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30 Mar 2023 at 01:44
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Bibliography on: Ecological Informatics


Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 30 Mar 2023 at 01:44 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: 2023-03-28

Yang D, Zhu H, Liu J, et al (2023)

Risk Assessment of Heavy Metals in Soils from Four Different Industrial Plants in a Medium-Sized City in North China.

Toxics, 11(3): pii:toxics11030217.

Laboratory experiments were carried out to analyze 39 soil samples collected from four industrial areas in Xuzhou City using inductively coupled plasma mass spectrometry and atomic fluorescence spectrometry. The descriptive statistics of heavy metals (HMs) in the soil profiles showed that the HM content at three depths was highly variable, and most coefficients of variation (CVs) showed moderate variability. The enrichment of Cd at all depths exceeded the risk screening value, and Cd pollution occurred in four plants. The enrichment of the other HMs at three depths was mainly concentrated in the pharmaceutical plant A and chemical plant C. It was found that the different HMs had different vertical distribution characteristics. For the different industrial plants, the raw materials and products not only made the spatial distribution characteristics of the HMs different, but also caused the HM types and contents to differ. The average single pollution indices of Cd in plant A, iron-steel plant B, and plant C indicated a slight pollution level. The other seven HMs in A, B, and C and all HMs in chemical plant D belonged to the safe category. The mean values of the Nemerow pollution index in the four industrial plants belonged to the warning category. The analysis showed that none of the HMs posed potential noncarcinogenic health risks, and only the carcinogenic health risks of Cr in plants A and C were unacceptable. The carcinogenic effect of Cr through the inhalation intake of resuspended soil particulates and that of Cd, Ni, and As via direct oral ingestion were the main exposure pathways.

RevDate: 2023-03-27

Cecchetto M, Peruzza L, Giubilato E, et al (2023)

An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment.

Environmental research pii:S0013-9351(23)00537-6 [Epub ahead of print].

The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.

RevDate: 2023-03-29
CmpDate: 2023-03-29

Beauchamp AM, Lehmann CU, Medford RJ, et al (2023)

The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.

Journal of medical Internet research, 25:e43623 pii:v25i1e43623.

BACKGROUND: Social connectedness decreases human mortality, improves cancer survival, cardiovascular health, and body mass, results in better-controlled glucose levels, and strengthens mental health. However, few public health studies have leveraged large social media data sets to classify user network structure and geographic reach rather than the sole use of social media platforms.

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

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

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

CONCLUSIONS: Social connectedness and depression showed, after adjusting for confounding factors such as income, education, cohabitation, natural resources, employment categories, accessibility, and urbanicity, that a greater social connectedness score is associated with a decreased prevalence of depression.

RevDate: 2023-03-26

Song W, W Song (2023)

Cropland fallow reduces agricultural water consumption by 303 million tons annually in Gansu Province, China.

The Science of the total environment pii:S0048-9697(23)01631-5 [Epub ahead of print].

The high-intensity utilization of global cropland causes water shortage and food crisis, which seriously affects the realization of SDG 2 (zero hunger), SDG 6 (clean water and sanitation) and SDG 15 (life on land), and threatens the sustainable social, economic and ecological development. Cropland fallow can not only improve the quality of cropland and maintain ecosystem balance, but also have a significant water-saving effect. However, in most developing countries, such as China, cropland fallow has not yet been widely promoted, and there are few reliable fallow cropland fallow identification methods, making it even more challenging to assess the water-saving effect. To remedy this deficit, we propose a framework for mapping cropland fallow and evaluating its water savings. First, we used the Landsat series of data to interpret the annual land use/cover changes in Gansu Province, China from 1991 to 2020. Subsequently, the spatial-temporal variation of cropland fallow in Gansu province (giving up farming for one to two years) was mapped. Finally, we evaluated the water-saving effect of cropland fallow using evapotranspiration, precipitation, irrigation maps, and crop-related data, instead of actual water consumption. The results showed that the mapping accuracy of fallow land in Gansu Province was 79.50 %, which was higher than that of most known fallow mapping studies. From 1993 to 2018, the average annual fallow rate in Gansu Province, China, was 10.86 %, which was at a low level in arid/semi-arid regions worldwide. More importantly, from 2003 to 2018, cropland fallow reduces annual water consumption of 303.26 million tons in Gansu Province, accounting for 3.44 % of agricultural water use in Gansu Province and equivalent to the annual water demand of 655,000 people in Gansu Province. Based on our research, we speculate that the increasing pilot projects of cropland fallow in China can bring significant water-saving effects and help achieve China's Sustainable Development Goals.

RevDate: 2023-03-28
CmpDate: 2023-03-28

Jin H, Zhihong P, Jiaqing Z, et al (2023)

Source apportionment and quantitative risk assessment of heavy metals at an abandoned zinc smelting site based on GIS and PMF models.

Journal of environmental management, 336:117565.

The abandoned smelters have caused serious hazards to the surrounding environment and residents. Taking an abandoned zinc smelter in southern China as an example, a total of 245 soil samples were collected to study spatial heterogeneity, source apportionment, and source-derived risk assessment of heavy metal(loid)s (HMs) in the region. The results showed that the mean values of all HMs concentrations were higher than the local background values, with Zn, Cd, Pb, and As contamination being the most serious and their plume penetrating to the bottom layer. Four sources were identified by principal component analysis and positive matrix factorization, with their contributions to the HMs contents ranked as: surface runoff (F2, 63.2%) > surface solid waste (F1, 22.2%) > atmospheric deposition (F3, 8.5%) > parent material (F4, 6.1%). Among these, F1 was a determinant source of human health risk with a contribution rate of 60%. Therefore, F1 was considered to be the priority control factor, but it only accounted for 22.2% of HMs contents contribution. Hg dominated the ecological risk with a contribution of 91.1%. Pb (25.7%) and As (32.9%) accounted for the non-carcinogenic risk, while As (95%) dominated the carcinogenic effect. The spatial characteristics of human health risk values derived from F1 indicated that high-risk areas were mainly distributed in the casting finished products area, electrolysis area, leaching-concentration area, and fluidization roasting area. The findings highlight the significance of priority control factors (including HMs, pollution sources and functional areas) for consideration in the integrated management of this region, thus saving costs for effective soil remediation.

RevDate: 2023-03-28
CmpDate: 2023-03-28

Hu Y, Wang X, Xu Y, et al (2023)

Molecular mechanisms of adaptive evolution in wild animals and plants.

Science China. Life sciences, 66(3):453-495.

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

RevDate: 2023-03-25

Dec E, Clement J, Cheng K, et al (2023)

Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity.

GeroScience [Epub ahead of print].

Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.

RevDate: 2023-03-27

Asaaga FA, Purse BV, Rahman M, et al (2023)

The role of social vulnerability in improving interventions for neglected zoonotic diseases: The example of Kyasanur Forest Disease in India.

PLOS global public health, 3(2):e0000758.

Forest-based communities manage many risks to health and socio-economic welfare including the increasing threat of emerging zoonoses that are expected to disproportionately affect poor and marginalised groups, and further impair their precarious livelihoods, particularly in Low-and-Middle Income (LMIC) settings. Yet, there is a relative dearth of empirical research on the vulnerability and adaptation pathways of poor and marginalised groups facing emerging zoonoses. Drawing on a survey of 229 households and a series of key-informant interviews in the Western Ghats, we examine the factors affecting vulnerability of smallholder and tribal households to Kyasanur Forest Disease (KFD), an often-fatal tick-borne viral haemorrhagic fever endemic in south India. Specifically, we investigate how different socio-demographic and institutional factors interact to shape KFD vulnerability and the strategies employed by households to adapt to disease consequences. Although surveyed households generally perceived KFD as an important health issue in the study region, there was variability in concern about contracting the disease. Overall results showed that poor access to land (AOR = 0.373, 95% CI: 0.152-0.916), being at or below the poverty line (AOR = 0.253, 95% CI: 0.094-0.685) and being headed by an older person (AOR = 1.038, 95% CI: 1.006-1.071) were all significant determinants of perceived KFD vulnerability. Furthermore, KFD vulnerability is also modulated by important extra-household factors including proximity to private hospitals (AOR = 3.281, 95% CI: 1.220-8.820), main roads (AOR = 2.144, 95% CI: 1.215-3.783) and study location (AOR = 0.226, 95% CI: 0.690-0.743). Our findings highlight how homogenous characterisation of smallholder and tribal communities and the 'techno-oriented' approach of existing interventions may further marginalise the most vulnerable and exacerbate existing inequalities. These findings are important for designing context-specific and appropriate health interventions (including the prioritisation of awareness raising, knowledge networks, livelihood diversification) that enhances the resilience of at-risk social groups within the KFD context. More broadly, our findings highlight how a focus on social vulnerability can help national and international health planners improve health interventions and prioritise among diseases with respect to neglected endemic zoonoses.

RevDate: 2023-03-26

Sawires R, Pearce C, Fahey M, et al (2022)

Snotwatch COVID-toes: An ecological study of chilblains and COVID-19 diagnoses in Victoria, Australia.

PLOS global public health, 2(10):e0000488.

The COVID-19 pandemic has caused widespread illness with varying clinical manifestations. One less-commonly-reported presentation of COVID-19 infection is chilblain-like lesions. We conducted an ecological analysis of chilblain presentations in comparison with confirmed and suspected COVID-19 infections in a primary care setting to establish that a relationship exists between the two. Our study collated data from three Primary Health Networks across Victoria, Australia, from 2017-2021, to understand patterns of chilblain presentations prior to and throughout the pandemic. Using a zero-inflated negative binomial regression analysis, we estimated the relationship between local minimum temperature, COVID-19 infections and the frequency of chilblain presentations. We found a 5.72 risk ratio of chilblain incidence in relation to COVID-19 infections and a 3.23 risk ratio associated with suspected COVID-19 infections. COVID-19 infections were also more strongly associated with chilblain presentations in 0-16-year-olds throughout the pandemic in Victoria. Our study statistically suggests that chilblains are significantly associated with COVID-19 infections in a primary care setting. This has major implications for clinicians aiming to diagnose COVID-19 infections or determine the cause of a presentation of chilblains. Additionally, we demonstrate the utility of large-scale primary care data in identifying an uncommon manifestation of COVID-19 infections, which will be significantly beneficial to treating physicians.

RevDate: 2023-03-24

Asaaga FA, Young JC, Srinivas PN, et al (2022)

Co-production of knowledge as part of a OneHealth approach to better control zoonotic diseases.

PLOS global public health, 2(3):e0000075.

There is increased global and national attention on the need for effective strategies to control zoonotic diseases. Quick, effective action is, however, hampered by poor evidence-bases and limited coordination between stakeholders from relevant sectors such as public and animal health, wildlife and forestry sectors at different scales, who may not usually work together. The OneHealth approach recognises the value of cross-sectoral evaluation of human, animal and environmental health questions in an integrated, holistic and transdisciplinary manner to reduce disease impacts and/or mitigate risks. Co-production of knowledge is also widely advocated to improve the quality and acceptability of decision-making across sectors and may be particularly important when it comes to zoonoses. This paper brings together OneHealth and knowledge co-production and reflects on lessons learned for future OneHealth co-production processes by describing a process implemented to understand spill-over and identify disease control and mitigation strategies for a zoonotic disease in Southern India (Kyasanur Forest Disease). The co-production process aimed to develop a joint decision-support tool with stakeholders, and we complemented our approach with a simple retrospective theory of change on researcher expectations of the system-level outcomes of the co-production process. Our results highlight that while co-production in OneHealth is a difficult and resource intensive process, requiring regular iterative adjustments and flexibility, the beneficial outcomes justify its adoption. A key future aim should be to improve and evaluate the degree of inter-sectoral collaboration required to achieve the aims of OneHealth. We conclude by providing guidelines based on our experience to help funders and decision-makers support future co-production processes.

RevDate: 2023-03-23

Lima GDS, Menegario AA, Suarez CA, et al (2023)

Pelagic and estuarine birds as sentinels of metal(loid)s in the South Atlantic Ocean: Ecological niches as main factors acting on bioaccumulation.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(23)00454-2 [Epub ahead of print].

Activities related to the offshore exploration and production of oil and natural gas provide economic development and an essential energy source. However, besides the risk of petroleum hydrocarbon contamination, these activities can also be sources of metals and metalloids for marine organism contamination. In this research, we evaluated the potential use of two pelagic (black-browed albatross Thalassarche melanophris and yellow-nosed albatross T. chlororhynchos) and one estuarine bird species (neotropical cormorant Nannopterum brasilianus) as sentinels of contamination of As, Cd, Cr, Cu, Pb, Mn, Mo, Zn, Ni, Ba, V, and Hg in an area under influence of oil and gas activities. The analyses were carried out in samples collected from 2015 to 2022 from 97 individuals. A factor alert; an adaptation from the contamination factor is proposed to identify individuals with high concentrations that possibly suffered contamination by anthropogenic origin. Grouping all species, the metal(loid)s with the highest concentrations were in decreasing order: Zn > Cu > Mn > Hg > As > Cd > Mo > V > Cr > Ba > Ni > Pb. Similar concentrations were observed for V, Mn, Cr and Pb among the three species. Pelagic birds showed higher levels of concentrations for Hg, As and Cd. Based on the correlations and multivariate analysis performed, the results indicate that the ecological niche factor has greater relevance in the bioaccumulation of these elements compared to the habitat. Although some individuals showed high concentrations in part of the trace elements, suggesting exposure to anthropic sources, the direct influence of oil production and exploration activities was not observed, suggesting that activities on the continent are the primary contamination source. The results of this work highlight the role of seabirds as sentinels for metal(loid)s, contributing to the knowledge of the occurrence of contaminants in the South Atlantic Ocean.

