, landscapes) with data management, analysis and synthesis, and communicates new findings to inform decisions by following the course of a loop. In comparison to the 2nd edition published in 2006, the 3rd edition of Ecological Informatics reflects the significant advances in data management, analysis and synthesis that have been made over the past 10 years, including new remote and in situ sensing techniques, the emergence of ecological and environmental observatories, novel evolutionary computations for knowledge discovery and forecasting, and new approaches to communicating results and informing decisions.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )