@article {pmid41106617,
year = {2025},
author = {Losiewicz, OM and Cohen, ZD and Akre, S and Welborn, A and Craske, MG},
title = {Daily spread of positive affect is associated with subsequent well-being: A study of idiographic network analysis and emotional inertia.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120461},
doi = {10.1016/j.jad.2025.120461},
pmid = {41106617},
issn = {1573-2517},
abstract = {Emotional inertia, or the persistence of affect over time, and emotion network density, a measurement of the interconnected or relatedness of one's emotions, both capture dynamics of emotional experiences. Previous research has found that higher levels of negative emotional inertia and network density are associated with anxiety and depression. However, there is a dearth of research examining inertia and density of positive emotions and prospective associations between emotion dynamics and subsequent wellbeing. This study sought to address these limitations by examining both cross-sectional and longitudinal associations between emotional inertia and network density and well-being. We examined inertia and density of both positive and negative emotions. Adults with moderate-to-severe depression (N = 333) completed two 8-day epochs of ecological momentary assessment (EMA) five times daily. Emotional inertia and idiographic networks were calculated separately for EMA measures of negative and positive affect, and associations with self-reported well-being were examined using nested comparison tests and Bayesian multilevel models. In partial support of hypotheses, contemporaneous network density of positive emotions was positively associated with self-reported well-being six months later. Conversely, inertia of positive affect was inversely associated with well-being six months later. Neither inertia nor network density of negative affect was associated with subsequent well-being. These results suggest that inertia and network density of positive affect may indicate likelihood of experiencing changes in well-being in the future. Future research should investigate the underlying mechanisms, discern differences between emotional inertia and emotion network density, and explore potential implications for treatment.},
}

@article {pmid41106353,
year = {2025},
author = {Asteraye, GB and Jobling, R and Jemberu, WT and Pinchbeck, G and Knight-Jones, TJD and Critchlow, R and Rushton, J and Chaters, GL},
title = {Classification of donkey systems in Ethiopia.},
journal = {Preventive veterinary medicine},
volume = {246},
number = {},
pages = {106719},
doi = {10.1016/j.prevetmed.2025.106719},
pmid = {41106353},
issn = {1873-1716},
abstract = {Working donkeys play a critical role in transportation, agriculture and household resilience in low- and middle-income countries. Other animals that are kept for production purposes, such as cattle, are often grouped into broad production system classes, such as dairy or pastoral, for comparison between and better understanding of the needs and outputs of animals within specific sectors. Despite the importance of working donkeys for sustaining livelihoods there are no systematic classifications of these populations. The aim of this study was to classify and characterise donkey systems in Ethiopia using household-level questionnaire data which included donkey ownership, husbandry, use and local environment data, through multiple factor and hierarchical cluster analysis. Household questionnaire data from 241 donkey-owning households in three districts of Ethiopia were used. Three distinct clusters of donkey ownership were identified: 'Domestic-Pastoral'; 'Domestic-Agricultural' and 'Commercial'. Differences between systems are primarily influenced by donkey purpose, environmental (agro-ecological) factors, and husbandry practices. Constraints associated with donkey ownership varied across clusters: households in the commercial system reported higher incidence of injuries and welfare concerns, in the pastoral system the main constraints were drought and feed shortage, and domestic-agricultural households reported infectious diseases as the main challenge. This new classification of donkey systems provides a framework for analysing donkey health and welfare data, enabling more context-specific needs assessments and facilitating the design of targeted interventions to improve equid health and household livelihoods.},
}

@article {pmid41103550,
year = {2025},
author = {McLean, BS and Bloom, D and Davis, EB and Guralnick, RP and Santana, SE and Allen, JM and Amarilla-Stevens, H and Bell, KC and Blackburn, DC and Bradley, JE and Bradley, RD and Carling, MD and Coconis, A and Colella, JP and Conroy, CJ and Cook, JA and de Bastos Cruz Machado, H and Demboski, JR and Derieg, KM and Doll, A and Dumbacher, JP and Duncan, WD and Dunnum, JL and Feldman, C and Ferguson, AW and Fitzgerald, KE and Flannery, ME and Hood, K and Hornsby, AD and Krejsa, D and LaFrance, R and Light, JE and Pavan, SE and Peterson, S and Raniszewski, A and Rickart, EA and Robson, S and Rowe, RJ and Rowsey, DM and Semerdjian, A and Stankowich, T and Steger, L and Stevens, R and Thibault, KM and Thompson, CW and Upham, NS and Wilkins, A and Wommack, EA},
title = {Extending mammal specimens with their essential phenotypic traits.},
journal = {Journal of mammalogy},
volume = {106},
number = {5},
pages = {1282-1291},
pmid = {41103550},
issn = {0022-2372},
abstract = {Natural history collections are repositories of biodiversity specimens that provide critical infrastructure for studies of mammals. Over the past 3 decades, digitization of collections has opened up the temporal and spatial properties of specimens, stimulating new data sharing, use, and training across the biodiversity sciences. These digital records are the cornerstones of an "extended specimen network," in which the diverse data derived from specimens become digital, linked, and openly accessible for science and policy. However, still missing from most digital occurrences of mammals are their morphological, reproductive, and life-history traits. Unlocking this information will advance mammalogy, establish richer faunal baselines in an era of rapid environmental change, and contextualize other types of specimen-derived information toward new knowledge and discovery. Here, we present the Ranges Digitization Network (Ranges), a community effort to digitize specimen-level traits from all terrestrial mammals of western North America, append them to digital records, publish them openly in community repositories, and make them interoperable with complimentary data streams. Ranges is a consortium of 23 institutions with an initial focus on non-marine mammal species (both native and introduced) occurring in western Canada, the western United States, and Mexico. The project will establish trait data standards and informatics workflows that can be extended to other regions, taxa, and traits. Reconnecting mammalogists, museum professionals, and researchers for a new era of collections digitization will catalyze advances in mammalogy and create a community-curated trait resource for training and engagement with global conservation initiatives.},
}

@article {pmid41102527,
year = {2025},
author = {Pei, Y and Forstmeier, W and Suh, A and Bambach, L and Borges, I and Low, GW and Dion-Côté, AM and Knief, U and Wolf, J and Kempenaers, B},
title = {Evolution of large polymorphic inversions in a panmictic songbird.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf262},
pmid = {41102527},
issn = {1537-1719},
abstract = {Chromosomal inversions have long been appreciated as an important source of genetic diversity, local adaptation and speciation. However, selection pressures maintaining ancestral and derived alleles at high frequency over extended periods of time remain poorly characterized. Using genome-wide single-nucleotide polymorphism (SNP) markers and shared barcodes of linked-read sequences from twenty wild and seven captive zebra finches Taeniopygia guttata, we systematically scanned a high-quality zebra finch reference genome and identified all large polymorphic inversions that segregate at high minor allele frequencies. Apart from the known polymorphic inversions on chromosomes Tgu5, Tug11, Tgu13 and TguZ, we characterized two inversions on microchromosomes Tgu26 and Tgu27 and identified another eight putative inversions, located mostly on microchromosomes and ranging in size from 0.42 to 65.22Mb. Population genomic analyses show that most of the six bona fide inversions are complex, containing short nested inversions. The early inversions emerged an estimated 0.6-2.2 million years ago and segregate at relatively high frequencies in the wild (minor haplotype frequency range: 0.289-0.429). Based on fitness-related measures of about 5,000 captive zebra finches, we conclude that three of the inversion polymorphisms (Tgu11, Tgu27, and TguZ) may be maintained by net heterosis. In the youngest of the six inversions (Tgu13), the derived haplotype showed weak positive additive effects on various fitness components. In combination with previous discoveries, we provide a comprehensive overview of the genomic distribution and evolutionary dynamics of large polymorphic inversions in the panmictic zebra finch. Our findings highlight (1) that microchromosomes may harbor quite a few additional inversion polymorphisms, (2) that most of the inversions contain smaller nested or overlapping inversions, and (3) that inversions were most likely maintained by weak heterosis with small fitness effects requiring large sample sizes to be detected.},
}

@article {pmid41102232,
year = {2025},
author = {Fassoni, AC and Yong, ASM and Clark, RE and Roeder, I and Glauche, I},
title = {Predicting treatment-free remission in chronic myeloid leukemia patients using an integrated model of tumor-immune dynamics.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {115},
pmid = {41102232},
issn = {2056-7189},
mesh = {Humans ; *Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology/drug therapy/therapy ; Killer Cells, Natural/immunology ; Remission Induction ; Treatment Outcome ; Models, Biological ; },
abstract = {The interactions between tumor and the immune system are main factors in determining cancer treatment outcomes. In Chronic Myeloid Leukemia (CML), considerable evidence shows that the dynamics between residual leukemia and the patient's immune system can result in either sustained disease control, leading to treatment-free remission (TFR), or disease recurrence. The question remains how to integrate mechanistic and data-driven models to support prediction of treatment outcomes. Starting from classical ecological modeling concepts, which allow to explicitly account for immune interactions at the cellular level, we incorporate time-course data on natural killer (NK) cell number, function, and their tumor-induced suppression into our general model of CML treatment. We identify relevant time scales governing treatment and immune response, enabling refined model calibration using tumor and NK cell time courses from different datasets. While the model successfully describes patient-specific response dynamics, critical parameters for predicting treatment outcome remain uncertain. However, by explicitly incorporating tumor load changes in response to TKI dose alterations, these parameters can be estimated and used to derive model predictions for treatment cessation. Further exploring dynamic changes in the number of functional immune cells, we suggest specific measurement strategies of immune effector cell populations to enhance prediction accuracy for CML recurrence following treatment cessation. The generalizability and flexibility of our approach represent a significant step towards quantitative, personalized medicine that integrates tumor-immune dynamics to guide clinical decisions and optimize dynamic cancer therapies.},
}

Humans
*Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology/drug therapy/therapy
Killer Cells, Natural/immunology
Remission Induction
Treatment Outcome
Models, Biological

@article {pmid41098171,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Yellow-barred Brindle, Acasis viretata (Hübner, 1799) (Lepidoptera: Geometridae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {516},
pmid = {41098171},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Acasis viretata (Yellow-barred Brindle; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 297.68 megabases. Most of the assembly (99.98%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.01 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid41096595,
year = {2025},
author = {Sakaguchi, T and Irifune, Y and Kamada, R and Sakaguchi, K},
title = {Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199326},
pmid = {41096595},
issn = {1422-0067},
support = {25K00273//Japan Society for the Promotion of Science/ ; 24K01633//Japan Society for the Promotion of Science/ ; 23K17966//Japan Society for the Promotion of Science/ ; 23H02098//Japan Society for the Promotion of Science/ ; JPMJSP2119//Japan Science and Technology Agency/ ; none//the Photo-excitonix Project at Hokkaido University/ ; },
mesh = {*Bacteria/genetics/metabolism ; *Genomics/methods ; Proteomics/methods ; Genome-Wide Association Study ; Systems Biology/methods ; Quantitative Trait Loci ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; Transcriptome ; Multiomics ; },
abstract = {The field of bacterial systems biology is rapidly advancing beyond static genomic analyses, and moving toward dynamic, integrative approaches that connect genetic variation with cellular function. This review traces the progression from genome-wide association studies (GWAS) to multi-omics frameworks that incorporate transcriptomics, proteomics, and interactome mapping. We emphasize recent breakthroughs in high-resolution transcriptomics, including single-cell, spatial, and epitranscriptomic technologies, which uncover functional heterogeneity and regulatory complexity in bacterial populations. At the same time, innovations in proteomics, such as data-independent acquisition (DIA) and single-bacterium proteomics, provide quantitative insights into protein-level mechanisms. Experimental and AI-assisted strategies for mapping protein-protein interactions help to clarify the architecture of bacterial molecular networks. The integration of these omics layers through quantitative trait locus (QTL) analysis establishes mechanistic links between single-nucleotide polymorphisms and systems-level phenotypes. Despite persistent challenges such as bacterial clonality and genomic plasticity, emerging tools, including deep mutational scanning, microfluidics, high-throughput genome editing, and machine-learning approaches, are enhancing the resolution and scope of bacterial genetics. By synthesizing these advances, we describe a transformative trajectory toward predictive, systems-level models of bacterial life. This perspective opens new opportunities in antimicrobial discovery, microbial engineering, and ecological research.},
}

*Bacteria/genetics/metabolism
*Genomics/methods
Proteomics/methods
Genome-Wide Association Study
Systems Biology/methods
Quantitative Trait Loci
*Genome, Bacterial
Polymorphism, Single Nucleotide
Transcriptome
Multiomics

@article {pmid41094481,
year = {2025},
author = {Karami, H and Bleichrodt, A and Luo, R and Chowell, G},
title = {BayesianFitForecast: a user-friendly R toolbox for parameter estimation and forecasting with ordinary differential equations.},
journal = {BMC medical informatics and decision making},
volume = {25},
number = {1},
pages = {385},
pmid = {41094481},
issn = {1472-6947},
mesh = {Bayes Theorem ; Humans ; Forecasting/methods ; *Software ; *Models, Theoretical ; },
abstract = {BACKGROUND: Mathematical models based on ordinary differential equations (ODEs) are essential tools across various scientific disciplines, including biology, ecology, epidemic modeling, and healthcare informatics, where they are used to simulate complex dynamic systems and inform decision-making. However, implementing Bayesian calibration and forecasting typically requires substantial coding in Stan or similar tools. To support Bayesian parameter estimation and forecasting for such systems, we introduce BayesianFitForecast, a user-friendly R toolbox specifically developed to streamline Bayesian parameter estimation and forecasting in ODE models, making it particularly relevant to health informatics and public health decision-making (https://github.com/gchowell/BayesianFitForecast/).

RESULTS: This toolbox enables automatic generation of Stan files, allowing users to configure models, define priors, and analyze results with minimal programming expertise. By eliminating manual coding, BayesianFitForecast significantly lowers the technical barrier to Bayesian inference with dynamical systems. We demonstrate its flexibility and usability through applications to historical epidemic datasets (e.g., the 1918 influenza pandemic in San Francisco and the 1896-1897 Bombay plague) and simulated data, showing robust parameter estimation and forecasting performance under Poisson and negative binomial observation error structures. The toolbox also provides robust tools for evaluating model performance, including convergence diagnostics, posterior distributions, credible intervals, and performance metrics.

CONCLUSION: By improving the accessibility of advanced Bayesian methods, BayesianFitForecast broadens the application of Bayesian inference in time-series modeling, healthcare forecasting, and epidemiological applications. In addition to the R scripting interface, a built-in Shiny web application is included, enabling interactive model configuration, visualization, and forecasting. A tutorial video demonstrating the toolbox's functionality is also available (https://youtu.be/jnxMjz3V3n8).},
}

Bayes Theorem
Humans
Forecasting/methods
*Software
*Models, Theoretical

@article {pmid41093425,
year = {2025},
author = {Guo, JX and Xie, Y and Qi, WX and Liao, YJ and Cao, XF and Peng, JF},
title = {[Pollution Characteristics and Identification of Risk Zones of Polycyclic Aromatic Hydrocarbons and Their Derivatives in Sediments and Soils of Chagan Lake].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {10},
pages = {6593-6602},
doi = {10.13227/j.hjkx.202409321},
pmid = {41093425},
issn = {0250-3301},
abstract = {Sediments and soils are primary reservoirs and potential secondary sources of polycyclic aromatic hydrocarbons （PAHs）. Investigating the pollution characteristics of PAHs and their derivatives in these environments is of significant environmental， health， and ecological relevance. In this study， Chagan Lake， a typical lake in the agricultural region of northeast China， was selected as the research area. Thirteen surface sediment and soil samples were collected in July 2021 to analyze the pollution characteristics， influencing factors， and ecological risks of 19 PAHs and 11 derivatives. The results showed that the contents of 19 PAHs in sediments ranged from 106.7 to 915.0 ng·g[-1]， higher values than those in soils， which ranged from 251.7 to 718.1 ng·g[-1]. The average contents of parent PAHs （PPAHs）， methylated PAHs （MPAHs）， oxygenated PAHs （OPAHs）， and nitro PAHs （NPAHs） in sediments and soils were 327.6， 57.7， 59.7， and 21.1 ng·g[-1]， respectively. The dominant congeners were primarily 3-ring （38%）， 2-ring （91%）， 3-ring （72%） and 2-ring （81%）， PAHs. An examination of derivatives of Nap， Flu， Ant， and BaA revealed that 2-MN and BA-7，12-D were the main derivatives of Nap and BaA， respectively， with contents lower than their parent compounds. In contrast， the contents of derivatives such as 9-FL， 2-NF， AQ， and 2-MAQ were higher than those of their parent compounds Flu and Ant. Quantitative results from the linear mixing model indicated that the sand ratio had a greater influence on the contents of PPAHs and MPAHs than TOC， particularly for 2-3 ring PPAHs， whereas the effect on 4-6 rings was opposite. Ecological risk assessments indicated that the contents of Nap and Phe in sediments and surrounding soils exceeded the threshold for adverse ecological effects， with 28% of the Chagan Lake area classified as a high-risk zone for overlapping Nap and Phe contamination.},
}

@article {pmid41093395,
year = {2025},
author = {Men, C and Cai, HJ and Fu, H and Zuo, JE},
title = {[Occurrence Characteristics， Ecological Risks， and Main Sources of Antibiotics in Rivers in Tongzhou District， Beijing].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {10},
pages = {6264-6273},
doi = {10.13227/j.hjkx.202408216},
pmid = {41093395},
issn = {0250-3301},
mesh = {Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Anti-Bacterial Agents/analysis ; *Environmental Monitoring ; China ; Beijing ; Risk Assessment ; Ecosystem ; Geographic Information Systems ; Wastewater/chemistry ; },
abstract = {China is a major producer and consumer of antibiotics. Because humans and animals have difficulty fully metabolizing antibiotics and the limited degradation efficiency of antibiotics in current wastewater treatment plants， antibiotic pollution is common in rivers in China， threatening the health of river ecosystems. Tongzhou District， Beijing， is the sub-center of Beijing， and all of the rivers flowing through the main urban area of Beijing converge in this district. A total of 16 antibiotics in the rivers of Tongzhou District， Beijing， were used as research objects， an analysis of the antibiotic concentration and spatial distribution characteristics was performed based on the geographic information system （GIS）， the ecological risk of the antibiotics and its uncertainty were evaluated by the coupling risk quotient method and Monte Carlo method， and the main sources of antibiotics were identified using the principal component analysis method. The results showed that the total concentrations of the 16 target antibiotics ranged from 69.52 to 1 913.05 ng·L[-1]. Ofloxacin （OFL） had the highest concentration among all antibiotics， with an average concentration of 279.95 ng·L[-1]， accounting for 50.07% of the total antibiotic concentration. Spatially， the concentrations of most of the antibiotics were relatively high in the Beiyun River and relatively low in the Wenyu River and Yunchaojian River. Compared to the Hai， Yangtze， Yellow， Pearl， Huai， and Liao Rivers， the concentrations of antibiotics in the rivers in Tongzhou District were low. The results of the ecological risk assessment showed that the ecological risk levels of sulfadimethoxine （SDM） and OFL were higher than those of the other antibiotics. The upper limits of the 90% confidence interval of the probability distribution of ecological risk for these antibiotics were 132.04 and 86.58 times the threshold of the high-risk class， respectively， and the probability of SDM leading to high ecological risk was higher than 95%. The results of source identification showed that the main sources of antibiotics were effluents of wastewater treatment plants， aquaculture， and livestock farming. Among these， effluent of wastewater treatment plants was the most dominant source， explaining 41.38% of the antibiotics. This study comprehensively explored the occurrence， ecological risks， and major sources of antibiotics in the rivers in Tongzhou District， Beijing， which is of great significance for targeted antibiotic pollution control and ecosystem health protection.},
}

Rivers/chemistry
*Water Pollutants, Chemical/analysis
*Anti-Bacterial Agents/analysis
*Environmental Monitoring
China
Beijing
Risk Assessment
Ecosystem
Geographic Information Systems
Wastewater/chemistry

@article {pmid41093232,
year = {2025},
author = {Lei, W and Guo, J and Liang, X and Wang, H and Qi, W and Mao, Z and He, S},
title = {Occurrence characteristics and environmental fate of neonicotinoid insecticides in mountain agricultural soils and river waters.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {386},
number = {},
pages = {127269},
doi = {10.1016/j.envpol.2025.127269},
pmid = {41093232},
issn = {1873-6424},
abstract = {Neonicotinoid insecticides (NNIs) have been widely detected in terrestrial ecosystems and may pose potential threats to ecosystem functions. Yet comprehensive evaluation of their occurrence characteristics, influencing factors, and soil-water connections remains limited. This study investigated NNIs occurrence patterns, transport dynamics, and ecological risks in soils and river waters of mountainous agricultural areas. The results revealed that NNIs were detected in soils and waters with a 100 % detection rate. Imidacloprid (IMI) was the predominant compound in soils (84.8 %), whereas river waters exhibited multi-component coexistence, with IMI, thiamethoxam (THIA), dinotefuran (DIN), and clothianidin (CLO) accounting for 30.9 %, 14.3 %, 12.9 %, and 11.8 % of NNIs, respectively. The mean concentration of eight NNIs (∑8NNIs) in stem mustard fields (11.45 ng/g) was higher than in forest soils (0.17 ng/g). The ∑8NNIs in water bodies near towns (102.65 ng/L) was 3.4 times higher than that in forest background areas. Additionally, A significant negative correlation between soil and water NNIs concentrations suggests that soil NNIs influence water NNIs levels. SEM and SHAP analyses identified soil NNIs concentration, bulk density, and elevation as primary factors regulating NNIs in adjacent waters. Ecological risk assessment outcomes indicate that the overall ecological risk in the study area was low. There were 13 % of soil sites with an α (risk entropy) exceeding 1, and 28 % of water sites with a risk coefficient surpassing the chronic HC5. These results provide theoretical support for understanding the occurrence characteristics and transfer trends of NNIs in soils and waters of agricultural areas.},
}

@article {pmid41092928,
year = {2025},
author = {, },
title = {Global burden of 292 causes of death in 204 countries and territories and 660 subnational locations, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(25)01917-8},
pmid = {41092928},
issn = {1474-547X},
abstract = {BACKGROUND: Timely and comprehensive analyses of causes of death stratified by age, sex, and location are essential for shaping effective health policies aimed at reducing global mortality. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2023 provides cause-specific mortality estimates measured in counts, rates, and years of life lost (YLLs). GBD 2023 aimed to enhance our understanding of the relationship between age and cause of death by quantifying the probability of dying before age 70 years (70q0) and the mean age at death by cause and sex. This study enables comparisons of the impact of causes of death over time, offering a deeper understanding of how these causes affect global populations.

METHODS: GBD 2023 produced estimates for 292 causes of death disaggregated by age-sex-location-year in 204 countries and territories and 660 subnational locations for each year from 1990 until 2023. We used a modelling tool developed for GBD, the Cause of Death Ensemble model (CODEm), to estimate cause-specific death rates for most causes. We computed YLLs as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. Probability of death was calculated as the chance of dying from a given cause in a specific age period, for a specific population. Mean age at death was calculated by first assigning the midpoint age of each age group for every death, followed by computing the mean of all midpoint ages across all deaths attributed to a given cause. We used GBD death estimates to calculate the observed mean age at death and to model the expected mean age across causes, sexes, years, and locations. The expected mean age reflects the expected mean age at death for individuals within a population, based on global mortality rates and the population's age structure. Comparatively, the observed mean age represents the actual mean age at death, influenced by all factors unique to a location-specific population, including its age structure. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2·5th and 97·5th percentiles from a 250-draw distribution for each metric. Findings are reported as counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2023 include a correction for the misclassification of deaths due to COVID-19, updates to the method used to estimate COVID-19, and updates to the CODEm modelling framework. This analysis used 55 761 data sources, including vital registration and verbal autopsy data as well as data from surveys, censuses, surveillance systems, and cancer registries, among others. For GBD 2023, there were 312 new country-years of vital registration cause-of-death data, 3 country-years of surveillance data, 51 country-years of verbal autopsy data, and 144 country-years of other data types that were added to those used in previous GBD rounds.

FINDINGS: The initial years of the COVID-19 pandemic caused shifts in long-standing rankings of the leading causes of global deaths: it ranked as the number one age-standardised cause of death at Level 3 of the GBD cause classification hierarchy in 2021. By 2023, COVID-19 dropped to the 20th place among the leading global causes, returning the rankings of the leading two causes to those typical across the time series (ie, ischaemic heart disease and stroke). While ischaemic heart disease and stroke persist as leading causes of death, there has been progress in reducing their age-standardised mortality rates globally. Four other leading causes have also shown large declines in global age-standardised mortality rates across the study period: diarrhoeal diseases, tuberculosis, stomach cancer, and measles. Other causes of death showed disparate patterns between sexes, notably for deaths from conflict and terrorism in some locations. A large reduction in age-standardised rates of YLLs occurred for neonatal disorders. Despite this, neonatal disorders remained the leading cause of global YLLs over the period studied, except in 2021, when COVID-19 was temporarily the leading cause. Compared to 1990, there has been a considerable reduction in total YLLs in many vaccine-preventable diseases, most notably diphtheria, pertussis, tetanus, and measles. In addition, this study quantified the mean age at death for all-cause mortality and cause-specific mortality and found noticeable variation by sex and location. The global all-cause mean age at death increased from 46·8 years (95% UI 46·6-47·0) in 1990 to 63·4 years (63·1-63·7) in 2023. For males, mean age increased from 45·4 years (45·1-45·7) to 61·2 years (60·7-61·6), and for females it increased from 48·5 years (48·1-48·8) to 65·9 years (65·5-66·3), from 1990 to 2023. The highest all-cause mean age at death in 2023 was found in the high-income super-region, where the mean age for females reached 80·9 years (80·9-81·0) and for males 74·8 years (74·8-74·9). By comparison, the lowest all-cause mean age at death occurred in sub-Saharan Africa, where it was 38·0 years (37·5-38·4) for females and 35·6 years (35·2-35·9) for males in 2023. Lastly, our study found that all-cause 70q0 decreased across each GBD super-region and region from 2000 to 2023, although with large variability between them. For females, we found that 70q0 notably increased from drug use disorders and conflict and terrorism. Leading causes that increased 70q0 for males also included drug use disorders, as well as diabetes. In sub-Saharan Africa, there was an increase in 70q0 for many non-communicable diseases (NCDs). Additionally, the mean age at death from NCDs was lower than the expected mean age at death for this super-region. By comparison, there was an increase in 70q0 for drug use disorders in the high-income super-region, which also had an observed mean age at death lower than the expected value.

INTERPRETATION: We examined global mortality patterns over the past three decades, highlighting-with enhanced estimation methods-the impacts of major events such as the COVID-19 pandemic, in addition to broader trends such as increasing NCDs in low-income regions that reflect ongoing shifts in the global epidemiological transition. This study also delves into premature mortality patterns, exploring the interplay between age and causes of death and deepening our understanding of where targeted resources could be applied to further reduce preventable sources of mortality. We provide essential insights into global and regional health disparities, identifying locations in need of targeted interventions to address both communicable and non-communicable diseases. There is an ever-present need for strengthened health-care systems that are resilient to future pandemics and the shifting burden of disease, particularly among ageing populations in regions with high mortality rates. Robust estimates of causes of death are increasingly essential to inform health priorities and guide efforts toward achieving global health equity. The need for global collaboration to reduce preventable mortality is more important than ever, as shifting burdens of disease are affecting all nations, albeit at different paces and scales.

FUNDING: Gates Foundation.},
}

@article {pmid41092926,
year = {2025},
author = {, },
title = {Burden of 375 diseases and injuries, risk-attributable burden of 88 risk factors, and healthy life expectancy in 204 countries and territories, including 660 subnational locations, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(25)01637-X},
pmid = {41092926},
issn = {1474-547X},
abstract = {BACKGROUND: For more than three decades, the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) has provided a framework to quantify health loss due to diseases, injuries, and associated risk factors. This paper presents GBD 2023 findings on disease and injury burden and risk-attributable health loss, offering a global audit of the state of world health to inform public health priorities. This work captures the evolving landscape of health metrics across age groups, sexes, and locations, while reflecting on the remaining post-COVID-19 challenges to achieving our collective global health ambitions.

METHODS: The GBD 2023 combined analysis estimated years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 375 diseases and injuries, and risk-attributable burden associated with 88 modifiable risk factors. Of the more than 310 000 total data sources used for all GBD 2023 (about 30% of which were new to this estimation round), more than 120 000 sources were used for estimation of disease and injury burden and 59 000 for risk factor estimation, and included vital registration systems, surveys, disease registries, and published scientific literature. Data were analysed using previously established modelling approaches, such as disease modelling meta-regression version 2.1 (DisMod-MR 2.1) and comparative risk assessment methods. Diseases and injuries were categorised into four levels on the basis of the established GBD cause hierarchy, as were risk factors using the GBD risk hierarchy. Estimates stratified by age, sex, location, and year from 1990 to 2023 were focused on disease-specific time trends over the 2010-23 period and presented as counts (to three significant figures) and age-standardised rates per 100 000 person-years (to one decimal place). For each measure, 95% uncertainty intervals [UIs] were calculated with the 2·5th and 97·5th percentile ordered values from a 250-draw distribution.

FINDINGS: Total numbers of global DALYs grew 6·1% (95% UI 4·0-8·1), from 2·64 billion (2·46-2·86) in 2010 to 2·80 billion (2·57-3·08) in 2023, but age-standardised DALY rates, which account for population growth and ageing, decreased by 12·6% (11·0-14·1), revealing large long-term health improvements. Non-communicable diseases (NCDs) contributed 1·45 billion (1·31-1·61) global DALYs in 2010, increasing to 1·80 billion (1·63-2·03) in 2023, alongside a concurrent 4·1% (1·9-6·3) reduction in age-standardised rates. Based on DALY counts, the leading level 3 NCDs in 2023 were ischaemic heart disease (193 million [176-209] DALYs), stroke (157 million [141-172]), and diabetes (90·2 million [75·2-107]), with the largest increases in age-standardised rates since 2010 occurring for anxiety disorders (62·8% [34·0-107·5]), depressive disorders (26·3% [11·6-42·9]), and diabetes (14·9% [7·5-25·6]). Remarkable health gains were made for communicable, maternal, neonatal, and nutritional (CMNN) diseases, with DALYs falling from 874 million (837-917) in 2010 to 681 million (642-736) in 2023, and a 25·8% (22·6-28·7) reduction in age-standardised DALY rates. During the COVID-19 pandemic, DALYs due to CMNN diseases rose but returned to pre-pandemic levels by 2023. From 2010 to 2023, decreases in age-standardised rates for CMNN diseases were led by rate decreases of 49·1% (32·7-61·0) for diarrhoeal diseases, 42·9% (38·0-48·0) for HIV/AIDS, and 42·2% (23·6-56·6) for tuberculosis. Neonatal disorders and lower respiratory infections remained the leading level 3 CMNN causes globally in 2023, although both showed notable rate decreases from 2010, declining by 16·5% (10·6-22·0) and 24·8% (7·4-36·7), respectively. Injury-related age-standardised DALY rates decreased by 15·6% (10·7-19·8) over the same period. Differences in burden due to NCDs, CMNN diseases, and injuries persisted across age, sex, time, and location. Based on our risk analysis, nearly 50% (1·27 billion [1·18-1·38]) of the roughly 2·80 billion total global DALYs in 2023 were attributable to the 88 risk factors analysed in GBD. Globally, the five level 3 risk factors contributing the highest proportion of risk-attributable DALYs were high systolic blood pressure (SBP), particulate matter pollution, high fasting plasma glucose (FPG), smoking, and low birthweight and short gestation-with high SBP accounting for 8·4% (6·9-10·0) of total DALYs. Of the three overarching level 1 GBD risk factor categories-behavioural, metabolic, and environmental and occupational-risk-attributable DALYs rose between 2010 and 2023 only for metabolic risks, increasing by 30·7% (24·8-37·3); however, age-standardised DALY rates attributable to metabolic risks decreased by 6·7% (2·0-11·0) over the same period. For all but three of the 25 leading level 3 risk factors, age-standardised rates dropped between 2010 and 2023-eg, declining by 54·4% (38·7-65·3) for unsafe sanitation, 50·5% (33·3-63·1) for unsafe water source, and 45·2% (25·6-72·0) for no access to handwashing facility, and by 44·9% (37·3-53·5) for child growth failure. The three leading level 3 risk factors for which age-standardised attributable DALY rates rose were high BMI (10·5% [0·1 to 20·9]), drug use (8·4% [2·6 to 15·3]), and high FPG (6·2% [-2·7 to 15·6]; non-significant).

INTERPRETATION: Our findings underscore the complex and dynamic nature of global health challenges. Since 2010, there have been large decreases in burden due to CMNN diseases and many environmental and behavioural risk factors, juxtaposed with sizeable increases in DALYs attributable to metabolic risk factors and NCDs in growing and ageing populations. This long-observed consequence of the global epidemiological transition was only temporarily interrupted by the COVID-19 pandemic. The substantially decreasing CMNN disease burden, despite the 2008 global financial crisis and pandemic-related disruptions, is one of the greatest collective public health successes known. However, these achievements are at risk of being reversed due to major cuts to development assistance for health globally, the effects of which will hit low-income countries with high burden the hardest. Without sustained investment in evidence-based interventions and policies, progress could stall or reverse, leading to widespread human costs and geopolitical instability. Moreover, the rising NCD burden necessitates intensified efforts to mitigate exposure to leading risk factors-eg, air pollution, smoking, and metabolic risks, such as high SBP, BMI, and FPG-including policies that promote food security, healthier diets, physical activity, and equitable and expanded access to potential treatments, such as GLP-1 receptor agonists. Decisive, coordinated action is needed to address long-standing yet growing health challenges, including depressive and anxiety disorders. Yet this can be only part of the solution. Our response to the NCD syndemic-the complex interaction of multiple health risks, social determinants, and systemic challenges-will define the future landscape of global health. To ensure human wellbeing, economic stability, and social equity, global action to sustain and advance health gains must prioritise reducing disparities by addressing socioeconomic and demographic determinants, ensuring equitable health-care access, tackling malnutrition, strengthening health systems, and improving vaccination coverage. We live in times of great opportunity.

FUNDING: Gates Foundation and Bloomberg Philanthropies.},
}

@article {pmid41087423,
year = {2025},
author = {Li, Z and Liu, J and Li, J and Zhou, Z and Huang, X and Gopinath, D and Luo, P and Wang, Q and Shan, D},
title = {Fusobacterium in the microbiome: from health to disease across the oral-gut axis and beyond.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {200},
pmid = {41087423},
issn = {2055-5008},
mesh = {Humans ; *Fusobacterium/physiology/pathogenicity/genetics ; *Mouth/microbiology ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; Animals ; Neoplasms/microbiology ; *Fusobacterium Infections/microbiology ; },
abstract = {Fusobacterium functions as both commensal and pathogen, linking the oral-gut axis to diverse diseases, including cancer. Evidence shows it modulates microbial balance, promotes dysbiosis, and contributes to carcinogenesis by driving inflammation, proliferation, invasion, and immune evasion. This review integrates ecological, molecular, and clinical insights, highlighting its roles in oral and systemic disease and discussing therapeutic potential, underscoring Fusobacterium's dualistic nature and implications for microbiome-targeted interventions.},
}

Humans
*Fusobacterium/physiology/pathogenicity/genetics
*Mouth/microbiology
Dysbiosis/microbiology
*Gastrointestinal Microbiome
*Microbiota
Animals
Neoplasms/microbiology
*Fusobacterium Infections/microbiology

@article {pmid40965023,
year = {2025},
author = {Li, S and Chen, P and Zhang, J and Wang, B},
title = {MBLEformer: Multi-Scale Bidirectional Lesion Enhancement Transformer for Cervical Cancer Image Segmentation.},
journal = {Current medical imaging},
volume = {21},
number = {},
pages = {e15734056357180},
doi = {10.2174/0115734056357180250516022218},
pmid = {40965023},
issn = {1573-4056},
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/diagnostic imaging ; Neural Networks, Computer ; *Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Colposcopy ; Iodides ; *Image Processing, Computer-Assisted/methods ; },
abstract = {BACKGROUND: Accurate segmentation of lesion areas from Lugol's Iodine Staining images is crucial for screening pre-cancerous cervical lesions. However, in underdeveloped regions lacking skilled clinicians, this method may lead to misdiagnosis and missed diagnoses. In recent years, deep learning methods have been widely applied to assist in medical image segmentation.

OBJECTIVE: This study aims to improve the accuracy of cervical cancer lesion segmentation by addressing the limitations of Convolutional Neural Networks (CNNs) and attention mechanisms in capturing global features and refining upsampling details.

METHODS: This paper presents a Multi-Scale Bidirectional Lesion Enhancement Network, named MBLEformer, which employs the Swin Transformer encoder to extract image features at multiple stages and utilizes a multi-scale attention mechanism to capture semantic features from different perspectives. Additionally, a bidirectional lesion enhancement upsampling strategy is introduced to refine the edge details of lesion areas.

RESULTS: Experimental results demonstrate that the proposed model exhibits superior segmentation performance on a proprietary cervical cancer colposcopic dataset, outperforming other medical image segmentation methods, with a mean Intersection over Union (mIoU) of 82.5%, accuracy, and specificity of 94.9% and 83.6%.

CONCLUSION: MBLEformer significantly improves the accuracy of lesion segmentation in iodine-stained cervical cancer images, with the potential to enhance the efficiency and accuracy of pre-cancerous lesion diagnosis and help address the issue of imbalanced medical resources.},
}

Humans
Female
*Uterine Cervical Neoplasms/diagnostic imaging
Neural Networks, Computer
*Image Interpretation, Computer-Assisted/methods
Deep Learning
Colposcopy
Iodides
*Image Processing, Computer-Assisted/methods

@article {pmid40915583,
year = {2026},
author = {Zhang, Y and Wang, B and Hassan, M and Zhang, X},
title = {Biochar-calcium alginate composite immobilizing Pseudomonas sp. H6 for phosphate and ammonium recovery: Multi-omics insights and practical application evaluation.},
journal = {Bioresource technology},
volume = {439},
number = {},
pages = {133274},
doi = {10.1016/j.biortech.2025.133274},
pmid = {40915583},
issn = {1873-2976},
mesh = {*Alginates/chemistry ; *Charcoal/chemistry ; *Ammonium Compounds/isolation & purification ; *Phosphates/isolation & purification ; *Pseudomonas/metabolism ; Wastewater/chemistry ; Glucuronic Acid/chemistry ; Hexuronic Acids/chemistry ; Cells, Immobilized/metabolism ; Adsorption ; Water Purification/methods ; Biodegradation, Environmental ; Water Pollutants, Chemical/isolation & purification ; Multiomics ; },
abstract = {Water eutrophication has emerged as a pervasive ecological challenge worldwide. To realize the resource utilization of waste and nutrients, a novel rape straw-derived biochar-calcium alginate composite (M-CA-RBC) immobilized Pseudomonas sp. H6 was synthesized to simultaneously remove phosphate (PO4[3-]) and ammonium (NH4[+]) from distillery wastewater. The removal performance of PO4[3-] and NH4[+] by M-CA-RBC were investigated. The removal mechanisms were explored by using different adsorption models combined with microbial degradation kinetics, analysis of dissolved organic matter components, electrochemical analysis, metagenomics, and metabolomics. The resource application potential of M-CA-RBC was evaluated. The results showed that M-CA-RBC had good removal performance for PO4[3-] (17.81 mg/g) and NH4[+] (25.78 mg/g). Surface precipitation, electrostatic attraction, Poly-P accumulation, microbial-induced calcium precipitation, and microbial assimilation were the main removal mechanisms of PO4[3-] by M-CA-RBC. The removal mechanisms of NH4[+] were micropore filling, ion exchange, electrostatic attraction, and heterotrophic nitrification-aerobic denitrification (HN-AD). M-CA-RBC had a good application potential in the practical distillery wastewater, with removal rates of PO4[3-] and NH4[+] reaching 88% and 65%, respectively. After adsorption saturation, M-CA-RBC exhibited good stability, which could be used as a slow-release fertilizer to promote the growth of mung beans. This study provides practical significance for the efficient removal and recovery of nitrogen and phosphorus in wastewater.},
}

*Alginates/chemistry
*Charcoal/chemistry
*Ammonium Compounds/isolation & purification
*Phosphates/isolation & purification
*Pseudomonas/metabolism
Wastewater/chemistry
Glucuronic Acid/chemistry
Hexuronic Acids/chemistry
Cells, Immobilized/metabolism
Adsorption
Water Purification/methods
Biodegradation, Environmental
Water Pollutants, Chemical/isolation & purification
Multiomics

@article {pmid40326463,
year = {2025},
author = {Vogelsmeier, LVDE and Jongerling, J and Ulitzsch, E},
title = {Accounting for Measurement Invariance Violations in Careless Responding Detection in Intensive Longitudinal Data: Exploratory vs. Partially Constrained Latent Markov Factor Analysis.},
journal = {Multivariate behavioral research},
volume = {60},
number = {5},
pages = {878-897},
doi = {10.1080/00273171.2025.2492016},
pmid = {40326463},
issn = {1532-7906},
mesh = {Humans ; Longitudinal Studies ; Factor Analysis, Statistical ; *Markov Chains ; *Models, Statistical ; Computer Simulation ; Data Interpretation, Statistical ; },
abstract = {Intensive longitudinal data (ILD) collection methods like experience sampling methodology can place significant burdens on participants, potentially resulting in careless responding, such as random responding. Such behavior can undermine the validity of any inferences drawn from the data if not properly identified and addressed. Recently, a confirmatory mixture model (here referred to as fully constrained latent Markov factor analysis, LMFA) has been introduced as a promising solution to detect careless responding in ILD. However, this method relies on the key assumption of measurement invariance of the attentive responses, which is easily violated due to shifts in how participants interpret items. If the assumption is violated, the ability of the fully constrained LMFA to accurately identify careless responding is compromised. In this study, we evaluated two more flexible variants of LMFA-fully exploratory LMFA and partially constrained LMFA-to distinguish between careless and attentive responding in the presence of non-invariant attentive responses. Simulation results indicated that the fully exploratory LMFA model is an effective tool for reliably detecting and interpreting different types of careless responding while accounting for violations of measurement invariance. Conversely, the partially constrained model struggled to accurately detect careless responses. We end by discussing potential reasons for this.},
}

Humans
Longitudinal Studies
Factor Analysis, Statistical
*Markov Chains
*Models, Statistical
Computer Simulation
Data Interpretation, Statistical

@article {pmid41087306,
year = {2025},
author = {Tang, Y and Qiu, S and Li, B and Sui, D and Jiang, K and Zheng, J and Zou, J and Lian, J and Wang, L and Yuan, Y},
title = {Integrative Physiological and Multi-Omics Insights: Salt Stress Adaptation and Functional Specialization in Suaeda salsa L.},
journal = {Physiologia plantarum},
volume = {177},
number = {5},
pages = {e70581},
doi = {10.1111/ppl.70581},
pmid = {41087306},
issn = {1399-3054},
support = {LYKJ[2023]01//Research on Breeding of Native Tree Species for Carbon Sequestration Afforestation in Jiangsu Coast/ ; Su[2024]TG14//Central Finance Forestry Science and Technology Extension Project/ ; JAF-2025-01//Youth Fund of Jiangsu Academy of Forestry Sciences/ ; LYKJ[2021]08//Long-Term Scientific Research Base for Cultivation of Salt-Tolerant Native Tree Species in Jiangsu/ ; },
mesh = {*Chenopodiaceae/physiology/genetics/metabolism ; Plant Leaves/physiology/metabolism/genetics ; Plant Roots/physiology/metabolism/genetics ; *Salt Stress/physiology ; Gene Expression Regulation, Plant ; Salt Tolerance/physiology ; Salt-Tolerant Plants/physiology/genetics ; Transcriptome ; Adaptation, Physiological ; Gene Expression Profiling ; Metabolomics ; Multiomics ; },
abstract = {Soil salinization, a major abiotic stress, severely limits plant growth and reduces crop yields. Understanding the salt tolerance mechanisms of halophytes is essential for the effective utilization of saline soils and improving crop resilience. Suaeda salsa L., a saline-alkali pioneer species with significant ecological and economic value, was investigated using physiological, metabolomic, and transcriptomic approaches under low, medium, and high soil electrical conductivities to elucidate its salt adaptation mechanisms. Physiological assays demonstrated that the responses were predominantly leaf-centered, with measurements of antioxidant enzymes, oxidative stress indicators, and osmolytes indicating that leaves play a key role in salt stress responses. Transcriptomic analysis revealed that the metabolic pathways were the most enriched across all conductivity comparisons. Metabolomic profiling showed that differential metabolites in the roots and leaves were enriched in starch and sucrose metabolism, whereas phenylpropanoid biosynthesis exhibited contrasting enrichment patterns in the roots and leaves under low- and high conductivity conditions. Based on these pathways, tissue-specific regulatory networks were constructed, revealing coordinated carbon allocation and the establishment of an efficient salt-tolerance network. Most genes exhibited divergent expression patterns between roots and leaves as conductivity increased, reflecting functional specialization. This study proposed that S. salsa uses a metabolic regulatory network characterized by gradient responses, functional differentiation, and energy optimization, providing a theoretical foundation for enhancing halophyte adaptation and improving crop salt tolerance.},
}

*Chenopodiaceae/physiology/genetics/metabolism
Plant Leaves/physiology/metabolism/genetics
Plant Roots/physiology/metabolism/genetics
*Salt Stress/physiology
Gene Expression Regulation, Plant
Salt Tolerance/physiology
Salt-Tolerant Plants/physiology/genetics
Transcriptome
Adaptation, Physiological
Gene Expression Profiling
Metabolomics
Multiomics

@article {pmid41085718,
year = {2025},
author = {Karaarslan, F and Güneri, FD and Özen, H and Odabaşı, E},
title = {The evaluation of medical mud pack treatment from the patient's perspective in different musculoskeletal disorders- A prospective study.},
journal = {International journal of biometeorology},
volume = {},
number = {},
pages = {},
pmid = {41085718},
issn = {1432-1254},
abstract = {This study evaluated patient satisfaction and expectation levels in individuals with chronic low back pain (LBP), myofascial pain syndrome (MPS), and knee osteoarthritis (KOA) who received mud pack therapy (MPT). It also investigated the relationship between these conditions and pain levels, global assessment results, and side effects. We assessed 250 patients (n = 74 for LBP, n = 75 for MPS, n = 101 for KOA) who underwent twelve sessions of MPT at 43 °C, lasting 30 min each. Patients continued their routine care and completed surveys on satisfaction and expectations, as well as measures of pain (VAS-pain), global assessment (VAS-PGA), and acceptable symptom state (PASS). Satisfaction levels were reported as "satisfied" or "definitely satisfied" by 93.1% to 96% of patients. Expectations were met by 86.7% to 89.2% of patients. Both VAS-pain and VAS-PGA showed statistically significant improvements after treatment (p < 0.001), though there were no differences between groups (p = 0.794 for VAS-pain, p = 0.234 for VAS-PGA). The PASS evaluation showed no significant group differences (p = 0.274). No serious side effects were reported, except for mild, short-term increases in pain. MPT is an effective treatment providing significant pain relief for LBP, MPS, and KOA patients, with high satisfaction and expectation fulfillment among participants.},
}

@article {pmid41082884,
year = {2025},
author = {, },
title = {The burden of bacterial antimicrobial resistance in the WHO Eastern Mediterranean Region 1990-2021: a cross-country systematic analysis with forecasts to 2050.},
journal = {The Lancet. Public health},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2468-2667(25)00201-4},
pmid = {41082884},
issn = {2468-2667},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is an urgent global crisis and one of the world's most complex challenges. Although there is increasing evidence of its impact on human mortality and morbidity, precise burden estimation has many challenges, and thus far has been elusive for the Eastern Mediterranean Region. Here, we present a comprehensive time-trend analysis of regional and country-level AMR burden estimates in the WHO Eastern Mediterranean Region (EMR), between 1990 and 2021, with forecasts up to 2050.

METHODS: We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 11 infectious syndromes, 22 bacterial pathogens, and 84 pathogen-drug combinations for the WHO EMR and each of its countries from 1990 to 2021. Data were obtained from mortality registries, surveillance systems, hospital records, systematic literature reviews, and other sources. We based our modelling approach on five broad components: the number of deaths in which infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antimicrobial drug of interest, and the excess risk of mortality (or duration of an infection) associated with this resistance. These components were then used to estimate the disease burden by using two counterfactual scenarios: deaths and DALYs attributable to AMR (considering an alternative scenario where drug-resistant infections are replaced with susceptible infections), and deaths and DALYs associated with AMR (considering an alternative scenario where infections would not occur at all). Predictive statistical modelling was applied to generate estimates of AMR burden for each country. We also generated AMR burden forecasts up to 2050. We generated 95% uncertainty intervals (UIs) for the final estimates by taking the 2·5th and 97·5th percentiles across 500 draws through the multistage computational pipeline, and models were cross-validated for out-of-sample predictive validity.

FINDINGS: We estimated 380 000 deaths (95% UI 332 000-426 000) associated with bacterial AMR and 92 800 deaths (78 300-111 000) attributable to bacterial AMR in the EMR in 2021. In the past 31 years, there was considerable variation in AMR mortality trends across countries of the region and different age groups. Between 1990 and 2021, associated deaths among children younger than 5 years decreased by 50·0% (38·2-62·0), while those among adults aged 70 and older rose by over 85·7% (95% UI 57·0-115·7). Six pathogens were identified as the primary generators of burden: Streptococcus pneumoniae, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa. A substantial increase in the AMR burden due to S aureus was observed between 1990 (28 200 deaths [21 600-34 000]) and 2021 (49 500 deaths [43 100-56 200]); consequently, in 2021, methicillin-resistant S aureus was a leading pathogen-drug combination for most countries in the region for deaths and DALYs attributable to, and associated with AMR. Somalia had the highest age-standardised mortality rates in the region: for deaths attributable to and associated with AMR per 100 000 population in both 1990 and 2021; conversely, the country with the lowest burden in the EMR was Qatar. By 2050, the number of deaths attributable to AMR in region is forecasted to reach 187 000 (157 000-223 000) and deaths associated with AMR were projected to reach 752 000 (629 000-879 000).

INTERPRETATION: Our study shows that bacterial AMR has been a serious public health threat in the EMR for more than 30 years, with a substantial fatal and non-fatal burden for priority bacterial pathogens and pathogen-drug combinations. The magnitude of this issue, future projects, and the inadequate response capacity in many countries underscore the need for more stringent regional leadership in this field. The insights gained from this study can direct targeted mitigation strategies for individual countries within the region, aiding in resource allocation and funding decisions, and emphasising the need for collaborative multisectoral endeavours among nations to address this issue.

FUNDING: Wellcome Trust, and the UK Department of Health and Social Care using aid funding managed by the Fleming Fund.},
}

@article {pmid41081996,
year = {2025},
author = {Yetişgin, SO and Bagci, HR and Coban, HO and Goktepe, S},
title = {From grazing to green: unraveling the ecological consequences of transhumance decline in Turkey's Mediterranean mountains.},
journal = {Tropical animal health and production},
volume = {57},
number = {8},
pages = {435},
pmid = {41081996},
issn = {1573-7438},
mesh = {Animals ; Turkey ; *Goats/physiology ; Geographic Information Systems ; *Animal Husbandry/methods ; *Ecosystem ; *Conservation of Natural Resources ; *Animal Migration ; },
abstract = {Transhumance, a millennia-old pastoral practice, has been instrumental in shaping the cultural, ecological and socio-economic fabric of Turkey's Mediterranean mountains while providing a range of ecosystem services. However, profound socio-economic shifts, policy constraints, and land-use changes have led to its rapid decline, triggering cascading environmental consequences. This study investigates the spatial and temporal associations between transhumance decline and land use/cover changes (LULC) along four transhumance migration routes in Turkey's Mediterranean Mountains over the past three decades. The migration routes of transhumant goat flocks were recorded using GPS collars. Digital Elevation Model data were sourced from the U.S. Geological Survey and analyzed using ArcGIS software to produce comprehensive maps illustrating the geographical and elevational characteristics of the study area. Furthermore, CORINE (Coordination of Information on the Environment) land cover maps derived from satellite imagery were employed to assess existing land cover and temporal shifts within the region. Through Geographic Information Systems (GIS), we conducted an in-depth analysis of land use/cover changes across the years 1990 and 2018, employing the Dynamic Degree Index to quantify the rate and extent of spatial transformations. Using Geographic Information Systems (GIS) and remote sensing, the findings reveal a loss of grasslands (- 9.96%) and shrublands (- 13.19%), while forests (+ 23.81%), agricultural land (+ 13.11%), and urban areas (+ 37.03%) expanded. Although direct causality cannot be confirmed, the spatial overlap between declining grazing areas and vegetation transitions suggests a strong association. Informal conversations with herders supported the observation that reduced grazing pressure contributed to shrub encroachment and forest expansion. These findings underscore the necessity of holistic rangeland governance strategies that reconcile conservation imperatives with the cultural and economic sustainability of pastoral communities. Ensuring the resilience of these landscapes requires a nuanced approach that acknowledges transhumance as a dynamic socio-ecological system rather than a relic of the past.},
}

Animals
Turkey
*Goats/physiology
Geographic Information Systems
*Animal Husbandry/methods
*Ecosystem
*Conservation of Natural Resources
*Animal Migration

@article {pmid41079487,
year = {2025},
author = {Owens, JBB and Wüster, W and Mulley, J and Graham, S and Morgan, R and Barlow, A and , and , and , and , and , },
title = {The genome sequence of the common adder, Vipera berus (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {11},
doi = {10.12688/wellcomeopenres.23470.2},
pmid = {41079487},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Vipera berus (common adder; Chordata; Lepidosauria; Squamata; Viperidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,695.0 megabases and 1,476.7 megabases, respectively. Most of haplotype 1 (98.45%) is scaffolded into 19 chromosomal pseudomolecules, while haplotype 2 is assembled to scaffold level. Haplotype 1 achieves the Earth Biogenome Project reference standard of 6.C.Q52. The mitochondrial genome has also been assembled and is 17.35 kilobases in length.},
}

@article {pmid41074313,
year = {2025},
author = {Lv, J and Wang, Y and Zhou, L and Zhang, S and Song, W and Dong, R and Liu, T and Wang, G and Shi, L},
title = {Multi-omics investigation unveils the role of Eurotium cristatum fermentation in potentiating thinned young apple pomace for colitis-induced liver disorders amelioration.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117095},
doi = {10.1016/j.foodres.2025.117095},
pmid = {41074313},
issn = {1873-7145},
mesh = {*Malus/microbiology ; *Fermentation ; Animals ; *Liver Diseases/etiology/prevention & control ; Gastrointestinal Microbiome ; Oxidative Stress ; *Fermented Foods ; Humans ; Male ; Mice ; Liver/metabolism ; *Colitis/complications ; Multiomics ; },
abstract = {Liver disorders are the most prevalent extraintestinal manifestations observed in patients with ulcerative colitis, impacting millions of individuals worldwide. The present study elucidated the novel role of Eurotium cristatum (E. cristatum) -fermented thinned young apples (E.YAP) in preventing colitis associated liver disorders and dissected potential mechanisms through multi-omics integration. Specifically, E.YAP exhibited superior efficacy in alleviating colitis symptoms, liver damage, lipid accumulation, inflammation cytokines and oxidative stress, compared to the unfermented sample and the anti-colitis drug mesalazine. Hepatic transcriptomics demonstrated that E.YAP suppressed genes belonging to the cytochrome P450 family, CXC chemokine ligands and pro-inflammatory cytokines while enhancing PPAR signaling and oxidative phosphorylation. E.YAP exclusively elevated hepatic levels of metabolites involved in glycerophospholipid metabolism, linoleic acid metabolism, biosynthesis of unsaturated fatty acids and glutathione metabolism, whereas suppressing urobilin, a microbial metabolite implicated in fatty liver disease. Moreover, E.YAP increased α-diversity and relative abundances of Lactobacillus, Akkermansia, Muribaculum, Blautia and Faecalibaculum, concurrently increasing short-chain fatty acids. Multi-omics integration revealed robust links between E.YAP- affected hepatic genes, metabolites and gut bacteria that were associated with liver health. Furthermore, E.YAP outperformed unfermented samples in mitigating palmitic acid-induced inflammation, dyslipidemia and ROS overproduction in HepG2 cells. Additionally, network pharmacology identified key metabolites enriched by E. cristatum fermentation, particularly flavonoids, polyphenols and indole derivatives, which may synergistically inhibit hepatic inflammation and oxidative stress. Collectively, our study establishes the novel function of E.YAP in preventing colitis associated liver disorders, providing a sustainable strategy to valorize apple thinning waste into functional foods.},
}

*Malus/microbiology
*Fermentation
Animals
*Liver Diseases/etiology/prevention & control
Gastrointestinal Microbiome
Oxidative Stress
*Fermented Foods
Humans
Male
Mice
Liver/metabolism
*Colitis/complications
Multiomics

@article {pmid40990718,
year = {2025},
author = {Sabino, AU and Guerreiro, DM and Kim, AR and Ramos, AF and Reinitz, J},
title = {Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {10},
pages = {},
doi = {10.1093/bioinformatics/btaf534},
pmid = {40990718},
issn = {1367-4811},
support = {R01 OD010936/OD/NIH HHS/United States ; R01 OD010936/NH/NIH HHS/United States ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES)/ ; //Programa Unificado de Bolsas-USP/ ; },
mesh = {Thermodynamics ; Animals ; Transcription Factors/metabolism ; *Transcription, Genetic ; Drosophila/genetics ; *Gene Expression Regulation ; Enhancer Elements, Genetic ; Drosophila Proteins/genetics/metabolism ; Binding Sites ; *Models, Genetic ; *DNA/chemistry/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Base Sequence ; },
abstract = {MOTIVATION: Understanding how the genome encodes the regulatory logic of transcription is a main challenge of the post-genomic era, and can be overcome with the aid of customized computational tools.

RESULTS: We report an automated framework for analyzing an ensemble of fits to data of a thermodynamics-based sequence-level model for transcriptional regulation. The fits are clustered accordingly with their intrinsic regulatory logic. A multiscale analysis enables visualization of quantitative features resulting from the deconvolution of the regulatory profile provided by multiple transcription factors interacting with the locus of a gene. Quantitative experimental data on reporters driven by the whole locus of the even-skipped gene in the blastoderm of Drosophila embryos was used for validating our approach. A few clusters of highly active DNA binding sites within the enhancers collectively modulate even-skipped gene transcription. Analysis of variable enhancers' length shows the importance of bound protein-protein interactions for transcriptional regulation. The interplay between activation and quenching enables function conservation of enhancers despite length variations.

The transcription factor level data used for performing the reported study is accessible in the input files in Zenodo and GitHub as well the full code. Additional data from formerly FlyEx database will be available under request.},
}

Thermodynamics
Animals
Transcription Factors/metabolism
*Transcription, Genetic
Drosophila/genetics
*Gene Expression Regulation
Enhancer Elements, Genetic
Drosophila Proteins/genetics/metabolism
Binding Sites
*Models, Genetic
*DNA/chemistry/genetics
*Sequence Analysis, DNA/methods
Computational Biology/methods
Base Sequence

@article {pmid41072345,
year = {2025},
author = {Liu, D and Yuan, J and Ren, P and Shi, L and Zhu, Z and Zhang, C and Dong, H and Liu, D},
title = {Electrochemical ammonia recovery from wastewater: The critical roles of electrode engineering toward scale-up.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124708},
doi = {10.1016/j.watres.2025.124708},
pmid = {41072345},
issn = {1879-2448},
abstract = {Ammonia is indispensable for producing fertilizers that sustain the global population, yet its agricultural application contributes significantly to water pollution. Electrochemical technologies offer a renewable-energy-driven and chemical-free pathway for recovering ammonia directly from wastewater, representing a critical step toward a circular nitrogen economy and net-zero emissions in the wastewater sector. Nevertheless, translating lab-scale advances to industrialization remains constrained by technological hurdles. Emerging electrode-engineering strategies promise scalable, membrane-less electrochemical systems, but a systematic and comparative assessment is lacking. In this review, we first present the electrochemical ammonia recovery pathway and elucidate the mechanisms of various electrode materials in this process. Secondly, we critically evaluate state-of-the-art scalable electrode systems for electrochemical ammonia recovery. Thirdly, we comparatively analyze the ammonia recovery performance at both the electrode-material and electrode-system levels, comprehensively discussing the current challenges and future research opportunities toward technological scale-up. Finally, we outline key research targets toward next-generation electrochemical engineering for sustainable ammonia recovery and wastewater treatment.},
}

@article {pmid41070750,
year = {2025},
author = {Seah, BKB},
title = {Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist-Prokaryote Symbioses.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {6},
pages = {e70049},
doi = {10.1111/jeu.70049},
pmid = {41070750},
issn = {1550-7408},
mesh = {*Symbiosis ; *Eukaryota/physiology/classification/genetics ; *Knowledge Bases ; *Archaea/physiology/genetics ; *Databases, Factual ; *Prokaryotic Cells/physiology ; *Bacteria/genetics/classification ; Software ; },
abstract = {As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of their diversity and the literature becomes a growing and ongoing challenge. Here I present the Protist-Prokaryote Symbiosis Database (PPSDB), comprising 1146 manually curated interaction statements sourced from 443 publications, where biological taxonomy, anatomical localization, and analytical methods applied have been annotated and mapped to external databases and ontologies, such as Wikidata, NCBI Taxonomy, and Gene Ontology. I describe how its data model deals practically with challenges such as incomplete information and inconsistent taxon concepts, which will be applicable to similar projects. Both the model and underlying Wikibase software platform are highly extensible, so new items and properties can easily be added. Unlike a static table or list of citations, PPSDB is a structured knowledge base that enables programmatic access and powerful, integrated semantic queries. The database is available at https://ppsdb.wikibase.cloud/.},
}

*Symbiosis
*Eukaryota/physiology/classification/genetics
*Knowledge Bases
*Archaea/physiology/genetics
*Databases, Factual
*Prokaryotic Cells/physiology
*Bacteria/genetics/classification
Software

@article {pmid41070261,
year = {2025},
author = {Câmara, J and de Aguiar, SC and Paulino, T and Faria, AL and Bermúdez I Badia, S and Vilar, M and Fermé, E},
title = {Comparing adaptive tablet-based cognitive training and paper-and-pencil cognitive training: a pilot randomized controlled trial with community-dwelling stroke survivors.},
journal = {International journal of clinical and health psychology : IJCHP},
volume = {25},
number = {3},
pages = {100627},
pmid = {41070261},
issn = {2174-0852},
abstract = {INTRODUCTION: This study explored the feasibility and the preliminary efficacy of adaptive tablet-based cognitive training (CT) and paper-and-pencil CT approaches for mitigating multidomain post-stroke cognitive and noncognitive deficits.

METHODS: In this two-arm pilot randomized controlled trial, participants were randomly assigned to the NeuroAIreh@b (NAIr; adaptive tablet-based CT inspired by activities of daily living) and the Task Generator (TG; adaptive paper-and-pencil CT). A non-randomized passive control group was recruited for comparative purposes. Interventions comprised 12 bi-weekly 30-minute sessions. Primary outcomes explored training effects on several cognitive (e.g., global cognition, episodic memory), and noncognitive domains (e.g., quality of life, functional abilities).

RESULTS: A total of 20 participants were randomized (NAIr: n = 10; TG = 10). Within-group analysis revealed that the NAIr group presented significant improvements in more cognitive domains than the TG, and reported less functional disability, increased quality of life and greater motivation for rehabilitation at post-intervention. At follow-up, the NAIr group further improved in several cognitive domains and reported greater quality of life, while TG only improved in global cognition. Between-group analysis exhibited a pattern of superior performance in the adaptive CT groups over passive controls.

CONCLUSIONS: Findings suggest that adaptive CT interventions are feasible to implement and lead to cognitive and noncognitive improvements in community-dwelling stroke survivors. However, while both training approaches yield different short and medium/long-term benefits, the NAIr - a more ecologically valid method - was the only to promote generalization of training effects to functionality and quality of life at post-intervention and three-month follow-up, respectively.

TRIAL REGISTRATION: The trial is registered at ClinicalTrials.gov, number NCT05929287. Registered July 3rd, 2023 (cf. https://classic.clinicaltrials.gov/ct2/show/NCT05929287).},
}

@article {pmid41066464,
year = {2025},
author = {O'Neill, X and White, A and Northrup, GR and Saad-Roy, CM and White, PS and Boots, M},
title = {Superspreading and the evolution of virulence.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013517},
pmid = {41066464},
issn = {1553-7358},
mesh = {Virulence/genetics ; Humans ; *COVID-19/transmission/epidemiology/virology ; *SARS-CoV-2/pathogenicity/genetics ; Animals ; *Biological Evolution ; Computer Simulation ; Computational Biology ; Host-Pathogen Interactions ; Models, Biological ; },
abstract = {Superspreading, where a small proportion of a population can cause a high proportion of infection transmission, is well known to be important to the epidemiology of a wide range of pathogens, including SARS-CoV-2. However, despite its ubiquity in important human and animal pathogens, the impact of superspreading on the evolution of pathogen virulence is not well understood. Using theory and both deterministic and stochastic simulations we examine the evolution of pathogen virulence under a range of different distributions of infection transmission for the host. Importantly, for many pathogens, superpreader events may be associated with increased tolerance to infection or asymptomatic infection and when we account for this superspreading selects for higher virulence. In contrast, in animal populations where highly connected individuals, that are linked to superspreader events, also have fitness benefits, superspreading may select for milder pathogens. In isolation, the transmission distribution of the host does not impact selection for pathogen virulence. However, superspreading reduces the rate of pathogen evolution and generates considerable variation in pathogen virulence. Therefore, the adaptation of an emerging infectious disease, that exhibits superspreading, is likely to be slowed and characterised by the maintenance of maladaptive variants. Taken as a whole, our results show that superspreading can have important impacts on the evolution of pathogens.},
}

Virulence/genetics
Humans
*COVID-19/transmission/epidemiology/virology
*SARS-CoV-2/pathogenicity/genetics
Animals
*Biological Evolution
Computer Simulation
Computational Biology
Host-Pathogen Interactions
Models, Biological

@article {pmid41052097,
year = {2025},
author = {Teitelbaum, CS and Casazza, ML and Overton, CT and Matchett, EL and Prosser, DJ},
title = {Host responses and viral traits interact to shape the impacts of climate warming on highly pathogenic avian influenza in migratory waterfowl.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013451},
doi = {10.1371/journal.pcbi.1013451},
pmid = {41052097},
issn = {1553-7358},
mesh = {Animals ; *Influenza in Birds/virology/epidemiology/transmission ; *Animal Migration ; *Climate Change ; Disease Outbreaks ; *Influenza A virus/pathogenicity ; Birds/virology ; Models, Biological ; Computational Biology ; Computer Simulation ; Host-Pathogen Interactions ; Animals, Wild/virology ; },
abstract = {Emerging infectious diseases pose threats to wildlife populations, as exemplified by recent outbreaks of avian influenza viruses in wild birds. Climate change can affect infection dynamics in wildlife through direct effects on pathogens (e.g., environmental decay rates) and changes to host ecology, including shifting migration patterns. Here, we adapt an existing mechanistic model that couples migration and infection to study how traits of highly pathogenic avian influenza (HPAI) viruses contribute to HPAI outcomes in migratory waterfowl, then apply this model to explore potential impacts of climate change on HPAI dynamics. We find that the simulated impacts of HPAI on the host population under baseline climate conditions varied from no impact to 100% mortality, depending on viral traits. In most cases, traits related to transmission (i.e., contact rates, shedding rates) were more important for HPAI establishment probability, infection prevalence, and mortality than were other viral traits (e.g., environmental temperature sensitivity, cross-protective immunity). We then simulated the effects of climate change (i.e., altered temperature regimes) on HPAI dynamics both via viral environmental decay and via changes in bird migration phenology. In these simulations, we found that a 9-day advancement in spring migration timing increased the duration of HPAI outbreaks by increasing time birds spent at their breeding grounds, leading to higher mortality and fewer infections. In contrast, increased viral decay in warmer years had a smaller, but opposite impact. These patterns depended on the primary transmission mode of HPAI (i.e., direct vs. environmental) and its sensitivity to environmental temperatures. Together, these results suggest that climate change is likely to increase the impacts of HPAI on waterfowl populations if HPAI relies strongly on direct transmission and birds advance their spring migration. Further integrating host-viral co-evolution and other climatic changes (e.g., salinity, humidity) could provide more precise predictions of how HPAI dynamics could change in the future.},
}

Animals
*Influenza in Birds/virology/epidemiology/transmission
*Animal Migration
*Climate Change
Disease Outbreaks
*Influenza A virus/pathogenicity
Birds/virology
Models, Biological
Computational Biology
Computer Simulation
Host-Pathogen Interactions
Animals, Wild/virology

@article {pmid41064473,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Pale Oak Beauty, Hypomecis punctinalis (Scopoli, 1763).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {531},
pmid = {41064473},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hypomecis punctinalis (the Pale Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 741.20 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,897 protein-coding genes.},
}

@article {pmid41063758,
year = {2025},
author = {Sivell, O and Sivell, D and Mitchell, R and Webb, JA and Falk, S and , and , and , and , and , and , and , and , },
title = {The genome sequence of a snipefly, Rhagio lineola Fabricius, 1794.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {154},
pmid = {41063758},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Rhagio lineola (snipefly; Arthropoda; Insecta; Diptera; Rhagionidae). The genome sequence has a total length of 1,654.96 megabases. Most of the assembly (97.13%) is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.64 kilobases.},
}

@article {pmid41063755,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Treble Lines, Charanyca trigrammica (Hufnagel, 1766) (Lepidoptera: Noctuidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {520},
pmid = {41063755},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Charanyca trigrammica (Treble Lines; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 546.43 megabases and 546.58 megabases. Most of haplotype 1 (99.97%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.44 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid41061878,
year = {2025},
author = {William, G and Qadir, A and Saqib, Z},
title = {Urbanization and pollution pressures drive functional homogenization in bird feeding guilds.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123029},
doi = {10.1016/j.envres.2025.123029},
pmid = {41061878},
issn = {1096-0953},
abstract = {Urbanization and pollution are rapidly transforming ecosystems across the Global South, yet their impacts on functional biodiversity remain underexplored. Birds, as ecologically diverse and responsive taxa, are valuable indicators of environmental change and functional simplification. We examined how urbanization and pollution jointly influence the functional structure of avian communities across an urban-rural gradient in Sialkot District, a rapidly industrializing region of northeastern Pakistan. Using standardized point counts across 18 sites stratified by urban intensity and pollution levels, we quantified bird community composition and feeding guilds. We applied multidimensional indices of functional diversity (FRic, FEve, FDis, RaoQ) and ordination methods to assess trait-based filtering. Functional richness and divergence contracted markedly with increasing pollution and urbanization. Functionally specialized guilds particularly insectivores, piscivores, and carnivores were absent from the most polluted urban sites, which were dominated by ecological generalists such as omnivores and scavengers. Trait dissimilarity and redundancy declined sharply with pollution, and ordination revealed clear guild turnover along the pollution gradient, indicating homogenization of trophic roles. Functional evenness and dispersion showed weaker responses, suggesting selective persistence of a few tolerant guilds in urban cores. Feeding guild richness also declined with pollution, reflecting a strong loss of trophic diversity under anthropogenic stress. These findings provide rare empirical evidence from South Asia linking environmental contamination to multidimensional losses of avian functional diversity. By integrating trait-based metrics with ecological gradients, this study highlights the need to incorporate functional indicators into conservation planning, particularly in rapidly urbanizing regions where ecological data remain limited.},
}

@article {pmid41042793,
year = {2025},
author = {Du, H and Zahn, MV and Loo, SL and Alleman, TW and Truelove, S and Patenaude, B and Gardner, LM and Papageorge, N and Hill, AL},
title = {Improving policy design and epidemic response using integrated models of economic choice and disease dynamics with behavioral feedback.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013549},
doi = {10.1371/journal.pcbi.1013549},
pmid = {41042793},
issn = {1553-7358},
mesh = {Humans ; *COVID-19/epidemiology/economics/transmission/prevention & control ; Pandemics/economics ; SARS-CoV-2 ; Choice Behavior ; Decision Making ; *Policy Making ; Computational Biology ; *Health Policy ; },
abstract = {Human behavior plays a crucial role in infectious disease transmission, yet traditional models often overlook or oversimplify this factor, limiting predictions of disease spread and the associated socioeconomic impacts. Here we introduce a feedback-informed epidemiological model that integrates human behavior with disease dynamics in a credible, tractable, and extendable manner. From economics, we incorporate a dynamic decision-making model where individuals assess the trade-off between disease risks and economic consequences, and then link this to a risk-stratified compartmental model of disease spread taken from epidemiology. In the unified framework, heterogeneous individuals make choices based on current and future payoffs, influencing their risk of infection and shaping population-level disease dynamics. As an example, we model disease-decision feedback during the early months of the COVID-19 pandemic, when the decision to participate in paid, in-person work was a major determinant of disease risk. Comparing the impacts of stylized policy options representing mandatory, incentivized/compensated, and voluntary work abstention, we find that accounting for disease-behavior feedback has a significant impact on the relative health and economic impacts of policies. Including two crucial dimensions of heterogeneity-health and economic vulnerability-the results highlight how inequities between risk groups can be exacerbated or alleviated by disease control measures. Importantly, we show that a policy of more stringent workplace testing can potentially slow virus spread and, surprisingly, increase labor supply since individuals otherwise inclined to remain at home to avoid infection perceive a safer workplace. In short, our framework permits the exploration of avenues whereby health and wealth need not always be at odds. This flexible and extendable modeling framework offers a powerful tool for understanding the interplay between human behavior and disease spread.},
}

Humans
*COVID-19/epidemiology/economics/transmission/prevention & control
Pandemics/economics
SARS-CoV-2
Choice Behavior
Decision Making
*Policy Making
Computational Biology
*Health Policy

@article {pmid41042792,
year = {2025},
author = {Chapman, D and Occhibove, F and Bullock, JM and Beck, PSA and Navas-Cortes, JA and White, SM},
title = {Modelling plant disease spread and containment: Simulation and approximate Bayesian Computation for Xylella fastidiosa in Puglia, Italy.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013539},
doi = {10.1371/journal.pcbi.1013539},
pmid = {41042792},
issn = {1553-7358},
mesh = {*Xylella/pathogenicity/physiology ; *Plant Diseases/microbiology/statistics & numerical data/prevention & control ; Italy ; Bayes Theorem ; Computer Simulation ; Disease Outbreaks ; *Models, Biological ; Olea/microbiology ; Computational Biology ; },
abstract = {Mathematical and computational models play a crucial role in understanding the epidemiology of economically important plant disease outbreaks, and in evaluating the effectiveness of surveillance and disease management measures. A case in point is Xylella fastidiosa, one of the world's most deadly plant pathogens. Since its European discovery in olives in Puglia, Italy in 2013, there remain key knowledge gaps that undermine landscape-scale containment efforts of the outbreak, most notably concerning the year of introduction, the rate of spread, dispersal mechanisms and control efficacy. To address this, we developed a spatially explicit simulation model for the outbreak spreading among olive groves coupled to a simulation of the real surveillance and containment measures. We used Approximate Bayesian Computation to fit the model to surveillance and remote-sensing infection data, comparing the fits for three alternative dispersal mechanisms (isotropic, wind and road). The model accurately explained the rate and spatiotemporal pattern of the outbreak and found weak support for the wind dispersal model over the isotropic model. It suggests that the bacterium may have been introduced as early as 2003 (95% CI [2000, 2009]), earlier than previous estimates and congruent with anecdotal evidence. The isotropic model estimates the pathogen is spreading at 5.7 km y-1 (95% CI [5.4-5.9]) under containment measures, down from 7.2 km y-1 (95% CI [6.9-7.5]) without containment measures. Our estimate of an approximately 10-year lag between introduction and detection highlights the need for stronger biosecurity and surveillance for earlier detection of emerging plant pathogens. The outputs from simulations without any disease management also suggest that while containment measures have caused some slowing of X. fastidiosa spread, stronger measures will be required to contain the outbreak fully.},
}

*Xylella/pathogenicity/physiology
*Plant Diseases/microbiology/statistics & numerical data/prevention & control
Italy
Bayes Theorem
Computer Simulation
Disease Outbreaks
*Models, Biological
Olea/microbiology
Computational Biology

@article {pmid41030989,
year = {2025},
author = {Carroll, RA and Ricemeyer, ES and Hillier, LW and DaCosta, JM and Osipova, E and Smith, S and Jamie, GA and Martinez, JG and Molina-Morales, M and Marques-Bonet, T and Manthey, JD and Haddad, D and Fuxjager, MJ and Lynch, KS and Wood, JMD and Jarvis, E and Masterson, P and Thibaud-Nissen, F and Hauber, M and Spottiswoode, CN and Sackton, TB and Balakrishnan, CN and Sorenson, MD and Warren, WC},
title = {Genomic resources for comparative analyses of obligate avian brood parasitism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41030989},
issn = {2692-8205},
abstract = {Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.},
}

@article {pmid41021637,
year = {2025},
author = {Maity, B and Banerjee, S and Senapati, A and Pitchford, J and Chattopadhyay, J},
title = {Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013523},
doi = {10.1371/journal.pcbi.1013523},
pmid = {41021637},
issn = {1553-7358},
mesh = {*Cholera/epidemiology/transmission/microbiology/prevention & control ; *Disease Outbreaks/statistics & numerical data/prevention & control ; Humans ; Vibrio cholerae/pathogenicity ; Animals ; *Plankton/microbiology ; Zooplankton/microbiology ; Models, Biological ; Phytoplankton ; Computational Biology ; },
abstract = {Despite extensive control efforts over the centuries, cholera remains a globally significant health issue. Seasonal emergence of cholera cases has been reported, particularly in the Bengal delta region, which is often synchronized with plankton blooms. This phenomenon has been widely attributed to the commensal interaction between Vibrio cholerae and zooplankton in aquatic environments. The role of plankton dynamics in cholera epidemiology has been acknowledged but remains poorly understood, and consequently, its importance in effective policymaking is largely overlooked. To this end, we propose and analyze a novel compartment-based transmission model that integrates phytoplankton-zooplankton interactions into a human-bacteria cholera framework. Our study shows that, beyond the reproduction number, the relative contribution of bacterial versus zooplankton-mediated transmission plays a crucial role in shaping epidemic progression and severity. In presence of zooplankton-mediated transmission, an outbreak with a delayed and lower peak may still result in a larger overall outbreak size. Additionally, contrary to common intuition, even for a large and early outbreak, the epidemic overshoot may intensify due to the maintenance of lower-level infections during the post-peak phase. Furthermore, our analysis reveals that the timing of filtration-like interventions can be strategically guided by ecological indicators, such as phytoplankton blooms. Our study underscores the importance of incorporating ecological aspects in epidemiological research to better predict and manage disease outbreaks.},
}

*Cholera/epidemiology/transmission/microbiology/prevention & control
*Disease Outbreaks/statistics & numerical data/prevention & control
Humans
Vibrio cholerae/pathogenicity
Animals
*Plankton/microbiology
Zooplankton/microbiology
Models, Biological
Phytoplankton
Computational Biology

@article {pmid40997859,
year = {2025},
author = {Hu, J and Bao, G and Wu, J and Chen, S and Xu, Y and Wang, H and Tian, L and Fu, Z and Li, N and Yuan, Y},
title = {Freeze-Thaw Cycles Accelerate Plastic Pollution Invasion in Agriculture: Trojan Horse Effect of Microplastic-Plasticizer Contamination Revealed in Rye via Computational Chemistry and Multiomics.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {40},
pages = {25285-25300},
doi = {10.1021/acs.jafc.5c08155},
pmid = {40997859},
issn = {1520-5118},
mesh = {*Soil Pollutants/chemistry/metabolism/toxicity ; *Microplastics/metabolism/chemistry/toxicity/analysis ; *Secale/metabolism/drug effects/chemistry/genetics/growth & development ; *Plasticizers/metabolism/chemistry/toxicity ; Freezing ; Phthalic Acids/metabolism/chemistry/toxicity ; Bacteria/genetics/metabolism/isolation & purification/classification/drug effects ; Agriculture ; Plant Roots/metabolism/drug effects/microbiology ; Multiomics ; },
abstract = {Climate change-related freeze-thaw (FT) cycles intensify combined contamination from diethyl phthalate (DEP) and microplastics (MPs) in agricultural systems. This study examines their synergistic phytotoxicity in hydroponic rye using multidisciplinary approaches, including physiology, transcriptomics, and computational modeling. FT dramatically increased cocontamination risks. Notably, DEP promoted MP uptake into plants by elevating MP surface charge─an effect intensified by FT─resulting in disrupted root function and nutrient absorption. Molecular analyses showed that DEP binds strongly to key proteins (e.g., HSP70; ΔG = -7.6 kcal/mol), inhibiting photosynthesis (net rate reduced by 20.1-64.5%) and altering antioxidant activity. MPs adsorbed DEP, reducing its mobility, while simultaneously reshaping the root microbiome to favor DEP-degrading bacteria (e.g., Rhizobium). Transcriptomic changes were observed in stress-responsive and phytohormone pathways. These results demonstrate that FT cycles exacerbate combined pollutant toxicity through surface charge modification, molecular disruption, and microbial community adaptation, offering important insights for assessing ecological risks under climate-induced stressors.},
}

*Soil Pollutants/chemistry/metabolism/toxicity
*Microplastics/metabolism/chemistry/toxicity/analysis
*Secale/metabolism/drug effects/chemistry/genetics/growth & development
*Plasticizers/metabolism/chemistry/toxicity
Freezing
Phthalic Acids/metabolism/chemistry/toxicity
Bacteria/genetics/metabolism/isolation & purification/classification/drug effects
Agriculture
Plant Roots/metabolism/drug effects/microbiology
Multiomics

@article {pmid40828878,
year = {2025},
author = {Fong, LJM and Johnson, BD and Darolti, I and Sandkam, BA and Mank, JE},
title = {Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {10},
pages = {},
doi = {10.1093/g3journal/jkaf188},
pmid = {40828878},
issn = {2160-1836},
support = {//NSERC/ ; //UBC/ ; //BRC Informatics/ ; },
mesh = {Animals ; *Poecilia/genetics ; *Dosage Compensation, Genetic ; Male ; Female ; *Sex Chromosomes/genetics ; *Genome ; *Genomics/methods ; X Chromosome/genetics ; },
abstract = {The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. The close relatives Poecilia reticulata, Poecilia picta, and Poecilia parae all share the same sex chromosome system, but with substantial diversity in the degree of Y degeneration and the extent of X chromosome dosage compensation. In order to identify if P. bifurca shares the same sex chromosome system, we built a female (XX) draft genome with 55X coverage of PacBio HiFi data, resulting in a 785 Mb assembly with 94.4% BUSCO completeness. We used this genome and found that P. bifurca shares the same sex chromosomes as related species and shows substantial Y chromosome degeneration. We combined this with RNA-Seq data and found similar expression of X-linked genes between sexes, revealing that P. bifurca also exhibits complete X chromosome dosage compensation. We further identify 11 putative autosome-to-Y gene duplications, 5 of which show gene expression in guppy male germ cells.},
}

Animals
*Poecilia/genetics
*Dosage Compensation, Genetic
Male
Female
*Sex Chromosomes/genetics
*Genome
*Genomics/methods
X Chromosome/genetics

@article {pmid41057836,
year = {2025},
author = {Rangachari, P and Al Arkoubi, K and Shindi, R},
title = {A multi-level framework for advancing digital health equity in learning health systems: aligning practice and theory with the Quintuple Aim.},
journal = {International journal for equity in health},
volume = {24},
number = {1},
pages = {253},
pmid = {41057836},
issn = {1475-9276},
abstract = {Achieving digital health equity is essential to realizing the transformative goals of the Quintuple. Aim: optimizing patient experience, improving population health, supporting provider well-being, reducing costs, and advancing health equity. Yet significant disparities persist in access to digital tools, driven by both traditional and digital social determinants of health (SDOH), such as housing instability and limited broadband access. Health system responses often focus on downstream interventions to meet immediate needs, such as referrals for housing assistance or smartphone distribution, while upstream strategies, like partnerships to expand access to affordable housing or advocacy to improve broadband access, remain underutilized. Similarly, targeted tools for specific populations often lack corresponding universal strategies like digital literacy campaigns. The absence of systematic Electronic Health Record (EHR) integration of SDOH data further limits health systems' ability to identify disparities, tailor interventions, and support structural change. This paper introduces a theoretically grounded, multi-level framework for advancing digital health equity within Learning Health Systems (LHS). Drawing on insights from information systems theories, socio-ecological models, organizational learning, implementation science, and systems thinking, the framework supports alignment of equity-centered strategies across micro- (individual), meso- (organizational), and macro- (policy) levels. The framework is organized around three strategic domains: (1) building equity-driven data infrastructure through SDOH-EHR integration, (2) designing scalable, equity-centered interventions that balance targeted and universal approaches, and (3) leveraging strategic starting points to transition from downstream efforts to upstream reforms. Grounded in the U.S. context yet informed by international evidence, this framework offers a roadmap for aligning theory and practice to advance digital health equity in LHS. It is both actionable and adaptable, translating evidence and theory into a structured approach that healthcare systems can use to guide health equity initiatives. It illustrates how SDOH data can inform person-centered care, how targeted tools like multilingual telehealth apps can be integrated with universal strategies such as digital literacy campaigns, and how enabling services, community partnerships, and policy advocacy can catalyze longer-term structural reforms. Emphasizing continuous learning through feedback loops and multi-level alignment, the framework equips stakeholders to embed equity into LHS design and function, ultimately advancing sustainable progress toward the Quintuple Aim.},
}

@article {pmid41056132,
year = {2025},
author = {Kourtesis, P and Lizarraga, A and MacPherson, SE},
title = {Immersive virtual reality assessments of working memory and psychomotor skills: A comparison between immersive and non-immersive assessments.},
journal = {Journal of neuropsychology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jnp.70014},
pmid = {41056132},
issn = {1748-6653},
abstract = {OBJECTIVE: Immersive virtual reality (VR) enhances ecological validity and facilitates intuitive and ergonomic hand interactions for performing neuropsychological assessments. However, its comparability to traditional computerized methods remains unclear. This study investigates the convergent validity, user experience and usability of VR-based versus PC-based assessments of short-term and working memory, as well as psychomotor skills, while also examining how demographic and IT-related skills influence performance in both modalities.

METHODS: Sixty-six participants performed the Digit Span Task (DST), Corsi Block Task (CBT) and Deary-Liewald Reaction Time Task (DLRTT) in both VR- and PC-based formats. Participants' experience in using computers and smartphones, and playing videogames, was considered. User experience and system usability of the formats were also evaluated.

RESULTS: While performance on DST was similar across modalities, PC assessments enabled better performance on CBT and faster reaction times in DLRTT. Significant correlations between VR and PC versions supported convergent validity. Regression analyses revealed that performance on PC versions was influenced by computing and gaming experience, whereas performance on VR versions was largely independent of these factors, except for gaming experience predicting performance on CBT backward recall. Moreover, VR assessments received higher ratings for user experience and usability than PC-based assessments.

CONCLUSION: Immersive VR assessments provide an engaging alternative to traditional computerized methods, with minimal reliance on prior IT experience and demographic factors. This resilience to individual differences suggests that VR may offer a more equitable and accessible platform for automated cognitive assessment. Future research should explore the long-term reliability of VR-based assessments.},
}

@article {pmid41053825,
year = {2025},
author = {Villette, R and Ortís Sunyer, J and Novikova, PV and Aho, VTE and Petrov, VA and Hickl, O and Busi, SB and De Rudder, C and Kunath, BJ and Heintz-Buschart, A and Trezzi, JP and Halder, R and Jäger, C and Lebrun, LA and Daujeumont, A and Schade, S and Janzen, A and Jehmlich, N and von Bergen, M and Laczny, CC and May, P and Trenkwalder, C and Oertel, W and Mollenhauer, B and Wilmes, P},
title = {Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {200},
pmid = {41053825},
issn = {2049-2618},
support = {863664//HORIZON EUROPE European Research Council/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/15/BM/10404093//Fonds National de la Recherche Luxembourg/ ; FNR11264123//Fonds National de la Recherche Luxembourg/ ; MJFF-019228//Michael J. Fox Foundation for Parkinson's Research/ ; MCI-BIOME_2019//Institute for Advanced Studies, Université of Luxembourg/ ; 101038088//European Union's Horizon 2020 Widening Fellowships/ ; INTER/DFG/19/14429377//DFG Research Unit FOR2488/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metabolomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Metabolome ; Prodromal Symptoms ; Multiomics ; },
abstract = {BACKGROUND: Parkinson's disease (PD) is associated with gut microbiome shifts. These shifts are mainly described at taxonomic level, but the functional consequences remain unclear. To obtain insight into the functional disruptions of the gut microbiome in PD, we used an integrated multi-omics approach, comparing gut microbiomes of individuals with PD, prodromal PD, and healthy controls.

RESULTS: Meta-metabolomics, the most discriminatory and robust omics level, was selected to Guide the analysis. We identified 11 metabolites that were differentially abundant between the groups, among which β-glutamate was increased in PD and prodromal PD, and correlated with the transcriptional activities of Methanobrevibacter smithii and Clostridium spp. We identified decreases in transcripts, but not in gene abundances, related to glutamate metabolism, bile acids biosynthesis, chemotaxis, and flagellar assembly in PD, particularly in keystone genera such as Roseburia, Agathobacter, and Blautia. Our findings, integrated into the Expobiome map, reveal multifactorial microbiome alterations which converge with PD pathways.

CONCLUSION: Our study highlights the apparent disruption of microbial gene expression in PD, particularly in genes associated to mobility. Moreover, we showcase the importance of investigating the gut microbiome's functional dimensions to better resolve microbiome-host interactions in health and disease.},
}

*Parkinson Disease/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Metabolomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
Male
Female
Middle Aged
Aged
Feces/microbiology
Metabolome
Prodromal Symptoms
Multiomics

@article {pmid41053814,
year = {2025},
author = {Huebner, C and Huebner, NO and Goerig, T and Flessa, S},
title = {A regional One Health approach to mapping antimicrobial resistance interactions via systems thinking.},
journal = {One health outlook},
volume = {7},
number = {1},
pages = {46},
pmid = {41053814},
issn = {2524-4655},
abstract = {BACKGROUND: Antimicrobial resistance (AMR), as an original One Health problem, combines inextricable interactions between the human, animal and environmental dimensions. Addressing this challenge requires systemic thinking and coordinated networking between different levels of society and regional institutions. Knowledge of causal relationships, their mutual influence and the ability to assess the impact of possible interventions are prerequisites for coherent action to combat the further spread of antimicrobial resistance in a region. An integrated regional approach has not yet been addressed in One Health research on antimicrobial resistance.

METHODS: This study is based on a systems thinking approach and uses a causal loop diagram to visualise the relationships between human, animal and ecological components in a circular AMR system map for a One Health model region. The participatory approach actively involved regional stakeholders in the data collection and modelling process through surveys, semi structured interviews and interactive workshops. Based on the developed causal loop diagram, leverage point analysis is applied to estimate which types of interventions would have the greatest ability to address antimicrobial resistance in the One Health region.

RESULTS: Our results show that the system mapping tool is suitable for demonstrating the relationships regarding AMR in the One Health context for a defined region. It provides an opportunity to identify and visualise important risk factors that are direct or indirect drivers of AMR. Specifically, two amplifying and two balancing loops have been constructed in the model, covering antibiotic stewardship, public awareness, regional data management and environmental impact. Interdisciplinary and intersectoral collaboration, homogeneity of data and public awareness were identified as important leverage points. The graphical illustration of the causal loop diagram enables political and economic decision-makers to develop a deeper understanding of regional resistance patterns and the rational use of antibiotics from a One Health perspective.

CONCLUSION: This study is one of the first applications of a participatory systems thinking approach to the topic of AMR in the context of a One Health region.

TRAIL REGISTRATION: Not applicable.},
}

@article {pmid40808268,
year = {2025},
author = {Xu, G and Guo, J and Yu, X and Zhao, N and Li, X and Yuan, T and Xu, Z and Zhao, T and Zhao, S and Li, X and Liu, X},
title = {Multi-Omics Analysis Reveals Adaptive Strategies of Meconopsis horridula to UV-B Radiation in the Qinghai-Tibet Plateau.},
journal = {Plant, cell & environment},
volume = {48},
number = {11},
pages = {8249-8263},
doi = {10.1111/pce.70117},
pmid = {40808268},
issn = {1365-3040},
support = {//This study was supported by the Local Development Funds of the Science and Technology Department of Tibet (Grants XZ202001YD0028C and XZ202102YD0031C), and by the Graduate High-Level Talent Training Program of Tibet University (Grant 2025-GSP-B017)./ ; },
mesh = {*Ultraviolet Rays ; Flavonoids/biosynthesis ; Tibet ; *Adaptation, Physiological ; Transcriptome ; Gene Expression Regulation, Plant ; Altitude ; Arabidopsis/genetics ; Multiomics ; Acyltransferases ; Papaveraceae ; },
abstract = {Meconopsis horridula, an endemic medicinal and alpine horticultural species of the Qinghai-Tibet Plateau, exhibits remarkable adaptation to high-altitude UV-B radiation. Despite its ecological and medicinal significance, the mechanisms underlying its UV-B adaptation remain poorly understood. Here, we used a PacBio full-length transcriptome as a reference, integrating RNA-seq and metabolomic data from altitudinal populations, with field-based transcriptomic and microbiome profiling under shade-controlled UV-B gradients, to elucidate UV-B adaptive regulatory networks. KEGG enrichment and environmental correlation analyses highlighted flavonoid biosynthesis as a central pathway in UV-B adaptation at high altitudes. Controlled UV-B gradient experiments identified 10 conserved flavonoid biosynthesis genes, including chalcone synthase (CHS). Overexpression of CHS in Arabidopsis thaliana increased flavonoid content by approximately 1.2-fold. Co-expression analysis further revealed that CHS-associated regulatory factors mediate coordinated responses, including reduced light signalling, enhanced antioxidant capacity and suppression of defence genes and anthocyanin biosynthesis inhibitors. CHS, in coordination with immune regulation, modulates high-centrality microbes, contributing to differential network regulation and microbiome stability. Enriched key microbes may mitigate the growth-defence trade-off under UV-B stress through antimicrobial, growth-promoting and antioxidant activities. Collectively, our findings reveal a flavonoid-centred adaptation framework that deepens our understanding of UV-B resilience in alpine plants and offers potential resources for crop improvement.},
}

*Ultraviolet Rays
Flavonoids/biosynthesis
Tibet
*Adaptation, Physiological
Transcriptome
Gene Expression Regulation, Plant
Altitude
Arabidopsis/genetics
Multiomics
Acyltransferases
Papaveraceae

@article {pmid41052276,
year = {2025},
author = {Sherwani, MK and Ruuskanen, MO and Feldner-Busztin, D and Nisantzis Firbas, P and Boza, G and Móréh, Á and Borman, T and Putu Erawijantari, P and Scheuring, I and Gopalakrishnan, S and Lahti, L},
title = {Multi-omics time-series analysis in microbiome research: a systematic review.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
doi = {10.1093/bib/bbaf502},
pmid = {41052276},
issn = {1477-4054},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {*Microbiota ; Humans ; *Computational Biology/methods ; Machine Learning ; *Genomics/methods ; Multiomics ; },
abstract = {Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. To address this gap, we performed the first systematic literature review that comprehensively categorizes, compares, and evaluates computational methods for longitudinal multi-omics integration, with a particular emphasis on four categories of the studies: (i) host and host-associated microbiome studies, (ii) microbiome-free host studies, (iii) host-free microbiome studies, and (iv) methodological framework studies. Our review highlights current methodological trends, identifies widely used and high-performing frameworks, and assesses each method across performance, interpretability, and ease of use. We further organize these methods into thematic groups-such as statistical modeling, machine learning, dimensionality reduction, and latent factor approaches-to provide a clear roadmap for future research and application. This work offers a critical foundation for advancing integrative longitudinal data science and supporting reproducible, scalable analysis in this rapidly evolving field.},
}

*Microbiota
Humans
*Computational Biology/methods
Machine Learning
*Genomics/methods
Multiomics

@article {pmid41047667,
year = {2025},
author = {Liang, S and Wang, W and Tan, C and Zhou, L and Ou, Z and Qu, Y},
title = {Multi-omics analysis reveals the potential role of MbDDC in tissue-specific alkaloid biosynthesis and distribution in Meconopsis betonicifolia.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {1},
pages = {e70515},
doi = {10.1111/tpj.70515},
pmid = {41047667},
issn = {1365-313X},
support = {32160404//National Natural Science Foundation of China/ ; 31460218//National Natural Science Foundation of China/ ; 202501BD070001-084//Yunnan Fundamental Research Projects- the General Program of the Agriculture Joint Special Project/ ; YNWR-QNBJ-2019-211//Ten Thousand Talent Plans for Young Top-notch Talents of Yunnan Province/ ; 2025Y0844//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; },
mesh = {*Alkaloids/biosynthesis/metabolism ; *Plant Proteins/metabolism/genetics ; Plant Roots/metabolism ; Plant Leaves/metabolism ; Gene Expression Regulation, Plant ; Nicotiana/metabolism/genetics ; Flowers/metabolism ; Plant Stems/metabolism ; Metabolomics ; Transcriptome ; Multiomics ; Papaveraceae ; },
abstract = {Plants of the Meconopsis (Meconopsis spp.), endemic to the Qinghai-Tibet Plateau, are prized in traditional Tibetan medicinal herbs for their bioactive alkaloids, particularly their antispasmodic and analgesic properties. To elucidate the mechanisms underlying tissue-specific alkaloid accumulation in Meconopsis betonicifolia, we integrated metabolomic and transcriptomic analyses across four organs (roots, stems, leaves, and flowers) and functionally characterized the rate-limiting enzyme MbDDC-3. Our results demonstrate that roots are the primary site of alkaloid accumulation, with codeinone and salutaridine identified as key intermediates in the isoquinoline pathway. Eleven differentially expressed genes (DEGs) were strongly correlated with these metabolites. Heterologous overexpression of MbDDC-3 in tobacco (Nicotiana tabacum) significantly increased total alkaloid by 274% in roots (P < 0.05), with (S)-cis-N-methylstylopine and its precursors (tyramine/dopamine) significantly enriched. Notably, MbDDC-3 protein contains a non-classical nuclear localization signal (NLS)-RLKPAAIFNRKLG-located near its C-terminal region and exhibits key residue substitutions compared to lowland species, suggesting adaptive evolution under high-altitude stress. Collectively, this study reveals how M. betonicifolia optimizes alkaloid distribution for ecological fitness, while offering a genetic tool for metabolic engineering of medicinal alkaloids.},
}

*Alkaloids/biosynthesis/metabolism
*Plant Proteins/metabolism/genetics
Plant Roots/metabolism
Plant Leaves/metabolism
Gene Expression Regulation, Plant
Nicotiana/metabolism/genetics
Flowers/metabolism
Plant Stems/metabolism
Metabolomics
Transcriptome
Multiomics
Papaveraceae

@article {pmid41047562,
year = {2025},
author = {Takata, K and Ogawa, M and Takahashi, T},
title = {Temporal Trends and Determinants of Low-Dose Estrogen-Progestin Prescription in Japan During 2014-2022: An Ecological Study Using a Nationwide Claims Database.},
journal = {The journal of obstetrics and gynaecology research},
volume = {51},
number = {10},
pages = {e70093},
doi = {10.1111/jog.70093},
pmid = {41047562},
issn = {1447-0756},
support = {24K13368//Japan Society for the Promotion of Science/ ; },
mesh = {Female ; Humans ; Adult ; Middle Aged ; Adolescent ; Japan ; Young Adult ; Child ; *Estrogens/administration & dosage ; *Progestins/administration & dosage ; Databases, Factual ; *Drug Prescriptions/statistics & numerical data ; *Practice Patterns, Physicians'/statistics & numerical data/trends ; *Estrogen Replacement Therapy/trends/statistics & numerical data ; },
abstract = {AIM: This study aimed to evaluate the trends and regional disparities in low-dose estrogen-progestin (LEP) prescription in Japan from 2014 to 2022 and the factors contributing to these disparities.

METHODS: LEP prescription data were obtained from the National Health Insurance Claims and Specific Health Examination Database; the prescriptions per 1000 women aged 10-54 years were calculated. Trends were analyzed in terms of the overall volume, age group distribution, and formulation type. The regional distribution in 2022 was also examined; the factors influencing regional differences were identified using multiple regression analysis.

RESULTS: LEP prescriptions showed a significant annual increase (p < 0.05), rising approximately five-fold over 9 years. A significant increase was observed in all age groups, except for those in their 50s (p < 0.05). Ethinylestradiol 0.035 mg/norethisterone 1 mg (p < 0.005) and ethinylestradiol 0.02 mg/drospirenone 3 mg (cyclic dosing regimen) (p < 0.001) usage declined. Conversely, ethinylestradiol 0.02 mg/drospirenone 3 mg (continuous dosing regimen) and ethinylestradiol 0.02 mg/levonorgestrel 0.09 mg usage increased significantly (p < 0.05). In 2022, regional disparities in LEP prescriptions reached a maximum of 2.7-fold. These disparities were not associated with the number of obstetricians and gynecologists and women's health specialists. However, the prescription of EE 0.02 mg/drospirenone 3 mg (continuous dosing regimen) showed a significant association with the number of women's health specialists (p = 0.002).

CONCLUSION: This study provides the first comprehensive analysis of real-world LEP prescription patterns in Japan, revealing significant regional disparities.},
}

Female
Humans
Adult
Middle Aged
Adolescent
Japan
Young Adult
Child
*Estrogens/administration & dosage
*Progestins/administration & dosage
Databases, Factual
*Drug Prescriptions/statistics & numerical data
*Practice Patterns, Physicians'/statistics & numerical data/trends
*Estrogen Replacement Therapy/trends/statistics & numerical data

@article {pmid41047557,
year = {2025},
author = {Rausch, P and Ratjen, I and Tittmann, L and Enderle, J and Wacker, EM and Jaeger, K and Rühlemann, MC and Franzpötter, K and Ellul, P and Kruse, R and Halfvarson, J and Roggenbuck, D and Ellinghaus, D and Jacobs, G and Krawczak, M and Schreiber, S and Bang, C and Lieb, W and Franke, A},
title = {First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2559119},
doi = {10.1080/19490976.2025.2559119},
pmid = {41047557},
issn = {1949-0984},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/epidemiology ; Male ; Female ; Adult ; *Bacteria/classification/isolation & purification/genetics ; *Dysbiosis/microbiology ; Prospective Studies ; *Gastrointestinal Microbiome ; Middle Aged ; Cohort Studies ; Feces/microbiology ; Germany/epidemiology ; Young Adult ; },
abstract = {The prospective Kiel Inflammatory Bowel Disease (IBD) Family Cohort Study (KINDRED cohort) was initiated in 2013 to systematically and extensively collect data and biosamples from index IBD patients and their relatives, a population at high risk for IBD development. Regular follow-ups were conducted to collect updated health and lifestyle information, to obtain new biosamples, and to capture the incidence of IBD during development. By combining microbial data collected at successive time points with extensive anthropometric, medical, nutritional, and social information, this study aimed to characterize the factors influencing the microbiota in health and disease via detailed ecological analyses. Using a microbial dysbiosis metric based on the German KINDRED cohort, we identified strong and generalizable gradients within and across different external IBD cohorts for validation. These community gradients correspond strongly with IBD pathologies, physiological manifestations of inflammation (e.g. Bristol stool score, ASCA IgA, ASCA IgG), and genetic risk for IBD. Anthropometric and medical factors influencing fecal transit time strongly modify bacterial communities. Various Enterobacteriaceae (e.g. Klebsiella sp.) and opportunistic Clostridia pathogens (e.g. C. XIVa clostridioforme), characterize in combination with ectopically colonizing oral taxa (e.g. Veillonella sp. Cand. Saccharibacteria sp. Fusobacterium nucleatum) the distinct and chaotic IBD-specific communities. Weak community and physiological changes are further traceable in a small number of individuals, who developed IBD in the study's runtime. Our findings demonstrate broad-scale ecological patterns which indicate drastic state transitions of communities in IBD patients. These patterns appear to be universal across cohorts and influence physiological signs of inflammation, display increased resilience, but show only limited heritability/intrafamily transmission.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/epidemiology
Male
Female
Adult
*Bacteria/classification/isolation & purification/genetics
*Dysbiosis/microbiology
Prospective Studies
*Gastrointestinal Microbiome
Middle Aged
Cohort Studies
Feces/microbiology
Germany/epidemiology
Young Adult

@article {pmid41041147,
year = {2024},
author = {Botham, M and , and , and , and , and , },
title = {The genome sequence of the Small Argent and Sable moth, Epirrhoe tristata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {541},
pmid = {41041147},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Small Argent and Sable moth Epirrhoe tristata (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence spans 313.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.92 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,469 protein-coding genes.},
}

@article {pmid41040654,
year = {2025},
author = {Boyes, D and Broad, GR and Lees, DC and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Brindled White-spot moth, Parectropis similaria (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {179},
pmid = {41040654},
issn = {2398-502X},
abstract = {We present a genome assembly from a female Parectropis similaria (Brindled White-spot; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 574.79 megabases. Most of the assembly (99.92%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.94 kilobases.},
}

@article {pmid41040651,
year = {2025},
author = {Boyes, D and Lees, DC and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Triangle-marked Roller, Ancylis achatana (Denis & Schiffermüller), 1775.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {128},
pmid = {41040651},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Ancylis achatana (Triangle-marked Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 547.27 megabases. Most of the assembly (99.25%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.0 kilobases.},
}

@article {pmid41040647,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Sycamore-seed Pygmy moth, Ectoedemia decentella (Herrich-Schäffer, 1855) van Nieukerken, 1986.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {182},
pmid = {41040647},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Ectoedemia decentella (Sycamore-seed Pygmy; Arthropoda; Insecta; Lepidoptera; Nepticulidae). The genome sequence has a total length of 418.14 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.25 kilobases.},
}

@article {pmid41041439,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Hoile, A and , },
title = {The genome sequence of the Brick, Agrochola circellaris (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {44},
pmid = {41041439},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agrochola circellaris (the Brick; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 572 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 15.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 18,319 protein coding genes.},
}

@article {pmid41038931,
year = {2025},
author = {Nganso, BT and Agboka, KM and Atagong, SD and Topé, SF and Massing, T and Landmann, T and Sevgan, S and Mwiza, W and Odera, F and Piiru, ED and Otieno-Ayayo, ZN and Soroker, V and Guimapi, RA},
title = {A Geospatial atlas of honey bee forage plants and their distribution patterns in Africa and beyond.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34384},
pmid = {41038931},
issn = {2045-2322},
support = {70054//JRS Biodiversity Foundation/ ; },
mesh = {Bees/physiology ; Animals ; Africa ; Pollination ; Biodiversity ; Ecosystem ; Conservation of Natural Resources ; Databases, Factual ; },
abstract = {Honey bee forage plants are essential for bee nutrition and wellbeing, and they also sustain multifunctional landscapes that support human livelihoods and biodiversity. Despite the critical need to conserve them, information on their identity and distribution across Africa remains limited. Through a systematic literature review, we compiled the first continental database of 1,248 honey bee forage plant species from 91 families and retrieved 1,572,790 occurrence records of these species from open-access biodiversity databases like iNaturalist and the Global Biodiversity Information Facility (GBIF). The database includes native and exotic species, with georeferenced records from Africa and beyond. An interactive web-based dashboard accompanies the database, allowing users to visualize species distributions. The dashboard reveals floral report gaps in Western, Central and Northern Africa, helping inform future conservation priorities. In Southern and Eastern Africa where considerable data exists, this resource promotes pollinator-friendly land management practices, supporting honey bees and other pollinators vital for ecosystem resilience. Overall, this resource provides a foundation for future integration with high-resolution imagery, climate models and field-collected data on plant-pollinator interactions to contextualize species distributions under varying land-use and climatic conditions. It offers a valuable tool to support pollinator conservation and climate-resilient strategies for agriculture and beekeeping across Africa.},
}

Bees/physiology
Animals
Africa
Pollination
Biodiversity
Ecosystem
Conservation of Natural Resources
Databases, Factual

@article {pmid41001448,
year = {2025},
author = {Evans, LM and Arehart, CH and Gibson, RA and Bowman, GI and Gignoux, CR},
title = {A simple approach for multiple observations improves power to detect genetic effects and genomic prediction accuracy.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41001448},
abstract = {Many datasets, including widely used biobanks, have more than one observation of numerous phenotypes for at least a portion of their sample. The majority of GWAS utilize only a single observation per individual, even when more than one observation may be available, and apply a standard model in which the additive allelic effect being estimated is assumed to be constant across the age or time range in the sample. Here, we test a set of simple approaches to utilize multiple observations per individual, under this same assumption. We find that utilizing the mean or median of the available observations rather than a single observation improves power to detect associated loci and enriched gene sets and yields higher out-of-sample polygenic score prediction accuracy. Despite growing biobanks, many deeply phenotyped samples are relatively small but have multiple observations. While explicitly modeling age- or time-dependent genetic effects can estimate time- or age-specific genetic effects, most GWAS apply a standard, additive-only model; a simple approach of using the mean or median can improve power by reducing "noise" in the phenotype, utilize standard, optimized software, and be particularly impactful for smaller samples, including samples of diverse genetic ancestry currently existing in widely used biobanks.},
}

@article {pmid40924543,
year = {2025},
author = {Baele, G and Carvalho, LM and Brusselmans, M and Dudas, G and Ji, X and McCrone, JT and Lemey, P and Suchard, MA and Rambaut, A},
title = {HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {10},
pages = {},
doi = {10.1093/bioinformatics/btaf488},
pmid = {40924543},
issn = {1367-4811},
support = {//Research Foundation-Flanders/ ; },
mesh = {*Software ; *Phylogeny ; *SARS-CoV-2/genetics/classification ; Bayes Theorem ; *Ebolavirus/genetics/classification ; Algorithms ; Humans ; *Computational Biology/methods ; COVID-19/virology ; },
abstract = {SUMMARY: In Bayesian phylogenetic and phylodynamic studies, it is common to summarize the posterior distribution of trees with a time-calibrated summary phylogeny. While the maximum clade credibility (MCC) tree is often used for this purpose, we here show that a novel summary tree method-the highest independent posterior subtree reconstruction, or (HIPSTR)-contains consistently higher supported clades over MCC. We also provide faster computational routines for estimating both summary trees in an updated version of TreeAnnotator X, an open-source software program that summarizes the information from a sample of trees and returns many helpful statistics such as individual clade credibilities contained in the summary tree.

RESULTS: HIPSTR and MCC reconstructions on two Ebola virus and two SARS-CoV-2 datasets show that HIPSTR yields summary trees that consistently contain clades with higher support compared to MCC trees. The MCC trees regularly fail to include several clades with very high posterior probability (≥0.95) as well as a large number of clades with moderate to high posterior probability (≥50%), whereas HIPSTR-in particular its majority-rule extension MrHIPSTR-achieves near-perfect performance in this respect. HIPSTR and MrHIPSTR also exhibit favourable computational performance over MCC in TreeAnnotator X. Comparison to the recent CCD0-MAP algorithm yielded mixed results and requires a more in-depth investigation in follow-up studies.

TreeAnnotator X is available as part of the BEAST X (v10.5.0) software package, available at https://github.com/beast-dev/beast-mcmc/releases, and on Zenodo (DOI: https://doi.org/10.5281/zenodo.4895234).},
}

*Software
*Phylogeny
*SARS-CoV-2/genetics/classification
Bayes Theorem
*Ebolavirus/genetics/classification
Algorithms
Humans
*Computational Biology/methods
COVID-19/virology

@article {pmid41034648,
year = {2025},
author = {Weingarten, A and Häusler, M and Serangeli, J and Verheijen, I and Reiter, E and Radzevičiūtė, R and Stoessel, A and Krause, J and Spyrou, MA and Conard, NJ and Nieselt, K and Posth, C},
title = {Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41034648},
issn = {2397-334X},
abstract = {Deep-time palaeogenomics offers rare insights into macroevolutionary events for both extant and extinct species. Aside from a Middle Pleistocene genome from North American permafrost (780-560 ka) and a number of Late Pleistocene specimens, most ancient horse DNA studies have focused on tracing the origins of domestication and subsequent periods. Here we present mitochondrial genomes from two Equus mosbachensis specimens from Schöningen, Germany, a Middle Pleistocene archaeological site complex with direct and repeated evidence of hominin-horse interactions on the shore of a palaeolake. Using petrous bone sampling, targeted enrichment and damage-aware and polarization-free mitochondrial DNA reconstruction methods, we extend the range of genome recovery in open-air sites to ~300,000 years ago. Phylogenetic analyses position these mitochondrial DNAs in two distinct, deeply divergent lineages, basal to both previously sequenced ancient Eurasian specimens and all modern-day horses. The Schöningen horse mitochondrial DNA data reveal a previously unrecognized diversification event within the clade, ultimately giving rise to modern-day horses, that is molecularly dated to ~570 ka and provides genetic support for the morphological species assignment. By extending the recoverable limits of ancient DNA from Middle Pleistocene open-air sites, our molecular findings bridge a temporal and geographic gap, providing insights on early evolutionary events within the genus Equus.},
}

@article {pmid41032589,
year = {2025},
author = {Yang, M and Adegbite, O and Chang, P and Cheng, J and Wang, Y and Held, M and Zhu, X and Li, Y and Dykes, GF and Chen, Y and Savage, N and Zhang, YZ and Gao, J and Hinton, JCD and Lian, LY and Liu, LN},
title = {Molecular basis of the biogenesis of a protein organelle for ethanolamine utilization.},
journal = {Science advances},
volume = {11},
number = {40},
pages = {eadx9774},
doi = {10.1126/sciadv.adx9774},
pmid = {41032589},
issn = {2375-2548},
mesh = {*Ethanolamine/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Organelles/metabolism ; *Salmonella/metabolism ; },
abstract = {Many pathogenic bacteria use proteinaceous ethanolamine utilization microcompartments (Eut BMCs) to catabolize ethanolamine. This ability gives pathogens a competitive edge over commensal microbiota, which can drive virulence in the inflamed gut. Despite such a critical function, the molecular mechanisms underlying the synthesis of Eut BMCs remain elusive. We report a systematic study for dissecting the molecular basis underlying Eut BMC assembly in Salmonella. We determined the functions of individual constituent proteins in the structure and function of Eut BMCs and demonstrated that EutQ is essential for cargo encapsulation and Eut BMC formation through specific association with the shell and cargo enzymes. We found that Eut proteins can self-assemble to form cargo and shell aggregates independently in vivo and that the biogenesis of Eut BMCs follows a "shell-initiated" pathway. Cargo enzymes exhibit dynamic liquid-like organization within the Eut BMC. Our findings provide mechanistic insights into the structure and assembly of the Eut BMC that serves as a paradigm for membraneless organelles.},
}

*Ethanolamine/metabolism
*Bacterial Proteins/metabolism/genetics/chemistry
*Organelles/metabolism
*Salmonella/metabolism

@article {pmid41032510,
year = {2025},
author = {Zhang, C and Teng, J and Liu, P and Liu, C},
title = {Ecological suitability evaluation of traditional village locations in Jiangxi Province based on multi-model integration using artificial intelligence.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332375},
doi = {10.1371/journal.pone.0332375},
pmid = {41032510},
issn = {1932-6203},
mesh = {*Artificial Intelligence ; China ; *Ecosystem ; Humans ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Neural Networks, Computer ; *Ecology ; Support Vector Machine ; },
abstract = {Traditional villages have evolved over time to adapt to their environmental characteristics, demonstrating high ecological suitability. Ideal village locations not only provide comfortable living spaces but also ensure safety and sustainability, reflecting the ancestors' profound understanding of the natural environment and ecological wisdom. This study employs an artificial intelligence-based multi-model integration approach to evaluate the ecological suitability of 413 traditional village sites in Jiangxi Province. Key influencing factors are identified, and the ecological wisdom of ancestral site selection is analyzed, resulting in an ecological suitability evaluation map for traditional village locations in Jiangxi Province. The study draws upon environmental characteristic data of Jiangxi Province, including topography, climate, habitat quality, land use, air quality, vegetation cover, and river network density. GIS technology is utilized for spatial analysis and result visualization, with raster data being extracted and standardized. Machine learning methods, such as Random Forest, Support Vector Machine, and Gradient Boosting Decision Trees, along with deep learning methods like Convolutional Neural Networks and Multilayer Perceptrons, are applied. Multi-model integration techniques combine diverse predictive outputs, thereby enhancing the overall accuracy and robustness of ecological suitability evaluations. Experimental results indicate that elevation, slope, habitat quality, actual distance to water bodies, and average temperature are the main influencing factors for village site selection. The multi-model integration method performs excellently in evaluating ecological suitability, effectively identifying key ecological factors. The model's accuracy and reliability are verified through confusion matrix, feature importance analysis, and ROC curve. By analyzing the impact weights of various ecological factors, this study constructs a Composite Suitability Index (CSI) and generates an ecological suitability evaluation map that clearly displays suitability levels. This provides a scientific basis for the protection and rational development of traditional villages and serves as a reference for ecological site selection studies in other regions.},
}

*Artificial Intelligence
China
*Ecosystem
Humans
*Conservation of Natural Resources/methods
Geographic Information Systems
Neural Networks, Computer
*Ecology
Support Vector Machine

@article {pmid41030122,
year = {2025},
author = {Robinson, JM and Brame, J and Cando-Dumancela, C and Deshmukh, S and Fickling, NW and Hawken, S and Hayward, C and Kuhn, E and Lee, K and Liddicoat, C and Ramesh, S and Robinson, K and Sun, X and Breed, MF},
title = {Mapping and Cataloguing Microbial and Biochemical Determinants of Health: Towards a 'Database of Salutogenic Potential'.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70243},
doi = {10.1111/1751-7915.70243},
pmid = {41030122},
issn = {1751-7915},
support = {//National Environmental Science Program/ ; 32361143523//National Natural Science Foundation of China/ ; UOWX2101//New Zealand Ministry of Business Innovation and Employment/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; 2023YFF1304600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Environmental Microbiology ; *Databases, Factual ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Microbial and biochemical research has historically focused on pathogenic agents due to their clear association with disease. This is a perspective that has saved countless lives but encourages a skewed, threat-centered view of microbes and biogenic compounds. Emerging evidence shows that exposure to diverse environmental microbiomes and natural biochemical products is also salutogenic-promoting health and resilience. Here we introduce the 'Database of Salutogenic Potential', a prototype relational repository cataloguing environmental microbes and biochemical compounds linked to health benefits. Drawing from more than 200 articles, we identified 124 potentially salutogenic microbial taxa, 14 biochemical compounds and 63 associated benefits. By creating a structured and open platform, we aim to shift the balance between pathogen-centric and salutogenic perspectives, potentially enabling future applications in public health, urban planning and ecosystem restoration. While the current iteration of the database primarily centers on human health outcomes, it is designed to expand into ecosystem health domains, embedding salutogenic thinking into One Health frameworks. We present this as a first step, not a ready-to-use tool, and invite collaborative refinement from the scientific community.},
}

Humans
*Microbiota
*Environmental Microbiology
*Databases, Factual
*Bacteria/metabolism/classification/genetics

@article {pmid41029229,
year = {2025},
author = {Nagy, KN and Károlyi, CE and Bakacsy, L},
title = {Multiscale assessment of conservation management for Amorpha fruticosa invasion in a marsh meadow.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {97},
pmid = {41029229},
issn = {2730-7182},
support = {7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; },
mesh = {*Introduced Species ; *Wetlands ; *Conservation of Natural Resources/methods ; Biodiversity ; Animals ; Cattle ; *Fabaceae/physiology ; },
abstract = {This study examined the ecological impact of the invasive shrub Amorpha fruticosa in marsh meadows and assessed the effectiveness of combined conservation management practices, i.e., mowing and cattle grazing, in on restoring native vegetation. Conducted in the Mártély Landscape Protection Area (Hungary), the research used a multiscale approach to compare treated non-invaded and treated invaded wetland vegetation. Information theory-based diversity metrics were employed to evaluate the impact of A. fruticosa on structural complexity and species composition. Results revealed that although A. fruticosa can significantly altered plant community structure, the implemented management strategies effectively reduced its impact. The treated invaded vegetation exhibited diversity levels compareable to native marshland communities, suggesting that mowing and grazing contributed to decreasing A. fruticose dominance. However, in the absence of untreated control stands, this pattern must be interpreted cautiously, as the observed similarity could be conclusively attributed to the applied management alone. A slight, but non-significant shift in structural diversity was also observed, implying a residual effect of invasion. This study underscores the value of active, combined conservation strategies in maintaining biodiversity and ecosystem resilience in wetland habitats. The results contribute to broader discussions on invasive species control, emphasizing the role of traditional land-use practices in mitigating the ecological effects of biological invasions.},
}

*Introduced Species
*Wetlands
*Conservation of Natural Resources/methods
Biodiversity
Animals
Cattle
*Fabaceae/physiology

@article {pmid41028195,
year = {2025},
author = {Yang, M and Wang, M and Cao, L and Zhang, H},
title = {Integrating trade-offs and supply-demand into ecosystem service zoning management to provide more targeted management strategies from the water-food-ecosystem nexus perspective.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33957},
pmid = {41028195},
issn = {2045-2322},
support = {42401384//National Natural Science Foundation of China/ ; 41971241//National Natural Science Foundation of China/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 25IRTSTHN008//Higher Education Institutions Scientific and Technological Innovation Team Support Program in Henan Province/ ; 25A170008//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; 24B170003//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; },
abstract = {The water-food-ecosystem nexus (WFE nexus) forms the foundation for achieving sustainable development. Managing ecosystem services (ESs) from this perspective is crucial for maintaining and enhancing ecosystem sustainability. However, synchronously mitigating trade-offs and supply-demand conflicts among ESs poses a significant challenge for sustainable ecosystem management. This study proposes a spatial management zoning framework integrating information on ESs trade-offs and supply-demand relationships from the perspective of the WFE nexus. This framework aims to precisely distinguish regional differences in ESs trade-off characteristics and supply-demand risk levels. We applied this framework to China's Loess Plateau (LP) in China, where the simultaneous safeguarding of water, food, and ecological security has become a major challenge for local sustainable development. Based on analyzing ESs trade-offs and supply-demand matching relationships, our framework divided the LP into ten management zones. Each of these zones faces similar ecological issues internally, while different zones confront distinct ecological problems. Consequently, we propose targeted management strategies for each zone based on their unique ecological issues. Our framework deepens the research on the WFE nexus and provides a new perspective for simultaneously resolving ESs trade-offs and supply-demand conflicts.},
}

@article {pmid41026600,
year = {2025},
author = {Liu, L and Han, P and Wang, J and Xiuqin, S and Xu, G and Wang, L and Liu, R and Shen, X and Chen, F},
title = {Approaches to the water environment and aquatic ecology governance in basin systems.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {6},
pages = {894-902},
pmid = {41026600},
issn = {0273-1223},
support = {ZR2024MD117//Natural Science Foundation of Shandong Province/ ; No.0031504//The Shandong Top Talent Special Foundation/ ; X20192Z//The Doctoral research fund project of Shandong Jianzhu University/ ; 42107496//The National Science Fund for Distinguished Young Scholars-Construction and application of remote sensing ecological index model of Tamarix shrubbery forest/ ; },
mesh = {*Ecology ; *Conservation of Natural Resources ; Ecosystem ; Sustainable Development ; },
abstract = {With the development of human civilization and the rapid progress of urbanization, the water environment and aquatic ecology need more systematic treatment to support the construction of ecological civilization and sustainable development. Based on a large number of research results and from the four dimensions including governance concept, governance technology, management and control platform and engineering strategy suggestions, this study systematically analysed the cutting-edge concepts such as reverse-driven governance, explored the application of key technologies such as remote sensing in the water environment and water ecological governance, put forward strategic suggestions on building an intelligent analysis and decision-making platform and avoiding great leap forward-style vanity projects in the water environment and aquatic ecology governance. Finally, six cutting-edge governance concepts, four key technologies, two types of governance and control platforms and two engineering strategies were sorted out and formed a governance system covering concept guidance, technical support, platform integration and application, and engineering strategy guarantee. The research enriches the theory of the water environment and aquatic ecology governance, and has important reference value for policy-making and engineering practice of watershed water environment and aquatic ecology governance.},
}

*Ecology
*Conservation of Natural Resources
Ecosystem
Sustainable Development

@article {pmid41021230,
year = {2025},
author = {Muzekari, B and Cooper, N and Resnick, A and Paul, AM and Torres-Grillo, OE and Andrews, ME and Mattan, B and Scholz, C and Johnson, D and Carreras-Tartak, J and Cakar, ME and Hao, S and Zhou, E and Beard, E and Mesquiti, S and Sayed, F and Fichman, MA and Lydon-Staley, DM and Barnett, IJ and Strasser, AA and Kirchner, TR and Henriksen, L and Falk, EB},
title = {Naturalistic Tobacco Retail Exposure and Smoking Outcomes in Adults Who Smoke Cigarettes Daily.},
journal = {JAMA network open},
volume = {8},
number = {9},
pages = {e2530132},
doi = {10.1001/jamanetworkopen.2025.30132},
pmid = {41021230},
issn = {2574-3805},
mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; *Tobacco Products/economics/statistics & numerical data ; Craving ; *Commerce/statistics & numerical data ; Aged ; *Cigarette Smoking/epidemiology/psychology ; Cohort Studies ; Young Adult ; Ecological Momentary Assessment ; New Jersey/epidemiology ; *Tobacco Industry ; },
abstract = {IMPORTANCE: The tobacco industry spends more than $8 billion annually in the US on marketing at the point of sale. Exposure to tobacco retail has been associated with smoking outcomes, but substantially less is known about how objectively logged everyday tobacco retail exposure is associated with smoking outcomes.

OBJECTIVE: To assess preregistered hypotheses that individuals would report (1) greater craving and (2) more cigarettes smoked on days when their exposure to tobacco retail is higher than usual.

This multimodal, within-person cohort study combined objectively logged geolocation tracking, public tobacco retail location records, and ecological momentary assessment data. Eligible participants recruited from the GeoSmoking Study were aged 21 to 65 years, smoked at least 5 cigarettes per day over the previous 6 months, owned a smartphone, and were a resident of Pennsylvania, New Jersey, or Delaware. Data were collected from May 25, 2022, to June 10, 2024.

EXPOSURE: Exposure to tobacco retail stores was assessed using mobility data matched with locations of tobacco retailers across Pennsylvania, New Jersey, and Delaware.

MAIN OUTCOMES AND MEASURES: Daily mean craving and daily number of cigarettes smoked were computed using ecological momentary assessment.

RESULTS: A total of 273 participants were included in the final analyses (mean [SD] age, 42.5 [10.7] years; 151 women [55.3%]). Multilevel models revealed support for both preregistered hypotheses. On days when individuals had more tobacco retail exposure than their own average, they reported significantly higher levels of craving (b = 0.04; 95% CI, 0.01-0.07; t3457 = 2.72; P = .01) and smoking significantly more cigarettes (b = 0.01; 95% CI, 0.0002-0.01; t3469 = 2.05; P = .04).

CONCLUSIONS AND RELEVANCE: In this cohort study of individuals who smoke cigarettes daily, exposure to tobacco retail in their everyday lives was associated with increases in craving and smoking. These findings highlight the importance of retail exposure and smoking outcomes, information that is critical for developing effective tobacco control interventions and lays the foundation for broader health research on environmental factors that shape health behaviors.},
}

Humans
Female
Male
Adult
Middle Aged
*Tobacco Products/economics/statistics & numerical data
Craving
*Commerce/statistics & numerical data
Aged
*Cigarette Smoking/epidemiology/psychology
Cohort Studies
Young Adult
Ecological Momentary Assessment
New Jersey/epidemiology
*Tobacco Industry

@article {pmid41020379,
year = {2025},
author = {Vázquez, E and Duong, I and Rabin, BA and Stadnick, NA and Watson, PL and Cain, KL and Pozar, M and Cheney, A},
title = {Ripple Effects Mapping: Evaluating Multilevel Perspectives and Impacts of a Statewide Community-Academic Partnership Network on Covid-19 Health Disparities.},
journal = {Health expectations : an international journal of public participation in health care and health policy},
volume = {28},
number = {5},
pages = {e70446},
doi = {10.1111/hex.70446},
pmid = {41020379},
issn = {1369-7625},
support = {//This paper was supported by the following funding NIH/NHLBI CEAL grant #21-312-0217571-66106L./ ; },
mesh = {Humans ; *COVID-19/epidemiology/ethnology ; *Health Status Disparities ; California/epidemiology ; Community-Based Participatory Research ; *Community-Institutional Relations ; Universities/organization & administration ; *Community Networks/organization & administration ; SARS-CoV-2 ; Female ; },
abstract = {INTRODUCTION: Community-academic partnerships played an important role in addressing Covid-19-related health disparities in historically marginalised groups such as racial ethnic minorities and low-income and rural communities in the pandemic. Part of the federal response involved establishing regional community academic networks that engaged highly impacted communities in health disparities research. The statewide Share, Trust, Organize, Partner COVID-19 California Alliance (STOP COVID-19 CA) network was part of the federal response.

METHODS: In spring 2024, ripple effects mapping (REM), a participatory action research method, was used to conduct an evaluation of the impact of the STOP COVID-19 network on the capacity of community-academic partnerships to carry out Covid-19-related health disparities research. This method uses group interviews to capture direct and indirect outcomes, that is, ripples, of community-based programmes. Short-, medium- and long-term changes and conditions related to community-academic partnerships in the statewide network were mapped onto the spheres of influence of the social ecological model.

RESULTS: A total of 24 participants took part in one of three REM sessions. Community and academic partners were represented in all sessions, and most had been involved in community-engaged research for 3 to 10+ years. Most identified as female, Hispanic/Latino, and between the ages of 40 and 49. Qualitative analysis of sessions indicated that most changes occurred at the individual and interpersonal levels and involved medium-term changes (e.g., increased capacity to partner in research and shared understanding). Neighbourhood- or community-level changes included identification of culturally and linguistically responsive intervention and dissemination efforts (e.g., promotora model). Policy and built environment conditions reveal the inequities in higher education and the need for structural-level changes to university infrastructure and grant administration.

CONCLUSION: Most outcomes were observed at the individual and interpersonal (group) levels and involved primarily medium-term changes. However, the network itself served as a platform to discuss the need for structural-level changes within university infrastructure to facilitate community-engaged scholarship. Such networks have the potential to facilitate capacity building for community-academic partnerships to collaborate in health disparities research that can generate evidence to move forward public health policy change.

Community partners, including grassroots leaders and staff of community-based organisations, were involved in the development of the research questions, the design of the study, and data collection, analysis and interpretation of the findings. Community partners also contributed to manuscript development.},
}

Humans
*COVID-19/epidemiology/ethnology
*Health Status Disparities
California/epidemiology
Community-Based Participatory Research
*Community-Institutional Relations
Universities/organization & administration
*Community Networks/organization & administration
SARS-CoV-2
Female

@article {pmid41016700,
year = {2025},
author = {Albertina, EA and Torres, L and Sauber, G and Hillard, CJ and Fitzgerald, JM and deRoon-Cassini, TA and Larson, CL},
title = {Endocannabinoids Mediate Racial/Ethnic Discrimination Prediction of Post-Traumatic Stress Disorder Symptoms Moderated by Resting-State Functional Connectivity in Black and African American Individuals.},
journal = {Biological psychiatry. Cognitive neuroscience and neuroimaging},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpsc.2025.09.016},
pmid = {41016700},
issn = {2451-9030},
abstract = {BACKGROUND: Individuals from marginalized ethnoracial groups face higher risk for posttraumatic stress disorder (PTSD) symptoms, exacerbated by experiencing racial/ethnic discrimination. Prior work separately explored the endocannabinoid (eCB) system and functional connectivity response to stress/trauma, and suggests that experiences of chronic minority stress, such as racial discrimination, contribute to eCB tone and resting state functional connectivity. We explored how circulating eCB tone, in conjunction with resting-state connectivity, contributes to increased risk for PTSD symptoms following trauma among individuals experiencing discrimination.

METHODS: Black/African Americans (n=74, Mage=33.81) were recruited from a Level 1 trauma center. Correlational and linear models explored whether experiences of racial/ethnic discrimination (PEDQ), eCB (AEA, 2-AG) concentrations, default mode network (DMN), or salience network (SN) functional connectivity were associated with PTSD symptoms (PCL-5). We then explored moderated mediation models where discrimination predicted PTSD symptoms with eCB concentration as a mediator and functional connectivity as a moderator.

RESULTS: Discrimination was correlated with PTSD symptoms (r=0.50), serum AEA concentration (r=0.43), and DMN connectivity (r=0.23). When including urine THC, lifetime trauma, age, and sex as covariates, AEA concentration was associated with PTSD symptoms (r=0.30) and DMN connectivity (r=0.24). AEA mediated the relationship between discrimination and PTSD symptoms, and SN connectivity moderated this mediation (B=52.46).

CONCLUSIONS: Our findings highlight how racial/ethnic discrimination impacts neurobiological systems that may lead to increased vulnerability for PTSD symptoms following an injury. Future work should continue to explore biological factors associated with the social-ecological model of health as mechanisms of risk for adverse outcomes following trauma.},
}

@article {pmid41013991,
year = {2025},
author = {Formanack, A and Ogle, K and Peltier, D},
title = {Flashy, decoupled, or declining? Single theories fail to explain the diversity of drought mortality signals in tree rings.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70605},
pmid = {41013991},
issn = {1469-8137},
abstract = {Growth patterns recorded in tree rings may predict drought 'winners' and 'losers'. Past studies of drought-killed trees have produced conflicting evidence. Some show killed trees were highly responsive to climate, while others suggest killed trees were climate-insensitive or became less sensitive over time. We leveraged ring width data from 2934 drought-killed and -surviving trees of seven species to compute growth sensitivity to seasonal climate variables via a Bayesian mixed effects model. Aided by clustering analyses, we evaluated how species conformed to three alternative hypotheses (theories): relative to surviving trees, killed trees (H1) have 'flashy' climate responses, (H2) are 'decoupled' from climate, or (H3) have 'declining' sensitivity over time. Differences in growth patterns were not consistent across species or status (surviving/killed). Drought-killed subalpine fir and Engelmann spruce exhibited 'flashy' growth - higher sensitivity of growth to climate over time - compared with survivors. Drought-killed aspen, Scots pine, and Norway spruce showed stable, climate-insensitive growth compared with survivors, suggesting 'decoupling' from climate. Most species showed nonstationary sensitivities, but rather than declining, some sensitivities increased, even in surviving trees. Our flashy-decoupled-declining framework links predictions for future drought-induced mortality to potential mechanisms, enhancing ecological and physiological understanding of growth-climate patterns preceding drought mortality events.},
}

@article {pmid41013625,
year = {2025},
author = {Li, M and Yang, H},
title = {Exploring spatial-temporal heterogeneity in new-type urbanization's impact on health expenditure: a GTWR analysis.},
journal = {International journal of health geographics},
volume = {24},
number = {1},
pages = {26},
pmid = {41013625},
issn = {1476-072X},
mesh = {Humans ; *Urbanization/trends ; *Health Expenditures/trends/statistics & numerical data ; China/epidemiology ; *Spatio-Temporal Analysis ; *Geographic Information Systems/trends ; },
abstract = {BACKGROUND: To address challenges arising from rapid urban development, China has formulated and implemented the New-Type Urbanization strategy. However, empirical research on the specific impacts between New-Type Urbanization and health expenditures remains limited.

METHODS: Using panel data from 31 Chinese provinces (2012-2019), this study constructed a comprehensive evaluation index system for New-Type Urbanization across four dimensions: demographic, economic, social, and ecological. Geographically and Temporally Weighted Regression was employed to examine the spatial effects, influencing factors, and spatial heterogeneity of New-Type Urbanization's impact on health expenditures.

RESULTS: The results show that China's health expenditures primarily exhibit High-High and Low-Low clustering patterns with spatial fluctuations. Meanwhile, the impact of New-Type Urbanization on health expenditures demonstrates spatiotemporal heterogeneity and non-stationarity. As urbanization levels increase, the negative effects of health expenditure clustering expand, while the influence of economic urbanization weaken.

CONCLUSIONS: Our findings fill the research gap regarding the impacts between New-Type Urbanization and health expenditures, while also providing direction for New-Type Urbanization development to support the implementation of health policies aimed at controlling health expenditure growth.},
}

Humans
*Urbanization/trends
*Health Expenditures/trends/statistics & numerical data
China/epidemiology
*Spatio-Temporal Analysis
*Geographic Information Systems/trends

@article {pmid41011672,
year = {2025},
author = {Song, C and Yan, M and Lin, S and Li, J and Zou, H and Hu, Z and Yan, X},
title = {Dual-Ionization SPME-GC-HRMS Metabolomic Profiling of Broccoli Volatiles for the Construction of a Broccoli Metabolic Database.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {18},
pages = {},
doi = {10.3390/molecules30183781},
pmid = {41011672},
issn = {1420-3049},
support = {2022YFE0108300//National Key R&D Program of China/ ; N20220013//the Basic Agricultural Research Project of Wenzhou/ ; },
mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; *Brassica/metabolism/chemistry ; Gas Chromatography-Mass Spectrometry/methods ; *Metabolomics/methods ; Solid Phase Microextraction/methods ; *Metabolome ; Principal Component Analysis ; Databases, Factual ; },
abstract = {Volatile organic compounds (VOCs) play critical roles in broccoli's sensory attributes, defense mechanisms, and ecological interactions, yet comprehensive profiling of its volatilome remains limited. This study aimed to construct a robust and inclusive volatile metabolite database for broccoli using advanced analytical techniques. A pooled sample comprising florets from 191 cultivars was prepared to capture broad chemical diversity and analyzed using solid-phase microextraction-gas chromatography-high-resolution mass spectrometry (SPME-GC-HRMS) under dual ionization modes: electron ionization (EI) and chemical ionization (CI). A total of 206 VOCs spanning nine chemical classes were detected, with 37 compounds further confirmed through synchronized CI analysis. To validate the database, broccoli florets from seven distinct cultivars were analyzed using the same workflow. Of the 206 compounds, 187 (90.78%) were detected in at least one cultivar, while 38 were consistently found across all samples, indicating a conserved core volatilome. Principal component analysis revealed distinct VOC profiles among cultivars, and freeze-dried samples were found suitable for reproducible large-scale analysis. This study demonstrates that a pooled-sample strategy coupled with dual-ionization GC-HRMS provides comprehensive and reliable VOC coverage. The resulting database offers a valuable resource for metabolomics studies in Brassica, with applications in cultivar differentiation, flavor research, and environmental response profiling.},
}

*Volatile Organic Compounds/analysis/metabolism/chemistry
*Brassica/metabolism/chemistry
Gas Chromatography-Mass Spectrometry/methods
*Metabolomics/methods
Solid Phase Microextraction/methods
*Metabolome
Principal Component Analysis
Databases, Factual

@article {pmid41009797,
year = {2025},
author = {Cheng, L and Shi, N and Du, X and Huang, T and Zhang, Y and Zhao, C and Zhao, K and Lin, Z and Ma, D and Li, Q and Wang, F and Yao, H and Shen, H},
title = {Bioinformatics Analysis and Expression Profiling Under Abiotic Stress of the DREB Gene Family in Glycyrrhiza uralensis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
doi = {10.3390/ijms26189235},
pmid = {41009797},
issn = {1422-0067},
support = {KY2025JBGS03//the Science and Technology Plan Project of the Third Division/ ; 32260083//the National Natural Science Foundation of China/ ; 2023AB052 and 2023CB008-17//a Science and Technology Project of Bingtuan/ ; RCZK202595//Scientific Research Startup Project for High-Level Talents, Shihezi University/ ; },
mesh = {*Gene Expression Regulation, Plant ; *Glycyrrhiza uralensis/genetics/metabolism ; *Stress, Physiological/genetics ; *Plant Proteins/genetics/metabolism ; *Computational Biology/methods ; Phylogeny ; *Transcription Factors/genetics/metabolism ; Gene Expression Profiling ; Droughts ; *Multigene Family ; Promoter Regions, Genetic ; Transcriptome ; },
abstract = {Glycyrrhiza uralensis is an important medicinal plant exhibiting strong tolerance to abiotic stresses, including drought and salinity. DREB (Dehydration-Responsive Element-Binding) transcription factors, key members of the AP2/ERF family, play crucial roles in plant growth, development, and stress responses. Based on transcriptome data, we identified 18 DREB transcription factors in G. uralensis, designated GuDREB1 to GuDREB18. Bioinformatics analysis revealed genomic sequences ranging from 534 to 2864 bp and coding sequence (CDS) lengths between 525 and 1509 bp. All GuDREB proteins contain a single AP2 domain, including the conserved YRG and RAYD elements, and were predicted to localize to the nucleus. Phylogenetic analysis clustered the G. uralensis DREBs with 61 Arabidopsis thaliana DREBs into five subgroups, indicating evolutionary conservation. Promoter analysis detected seventeen stress-responsive cis-acting elements, encompassing hormone-responsive and abiotic stress-responsive motifs, suggesting diverse biological functions. Tissue-specific expression profiling revealed GuDREB transcription in both aerial and underground parts. Drought stress induced varying degrees of GuDREB expression, confirming their involvement in stress responses. Notably, GuDREB10 expression increased significantly in underground parts, while GuDREB15 showed pronounced upregulation in aerial parts under drought; the GuDREB15 promoter contained the highest number of light-responsive elements (23), potentially explaining its aerial tissue specificity. Drought stress significantly increased abscisic acid (ABA) content. Underground parts exhibited higher initial sensitivity to drought, whereas aerial parts displayed a more sustained response; ABA levels overall showed an initial increase followed by a decline. This study expands the G. uralensis DREB gene database, provides a foundation for selecting stress-resistance genes, and offers insights into DREB functional roles in abiotic stress responses in this key medicinal species.},
}

*Gene Expression Regulation, Plant
*Glycyrrhiza uralensis/genetics/metabolism
*Stress, Physiological/genetics
*Plant Proteins/genetics/metabolism
*Computational Biology/methods
Phylogeny
*Transcription Factors/genetics/metabolism
Gene Expression Profiling
Droughts
*Multigene Family
Promoter Regions, Genetic
Transcriptome

@article {pmid41007943,
year = {2025},
author = {Zhu, Y and Zhao, Y and He, Y and Wu, B and Su, X},
title = {YOLO-WildASM: An Object Detection Algorithm for Protected Wildlife.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/ani15182699},
pmid = {41007943},
issn = {2076-2615},
support = {QNTD202308//Outstanding Youth Team Project of Central Universities/ ; 2023YFD2201700//National Key R&D Program of China/ ; },
abstract = {Wild animals are an essential component of natural ecosystems, and the accurate identification of wildlife targets plays a critical role in ecological conservation and species monitoring. However, the effectiveness of conventional object detection algorithms is often limited by the challenges posed by complex outdoor environments, small target sizes, and group occlusions. To address these issues, this study constructs a dataset comprising over 8000 images of 10 protected wildlife species and investigates effective detection methods for wildlife in natural habitats. We propose a novel deep learning-based detection framework, YOLO-WildASM, which incorporates three key improvements to the YOLOv8 architecture: a P2 detection layer for small objects, a multi-head self-attention (MHSA) mechanism, and a bidirectional feature pyramid network (BiFPN). Experimental results demonstrate that YOLO-WildASM significantly outperforms YOLOv8 and other state-of-the-art models on the custom wildlife dataset, achieving a mAP50 of 94.1%, which is 2.8% higher than the baseline model and superior to the latest YOLOv12 model (92.2%). Furthermore, ablation and generalization experiments validate the model's enhanced performance and adaptability in multi-scale wildlife detection tasks. The proposed deep learning-based detection framework provides an efficient and robust solution for wildlife monitoring and ecological conservation in complex natural ecosystems.},
}

@article {pmid41006295,
year = {2025},
author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J},
title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1568},
pmid = {41006295},
issn = {2052-4463},
support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; },
abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.},
}

*Soil Microbiology
*Phospholipids
*Fatty Acids
*Databases, Factual
*Enzymes
Soil/chemistry
Ecosystem

@article {pmid41004955,
year = {2025},
author = {Qin, J and Wang, Q and Li, W},
title = {Incorporating regional green spaces into greenspace exposure assessment: A nationwide study of 244 Chinese cities.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127369},
doi = {10.1016/j.jenvman.2025.127369},
pmid = {41004955},
issn = {1095-8630},
abstract = {Green spaces are essential components of urban ecosystems, offering ecological services that support environmental sustainability and enhance human well-being. However, rapid urbanization has caused substantial declines in green space, particularly in rapidly growing cities. In this context, regional green spaces (RGSs), which are defined as green areas located beyond the boundaries of built-up areas, have gained attention for their ecological value and strategic role in enhancing urban resilience. Despite their importance, RGSs remain underrepresented in current greenspace exposure assessment frameworks. To fill this gap, we propose a novel transportation-weighted global greenspace exposure model that integrates RGSs, urban green spaces, and transportation proximity. Using greenspace exposure (GE) as an indicator, the model assesses the spatial distribution and exposure contribution of RGSs. We applied this model to 244 Chinese cities and obtained the following findings: (1) Incorporating RGSs significantly improves GE levels in many cities, particularly in southern and western regions, while also amplifying spatial disparities; (2) The compensatory effect of RGSs was validated, as substantial GE increases were observed under larger RGSs buffer zones; (3) Nighttime light intensity, elevation, and land surface temperature correlate strongly with GE, indicating the influence of both anthropogenic and natural factors. The proposed framework enhances the accuracy of GE assessments by integrating RGSs and transportation networks. Its scalable structure and moderate data requirements enable its application across diverse regions, supporting international efforts toward sustainable urban development.},
}

@article {pmid41003170,
year = {2025},
author = {Francesconi, L and Conti, M and Martellos, S and Di Nuzzo, L and Gheza, G and Nimis, PL and Pistocchi, C and Nascimbene, J},
title = {Dolichens: An Information System on the Lichens of the Dolomites.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/jof11090624},
pmid = {41003170},
issn = {2309-608X},
support = {DOT199RYN9-2//Ministero dell'università e della ricerca/ ; },
abstract = {Lichens, despite their key role as environmental indicators and their ecological importance, remain underrepresented in conservation policies, largely due to fragmented exploration of several areas, as well as limited availability of data in digital platforms. The UNESCO World Heritage area of the Dolomites (N Italy) is well-investigated as far as lichen diversity is concerned, with a long history of lichenological exploration since the 19th century. However, the relevant amount of data produced by these efforts was scattered and often not accessible in digital format, thus hindering data accessibility and usability. In this paper, we present Dolichens, a novel web platform designed to aggregate data about lichen diversity in the Dolomites. The platform aims at making available a comprehensive resource to support research, monitoring, and conservation of lichen diversity in the Dolomites, while ensuring data interoperability with the most relevant global repositories.},
}

@article {pmid41001881,
year = {2025},
author = {Rutz, A and Probst, D and Aguilar, C and Akiyama, DY and Alberti, F and Augustijn, HE and Avalon, NE and Beemelmanns, C and Barbieri, HB and Biermann, F and Bridge, AJ and Girón, EC and Cox, R and Crüsemann, M and D'Agostino, PM and Feuermann, M and Gerke, J and García, KG and Holme, JE and Hwang, JY and Iacovelli, R and Jeronimo Barbosa, JC and Kaur, N and Klapper, M and Köhler, AM and Korenskaia, A and Kubach, N and Lee, BT and Loureiro, C and Mantri, S and Narula, S and Meijer, D and Navarro-Muñoz, JC and Nguyen, GS and Paliyal, S and Panghal, M and Rao, L and Sieber, S and Sokolova, N and Sowa, ST and Szenei, J and Terlouw, BR and Weddeling, HG and Yu, J and Ziemert, N and Weber, T and Blin, K and van der Hooft, JJJ and Medema, MH and Zdouc, MM},
title = {MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf969},
pmid = {41001881},
issn = {1362-4962},
support = {21/07038-0//São Paulo Research Foundation/ ; 2021/08947-3//São Paulo Research Foundation/ ; 2023/06874-4//São Paulo Research Foundation/ ; MR/V022334/1//UKRI/ ; /AT/NCCIH NIH HHS/United States ; F32AT011475/GF/NIH HHS/United States ; 802736, MORPHEUS//Horizon 2020/ ; 101 000 392//Horizon 2020/ ; 101 081 957//Horizon 2020/ ; 862 923//Horizon 2020/ ; 101 000 392//Horizon 2020/ ; 101 081 957//Horizon 2020/ ; 862 923//Horizon 2020/ ; //German Research Foundation/ ; 239748522//Deutsche Forschungsgemeinschaft/ ; 495740318//German Research Foundation/ ; //Hans-Fischer-Gesellschaft/ ; //State Secretariat for Education, Research and Innovation/ ; 102 022 750//SINTEF/ ; 102 029 187//SINTEF/ ; 102024676-14//SINTEF/ ; 102 029 407//SINTEF/ ; NNF23OC0086472//Novo Nordisk Foundation/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Department of Biotechnology/ ; //the Werner Siemens Foundation/ ; //DFG/ ; 101 072 485//Horizon Europe Marie Skłodowska-Curie/ ; //National Agri-Food and Biomanufacturing Institute (NABI)/ ; 948770-DECIPHER/ERC_/European Research Council/International ; 102 022 750//SINTEF/ ; 102 029 187//SINTEF/ ; 102024676-14//SINTEF/ ; 102 029 407//SINTEF/ ; //University Grants Commission/ ; //Horizon Europe programme/ ; 101 072 485//Marie Skłodowska-Curie/ ; 101 072 485//Marie Skłodowska-Curie/ ; 101 072 485//Marie Skłodowska-Curie/ ; 101 072 485//Marie Skłodowska-Curie/ ; //German Center for Infection Research/ ; //Danish National Research Foundation/ ; //Horizon Europe programme/ ; //NWO/ ; //Horizon Europe programme/ ; KICH1.LWV04.21.013//Netherlands Organisation for Scientific Research/ ; },
abstract = {Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core 'scaffold', which is subsequently modified by tailoring enzymes to define the molecule's final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, for in silico biosynthesis, or to train machine-learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.},
}

@article {pmid40840863,
year = {2025},
author = {Zong, Z and Sun, X and Chen, J and Yu, Y and Ni, Z and Wang, Y},
title = {Identification of the full-length GbERD7 gene family in Gossypium barbadense and functional analysis of the role of the GbERD7g gene in drought and salt tolerance.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {360},
number = {},
pages = {112715},
doi = {10.1016/j.plantsci.2025.112715},
pmid = {40840863},
issn = {1873-2259},
mesh = {*Gossypium/genetics/physiology ; Plant Proteins/genetics ; *Salt Tolerance/genetics/physiology ; Droughts ; Dehydration/genetics/metabolism ; *Stress, Physiological/genetics/physiology ; Computational Biology ; Genes, Plant ; *Acclimatization/genetics/physiology ; Sodium Chloride ; Polyethylene Glycols ; Hot Temperature ; Malondialdehyde/metabolism ; },
abstract = {ERD (early response to dehydration) genes are promptly upregulated under dehydration stress and are pivotal in plant development. Nonetheless, the precise impact of the ERD7 gene on the response of cotton to abiotic stress remains unclear. The physical and chemical characteristics, gene architecture, gene collinearity, and transcriptomic profiles were examined. Using bioinformatics techniques, we investigated the evolutionary relationships among the genes within the GbERD7 gene family of sea island cotton. The GbERD7 genes are unevenly distributed across the seven chromosomes of sea island cotton, with multiple gene duplications. The GbERD7 gene family was subjected to phylogenetic analysis, leading to the classification of its members into the SENA and SENB subfamilies. The expression of the GbERD7 genes was investigated in relation to heat, low-temperature, salt (NaCl), and polyethylene glycol (PEG) treatments. Some genes presented greater expression in specific organs and different periods of fiber development. The functional role of GbERD7g was subsequently investigated using molecular biological techniques. GbERD7g exhibited pronounced expression in sea island cotton leaves and was upregulated following exposure to PEG, NaCl, and ABA. Subcellular localization studies revealed that the GbERD7g protein is located within the nucleus as well as the plasma membrane of the cell. When the GbERD7g gene was silenced under drought and salt stress, the sea island cotton plants were significantly less resistant to drought and salinity and exhibited lower survival than the control plants. The proline levels, catalase activity, and superoxide dismutase activity were reduced, and the malondialdehyde and hydrogen peroxide levels were elevated. In addition, compared with those in the control plants, the expression of all three stress-responsive genes, namely, GbRD22, GbRD26, and GbCDPK1, was significantly lower in the mutant plants.},
}

*Gossypium/genetics/physiology
Plant Proteins/genetics
*Salt Tolerance/genetics/physiology
Droughts
Dehydration/genetics/metabolism
*Stress, Physiological/genetics/physiology
Computational Biology
Genes, Plant
*Acclimatization/genetics/physiology
Sodium Chloride
Polyethylene Glycols
Hot Temperature
Malondialdehyde/metabolism

@article {pmid41000208,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brown House-moth, Hofmannophila pseudospretella (Stainton, 1849).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {230},
pmid = {41000208},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hofmannophila pseudospretella (the Brown House-moth; Arthropoda; Insecta; Lepidoptera; Oecophoridae). The genome sequence is 406.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.},
}

@article {pmid40998880,
year = {2025},
author = {Le Scornec, E and Chimienti, M and Corbeau, A and Pajot, A and Weimerskirch, H and Collet, J},
title = {Predicting fisheries from albatross movements requires accounting for individual variability in interaction.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32807},
pmid = {40998880},
issn = {2045-2322},
mesh = {Animals ; *Fisheries ; *Birds/physiology ; Geographic Information Systems ; *Animal Migration ; },
abstract = {Fisheries have major ecological impacts including bycatch of foraging seabirds, but it is often difficult to obtain comprehensive information on the presence of fishing vessels. Automatic Identification System (AIS) data can be used to monitor fisheries and their interactions with GPS-tracked seabirds, but not all vessels have their AIS operational. Bird-tied radar detectors can overcome this limit and complement monitoring, but the technology is recent and costly. We used both methods combined as a training dataset for classification algorithms, to extend the identification of interactions to GPS tracks without radar detectors nor AIS. We studied over 3 years wandering albatrosses from the French Southern Territories, interacting with toothfish and tuna longliners. We used 196 GPS tracks combined with radar detectors, to calculate different movement variables over various scales (time spent in an area, sinuosity, speed) and used a Random Forest to distinguish behaviour in presence or absence of fishing vessels. Our model reached high classification accuracy (ca. 85%) for individual birds included in the training dataset. However, we lost predictive power (around 72% of accuracy, with a drop of specificity from 76 to 59%) when predicting on individuals not included in the training dataset. Our results emphasize the importance of documenting and accounting for individual variations to use animals as sentinels. We discuss the pros and cons of different research avenues (data sampling, classification model, bird species, etc.) to eventually get to predict fisheries from bird movements only.},
}

Animals
*Fisheries
*Birds/physiology
Geographic Information Systems
*Animal Migration

@article {pmid40997692,
year = {2025},
author = {Zang, H and Feng, Y and Yang, F and Gao, S and Su, M and Li, H},
title = {Multi-media distribution, partitioning behavior, and environmental risk of per- and polyfluoroalkyl substances (PFASs) in the southern coastal zone of Shandong Peninsula, China.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107562},
doi = {10.1016/j.marenvres.2025.107562},
pmid = {40997692},
issn = {1879-0291},
abstract = {Per- and polyfluoroalkyl substances (PFASs) pose significant ecological threats due to their persistence and toxicity. This study investigates the occurrence, partitioning behavior, and environmental risks of 33 legacy and emerging PFASs in the southern coastal zone of Shandong Peninsula, China. Paired water and sediment samples were collected from 55 sites across groundwater, river, estuarine, tourist beaches and marine ranches. PFASs were ubiquitously detected, with total concentrations (∑PFASs) ranging from 23.41 to 80.62 ng/L in water and 0.38-6.49 ng/g dry weight (dw) in sediment. Except perfluorooctanoic acid (PFOA), perfluorobutanoic acid (PFBA) (6.42 ± 2.26 ng/L) and perfluorobutanesulfonic acid (PFBS) (3.03 ± 1.44 ng/L) dominated aqueous phases, reflecting phased-out replacements of long-chain homologs. Sediments accumulated long-chain compounds (e.g., Perfluorohexanoic acid (PFHxA): 0.92 ± 1.08 ng/g dw; perfluorooctane sulfonic acid (PFOS): 0.45 ± 0.28 ng/g dw), driven by hydrophobic partitioning. Strong positive correlations among long-chain PFASs (e.g., Perfluorododecanoic acid (PFDoDA)- perfluorotetradecanoic acid (PFTeDA), r = 0.882) indicated co-accumulation in organic-rich sediments. Spatial analysis revealed land-to-sea concentration gradients, with maxima in estuaries (52.72 ng/L) and industrial-adjacent sediments (6.48 ng/g dw). Groundwater infiltration (up to 51.53 ng/L) highlighted subsurface transport risks. Sediment-water partition coefficients (log Kd) increased with carbon chain length and salinity, consistent with salting-out effects and reduced electrostatic repulsion. Organic carbon-normalized log Koc values (Kow method) aligned with model predictions for most PFASs. Risk assessment identified high ecological risk for sediment-bound PFOS (RQ > 1) near river discharges, while PFOA posed greater aqueous-phase risks. Emerging PFASs (e.g., 6:2 chlorinated polyfluoroalkyl ether sulfonic acid (6:2 Cl-PFESA)) showed negligible risks. Coastal sediments act as significant PFASs reservoirs, with resuspension potential enabling secondary pollution.},
}

@article {pmid40996892,
year = {2025},
author = {Njoroge, SM and Kulohoma, BW and Falzon, LC and Kamanu, TK and Momanyi, K and Muinde, P and Murungi, MK and Ogendo, A and Ogola, J and Wambua, L and Kangethe, E and Rushton, J and Woolhouse, M and Thomson, NR and Kariuki, S and von Mentzer, A and Fèvre, EM},
title = {Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001515},
pmid = {40996892},
issn = {2057-5858},
mesh = {*Enterotoxigenic Escherichia coli/genetics/isolation & purification/pathogenicity ; Kenya/epidemiology ; Animals ; *Livestock/microbiology ; *Escherichia coli Infections/microbiology/veterinary ; *Enterotoxins/genetics ; *Escherichia coli Proteins/genetics ; *Adhesins, Bacterial/genetics ; *Bacterial Toxins/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; Humans ; Feces/microbiology ; Cattle ; *Adhesins, Escherichia coli/genetics ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhoea in livestock and humans. The epidemiology of ETEC in animals remains understudied, prompting an investigation into the virulence factors and associated adhesins of ETEC in livestock from Western Kenya. Also, there is limited evidence supporting the role of livestock as possible zoonotic reservoirs for ETEC. ETEC strains harbour colonization factors/adhesins and enterotoxins, with animal ETECs exhibiting various adhesins (F4, F5, F6, F17, F18 and F41). Enterotoxins include heat-labile (LT) and heat-stable (ST) toxins and are further divided into LT-I and LT-II and STa and STb, respectively. Additional toxin combinations occur, with ETEC and Shiga toxin-producing E. coli (STEC) hybrids garnering public health significance. Here, we analysed faecal and mesenteric lymph node samples from diverse livestock across three Western Kenyan counties (Busia, Bungoma and Kakamega), using whole-genome sequencing. In silico screening determined the presence of AB5 and A2B5-like toxin genes, including cytolethal distending toxin (cdtABC) along with associated adhesins. To broaden the screening panel, adhesin genes identified were further characterized to identify both known and novel alleles, particularly focusing on human-ETEC colonization factors. Two estA alleles (estA-4-06, estA-6-02) and six eltAB-II toxin alleles (eltAB-II-a2-01, eltAB-II-a3-01, eltAB-II-c1-02, eltAB-II-c6-03, eltAB-II-c6-04 and eltAB-II-c7-02) were identified in livestock. Hybrid ETECs identified were ETEC/STEC present in 6.7% (4/60) of ETEC strains and ETEC with cdtABC type I. An A2B5-like tripartite toxin, potentially resembling the typhoid toxin, was detected in 8.7% (4/46) of the eltAB-II-positive strains. It may have unique effects on enterocytes distinct from known toxins. These findings expand our understanding of ETEC pathogenicity and genetic diversity in animal reservoirs, while also highlighting potential zoonotic risks. They broaden the toxin repertoire, offer adhesin-based vaccine candidates for livestock and provide valuable insights for future vaccine development and public health strategies in the Lake Victoria Crescent ecosystem and beyond.},
}

*Enterotoxigenic Escherichia coli/genetics/isolation & purification/pathogenicity
Kenya/epidemiology
Animals
*Livestock/microbiology
*Escherichia coli Infections/microbiology/veterinary
*Enterotoxins/genetics
*Escherichia coli Proteins/genetics
*Adhesins, Bacterial/genetics
*Bacterial Toxins/genetics
Virulence Factors/genetics
Whole Genome Sequencing
Humans
Feces/microbiology
Cattle
*Adhesins, Escherichia coli/genetics

@article {pmid40996715,
year = {2025},
author = {Fruggiero, I and Maisto, A and Passaro, S and Gentile, D and Nunziata, A and D'Agostino, N},
title = {A new database of chestnut DNA fingerprints for genetic diversity assessment, precise varietal identification, and traceability.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baaf056},
pmid = {40996715},
issn = {1758-0463},
support = {//Italy-Rural Development Programme/ ; //Italian Ministry of Agriculture/ ; },
mesh = {*Fagaceae/genetics ; *Genetic Variation ; Polymorphism, Single Nucleotide ; *DNA Fingerprinting ; *Databases, Genetic ; *DNA, Plant/genetics ; },
abstract = {The European chestnut (Castanea sativa Mill., Fagaceae) is ecologically and economically important, particularly in countries like Italy, Greece, Spain, and Turkey, where it supports rural economies and ecosystems. Accurate varietal recognition is crucial for managing chestnut groves but is hindered by the limitations of traditional methods, which require costly expertise and struggle to identify young, dormant, or scion trees. Recent advances in molecular tools, particularly single nucleotide polymorphism (SNP) markers identified through Kompetitive Allele-Specific PCR (KASP) technology, have transformed cultivar identification. To harness this potential, we developed KASTRACKdb, a genetic fingerprinting database for European chestnut that now integrates genotypic and phenotypic data for 150 chestnut accessions. Designed to translate KASP analysis results into practical and actionable insights, KASTRACKdb serves as a powerful tool for cultivar identification and management. The database offers three primary query modes and is designed for continuous upgrades, serving a crucial role in cataloguing the genetic diversity of chestnut trees, characterized by broad geographic distributions and significant genetic variation. This diversity is critical for conservation and breeding programs, enabling precise varietal identification and traceability to protect intellectual property, verify authenticity, and support the commercialization of high-value cultivars. Database URL: KASTRACKdb is available online at https://kastrack.crea.gov.it/kastrackdb/?lang=en.},
}

*Fagaceae/genetics
*Genetic Variation
Polymorphism, Single Nucleotide
*DNA Fingerprinting
*Databases, Genetic
*DNA, Plant/genetics

@article {pmid40996703,
year = {2025},
author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE},
title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baaf060},
pmid = {40996703},
issn = {1758-0463},
support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; },
mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; },
abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.},
}

*Microbiota/genetics
Humans
*Databases, Genetic
Data Curation
Metadata
Animals
Metagenomics

@article {pmid40995615,
year = {2025},
author = {Kuhara, S and Matsugaki, R and Itoh, H and Oginosawa, Y and Fushimi, K and Matsuda, S and Saeki, S},
title = {Factors Influencing the Availability of Cardiopulmonary Exercise Testing for Patients Undergoing Cardiac Resynchronization Therapy in Japan.},
journal = {Journal of arrhythmia},
volume = {41},
number = {5},
pages = {e70198},
pmid = {40995615},
issn = {1880-4276},
abstract = {BACKGROUND: This study aimed to investigate the implementation rate of cardiopulmonary exercise testing (CPET) in patients undergoing cardiac resynchronization therapy (CRT) or cardiac resynchronization therapy-defibrillator (CRT-D), as well as the associated factors, using real-world data.

METHODS AND RESULTS: Data from the Diagnostic Procedure Combination System in Japan (2014-2018) was analyzed. The participants were cardiac patients who underwent CRT or CRT-D device implantation (n = 3859). The primary outcome was whether CPET was performed after device implantation. Unpaired t-tests and chi-squared tests were used to compare the characteristics of the CPET (+) and CPET (-) groups. Multivariate analysis was used to identify factors associated with CPET performance. CPET was performed in 134 patients (3%). The CPET (-) group was older and had lower Barthel Index (BI) scores at discharge. CPET (+) patients had a higher rate of cardiac rehabilitation. Multivariate analysis revealed that age < 70 years and BI score ≥ 85 at discharge were associated with CPET implementation. In-hospital cardiac rehabilitation is also an important determinant.

CONCLUSIONS: The CPET implementation after CRT or CRT-D was low. Emphasizing the importance of CPET may improve these rates. Future studies should explore strategies to increase its use in this patient population.},
}

@article {pmid40947031,
year = {2025},
author = {Onyeka, OC and Cheng, JS and Sanei, S and Clark, SL and Pinciotti, CM and Guzick, AG and Storch, EA and Stewart, S and Sandoval, JF and Taylor, L and Riddle, D and Garza, C and Liberzon, I and Rousseau, J and Shahidullah, JD and Newport, DJ and Wagner, KD and Nemeroff, C},
title = {Exploring resource profiles among trauma exposed youth: An identity-focused, cultural, and person-centered approach.},
journal = {Journal of affective disorders},
volume = {393},
number = {Pt A},
pages = {120298},
doi = {10.1016/j.jad.2025.120298},
pmid = {40947031},
issn = {1573-2517},
abstract = {OBJECTIVE: Resilience is a multi-faceted construct comprised of both internal and external resources that support adaptive functioning following trauma exposure. The role of resilience in ameliorating internalizing symptoms may depend on its typology as opposed to its presence alone, suggesting the existence of distinct subpopulations with heterogeneous resource profiles. The current study employs Latent Profile Analysis (LPA) to identify and characterize profiles of resilience-related resources among youth exposed to trauma from an identity-focused, cultural lens.

METHOD: Patterns of resources were examined in 1,538 youth (Mage = 13.4, 51.9% female) from a large longitudinal registry of trauma exposed youth in Texas using LPA. Profiles were related to demographic variables and internalizing symptoms (post-traumatic stress symptoms [PTSS], depression, and anxiety) using multinomial regression.

RESULTS: Results demonstrated an optimal four-class solution (Low Social Support and Average ERI, 31.2 %; Average Level of Protective Factors, 27.4 %; Ethnic Identity Diffusion, 18.1 %; Social Support Dominant, 23.2 %). Depressive symptoms significantly differentiated between classes in the four-class model as well as youth race, age, and ethnicity. Anxiety symptoms and PTSS did not differentiate the classes as clearly.

CONCLUSION: Person-centered analyses such as LPA underscore the value of examining resilience as a multi-faceted and heterogenous pattern of resources shaped by socio-ecological and cultural contexts among trauma-exposed youth. Implications for clinical intervention are discussed.},
}

@article {pmid40824055,
year = {2025},
author = {Grigson, SR and Bouras, G and Dutilh, BE and Olson, RD and Edwards, RA},
title = {Computational function prediction of bacteria and phage proteins.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {3},
pages = {e0002225},
pmid = {40824055},
issn = {1098-5557},
support = {865694/ERC_/European Research Council/International ; 390713860//Deutsche Forschungsgemeinschaft/ ; RC2DK116713/DK/NIDDK NIH HHS/United States ; DP250103825//Australian Research Council/ ; DP220102915//Australian Research Council/ ; FL250100019//Australian Research Council/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Computational Biology/methods ; *Viral Proteins/genetics/metabolism/chemistry ; *Bacteria/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; Machine Learning ; Molecular Sequence Annotation/methods ; },
abstract = {SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial and ~65% of all bacteriophage (phage) protein sequences cannot be confidently annotated. In this review, we examine state-of-the-art bioinformatics tools and methodologies for annotating bacterial and phage proteins, particularly those of unknown or poorly characterized function. We describe the process of identifying protein-coding regions and the systems to classify protein functionalities. Additionally, we explore a range of protein annotation methods, from traditional homology-based methods to cutting-edge machine learning models. In doing so, we provide a toolbox for confidently annotating previously unknown bacterial and phage proteins, advancing the discovery of novel functions and our understanding of microbial systems.},
}

*Bacteriophages/genetics/metabolism
*Computational Biology/methods
*Viral Proteins/genetics/metabolism/chemistry
*Bacteria/genetics/metabolism
*Bacterial Proteins/genetics/metabolism/chemistry
Machine Learning
Molecular Sequence Annotation/methods

@article {pmid40571080,
year = {2025},
author = {Han, H and Zhang, JM and Li, K and Amankwah, JF and Zeng, XB and Shen, ZQ and Jin, XC and Chen, TY and Liu, JW and Liu, LP},
title = {Multi-omics and random forest reveal lipid metabolism disruption and biomarkers in grass carp (Ctenopharyngodon idellus) exposed to 2-methylisoborneol.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122226},
doi = {10.1016/j.envres.2025.122226},
pmid = {40571080},
issn = {1096-0953},
mesh = {Animals ; *Carps/metabolism ; *Lipid Metabolism/drug effects ; Biomarkers/metabolism ; *Water Pollutants, Chemical/toxicity ; *Camphanes/toxicity ; Liver/metabolism/drug effects ; Lipidomics ; Random Forest ; Multiomics ; },
abstract = {The lipophilic nature of 2-methylisoborneol (2-MIB), a prevalent off-flavor compound in aquatic systems, raises concerns about its bioaccumulation potential and metabolic interference in fish. Most studies have focused on removing this compound from water and fish. However, the effect of lipid metabolism in fish exposed to 2-MIB remains poorly defined. This study investigated lipid metabolism disruption in grass carp (Ctenopharyngodon idellus) induced by 96 h of exposure to 5 and 20 μg/L of 2-MIB through integrated serum biochemistry, hepatic lipidomics, and multi-omics analysis. Grass carp exhibited varying degrees of oxidative stress, immune response, and lipid metabolism disruption. Non-targeted lipidomic analysis reveals that 2-MIB alters the levels of phosphatidylcholine (PC), sphingomyelin (SM), and phosphatidylmethanol (PMeOH) in the liver, potentially affecting the structure and function of cell membranes. Multi-omics analysis suggests that pathways related to carbohydrate metabolism, lipid metabolism, and amino acid biosynthesis may be crucial in regulating the physiological status of grass carp. Additionally, random forest and correlation analysis identified pregnenolone and 1-cyano-2-methyl-2-propen-1-yl docosanoate as potential biomarkers for 2-MIB exposure. Collectively, this study highlights the lipid characteristics and mechanisms of grass carp under 2-MIB exposure, contributing to the evaluation of its impact on fish health and improving aquaculture management.},
}

Animals
*Carps/metabolism
*Lipid Metabolism/drug effects
Biomarkers/metabolism
*Water Pollutants, Chemical/toxicity
*Camphanes/toxicity
Liver/metabolism/drug effects
Lipidomics
Random Forest
Multiomics

@article {pmid38695096,
year = {2025},
author = {Liu, H and Zhao, X and Xu, S and Zhao, L and Han, X and Xu, X and Zhao, N and Hu, L and Luo, C and Wang, X and Zhang, Q and Guo, T},
title = {Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China.},
journal = {Integrative zoology},
volume = {20},
number = {5},
pages = {916-935},
doi = {10.1111/1749-4877.12830},
pmid = {38695096},
issn = {1749-4877},
support = {32100100//Youth Fund Project of National Natural Science Foundation of China/ ; 2022-ZJ-943Q//National Science Foundation of Qinghai Province/ ; LHZX-2022-02//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; China ; *Antelopes/microbiology/physiology ; Sheep/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; *Ruminants/microbiology/physiology ; *Adaptation, Physiological ; Parks, Recreational ; Bacteria/classification/genetics ; Feeding Behavior ; Multiomics ; },
abstract = {The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.},
}

Animals
*Gastrointestinal Microbiome/physiology
China
*Antelopes/microbiology/physiology
Sheep/physiology/microbiology
RNA, Ribosomal, 16S/genetics
*Ruminants/microbiology/physiology
*Adaptation, Physiological
Parks, Recreational
Bacteria/classification/genetics
Feeding Behavior
Multiomics

@article {pmid40993501,
year = {2025},
author = {Garnier, É and Delalandre, L and Segrestin, J and Barkaoui, K and Kazakou, E and Navas, ML and Vile, D and Violle, C and Bernard-Verdier, M and Birouste, M and Blanchard, A and Bumb, I and Cruz, P and Debain, S and Fayolle, A and Fortunel, C and Grigulis, K and Laurent, G and Lavorel, S and Lloret, F and Pérez-Ramos, IM and Prieto, I and Roumet, C},
title = {FAIRTraits: An enriched, FAIR-compliant database of plant traits from Mediterranean populations of 240 species.},
journal = {Ecology},
volume = {106},
number = {9},
pages = {e70219},
doi = {10.1002/ecy.70219},
pmid = {40993501},
issn = {1939-9170},
support = {AAPFNSO2019OpenMetaPaper-14026//Ministère de l'Enseignement supérieur et de la Recherche (FNSO Project)/ ; },
abstract = {Trait-based ecology relies on high-quality, well-documented data to explore how plant traits relate to environmental conditions, community assembly, and ecosystem functioning. However, the reuse and synthesis of trait data across studies remain limited by several constraints: a lack of detailed metadata, heterogeneous protocols, absence of individual-level measurements, and underrepresentation of certain trait types-particularly below-ground traits. Many existing datasets also lack the environmental details necessary to investigate trait-environment relationships at local scales. Here, we present FAIRTraits, a comprehensive dataset that addresses these limitations by compiling 189,452 records of quantitative trait measurements collected between 1997 and 2023 from 1955 populations of 240 vascular plant species in the Northern Mediterranean Basin, a region known both for its exceptional biodiversity and as a climate change hotspot. All data were collected by a single research group using consistent and well-documented field and laboratory protocols, ensuring internal consistency across traits, species, sites, and years. FAIRTraits includes 180 traits measured at the individual or replicate level, with no aggregation. It features an unprecedented diversity of traits spanning all major plant organs-leaves, stems, roots, and reproductive parts. These include widely used traits such as specific leaf area and plant height, but also traits that are rarely reported, especially below-ground traits related to root morphology, as well as mechanical properties, phenology, and microbial associations. In addition to raw measurements, species are annotated with categorical descriptors (e.g., life form, photosynthetic pathway, and successional status), and species-level values taken from a Mediterranean flora, for key traits such as reproductive phenology and maximum height. To support analyses that account for environmental variability, each observation is linked to detailed descriptors of the plot where the individual was sampled, including climate data, soil physicochemical properties, and disturbance regime. Full metadata on sampling protocols and measurement methods are provided for every trait and environmental variable. FAIRTraits was built in compliance with the FAIR principles of data management (Findable, Accessible, Interoperable, and Reusable). Metadata are described using the Ecological Metadata Language (EML); trait definitions are standardized using community-endorsed semantic resources. The data are archived across two interoperable repositories: GBIF (via Darwin Core and trait-specific extensions) for taxon-trait associations and InDoRES for environmental and contextual data. These efforts ensure long-term preservation, data traceability, and seamless integration with plant trait databases such as BROT or TRY, and cross-organism initiatives such as the Open Traits Network or the Encyclopedia of Life. FAIRTraits offers a robust, richly documented, and reusable resource for investigating plant functional strategies, trait-environment relationships, and scaling from individuals to communities and ecosystems. It also provides a concrete example of how trait datasets can meet the highest standards of data quality and interoperability-serving as a model for future community-led initiatives in functional ecology. The FAIRTraits database is released under the CC-BY Attribution 4.0 International license.},
}

@article {pmid40991430,
year = {2025},
author = {Pascal, LV and Chadès, I and Adams, MP and Helmstedt, KJ},
title = {Developing new technologies to protect ecosystems: Planning with adaptive management.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {39},
pages = {e2422002122},
doi = {10.1073/pnas.2422002122},
pmid = {40991430},
issn = {1091-6490},
support = {DE200101791//Department of Education and Training | Australian Research Council (ARC)/ ; DE200100683//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; Climate Change ; Biodiversity ; Australia ; Coral Reefs ; },
abstract = {Technology development is an essential investment for policymakers to address contemporary global crises, including climate change, biodiversity loss, the energy transition, and emergent infectious diseases. However, investing limited resources in the development of new technologies is risky. The research and development process is unpredictable, with unknown timelines and outcomes. In addition, even after successful development, the effects of deploying a new technology remain uncertain. When confronted with these uncertainties, policymakers must determine how long they should allocate resources to developing new technologies. Informed decisions require anticipating possible successes and failures of both technology development and deployment, which is a challenging optimization task when managing dynamic systems, such as threatened ecological systems. Using an adaptive management approach from AI, we find a time limit new technologies should be developed for, which balances costs, benefits, and uncertainties during development and deployment. We extract clear and transparent general rules for investing in new technologies, building on an analytical approximation. Using Australia's Great Barrier Reef as a case study, we demonstrate that the development time limit ranges between 0 to 45 y before surrendering. We also show how characteristics of an ecological system influence the optimal investment strategy. Our approach can inform the development of new technologies in multiple domains including biodiversity conservation, public health, energy production, and the technology industry more broadly.},
}

*Conservation of Natural Resources/methods
*Ecosystem
Climate Change
Biodiversity
Australia
Coral Reefs

@article {pmid40920894,
year = {2025},
author = {Kawam, B and Ostner, J and McElreath, R and Schülke, O and Redhead, D},
title = {A causal framework for the drivers of animal social network structure.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013370},
doi = {10.1371/journal.pcbi.1013370},
pmid = {40920894},
issn = {1553-7358},
mesh = {Animals ; Bayes Theorem ; *Behavior, Animal/physiology ; Computational Biology ; *Social Behavior ; Computer Simulation ; Models, Biological ; },
abstract = {A major goal of behavioural ecology is to explain how phenotypic and ecological factors shape the networks of social relationships that animals form with one another. This inferential task is notoriously challenging. The social networks of interest are generally not observed, but must be approximated from behavioural samples. Moreover, these data are highly dependent: the observed network edges correlate with one another, due to biological and sampling processes. Failing to account for the resulting uncertainty and biases can lead to dysfunctional statistical procedures, and thus to incorrect results. Here, we argue that these problems should be understood-and addressed-as problems of causal inference. For this purpose, we introduce a Bayesian causal modelling framework that explicitly defines the links between the target interaction network, its causes, and the data. We illustrate the mechanics of our framework with simulation studies and an empirical example. First, we encode causal effects of individual-, dyad-, and group-level features on social interactions using Directed Acyclic Graphs and Structural Causal Models. These quantities are the objects of inquiry, our estimands. Second, we develop estimators for these effects-namely, Bayesian multilevel extensions of the Social Relations Model. Third, we recover the structural parameters of interest, map statistical estimates to the underlying causal structures, and compute causal estimates from the joint posterior distribution. Throughout the manuscript, we develop models layer by layer, thereby illustrating an iterative workflow for causal inference in social networks. We conclude by summarising this workflow as a set of seven steps, and provide practical recommendations.},
}

Animals
Bayes Theorem
*Behavior, Animal/physiology
Computational Biology
*Social Behavior
Computer Simulation
Models, Biological

@article {pmid40779849,
year = {2025},
author = {Zhu, J and Ding, X and Xu, Q and Fan, Y and Zhu, P and Li, X and Zhang, X and Zhang, Q and Du, X and Zhou, W and Jiao, J and Lu, B and Lu, C},
title = {Insights into the disinfection byproduct bromochloroacetamide-induced cardiotoxicity of zebrafish embryo-larvae: A multiomics approach and comparison of biomarker responsiveness.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118805},
doi = {10.1016/j.ecoenv.2025.118805},
pmid = {40779849},
issn = {1090-2414},
mesh = {Animals ; *Zebrafish/embryology ; Biomarkers/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cardiotoxicity/etiology ; *Acetamides/toxicity ; Embryo, Nonmammalian/drug effects ; Larva/drug effects ; *Disinfectants/toxicity ; Heart/drug effects ; Metabolomics ; Disinfection ; Multiomics ; },
abstract = {Bromochloroacetamide (BCAcAm), an inevitable byproduct of the water treatment disinfection process, is widely detected in drinking water. Previous toxicological and in silico results suggested that developmental effects are associated with analogous chemical exposure; however, the key molecular events and underlying mechanisms remain unclear, especially in the early stages of aquatic organisms. In the present study, a zebrafish larval model was used to comprehensively assess the developmental toxicity of BCAcAm via transcriptional, metabolic, biochemical and morphological tests. Integration analyses of RNA sequencing and untargeted metabolomic data revealed crucial biological processes related to drug metabolism, cardiac muscle contraction and oxidative phosphorylation, which started from the initial stage, and ferroptosis progressed to the advanced stage in validated cardiac defects. Biochemical assays further verified ATP depletion, ROS and MDA accumulation, and hyperactivation of detoxification (increased GST activity) and the antioxidative system (increased GSH and GSSG levels). Transcriptionally, BCAcAm led to gpx4 downregulation, iron homeostasis perturbation (upregulated tfr and tf and downregulated fth) and lipid peroxidation (elevated alox12 and lpcat3), suggesting the involvement of ferroptosis. Moreover, the application of Fer-1 (a ferroptosis inhibitor) reversed BCAcAm-induced mitochondrial dysfunction and subsequent cardiotoxicity. In addition, the BMD and IBRv2 indices were derived from molecules across various biological levels. The general ranking of the different biomarkers in terms of better responsiveness and sensitivity performance is as follows: transcriptomics > metabolomics > biochemical assays. In the present study, an approach to detecting chemical-induced adverse outcomes and deciphering the underlying mechanisms through high-throughput data analysis is applied. This study provides valuable insights into the responsiveness and sensitivity of biomarkers, which may be instrumental for evaluating the ecological and health risks associated with newly emerged contaminants.},
}

Animals
*Zebrafish/embryology
Biomarkers/metabolism
*Water Pollutants, Chemical/toxicity
*Cardiotoxicity/etiology
*Acetamides/toxicity
Embryo, Nonmammalian/drug effects
Larva/drug effects
*Disinfectants/toxicity
Heart/drug effects
Metabolomics
Disinfection
Multiomics

@article {pmid40053082,
year = {2025},
author = {Alibardi, L},
title = {Immunoreactivity of flexible and inflexible scales in different lizards indicates that the mature beta-layer contains different corneous proteins.},
journal = {Protoplasma},
volume = {262},
number = {5},
pages = {1129-1149},
pmid = {40053082},
issn = {1615-6102},
mesh = {Animals ; *Lizards/anatomy & histology/genetics/immunology/metabolism ; Immunohistochemistry ; *Animal Scales/cytology/immunology/metabolism ; *Reptilian Proteins/chemistry/genetics/immunology/metabolism ; Computational Biology ; Amino Acid Sequence ; Epitopes/immunology ; Peptides/chemistry/metabolism ; Keratins/chemistry/metabolism ; },
abstract = {We have analyzed by immunohistochemical methods the Oberhautchen-beta layer, here abbreviated as beta-layer, of lizards with hard scales and lizards with softer scales. Different antibodies for detecting Corneous Beta Proteins (CBPs) have been utilized. The agamid beta-corneous layer is generally 3-4 times thicker than in geckos, and the surface microornamentation forms a honeycomb pattern. Geckos feature thinner beta-layers and a spinulated pattern and show immunolocalization for CBPs and isopeptide bonds, a product of transglutaminase catalysis, in their thin beta-layer. CBPs and isopeptide-bonds are detected in the superficial Oberhautchen and alpha-layer of agamids while the beta-layer is immuno-negative. Considering the limitations of immunolabeling methods, the unexpected result might derive from inaccessibility of antibodies to epitopes that are masked within the packed corneous material of the agamid beta-layer. However, bioinformatics analysis for CBPs sequenced in the few species of agamids so far known indicates that these proteins have low identity with those of other lizards. This suggests that agamids possess peculiar CBPs but low isopeptide bonds in their inflexible beta-layer. In contrast, the thinner and pliable beta-corneous layers of geckos may derive from the presence of isopeptide bonds mixed with lower amounts of CBPs. The differences in material properties of lizard scales, inflexibility versus pliability, are adaptive for the different ecological conditions of the species here analyzed.},
}

Animals
*Lizards/anatomy & histology/genetics/immunology/metabolism
Immunohistochemistry
*Animal Scales/cytology/immunology/metabolism
*Reptilian Proteins/chemistry/genetics/immunology/metabolism
Computational Biology
Amino Acid Sequence
Epitopes/immunology
Peptides/chemistry/metabolism
Keratins/chemistry/metabolism

@article {pmid40986865,
year = {2025},
author = {Sun, Y and Jaiswal, A and Slade, C and Phillips, KT and Benzo, RM and Washington, P},
title = {Associations Between Social Determinants of Health and Adherence in Mobile-Based Ecological Momentary Assessment: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e69831},
doi = {10.2196/69831},
pmid = {40986865},
issn = {1438-8871},
mesh = {Humans ; *Social Determinants of Health ; *Ecological Momentary Assessment ; *Patient Compliance ; Telemedicine ; Mobile Applications ; Male ; },
abstract = {BACKGROUND: Ecological momentary assessment (EMA) involves repeated prompts to capture real-time self-reported health outcomes and behaviors via mobile devices. With the rise of mobile health (mHealth) technologies, EMA has been applied across diverse populations and health domains. However, the extent to which EMA engagement and data quality vary across social determinants of health (SDoH) remains underexplored. Emerging evidence suggests that EMA adherence and data completeness may be sometimes associated with participant characteristics such as socioeconomic status, race/ethnicity, and education level. These associations may sometimes influence who engages with EMA protocols and the types of contextual data captured. Despite growing interest in these patterns, no review to date has synthesized evidence on how SDoH relate to EMA compliance and engagement.

OBJECTIVE: We conducted a scoping review to study two research questions: (R1) how EMA compliance rates in health studies can differ across SDoH and (R2) what types of SDoH have been identified through EMA health studies.

METHODS: Following PRISMA-ScR guidelines, we searched PubMed, Web of Science, and EBSCOhost using two sets of queries targeting EMA and its relationship to SDoH. Eligible studies were peer reviewed, were published in English between 2013 and 2024, and used mobile-based EMA methods. Studies were included if they (1) reported on differences in EMA compliance by SDoH or (2) reported at least one SDoH observed or uncovered during an EMA study. We used the social ecological model (SEM) as a guiding framework to categorize and interpret SDoH across individual, interpersonal, community, and societal levels. A qualitative thematic synthesis was conducted to iteratively and collaboratively extract, categorize, and review determinants.

RESULTS: We analyzed 48 eligible studies, of which 35 addressed R1 by examining compliance patterns across various SDoH. Using the SEM, we identified 13 determinants categorized across 4 levels: individual (eg, daily routine, biological sex, age, socioeconomic status, language, education, and race or ethnicity), interpersonal (eg, social support), community and organizational (eg, social context, social acceptance, stigmatization, and youth culture), and policy or societal (eg, systemic and structural barriers). These studies described differences in EMA response rates, compliance, and dropout associated with these determinants, often among vulnerable populations. The remaining 13 studies addressed R2, demonstrating examples of the types of SDoH that EMA research can uncover, including family culture, social support, social contexts, stigmatization, gender norms, heroic narratives, LGBTQ+ culture, racial discrimination, and systematic and structural barriers.

CONCLUSIONS: This scoping review illustrates how EMA compliance rates can differ across SDoH and highlights the potential of EMA to uncover social and cultural factors linked to health behaviors and outcomes. Our findings underscore the importance of integrating SDoH considerations into EMA study designs to capture context-specific sociocultural dynamics.},
}

Humans
*Social Determinants of Health
*Ecological Momentary Assessment
*Patient Compliance
Telemedicine
Mobile Applications
Male

@article {pmid40986480,
year = {2025},
author = {Constant, A and Paquin, V and Ackerman, RA and Depp, CA and Moore, RC and Harvey, PD and Pinkham, AE},
title = {Exploring the clinical utility of rhythmic digital markers for schizophrenia.},
journal = {PLOS digital health},
volume = {4},
number = {9},
pages = {e0001010},
doi = {10.1371/journal.pdig.0001010},
pmid = {40986480},
issn = {2767-3170},
abstract = {This study investigates the clinical utility of rhythmic digital markers (RDMs) in schizophrenia. RDMs are digital markers capturing behavioral rhythms over different timescales - within 24 hours span (ultradian), at a span of 24 hours (circadian), or over cycles of more than 24 hours (infradian). While previous research has explored digital markers for schizophrenia, the focus has primarily been on sensor data variability rather than rhythmic patterns. This study introduces two RDMs: an entropy RDM, which quantifies uncertainty in activity distribution over the infradian cycles, and a dynamic RDM, which is derived from models of transitions in entropy and psychotic symptom intensity using Markov chain analysis. Data were ecological momentary assessments (EMAs) of 39 activities collected from 390 individuals diagnosed with schizophrenia (N = 153) or bipolar disorder (N = 192) and controls (N = 45). We assessed associations between RDMs and symptom severity and whether participants could be differentiated based on these RDMs. We found that participants with schizophrenia significantly differed on dynamic RDMs, suggesting a potential diagnostic utility. However, dynamic RDMs were not associated with symptom severity, and entropy RDM had no significant clinical correlate. Our findings contribute to the growing evidence on digital markers in psychiatry and highlight the potential of rhythmic digital markers (RDMs) in characterizing digital phenotypes for schizophrenia.},
}

@article {pmid40481658,
year = {2025},
author = {von Mering, S and Leachman, S and Santos, J and Meudt, HM},
title = {Wikidata for botanists: benefits of collaborating and sharing Linked Open Data.},
journal = {Annals of botany},
volume = {136},
number = {3},
pages = {491-511},
doi = {10.1093/aob/mcaf062},
pmid = {40481658},
issn = {1095-8290},
support = {//Fundação para a Ciência e Tecnologia/ ; },
mesh = {*Botany ; *Information Dissemination/methods ; *Internet ; Knowledge Bases ; *Databases, Factual ; },
abstract = {BACKGROUND: Wikidata is a multilingual linked open knowledge base to which anyone can contribute that contains multitudes of botany-related information. Wikidata reveals interactions between entities and connects botany-related information from multiple institutions and other sources, benefiting the botanical community in numerous ways. The aim of this article is to give an overview of Wikidata from a botany perspective and issue a call to action to the botanical community to collectively improve the quantity and quality of information related to botany, botanists and botanical collections, in Wikidata. Here, we use a broad definition of botany to include the study of many different taxa and specializations.

SCOPE: Wikidata contains botany-related data and identifiers for botanists and botanical collectors, botanical taxa, natural history institutions and collections, botany-related publications, geographical locations and research expeditions, as well as genes, genetic variants, chemical compounds, diseases, and more. As an open, collaborative and community-curated knowledge base, Wikidata enables different communities to add and link data related to botany and empowers the querying and reuse of this data via digital tools such as the Wikidata Query Service, Bionomia, Scholia, TL-2 and Expeditia.

CONCLUSIONS: Collaboration is key in botany and Wikidata, and the sharing and enriching of botany-related Linked Open Data benefits us all. Several resources, including ethical and legal guidelines, are available for botanists to edit, use, reuse, roundtrip and teach Wikidata. We call on all botanists to be active participants in Wikidata, improving the quality, quantity and linking of botany-related data. Our individual and collective actions can help harness the power of Linked Open Data to answer important queries in the field, improve accessibility of herbaria, increase visibility of botanists and their scientific contributions, integrate Wikidata into the classroom, support the Madrid Declaration strategic actions, achieve our collective goals, and ultimately make botany-related information more FAIR (Findable, Accessible, Interoperable, Reusable) and equitable.},
}

*Botany
*Information Dissemination/methods
*Internet
Knowledge Bases
*Databases, Factual

@article {pmid40296452,
year = {2025},
author = {Wang, S and Kaur, S and Kunath, BJ and May, P and Richardson, L and Rogers, AB and Wilmes, P and Finn, RD and Vizcaíno, JA},
title = {An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.},
journal = {Proteomics},
volume = {25},
number = {17-18},
pages = {33-42},
doi = {10.1002/pmic.202500002},
pmid = {40296452},
issn = {1615-9861},
support = {C19/BM/13684739//National Research Fund Luxembourg (FNR)/ ; 223745/Z/21/Z//Wellcome/ ; //EMBL Core Funding/ ; },
mesh = {*Metagenomics/methods ; *Proteomics/methods ; Humans ; Databases, Protein ; Metagenome ; *Transcriptome ; Animals ; Pilot Projects ; },
abstract = {The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.},
}

*Metagenomics/methods
*Proteomics/methods
Humans
Databases, Protein
Metagenome
*Transcriptome
Animals
Pilot Projects

@article {pmid40979437,
year = {2025},
author = {Atagong, SD and Tonnang, H and Senagi, K and Wamalwa, M and Agboka, KM and Odindi, J},
title = {A review on knowledge and information extraction from PDF documents and storage approaches.},
journal = {Frontiers in artificial intelligence},
volume = {8},
number = {},
pages = {1466092},
pmid = {40979437},
issn = {2624-8212},
abstract = {INTRODUCTION: Automating the extraction of information from Portable Document Format (PDF) documents represents a major advancement in information extraction, with applications in various domains such as healthcare, law, or biochemistry. However, existing solutions face challenges related to accuracy, domain adaptability, and implementation complexity.

METHODS: A systematic review of the literature was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology to examine approaches and trends in PDF information extraction and storage approaches.

RESULTS: The review revealed three dominant methodological categories: rule-based systems, statistical learning models, and neural network-based approaches. Key limitations include the rigidity of rule-based methods, the lack of annotated domain-specific datasets for learning-based approaches, and issues such as hallucinations in large language models.

DISCUSSION: To overcome these limitations, a conceptual framework is proposed comprising nine core components: project manager, document manager, document pre-processor, ontology manager, information extractor, annotation engine, question-answering tool, knowledge visualizer, and data exporter. This framework aims to improve the accuracy, adaptability, and usability of PDF information extraction systems.},
}

@article {pmid40963762,
year = {2025},
author = {Dey, D and Lateef, HA and Leroux, A and Zipunnikov, V and Merikangas, K},
title = {Associations Between Daily Outdoor Temperature and Subjective Real-time Ratings of Emotional States and Sleep in Mood Disorder Subtypes.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40963762},
abstract = {Growing evidence for the influence of weather on mental health at both the aggregate level indices of mental health statistics of hospitalizations, morbidity, and mortality, and individual level dynamics of mood states. Most research on this topic has focused on light exposure and depressed mood as the sole indicators of seasonal fluctuations of mood disorders. This paper evaluates the association between daily maximum outdoor temperature (DMOT) and contemporaneously reported mood, energy, anxiousness, and sleep quality assessed with Ecological Momentary Assessment (EMA) in a community-based sample of 452 people, aged 11 to 85 years, comprising people with or without a history of mood disorders. After controlling for demographics, daily activity levels, and daytime cloud coverage as an index of light exposure, we found that higher DMOT was associated with better mood, increased energy, and better sleep quality among those with with a history of mood disorders, particularly in the spring among people with a history of Bipolar Disorder (BD) who tended to exhibit more seasonal changes than controls. These findings suggest that the dynamics of mood, energy, and sleep may underlie the aggregate population-level influences of temperature and correlated environmental influences on negative mental health outcomes, particularly among those with BD. Therefore, the conceptualization of risk and intervention for mood disorders should consider both the aggregate influences of temperature and light and associated environmental conditions, as well as individual-level sleep quality and energy as potential mechanisms for seasonal patterns of emotional states.},
}

@article {pmid40886889,
year = {2025},
author = {Furxhi, I and Perucca, M and Baldi, G and Dami, V and Cioni, A and Koivisto, AJ and Bengalli, R and Mantecca, P and Motta, G and Carriere, M and Kose, O and Nicosia, A and Ravegnani, F and Burrueco-Subirà, D and Candalija, A and Cabellos, J and Vázquez-Campos, S and Lahive, E and Eagles, E and de Ipiña, JL and Oliveira, J and Conin, P and Zanoni, I and Brigliadori, A and Faccani, L and Syed, T and Haq, EU and O'Mahony, C and Serantoni, M and Blosi, M and Exner, T and Costa, A},
title = {The fruits of data shepherding: A collection of open FAIR datasets for titanium dioxide coated photocatalytic surfaces.},
journal = {NanoImpact},
volume = {39},
number = {},
pages = {100583},
doi = {10.1016/j.impact.2025.100583},
pmid = {40886889},
issn = {2452-0748},
mesh = {*Titanium/chemistry ; Catalysis ; *Databases, Factual ; Surface Properties ; *Nanostructures/chemistry ; Information Dissemination ; },
abstract = {This paper presents a large-scale collaborative effort within a multi-partner consortium, to systematically structure, curate, and openly share data in alignment with the FAIR principles. The data result from a case study of titanium dioxide (TiO2) nanomaterials (NMs) for photocatalytic depolluting surfaces, produced via various spray coating techniques under the Safe and Sustainable by Design (SSbD) approach. The data are publicly available through a dedicated Zenodo community (https://zenodo.org/communities/asina/records), comprising of individual records that separately host the data and the corresponding metadata. Each dataset is systematically named to reflect its context beginning with "ASINA dataset," followed by i) the relevant life cycle stage (LCS) from synthesis to end-of-life, ii) the SSbD dimension (i.e., functionality, safety, and environmental aspects), and iii) the assessed features (e.g., physicochemical properties, hazard evaluation, functionality assessment) facilitating searchability. The data files include "descriptors" excel tab, which is a harmonized version derived from primary data for visualization, data integration and future modeling applications. Metadata are provided in separate records and include detailed information such as contributor name and affiliations, experimental protocols, instrumentation, dictionary definitions, ontologies, and licensing terms. The data and metadata files are mutually paired in Zenodo using related identifiers, where each data file includes the DOI of its corresponding metadata file, and vice versa. In total, 43 interlinked records are provided capturing the case study, offering structured and machine-actionable resources that support modeling, data integration and harmonization efforts within the nanosafety and nanoinformatics communities. This effort was coordinated through dedicated data shepherding, which enabled trust-building, metadata alignment, and consistent FAIR implementation across partners.},
}

*Titanium/chemistry
Catalysis
*Databases, Factual
Surface Properties
*Nanostructures/chemistry
Information Dissemination

@article {pmid40980745,
year = {2024},
author = {Boyes, D and Broad, GR and Sivess, L and Holt, S and Holland, PWH and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Brown China-mark moth, Elophila nymphaeata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {155},
pmid = {40980745},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Elophila nymphaeata (the Brown China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 734.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,079 protein coding genes.},
}