RevDate: 2023-03-23

Bautista J, SM Schueller (2023)

Understanding the Adoption and Use of Digital Mental Health Apps Among College Students: Secondary Analysis of a National Survey.

JMIR mental health, 10:e43942 pii:v10i1e43942.

BACKGROUND: Increasing rates of mental health diagnoses in college students signal the need for new opportunities to support the mental health of this population. With many mental health apps being efficacious, they may be a promising resource for college campuses to provide support to their students. However, it is important to understand why (or why not) students might want to use apps and their desired features.

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

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

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

CONCLUSIONS: The findings from this study underscore that simply providing digital mental health apps as tools may be insufficient to support their use in college campuses. Although many students were open to using a mental health app, hesitation and uncertainty were common in the participant responses. Working with colleges and universities to increase digital literacy and provide resources that allow students to gauge when app use is appropriate may be helpful when implementing mental health apps as resources in college campuses.

RevDate: 2023-03-22

Oliveira HC, Seabra AB, Kondak S, et al (2023)

Multilevel approach of plant-nanomaterial relationship: from cells to living ecosystems.

Journal of experimental botany pii:7083643 [Epub ahead of print].

Due to their unique properties, nanomaterials (NMs) behave peculiarly in biosystems. Regarding plants, the interactions of NMs can be interpreted on a spatial scale: from local interactions in cells to systemic effects on whole plants and on ecosystems. Interpreted on a time scale, the effects of NMs on plants may be immediate or subsequent. At the cellular level, the composition and structure of the cell wall and membranes are modified by NMs, promoting internalization. The effects of NMs on germination and seedling physiology and on the primary and secondary metabolisms in the shoot are realized at organ and organism levels. Nanomaterials interact with the beneficial ecological partners of plants. The effects of NMs on plant growth-promoting rhizobacteria and legume-rhizobia symbiosis can be stimulating or inhibitory, depending on the concentration and type of NM. Nanomaterials exert a negative effect on arbuscular mycorrhiza, and vice versa. Pollinators are exposed to NMs, which may affect plant reproduction. The substances released by the roots influence the availability of NMs in the rhizosphere and components of plant cells trigger internalization, translocation, and transformation of NMs. Understanding of the multilevel and bidirectional relationship between plants and NMs is of great relevance in practice.

RevDate: 2023-03-22
CmpDate: 2023-03-22

Forootan E (2023)

GIS-based slope-adjusted curve number methods for runoff estimation.

Environmental monitoring and assessment, 195(4):489.

Accurate estimation of surface runoff and determination of susceptible lands to runoff generation in ungauged watersheds were the problems for hydrologic engineering which could be predicted through a simple model such as Soil Conservation Service Curve Number (SCS-CN). Due to the slope effects on this method, slope adjustment for curve number was developed to improve its precision. So, the main objectives of this study were to apply GIS-based slope SCS-CN approaches for surface runoff estimation and compare the accuracy of three slope-adjusted models including: (a) model with three empirical parameters, (b) model with two parameters slope function, and (c) model with one parameter in the region located in the central part of Iran. For this purpose, soil texture, hydrologic soil group, land use, slope, and daily rainfall volume maps were utilized. In order to provide the curve number map of the study area, land use and hydrologic soil group layers built in Arc-GIS were intersected and the curve number was determined. Then, three slope adjustment equations were used to modify curve numbers of AMC-II by employing slope map. Finally, recorded runoff data of the hydrometric station were applied to assess the performance of the models through four statistical indicators of the root mean square error (RMSE), the Nash-Sutcliffe efficiency (E), the coefficient of determination [Formula: see text], and percent bias (PB). Land use map analysis showed that rangeland was the dominant land use, whereas the soil texture map specified the greatest and smallest area belonging to loam and sandy loam textures, respectively. Although the runoff results showed the overestimation of large rainfall values and underestimation for rainfall with less than 40 mm volume in both models, the values of E (0.78), RMSE (2), PB (16), and [Formula: see text] (0.88) revealed that eq. (a) with three empirical parameters was the most accurate equation. The maximum percent of runoff generated by rainfall for eqs. (a), (b), and (c) were 68.43, 67.28, and 51.57% which showed that bareland located in south part with the slope of more than 5% was susceptible to runoff generation and should be paid attention to watershed management.

RevDate: 2023-03-23
CmpDate: 2023-03-23

D'Emic MD, O'Connor PM, Sombathy RS, et al (2023)

Developmental strategies underlying gigantism and miniaturization in non-avialan theropod dinosaurs.

Science (New York, N.Y.), 379(6634):811-814.

In amniotes, the predominant developmental strategy underlying body size evolution is thought to be adjustments to the rate of growth rather than its duration. However, most theoretical and experimental studies supporting this axiom focus on pairwise comparisons and/or lack an explicit phylogenetic framework. We present the first large-scale phylogenetic comparative analysis examining developmental strategies underlying the evolution of body size, focusing on non-avialan theropod dinosaurs. We reconstruct ancestral states of growth rate and body mass in a taxonomically rich dataset, finding that contrary to expectations, changes in the rate and duration of growth played nearly equal roles in the evolution of the vast body size disparity present in non-avialan theropods-and perhaps that of amniotes in general.

RevDate: 2023-03-21
CmpDate: 2023-03-21

Wabnitz K, Schwienhorst-Stich EM, Asbeck F, et al (2022)

National Planetary Health learning objectives for Germany: A steppingstone for medical education to promote transformative change.

Frontiers in public health, 10:1093720.

Physicians play an important role in adapting to and mitigating the adverse health effects of the unfolding climate and ecological crises. To fully harness this potential, future physicians need to acquire knowledge, values, skills, and leadership attributes to care for patients presenting with environmental change-related conditions and to initiate and propel transformative change in healthcare and other sectors of society including, but not limited to, the decarbonization of healthcare systems, the transition to renewable energies and the transformation of transport and food systems. Despite the potential of Planetary Health Education (PHE) to support medical students in becoming agents of change, best-practice examples of mainstreaming PHE in medical curricula remain scarce both in Germany and internationally. The process of revising and updating the Medical Licensing Regulations and the National Competency-based Catalog of Learning Objectives for Medical Education in Germany provided a window of opportunity to address this implementation challenge. In this article, we describe the development and content of national Planetary Health learning objectives for Germany. We anticipate that the learning objectives will stimulate the development and implementation of innovative Planetary Health teaching, learning and exam formats in medical schools and inform similar initiatives in other health professions. The availability of Planetary Health learning objectives in other countries will provide opportunities for cross-country and interdisciplinary exchange of experiences and validation of content, thus supporting the consolidation of Planetary Health learning objectives and the improvement of PHE for all health professionals globally.

RevDate: 2023-03-19

Newbury JB, Arseneault L, Moffitt TE, et al (2023)

Socioenvironmental Adversity and Adolescent Psychotic Experiences: Exploring Potential Mechanisms in a UK Longitudinal Cohort.

Schizophrenia bulletin pii:7080660 [Epub ahead of print].

BACKGROUND AND HYPOTHESIS: Children exposed to socioenvironmental adversities (eg, urbanicity, pollution, neighborhood deprivation, crime, and family disadvantage) are more likely to subsequently develop subclinical psychotic experiences during adolescence (eg, hearing voices, paranoia). However, the pathways through which this occurs have not been previously investigated. We hypothesized that cognitive ability and inflammation would partly explain this association.

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

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

CONCLUSIONS: Cognitive ability, especially crystallized ability, may partly explain the association between childhood socioenvironmental adversity and adolescent psychotic experiences. Interventions to support cognitive development among children living in disadvantaged settings could buffer them against developing subclinical psychotic phenomena.

RevDate: 2023-03-21
CmpDate: 2023-03-21

Kasmi Y, Eschbach E, R Hanel (2023)

Mare-MAGE curated reference database of fish mitochondrial genes.

BMC genomic data, 24(1):18.

Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.

RevDate: 2023-03-17

Zhang B, Zheng T, Zheng X, et al (2023)

Dynamics of upstream saltwater intrusion driven by tidal river in coastal aquifers.

The Science of the total environment pii:S0048-9697(23)01473-0 [Epub ahead of print].

For the coastal aquifers, recent research have shown that the tidal has a significant effect on saltwater intrusion in the near-shore aquifer. However, it is currently unclear how the tidal river contributes to the groundwater flow and salinity distribution in the upstream aquifer of the estuary. This study examined the effects of a tidal river on the dynamic characteristics of groundwater flow and salt transport in a tidal river-coastal aquifer system using field monitoring data and numerical simulations. It was found that changes in tidal-river level led to the reversal of groundwater flow. For a tidal cycle, the maximum area of seawater intrusion is about 41.16 km[2] at the end of the high tide stage. Then the area gradually decreased to 39.02 km[2] at the end of the low tide stage. More than 2 km[2] area variation can be observed in a tidal cycle. Compared to the low tide stage, the area of SWI increased by 5 % at high tide stage. The SWI region was also spreading landward from the tidal river. In addition, we quantified the water exchange and salt flux between the tidal river and aquifer. When the tidal fell below the level of the riverbed, the water exchange rate was stabilized at about -1.6 m/h. The negative value indicated that the river was recharged by the groundwater. With the increasing of tidal water level, the water exchange rate gradually changes from negative to positive and reached the maximum value of 3.2 m/h at the beginning of the falling tide stage. The presence of a physical river dam can amplify the difference in water level between high and low tides, thereby enhancing the influence of a tidal river on water exchange and salt flux. The findings lay the foundation for gaining a comprehensive understanding of the tidal river on groundwater flow and salt transport in upstream aquifers.

RevDate: 2023-03-18

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 garden grass-veneer, Chrysoteuchia culmella (Linnaeus, 1758).

Wellcome open research, 7:248.

We present a genome assembly from an individual male Chrysoteuchia culmella (the garden grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 645 megabases in span. The majority of the assembly (99.81%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 21,251 protein coding genes.

RevDate: 2023-03-20
CmpDate: 2023-03-20

Morais LS, Pimentel SVT, Kawa H, et al (2023)

Temporal trend of congenital syphilis in the most populous municipality of metropolitan region II of Rio de Janeiro state.

Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo, 41:e2021337.

OBJECTIVE: This study aimed to explore the temporal trend in congenital syphilis, according to sociodemographic and prenatal care in the city of São Gonçalo - Rio de Janeiro, from 2007 to 2018.

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

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

CONCLUSIONS: We identified high congenital syphilis incidences and crescent trends, especially in more vulnerable groups, pointing to social and healthcare inequalities. Prenatal care needs to be more comprehensive and qualified, primarily for young, low-educated, and black women.

RevDate: 2023-03-20
CmpDate: 2023-03-20

Zhang X, Shao W, Huo Y, et al (2023)

The effects of short-term dietary exposure to SiO2 nanoparticle on the domesticated lepidopteran insect model silkworm (Bombyx mori): Evidence from the perspective of multi-omics.

Chemosphere, 323:138257.

Silicon dioxide nanoparticles (nSiO2) are one of the widely utilized nanoparticle (NPSs) materials, and exposure to nSiO2 is ubiquitous. With the increasing commercialization of nSiO2, the potential risk of nSiO2 release to the health and the ecological environment have been attracted more attention. In this study, the domesticated lepidopteran insect model silkworm (Bombyx mori) was utilized to evaluate the biological effects of dietary exposure to nSiO2. Histological investigations showed that nSiO2 exposure resulted in midgut tissue injury in a dose-dependent manner. Larval body mass and cocoon production were reduced by nSiO2 exposure. ROS burst was not triggered, and the activities of antioxidant enzymes were induced in the midgut of silkworm exposure to nSiO2. RNA-sequencing revealed that the differentially expressed genes induced by nSiO2 exposure were predominantly enriched into xenobiotics biodegradation and metabolism, lipid, and amino acid metabolism pathways. 16 S rDNA sequencing revealed that nSiO2 exposure altered the microbial diversity in the gut of the silkworm. Metabolomics analysis showed that the combined uni- and multivariate analysis identified 28 significant differential metabolites from the OPLS-DA model. These significant differential metabolites were predominantly enriched into the metabolic pathways, including purine metabolism and tyrosine metabolism and so. Spearman correlation analysis and the Sankey diagram established the relationship between microbe and metabolites, and some genera may play crucial and pleiotropic functions in the interaction between microbiome and host. These findings indicated that nSiO2 exposure could impact the dysregulation of genes related to xenobiotics metabolism, gut dysbiosis, and metabolic pathways and provided a valuable reference for assessing nSiO2 toxicity from a multi-dimensional perspective.

RevDate: 2023-03-20
CmpDate: 2023-03-20

Jiang X, Sun Y, Qu Y, et al (2023)

The development and future frontiers of global ecological restoration projects in the twenty-first century: a systematic review based on scientometrics.

Environmental science and pollution research international, 30(12):32230-32245.

Ecological restoration projects are becoming a mainstream of research, and their studies are widely followed by scholars worldwide, yet there is no comprehensive review of this research. Nowadays, bibliometrics has attracted much attention from the scientific community, and its methodological approach allows quantitative and qualitative analysis of research performance in journals or subject areas. This paper provides a systematic and comprehensive description of the progress and hotspots of ecological restoration projects from a bibliometric perspective, based on 1173 articles in the Web of Science Core Collection (WOSCC) database. Research on ecological restoration projects has shown a positive growth trend since the twenty-first century. China and the USA are the most active countries in terms of the number of relevant articles published, and more than half of the top 10 active institutions are from China, but there is less collaboration between different countries/institutions. Research in ecological restoration projects is summarized into three main research areas: the main ecological damage problems, the impact of human beings on ecological damage, and the main methods of ecological restoration. Finally, some challenges and outlooks conducive to the rapid and balanced development of ecological restoration projects are presented, which provide valuable references and help for future researchers.

RevDate: 2023-03-18

Viner AC, Malata MP, Mtende M, et al (2022)

Implementation of a novel ultrasound training programme for midwives in Malawi: A mixed methods evaluation using the RE-AIM framework.

Frontiers in health services, 2:953677.

INTRODUCTION: Despite recommendation that all women receive an ultrasound in pregnancy prior to 24 weeks', this remains unavailable to many women in low-income countries where trained practitioners are scarce. Although many programmes have demonstrated efficacy, few have achieved longterm sustainability, with a lack of information about how best to implement such programmes. This mixed-methods study aimed to evaluate the implementation of a novel education package to teach ultrasound-naive midwives in Malawi basic obstetric ultrasound, assessing its impact in the context of the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework.

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

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

CONCLUSION: This programme was successful in improving trainees' knowledge, confidence and skill in performing basic obstetric ultrasound, largely on account of an adaptive approach to implementation. The maintenance of ongoing support was challenging, reflected by trainee dissatisfaction. By evaluating the success of this education package based on its implementation and not just its efficacy, we have generated new insights into the barriers to sustainable upscale, specifically those surrounding maintenance.

RevDate: 2023-03-15

Zhang H, Wang X, Song R, et al (2023)

Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational-Experimental Synergy Study on Emerging Pollutants.

Environmental science & technology [Epub ahead of print].

Metabolism, especially by CYP450 enzymes, is the main reason for mediating the toxification and detoxification of xenobiotics in humans, while some uncommon metabolic pathways, especially for emerging pollutants, probably causing idiosyncratic toxicity are easily overlooked. The pollution of sulfonamide antibiotics in aqueous system has attracted increasing public attention. Hydroxylation of the central amine group can trigger a series of metabolic processes of sulfonamide antibiotics in humans; however, this work parallelly reported the coupling and fragmenting initiated by amino H-abstraction of sulfamethoxazole (SMX) catalyzed by human CYP450 enzymes. Elucidation of the emerging metabolic profiles was mapped via a multistep synergy between computations and experiments, involving preliminary DFT computations and in vitro and in vivo assays, profiling adverse effects, and rationalizing the fundamental factors via targeted computations. Especially, the confirmed SMX dimer was shown to potentially act as a metabolism disruptor in humans, while spin aromatic delocalization resulting in the low electron donor ability of amino radicals was revealed as the fundamental factor to enable coupling of sulfonamide antibiotics by CYP450 through the nonconventional nonrebound pathway. This work may further strengthen the synergistic use of computations prior to experiments to avoid wasteful experimental screening efforts in environmental chemistry and toxicology.

RevDate: 2023-03-16

Helmer EH, Kay S, Marcano-Vega H, et al (2023)

Multiscale predictors of small tree survival across a heterogeneous tropical landscape.

PloS one, 18(3):e0280322 pii:PONE-D-22-10318.

Uncertainties about controls on tree mortality make forest responses to land-use and climate change difficult to predict. We tracked biomass of tree functional groups in tropical forest inventories across Puerto Rico and the U.S. Virgin Islands, and with random forests we ranked 86 potential predictors of small tree survival (young or mature stems 2.5-12.6 cm diameter at breast height). Forests span dry to cloud forests, range in age, geology and past land use and experienced severe drought and storms. When excluding species as a predictor, top predictors are tree crown ratio and height, two to three species traits and stand to regional factors reflecting local disturbance and the system state (widespread recovery, drought, hurricanes). Native species, and species with denser wood, taller maximum height, or medium typical height survive longer, but short trees and species survive hurricanes better. Trees survive longer in older stands and with less disturbed canopies, harsher geoclimates (dry, edaphically dry, e.g., serpentine substrates, and highest-elevation cloud forest), or in intervals removed from hurricanes. Satellite image phenology and bands, even from past decades, are top predictors, being sensitive to vegetation type and disturbance. Covariation between stand-level species traits and geoclimate, disturbance and neighboring species types may explain why most neighbor variables, including introduced vs. native species, had low or no importance, despite univariate correlations with survival. As forests recovered from a hurricane in 1998 and earlier deforestation, small trees of introduced species, which on average have lighter wood, died at twice the rate of natives. After hurricanes in 2017, the total biomass of trees ≥12.7 cm dbh of the introduced species Spathodea campanulata spiked, suggesting that more frequent hurricanes might perpetuate this light-wooded species commonness. If hurricane recovery favors light-wooded species while drought favors others, climate change influences on forest composition and ecosystem services may depend on the frequency and severity of extreme climate events.

RevDate: 2023-03-17
CmpDate: 2023-03-16

Young WJ, Haessler J, Benjamins JW, et al (2023)

Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.

Nature communications, 14(1):1411.

The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.

RevDate: 2023-03-16
CmpDate: 2023-03-16

Tucker C, Brandt M, Hiernaux P, et al (2023)

Sub-continental-scale carbon stocks of individual trees in African drylands.

Nature, 615(7950):80-86.

The distribution of dryland trees and their density, cover, size, mass and carbon content are not well known at sub-continental to continental scales[1-14]. This information is important for ecological protection, carbon accounting, climate mitigation and restoration efforts of dryland ecosystems[15-18]. We assessed more than 9.9 billion trees derived from more than 300,000 satellite images, covering semi-arid sub-Saharan Africa north of the Equator. We attributed wood, foliage and root carbon to every tree in the 0-1,000 mm year[-1] rainfall zone by coupling field data[19], machine learning[20-22], satellite data and high-performance computing. Average carbon stocks of individual trees ranged from 0.54 Mg C ha[-1] and 63 kg C tree[-1] in the arid zone to 3.7 Mg C ha[-1] and 98 kg tree[-1] in the sub-humid zone. Overall, we estimated the total carbon for our study area to be 0.84 (±19.8%) Pg C. Comparisons with 14 previous TRENDY numerical simulation studies[23] for our area found that the density and carbon stocks of scattered trees have been underestimated by three models and overestimated by 11 models, respectively. This benchmarking can help understand the carbon cycle and address concerns about land degradation[24-29]. We make available a linked database of wood mass, foliage mass, root mass and carbon stock of each tree for scientists, policymakers, dryland-restoration practitioners and farmers, who can use it to estimate farmland tree carbon stocks from tablets or laptops.

RevDate: 2023-03-16
CmpDate: 2023-03-16

Cai S, Zhao X, Pittelkow CM, et al (2023)

Optimal nitrogen rate strategy for sustainable rice production in China.

Nature, 615(7950):73-79.

Avoiding excessive agricultural nitrogen (N) use without compromising yields has long been a priority for both research and government policy in China[1,2]. Although numerous rice-related strategies have been proposed[3-5], few studies have assessed their impacts on national food self-sufficiency and environmental sustainability and fewer still have considered economic risks faced by millions of smallholders. Here we established an optimal N rate strategy based on maximizing either economic (ON) or ecological (EON) performance using new subregion-specific models. Using an extensive on-farm dataset, we then assessed the risk of yield losses among smallholder farmers and the challenges of implementing the optimal N rate strategy. We find that meeting national rice production targets in 2030 is possible while concurrently reducing nationwide N consumption by 10% (6-16%) and 27% (22-32%), mitigating reactive N (Nr) losses by 7% (3-13%) and 24% (19-28%) and increasing N-use efficiency by 30% (3-57%) and 36% (8-64%) for ON and EON, respectively. This study identifies and targets subregions with disproportionate environmental impacts and proposes N rate strategies to limit national Nr pollution below proposed environmental thresholds, without compromising soil N stocks or economic benefits for smallholders. Thereafter, the preferable N strategy is allocated to each region based on the trade-off between economic risk and environmental benefit. To facilitate the adoption of the annually revised subregional N rate strategy, several recommendations were provided, including a monitoring network, fertilization quotas and smallholder subsidies.

RevDate: 2023-03-15
CmpDate: 2023-03-15

Kohyama TI, Sheil D, Sun IF, et al (2023)

Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia.

Nature communications, 14(1):1113.

Despite their fundamental importance the links between forest productivity, diversity and climate remain contentious. We consider whether variation in productivity across climates reflects adjustment among tree species and individuals, or changes in tree community structure. We analysed data from 60 plots of humid old-growth forests spanning mean annual temperatures (MAT) from 2.0 to 26.6 °C. Comparing forests at equivalent aboveground biomass (160 Mg C ha[-1]), tropical forests ≥24 °C MAT averaged more than double the aboveground woody productivity of forests <12 °C (3.7 ± 0.3 versus 1.6 ± 0.1 Mg C ha[-1] yr[-1]). Nonetheless, species with similar standing biomass and maximum stature had similar productivity across plots regardless of temperature. We find that differences in the relative contribution of smaller- and larger-biomass species explained 86% of the observed productivity differences. Species-rich tropical forests are more productive than other forests due to the high relative productivity of many short-stature, small-biomass species.

RevDate: 2023-03-14

Lim T, Lee K, Kim RH, et al (2023)

Effects of black raspberry extract on gut microbiota, microbial metabolites, and expressions of the genes involved in cholesterol and bile acid metabolisms in rats fed excessive choline with a high-fat diet.

Food science and biotechnology, 32(4):577-587.

UNLABELLED: In our previous study, black raspberry (BR) reduced the serum levels of trimethylamine-N-oxide and cholesterol in rats fed excessive choline with a high-fat diet (HFC). We hypothesized that gut microbiota could play a crucial role in the production of trimethylamine and microbial metabolites, and BR could influence gut microbial composition. This study aimed to elucidate the role of BR on changes in gut microbiota and microbial metabolites in the rats. The phylogenetic diversity of gut microbiota was reduced in the rats fed HFC, while that in the BR-fed group was restored. The BR supplementation enriched Bifidobacterium and reduced Clostridium cluster XIVa. In the BR-fed group, most cecal bile acids and hippuric acid increased, while serum lithocholic acid was reduced. The BR supplementation upregulated Cyp7a1 and downregulated Srebf2. These results suggest that BR extract may change gut bacterial community, modulate bile acids, and regulate gene expression toward reducing cholesterol.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01267-4.

RevDate: 2023-03-14

Martinez ND (2023)

Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology.

Ecology and evolution, 13(3):e9872.

Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.

RevDate: 2023-03-14
CmpDate: 2023-03-14

Zeng L, C Liu (2023)

Exploring Factors Affecting Urban Park Use from a Geospatial Perspective: A Big Data Study in Fuzhou, China.

International journal of environmental research and public health, 20(5):.

Promoting research on urban park use is important for developing the ecological and environmental health benefits of parks. This study proposes uniquely integrated methods combined with big data to measure urban park use. It combines comprehensive geographic detectors and multiscale geographically weighted regression from a geospatial perspective to quantify the individual and interactive effects of the parks' characteristics, accessibility, and surrounding environment features on weekday and weekend park use. The study also explores the degree of influence of spatial changes. The results indicate that the park-surrounding facilities and services factor contributed most to use, while its interaction effect with park service capacity had the greatest impact on park use. The interaction effects showed binary or nonlinear enhancement. This suggests that park use should be promoted within multiple dimensions. Many influencing factors had significant changes in the geographic space, suggesting that city-level park zoning construction should be adopted. Finally, park use was found to be affected by users' subjective preference on weekends and convenience factors on weekdays. These findings provide a theoretical basis for the influencing mechanisms of urban park use, which can help urban planners and policymakers formulate more specific policies to successfully manage and plan urban parks.

RevDate: 2023-03-13

Würstle S, Hapfelmeier A, Karapetyan S, et al (2023)

Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study.

Diagnostics (Basel, Switzerland), 13(5):.

Ascitic fluid infection is a serious complication of liver cirrhosis. The distinction between the more common spontaneous bacterial peritonitis (SBP) and the less common secondary peritonitis in patients with liver cirrhosis is crucial due to the varying treatment approaches. This retrospective multicentre study was conducted in three German hospitals and analysed 532 SBP episodes and 37 secondary peritonitis episodes. Overall, >30 clinical, microbiological, and laboratory parameters were evaluated to identify key differentiation criteria. Microbiological characteristics in ascites followed by severity of illness and clinicopathological parameters in ascites were the most important predictors identified by a random forest model to distinguish between SBP and secondary peritonitis. To establish a point-score model, a least absolute shrinkage and selection operator (LASSO) regression model selected the ten most promising discriminatory features. By aiming at a sensitivity of 95% either to rule out or rule in SBP episodes, two cut-off scores were defined, dividing patients with infected ascites into a low-risk (score ≥ 45) and high-risk group (score < 25) for secondary peritonitis. Overall, the discrimination of secondary peritonitis from SBP remains challenging. Our univariable analyses, random forest model, and LASSO point score may help clinicians with the crucial differentiation between SBP and secondary peritonitis.

RevDate: 2023-03-14

Paixão TM, Siqueira CEG, Tristan-Cheever E, et al (2023)

Overweight and Obesity in Brazilian Immigrants in Massachusetts, USA: A Time Series Analysis (2009-2020).

Obesity facts, 16(2):109-118.

INTRODUCTION: Obesity is considered a growing public health problem by the Brazilian Ministry of Health and a global epidemic by the World Health Organization (WHO). In 2020, the Centers for Disease Control and Prevention (CDC) estimated the prevalence of adult obesity at 31.9% in the USA. The USA is one of the main destinations for Brazilian immigrants in search of better living conditions, and Massachusetts is one of the states with the highest presence of Brazilians. Changes in lifestyle and eating habits are often associated with increases in overweight and obesity in immigrants in the USA, especially Hispanics, an official classification that does not, however, include Brazilians. The aim of this study was to describe the temporal trend of overweight and obesity in Brazilian immigrants assisted by the Cambridge Health Alliance (CHA) healthcare network in Massachusetts.

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

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

CONCLUSION: As little is known about the health of Brazilian immigrants in the USA, this study contributes to the literature on the subject. The observed increasing trends agree with the worldwide increase in obesity and indicate the need for future research exploring individual factors associated with immigrant acculturation.

RevDate: 2023-03-13

Chan YO, Dietz N, Zeng S, et al (2023)

The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis.

BMC genomics, 24(1):107.

BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize.

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

CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website (https://soykb.org/SoybeanAlleleCatalogTool/), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website (https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana). Researchers can use this tool to connect variant alleles of genes with meta-information of species.

RevDate: 2023-03-13
CmpDate: 2023-03-13

de Nies L, Galata V, Martin-Gallausiaux C, et al (2023)

Altered infective competence of the human gut microbiome in COVID-19.

Microbiome, 11(1):46.

BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

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

CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.

RevDate: 2023-03-13
CmpDate: 2023-03-13

Rubenstein DR, J Solomon (2023)

Target-enriched enzymatic methyl sequencing: Flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation.

PloS one, 18(3):e0282672.

The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling (Lamprotornis superbus), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.

RevDate: 2023-03-11

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 yellow-legged clearwing, Synanthedon vespiformis (Linnaeus, 1761).

Wellcome open research, 7:233.

We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length.

RevDate: 2023-03-09

Mallinson DC, Elwert F, DB Ehrenthal (2023)

Spillover Effects of Prenatal Care Coordination on Older Siblings Beyond the Mother-Infant Dyad.

Medical care, 61(4):206-215.

BACKGROUND: Pregnancy care coordination increases preventive care receipt for mothers and infants. Whether such services affect other family members' health care is unknown.

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

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

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

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

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

CONCLUSION: PNCC may only have spillover effects on siblings' preventive care in selected subpopulations but not in the broader population of Wisconsin families.

RevDate: 2023-03-10
CmpDate: 2023-03-08

Wei Z, Jian Z, Sun Y, et al (2023)

Ecological sustainability and high-quality development of the Yellow River Delta in China based on the improved ecological footprint model.

Scientific reports, 13(1):3821.

Aiming at the traditional ecological footprint model, the improved ecological footprint of the carbon footprint effectively makes up for the singularity of the ecological footprint's consideration of carbon emissions, and plays an important role in promoting high-quality development and ecological sustainability. This paper selects 2015, 2018 and 2020 as important time points for the study, corrects the ecological footprint parameter factors based on net primary productivity (NPP), measures the ecological footprint after the improvement of the carbon footprint, studies the spatial and temporal variation in the ecological footprint at the 100-m grid scale with the support of IPCC greenhouse gas inventory analysis, and analyzes the current ecological conservation status of the Yellow River Delta. Additionally, in the context of a low carbon economy, the decoupling index of carbon emissions and GDP is extended to the evaluation and analysis of high-quality development. The study showed that (1) the ecological footprint of the Yellow River Delta has increased year by year, from 0.721 hm[2]·person[- 1] to 0.758 hm[2]·person[- 1], an average annual increase of 2.9%; the ecological carrying capacity has decreased from 0.40 hm[2]·person[- 1] to 0.31 hm[2]·person[- 1], an overall decrease of 28.59%. (2) The overall ecological deficit of the Yellow River Delta grid is lightly overloaded, with most of the ecological surplus occurring in the northern and eastern parts of the study area and a few moderate and heavy overloads in the center of the core area where there is a lot of built-up land and the area is small and easy to gather. (3) Based on the low-carbon economy analysis, 2015, 2017 and 2020 reach absolute decoupling and are in the ideal scenario. However, in the rest of the years, carbon emissions and economic development are still in a large contradiction, and decoupling has fluctuated and varied greatly in the last six years. The effective combination of ecological footprint and low carbon economy analysis provides an important theoretical basis for improving ecological conservation and achieving high-quality development.

RevDate: 2023-03-10
CmpDate: 2023-03-10

Wang H, Harrison SP, Li M, et al (2022)

The China plant trait database version 2.

Scientific data, 9(1):769.

Plant functional traits represent adaptive strategies to the environment, linked to biophysical and biogeochemical processes and ecosystem functioning. Compilations of trait data facilitate research in multiple fields from plant ecology through to land-surface modelling. Here we present version 2 of the China Plant Trait Database, which contains information on morphometric, physical, chemical, photosynthetic and hydraulic traits from 1529 unique species in 140 sites spanning a diversity of vegetation types. Version 2 has five improvements compared to the previous version: (1) new data from a 4-km elevation transect on the edge of Tibetan Plateau, including alpine vegetation types not sampled previously; (2) inclusion of traits related to hydraulic processes, including specific sapwood conductance, the area ratio of sapwood to leaf, wood density and turgor loss point; (3) inclusion of information on soil properties to complement the existing data on climate and vegetation (4) assessments and flagging the reliability of individual trait measurements; and (5) inclusion of standardized templates for systematical field sampling and measurements.

RevDate: 2023-03-08

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 sallow kitten, Furcula furcula (Clerck, 1759).

Wellcome open research, 7:229.

We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.

RevDate: 2023-03-09
CmpDate: 2023-03-09

Zhu M, Wang Z, Yang Y, et al (2023)

Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau.

Molecular ecology, 32(6):1411-1424.

Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. Numerous genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.

RevDate: 2023-03-08
CmpDate: 2023-03-08

Lippi CA, Rund SSC, SJ Ryan (2023)

Characterizing the Vector Data Ecosystem.

Journal of medical entomology, 60(2):247-254.

A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct control and mitigation efforts. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and serving approaches, means that it is distributed across many formats and data types. Data ranges from collections records to molecular characterization, geospatial data to interactions of vectors and traits, infection experiments to field trials. New initiatives arise, often spanning the effort traditionally siloed in specific research disciplines, and other efforts wane, perhaps in response to funding declines, different research directions, or lack of sustained interest. Thusly, the world of vector data - the Vector Data Ecosystem - can become unclear in scope, and the flows of data through these various efforts can become stymied by obsolescence, or simply by gaps in access and interoperability. As increasing attention is paid to creating FAIR (Findable Accessible Interoperable, and Reusable) data, simply characterizing what is 'out there', and how these existing data aggregation and collection efforts interact, or interoperate with each other, is a useful exercise. This study presents a snapshot of current vector data efforts, reporting on level of accessibility, and commenting on interoperability using an illustration to track a specimen through the data ecosystem to understand where it occurs for the database efforts anticipated to describe it (or parts of its extended specimen data).

RevDate: 2023-03-07

Zhang J, H Qian (2023)

U.Taxonstand: An R package for standardizing scientific names of plants and animals.

Plant diversity, 45(1):1-5.

The scientific names of organisms are key identifiers of plants and animals. Correctly treating scientific names is a prerequisite for biodiversity research and documentation. Here, we present an R package, 'U.Taxonstand', which can standardize and harmonize scientific names in plant and animal species lists at a fast speed and at a high rate of matching success. Unlike most of other similar R packages each of which works with only one taxonomic database, U.Taxonstand can work with all taxonomic databases, as long as they are properly formatted. Multiple databases for plants and animals that can be directly used by U.Taxonstand, which include bryophytes, vascular plants, amphibians, birds, fishes, mammals, and reptiles, are available online. U.Taxonstand can be a very useful tool for botanists, zoologists, ecologists and biogeographers to standardize and harmonize scientific names of organisms.

RevDate: 2023-03-07

Hayward A, Lohse K, Laetsch DR, et al (2022)

The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758).

Wellcome open research, 7:315.

We present a genome assembly from an individual male Plebejus argus (silver-studded blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 382 megabases in span. The entire assembly (100%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 27.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,693 protein coding genes.

RevDate: 2023-03-07
CmpDate: 2023-03-07

Nosenko T, Zimmer I, Ghirardo A, et al (2023)

Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis.

Fungal genetics and biology : FG & B, 165:103779.

Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.

RevDate: 2023-03-06

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 Seraphim, Lobophora halterata (Hufnagel, 1767).

Wellcome open research, 7:313.

We present a genome assembly from an individual female Lobophora halterata (the Seraphim; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 315 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules with the Z and W sex chromosomes assembled. The mitochondrial genome has also been assembled and is 15.7 kilobases in length.

RevDate: 2023-03-06

Hawkes W, Wotton K, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2022)

The genome sequence of the dumpy grass hoverfly, Melanostoma mellinum (Linnaeus, 1758).

Wellcome open research, 7:59.

We present a genome assembly from an individual male Melanostoma mellinum (the dumpy grass hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 731 megabases in span. The majority of the assembly (99.67%) is scaffolded into five chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 16.1 kilobases in length.

RevDate: 2023-03-06

Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2022)

The genome sequence of the large yellow underwing, Noctua pronuba (Linnaeus, 1758).

Wellcome open research, 7:119.

We present a genome assembly from an individual female Noctua pronuba (the large yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 529 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.

RevDate: 2023-03-05

Zhang GZ, Chen SL, LL Dong (2023)

[Traditional Chinese medicine microbiomics and its research strategies].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 48(3):596-607.

The tight relationships between microbiome and traditional Chinese medicine(TCM)have been widely recognized. New technologies, results, and theories are emerging in the field of microbiomics in recent years with the advances in high-throughput sequencing and multi-omics technologies. Based on the previous research, the present study has proposed the concept of TCM microbiomics(TCMM), which is an interdisciplinary subject aiming at elucidating the functions and applications of microbiome in the areas of herb resources, herb processing, herb storage, and clinical effects by using modern technology of biology, ecology, and informatics. This subject essentially contains the structures, functions, interactions, molecular mechanisms, and application strategies of the microbiome associated with the quality, safety, and efficacy of TCM. Firstly, the development of the TCMM concept was summarized, with the profound understanding of TCMM on the complexity and entirety of microbiome being emphasized. Then, the research contents and applications of TCMM in promoting the sustainable development of herb resources, improving the standardization and diversification of herb fermentation, strengthening the safety of herb storage, and resolving the scientific connotation of theories and clinical efficacy of TCM are reviewed. Finally, the research strategies and methods of TCM microbiomics were elaborated from basic research, application research, and system research. TCMM is expected to promote the integrative development of TCM with frontier science and technology, thereby expanding the depth and scope of TCM study and facilitating TCM modernization.

RevDate: 2023-03-04

Lin J, Yu D, Pan R, et al (2023)

Improved YOLOX-Tiny network for detection of tobacco brown spot disease.

Frontiers in plant science, 14:1135105.

INTRODUCTION: Tobacco brown spot disease caused by Alternaria fungal species is a major threat to tobacco growth and yield. Thus, accurate and rapid detection of tobacco brown spot disease is vital for disease prevention and chemical pesticide inputs.

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

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

DISCUSSION: Therefore, the YOLO-Tobacco network satisfies both the advantages of high detection accuracy and fast detection speed. It will likely have a positive impact on early monitoring, disease control, and quality assessment in diseased tobacco plants.

RevDate: 2023-03-06
CmpDate: 2023-03-06

Nanjala R, Nyasimi F, Masiga D, et al (2023)

A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya.

PLoS computational biology, 19(3):e1010904.

The demand for well-trained bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialization in bioinformatics. Graduates are often unaware of the career opportunities in bioinformatics, and those who are may lack mentors to help them choose a specialization. The Bioinformatics Mentorship and Incubation Program seeks to bridge the gap by laying the foundation for a bioinformatics training pipeline using project-based learning. The program selects six participants through an intensive open recruitment exercise for highly competitive students to join the program for four months. The six interns undergo intensive training within the first one and a half months before being assigned to mini-projects. We track the progress of the interns weekly through code review sessions and a final presentation at the end of the four months. We have trained five cohorts, most of whom have secured master's scholarships within and outside the country and job opportunities. We demonstrate the benefit of structured mentorship using project-based learning in filling the training gap after undergraduate programs to generate well-trained bioinformaticians who are competitive in graduate programs and bioinformatics jobs.

RevDate: 2023-03-06

Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2021)

The genome sequence of the swallow prominent, Pheosia tremula (Clerck, 1759).

Wellcome open research, 6:335.

We present a genome assembly from an individual male Pheosia tremula (the swallow prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 290 megabases in span. The majority of the assembly, 99.94%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.

RevDate: 2023-03-06

Hawkes W, Wotton K, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2021)

The genome sequence of the tapered dronefly, Eristalis pertinax (Scopoli, 1763).

Wellcome open research, 6:292.

We present a genome assembly from an individual male Eristalis tenax (the tapered dronefly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 487 megabases in span. The majority of the assembly (95.23%) is scaffolded into seven chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.

RevDate: 2023-03-04

Hawkes W, Wotton K, Smith M, et al (2021)

The genome sequence of the two-banded wasp hoverfly, Chrysotoxum bicinctum (Linnaeus, 1758).

Wellcome open research, 6:321.

We present a genome assembly from an individual female Chrysotoxum bicinctum (the two-banded wasp hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 913 megabases in span. The majority of the assembly (98.81%) is scaffolded into five chromosomal pseudomolecules, with the X sex chromosome assembled.

RevDate: 2023-03-03

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 merveille du jour, Griposia aprilina (Linnaeus, 1758).

Wellcome open research, 7:247.

We present a genome assembly from an individual Griposia aprilina (the merveille du jour; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 720 megabases in span. The majority of the assembly (99.89%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

RevDate: 2023-03-03

Broad GR, Boyes D, Natural History Museum Genome Acquisition Lab, et al (2022)

The genome sequence of the setaceous Hebrew character, Xestia c-nigrum, (Linnaeus, 1758).

Wellcome open research, 7:295.

We present a genome assembly from an individual male Xestia c-nigrum (the setaceous Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 760 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.

RevDate: 2023-03-02

Keuschnig C, Vogel TM, Barbaro E, et al (2023)

Selection processes of Arctic seasonal glacier snowpack bacterial communities.

Microbiome, 11(1):35.

BACKGROUND: Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.

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

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

CONCLUSIONS: These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.

RevDate: 2023-03-02

Liu X, Wang Y, Meng X, et al (2023)

Improved method for benthic ecosystem health assessment by integrating chemical indexes into multiple biological indicator species-A case study of the Baiyangdian Lake, China.

Journal of environmental management, 335:117530 pii:S0301-4797(23)00318-3 [Epub ahead of print].

A comprehensive and scientific assessment of benthic ecosystem health is key to the rational selection of endogenous pollution reduction technologies for lakes. However, current assessments are mainly limited to biological indicators and ignore the actual benthic ecosystem situations, such as the impact of eutrophication and heavy metal pollution, which may lead to the one-sidedness of the evaluation results. In this study, taking Baiyangdian Lake, the largest shallow mesotrophic-eutrophic lake in the North China Plain, as an example, the chemical assessment index and biological integrity index were first combined to estimate the biological conditions, nutritional status and heavy metal pollution of lakes. The indicator system incorporated three biological assessments (benthic index of biotic integrity (B-IBI), submerged aquatic vegetation index of biological integrity (SAV-IBI) and microbial index of biological integrity (M-IBI)) and three chemical assessments (dissolved oxygen (DO), comprehensive trophic level index (TLI) and index of geoaccumulation (Igeo)). Twenty-three attributes of B-IBI, fourteen attributes of SAV-IBI and twelve attributes of M-IBI were screened by range, responsiveness, and redundancy tests to keep the core metrics that were significantly correlated with disturbance gradients or showed strong discriminatory power between reference and impaired sites. The assessment results of B-IBI, SAV-IBI, and M-IBI showed significant differences in the response to anthropogenic activities and seasonal change, among which the submerged plants showed more significant seasonal differences. It is difficult to reach a comprehensive conclusion regarding the benthic ecosystem health status based on a single biological community. In comparison with biological indicators, the score of chemical indicators is relatively low. DO, TLI and Igeo provide an essential supplement for the benthic ecosystem health assessment of lakes with eutrophication and heavy metal pollution problems. Using the new integrated assessment method, the benthic ecosystem health of Baiyangdian Lake was rated as fair, especially the northern parts of the lake adjacent to the inflow mouth of the Fu River, which were in poor condition, indicating that the lake has experienced anthropogenic disturbance, resulting in eutrophication, heavy metal pollution and biological community degradation. Whether it's spring or summer, the integrated assessment method provides a more plausible and comprehensive view of benthic ecosystem health under the pressure of increasing human activities and changing habitat and hydrological conditions, overcoming the narrow perspective and uncertainties of the single-index method. Thus, it can assist lake managers in providing technical support for ecological indication and restoration.

RevDate: 2023-03-03

Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2021)

The genome sequence of the snout, Hypena proboscidalis (Linnaeus, 1758).

Wellcome open research, 6:236.

We present a genome assembly from an individual female Hypena proboscidalis (the snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 637 megabases in span. The majority of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.

RevDate: 2023-03-01

Nocci M, Villa G, Ragazzoni L, et al (2023)

Relationship between intensive care surge capacity and hospital factors: an extensive experience.

Internal and emergency medicine [Epub ahead of print].

As a prolonged surge scenario, the COVID-19 pandemic has offered an unparalleled opportunity to improve hospital surge capacity (SC) understanding and the ability to manage it. In this study, the authors report the experience of a large hospital network and evaluate potential relationships between Intensive Care Units SC (ICU-SC) and some hospital-related variables: bed occupancy, emergency department admissions, ward admission from ED, and elective surgery procedures. Pearson's partial correlation coefficient (r) has been used to define the relationship between SC and the daily values of the above variables, collected through a dedicated digital platform that also ensured a regular quality check of the data. The observation has concerned several levels of analysis, namely two different types of SC calculation (SC base-SCb and SC actual-SCa), hospital category level and multi-hospital level, and two consecutive pandemic waves. Among the 16 hospitals observed, the correlation was shown to be moderate-positive with non-ICU bed occupancy (r/ = 0.62, r/ = 0.54), strong/moderate with ICU bed occupancy (r/ = 0.72, r/ = 0.54), and moderate with ward admissions from ED (r/ = 0.50, r/ = 0.51) On the contrary, the correlation proved to be moderate-negative with ED admissions (r/ = - 0.69, r/ = - 0.62) and low with the number of elective surgery procedures (r/ = - 0.10, r/ = - 0.16). This study identified a positive correlation between SC and three variables monitored: ICU bed occupancy, non-ICU bed occupancy, and ward admissions from ED. On the contrary, the correlation was negative for ED admission and the number of elective surgery procedures. The results have been confirmed across all levels of analysis adopted.

RevDate: 2023-03-01

Jones DL, Rhymes JM, Green E, et al (2023)

Poor air passenger knowledge of COVID-19 symptoms and behaviour undermines strategies aimed at preventing the import of SARS-CoV-2 into the UK.

Scientific reports, 13(1):3494.

Air travel mediates transboundary movement of SARS-CoV-2. To prepare for future pandemics, we sought to understand air passenger behaviour and perceived risk during the COVID-19 pandemic. This study of UK adults (n = 2103) quantified knowledge of COVID-19 symptoms, perceived health risk of contracting COVID-19, likelihood of returning to the UK with COVID-19 symptoms, likelihood to obey self-quarantining guidelines, how safe air travellers felt when flying during the pandemic (n = 305), and perceptions towards face covering effectiveness.Overall knowledge of COVID-19 symptoms was poor. Men and younger age groups (18-44) were less informed than women and older age groups (44 +). A significant proportion (21%) of the population would likely travel back to the UK whilst displaying COVID-19 symptoms with many expressing that they would not fully comply with self-isolation guidelines. Overall, males and younger age groups had a reduced perceived personal risk from contracting COVID-19, posing a higher risk of transporting SARS-CoV-2 back to the UK. Poor passenger knowledge and behaviour undermines government guidelines and policies aimed at preventing SARS-CoV-2 entry into the UK. This supports the need for stricter, clearer and more targeted guidelines with point-of-departure viral testing and stricter quarantining upon arrival.

RevDate: 2023-03-01

Kushwaha B, Nagpure NS, Srivastava S, et al (2023)

Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes.

Gene pii:S0378-1119(23)00135-X [Epub ahead of print].

Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (28 commercially important, 10 vulnerable and 14 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.

RevDate: 2023-03-01

Streng K, de Best PA, Timen A, et al (2023)

Rapid response screening for emerging zoonotic pathogens, barriers and opportunities: A study for enhanced preparedness of the Netherlands.

One health (Amsterdam, Netherlands), 16:100507.

BACKGROUND: Outbreaks of zoonotic emerging infectious diseases (EIDs) require rapid identification of potential reservoir hosts and mapping disease spread in these hosts to inform risk assessment and adequate control measures. Animals are often understudied when a novel EID is detected in humans and acquisition of animal samples is hampered by practical, ethical, and legal barriers, of which there is currently no clear overview. Therefore, the three aims of this study are (1) to map potentially available collections of animal samples, (2) to assess possibilities and barriers for reuse of these samples and (3) to assess possibilities and barriers for active animal and environmental sampling in the Netherlands.

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

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

CONCLUSION: The animal sample collections identified would be very valuable for use in outbreak investigations. Barriers for sharing may be overcome by increasing familiarity with legislation, building (international) sharing networks and agreements before crises occur and developing systems for sample registration and biobanking. Proactive setting up of ethical approvals will allow for rapid animal sample collection to identify EID hosts and potential spillovers.

RevDate: 2023-03-01
CmpDate: 2023-03-01

Di Paolo S, Nijmeijer EM, Bragonzoni L, et al (2023)

Definition of High-Risk Motion Patterns for Female ACL Injury Based on Football-Specific Field Data: A Wearable Sensors Plus Data Mining Approach.

Sensors (Basel, Switzerland), 23(4):.

The aim of the present study was to investigate if the presence of anterior cruciate ligament (ACL) injury risk factors depicted in the laboratory would reflect at-risk patterns in football-specific field data. Twenty-four female footballers (14.9 ± 0.9 year) performed unanticipated cutting maneuvers in a laboratory setting and on the football pitch during football-specific exercises (F-EX) and games (F-GAME). Knee joint moments were collected in the laboratory and grouped using hierarchical agglomerative clustering. The clusters were used to investigate the kinematics collected on field through wearable sensors. Three clusters emerged: Cluster 1 presented the lowest knee moments; Cluster 2 presented high knee extension but low knee abduction and rotation moments; Cluster 3 presented the highest knee abduction, extension, and external rotation moments. In F-EX, greater knee abduction angles were found in Cluster 2 and 3 compared to Cluster 1 (p = 0.007). Cluster 2 showed the lowest knee and hip flexion angles (p < 0.013). Cluster 3 showed the greatest hip external rotation angles (p = 0.006). In F-GAME, Cluster 3 presented the greatest knee external rotation and lowest knee flexion angles (p = 0.003). Clinically relevant differences towards ACL injury identified in the laboratory reflected at-risk patterns only in part when cutting on the field: in the field, low-risk players exhibited similar kinematic patterns as the high-risk players. Therefore, in-lab injury risk screening may lack ecological validity.

RevDate: 2023-03-01
CmpDate: 2023-03-01

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

How to avoid a local epidemic becoming a global pandemic.

Proceedings of the National Academy of Sciences of the United States of America, 120(10):e2220080120.

Here, we combine international air travel passenger data with a standard epidemiological model of the initial 3 mo of the COVID-19 pandemic (January through March 2020; toward the end of which the entire world locked down). Using the information available during this initial phase of the pandemic, our model accurately describes the main features of the actual global development of the pandemic demonstrated by the high degree of coherence between the model and global data. The validated model allows for an exploration of alternative policy efficacies (reducing air travel and/or introducing different degrees of compulsory immigration quarantine upon arrival to a country) in delaying the global spread of SARS-CoV-2 and thus is suggestive of similar efficacy in anticipating the spread of future global disease outbreaks. We show that a lesson from the recent pandemic is that reducing air travel globally is more effective in reducing the global spread than adopting immigration quarantine. Reducing air travel out of a source country has the most important effect regarding the spreading of the disease to the rest of the world. Based upon our results, we propose a digital twin as a further developed tool to inform future pandemic decision-making to inform measures intended to control the spread of disease agents of potential future pandemics. We discuss the design criteria for such a digital twin model as well as the feasibility of obtaining access to the necessary online data on international air travel.

RevDate: 2023-02-27

Hou H, Liu H, Xiong J, et al (2023)

Comparison of Soil Bacterial Communities under Canopies of Pinus tabulaeformis and Populus euramericana in a Reclaimed Waste Dump.

Plants (Basel, Switzerland), 12(4):.

To compare the effects of different remediation tree species on soil bacterial communities and provide a theoretical basis for the selection of ecosystem function promotion strategies after vegetation restoration, the characteristic changes in soil bacterial communities after Pinus tabulaeformis and Populus euramericana reclamation were explored using high-throughput sequencing and molecular ecological network methods. The results showed that: (1) With the increase in reclamation years, the reclaimed soil properties were close to the control group, and the soil properties of Pinus tabulaeformis were closer to the control group than those of P. euramericana. (2) The dominant bacteria under the canopies of P. tabulaeformis and P. euramericana was the same. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Bacteroidetes, and Cyanobacteria were the dominant bacteria in the restored soil, accounting for more than 95% of the total abundance. The average values of the Shannon diversity index, Simpson diversity index, Chao 1 richness estimator, and abundance-based coverage estimator of the bacterial community in the P. euramericana reclaimed soil were higher than those in the P. tabulaeformis reclaimed soil. The influence of reclamation years on the bacterial community of samples is greater than that of species types. (3) The results of ecological network construction showed that the total number of nodes, total number of connections, and average connectivity of the soil bacterial network under P. euramericana reclamation were greater than those under P. tabulaeformis reclamation. The bacterial molecular ecological network under P. euramericana was more abundant. (4) Among the dominant bacteria, the relative abundance of Actinobacteria was negatively correlated with soil pH, soil total nitrogen content, and the activities of urease, invertase, and alkaline phosphatase, while the relative abundance of Proteobacteria and Bacteroidetes was positively correlated with these environmental factors. The relationship between the soil bacterial community of P. tabulaeformis and P. euramericana and the environmental factors is not completely the same, and even the interaction between some environmental factors and bacteria is opposite.

RevDate: 2023-02-27

Jocienė L, Krokaitė E, Rekašius T, et al (2023)

Ionomic Parameters of Populations of Common Juniper (Juniperus communis L.) Depending on the Habitat Type.

Plants (Basel, Switzerland), 12(4):.

For the study of the ionomic parameters of Juniperus communis needles, fourteen sites covering most of the territory of Lithuania and belonging to distinct habitats (coastal brown dunes covered with natural Scots pine forests (G), Juniperus communis scrubs (F), transition mires and quaking bogs (D), subcontinental moss Scots pine forests (G), and xero-thermophile fringes) were selected. Concentrations of macro-, micro-, and non-essential elements were analyzed in current-year needles, sampled in September. According to the concentrations of elements in J. communis needles, the differences between the most contrasting populations were as follows: up to 2-fold for Mg, N, K, Ca, and Zn; 2- to 7-fold for P, Na, Fe, Cu, Al, Cr, Ni, and Pb; and 26- to 31-fold for Mn and Cd. The concentrations of Cd, Cr, and Ni in needles of J. communis did not reach levels harmful for conifers. When compared to all other habitats (B, F, G, and E), the populations from transition mires and quaking bogs (D) had significantly lower concentrations of main nutritional elements N (12176 µg/g d. m.), P (1054 µg/g d. m.), and K (2916 µg/g d. m.). In Juniperus communis scrubs (F), a habitat protected by EUNIS, the concentration of K in the needles was highest, while Zn and Cu concentrations were the lowest. Principal component (PC) analyses using concentrations of 15 elements as variables for the discrimination of populations or habitats allowed authors to distinguish F and B habitats from the E habitat (PC1) and F and D habitats from the G habitat (PC2). Discriminating between populations, the most important variables were concentrations of P, N, Mg, Ca, Cu, and K. Discriminating between habitats, the important variables were concentrations of N and P.

RevDate: 2023-02-27
CmpDate: 2023-02-27

Ben Aribi H, Ding M, A Kiran (2022)

Gene expression data visualization tool on the o[2]S[2]PARC platform.

F1000Research, 11:1267.

Background: The identification of differentially expressed genes and their associated biological processes, molecular function, and cellular components are essential for genetic disease studies because they present potential biomarkers and therapeutic targets. Methods: In this study, we developed an o[2]S[2]PARC template to instantiate an interactive pipeline for gene expression data visualization, ontological mapping, and statistical evaluation. To demonstrate the tool's usefulness, we performed a case study on a publicly available dataset. Results: The tool enables users to identify the differentially expressed genes (DEGs) and visualize them in a volcano plot format. Ontologies associated with the DEGs are assigned and visualized in barplots. Conclusions: The "Expression data visualization" template is publicly available on the o[2]S[2]PARC platform.

RevDate: 2023-02-27
CmpDate: 2023-02-27

Huo J, Hu X, Bai J, et al (2023)

Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection.

Frontiers in immunology, 14:1098455.

The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.

RevDate: 2023-02-27
CmpDate: 2023-02-27

Wylie MS, Colasante T, De France K, et al (2023)

Momentary emotion regulation strategy use and success: Testing the influences of emotion intensity and habitual strategy use.

Emotion (Washington, D.C.), 23(2):375-386.

Successful emotion regulation (ER) is important for a wide range of psychosocial outcomes. Specific ER strategies have been identified as being more or less likely to be successful. However, recent evidence suggests significant individual differences in the association between strategy implementation and ER success. Indeed, 2 key factors may play an important role in moderating the link between ER strategy use and ER success in the moment: (a) the intensity of the specific emotional experience, and (b) the relative frequency in using a given ER strategy. Experience-sampling across 14-days (N = 304, Mage = 19.14, % female = 87.5) was used to assess whether emotion intensity and trait ER strategy use were differentially associated with perceived regulatory success depending on which ER strategy was used. Multilevel modeling revealed that more intense emotions were associated with lower perceived success for all strategies. Additionally, habitual reappraisal predicted greater success and habitual rumination predicted lower success. We discuss the possibility that results reflected intensity-based ER strategy choices and add to the growing call to abandon the reductive labeling of ER strategies as either "adaptive" or "maladaptive." (PsycInfo Database Record (c) 2023 APA, all rights reserved).

RevDate: 2023-02-25

Visztra GV, Frei K, Hábenczyus AA, et al (2023)

Applicability of Point- and Polygon-Based Vegetation Monitoring Data to Identify Soil, Hydrological and Climatic Driving Forces of Biological Invasions-A Case Study of Ailanthus altissima, Elaeagnus angustifolia and Robinia pseudoacacia.

Plants (Basel, Switzerland), 12(4): pii:plants12040855.

Invasive tree species are a significant threat to native flora. They modify the environment with their allelopathic substances and inhibit the growth of native species by shading, thus reducing diversity. The most effective way to control invasive plants is to prevent their spread which requires identifying the environmental parameters promoting it. Since there are several types of invasive plant databases available, determining which database type is the most relevant for investigating the occurrence of alien plants is of great importance. In this study, we compared the efficiency and reliability of point-based (EUROSTAT Land Use and Coverage Area Frame Survey (LUCAS)) and polygon-based (National Forestry Database (NFD)) databases using geostatistical methods in ArcGIS software. We also investigated the occurrence of three invasive tree species (Ailanthus altissima, Elaeagnus angustifolia, and Robinia pseudoacacia) and their relationships with soil, hydrological, and climatic parameters such as soil organic matter content, pH, calcium carbonate content, rooting depth, water-holding capacity, distance from the nearest surface water, groundwater depth, mean annual temperature, and mean annual precipitation with generalized linear models in R-studio software. Our results show that the invasion levels of the tree species under study are generally over-represented in the LUCAS point-based vegetation maps, and the point-based database requires a dataset with a larger number of samples to be reliable. Regarding the polygon-based database, we found that the occurrence of the invasive species is generally related to the investigated soil and hydrological and climatic factors.

RevDate: 2023-02-25

Wang J, Qin S, Fan R, et al (2023)

Plant Growth Promotion and Biocontrol of Leaf Blight Caused by Nigrospora sphaerica on Passion Fruit by Endophytic Bacillus subtilis Strain GUCC4.

Journal of fungi (Basel, Switzerland), 9(2): pii:jof9020132.

Passion fruit (Passiflora edulis Sims) is widely cultivated in tropic and sub-tropic regions for the production of fruit, flowers, cosmetics, and for pharmacological applications. Its high economic, nutritional, and medical values elicit the market demand, and the growing areas are rapidly increasing. Leaf blight caused by Nigrospora sphaerica is a new and emerging disease of passion fruit in Guizhou, in southwest China, where the unique karst mountainous landscape and climate conditions are considered potential areas of expansion for passion fruit production. Bacillus species are the most common biocontrol and plant-growth-promotion bacteria (PGPB) resources in agricultural systems. However, little is known about the endophytic existence of Bacillus spp. in the passion fruit phyllosphere as well as their potential as biocontrol agents and PGPB. In this study, 44 endophytic strains were isolated from 15 healthy passion fruit leaves, obtained from Guangxi province, China. Through purification and molecular identification, 42 of the isolates were ascribed to Bacillus species. Their inhibitory activity against N. sphaerica was tested in vitro. Eleven endophytic Bacillus spp. strains inhibited the pathogen by >65%. All of them produced biocontrol- and plant-growth-promotion-related metabolites, including indole-3-acetic acid (IAA), protease, cellulase, phosphatase, and solubilized phosphate. Furthermore, the plant growth promotion traits of the above 11 endophytic Bacillus strains were tested on passion fruit seedlings. One isolate, coded B. subtilis GUCC4, significantly increased passion fruit stem diameter, plant height, leaf length, leaf surface, fresh weight, and dry weight. In addition, B. subtilis GUCC4 reduced the proline content, which indicated its potential to positively regulate passion fruit biochemical properties and resulted in plant growth promotion effects. Finally, the biocontrol efficiencies of B. subtilis GUCC4 against N. sphaerica were determined in vivo under greenhouse conditions. Similarly to the fungicide mancozeb and to a commercial B. subtilis-based biofungicide, B. subtilis GUCC4 significantly reduced disease severity. These results suggest that B. subtilis GUCC4 has great potential as a biological control agent and as PGPB on passion fruit.

RevDate: 2023-02-25

Srygley RB, Dudley R, Hernandez EJ, et al (2023)

Quantifying the Aerodynamic Power Required for Flight and Testing for Adaptive Wind Drift in Passion-Vine Butterflies Heliconius sara (Lepidoptera: Nymphalidae).

Insects, 14(2): pii:insects14020112.

Although theoretical work on optimal migration has been largely restricted to birds, relevant free-flight data are now becoming available for migratory insects. Here we report, for the first time in passion-vine butterflies, that Heliconius sara migrates directionally. To test optimal migration models for insects, we quantified the aerodynamic power curve for free-flying H. sara as they migrated across the Panama Canal. Using synchronized stereo-images from high-speed video cameras, we reconstructed three-dimensional flight kinematics of H. sara migrating naturally across the Panama Canal. We also reconstructed flight kinematics from a single-camera view of butterflies flying through a flight tunnel. We calculated the power requirements for flight for H. sara over a range of flight velocities. The relationship between aerodynamic power and velocity was "J"-shaped across the measured velocities with a minimum power velocity of 0.9 m/s and a maximum range velocity of 2.25 m/s. Migrating H. sara did not compensate for crosswind drift. Changes in airspeed with tailwind drift were consistent with the null hypothesis that H. sara did not compensate for tailwind drift, but they were also not significantly different from those predicted to maximize the migratory range of the insects.

RevDate: 2023-02-25

Liu J, Chen J, Yang Y, et al (2023)

Construction and Optimization of an Ecological Network in the Yellow River Source Region Based on MSPA and MCR Modelling.

International journal of environmental research and public health, 20(4): pii:ijerph20043724.

The source region of the Yellow River (SRYR) is an important water conservation and farming area in China. Under the dual influence of the natural environment and external pressure, ecological patches in the region are becoming increasingly fragmented, and landscape connectivity is continuously declining, which directly affect the landscape patch pattern and SRYR sustainable development. In the SRYR, morphological spatial pattern analysis (MSPA) and landscape index methods were used to extract ecologically important sources. Based on the minimum cumulative resistance model (MCR), Linkage Mapper was used to generate a potential corridor, and then potential stepped stone patches were identified and extracted by the gravity model and betweenness centrality to build an optimal SRYR ecological network. The distribution of patches in the core area of the SRYR was fragmented, accounting for 80.53% of the total grassland area. The 10 ecological sources based on the landscape connectivity index and 15 important corridors identified based on the MCR model were mainly distributed in the central and eastern regions of the SRYR. Through betweenness centrality, 10 stepped stone patches were added, and 45 planned ecological corridors were obtained to optimize the SRYR ecological network and enhance east and west connectivity. Our research results can provide an important reference for the protection of the SRYR ecosystem, and have important guiding significance and practical value for ecological network construction in ecologically fragmented areas.

RevDate: 2023-02-25

Li Y, Liu H, Su L, et al (2023)

Developmental Features, Influencing Factors, and Formation Mechanism of Underground Mining-Induced Ground Fissure Disasters in China: A Review.

International journal of environmental research and public health, 20(4): pii:ijerph20043511.

Mining-induced ground fissures are one of the major geological disasters affecting coal mines. In recent years, many effective monitoring methods have been developed to explore the developmental characteristics and nature of mining-induced ground fissures for being treated scientifically. This paper is mainly on the development law and mechanism of mining ground fissure research results which have been comprehensively combed, highlighting the development trend, including the formation condition, development features, influencing factors, and mechanical mechanism of mining-induced ground fissures. Outstanding issues are discussed and future research hot spots and trends are pointed out. The major conclusions include: (1) under the shallow coal mining condition, because the rock layer fault zone directly reaches the surface, the ground fissure usually develops seriously; (2) mining-induced ground fissures are generally divided into four types: tensile fissures, compression fissures, collapsed fissures, and sliding fissures; (3) mining-induced ground fissures are affected by the coupling effect of underground mining and surface topography. The main factors are geological mining conditions, surface deformation, and surface topography, including rock and soil structure, rock and soil mechanical properties, surface horizontal deformation, surface slope, and so on; and (4) to ensure the safety of underground mining, temporary ground fissures formed during the process of coal mining must be treated when ground fissures and rock ground fissures are connected. The results of this article make up for the deficiencies of the relevant research, provide the basis and direction for future research, and have universal applicability and scientific guiding significance.

RevDate: 2023-02-24

Martínez-Pernía D, Olavarría L, Fernández-Manjón B, et al (2023)

The limitations and challenges in the assessment of executive dysfunction associated with real-world functioning: The opportunity of serious games.

Applied neuropsychology. Adult [Epub ahead of print].

Nowadays, there is a broad range of methods for detecting and evaluating executive dysfunction ranging from clinical interview to neuropsychological evaluation. Nevertheless, a critical issue of these assessments is the lack of correspondence of the neuropsychological test's results with real-world functioning. This paper proposes serious games as a new framework to improve the neuropsychological assessment of real-world functioning. We briefly discuss the contribution and limitations of current methods of evaluation of executive dysfunction (paper-and-pencil tests, naturalistic observation methods, and Information and Communications Technologies) to inform on daily life functioning. Then, we analyze what are the limitations of these methods to predict real-world performance: (1) A lack of appropriate instruments to investigate the complexity of real-world functioning, (2) the vast majority of neuropsychological tests assess well-structured tasks, and (3) measurement of behaviors are based on simplistic data collection and statistical analysis. This work shows how serious games offer an opportunity to develop more efficient tools to detect executive dysfunction in everyday life contexts. Serious games provide meaningful narrative stories and virtual or real environments that immerse the user in natural and social environments with social interactions. In those highly interactive game environments, the player needs to adapt his/her behavioral performance to novel and ill-structured tasks which are suited for collecting user interaction evidence. Serious games offer a novel opportunity to develop better tools to improve diagnosis of the executive dysfunction in everyday life contexts. However, more research is still needed to implement serious games in everyday clinical practice.

RevDate: 2023-02-24

Wei T, Guo G, Li H, et al (2023)

A novel probability integral method segmental modified model for subsidence prediction applicable to thick loose layer mining areas.

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

In response to the problem that the actual extent of coal mining impacts on the surface in thick loose layer mines significantly exceeds the theoretical predictions, based on the literature study, the form of influence of thick loose layer on the predicted parameters of the probability integral method is summarized and analyzed; taking into account the influence of the subsidence coefficient, the sine modification formula of the major influence radius and the logistic modification formula of the subsidence coefficient are established, respectively, and based on the characteristics of the major influence radius, a new subsidence basin demarcation point is proposed and a novel probability integral method segmental parameter modified prediction model is constructed. The simulated experiment and real data experiment results prove that the constructed probability integral method segmented parameter modified model can both reduce the convergence of surface subsidence basin edge better and take into account the predicted accuracy inside the subsidence basin. The research achievements provide scientific data support for disaster warning, pollution management, ecological restoration, and coordination between coal mining and surface city construction in thick loose layer mining areas.

RevDate: 2023-02-24
CmpDate: 2023-02-24

Woodhouse A, Swain A, Fagan WF, et al (2023)

Late Cenozoic cooling restructured global marine plankton communities.

Nature, 614(7949):713-718.

The geographic ranges of marine organisms, including planktonic foraminifera[1], diatoms, dinoflagellates[2], copepods[3] and fish[4], are shifting polewards owing to anthropogenic climate change[5]. However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear[6]. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences[7]. The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms[1,2,8] in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios.

RevDate: 2023-02-24
CmpDate: 2023-02-24

Zhou T, W Li (2023)

Analysis on Logistics Efficiency Measurement of New Western Land-Sea Corridor under the Background of "Double Carbon" and Ecological Environment Protection.

Journal of environmental and public health, 2023:8642841.

Under the research background of ecological environment protection and "double carbon" goal, this paper applies panel data on the logistics industry from 2010 to 2019 in 12 provinces of China's new western land-sea corridor to statically measure the logistics industry's technical efficiency after taking into account the impact of different environmental elements and to analyze the dynamics trends of total factor productivity in the logistics sector. It is measured by using the three-stage SBM model and the Malmquist-Luenberger productivity index, which considers undesirable output. The findings indicate the following: (1) In the context of "double carbon," the overall technical efficiency of the logistics sector in the new western land-sea corridor seems to be relatively low; however, the average technical efficiency of the logistics sector in the southern portion of the new western land-sea corridor does seem to be higher than that of the northern part. (2) The logistics industry's technical efficiency varies greatly by region, with locations near central China having much higher technical efficiency than remote inland areas. (3) The fundamental reason for the improvement of technical efficiency in the logistics industry is pure technical efficiency, and the driving force behind the increase in total factor productivity is technological advancement. (4) Economic development, informatization development, industrial market scale, and import and export all have a substantial influence on the logistics industry's technical efficiency. Finally, depending on the findings, policy recommendations are offered.

RevDate: 2023-02-22

Rivera-Colón AG, Rayamajhi N, Fazal Minhas B, et al (2023)

Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.

Molecular biology and evolution pii:7035026 [Epub ahead of print].

White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.

RevDate: 2023-02-24
CmpDate: 2023-02-24

Tian L, Wang L, Zhang X, et al (2023)

Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.

Environmental science and pollution research international, 30(9):24284-24298.

The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.

RevDate: 2023-02-23
CmpDate: 2023-02-23

Niu L, Zhagn L, Xi F, et al (2023)

[Influencing factors and scenario forecasting of carbon emissions in Liaoning Province, China].

Ying yong sheng tai xue bao = The journal of applied ecology, 34(2):499-509.

Liaoning is a province with large energy consumption and carbon emissions. Management of carbon emissions in Liaoning Province is crucial to realizing China's carbon peaking and carbon neutrality goals. To clarify the driving factors and trends of carbon emissions in Liaoning Province, we analyzed the impacts of six factors on carbon emissions in Liaoning Province through STIRPAT model based on carbon emission data from 1999 to 2019. The impact factors included population, urbanization rate, per-capita GDP, secondary industry ratio, energy consumption per unit GDP, and coal consumption ratio. Nine forecasting scenarios with three economic and population growth models and three emission reduction models were set up, and their carbon emission trends under the above nine forecasting scenarios were predicted. The results showed that the main driving factor of carbon emissions in Liaoning Province was per-capita GDP, and that the main inhibitor was energy consumption per unit GDP. The carbon peak year in Liaoning Province would fluctuate between 2020 and 2055 under the nine forecasting scenarios, with peak values ranging from 544 to 1088 million tons CO2. The medium economic development growth and high carbon emission reduction scenario would be the optimal carbon emission scenario in Liaoning Province. Under this forecasting scenario, Liaoning Province could achieve carbon peak (611 million tons CO2) by 2030 without affec-ting economic development through optimizing energy structure and controlling the intensity of energy consumption. Our results would be helpful for seeking the best path for carbon emission reduction in Liaoning Province and providing a reference for its realization of carbon peaking and carbon neutrality goals.

RevDate: 2023-02-16

Wang J, Ding R, Ouyang T, et al (2023)

Systematic investigation of the mechanism of herbal medicines for the treatment of prostate cancer.

Aging, 15: pii:204516 [Epub ahead of print].

Due to various unpleasant side effects and general ineffectiveness of current treatments for prostate cancer (PCa), more and more people with PCa try to look for complementary and alternative medicine such as herbal medicine. However, since herbal medicine has multi-components, multi-targets and multi-pathways features, its underlying molecular mechanism of action is not yet known and still needs to be systematically explored. Presently, a comprehensive approach consisting of bibliometric analysis, pharmacokinetic assessment, target prediction and network construction is firstly performed to obtain PCa-related herbal medicines and their corresponding candidate compounds and potential targets. Subsequently, a total of 20 overlapping genes between DEGs in PCa patients and the target genes of the PCa-related herbs, as well as five hub genes, i.e., CCNA2, CDK2, CTH, DPP4 and SRC were determined employing bioinformatics analysis. Further, the roles of these hub genes in PCa were also investigated through survival analysis and tumour immunity analysis. Moreover, to validate the reliability of the C-T interactions and to further explore the binding modes between ingredients and their targets, the molecular dynamics (MD) simulations were carried out. Finally, based on the modularization of the biological network, four signaling pathways, i.e., PI3K-Akt, MAPK, p53 and cell cycle were integrated to further analyze the therapeutic mechanism of PCa-related herbal medicine. All the results show the mechanism of action of herbal medicines on treating PCa from the molecular to systematic levels, providing a reference for the treatment of complex diseases using TCM.

RevDate: 2023-02-22
CmpDate: 2023-02-17

Suzuki S, Nishikawa Y, Okada H, et al (2023)

Information-seeking behaviour of community pharmacists during the COVID-19 pandemic: an ecological study.

BMJ open, 13(2):e062465.

OBJECTIVE: To evaluate the information-seeking behaviour of pharmacists during the COVID-19 pandemic and its relation to COVID-19 and related infections and deaths within the local prefecture.

DESIGN: Ecological study.

SETTING: Japan-47 prefectures.

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

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

CONCLUSIONS: The information-seeking behaviour of community pharmacists correlated positively with infection status within the community.

RevDate: 2023-02-22
CmpDate: 2023-02-22

Gautam P, Pandey AK, SK Dubey (2023)

Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid.

Environmental research, 221:115271.

The residual imidacloprid, a widely used insecticide is causing serious environmental concerns. Knowledge of its biodegradation will help in assessing its residual mass in soil. In view of this, a soil microcosm-based study was performed to test the biodegradation potential of Agrobacterium sp. InxBP2. It achieved ∼88% degradation in 20 days and followed the pseudo-first-order kinetics (k = 0.0511 day[-1] and t1/2=7 days). Whole genome sequencing of Agrobacterium sp. InxBP2 revealed a genome size of 5.44 Mbp with 5179 genes. Imidacloprid degrading genes at loci K7A42_07110 (ABC transporter substrate-binding protein), K7A42_07270 (amidohydrolase family protein), K7A42_07385 (ABC transporter ATP-binding protein), K7A42_16,845 (nitronate monooxygenase family protein), and K7A42_20,660 (FAD-dependent monooxygenase) having sequence and functional similarity with known counterparts were identified. Molecular docking of proteins encoded by identified genes with their respective degradation pathway intermediates exhibited significant binding energies (-6.56 to -4.14 kcal/mol). Molecular dynamic simulation discovered consistent interactions and binding depicting high stability of docked complexes. Proteome analysis revealed differential protein expression in imidacloprid treated versus untreated samples which corroborated with the in-silico findings. Further, the detection of metabolites proved the bacterial degradation of imidacloprid. Thus, results provided a mechanistic link between imidacloprid and associated degradative genes/enzymes of Agrobacterium sp. InxBP2. These findings will be of immense significance in carrying out the lifecycle analysis and formulating strategies for the bioremediation of soils contaminated with insecticides like imidacloprid.

RevDate: 2023-02-22
CmpDate: 2023-02-22

Petrén H, Köllner TG, RR Junker (2023)

Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv.

The New phytologist, 237(6):2478-2492.

Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and - most importantly - structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.

RevDate: 2023-02-22
CmpDate: 2023-02-22

Nasiruddin M, Islam ARMT, Siddique MAB, et al (2023)

Distribution, sources, and pollution levels of toxic metal(loid)s in an urban river (Ichamati), Bangladesh using SOM and PMF modeling with GIS tool.

Environmental science and pollution research international, 30(8):20934-20958.

Indexical assessment coupled with a self-organizing map (SOM) and positive matrix factorization (PMF) modeling of toxic metal(loid)s in sediment and water of the aquatic environment provides valuable information from the environmental management perspective. However, in northwest Bangladesh, indexical and modeling assessments of toxic metal(loid)s in surface water and sediment are still rare. Toxic metal(loid)s were measured in sediment and surface water from an urban polluted river (Ichamati) in northwest Bangladesh using an atomic absorption spectrophotometer to assess distribution, pollution levels, sources, and potential environmental risks to the aquatic environment. The mean concentrations (mg/kg) of metal(loid)s in water are as follows: Fe (871) > Mn (382) > Cr (72.4) > Zn (34.2) > Co (20.8) > Pb (17.6) > Ni (16.7) > Ag (14.9) > As (9.0) > Cu (5.63) > Cd (2.65), while in sediment, the concentration follows the order, Fe (18,725) > Mn (551) > Zn (213) > Cu (47.6) > Cr (30.2) > Ni (24.2) > Pb (23.8) > Co (9.61) > As (8.23) > Cd (0.80) > Ag (0.60). All metal concentrations were within standard guideline values except for Cr and Pb for water and Cd, Zn, Cu, Pb, and As for sediment. The outcomes of eco-environmental indices, including contamination and enrichment factors and geo-accumulation index, differed spatially, indicating that most of the sediment sites were moderately to highly polluted by Cd, Zn, and As. Cd and Zn content can trigger ecological risks. The positive matrix factorization (PMF) model recognized three probable sources of sediment, i.e., natural source (49.39%), industrial pollution (19.72%), and agricultural source (30.92%), and three possible sources of water, i.e., geogenic source (45.41%), industrial pollution (22.88%), and industrial point source (31.72%), respectively. SOM analysis identified four spatial patterns, e.g., Fe-Mn-Ag, Cd-Cu, Cr-Pb-As-Ni, and Zn-Co in water and three patterns, e.g., Mn-Co-Ni-Cr, Cd-Cu-Pb-Zn, and As-Fe-Ag in sediment. The spatial distribution of entropy water quality index values shows that the southwestern area possesses "poor" quality water. Overall, the levels of metal(loid) pollution in the investigated river surpassed a critical threshold, which might have serious consequences for the river's aquatic biota and human health in the long run.

RevDate: 2023-02-14

Bayer N, Hausmann B, Pandey RV, et al (2023)

Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.

RevDate: 2023-02-16
CmpDate: 2023-02-16

Zhou Y, Hu Z, Geng Q, et al (2023)

Monitoring and analysis of desertification surrounding Qinghai Lake (China) using remote sensing big data.

Environmental science and pollution research international, 30(7):17420-17436.

Desertification is one of the most serious ecological environmental problems in the world. Monitoring the spatiotemporal dynamics of desertification is crucial for its control. The region around Qinghai Lake, in the northeastern part of the Qinghai-Tibet Plateau in China, is a special ecological function area and a climate change sensitive area, making its environmental conditions a great concern. Using cloud computing via Google Earth Engine (GEE), we collected Landsat 5 TM, Landsat 8 OLI/TIRS, and MODIS Albedo images from 2000 to 2020 in the region around Qinghai Lake, acquired land surface albedo (Albedo), and normalized vegetation index (NDVI) to build a remote sensing monitoring model of desertification. Our results showed that the desertification difference index based on the Albedo-NDVI feature space could reflect the degree of desertification in the region around Qinghai Lake. GEE offers significant advantages, such as massive data processing and long-term dynamic monitoring. The desertification land area fluctuated downward in the study area from 2000 to 2020, and the overall desertification status improved. Natural factors, such as climate change from warm-dry to warm-wet and decreased wind speed, and human factors improved the desertification situation. The findings indicate that desertification in the region around Qinghai Lake has been effectively controlled, and the overall desertification trend is improving.

RevDate: 2023-02-14

Dennis A, Cuthbertson DJ, Wootton D, et al (2023)

Multi-organ impairment and long COVID: a 1-year prospective, longitudinal cohort study.

Journal of the Royal Society of Medicine [Epub ahead of print].

OBJECTIVES: To determine the prevalence of organ impairment in long COVID patients at 6 and 12 months after initial symptoms and to explore links to clinical presentation.

DESIGN: Prospective cohort study.

PARTICIPANTS: Individuals.

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

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

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

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

CONCLUSIONS: Organ impairment persisted in 59% of 331 individuals followed up at 1 year post COVID-19, with implications for symptoms, quality of life and longer-term health, signalling the need for prevention and integrated care of long COVID.Trial Registration: ClinicalTrials.gov Identifier: NCT04369807.

RevDate: 2023-02-14

Amin M, Aziz MA, Pieroni A, et al (2023)

Edible wild plant species used by different linguistic groups of Kohistan Upper Khyber Pakhtunkhwa (KP), Pakistan.

Journal of ethnobiology and ethnomedicine, 19(1):6.

BACKGROUND: The mountainous territory of Kohistan shelters diverse food plant species and is considered one of the important hotspots of local plant knowledge. In the era of globalization and food commodification, wild food plants (WFPs) play an important role in supporting local food systems and related local knowledge is one of the important pillars of food sustainability across the region. Since the area is populated by different cultural groups and each culture has retained particular knowledge on the local plant species, therefore, to make a cross-culturally comparison, the study was planned to record and compare the local plants knowledge among three linguistic groups viz Gujjar, Kohistani and Shina in order to not only protect the local knowledge but to determine the food cultural adaptations among these groups looking through the lens of their food ethnobotanies.

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

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

CONCLUSIONS: The study indicates that Kohistan is one of the important spots of biocultural diversity and could be recognized as biocultural refugia. WFPs have been an integral part of the traditional food systems among the studied groups, particularly the Gujjars have reported more distinct plant uses which could be referred to their distinctive ecological experiences among others. However, social change is one of the challenges that might lead to the erosion of local plant knowledge. Moreover, intercultural negotiations among the studied groups are also a matter of concern which could homogenize the local knowledge among them. Therefore, we suggest solid policy measures to protect the local knowledge and celebrate diversity across this mountain territory.

RevDate: 2023-02-13

Mayne SL, DiFiore G, Hannan C, et al (2023)

Feasibility and acceptability of mobile methods to assess home and neighborhood environments related to adolescent sleep.

Sleep health pii:S2352-7218(23)00027-X [Epub ahead of print].

OBJECTIVE: A growing evidence base suggests home and neighborhood environmental exposures may influence adolescent sleep, but few studies have assessed these relationships using methods that account for time-varying, location-specific exposures, or multiple neighborhood contexts. This study aimed to assess the feasibility and acceptability of using smartphone global positioning system (GPS) tracking and ecological momentary assessment (EMA) to assess time-varying home and neighborhood environmental exposures hypothesized to be associated with adolescent sleep.

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

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

CONCLUSIONS: Results demonstrate the feasibility and acceptability of mobile methods for assessing time-varying home and neighborhood exposures relevant to adolescent sleep for up to 1 week.

RevDate: 2023-02-14
CmpDate: 2023-02-14

Liu L, Zhang WQ, Hu FC, et al (2023)

[Evaluation and Optimization of Rural Sewage Treatment Technologies in the Middle Reaches of the Yangtze River Based on Group Decision Making and Analytic Hierarchy Process].

Huan jing ke xue= Huanjing kexue, 44(2):1191-1200.

Rural sewage treatment in the Yangtze River basin is an important link to achieve the great protection of the Yangtze River, but the existing treatment technologies are difficult to choose and have various techniques and a lack of evaluation. Therefore, this study researched and collected the case information of rural sewage treatment projects in the middle reaches of the Yangtze River, analyzed the application of each treatment technology under different collection modes and discharge standards, constructed the evaluation index system of rural sewage treatment technologies, and then conducted a classification evaluation of processing technologies for each application scenario based on group decision making and the Analytic Hierarchy Process. The results showed that:the collection modes of rural sewage in the middle reaches of the Yangtze River were mainly single village or small-scale joint village, the treatment scale was mainly concentrated below 200 m[3]·d[-1], the treatment technology was most applied by the anaerobic+ecological process (28.05%), and the application of integrated equipment was also more widely used (22.47%). The technical performance in the criterion layer had the largest weight (0.5039) in the evaluation index system, followed by those of economic benefits (0.2474), operation and management (0.1559), and environmental impact (0.0928), respectively; the four indicators of TP removal rate, ton water operation cost, ammonia nitrogen removal rate, and maintenance difficulty had higher weights. The evaluation and optimization results showed that the enhanced ecological and anaerobic+ecological treatment technologies were suitable for promotion and application in the rural areas of the middle reaches of the Yangtze River. The results of this study can provide scientific basis and reference for the selection of rural sewage treatment technologies in the middle reaches of the Yangtze River.

RevDate: 2023-02-14
CmpDate: 2023-02-14

Cao H, Ou H, Ju W, et al (2023)

Visual Analysis of International Environmental Security Management Research (1997-2021) Based on VOSviewer and CiteSpace.

International journal of environmental research and public health, 20(3):.

To investigate the international development status and hot trends in the field of environmental security management in recent years, the published the environmental security management literature from 1997 to 2021, which was retrieved from Web of Science, with VOSviewer as the main and CiteSpace as the auxiliary, through the cooperation network of authors, scientific research institutions, and countries. The keywords were visualized by clustering, time zone analysis, and burst analysis. A total of 7596 articles were retrieved, forming six main clustering labels, including 28,144 authors. The research hotspots are from the fields of personal health, society, agriculture, ecological environment, energy, and sustainable development, as well as the development of internet environmental safety management, such as big data, Bayesian networks, and conceptual frameworks. Through cluster analysis, the cooperation of major research teams and scientific research institutions and the cooperation and development between countries were analyzed. The cooperation between scientific research institutions in various countries is relatively close. The United States currently occupies a dominant and authoritative position in this field. China has cooperated more closely with the United States, Britain, Australia, and India.

RevDate: 2023-02-14

Dussex N, van der Valk T, Morales HE, et al (2021)

Population genomics of the critically endangered kākāpō.

Cell genomics, 1(1):100002.

The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.

RevDate: 2023-02-13

Glasgow L, Lewis R, S Charles (2022)

The cancer epidemic in the Caribbean region: Further opportunities to reverse the disease trend.

Lancet regional health. Americas, 13:100295.

Cancer incidence has been rising in the Caribbean and is expected to have significant adverse implications for the health of people in the region and health systems in this decade. While developed countries, for the most part, enjoy the benefits of advanced technologies and adaptive systems in cancer control and management, a different experience confronts a large segment of the Caribbean population. The region has experienced some success in enhancing cancer services, however, there is a need to address gaps in several areas through nationally and regionally tailored initiatives. This Review complements previous publications on the challenges, actions, and progress towards cancer prevention and care in Caribbean countries but also further outlines potential positive impacts that can be derived from addressing gaps pertaining to cancer education, data management, screening and risk assessment, navigation services, gender factors, and resource development. The proposed approaches encapsulate concepts of health theories that are applicable across the ecological domains. When implemented in combination, the proposals may effectively contribute to reducing the cancer burden in the region.

RevDate: 2023-02-13

Shah AA, Badshah L, Khalid N, et al (2023)

Disadvantaged Economic Conditions and Stricter Border Rules Shape Afghan Refugees' Ethnobotany: Insights from Kohat District, NW Pakistan.

Plants (Basel, Switzerland), 12(3):.

The study of migrants' ethnobotany can help to address the diverse socio-ecological factors affecting temporal and spatial changes in local ecological knowledge (LEK). Through semi-structured and in-depth conversations with ninety interviewees among local Pathans and Afghan refugees in Kohat District, NW Pakistan, one hundred and forty-five wild plant and mushroom folk taxa were recorded. The plants quoted by Afghan refugees living inside and outside the camps tend to converge, while the Afghan data showed significant differences with those collected by local Pakistani Pathans. Interviewees mentioned two main driving factors potentially eroding folk plant knowledge: (a) recent stricter border policies have made it more difficult for refugees to visit their home regions in Afghanistan and therefore to also procure plants in their native country; (b) their disadvantaged economic conditions have forced them to engage more and more in urban activities in the host country, leaving little time for farming and foraging practices. Stakeholders should foster the exposure that refugee communities have to their plant resources, try to increase their socio-economic status, and facilitate both their settling outside the camps and their transnational movement for enhancing their use of wild plants, ultimately leading to improvements in their food security and health status.


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

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Curriculum Vitae for R J Robbins

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