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Bibliography on: Ecological Informatics

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ESP: PubMed Auto Bibliography 28 Mar 2024 at 01:47 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 National Science Foundation Datanet projects, DataONE and Data Conservancy.

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®)

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RevDate: 2024-03-26
CmpDate: 2024-03-26

Ouyang YY, Su ZW, Li CH, et al (2024)

Forest fire risk zoning based on fuzzy logic and analytical network process.

Ying yong sheng tai xue bao = The journal of applied ecology, 35(2):354-362.

Forest fires have a significant impact on human life, property safety, and ecological environment. Deve-loping high-quality forest fire risk maps is beneficial for preventing forest fires, guiding resource allocation for firefighting, assisting in fire suppression efforts, and supporting decision-making. With a multi-criteria decision analysis (MCDA) method based on geographic information systems (GIS) and literature review, we assessed the main factors influencing the occurrences of forest fires in Youxi County, Fujian Province. We analyzed the importance of each fire risk factor using the analytic network process (ANP) and assigned weights, and evaluated the sub-standard weights using fuzzy logic assessment. Using ArcGIS aggregation functions, we generated a forest fire risk map and validated it with satellite fire points. The results showed that the areas classified as level 4 or higher fire risk accounted for a considerable proportion in Youxi County, and that the central and northern regions were at higher risk. The overall fire risk situation in the county was severe. The fuzzy ANP model demonstrated a high accuracy of 85.8%. The introduction of this novel MCDA method could effectively improve the accuracy of forest fire risk mapping at a small scale, providing a basis for early fire warning and the planning and allocation of firefighting resources.

RevDate: 2024-03-26
CmpDate: 2024-03-25

Wu J, Lv Y, Hao P, et al (2024)

Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.

Journal of translational medicine, 22(1):300.

BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.

METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.

RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.

CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Liu Y, You S, Ding L, et al (2024)

Hepatotoxic effects of chronic exposure to environmentally relevant concentrations of Di-(2-ethylhexyl) phthalate (DEHP) on crucian carp: Insights from multi-omics analyses.

The Science of the total environment, 923:171447.

Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used phthalate esters (PAEs) that raise growing ecotoxicological concerns due to detrimental effects on living organisms and ecosystems. This study performed hepatotoxic investigations on crucian carp under chronic low-dosage (CLD) exposure to DEHP at environmentally relevant concentrations (20-500 μg/L). The results demonstrated that the CLD exposure induced irreversible damage to the liver tissue. Multi-omics (transcriptomics and metabolomics) analyses revealed the predominant toxicological mechanisms underlying DEHP-induced hepatotoxicity by inhibiting energy production pathways and the up-regulation of the purine metabolism. Disruption of metabolic pathways led to excessive reactive oxygen species (ROS) production and subsequent oxidative stress. The adverse metabolic effects were exacerbated by an interplay between oxidative stress and endoplasmic reticulum stress. This study not only provides new mechanistic insights into the ecotoxicological effects of DEHP under chronic low-dosage exposure, but also suggests a potential strategy for further ecological risk assessment of PAEs.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Alari A, Ranzani O, Olmos S, et al (2024)

Short-term exposure to air pollution and hospital admission after COVID-19 in Catalonia: the COVAIR-CAT study.

International journal of epidemiology, 53(2):.

BACKGROUND: A growing body of evidence has reported positive associations between long-term exposure to air pollution and poor COVID-19 outcomes. Inconsistent findings have been reported for short-term air pollution, mostly from ecological study designs. Using individual-level data, we studied the association between short-term variation in air pollutants [nitrogen dioxide (NO2), particulate matter with a diameter of <2.5 µm (PM2.5) and a diameter of <10 µm (PM10) and ozone (O3)] and hospital admission among individuals diagnosed with COVID-19.

METHODS: The COVAIR-CAT (Air pollution in relation to COVID-19 morbidity and mortality: a large population-based cohort study in Catalonia, Spain) cohort is a large population-based cohort in Catalonia, Spain including 240 902 individuals diagnosed with COVID-19 in the primary care system from 1 March until 31 December 2020. Our outcome was hospitalization within 30 days of COVID-19 diagnosis. We used individual residential address to assign daily air-pollution exposure, estimated using machine-learning methods for spatiotemporal prediction. For each pandemic wave, we fitted Cox proportional-hazards models accounting for non-linear-distributed lagged exposure over the previous 7 days.

RESULTS: Results differed considerably by pandemic wave. During the second wave, an interquartile-range increase in cumulative weekly exposure to air pollution (lag0_7) was associated with a 12% increase (95% CI: 4% to 20%) in COVID-19 hospitalizations for NO2, 8% (95% CI: 1% to 16%) for PM2.5 and 9% (95% CI: 3% to 15%) for PM10. We observed consistent positive associations for same-day (lag0) exposure, whereas lag-specific associations beyond lag0 were generally not statistically significant.

CONCLUSIONS: Our study suggests positive associations between NO2, PM2.5 and PM10 and hospitalization risk among individuals diagnosed with COVID-19 during the second wave. Cumulative hazard ratios were largely driven by exposure on the same day as hospitalization.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Chanda MM, Purse BV, Hemadri D, et al (2024)

Spatial and temporal analysis of haemorrhagic septicaemia outbreaks in India over three decades (1987-2016).

Scientific reports, 14(1):6773.

Haemorrhagic septicaemia (HS) is an economically important disease affecting cattle and buffaloes and the livelihoods of small-holder farmers that depend upon them. The disease is caused by Gram-negative bacterium, Pasteurella multocida, and is considered to be endemic in many states of India with more than 25,000 outbreaks in the past three decades. Currently, there is no national policy for control of HS in India. In this study, we analysed thirty year (1987-2016) monthly data on HS outbreaks using different statistical and mathematical methods to identify spatial variability and temporal patterns (seasonality, periodicity). There was zonal variation in the trend and seasonality of HS outbreaks. Overall, South zone reported maximum proportion of the outbreaks (70.2%), followed by East zone (7.2%), Central zone (6.4%), North zone (5.6%), West zone (5.5%) and North-East zone (4.9%). Annual state level analysis indicated that the reporting of HS outbreaks started at different years independently and there was no apparent transmission between the states. The results of the current study are useful for the policy makers to design national control programme on HS in India and implement state specific strategies. Further, our study and strategies could aid in implementation of similar approaches in HS endemic tropical countries around the world.

RevDate: 2024-03-21

Morel B, Williams TA, Stamatakis A, et al (2024)

AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.

Bioinformatics (Oxford, England) pii:7633408 [Epub ahead of print].

MOTIVATION: Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree.

RESULTS: We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as DTL probabilities for genome-scale datasets with hundreds of taxa.

GNU GPL at https://github.com/BenoitMorel/AleRax and data are made available at https://cme.h-its.org/exelixis/material/alerax_data.tar.gz.

SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

RevDate: 2024-03-26
CmpDate: 2024-03-26

Chandel AS (2024)

Geo-spatial technology based on a multi-criteria evaluation technique used to find potential landfill sites in the town of Bule Hora in southern Ethiopia.

Journal of the Air & Waste Management Association (1995), 74(4):207-239.

Solid waste has surfaced as an eminent and critical concern of environmental and social significance on a global scale, and Ethiopia, a developing country with limited income, has also encountered unfavorable outcomes due to substandard waste management practices. When pinpointing a fitting landfill location in the town of Bule Hora, various ecological, economic, and societal aspects must be considered; these may result in discord and exacerbate a multifaceted and lengthy process. Hence, this research aims to identify prospective landfill sites within the town and utilize geospatial methods, such as Multi-Criteria Evaluation and Analytic Hierarchy Process, to accomplish its objectives. The utilization of geospatial technology and multi-criteria evaluation provides an efficient manner to simultaneously address all bottlenecks involved in the selection of an appropriate landfill location. Geospatial technology evaluates and manages environmental constraints, whereas multi-criteria assessment categorizes choices based on their desirability. Furthermore, by employing a restriction map adhering to established standards, seven landfill sites have successfully been identified within the town. The Land Suitability Index assesses site suitability based on ecological factors, while the Total Hauling Distance evaluates sites within an economic framework. AHP determines weightings through 25.4 pairwise comparisons, resulting in a consistency ratio of 1.95%. The cartographic analysis is conducted using ESRI ArcGIS version 10.8 software. The findings of this study reveal that 98.69% of the area under study is subject to restrictions. The study recommends the implementation of geospatial methods for identifying suitable landfill sites, which would aid in the decision-making process and prevent hasty decisions from triggering environmental degradation. Proper waste disposal would augment the quality of life for residents by diminishing health hazards. The study endeavors to serve as a reference for other developing countries in selecting appropriate landfill sites.Implications: The town of Bule Hora also faces the problem of waste disposal; there is no scientifically selected suitable landfill. Residents of the town of Bule Hora practice waste disposal in open fields, near settlements, water bodies, roads, agricultural land, and other places. The main sources of solid waste in the town are homes, shops, hotels, restaurants, open markets, hospitals, educational institutions, private clinics, etc. Water pollution can potentially lead to the spread of waterborne diseases. According to reports from the Bule Horas Health Department, many people are affected by water-related diseases every year. These open landfill systems with no regard for settlement, topography, geology, surface, or groundwater conditions are the consequences of these unsuitable habitats and health problems. To reduce these problems, this study plays an important role in determining the suitability of landfills for the town and proposing alternative measures that can minimize negative environmental impacts from waste. This study aims to apply geospatial-based technology to a multi-criteria assessment technique to select perfectly suitable landfill sites that are environmentally friendly, economically cost-effective, and socially responsible; examine the town's current waste management system; calculate the selected parameter weights for feature ranking; and delineate solid waste landfills.

RevDate: 2024-03-22
CmpDate: 2024-03-15

Delavaux CS, Crowther TW, Bever JD, et al (2024)

Mutualisms weaken the latitudinal diversity gradient among oceanic islands.

Nature, 627(8003):335-339.

The latitudinal diversity gradient (LDG) dominates global patterns of diversity[1,2], but the factors that underlie the LDG remain elusive. Here we use a unique global dataset[3] to show that vascular plants on oceanic islands exhibit a weakened LDG and explore potential mechanisms for this effect. Our results show that traditional physical drivers of island biogeography[4]-namely area and isolation-contribute to the difference between island and mainland diversity at a given latitude (that is, the island species deficit), as smaller and more distant islands experience reduced colonization. However, plant species with mutualists are underrepresented on islands, and we find that this plant mutualism filter explains more variation in the island species deficit than abiotic factors. In particular, plant species that require animal pollinators or microbial mutualists such as arbuscular mycorrhizal fungi contribute disproportionately to the island species deficit near the Equator, with contributions decreasing with distance from the Equator. Plant mutualist filters on species richness are particularly strong at low absolute latitudes where mainland richness is highest, weakening the LDG of oceanic islands. These results provide empirical evidence that mutualisms, habitat heterogeneity and dispersal are key to the maintenance of high tropical plant diversity and mediate the biogeographic patterns of plant diversity on Earth.

RevDate: 2024-03-21

Scalabrin E, Radaelli M, Capodaglio G, et al (2024)

Hemp cultivation opportunities for marginal lands development.

PloS one, 19(3):e0299981 pii:PONE-D-23-37006.

Agricultural diversification and high-quality products deriving from sustainable crops such as hemp can represent a solution to revitalize marginal areas and reverse land abandonment. This study aimed at comparing four different hemp cultivars (Carmagnola Selezionata, "CS"; Futura 75, "FUT"; Felina 32, "FEL"; Secuieni Jubileu, "JUB") to provide information to select the best suited cultivar for cultivation in mountain marginal areas and for specific end-use applications. Hemp cultivars were cultivated in a single experimental field to compare their ecological and agronomic behavior (duration of life cycle phases, plant size and biomass allocation, and plant resource-use strategies). Through metabolomic analysis of both vegetative and reproductive parts of the plants we tested the presence of substances of nutraceutical interest and traced seed nutritional profile. The four cultivars had different ecological and agronomic behavior, and nutritional profile. We found several compounds with potential pharmaceutical and nutraceutical values in all parts of the plant (leaves, inflorescences, and stems). JUB resulted the most suitable for seed production while CS showed the highest content of bioactive compounds in flowers and leaves. FUT, showed the best suitability for multi-purpose cultivation, while FEL seemed to be not appropriate for the cultivation in mountain area. The multi-disciplinary approach we adopted was effective in distinguish across hemp cultivars and provided information to farmers for the selection of the best hemp cultivar to select. Hemp had a high potential for cultivation in marginal lands, demonstrating to be an economic resource due to its multi-purpose use and to the possibility to generate high-added values products. Our results could serve as a stimulus for the reintroduction of this culture in the study area and in other similar environments.

RevDate: 2024-03-22
CmpDate: 2024-03-22

Berner LT, Orndahl KM, Rose M, et al (2024)

The Arctic Plant Aboveground Biomass Synthesis Dataset.

Scientific data, 11(1):305.

Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m[-2]) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.

RevDate: 2024-03-22
CmpDate: 2024-03-22

Mueller HM, Franzisky BL, Messerer M, et al (2024)

Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water.

The plant genome, 17(1):e20372.

Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well-known salt-tolerance strategies are combined to fine-tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt-tolerance mechanisms are integrated to fine-tune this remarkable resilience. To address this shortcoming, we exposed date palm to a salt stress dose equivalent to seawater for up to 4 weeks and applied integrative multi-omics analyses followed by targeted metabolomics, hormone, and ion analyses. Integration of proteomic into transcriptomic data allowed a view beyond simple correlation, revealing a remarkably high degree of convergence between gene expression and protein abundance. This sheds a clear light on the acclimatization mechanisms employed, which depend on reprogramming of protein biosynthesis. For growth in highly saline habitats, date palm effectively combines various salt-tolerance mechanisms found in both halophytes and glycophytes: "avoidance" by efficient sodium and chloride exclusion at the roots, and "acclimation" by osmotic adjustment, reactive oxygen species scavenging in leaves, and remodeling of the ribosome-associated proteome in salt-exposed root cells. Combined efficiently as in P. dactylifera L., these sets of mechanisms seem to explain the palm's excellent salt stress tolerance.

RevDate: 2024-03-22
CmpDate: 2024-03-22

Kudapa H, Ghatak A, Barmukh R, et al (2024)

Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.).

The plant genome, 17(1):e20337.

Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (drought-sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4'-O-methyltransferase, UDP-d-glucose/UDP-d-galactose 4-epimerase, and delta-1-pyrroline-5-carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root-omics data also revealed some key candidate genes underlying the drought-responsive "QTL-hotspot" region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.

RevDate: 2024-03-21
CmpDate: 2024-03-21

Stefanovic M, Takano K, Wittekind CE, et al (2024)

Dynamic symptom associations in posttraumatic stress disorder: a network approach.

European journal of psychotraumatology, 15(1):2317675.

Background and objective: The current study aimed to investigate the within-day symptom dynamics in PTSD patients, specifically focusing on symptoms that most predict changes in other symptoms. The study included a baseline diagnostic assessment, followed by an assessment using the experience sampling method (ESM) via a smartphone.Method: Participants answered questions related to their PTSD symptoms four times per day for 15 consecutive days (compliance rate 75%). The clinical sample consisted of 48 treatment-seeking individuals: 44 with PTSD as a primary diagnosis, and four patients with subsyndromal PTSD, all of whom had not yet begun trauma-focused treatment. The ESM assessment included the 20 items from the PTSD Checklist for DSM-5, five items from the International Trauma Questionnaire (ITQ) assessing disturbances in relationships and functional impairment, and two items from the Clinician-Administered PTSD Scale for DSM-5 assessing symptoms of depersonalization and derealization.Results: Temporal networks (prospective associations between symptoms) showed that changes in hypervigilance predicted changes in the greatest number of symptoms at the next time point. Furthermore, hypervigilance showed temporal connections with at least one additional symptom from each of the DSM-5 PTSD symptom clusters.Conclusions: Results show that the contemporaneous network (representing the relationship between given symptoms within the same assessment occasion) and the temporal network (representing prospective associations between symptoms) differ and that it is important to estimate both. Some findings from earlier research are replicated, but heterogeneity across studies remains. Future studies should include potential moderators.

RevDate: 2024-03-21

Clifton-Brown J, Hastings A, von Cossel M, et al (2023)

Perennial biomass cropping and use: Shaping the policy ecosystem in European countries.

Global change biology. Bioenergy, 15(5):538-558.

Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023-27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&D requirements; (v) utilisation options; and (vi) market systems and the socio-economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low-carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long-term, strategic R&D and education for positive environmental, economic and social sustainability impacts.

RevDate: 2024-03-17

Ketterer T, Sieke E, Min J, et al (2024)

Contraception Initiation in the Emergency Department: Adolescent Perspectives.

The Journal of adolescent health : official publication of the Society for Adolescent Medicine pii:S1054-139X(24)00112-5 [Epub ahead of print].

PURPOSE: The purpose of this study was to identify factors affecting contraceptive intention and behavior among adolescent females in the pediatric Emergency Department.

METHODS: We conducted a qualitative interview study nested within a larger prospective cohort study examining adolescent contraceptive counseling for females ages 15-18 years at-risk of unintended pregnancy presenting to the pediatric Emergency Department. Interviews were conducted in a subset of participants. The ecologically expanded Theory of Planned Behavior, expert opinion, and literature review informed the interview guide. Interviews were recorded, transcribed, coded and monitored for thematic saturation.

RESULTS: Twenty-eight interviews were analyzed. Mean age was 17.1 years. Themes were mapped to ecologically expanded Theory of Planned Behavior constructs. Within health system influences, prior contraceptive experiences and patient-clinician interactions were described. Within community influences, contraceptive education, knowledge and misinformation, teen pregnancy norms, and social media impacts were described. Within attitudes influences, side-effect and safety concerns, contraceptive motivations and teen pregnancy beliefs were described. Within subjective norm influences, peer and family impacts were described. Within perceived behavioral control, Emergency Department (ED) counseling intervention impacts were described.

DISCUSSION: We identified factors affecting contraceptive initiation/behavior among an ED adolescent population that otherwise may not have received contraceptive education in similar detail as provided by study clinicians. Adolescents' prior contraceptive and clinician interactions, limited access to contraceptive education, knowledge and misinformation, and side-effect and safety concerns affected initiation. Peer/family sharing and social media were leading contraceptive information sources. Future studies should incorporate insights into adolescent ED intervention design to make optimal use of resources while maximizing potential benefit.

RevDate: 2024-03-19
CmpDate: 2024-03-18

Arslan D, Akdağ B, Yaşar Ç, et al (2024)

An extensive database on the traits and occurrences of amphibian species in Turkey.

Scientific data, 11(1):292.

Amphibians are the most endangered taxa among vertebrates, and they face many threats during their complex life cycles. The species' life history traits and occurrence database help understand species responses against ecological factors. Consequently, the species-level-trait database has gained more prominence in recent years as a useful tool for understanding the dimensions of communities, assembly processes of communities, and conserving biodiversity at the ecosystem level against environmental changes. However, in Turkey, there are deficiencies in the knowledge of the ecological traits of amphibians compared to other vertebrate taxa, as most studies have focused on their distribution or taxonomic status. Consequently, there is a need to create such a database for future research on all known extant amphibians in Turkey. We compiled a species-level data set of species traits and occurrences for all amphibians in Turkey using 436 literature sources. We completed 36 trait categories with 5611 occurrence data for 37 amphibian species in Turkey. This study provides an open, useful, and comprehensive database for macroecological and conservation studies on amphibians in Turkey.

RevDate: 2024-03-18
CmpDate: 2024-03-18

Guo Y, Li X, Li Q, et al (2024)

Environmental impact assessment of acidic coal gangue leaching solution on groundwater: a coal gangue pile in Shanxi, China.

Environmental geochemistry and health, 46(4):120.

With the continual advancement of coal resource development, the comprehensive utilization of coal gangue as a by-product encounters certain constraints. A substantial amount of untreated coal gangue is openly stored, particularly acidic gangue exposed to rainfall. The leaching effect of acidic solutions, containing heavy metal ions and other pollutants, results in environmental challenges such as local soil or groundwater pollution, presenting a significant concern in the current ecological landscape of mining areas. Investigating the migration patterns of pollutants in the soil-groundwater system and elucidating the characteristics of polluted solute migration are imperative. To understand the migration dynamics of pollutants and unveil the features of solute migration, this study focuses on a coal gangue dump in a mining area in Shanxi. Utilizing indoor leaching experiments and soil column migration experiments, a two-dimensional soil-groundwater model is established using the finite element method of COMSOL. This model quantitatively delineates the migration patterns of key pollutant components leached from coal gangue into the groundwater. The findings reveal that sulfate ions can migrate and infiltrate groundwater within a mere 7 years in the vadose zone of aeration. Moreover, the average concentration of iron ions in groundwater can reach approximately 58.3 mg/L. Convection, hydrodynamic dispersion, and adsorption emerge as the primary factors influencing pollution transport. Understanding the leaching patterns and environmental impacts of major pollutants in acidic coal gangue is crucial for predicting soil-groundwater pollution and implementing effective protective measures.

RevDate: 2024-03-20
CmpDate: 2024-03-20

Ulanova A, C Mansfeldt (2024)

EcoGenoRisk: Developing a computational ecological risk assessment tool for synthetic biology.

Environmental pollution (Barking, Essex : 1987), 346:123647.

The expanding field of synthetic biology (synbio) supports new opportunities in the design of targeted bioproducts or modified microorganisms. However, this rapid development of synbio products raises concerns surrounding the potential risks of modified microorganisms contaminating unintended environments. These potential invasion risks require new bioinformatic tools to inform the design phase. EcoGenoRisk is a newly constructed computational risk assessment tool for invasiveness that aims to predict where synbio microorganisms may establish a population by screening for habitats of genetically similar microorganisms. The first module of the tool identifies genetically similar microorganisms and potential ecological relationships such as competition, mutualism, and inhibition. In total, 520 archaeal and 32,828 bacterial complete assembly genomes were analyzed to test the specificity and accuracy of the tool as well as to characterize the enzymatic profiles of different taxonomic lineages. Additionally, ecological relationships were analyzed to determine which would result in the greatest potential overlap between shared functional profiles. Notably, competition displayed the significantly highest overlap of shared functions between compared genomes. Overall, EcoGenoRisk is a flexible software pipeline that assists environmental risk assessors to query large databases of known microorganisms and prioritize follow-up bench scale studies.

RevDate: 2024-03-15
CmpDate: 2024-03-15

Yang R, Feng J, Tang J, et al (2024)

Risk assessment and classification prediction for water environment treatment PPP projects.

Water science and technology : a journal of the International Association on Water Pollution Research, 89(5):1264-1281.

Water treatment public-private partnership (PPP) projects are pivotal for sustainable water management but are often challenged by complex risk factors. Efficient risk management in these projects is crucial, yet traditional methodologies often fall short of addressing the dynamic and intricate nature of these risks. Addressing this gap, this comprehensive study introduces an advanced risk classification prediction model tailored for water treatment PPP projects, aimed at enhancing risk management capabilities. The proposed model encompasses an intricate evaluation of crucial risk areas: the natural and ecological environments, socio-economic factors, and engineering entities. It delves into the complex relationships between these risk elements and the overall risk profile of projects. Grounded in a sophisticated ensemble learning framework employing stacking, our model is further refined through a weighted voting mechanism, significantly elevating its predictive accuracy. Rigorous validation using data from the Jiujiang City water environment system project Phase I confirms the model's superiority over standard machine learning models. The development of this model marks a significant stride in risk classification for water treatment PPP projects, offering a powerful tool for enhancing risk management practices. Beyond accurately predicting project risks, this model also aids in developing effective government risk management strategies.

RevDate: 2024-03-19
CmpDate: 2024-02-29

Xu W, Pan Z, Wu Y, et al (2024)

A database on the abundance of environmental antibiotic resistance genes.

Scientific data, 11(1):250.

Antimicrobial resistance (AMR) poses a severe threat to global health. The wide distribution of environmental antibiotic resistance genes (ARGs), which can be transferred between microbiota, especially clinical pathogens and human commensals, contributed significantly to AMR. However, few databases on the spatiotemporal distribution, abundance, and health risk of ARGs from multiple environments have been developed, especially on the absolute level. In this study, we compiled the ARG occurrence data generated by a high-throughput quantitative PCR platform from 1,403 samples in 653 sampling sites across 18 provinces in China. The database possessed 291,870 records from five types of habitats on the abundance of 290 ARGs, as well as 8,057 records on the abundance of 30 mobile genetic elements (MGEs) from 2013 to 2020. These ARGs conferred resistance to major common types of antibiotics (a total of 15 types) and represented five major resistance mechanisms, as well as four risk ranks. The database can provide information for studies on the dynamics of ARGs and is useful for the health risk assessment of AMR.

RevDate: 2024-03-18
CmpDate: 2024-03-18

Thenmozhi M, Sujatha M, Kavitha M, et al (2024)

Assessment of cyclone risk and case study of Gaja cyclone using GIS techniques and machine learning algorithms in coastal zone of Tamil Nadu, India.

Environmental research, 246:118089.

Cyclones can cause devastating impacts, including strong winds, heavy rainfall, storm surges, and flooding. The aftermath includes infrastructure damage, loss of life, displacement of communities, and ecological disruptions. Timely response and recovery efforts are crucial to minimize the socio-economic and environmental consequences of cyclones. To accelerate the time-consuming risk assessment process, particularly in geographically diverse regions, a blend of multi-criteria decision-making and machine learning models was utilized. This novel approach swiftly assessed cyclone risk and the impact of the Gaja cyclone in Nagapattinam, India. The method involved assigning weights to distinct criteria, unveiling notable vulnerability aspects like elevation, slope, proximity to the coast, distance from cyclone tracts, Lu/Lc, population density, proximity to cyclone shelters, household density, accessibility to healthcare facilities, NDVI, and levels of awareness. Daddavari, Ettugudi, Kodikarai, Vedharanyam, Velankanni, and Thirupoondi face high/extreme cyclone risk. Nagore, Nagapattinam, Pillai, Enangudi, and Sannanllur have low/no threat. To further enhance the precision of the study, machine learning algorithms like SVM, SAM, and MLC were deployed. These models were instrumental in generating pre- and post-cyclone land use maps. The influence of Gaja cyclones effects shows decreasing of agriculture land from 34% to 30%, aquaculture increase 1%, barren land decrease from 8% to 6%, Built-up land decrease from 15% to 13%, land with scrub and salt pan also decrease from 21% to 17% and 10%-8%. Mostly effect of Gaja cyclone is dramatic increase of water body from 8% to 21%. Conducting cyclone risk zone analysis and pre/post-cyclone Land Use Land Cover (LULC) detection in Nagapattinam offers valuable insights for disaster preparedness, infrastructure planning, and climate resilience. This study can enhance understanding of vulnerability and aid in formulating strategies to mitigate cyclone impacts, ensuring sustainable development in the region.

RevDate: 2024-03-18
CmpDate: 2024-03-18

Chaves T, Azevedo Á, IM Caldas (2024)

Cheiloscopy in sex estimation: a systematic review.

Forensic science, medicine, and pathology, 20(1):280-292.

This study aimed to conduct a systematic review to gather evidence to clarify if cheiloscopy can be used in sex estimation and identify the reasons behind the lack of consensus in the scientific community. The systematic review was performed following the PRISMA guidelines. A bibliographic survey was conducted in PubMed, Scopus, and Web of Science databases, restricted to articles published between 2010 and 2020. Studies were selected according to eligibility criteria, and then the study data were collected. The risk of bias in each study was assessed and applied as additional inclusion or exclusion criteria. The results of the articles eligible for analysis were synthesized using a descriptive approach. In the 41 included studies, several methodological flaws and variations between studies that contribute to the discrepancy in results were identified. The data gathered allowed us to conclude that there is no strong scientific evidence to support the use of cheiloscopy in sex estimation, as there is no specific pattern for each sex, which reduces the criminalistic interest of cheiloscopy in estimating this parameter.

RevDate: 2024-03-14

Furuya S, Zheng F, Lu Q, et al (2024)

Separating Scarring Effect and Selection of Early-Life Exposures With Genetic Data.

Demography pii:386301 [Epub ahead of print].

Causal life course research examining consequences of early-life exposures has largely relied on associations between early-life environments and later-life outcomes using exogenous environmental shocks. Nonetheless, even with (quasi-)randomized early-life exposures, these associations may reflect not only causation ("scarring") but also selection (i.e., which members are included in data assessing later life). Investigating this selection and its impacts on estimated effects of early-life conditions has, however, often been ignored because of a lack of pre-exposure data. This study proposes an approach for assessing and correcting selection, separately from scarring, using genetic measurements. Because genetic measurements are determined at the time of conception, any associations with early-life exposures should be interpreted as selection. Using data from the UK Biobank, we find that in utero exposure to a higher area-level infant mortality rate is associated with genetic predispositions correlated with better educational attainment and health. These findings point to the direction and magnitude of selection from this exposure. Corrections for this selection in examinations of effects of exposure on later educational attainment suggest underestimates of 26-74%; effects on other life course outcomes also vary across selection correction methods.

RevDate: 2024-03-13

Kekalih A, Adi NP, DS Soemarko (2024)

Preparation and Challenges in Developing a Big Data Analysis Framework in Occupational Medicine in Indonesia.

Journal of UOEH, 46(1):113-118.

This mini review explores the transformative potential of big data analysis and artificial intelligence (AI) in reforming occupational medicine in Indonesia. Emphasizing the preconditions, case studies, and benefits, it underscores the role of big data in enhancing worker well-being. The review highlights the importance of informative health big data, especially in high-risk industries, with examples of case studies of AI implementation in occupational medicine during the COVID-19 pandemic and other relevant scenarios. While acknowledging the challenges of AI implementation, the essay identifies the role of academic and professional organizations as pioneers in big data utilization. Six potential benefits that are identified, including improved patient care and efficient resource allocation, demonstrate the transformative impact of big data analysis. The proposed pathway of preparation underscores the need for awareness, skill enhancement, and collaboration, addressing challenges in data management and stakeholder engagement. The conclusion emphasizes continuous assessment, feasibility studies, and commitment as essential steps in advancing occupational medicine through big data analysis.

RevDate: 2024-03-14

Kearsley E, Verbeeck H, Stoffelen P, et al (2024)

Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest.

Plant-environment interactions (Hoboken, N.J.), 5(2):e10136.

Tropical forest phenology directly affects regional carbon cycles, but the relation between species-specific and whole-canopy phenology remains largely uncharacterized. We present a unique analysis of historical tropical tree phenology collected in the central Congo Basin, before large-scale impacts of human-induced climate change. Ground-based long-term (1937-1956) phenological observations of 140 tropical tree species are recovered, species-specific phenological patterns analyzed and related to historical meteorological records, and scaled to characterize stand-level canopy dynamics. High phenological variability within and across species and in climate-phenology relationships is observed. The onset of leaf phenophases in deciduous species was triggered by drought and light availability for a subset of species and showed a species-specific decoupling in time along a bi-modal seasonality. The majority of the species remain evergreen, although central African forests experience relatively low rainfall. Annually a maximum of 1.5% of the canopy is in leaf senescence or leaf turnover, with overall phenological variability dominated by a few deciduous species, while substantial variability is attributed to asynchronous events of large and/or abundant trees. Our results underscore the importance of accounting for constituent signals in canopy-wide scaling and the interpretation of remotely sensed phenology signals.

RevDate: 2024-03-14
CmpDate: 2024-03-14

Omega RL, Ishigaki Y, Permana S, et al (2024)

Low-Cost Sensor Deployment on a Public Minibus in Fukushima Prefecture.

Sensors (Basel, Switzerland), 24(5):.

This study analyzed radiation dose data to observe the annual decline in ambient radiation doses and assess the factors contributing to fluctuations in reconstructed areas of the Fukushima prefecture. Utilizing a novel mobile monitoring system installed on a community minibus, the study employed a cost-effective sensor, namely, Pocket Geiger which was integrated with a microcontroller and telecommunication system for data transfer, access, visualization, and accumulation. The study area included the region between Okuma and Tomioka towns. The ambient dose rate recorded along the minibus route was depicted on a map, averaged within a 1 × 1 km mesh created with the Quantum Geographic Information System. To ensure accuracy, the shielding factor of the minibus material is determined to adjust the dose readings. A significant decrease (p < 0.001) in the radiation dose ranges from 2022 to 2023 was observed. The land use classification by the Advanced Land Observation Satellite revealed an ecological half-life ranging from 2.41 years to 1 year, suggesting a rapid radiation decay across all land types. This underscores the close connection between radiation attenuation and environmental factors, as well as decontamination efforts across diverse land categories.

RevDate: 2024-03-14
CmpDate: 2024-03-14

Li Z, Fan H, Yang L, et al (2024)

Multi-Omics Analysis of the Effects of Soil Amendment on Rapeseed (Brassica napus L.) Photosynthesis under Drip Irrigation with Brackish Water.

International journal of molecular sciences, 25(5):.

Drip irrigation with brackish water increases the risk of soil salinization while alleviating water shortage in arid areas. In order to alleviate soil salinity stress on crops, polymer soil amendments are increasingly used. But the regulation mechanism of a polymer soil amendment composed of polyacrylamide polyvinyl alcohol, and manganese sulfate (PPM) on rapeseed photosynthesis under drip irrigation with different types of brackish water is still unclear. In this field study, PPM was applied to study the responses of the rapeseed (Brassica napus L.) phenotype, photosynthetic physiology, transcriptomics, and metabolomics at the peak flowering stage under drip irrigation with water containing 6 g·L[-1] NaCl (S) and Na2CO3 (A). The results showed that the inhibitory effect of the A treatment on rapeseed photosynthesis was greater than that of the S treatment, which was reflected in the higher Na[+] content (73.30%) and lower photosynthetic-fluorescence parameters (6.30-61.54%) and antioxidant enzyme activity (53.13-77.10%) of the A-treated plants. The application of PPM increased the biomass (63.03-75.91%), photosynthetic parameters (10.55-34.06%), chlorophyll fluorescence parameters (33.83-62.52%), leaf pigment content (10.30-187.73%), and antioxidant enzyme activity (28.37-198.57%) under S and A treatments. However, the difference is that under the S treatment, PPM regulated the sulfur metabolism, carbon fixation and carbon metabolism pathways in rapeseed leaves. And it also regulated the photosynthesis-, oxidative phosphorylation-, and TCA cycle-related metabolic pathways in rapeseed leaves under A treatment. This study will provide new insights for the application of polymer materials to tackle the salinity stress on crops caused by drip irrigation with brackish water, and solve the difficulty in brackish water utilization.

RevDate: 2024-03-14
CmpDate: 2024-03-14

Viera A, Ondrusek A, Tengatenga C, et al (2024)

A Qualitative Exploration of Attitudes Toward Global Positioning System Tracking and Ecological Momentary Assessment Among Individuals in Substance Use Treatment.

Substance use & addiction journal, 45(2):260-267.

BACKGROUND: The use of tracking technology in substance use research can uncover the role of contextual factors, such as social networks and environmental cues, in triggering cravings and precipitating return to use. Few studies have explored the opinions of individuals in substance use treatment related to tracking technology.

METHODS: We conducted 30 semi-structured interviews with individuals in substance use treatment facilities in Connecticut and Georgia. Interviews were not limited to individuals with any specific substance use disorder. Interviewers described a hypothetical study involving ecological momentary assessment and global positioning system tracking to examine place-based predictors of substance use. Participants were invited to share reactions to this description. We used thematic analysis to identify themes in participant perceptions of this hypothetical research study.

RESULTS: Most participants shared positive opinions about study participation and expressed little to no concern about the tracking components. Participant concerns focused on the security of their information and the potential burden of responding to study questions. Participants largely understood the importance of study participation for promoting greater understanding of substance use and identified potential therapeutic effects of study participation on their own recovery.

CONCLUSIONS: Individuals in substance use treatment expressed little concern with research studies or interventions incorporating mobile-tracking elements. Future studies should explore the responsible use of tracking elements in recovery support interventions.

RevDate: 2024-03-13

Kozicki M, Sąsiadek-Andrzejczak E, Wach R, et al (2024)

Flexible Cotton Fabric-Based Ionizing Radiation Dosimeter for 2D Dose Distribution Measurements over a Wide Dose Range at High Dose Rates.

International journal of molecular sciences, 25(5): pii:ijms25052916.

This work presents an ecological, flexible 2D radiochromic dosimeter for measuring ionizing radiation in the kilogray dose range. Cotton woven fabric made of cellulose was volume-modified with nitrotetrazolium blue chloride as a radiation-sensitive compound. Its features include a color change during exposure from yellowish to purple-brown and flexibility that allows it to adapt to various shapes. It was found that (i) the dose response is up to ~80 kGy, (ii) it is independent of the dose rate for 1.1-73.1 kGy/min, (iii) it can be measured in 2D using a flatbed scanner, (iv) the acquired images can be filtered using a mean filter, which improves its dose resolution, (v) the dose resolution is -0.07 to -0.4 kGy for ~0.6 to ~75.7 kGy for filtered images, and (vi) two linear dose subranges can be distinguished: ~0.6 to ~7.6 kGy and ~9.9 to ~62.0 kGy. The dosimeter combined with flatbed scanner reading and data processing using dedicated software packages constitutes a comprehensive system for measuring dose distributions for objects with complex shapes.

RevDate: 2024-03-12

Bhosle A, Bae S, Zhang Y, et al (2024)

Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.

Molecular systems biology [Epub ahead of print].

Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.

RevDate: 2024-03-11

Rivero-Marcos M, Lasa B, Neves T, et al (2024)

Plant ammonium sensitivity is associated with the external pH adaptation, repertoire of nitrogen transporters, and nitrogen requirement.

Journal of experimental botany pii:7625386 [Epub ahead of print].

Modern crops exhibit diverse sensitivities to ammonium as the primary nitrogen source, influenced by environmental factors such as external pH and nutrient availability. Despite its significance, there is currently no systematic classification of plant species based on their ammonium sensitivity. This study conducts a meta-analysis of 50 plant species and presents a new classification method based on the comparison of fresh biomass obtained under ammonium and nitrate nutrition. The classification uses the natural logarithm of biomass ratio as the size effect indicator of ammonium sensitivity. This numerical parameter is associated with critical factors for nitrogen demand and form preference, such as Ellenberg indicators and the repertoire of nitrogen transporters for ammonium and nitrate uptake. Finally, a comparative analysis of the developmental and metabolic responses, including hormonal balance, is conducted in two species with divergent ammonium sensitivity values in the classification. Results indicate that nitrate has a key counteracting role of ammonium toxicity in species with a higher abundance of genes encoding NRT2-type proteins and fewer of the AMT2-type proteins. Additionally, the study confirms the reliability of the phytohormone balance and methylglyoxal content as indicators for anticipating ammonium toxicity.

RevDate: 2024-03-12
CmpDate: 2024-03-11

Zhang L, Li H, Shi M, et al (2024)

FishSNP: a high quality cross-species SNP database of fishes.

Scientific data, 11(1):286.

The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP (http://bioinfo.ihb.ac.cn/fishsnp), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.

RevDate: 2024-03-13
CmpDate: 2024-03-13

Akar AU, Sisman S, Ulku H, et al (2024)

Evaluating lake water quality with a GIS-based MCDA integrated approach: a case in Konya/Karapınar.

Environmental science and pollution research international, 31(13):19478-19499.

Considering water quality is an essential requirement in terms of environmental planning and management. To protect and manage water resources effectively, it is necessary to develop an analytical decision-support system. In this study, a systematic approach was suggested to evaluate the lake water quality. The methodology includes the prediction of the values in different locations of the lakes from experimental data through inverse distance weighting (IDW) method, creation of maps by using Geographic Information System (GIS) integrated with analytic hierarchy process (AHP) from multi-criteria decision analysis (MCDA), reclassification into five class, combining the time-related spatial data into a single map to predict the whole lake water quality from the data of sampling points, and finally overlapping the final maps with topography/geology and land use. The proposed approach was verified and presented as case study for Meke and Acigol Lakes in Konya/Turkey which were affected by human and natural factors although they have ecological, hydromorphological, and socio-economic importance. In the proposed approach, categorizing water quality parameters as "hardness and minerals," "substrates and nutrients," "solids content," "metals," and "oil-grease" groups was helpful for AHP with the determined group weights of 0.484, 0.310, 0.029, and 0.046, respectively. Assigning weights within each group and then assigning weights between groups resulted in creating accurate final map. The proposed approach is flexible and applicable to any lake water quality data; even with a limited number of data, the whole lake water quality maps could be created for assessment.

RevDate: 2024-03-13
CmpDate: 2024-02-14

Brehm AM, JL Orrock (2023)

Extensive behavioral data contained within existing ecological datasets.

Trends in ecology & evolution, 38(12):1129-1133.

Long-term ecological datasets contain vast behavioral data, enabling the quantification of among-individual behavioral variation at unprecedented spatiotemporal scales. We detail how behaviors can be extracted and describe how such data can be used to test new hypotheses, inform population and community ecology, and address pressing conservation needs.

RevDate: 2024-03-08
CmpDate: 2024-03-08

Souza IM, Araújo EM, AMD Silva Filho (2024)

Incomplete recording of race/colour in health information systems in Brazil: time trend, 2009-2018.

Ciencia & saude coletiva, 29(3):e05092023.

This ecological study of time trends and multiple groups evaluated incompleteness in the race/colour field of Brazilian health information system records and the related time trend, 2009-2018, for the diseases and disorders most prevalent in the black population. The Romero and Cunha (2006) classification was applied in order to examine incompleteness using secondary data from Brazil's National Notifiable Diseases System, Hospital Information System and Mortality Information System, by administrative regions of Brazil, while percentage underreporting and time trend were calculated using simple linear regression models with Prais-Winsten correction (p-value<0.05). All records scored poorly except those for mortality from external causes (excellent), tuberculosis (good) and infant mortality (fair). An overall downward trend was observed in percentage incompleteness. Analysis by region found highest mean incompleteness in the North (30.5%), Northeast (33.3%) and Midwest (33.0%) regions. The Southeast and Northeast regions showed the strongest downward trends. The findings intended to increase visibility on the implications of the race/color field for health equity.

RevDate: 2024-03-11
CmpDate: 2024-03-08

Tao F, Houlton BZ, Frey SD, et al (2024)

Reply to: Model uncertainty obscures major driver of soil carbon.

Nature, 627(8002):E4-E6.

RevDate: 2024-03-06

van der Feltz-Cornelis C, Turk F, Sweetman J, et al (2024)

Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis.

General hospital psychiatry, 88:10-22 pii:S0163-8343(24)00039-2 [Epub ahead of print].

OBJECTIVE: Long COVID can include impaired cognition ('brain fog'; a term encompassing multiple symptoms) and mental health conditions. We performed a systematic review and meta-analysis to estimate their prevalence and to explore relevant factors associated with the incidence of impaired cognition and mental health conditions.

METHODS: Searches were conducted in Medline and PsycINFO to cover the start of the pandemic until August 2023. Included studies reported prevalence of mental health conditions and brain fog in adults with long COVID after clinically-diagnosed or PCR-confirmed SARS-CoV-2 infection.

FINDINGS: 17 studies were included, reporting 41,249 long COVID patients. Across all timepoints (3-24 months), the combined prevalence of mental health conditions and brain fog was 20·4% (95% CI 11·1%-34·4%), being lower among those previously hospitalised than in community-managed patients(19·5 vs 29·7% respectively; p = 0·047). The odds of mental health conditions and brain fog increased over time and when validated instruments were used. Odds of brain fog significantly decreased with increasing vaccination rates (p = ·000).

CONCLUSIONS: Given the increasing prevalence of mental health conditions and brain fog over time, preventive interventions and treatments are needed. Research is needed to explore underlying mechanisms that could inform further research in development of effective treatments. The reduced risk of brain fog associated with vaccination emphasizes the need for ongoing vaccination programs.

RevDate: 2024-03-11
CmpDate: 2024-03-11

Gonyo SB, Burkart H, S Regan (2024)

Leveraging big data for outdoor recreation management: A case study from the York river in Virginia.

Journal of environmental management, 354:120482.

Outdoor recreation is important for improving quality of life, well-being, and local economies, but quantifying its value without direct monetary transactions can be challenging. This study explores combining non-market valuation techniques with emerging big data sources to estimate the value of recreation for the York River and surrounding parks in Virginia. By applying the travel cost method to anonymous human mobility data, we gain deeper insights into the significance of recreational experiences for visitors and the local economy. Results of a zero-inflated Negative Binomial model show a mean consumer surplus value of $26.91 per trip, totaling $15.5 million across nearly 600,000 trips observed in 2022. Further, weekends, holidays, and the summer and fall months are found to be peak visitation times, whereas those with young children and who are Hispanic or over 64 years old are less likely to visit. These findings shed light on various factors influencing visitation patterns and recreation values, including temporal effects and socio-demographics, revealing disparities that warrant targeted efforts for inclusivity and accessibility. Policymakers can use these insights to make informed and sustainable choices in outdoor recreation management, fostering the preservation of natural resources for the benefit of both visitors and the environment.

RevDate: 2024-03-08
CmpDate: 2024-03-07

Kudamba A, Kasolo JN, Bbosa GS, et al (2024)

Review of Herbal Medicinal Plants Used in the Management of Cancers in the East Africa Region from 2019 to 2023.

Integrative cancer therapies, 23:15347354241235583.

BACKGROUND: In the East African region, herbal plants are essential in the treatment and control of cancer. Given the diverse ecological and cultural makeup of the regional states, it is likely that different ethnic groups will use the same or different plants for the same or different diseases. However, since 2019, this has not been compiled into a single study.

PURPOSE: The study aimed to compile and record the medicinal plants utilized in East Africa from April 2019 to June 2023 to treat various cancer types.

MATERIALS AND METHODS: The study examined 13 original studies that included ethnobotanical research conducted in East Africa. They were retrieved from several internet databases, including Google Scholar, Scopus, PubMed/Medline, Science Direct, and Research for Life. The study retrieved databases on plant families and species, plant parts used, preparation methods and routes of administration, and the country where the ethnobotanical field surveys were conducted. Graphs were produced using the GraphPad Prism 8.125 program (GraphPad Software, Inc., San Diego, CA). Tables and figures were used to present the data, which had been condensed into percentages and frequencies.

RESULTS: A total of 105 different plant species from 45 different plant families were identified, including Asteraceae (14), Euphorbiaceae (12), Musaceae (8), and Apocynaceae (7). Uganda registered the highest proportion (46% of the medicinal plants used). The most commonly mentioned medicinal plant species in cancer management was Prunus africana. Herbs (32%), trees and shrubs (28%), and leaves (45%) constituted the majority of herbal remedies. Most herbal remedies were prepared by boiling (decoction) and taken orally (57%).

CONCLUSION: East Africa is home to a wide variety of medicinal plant species that local populations and herbalists, or TMP, frequently use in the treatment of various types of cancer. The most frequently used families are Asteraceae and Euphorbiaceae, with the majority of species being found in Uganda. The most frequently utilized plant species is Prunus africana. Studies on the effectiveness of Prunus africana against other malignancies besides prostate cancer are required.

RevDate: 2024-03-07
CmpDate: 2024-03-07

Liu Y, Li L, Feng J, et al (2024)

Modulation of chronic obstructive pulmonary disease progression by antioxidant metabolites from Pediococcus pentosaceus: enhancing gut probiotics abundance and the tryptophan-melatonin pathway.

Gut microbes, 16(1):2320283.

Chronic obstructive pulmonary disease (COPD), a condition primarily linked to oxidative stress, poses significant health burdens worldwide. Recent evidence has shed light on the association between the dysbiosis of gut microbiota and COPD, and their metabolites have emerged as potential modulators of disease progression through the intricate gut-lung axis. Here, we demonstrate the efficacy of oral administration of the probiotic Pediococcus pentosaceus SMM914 (SMM914) in delaying the progression of COPD by attenuating pulmonary oxidative stress. Specially, SMM914 induces a notable shift in the gut microbiota toward a community structure characterized by an augmented abundance of probiotics producing short-chain fatty acids and antioxidant metabolisms. Concurrently, SMM914 synthesizes L-tryptophanamide, 5-hydroxy-L-tryptophan, and 3-sulfino-L-alanine, thereby enhancing the tryptophan-melatonin pathway and elevating 6-hydroxymelatonin and hypotaurine in the lung environment. This modulation amplifies the secretion of endogenous anti-inflammatory factors, diminishes macrophage polarization toward the M1 phenotype, and ultimately mitigates the oxidative stress in mice with COPD. The demonstrated efficacy of the probiotic intervention, specifically with SMM914, not only highlights the modulation of intestine microbiota but also emphasizes the consequential impact on the intricate interplay between the gastrointestinal system and respiratory health.

RevDate: 2024-03-07
CmpDate: 2024-03-07

Ge X, Peng L, Deng Z, et al (2024)

Chromosome-scale genome assemblies of Himalopsyche anomala and Eubasilissa splendida (Insecta: Trichoptera).

Scientific data, 11(1):267.

Trichoptera is one of the most evolutionarily successful aquatic insect lineages and is highly valued value in adaptive evolution research. This study presents the chromosome-level genome assemblies of Himalopsyche anomala and Eubasilissa splendida achieved using PacBio, Illumina, and Hi-C sequencing. For H. anomala and E. splendida, assembly sizes were 663.43 and 859.28 Mb, with scaffold N50 lengths of 28.44 and 31.17 Mb, respectively. In H. anomala and E. splendida, we anchored 24 and 29 pseudochromosomes, and identified 11,469 and 10,554 protein-coding genes, respectively. The high-quality genomes of H. anomala and E. splendida provide critical genomic resources for understanding the evolution and ecology of Trichoptera and performing comparative genomics analyses.

RevDate: 2024-03-07
CmpDate: 2024-03-07

Zhou H, Zhang X, Liu H, et al (2024)

Chromosome-level genome assembly of Platycarya strobilacea.

Scientific data, 11(1):269.

Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.

RevDate: 2024-03-07
CmpDate: 2024-02-09

Del Campo J, Carlos-Oliveira M, Čepička I, et al (2024)

The protist cultural renaissance.

Trends in microbiology, 32(2):128-131.

Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.

RevDate: 2024-03-05

Zhang Z, Xu H, G Zhu (2024)

Incorporating high-frequency information into edge convolution for link prediction in complex networks.

Scientific reports, 14(1):5437.

Link prediction in complex networks aims to mine hidden or to-be-generated links between network nodes, which plays a significant role in fields such as the cold start of recommendation systems, knowledge graph completion and biomedical experiments. The existing link prediction models based on graph neural networks, such as graph convolution neural networks, often only learn the low-frequency information reflecting the common characteristics of nodes while ignoring the high-frequency information reflecting the differences between nodes when learning node representation, which makes the corresponding link prediction models show over smoothness and poor performance. Focusing on links in complex networks, this paper proposes an edge convolutional graph neural network EdgeConvHiF that fuses high-frequency node information to achieve the representation learning of links so that link prediction can be realized by implementing the classification of links. EdgeConvHiF can also be employed as a baseline, and extensive experiments on real-world benchmarks validate that EdgeConvHiF not only has high stability but also has more advantages than the existing representative baselines.

RevDate: 2024-03-05

Tamosiunaite M, Tetzlaff C, F Wörgötter (2024)

Unsupervised learning of perceptual feature combinations.

PLoS computational biology, 20(3):e1011926 pii:PCOMPBIOL-D-23-01087 [Epub ahead of print].

In many situations it is behaviorally relevant for an animal to respond to co-occurrences of perceptual, possibly polymodal features, while these features alone may have no importance. Thus, it is crucial for animals to learn such feature combinations in spite of the fact that they may occur with variable intensity and occurrence frequency. Here, we present a novel unsupervised learning mechanism that is largely independent of these contingencies and allows neurons in a network to achieve specificity for different feature combinations. This is achieved by a novel correlation-based (Hebbian) learning rule, which allows for linear weight growth and which is combined with a mechanism for gradually reducing the learning rate as soon as the neuron's response becomes feature combination specific. In a set of control experiments, we show that other existing advanced learning rules cannot satisfactorily form ordered multi-feature representations. In addition, we show that networks, which use this type of learning always stabilize and converge to subsets of neurons with different feature-combination specificity. Neurons with this property may, thus, serve as an initial stage for the processing of ecologically relevant real world situations for an animal.

RevDate: 2024-03-06
CmpDate: 2024-03-06

Wu LF, Zhu WG, Yu EP, et al (2024)

Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant.

BMC genomic data, 25(1):24.

OBJECTIVES: Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation.

DATA DESCRIPTION: Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839 bp in length, with 92 contigs and an N50 of 22,379,495 bp. The repetitive elements in the assembly were 555,442,205 bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.

RevDate: 2024-03-04

Qian J, Qian L, Pu N, et al (2024)

An Intelligent Early Warning System for Harmful Algal Blooms: Harnessing the Power of Big Data and Deep Learning.

Environmental science & technology [Epub ahead of print].

Harmful algal blooms (HABs) pose a significant ecological threat and economic detriment to freshwater environments. In order to develop an intelligent early warning system for HABs, big data and deep learning models were harnessed in this study. Data collection was achieved utilizing the vertical aquatic monitoring system (VAMS). Subsequently, the analysis and stratification of the vertical aquatic layer were conducted employing the "DeepDPM-Spectral Clustering" method. This approach drastically reduced the number of predictive models and enhanced the adaptability of the system. The Bloomformer-2 model was developed to conduct both single-step and multistep predictions of Chl-a, integrating the " Alert Level Framework" issued by the World Health Organization to accomplish early warning for HABs. The case study conducted in Taihu Lake revealed that during the winter of 2018, the water column could be partitioned into four clusters (Groups W1-W4), while in the summer of 2019, the water column could be partitioned into five clusters (Groups S1-S5). Moreover, in a subsequent predictive task, Bloomformer-2 exhibited superiority in performance across all clusters for both the winter of 2018 and the summer of 2019 (MAE: 0.175-0.394, MSE: 0.042-0.305, and MAPE: 0.228-2.279 for single-step prediction; MAE: 0.184-0.505, MSE: 0.101-0.378, and MAPE: 0.243-4.011 for multistep prediction). The prediction for the 3 days indicated that Group W1 was in a Level I alert state at all times. Conversely, Group S1 was mainly under an Level I alert, with seven specific time points escalating to a Level II alert. Furthermore, the end-to-end architecture of this system, coupled with the automation of its various processes, minimized human intervention, endowing it with intelligent characteristics. This research highlights the transformative potential of integrating big data and artificial intelligence in environmental management and emphasizes the importance of model interpretability in machine learning applications.

RevDate: 2024-03-06
CmpDate: 2024-03-06

Han K, Li J, Yang D, et al (2024)

Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.

Microbiology spectrum, 12(3):e0360223.

Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.

RevDate: 2024-03-05
CmpDate: 2024-03-05

Specker F, Paz A, Crowther TW, et al (2024)

Treemendous: an R package for integrating taxonomic information across backbones.

PeerJ, 12:e16896.

Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful name-cleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graph-based iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to 'translate' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology.

RevDate: 2024-03-05

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

The genome sequence of the Diamond-back Marble, Eudemis profundana (Denis & Schiffermüller, 1775).

Wellcome open research, 8:184.

We present a genome assembly from an individual male Eudemis profundana (the Diamond-back Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.

RevDate: 2024-03-05
CmpDate: 2024-03-05

Thiébaut A, Altenhoff AM, Campli G, et al (2023)

DrosOMA: the Drosophila Orthologous Matrix browser.

F1000Research, 12:936.

BACKGROUND: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking.

METHODS: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results.

RESULTS: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation.

CONCLUSIONS: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.

RevDate: 2024-03-04

Boyes D, Lees DC, Hammond J, et al (2023)

The genome sequence of the Ashy Button, Acleris sparsana (Denis & Schiffermüller, 1775).

Wellcome open research, 8:241.

We present a genome assembly from an individual male Acleris sparsana (the Ashy Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 589.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,123 protein coding genes.

RevDate: 2024-03-04

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

The genome sequence of the Minor Shoulder-knot, Brachylomia viminalis (Fabricius, 1777).

Wellcome open research, 8:245.

We present a genome assembly from an individual male Brachylomia viminalis (the Minor Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 782.2 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,191 protein coding genes.

RevDate: 2024-03-04

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

The genome sequence of the Orange Footman, Eilema sororcula (Hufnagel, 1766).

Wellcome open research, 8:282.

We present a genome assembly from an individual male Eilema sororcula (the Orange Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 729.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,093 protein coding genes.

RevDate: 2024-03-04

Mallinson DC, Elwert F, DB Ehrenthal (2024)

Spillover effects of gestational age on sibling's literacy.

Early child development and care, 194(2):244-259.

Adverse health events within families can harm children's development, including their early literacy. Using data from a longitudinal Wisconsin birth cohort, we estimated the spillover effect of younger siblings' gestational ages on older siblings' kindergarten-level literacy. We sampled 20,014 sibling pairs born during 2007-2010 who took Phonological Awareness Literacy Screening-Kindergarten tests during 2012-2016. Exposures were gestational age (completed weeks), preterm birth (gestational age <37 weeks), and very preterm birth (gestational age <32 weeks). We used gain-score regression-a fixed effects strategy-to estimate spillover effect. A one-week increase in younger siblings' gestational age improved the older siblings' test score by 0.011 SD (95% confidence interval: 0.001, 0.021 SD). The estimated spillover effect was larger among siblings whose mothers reported having a high school diploma/equivalent only (0.024 SD; 95% CI: 0.004, 0.044 SD). The finding underscores the networked effects of one individual's early-life health shocks on their family members.

RevDate: 2024-03-03

Freitas IBF, Duarte-Neto PJ, Sorigotto LR, et al (2024)

Effects of pasture intensification and sugarcane cultivation on non-target species: A realistic evaluation in pesticide-contaminated mesocosms.

The Science of the total environment pii:S0048-9697(24)01566-3 [Epub ahead of print].

Conventional soil management in agricultural areas may expose non-target organisms living nearby to several types of contaminants. In this study, the effects of soil management in extensive pasture (EP), intensive pasture (IP), and sugarcane crops (C) were evaluated in a realistic-field-scale study. Thirteen aquatic mesocosms embedded in EP, IP, and C treatments were monitored over 392 days. The recommended management for each of the areas was simulated, such as tillage, fertilizer, pesticides (i.e. 2,4-D, fipronil) and vinasse application, and cattle pasture. To access the potential toxic effects that the different steps of soil management in these areas may cause, the cladoceran Ceriophania silvestrii was used as aquatic bioindicator, the dicot Eruca sativa as phytotoxicity bioindicator in water, and the dipteran Chironomus sancticaroli as sediment bioindicator. Generalized linear mixed models were used to identify differences between the treatments. Low concentrations of 2,4-D (<97 μg L[-1]) and fipronil (<0.21 μg L[-1]) in water were able to alter fecundity, female survival, and the intrinsic rate of population increase of C. silvestrii in IP and C treatments. Similarly, the dicot E. sativa had germination, shoot and root growth affected mainly by 2,4-D concentrations in the water. For C. sancticarolli, larval development was affected by the presence of fipronil (<402.6 ng g[-1]). The acidic pH (below 5) reduced the fecundity and female survival of C. silvestrii and affected the germination and growth of E. sativa. Fecundity and female survival of C. silvestrii decrease in the presence of phosphorus-containing elements. The outcomes of this study may improve our understanding of the consequences of exposure of freshwater biota to complex stressors in an environment that is rapidly and constantly changing.

RevDate: 2024-03-04
CmpDate: 2024-03-04

Rillig MC, Mansour I, Hempel S, et al (2024)

How widespread use of generative AI for images and video can affect the environment and the science of ecology.

Ecology letters, 27(3):e14397.

Generative artificial intelligence (AI) models will have broad impacts on society including the scientific enterprise; ecology and environmental science will be no exception. Here, we discuss the potential opportunities and risks of advanced generative AI for visual material (images and video) for the science of ecology and the environment itself. There are clearly opportunities for positive impacts, related to improved communication, for example; we also see possibilities for ecological research to benefit from generative AI (e.g., image gap filling, biodiversity surveys, and improved citizen science). However, there are also risks, threatening to undermine the credibility of our science, mostly related to actions of bad actors, for example in terms of spreading fake information or committing fraud. Risks need to be mitigated at the level of government regulatory measures, but we also highlight what can be done right now, including discussing issues with the next generation of ecologists and transforming towards radically open science workflows.

RevDate: 2024-03-04
CmpDate: 2024-03-04

Chen C, He Y, Ni Y, et al (2024)

Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning.

Journal of cellular and molecular medicine, 28(6):e18156.

This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes. The coexpression network of co-expression pairs (CP) genes was integrated with its protein-protein interaction (PPI) network, and machine learning was employed to identify essential disease-representing genes. Finally, immuno-penetration analysis was performed on the MASH and DN gene datasets using the CIBERSORT algorithm to evaluate the plausibility of these genes in diseases. We found 19 key CP genes. Fos proto-oncogene (FOS), belonging to the IL-17 signalling pathway, showed greater centrality PPI network; Hyaluronan Mediated Motility Receptor (HMMR), belonging to ECM-receptor interaction genes, showed most critical in the co-expression network map of 19 CP genes; Forkhead Box C1 (FOXC1), like FOS, showed a high ability to predict disease in XGBoost analysis. Further immune infiltration showed a clear positive correlation between FOS/FOXC1 and mast cells that secrete IL-17 during inflammation. Combining the results of previous studies, we suggest a FOS/FOXC1/HMMR regulatory axis in MASH and DN may be associated with mast cells in the acting IL-17 signalling pathway. Extracellular HMMR may regulate the IL-17 pathway represented by FOS through the Mitogen-Activated Protein Kinase 1 (ERK) or PI3K-Akt-mTOR pathway. HMMR may serve as a signalling carrier between MASH and DN and could be targeted for therapeutic development.

RevDate: 2024-03-04
CmpDate: 2024-03-04

Huo J, Li X, Hu X, et al (2024)

Multi-omics analysis of miRNA-mediated intestinal microflora changes in crucian carp Carassius auratus infected with Rahnella aquatilis.

Frontiers in immunology, 15:1335602.

Infection by an emerging bacterial pathogen Rahnella aquatilis caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by R. aquatilis infection and its interacting mechanism of the intestinal microflora associated with microRNA (miRNA) immune regulation in crucian carp Carassius auratus are still unclear. In this study, C. auratus intraperitoneally injected with R. aquatilis KCL-5 was used as an experimental animal model, and the intestinal pathological changes, microflora, and differentially expressed miRNAs (DEMs) were investigated by multi-omics analysis. The significant changes in histopathological features, apoptotic cells, and enzyme activities (e.g., lysozyme (LYS), alkaline phosphatase (AKP), alanine aminotransferase (ALT), aspartate transaminase (AST), and glutathione peroxidase (GSH-Px)) in the intestine were examined after infection. Diversity and composition analysis of the intestinal microflora clearly demonstrated four dominant bacteria: Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes. A total of 87 DEMs were significantly screened, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes were mainly involved in the regulation of lipid, glutathione, cytosine, and purine metabolism, which participated in the local immune response through the intestinal immune network for IgA production, lysosome, and Toll-like receptor (TLR) pathways. Moreover, the expression levels of 11 target genes (e.g., TLR3, MyD88, NF-κB, TGF-β, TNF-α, MHC II, IL-22, LysC, F2, F5, and C3) related to inflammation and immunity were verified by qRT-PCR detection. The correlation analysis indicated that the abundance of intestinal Firmicutes and Proteobacteria was significantly associated with the high local expression of miR-203/NF-κB, miR-129/TNF-α, and miR-205/TGF-β. These findings will help to elucidate the molecular regulation mechanism of the intestinal microflora, inflammation, and immune response-mediated miRNA-target gene axis in cyprinid fish.

RevDate: 2024-03-04
CmpDate: 2024-03-04

Barrenechea Angeles I, Nguyen NL, Greco M, et al (2024)

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity.

PloS one, 19(2):e0298440.

Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.

RevDate: 2024-03-04
CmpDate: 2024-03-04

Li X, Cheng X, Wu J, et al (2024)

Multi-omics reveals different impact patterns of conventional and biodegradable microplastics on the crop rhizosphere in a biofertilizer environment.

Journal of hazardous materials, 467:133709.

Microplastics (MPs) from the incomplete degradation of agricultural mulch can stress the effectiveness of biofertilizers and ultimately affect the rhizosphere environment of crops. Yet, the involved mechanisms are poorly known and robust empirical data is generally lacking. Here, conventional polyethylene (PE) MPs and poly(butylene adipate-co-butylene terephthalate) (PBAT) / poly(lactic acid) (PLA) biodegradable MPs (PBAT-PLA BioMPs) were investigated to assess their potential impact on the rhizosphere environment of Brassica parachinensis in the presence of Bacillus amyloliquefaciens biofertilizer. The results revealed that both MPs caused different levels of inhibited crop both above- and belowground crop biomass (up to 50.11% and 57.09%, respectively), as well as a significant decrease in plant height (up to 48.63% and 25.95%, respectively), along with an imbalance of microbial communities. Transcriptomic analyses showed that PE MPs mainly affected root's vitamin metabolism, whereas PBAT-PLA BioMPs mainly interfered with the lipid's enrichment. Metabolomic analyses further indicated that PE MPs interfered with amino acid synthesis that involved in crops' oxidative stress, and that PBAT-PLA BioMPs mainly affected the pathways associated with root growth. Additionally, PBAT-PLA BioMPs had a bigger ecological negative impact than did PE MPs, as evidenced by more pronounced alterations in root antioxidant abilities, a higher count of identified differential metabolites, more robust interrelationships among rhizosphere parameters, and a more intricate pattern of impacts on rhizosphere metrics. This study highlights the MPs' impact on crop rhizosphere in a biofertilizer environment from a rhizosphere multi-omics perspective, and has theoretical implications for scientific application of biofertilizers.

RevDate: 2024-03-04
CmpDate: 2024-03-04

IHME-CHAIN Collaborators (2024)

Effects of education on adult mortality: a global systematic review and meta-analysis.

The Lancet. Public health, 9(3):e155-e165.

BACKGROUND: The positive effect of education on reducing all-cause adult mortality is known; however, the relative magnitude of this effect has not been systematically quantified. The aim of our study was to estimate the reduction in all-cause adult mortality associated with each year of schooling at a global level.

METHODS: In this systematic review and meta-analysis, we assessed the effect of education on all-cause adult mortality. We searched PubMed, Web of Science, Scopus, Embase, Global Health (CAB), EconLit, and Sociology Source Ultimate databases from Jan 1, 1980, to May 31, 2023. Reviewers (LD, TM, HDV, CW, IG, AG, CD, DS, KB, KE, and AA) assessed each record for individual-level data on educational attainment and mortality. Data were extracted by a single reviewer into a standard template from the Global Burden of Diseases, Injuries, and Risk Factors Study. We excluded studies that relied on case-crossover or ecological study designs to reduce the risk of bias from unlinked data and studies that did not report key measures of interest (all-cause adult mortality). Mixed-effects meta-regression models were implemented to address heterogeneity in referent and exposure measures among studies and to adjust for study-level covariates. This study was registered with PROSPERO (CRD42020183923).

FINDINGS: 17 094 unique records were identified, 603 of which were eligible for analysis and included data from 70 locations in 59 countries, producing a final dataset of 10 355 observations. Education showed a dose-response relationship with all-cause adult mortality, with an average reduction in mortality risk of 1·9% (95% uncertainty interval 1·8-2·0) per additional year of education. The effect was greater in younger age groups than in older age groups, with an average reduction in mortality risk of 2·9% (2·8-3·0) associated with each additional year of education for adults aged 18-49 years, compared with a 0·8% (0·6-1·0) reduction for adults older than 70 years. We found no differential effect of education on all-cause mortality by sex or Socio-demographic Index level. We identified publication bias (p<0·0001) and identified and reported estimates of between-study heterogeneity.

INTERPRETATION: To our knowledge, this is the first systematic review and meta-analysis to quantify the importance of years of schooling in reducing adult mortality, the benefits of which extend into older age and are substantial across sexes and economic contexts. This work provides compelling evidence of the importance of education in improving life expectancy and supports calls for increased investment in education as a crucial pathway for reducing global inequities in mortality.

FUNDING: Research Council of Norway and the Bill & Melinda Gates Foundation.

RevDate: 2024-03-04
CmpDate: 2024-03-04

Chen Y, Shi Y, Liang C, et al (2024)

MicrobeTCM: A comprehensive platform for the interactions of microbiota and traditional Chinese medicine.

Pharmacological research, 201:107080.

Thanks to the advancements in bioinformatics, drugs, and other interventions that modulate microbes to treat diseases have been emerging continuously. In recent years, an increasing number of databases related to traditional Chinese medicine (TCM) or gut microbes have been established. However, a database combining the two has not yet been developed. To accelerate TCM research and address the traditional medicine and micro ecological system connection between short board, we have developed the most comprehensive micro-ecological database of TCM. This initiative includes the standardization of the following advantages: (1) A repeatable process achieved through the standardization of a retrieval strategy to identify literature. This involved identifying 419 experiment articles from PubMed and six authoritative databases; (2) High-quality data integration achieved through double-entry extraction of literature, mitigating uncertainties associated with natural language extraction; (3) Implementation of a similar strategy aiding in the prediction of mechanisms of action. Leveraging drug similarity, target entity similarity, and known drug-target entity association, our platform enables the prediction of the effects of a new herb or acupoint formulas using the existing data. In total, MicrobeTCM includes 171 diseases, 725 microbes, 1468 herb-formulas, 1032 herbs, 15780 chemical compositions, 35 acupoint-formulas, and 77 acupoints. For further exploration, please visit https://www.microbetcm.com.

RevDate: 2024-02-29

Hitchings L, Fleet B, Smith DT, et al (2024)

Determining the distance patterns in the movements of future doctors in UK between 2002 and 2015: a retrospective cohort study.

BMJ open, 14(3):e077635 pii:bmjopen-2023-077635.

OBJECTIVE: To determine and identify distance patterns in the movements of medical students and junior doctors between their training locations.

DESIGN: A retrospective cohort study of UK medical students from 2002 to 2015 (UKMED data).

SETTING: All UK medical schools, foundations and specialty training organisation.

PARTICIPANTS: All UK medical students from 2002 to 2015, for a total of 97 932 participants.

OUTCOME MEASURES: Individual movements and number of movements by county of students from family home to medical school training, from medical school to foundation training and from foundation to specialty training.

METHODS: Leslie matrix, principal components analysis, Gini coefficient, χ[2] test, generalised linear models and variable selection methods were employed to explore the different facets of students' and junior doctors' movements from the family home to medical school and for the full pathway (from family home to specialty training).

RESULTS: The majority of the movements between the different stages of the full pathway were restricted to a distance of up to 50 km; although the proportion of movements changed from year-to-year, with longer movements during 2007-2008. At the individual level, ethnicity, socioeconomic class of the parent(s) and the deprivation score of the family home region were found to be the most important factors associated with the length of the movements from the family home to medical school. Similar results were found when movements were aggregated at the county level, with the addition of factors such as gender and qualification at entry (to medical school) being statistically associated with the number of new entrant students moving between counties.

CONCLUSION: Our findings show that while future doctors do not move far from their family home or training location, this pattern is not homogeneous over time. Distances are influenced by demographics, socioeconomic status and deprivation. These results may contribute in designing interventions aimed at solving the chronic problems of maldistribution and underdoctoring in the UK.

RevDate: 2024-02-28

Vigna-Taglianti FD, Martorana M, Viola E, et al (2024)

Evaluation of Effectiveness of the Unplugged Program on Gambling Behaviours among Adolescents: Study Protocol of the Experimental Controlled Study "GAPUnplugged".

Journal of prevention (2022) [Epub ahead of print].

Gambling risk behaviour is an emerging problem among adolescents. "Unplugged" is an effective Social Influence curriculum for preventing substance use among students. This study aims to develop and test a new component focused on gambling added to the Unplugged program. Schools of Piedmont region and Rome city were invited to participate in the study. A self-completed anonymous questionnaire including questions on socio-demographic characteristics, addictive behaviours, beliefs, attitudes and risk perceptions about gambling, normative perceptions, parental practices, school climate, refusal skills, impulsiveness, self-esteem, antisocial behaviours and sensation seeking was prepared for baseline and follow-up surveys. The protocol of the study was submitted and approved by the Novara Ethical Committee and registered in ClinicalTrials.gov (NCT05630157, Protocol ID: 080.742, 11/17/2022). Twenty-nine schools accepted to participate in the study. Sixty-three classes (1325 students) satisfied the eligibility criteria for intervention and were allocated to the intervention arm, and the other 61 (1269 students) were allocated to the control arm. Because of drop-out, absentees, refusals, and invalid questionnaires, data on 1874 students (998 in the intervention and 876 in the control arm), were available for the analysis at baseline. Data management of follow-up questionnaires is in progress. Results of the present study will be useful to clarify the effectiveness of prevention interventions in reducing gambling behaviours among adolescents. Moreover, this will be the first experience of evaluating a new component focused on a different risk behaviour, added to a curriculum previously shown as effective on other risk behaviours.

RevDate: 2024-02-29
CmpDate: 2024-02-29

Lemane T, Lezzoche N, Lecubin J, et al (2024)

Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.

Nature computational science, 4(2):104-109.

Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.

RevDate: 2024-02-27

Boyes D, Sims I, Lees DC, et al (2024)

The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794).

Wellcome open research, 9:6.

We present a genome assembly from an individual male Pandemis corylana (the Chequered Fruit-tree Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 441.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.53 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,608 protein coding genes.

RevDate: 2024-02-29
CmpDate: 2024-02-29

Schloss PD (2024)

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.

mSphere, 9(2):e0035423.

UNLABELLED: Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.

IMPORTANCE: Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.

RevDate: 2024-02-27

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

The genome sequence of the Light Emerald, Campaea margaritaria (Linnaeus, 1761).

Wellcome open research, 8:476.

We present a genome assembly from an individual male Campaea margaritaria (the Light Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 335.2 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,403 protein coding genes.

RevDate: 2024-02-26

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

The genome sequence of the Phoenix, Eulithis prunata (Linnaeus, 1758).

Wellcome open research, 8:185.

We present a genome assembly from an individual male Eulithis prunata (the Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 263.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,023 protein coding genes.

RevDate: 2024-02-26

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

The genome sequence of the Flame Shoulder, Ochropleura plecta (Linnaeus, 1761).

Wellcome open research, 8:506.

We present a genome assembly from an individual female Ochropleura plecta (the Flame Shoulder; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 643.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,016 protein coding genes.

RevDate: 2024-02-26

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

The genome sequence of the Brown Argus, Aricia agestis (Denis & Schiffermüller, 1775).

Wellcome open research, 8:336.

We present genome assemblies from two male Aricia agestis specimens (the Brown Argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequences are 435.3 and 437.4 megabases in span. Each assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genomes were assembled and are 15.47 and 15.45 kilobases in length. Gene annotation of these assemblies on Ensembl identified 12,688 and 12,654 protein coding genes.

RevDate: 2024-02-25

Zhu Y, Wang L, Ma J, et al (2024)

Assessment of carbon sequestration potential of mining areas under ecological restoration in China.

The Science of the total environment pii:S0048-9697(24)01318-4 [Epub ahead of print].

Mining activities aggravate the ecological degradation and emission of greenhouse gases throughout the world, thereby affecting the global climate and posing a serious threat to the ecological safety. Vegetation restoration is considered to be an effective and sustainable strategy to improve the post-mining soil quality and functions. However, we still have a limited knowledge of the impact of vegetation restoration on carbon sequestration potential in mining areas. In this pursuit, the present study was envisaged to integrate the findings from studies on soil organic carbon (SOC) sequestration in mining areas under vegetation restoration with field monitoring data. The carbon sequestration potential under vegetation restoration in China's mining areas was estimated by using a machine learning model. The results showed that (1) Vegetation restoration exhibited a consistently positive impact on the changes in the SOC reserves. The carbon sequestration potential was the highest in mixed forests, followed by broad-leaved forests, coniferous forests, grassland, shrubland, and farmland; (2) The number of years of vegetation restoration and mean annual precipitation were found to be the important moderating variables affecting the SOC reserves in reclaimed soils in mining areas; (3) There were significant differences in the SOC sequestration potential under different vegetation restoration scenarios in mining areas in China. The SOC sequestration potential reached up to 9.86 million t C a[-1], when the soil was restored to the initial state. Based on the meta-analysis, the maximal attainable SOC sequestration potential was found to be 4.26 million t C a[-1]. The SOC sequestration potential reached the highest level of 12.86 million t C a[-1], when the optimal vegetation type in a given climate was restored. The results indicated the importance of vegetation restoration for improving the soil sequestration potential in mining areas. The time lag in carbon sequestration potential for different vegetation types in mining areas was also revealed. Our findings can assist the development of ecological restoration regimens in mining areas to mitigate the global climate change.

RevDate: 2024-02-26
CmpDate: 2024-02-26

Navratilova HF, Lanham-New S, Whetton AD, et al (2024)

Associations of Diet with Health Outcomes in the UK Biobank: A Systematic Review.

Nutrients, 16(4):.

The UK Biobank is a cohort study that collects data on diet, lifestyle, biomarkers, and health to examine diet-disease associations. Based on the UK Biobank, we reviewed 36 studies on diet and three health conditions: type 2 diabetes (T2DM), cardiovascular disease (CVD), and cancer. Most studies used one-time dietary data instead of repeated 24 h recalls, which may lead to measurement errors and bias in estimating diet-disease associations. We also found that most studies focused on single food groups or macronutrients, while few studies adopted a dietary pattern approach. Several studies consistently showed that eating more red and processed meat led to a higher risk of lung and colorectal cancer. The results suggest that high adherence to "healthy" dietary patterns (consuming various food types, with at least three servings/day of whole grain, fruits, and vegetables, and meat and processed meat less than twice a week) slightly lowers the risk of T2DM, CVD, and colorectal cancer. Future research should use multi-omics data and machine learning models to account for the complexity and interactions of dietary components and their effects on disease risk.

RevDate: 2024-02-23

Wang F, Sun N, Zhang C, et al (2024)

Experimental study on mine water purification mechanism for broken coal and rock masses in the underground reservoir of ecologically vulnerable mining area.

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

Water-rock interaction mechanism and water purification capacity of broken coal and rock masses are very important for the efficient operation of the underground reservoir. In this paper, a water purification simulation device for an underground mine reservoir was designed. The experimental study on the dynamic interaction between broken coal and rock masses and mine water was carried out. The water purification mechanism is analyzed from the changes in rock mineral composition and mine water quality before and after the test. The results show that after the broken coal and rock mass purification, the water turbidity and the concentration of chlorides and suspended solids decreased obviously. The water purification capacities of mudstone and sandstone are stronger than that of coal samples. After 60 days of reaction between the working face sewage and the broken samples (mudstone, sandstone, and coal), the turbidity, chromaticity, and residual chlorine decreased by > 90%, 90%, and 60%, respectively; and COD decreased by 35.29%, 30.59%, and 28.99%, respectively. While the TDS and the total hardness increased by about 40%, 30%, and 10% for the mudstone, sandstone, and coal, respectively. It shows that coal also has the worst degradation performance. The water purification effect of broken coal and rock masses has a significant time effect. The early stage of water-rock interaction is dominated by mineral dissolution, and the middle stage is dominated by precipitation and adsorption. The pH value of the solution has a certain influence on the ion change. In the later stage, the water-rock interaction is weak in a dynamic equilibrium state, and the change in the mine water quality index is not obvious. Considering the influence of rock lithology on water quality and the law of water-rock interaction time, the construction site selection and water storage time optimization of underground reservoirs in Jinjie Coal Mine were carried out, respectively.

RevDate: 2024-02-26
CmpDate: 2024-02-26

Ou AH, Rosenthal SB, Adli M, et al (2024)

Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study.

Translational psychiatry, 14(1):109.

Lithium is the gold standard treatment for bipolar disorder (BD). However, its mechanism of action is incompletely understood, and prediction of treatment outcomes is limited. In our previous multi-omics study of the Pharmacogenomics of Bipolar Disorder (PGBD) sample combining transcriptomic and genomic data, we found that focal adhesion, the extracellular matrix (ECM), and PI3K-Akt signaling networks were associated with response to lithium. In this study, we replicated the results of our previous study using network propagation methods in a genome-wide association study of an independent sample of 2039 patients from the International Consortium on Lithium Genetics (ConLiGen) study. We identified functional enrichment in focal adhesion and PI3K-Akt pathways, but we did not find an association with the ECM pathway. Our results suggest that deficits in the neuronal growth cone and PI3K-Akt signaling, but not in ECM proteins, may influence response to lithium in BD.

RevDate: 2024-02-26
CmpDate: 2024-02-26

Kumar A, Ojha PK, K Roy (2024)

First report on pesticide sub-chronic and chronic toxicities against dogs using QSAR and chemical read-across.

SAR and QSAR in environmental research, 35(3):241-263.

Excessive use of chemicals is the outcome of the industrialization of agricultural sectors which leads to disturbance of ecological balance. Various agrochemicals are widely used in agricultural fields, urban green areas, and to protect from various pest-associated diseases. Due to their long-term health and environmental hazards, chronic toxicity assessment is crucial. Since in vivo and in vitro toxicity assessments are costly, lengthy, and require a large number of animal experiments, in silico toxicity approaches are better alternatives to save time, cost, and animal experimentation. We have developed the first regression-based 2D-QSAR models using different sub-chronic and chronic toxicity data of pesticides against dogs employing 2D descriptors. From the statistical results (ntrain=53-62, r2 = 0.614 to 0.754, QLOO2 = 0.501 to 0.703 and QF12 = 0.531 to 0.718, QF22=0.523-0.713), it was concluded that the models are robust, reliable, interpretable, and predictive. Similarity-based read-across algorithm was also used to improve the predictivity (QF12=0.595-0.813,QF22=0.573-0.809) of the models. 5132 chemicals obtained from the CPDat and 1694 pesticides obtained from the PPDB database were also screened using the developed models, and their predictivity and reliability were checked. Thus, these models will be helpful for eco-toxicological data-gap filling, toxicity prediction of untested pesticides, and development of novel, safer & eco-friendly pesticides.

RevDate: 2024-02-26
CmpDate: 2024-02-26

Messer LF, Lee CE, Wattiez R, et al (2024)

Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics.

Microbiome, 12(1):36.

BACKGROUND: Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment.

RESULTS: For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community.

CONCLUSION: Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.

RevDate: 2024-02-26
CmpDate: 2024-02-26

Wang Y, Chen Y, Lu S, et al (2024)

Development and trends of constructed wetland substrates over the past 30 years: a literature visualization analysis based on CiteSpace.

Environmental science and pollution research international, 31(10):14537-14552.

Constructed wetland substrates (CWSs) have received considerable attention owing to their importance in adsorbing and degrading pollutants, providing growth attachment points for microorganisms, and supporting wetland plants. There are differences in the configurations and functions of constructed wetlands (CWs) for treating different water bodies and sewage, resulting in a wide variety of substrates. Research on the application and mechanism of CWSs is not sufficiently systematic. Therefore, the current research advancements and hotspots must be identified. Hence, we used CiteSpace to analyze 1955 English publications from the core collection database of the Web of Science to assess the current state of the CWS research field. Based on the cooperative network analysis, the roles of various countries, institutions, and authors in research on CWSs were reviewed. Keyword co-occurrence and cluster analyses were used to discuss the transformation of CWSs from removing traditional pollutants to emerging pollutants and the transition from incorporating natural substrates to artificial substrates. Finally, we underscored the need for more emphasis to be placed on the collocation and application of the CWSs at different latitudes. Furthermore, the substrate micro-interface process and its effects on the interaction patterns of pollutants and microorganisms should be thoroughly investigated to provide theoretical guidance for the development of wetland applications and mechanisms.

RevDate: 2024-02-26
CmpDate: 2024-02-23

Xu P, Li G, Zheng Y, et al (2024)

Fertilizer management for global ammonia emission reduction.

Nature, 626(8000):792-798.

Crop production is a large source of atmospheric ammonia (NH3), which poses risks to air quality, human health and ecosystems[1-5]. However, estimating global NH3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy[4,5]. Here we develop a machine learning model for generating crop-specific and spatially explicit NH3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr[-1], lower than previous estimates that did not fully consider fertilizer management practices[6-9]. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr[-1]) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44-56%) for rice, 27% (24-28%) for maize and 26% (20-28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1-2.6 and 5.5 ± 5.7% under SSP5-8.5 by 2030-2060. However, targeted fertilizer management has the potential to mitigate these increases.

RevDate: 2024-02-26
CmpDate: 2024-02-26

Rojo J, Cervigón P, Ferencova Z, et al (2024)

Assessment of environmental risk areas based on airborne pollen patterns as a response to land use and land cover distribution.

Environmental pollution (Barking, Essex : 1987), 344:123385.

Allergic respiratory diseases are considered to be among the most important public health concerns, and pollen is the main cause of allergic respiratory diseases worldwide. However, the biological component of air quality is largely underestimated, and there is an important gap in the legislation in this area. The aims of this study were to characterise the occurrence and incidence of pollen exposure in relation to potential pollen sources and to delineate the main areas of aerobiological risk in the Madrid Autonomous Region based on homogeneous patterns of pollen exposure. This study uses the historical aerobiological database of the Madrid Region Palynological Network (central Spain) from ten pollen stations from 1994 to 2022, and the land-use information from the Corine Land Cover. Multiple clustering approaches were followed to group the sampling stations and subsequently all the 1 × 1km pixels for the Madrid Autonomous Region. The clustering dendrogram for land-use distribution was compared to the dendrogram for historical airborne pollen data. The two dendrograms showed a good alignment with a very high correlation (0.95) and very low entanglement (0.15), which indicates a close correspondence between the distribution of the potential pollen sources and the airborne pollen dynamics. Based on this knowledge, the Madrid Autonomous Region was divided into six aerobiological risk areas following a clear anthropogenic gradient in terms of the potential pollen sources that determine pollen exposure in the Madrid Region. Spatial regionalisation is a common practice in environmental risk assessment to improve the application of management plans and optimise the air quality monitoring networks. The risk areas proposed by scientific criteria in the Madrid Autonomous Region can be adjusted to other operational criteria following a framework equivalent to other air quality networks.

RevDate: 2024-02-23

Gauzens B, Kalinkat G, Antunes AC, et al (2024)

Quantitative description of six fish species' gut contents and prey abundances in the Baltic Sea (1968-1978).

Scientific data, 11(1):236.

The dataset presents a compilation of stomach contents from six demersal fish species from two functional groups inhabiting the Baltic Sea. It includes detailed information on prey identities, body masses, and biomasses recovered from both the fish's digestive systems and their surrounding environment. Environmental parameters, such as salinity and temperature levels, have been integrated to enrich this dataset. The juxtaposition of information on prey found in stomachs and in the environment provides an opportunity to quantify trophic interactions across different environmental contexts and investigate how fish foraging behaviour adapts to changes in their environment, such as an increase in temperature. The compilation of body mass and taxonomic information for all species allows approaching these new questions using either a taxonomic (based on species identity) or functional trait (based on body mass) approach.

RevDate: 2024-02-23

Brunelli A, Cazzagon V, Faraggiana E, et al (2024)

An overview on dispersion procedures and testing methods for the ecotoxicity testing of nanomaterials in the marine environment.

The Science of the total environment pii:S0048-9697(24)01271-3 [Epub ahead of print].

Considerable efforts have been devoted to develop or adapt existing guidelines and protocols, to obtain robust and reproducible results from (eco)toxicological assays on engineered nanomaterials (NMs). However, while many studies investigated adverse effects of NMs on freshwater species, less attention was posed to the marine environment, a major sink for these contaminants. This review discusses the procedures used to assess the ecotoxicity of NMs in the marine environment, focusing on the use of protocols and methods for preparing NMs dispersions and on the NMs physicochemical characterization in exposure media. To this purpose, a critical analysis of the literature since 2010 was carried out, based on the publication of the first NMs dispersion protocols. Among the 89 selected studies, only <5 % followed a standardized dispersion protocol combined with NMs characterization in ecotoxicological media, while more than half used a non-standardized dispersion method but performed NMs characterization. In the remaining studies, only partial or no information on dispersion procedures or on physicochemical characterization was provided. This literature review also highlighted that metal oxides NMs were the most studied (42 %), but with an increasing interest in last years towards nanoplastics (14 %) and multicomponent nanomaterials (MCNMs, 7 %), in line with the growing attention on these emerging contaminants. For all these NMs, primary producers as algae and bacteria were the most studied groups of marine species, in addition to mollusca, while organisms at higher trophic levels were less represented, likely due to challenges in evaluating adverse effects on more complex organisms. Thus, despite the wide use of NMs in different applications, standard dispersion protocols are not often used for ecotoxicity testing with marine species. However, the efforts to characterize NMs in ecotoxicological media recognize the importance of following conditions that are as standardized as possible to support the ecological hazard assessment of NMs.

RevDate: 2024-02-22

Ambrosini E, Giangregorio C, Lomurno E, et al (2024)

Automatic spontaneous speech analysis for the detection of cognitive functional decline in the elderly: a multi-language study.

JMIR aging [Epub ahead of print].

BACKGROUND: The rise in life expectancy is associated with an increase in long-term and gradual cognitive decline. Treatment effectiveness is enhanced at the early stage of the disease. Therefore, there is a need to find low-cost and ecological solutions for mass screening of community-dwelling elderly people.

OBJECTIVE: This work aimed to exploit automatic analysis of free speech to identify signs of cognitive function decline.

METHODS: A sample of 266 subjects aged over 65 years were recruited in Italy and Spain and were divided into three groups according to their Mini-Mental Status Examination (MMSE) score. People were asked to tell a story and describe a picture, and voice recordings were used to extract high-level features on different time scales automatically. Based on these features, machine learning algorithms were trained to solve binary and multi-class classification problems using both mono- and cross-lingual approaches. The algorithms were enriched using SHAP for model explainability.

RESULTS: On the Italian dataset, healthy subjects (MMSE≥27) were automatically discriminated from subjects with a mildly impaired cognitive function (20≤MMSE≤26) and from those with a moderate to severe impairment of cognitive function (11≤MMSE≤19) with an accuracy of 80% and 86%, respectively. Slightly lower performance was achieved on the Spanish and multi-language datasets.

CONCLUSIONS: This work proposed a transparent and unobtrusive assessment method, which might be included in a mobile app for large-scale monitoring of cognitive functionality in elderly people. Voice is confirmed to be an important biomarker of cognitive decline due to its non-invasive and easily accessible nature.

RevDate: 2024-02-24

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

The genome sequence of the Hornet Moth, Sesia apiformis (Clerck, 1759).

Wellcome open research, 8:499.

We present a genome assembly from an individual male Sesia apiformis (the Hornet Moth; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 546.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,358 protein coding genes.

RevDate: 2024-02-23
CmpDate: 2024-02-23

Yu D, Zhang Y, Dang H, et al (2024)

Multiomics analyses reveal the mechanisms of the responses of subalpine treeline trees to phenology and winter low-temperature stress.

Physiologia plantarum, 176(1):e14218.

Withstanding extreme cold stress is a prerequisite for alpine treeline trees to persist and survive. However, the underlying mechanism by which treeline trees sense phenological changes and survive hard winters has not been fully elucidated. Here, we investigated the physiology, transcriptome, and metabolome of the subalpine treeline species Larix chinensis to identify the molecular mechanism of phenological and cold resistance. Calcium and antioxidant enzyme activities (e.g., superoxide dismutase and glutathione peroxidase) are essential for coping with winter cold stress in L. chinensis. Transcriptome analysis revealed that circadian rhythm and phytohormone signalling transduction played important roles in regulating L. chinensis phenological changes and cold stress responses. The variations in the transcriptome identified were accompanied by the specific accumulation of flavones, flavonols, and monosaccharides. The flavonoid biosynthesis and phenylpropanoid biosynthesis pathways played important roles in the adaptation of L. chinensis to the extreme winter environment, and flavone and flavonol biosynthesis was an important pathway involved in bud burst. In addition, temperature and photoperiod had synergistic influences on the formation and release of bud dormancy. Thus, our findings provided new insights into the mechanism of subalpine treeline formation.

RevDate: 2024-02-23
CmpDate: 2024-02-23

Shen Z, Shi H, Jiang Y, et al (2024)

Diurnal variation in the urban thermal environment and its relationship to human activities in China: a Tencent location-based service geographic big data perspective.

Environmental science and pollution research international, 31(9):14218-14228.

The main factor of the formation and deterioration in China's urban thermal environment is human activity, which is difficult to describe and measure. A new perspective on the effect of human activity on the urban thermal environment can be obtained by examining the interaction between location-based service (LBS) data and the urban thermal environment in China. However, relevant research is still limited. In this study, we used Tencent LBS data, Terra/Aqua MODIS land surface temperature (LST) data, and land use data to investigate the relationship between LBS and the urban thermal environment, specifically the LST and surface urban heat island intensity (SUHII) across China and its provinces. Our results showed that (1) in summer, the heat island effect was an issue in 94% of the urban areas in China, which was worse during the day. The high- and low-value periods of LBS data on a given day coincided with the acquisition times of MODIS LST products during the day and at night, respectively. (2) During both the day and at night, there was a significant connection between LBS data and the urban thermal environment in China. The highest correlation coefficient (r) between LBS data and the LST could reach 0.55 (p < 0.01) at the provincial level, and the highest correlation coefficient (r) between LBS data and the SUHII could reach 0.78 (p < 0.01) at the provincial level. (3) The urban thermal environment diurnal difference and LBS data exhibited a significant relationship. The ΔLBS diurnal differences were significantly positively related to the SUHII diurnal differences in China. The overall study findings revealed that LBS data constitute an important parameter to represent the human activity intensity when investigating the formation of the urban thermal environment in China.

RevDate: 2024-02-22

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

The genome sequence of the Shuttle-shaped Dart, Agrotis puta (Hübner, 1803).

Wellcome open research, 8:84.

We present a genome assembly from an individual male Agrotis puta (the Shuttle-shaped Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 522 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,136 protein coding genes.

RevDate: 2024-02-22

Tran T, S Xie (2024)

Mitigating Wildlife Spillover in the Clinical Setting: How Physicians and Veterinarians Can Help Prevent Future Disease Outbreaks.

AJPM focus, 3(2):100193.

INTRODUCTION: The transmission of pathogens from wildlife to humans is a major global health threat that has been highlighted by the proposed origins of the COVID-19 pandemic. Numerous barriers impede pathogen spillover events from ensuing widespread human transmission, but human activity has accelerated the frequency of spillovers and subsequent disease outbreaks, in part through a booming wildlife trade whose impacts on health are not well understood.

METHODS: A literature review was conducted to examine the risk that the wildlife trade poses to public health and the degree to which these risks are recognized and addressed in clinical practice and medical and veterinary education.

RESULTS: The illicit aspects of the wildlife trade challenge efforts to understand its impacts on health. The U.S. and Europe play a leading role in the global wildlife trade that often goes unacknowledged. In particular, the consumption of wild meat and ownership of exotic pets poses public health risks. The potential role of clinicians is underutilized, both in the clinical setting and in clinical education.

DISCUSSION: Physicians and veterinarians have the unique opportunity to utilize their clinical roles to address these knowledge gaps and mitigate future outbreaks. We outline a multifaceted approach that includes increasing clinical knowledge about the ecology of zoonotic diseases, leveraging opportunities for mitigation during patient/client-clinician interactions, and incorporating One Health core competencies into medical and veterinary school curricula.

RevDate: 2024-02-20

Townley B, Akin D, Dimaguila GL, et al (2024)

Exploring the infectious contribution to intussusception causality using the effects of COVID-19 lockdowns in Australia: An ecological study.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:7611512 [Epub ahead of print].

INTRODUCTION: Intussusception is the primary cause of acute bowel obstruction in infants. The majority of cases under 2 years of age are classed as idiopathic with viral infection implicated as one of the causes. COVID-19 public health measures led to significant decreases in communicable disease prevalence. During these times, reductions in intussusception frequency were reported - reductions greater than would be expected with our previous understanding of its infectious aetiology.

METHODS: We conducted a retrospective, multi-state, ecological study over a twelve-year period. Monthly case numbers of ICD-10-AM K56.1 'Intussusception' coded admissions were acquired from state-wide admissions datasets from New South Wales (NSW), Victoria and Queensland, representing 77.62% of the eligible Australian population. These counts within differing jurisdictional lockdowns were compared to non-lockdown periods in order to investigate a correlation between intussusception frequency and lockdown periods.

RESULTS: We found a negative association between intussusception frequency and lockdown periods in both eligible states. The largest reductions were seen in the under 2 year age groups with Victoria experiencing a 62.7% reduction (Rate ratio (RR) = 0.37, p < 0.0001) and NSW a 40.1% reduction (RR = 0.599, p = 0.006) during lockdown times. Controls for variations in lockdown restrictions between both regional and metropolitan areas also showed expected decreases.

CONCLUSION: Our ecological study demonstrates significant decreases in the frequency of paediatric intussusception admissions during the COVID-19 lockdown periods. The unexpected magnitude of the reductions suggests that the true proportion of infectious disease-caused idiopathic intussusception is greatly underestimated.

RevDate: 2024-02-20

Schaan AP, Vidal A, Zhang A-N, et al (2024)

Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.

mSystems [Epub ahead of print].

Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Ramakodi MP (2024)

Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.

FEMS microbiology letters, 371:.

A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Omondi VO, Bosire GO, Onyari JM, et al (2024)

Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.

mSystems, 9(2):e0122823.

Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.

RevDate: 2024-02-20

Hegarty B, Riddell V J, Bastien E, et al (2024)

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.

mSystems [Epub ahead of print].

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.IMPORTANCEThe identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.

RevDate: 2024-02-20

Meyer F, Sandbakk Ø, GP Millet (2024)

Editorial: Sport performance analysis: from the laboratory to the field.

Frontiers in sports and active living, 6:1372080.

RevDate: 2024-02-18

Shchepin ON, López Villalba Á, Inoue M, et al (2024)

DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia.

Protist, 175(2):126023 pii:S1434-4610(24)00015-4 [Epub ahead of print].

The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.

RevDate: 2024-02-19
CmpDate: 2024-02-19

Jensen PM, Danielsen F, Jacobsen SK, et al (2024)

Fair concordance between Google Trends and Danish ornithologists in the assessment of temporal trends in Danish bird populations highlights the informational value of big data.

Environmental monitoring and assessment, 196(3):276.

The ongoing depletion of natural systems and associated biodiversity decline is of growing international concern. Climate change is expected to exacerbate anthropogenic impacts on wild populations. The scale of impact on ecosystems and ecosystem services will be determined by the impact on a multitude of species and functional groups, which due to their biology and numbers are difficult to monitor. The IPCC has argued that surveillance or monitoring is critical and proposed that monitoring systems should be developed, which not only track developments but also function as "early warning systems." Human populations are already generating large continuous datasets on multiple taxonomic groups through internet searches. These time series could in principle add substantially to current monitoring if they reflect true changes in the natural world. We here examined whether information on internet search frequencies delivered by the Danish population and captured by Google Trends (GT) appropriately informs on population trends in 106 common Danish bird species. We compared the internet search activity with independent equivalent population trend assessments from the Danish Ornithological Society (BirdLife Denmark/DOF). We find a fair concordance between the GT trends and the assessments by DOF. A substantial agreement can be obtained by omitting species without clear temporal trends. Our findings suggest that population trend proxies from internet search frequencies can be used to supplement existing wildlife population monitoring and to ask questions about an array of ecological phenomena, which potentially can be integrated into an early warning system for biodiversity under climate change.

RevDate: 2024-02-19
CmpDate: 2024-02-19

Yu XA, McLean C, Hehemann JH, et al (2024)

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.

The ISME journal, 18(1):.

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

RevDate: 2024-02-18

Lyu Y, Gao Y, Pang X, et al (2024)

Elucidating contributions of volatile organic compounds to ozone formation using random forest during COVID-19 pandemic: A case study in China.

Environmental pollution (Barking, Essex : 1987), 346:123532 pii:S0269-7491(24)00246-X [Epub ahead of print].

Ozone has been reported to increase despite nitrogen oxides reductions during the COVID-19 pandemic, and ozone formation needs to be revisited using volatile organic compounds (VOCs), which are rarely measured during the pandemic. Here, a total of 98 VOCs species were monitored in an economy-active city in China from January 2021 to August 2022 to assess contributions to ozone formation during the pandemic. Total VOCs concentrations were 35.55 ± 21.47 ppb during the entire period, among which alkanes account for the largest fraction (13.78 ppb, 38.0%), followed by aromatics (6.16 ppb, 16.8%) and oxygenated VOCs (OVOCs, 5.69 ppb, 15.7%). Most VOCs groups (e.g., alkenes, OVOCs) and individual species (e.g., isoprene, methyl vinyl ketone) display obvious seasonal and diurnal variations, which are related to their sources and reactivities. No weekend effects of VOCs suggest limited influences from traffic emissions during pandemic. Aromatics and alkenes are the major contributors (39% and 33%) to ozone formation potential, largely driven by o/m/p-xylene (21%), ethylene (15%), toluene (9%). Secondary organic aerosol formation potential is dominated by toluene (>50%) despite its low proportion (5%). Further inclusion of VOCs and meteorology in the Random Forest model shows good ozone prediction performance (R[2] = 0.77-0.86, RMSE = 11.95-19.91 μg/m[3], MAE = 8.89-14.58 μg/m[3]). VOCs and NO2 contribute >50% of total importance with the largest difference in importance ratio of VOCs/NO2 in the summer and winter, implying ozone formation regime may vary. No seasonal variations in importance of meteorology are observed, while importance of other variables (e.g., PM2.5) is highest in the summer. This work identifies critical VOCs groups and species for ozone formation during the pandemic, and demonstrates the feasibility of machine learning algorithms in elucidation of ozone formation mechanisms.

RevDate: 2024-02-15

Ko CY, Lee YC, Wang YC, et al (2024)

Modulations of ocean-atmosphere interactions on squid abundance over Southwest Atlantic.

Environmental research pii:S0013-9351(24)00348-7 [Epub ahead of print].

Anthropogenic shifts in seas are reshaping fishing trends, with significant implications for aquatic food sources throughout this century. Examining a 21-year abundance dataset of Argentine shortfin squids Illex argentines paired with a regional oceanic analysis, we noted strong correlations between squid annual abundance and sea surface temperature (SST) in January and February and eddy kinetic energy (EKE) from March to May in the Southwest Atlantic. A deeper analysis revealed combined ocean-atmosphere interactions, pinpointed as the primary mode in a rotated empirical orthogonal function analysis of SST. This pattern produced colder SST and amplified EKE in the surrounding seas, factors crucial for the unique life stages of squids. Future projections from the CMIP6 archive indicated that this ocean-atmosphere pattern, referred to as the Atlantic symmetric pattern, would persist in its cold SST phase, promoting increased squid abundance. However, rising SSTs due to global warming might counteract the abundance gains. Our findings uncover a previously unrecognized link between squids and specific environmental conditions governed by broader ocean-atmosphere interactions in the Southwest Atlantic. Integrating these insights with seasonal and decadal projections can offer invaluable information to stakeholders in squid fisheries and marine conservation under a changing climate.

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ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

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In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

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Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

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In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

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Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

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When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

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With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

Electronic Scholarly Publishing
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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin and even a collection of poetry — Chicago Poems by Carl Sandburg.

Timelines

ESP now offers a large collection of user-selected side-by-side timelines (e.g., all science vs. all other categories, or arts and culture vs. world history), designed to provide a comparative context for appreciating world events.

Biographies

Biographical information about many key scientists (e.g., Walter Sutton).

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )