@article {pmid40344046,
year = {2025},
author = {Ramihangihajason, TA and Weber, JL and Rakotondraompiana, S and Roger, E and Faramalala, MH and Rakotoniaina, S},
title = {Natural capital accounting as a decision support tool for environmental management of a protected area in Madagascar.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321948},
pmid = {40344046},
issn = {1932-6203},
mesh = {Madagascar ; *Conservation of Natural Resources/methods ; Ecosystem ; Biodiversity ; Forests ; Animals ; *Decision Support Techniques ; Humans ; Birds ; },
abstract = {Ecosystem change affects the availability of resources and services provided by nature. Ecosystem Natural capital accounting helps track these changes and supports better decision-making for managing the environment. This approach aims to assess changes in the stocks and flows of natural resources and the possibility to integrate them into economic and political decisions. The protected area of Mahavavy-Kinkony Complex, in North-Western of Madagascar, was chosen to implement this approach due to its many types of ecosystems as well as important reserves of threatened birds. In five years (2013-2018), we have observed a reduction in woodland cover (forest and mangrove) due to both regulated and illegal logging, linked to urban expansion and increasing of human pressure. This loss of woodland compromises not only biodiversity but also the capacity of ecosystems to provide ecosystem services. At the same time, the silting up of surface waters is compromising water quality and the health of aquatic ecosystems. In addition, the increase in agricultural land at the expense of forested areas raises concerns about the continuing degradation of natural ecosystems. All of these changes can be observed inside local socio-ecological landscape type. Each socio-ecological landscape type shows the potential variation in the production of ecosystem services.},
}

Madagascar
*Conservation of Natural Resources/methods
Ecosystem
Biodiversity
Forests
Animals
*Decision Support Techniques
Humans
Birds

@article {pmid40343940,
year = {2025},
author = {Longo, L and Veronese, M and Cagnato, C and Sorrentino, G and Tetruashvili, A and Belfer-Cohen, A and Jakeli, N and Meshveliani, T and Meneghetti, M and Zoleo, A and Marcomini, A and Artioli, G and Badetti, E and Hardy, K},
title = {Direct evidence for processing Isatis tinctoria L., a non-nutritional plant, 32-34,000 years ago.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321262},
pmid = {40343940},
issn = {1932-6203},
mesh = {*Plant Leaves/chemistry/ultrastructure ; Humans ; *Isatis/chemistry/anatomy & histology ; Spectrum Analysis, Raman ; Spectroscopy, Fourier Transform Infrared ; Archaeology ; History, Ancient ; },
abstract = {Recovering evidence for the intentional use of plants in the Palaeolithic is challenging due to their perishable nature as, unlike chipped stone or bone artefacts, plant remains are rarely preserved. This has created a paradigm for the Palaeolithic in which plants seldom feature, resulting in a partial and skewed perspective; in fact, plants were as essential to human life then as they are today. Here, we combine morphological and spectroscopic analyses (µ-Raman, µ-FTIR) to provide robust multiscale physical and biomolecular evidence for the deliberate pounding and grinding of Isatis tinctoria L. leaves 34-32,000 years ago. The leaf epidermis fragments were found entrapped in the topography of the used surface of unmodified pebbles, in association with use-wear traces. Although their bitter taste renders them essentially inedible, the leaves have well-recognised medicinal properties and contain indigotin precursors, the chromophore responsible for the blue colour of woad, a plant-based dye that is insoluble in water. We used a stringent approach to contamination control and biomolecular analysis to provide evidence for a new perspective on human behaviour, and the applied technical and ecological knowledge that is likely to have prevailed in the Upper Palaeolithic. Whether this plant was used as a colourant, as medicine, or indeed for both remains unknown, but offers a new perspective on the fascinating possibilities of non-edible plant use.},
}

*Plant Leaves/chemistry/ultrastructure
Humans
*Isatis/chemistry/anatomy & histology
Spectrum Analysis, Raman
Spectroscopy, Fourier Transform Infrared
Archaeology
History, Ancient

@article {pmid40343039,
year = {2025},
author = {Cuenca, PR and Souza, FN and do Nascimento, RC and da Silva, AG and Eyre, MT and Santana, JO and de Oliveira, DS and de Souza, EVR and Palma, FAG and de Carvalho Santiago, DC and Dos Santos Ribeiro, P and Read, JM and Cremonese, C and Costa, F and Giorgi, E},
title = {Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40343039},
abstract = {Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis-a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease. We recruited individuals living in urban slums in Salvador, Brazil to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step-selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors. With 124 participants wearing GPS devices for 24 to 48 hours, recording locations every 35 seconds during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers. This study introduces a novel method for analysing human telemetry data in infectious disease research, providing critical insights for targeted interventions.},
}

@article {pmid40339581,
year = {2025},
author = {Pekar, JE and Lytras, S and Ghafari, M and Magee, AF and Parker, E and Wang, Y and Ji, X and Havens, JL and Katzourakis, A and Vasylyeva, TI and Suchard, MA and Hughes, AC and Hughes, J and Rambaut, A and Robertson, DL and Dellicour, S and Worobey, M and Wertheim, JO and Lemey, P},
title = {The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.03.035},
pmid = {40339581},
issn = {1097-4172},
abstract = {The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.},
}

@article {pmid40338955,
year = {2025},
author = {Benjamin, JR and Neibauer, J and Anthony, H and Vazquez, J and Rawhouser, A and Dunham, JB},
title = {A partner-driven decision support model to inform the reintroduction of bull trout.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323427},
pmid = {40338955},
issn = {1932-6203},
mesh = {Animals ; *Trout/physiology ; *Conservation of Natural Resources/methods ; Ecosystem ; *Decision Support Techniques ; Decision Making ; },
abstract = {Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout (Salvelinus confluentus) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.},
}

Animals
*Trout/physiology
*Conservation of Natural Resources/methods
Ecosystem
*Decision Support Techniques
Decision Making

@article {pmid40335533,
year = {2025},
author = {Pakulnicka, J and Kruk, M},
title = {Water beetle networks differences and migration between natural lakes and post-exploitation water bodies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15898},
pmid = {40335533},
issn = {2045-2322},
mesh = {Animals ; *Coleoptera/physiology ; *Lakes ; Ecosystem ; *Animal Migration ; Biodiversity ; },
abstract = {Water deficits are a serious problem around the world, which also affects young landscapes, where lakes are most abundant. This poses a threat to many habitats and biological diversity found here. The relationships between species in the ecological networks of lakes at different stages of development and in nearby post-exploitation water bodies remain poorly understood. To better understand the functioning of beetle communities in different ecosystems, we created five network models that we subjected to graph analysis. By analysing the general attributes of the network (number of neighbours, shortest path, characteristic path length, clustering coefficient, network centralisation, network density and network heterogeneity) and those related to the nodes (NCC-Node Closeness Centrality, NBC-Node Betweenness Centrality, NDC-Node Degree Centrality) and to the edges (EBC-Edge Betweenness Centrality and correlations between the biomass of species as nodes), we were able to determine the role of each species in the networks and the relationships between the species. We then used the machine learning ensemble modelling XGBoost-SHAP to identify species that are particularly important in migrations between water bodies and to assess the direction and strength of migrations using Shapley values. Our analyses are based on faunal material from 25 lakes (mesotrophic, eutrophic, dystrophic) and 31-post-exploitation water bodies (clay pits and gravel pits) in northern Poland, in the Masurian Lake District. We found a total of 169 species representing different ecological and functional components. We have shown that the structures of the network between the biomass of species in the analysed five water types differ significantly. The highest value for network density was recorded in eutrophic lakes and clay ponds, the lowest in dystrophic lakes. In eutrophic lakes these are mainly eurybionts, in clay pits-rheophiles and in gravel pits-argilophiles and tyrphophiles. The relationship between the species with the highest NBC and EBC values is particularly important in order to maintain the stability of the network. The periphery of the network usually consists of larger predators that do not compete with each other. By analysing the migration directions of beetles between different ecosystems, we were able to demonstrate a greater affinity of the beetle fauna, especially the argilophiles (e.g. Scarodytes halensis and Laccobius minutus) inhabiting gravel pits, to dystrophic lakes. The beetles in clay pits originate mainly from mesotrophic lakes. These are mainly rheophiles, mostly weakly flying species, such as: Haliplus fluviatilis, Haliplus fulvus, Ilybius fenestratus, Hygrotus vericolor and Haliplus flavicollis. These species are important for the stability of ecological networks in the studied lake types. Their movements between the ecosystems studied in turn contribute to the functional connectivity between the individual lakes, which ensures the stabilisation of biotic relationships at the landscape level. At the same time, they generally also indicate the optimisation of environmental conditions in post-exploitation water bodies, which makes them potential substitute habitats for natural lakes.},
}

Animals
*Coleoptera/physiology
*Lakes
Ecosystem
*Animal Migration
Biodiversity

@article {pmid40324147,
year = {2025},
author = {Gilpin, W},
title = {Optimization hardness constrains ecological transients.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013051},
pmid = {40324147},
issn = {1553-7358},
mesh = {*Ecosystem ; *Models, Biological ; Computer Simulation ; Computational Biology ; Biological Evolution ; },
abstract = {Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of interactions within versus among subcommunities. Here, we use tools from computational complexity theory to frame equilibration in complex ecosystems as the process of solving an analogue optimization problem. We show that functional redundancies among species in an ecosystem produce difficult, ill-conditioned problems, which physically manifest as transient chaos. We find that the recent success of dimensionality reduction methods in describing ecological dynamics arises due to preconditioning, in which fast relaxation decouples from slow solving timescales. In evolutionary simulations, we show that selection for steady-state species diversity produces ill-conditioning, an effect quantifiable using scaling relations originally derived for numerical analysis of complex optimization problems. Our results demonstrate the physical toll of computational constraints on biological dynamics.},
}

*Ecosystem
*Models, Biological
Computer Simulation
Computational Biology
Biological Evolution

@article {pmid40132265,
year = {2025},
author = {Gu, J and Shen, Y and Guo, L and Chen, Z and Zhou, D and Ji, G and Gu, A},
title = {Investigation of the mechanisms of liver injury induced by emamectin benzoate exposure at environmental concentrations in zebrafish: A multi-omics approach to explore the role of the gut-liver axis.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {138008},
doi = {10.1016/j.jhazmat.2025.138008},
pmid = {40132265},
issn = {1873-3336},
mesh = {Animals ; Zebrafish ; *Ivermectin/analogs & derivatives/toxicity ; *Liver/drug effects/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology ; *Water Pollutants, Chemical/toxicity ; Metabolomics ; Lipid Metabolism/drug effects ; *Insecticides/toxicity ; RNA, Ribosomal, 16S/genetics ; Multiomics ; },
abstract = {Emamectin benzoate (EMB) is a lipophilic pesticide that enters aquatic systems and adversely affects non-target organisms. This study investigated the long-term effects of EMB on zebrafish, exposing them to concentrations of 0, 0.1, 1, and 10 μg/L from the 4-hour post-fertilization (hpf) embryo stage to the 120-day post-fertilisation (dpf) adult stage. We found that exposure to 1 μg/L EMB induced liver damage, manifested as impaired liver function (elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT)), histopathological damage (lipid accumulation), as well as inflammatory and oxidative damage, with a dose - dependent effect. Non-targeted metabolomic analysis revealed an increase in lipid molecules in the liver, affecting the pathways related to glycerophospholipid metabolism. In addition, EMB exposure resulted in damage to the intestinal barrier and inflammatory responses in zebrafish. 16S rRNA sequencing demonstrated that EMB exposure resulted in notable alterations in the gut microbiota composition. Notably, the abundance of Plesiomonas and Cetobacterium increased in the EMB exposure group and exhibited a positive correlation with the majority of liver lipid metabolites. In contrast, reductions in Muribaculaceae and Alloprevotella were negatively correlated. The results of this study indicate that long-term exposure to EMB disrupts the gut microbiota, leading to the dysregulation of hepatic phospholipid metabolism. These findings provide new insights into the health risks associated with EMB and highlight its potential threats to higher organisms, including mammals.},
}

Animals
Zebrafish
*Ivermectin/analogs & derivatives/toxicity
*Liver/drug effects/metabolism/pathology
Gastrointestinal Microbiome/drug effects
*Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology
*Water Pollutants, Chemical/toxicity
Metabolomics
Lipid Metabolism/drug effects
*Insecticides/toxicity
RNA, Ribosomal, 16S/genetics
Multiomics

@article {pmid40117176,
year = {2025},
author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP},
title = {Healthy microbiome-moving towards functional interpretation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40117176},
issn = {2047-217X},
support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Dysbiosis/microbiology ; Phylogeny ; *Microbiota ; Principal Component Analysis ; Computational Biology/methods ; },
abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).},
}

Humans
*Gastrointestinal Microbiome/genetics
*Inflammatory Bowel Diseases/microbiology
*Metagenomics/methods
Dysbiosis/microbiology
Phylogeny
*Microbiota
Principal Component Analysis
Computational Biology/methods

@article {pmid40017036,
year = {2025},
author = {Han, Y and Du, Q and Dai, Y and Gu, S and Lei, M and Liu, W and Zhang, W and Zhu, M and Feng, L and Si, H and Liu, J and Zan, Y},
title = {EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization.},
journal = {Plant communications},
volume = {6},
number = {5},
pages = {101293},
doi = {10.1016/j.xplc.2025.101293},
pmid = {40017036},
issn = {2590-3462},
mesh = {*Software ; *Genomics/methods ; Genome-Wide Association Study ; *Computational Biology/methods ; User-Computer Interface ; Computer Graphics ; Quantitative Trait Loci ; Proteomics ; Metabolomics ; },
abstract = {The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.},
}

*Software
*Genomics/methods
Genome-Wide Association Study
*Computational Biology/methods
User-Computer Interface
Computer Graphics
Quantitative Trait Loci
Proteomics
Metabolomics

@article {pmid38319551,
year = {2025},
author = {Fuller, TJ and Lambert, DN and DiClemente, RJ and Wingood, GM},
title = {Reach and Capacity of Black Protestant Health Ministries as Sites of Community-Wide Health Promotion: A Qualitative Social Ecological Model Examination.},
journal = {Journal of racial and ethnic health disparities},
volume = {12},
number = {2},
pages = {887-898},
pmid = {38319551},
issn = {2196-8837},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Black or African American/statistics & numerical data/psychology ; Georgia ; *Health Promotion/organization & administration ; Interviews as Topic ; *Protestantism ; Qualitative Research ; Secondary Data Analysis ; },
abstract = {Black communities in the Southeast United States experience a disproportionate burden of illness and disease. To address this inequity, public health practitioners are partnering with Black Protestant churches to deliver health promotion interventions. Yet, the reach of these programs beyond the organizational level of the Social Ecological Model (SEM) is not well defined. Thus, the aim of this study is to understand Black Protestant church leaders' and members' perceptions about the capacity of their ministries to reach into their communities, beyond their congregations, as providers or hosts of health education or promotion interventions. From 20 Black Protestant churches in Atlanta, GA, 92 church leaders and members participated in semi-structured interviews. Grounded theory guided data analysis and a diverse team coded the interviews. Most participating churches had health ministries. Participants saw the boundaries between their churches at the organizational level of the SEM and the broader Black community to be porous. Those who described their "community" as being broader than their congregation also tended to describe community-wide health promotion their church engaged in. They described church-based health fairs as a strategy to promote engagement in their communities. Some participants, particularly those in a health-related profession, discussed visions of how to utilize their church as a site for community-wide health promotion. We suggest these participants may be boundary leaders who can build relationships between public health professionals, pastors, and congregants. Based on the findings, we suggest that church-based health fairs may be effective sites of community-wide health promotion.},
}

Adult
Female
Humans
Male
Middle Aged
*Black or African American/statistics & numerical data/psychology
Georgia
*Health Promotion/organization & administration
Interviews as Topic
*Protestantism
Qualitative Research
Secondary Data Analysis

@article {pmid40333133,
year = {2025},
author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO},
title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333133},
issn = {2076-0817},
support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; },
abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.},
}

Humans
*Microbiota/drug effects
Anti-Bacterial Agents/pharmacology/therapeutic use
*Respiratory Tract Infections/microbiology/drug therapy
*Drug Resistance, Microbial
Probiotics
*Drug Resistance, Bacterial
*Respiratory System/microbiology

@article {pmid40319682,
year = {2025},
author = {Hwang, H and Kim, D and Kim, S and Kim, JY and Kim, ES and Yang, T and Lee, N and Piao, Y and Park, BJ and Lee, DK},
title = {Optimizing urban green spaces using a decision-support model for carbon sequestration and ecological connectivity.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125058},
doi = {10.1016/j.jenvman.2025.125058},
pmid = {40319682},
issn = {1095-8630},
mesh = {*Carbon Sequestration ; *Decision Support Techniques ; Cities ; *Conservation of Natural Resources/methods ; Ecosystem ; },
abstract = {Urban green spaces (UGSs) are vital for enhancing urban ecological health and resident well-being. However, their diverse functions need to be balanced based on spatial limitations and varying stakeholder preferences. Integrated planning approaches are needed to exploit the multiple benefits of UGSs. This study introduces a multi-objective decision-support model designed to optimize UGS planning by simultaneously addressing carbon sequestration, ecological connectivity, and cost constraints. The model incorporates the non-dominated sorting genetic algorithm II to identify Pareto-optimal solutions for tailored decision-making strategies that balance different priorities. The model indicated that ecological connectivity can be improved by 7.57 % while meeting carbon-reduction and budgetary targets. The model effectively balanced trade-offs, underscoring the importance of both the quantity and strategic placement of green space. This decision-support framework empowers decision-makers to rapidly simulate and validate optimal scenarios, effectively balance competing objectives, and provide a scientific basis through verifiable feedback, ultimately promoting the development of sustainable urban environments.},
}

*Carbon Sequestration
*Decision Support Techniques
Cities
*Conservation of Natural Resources/methods
Ecosystem

@article {pmid40273607,
year = {2025},
author = {Nkoh, JN and Ye, T and Shang, C and Li, C and Tu, J and Li, S and Wu, Z and Chen, P and Hussain, Q and Esemu, SN},
title = {Deciphering the mechanisms for preferential tolerance of Escherichia coli BL21 to Cd(II) over Cu(II) and Ni(II): A combined physiological, biochemical, and multiomics perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {297},
number = {},
pages = {118195},
doi = {10.1016/j.ecoenv.2025.118195},
pmid = {40273607},
issn = {1090-2414},
mesh = {*Escherichia coli/drug effects/physiology/metabolism ; *Cadmium/toxicity ; *Nickel/toxicity ; *Copper/toxicity ; Oxidative Stress/drug effects ; Escherichia coli Proteins/metabolism/genetics ; Hydrogen Peroxide/metabolism ; Multiomics ; },
abstract = {Environmental pollution severely affects ecological functions/health, and nondegradable pollutants such as heavy metals (HMs) cause significant damage to living organisms. Escherichia coli is one of the most studied life forms, and its response to oxidative stress is driven by a complex ensemble of mechanisms driven by transcriptomic-level adjustments. However, the magnitude of the physiological, metabolic, and biochemical alterations and their relationships with transcriptomic changes remain unclear. Studying the growth of E. coli in Cd-, Cu-, and Ni-polluted media at pH 5.0, we observed that (i) downregulation of the alkyl hydroperoxide complex, glutathione reductase, and glutathione S-transferase by Cd inhibited H2O2 degradation, and the accumulated H2O2 was respectively 2.7, 1.7, and 2.4 times greater than that in the control, Cu, and Ni treatments; (ii) Zn-associated resistance protein (ZraP) was the major scavenger of Cd, with a 140.7-fold increase in its expression; (iii) the P-type Cu[+] transporter (CopA), multicopper oxidase (CueO), and heteromultimeric transport system (CusCBAF) controlled the excretion and detoxification of Cu; (iv) the Cd[2+]/Zn[2+]/Pb[2+]-exporting P-type ATPase (ZntA) and transcriptional activator ZntR were the major transporters of Ni; (v) Cd upregulated biofilm formation and synthesis of secondary metabolites more than Cu and Ni, which resulted in increased adsorption and improved tolerance; and (vi) the activity of superoxide dismutase in Cu-spiked cells was 153.2 %, 141.7 %, and 172.7 % higher and corresponded to 85.7 %, 524.5 %, and 491.5 % lower O2[●][-] in the control, Cd-, and Ni-spiked cells, respectively. This study reveals E. coli's preferential tolerance mechanisms to Cd rather than Cu and Ni and demonstrates mechanisms for its survival in highly polluted environments.},
}

*Escherichia coli/drug effects/physiology/metabolism
*Cadmium/toxicity
*Nickel/toxicity
*Copper/toxicity
Oxidative Stress/drug effects
Escherichia coli Proteins/metabolism/genetics
Hydrogen Peroxide/metabolism
Multiomics

@article {pmid40332368,
year = {2025},
author = {Zheng, K and Feng, Y and Liu, R and Zhang, Y and Fan, D and Zhong, K and Tang, X and Zhang, Q and Cao, S},
title = {Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40332368},
issn = {1422-0067},
mesh = {*Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; Phylogeny ; *Evolution, Molecular ; *Computational Biology/methods ; *Plant Proteins/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; *Multigene Family ; *Adaptation, Physiological/genetics ; *Poaceae/genetics ; Indoleacetic Acids/metabolism ; Promoter Regions, Genetic ; },
abstract = {Auxin response factors (ARFs) are pivotal transcription factors that regulate plant growth, development, and stress responses. Yet, the genomic characteristics and functions of ARFs in Phoebe bournei remain undefined. In this study, 25 PbARF genes were identified for the first time across the entire genome of P. bournei. Phylogenetic analysis categorized these genes into five subfamilies, with members of each subfamily displaying similar conserved motifs and gene structures. Notably, Classes III and V contained the largest number of members. Collinearity analysis suggested that segmental duplication events were the primary drivers of PbARF gene family expansion. Structural analysis revealed that all PbARF genes possess a conserved B3 binding domain and an auxin response element, while additional motifs varied among different classes. Promoter cis-acting element analysis revealed that PbARF genes are extensively involved in hormonal responses-particularly to abscisic acid and jasmonic acid and abiotic stresses-as well as abiotic stresses, including heat, drought, light, and dark. Tissue-specific expression analysis showed that PbARF25, PbARF23, PbARF19, PbARF22, and PbARF20 genes (class III), and PbARF18 and PbARF11 genes (class V) consistently exhibited high expression levels in the five tissues. In addition, five representative PbARF genes were analyzed using qRT-PCR. The results demonstrated significant differences in the expression of PbARF genes under various abiotic stress conditions (drought, salt stress, light, and dark), indicating their important roles in stress response. This study laid a foundation for elucidating the molecular evolution mechanism of ARF genes in P. bournei and for determining the candidate genes for stress-resistance breeding.},
}

*Gene Expression Regulation, Plant
*Stress, Physiological/genetics
Phylogeny
*Evolution, Molecular
*Computational Biology/methods
*Plant Proteins/genetics/metabolism
*Transcription Factors/genetics/metabolism
*Multigene Family
*Adaptation, Physiological/genetics
*Poaceae/genetics
Indoleacetic Acids/metabolism
Promoter Regions, Genetic

@article {pmid40331936,
year = {2025},
author = {Li, H and Wang, R and Pan, J and Chen, J and Hao, X},
title = {Bioinformatics Analysis of the Glutamate-Gated Chloride Channel Family in Bursaphelenchus xylophilus.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40331936},
issn = {1422-0067},
support = {202403//Key Laboratory of National Forestry and Grassland Administration on Prevention and Control Technology of Pine Wilt Disease/ ; 202401BD070001-115//Yunnan Fundamental Research Projects/ ; LXXK-2023M06, LXXK-2024Z04//Southwest Forestry University Forestry major in Yunnan Province First-Class Construction Discipline/ ; },
mesh = {*Chloride Channels/genetics/metabolism/chemistry ; Animals ; *Computational Biology/methods ; Phylogeny ; *Tylenchida/genetics/metabolism ; Multigene Family ; Amino Acid Sequence ; },
abstract = {Glutamate-gated chloride channels (GluCls), a class of ion channels found in the nerve and muscle cells of invertebrates, are involved in vital life processes. Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has induced major economic and ecological losses in invaded areas of Asia and Europe. We identified 33 GluCls family members by sequence alignment analysis. A subsequent bioinformatic analysis revealed the physicochemical properties, protein structure, and gene expression patterns in different developmental stages. The results showed that GluCls genes are distributed across all six chromosomes of B. xylophilus. These proteins indicated a relatively conserved structure by NCBI-conserved domains and InterPro analysis. A gene structure analysis revealed that GluCls genes consist of 5 to 14 exons. Expression pattern analysis revealed BxGluCls were extensively involved in the development of second instar larvae of B. xylophilus. Furthermore, BxGluCls15, BxGluCls25, and BxGluCls28 were mainly associated with the development of eggs of B. xylophilus. BxGluCls12, BxGluCls18, and BxGluCls32 were predominantly linked to nematode resistance and adaptation. Investigation the structure and expression patterns of BxGluCls is crucial to understand the developmental trends of B. xylophilus. It also helps identify molecular targets for the development of biopesticides or drugs designed to control this nematode.},
}

*Chloride Channels/genetics/metabolism/chemistry
Animals
*Computational Biology/methods
Phylogeny
*Tylenchida/genetics/metabolism
Multigene Family
Amino Acid Sequence

@article {pmid40053042,
year = {2025},
author = {Duarte, T and Martin, GM and Anjos-Santos, D and Pessacq, P},
title = {Unraveling Plecoptera Diversity in Two Protected Areas of Argentine Patagonia.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {97},
number = {1},
pages = {e20240085},
doi = {10.1590/0001-3765202520240085},
pmid = {40053042},
issn = {1678-2690},
mesh = {Animals ; Argentina ; *Biodiversity ; *Neoptera/classification ; Forests ; Population Density ; Cluster Analysis ; *Animal Distribution ; *Insecta/classification ; Conservation of Natural Resources ; Parks, Recreational ; Geographic Information Systems ; },
abstract = {The Plecoptera taxonomy in Patagonia is well-documented, yet their distribution remains poorly understood, hindering comprehensive ecological and biogeographical studies. This study enhances knowledge of stonefly distribution in two Patagonian national parks: Nahuel Huapi and Los Alerces. Extensive fieldwork, georeferenced species records, and geographic information system data integration were conducted. Species richness was calculated using polygons (0.1° x 0.1° pixels) across ecoregions, with species indexed from rare to ubiquitous. Cluster analyses revealed faunal affinities across ecosystem complexes, and richness estimators (Jack1, Jack2, and Chao2) highlighted knowledge gaps. Results showed uneven species distribution, with the highest richness polygon (n = 19) in Los Alerces. The Northern Moist Forests hosted the most species, followed by the Transitional Cypress-Beech Forests. The rarest species were also found in these two complexes, as well as the Ecotone Steppe-Forest. Cluster analysis revealed strong affinities between the Northern Moist Forests of Nahuel Huapi and Ecotone Steppe-Forest. Richness estimators suggested up to 23 undocumented species. Though much remains to be learned about Plecoptera distribution in Patagonia, this study emphasizes the critical role of national parks in conserving biodiversity and provides a foundation for future conservation strategies, identifying new taxa records, including southernmost distributions.},
}

Animals
Argentina
*Biodiversity
*Neoptera/classification
Forests
Population Density
Cluster Analysis
*Animal Distribution
*Insecta/classification
Conservation of Natural Resources
Parks, Recreational
Geographic Information Systems

@article {pmid40045055,
year = {2025},
author = {Shi, J and Gong, J and Zhang, Y and Kan, G},
title = {Spatiotemporal change in ecological quality of the Qinghai-Tibetan Plateau based on an improved remote sensing ecological index and Google Earth Engine platform.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {4},
pages = {355},
pmid = {40045055},
issn = {1573-2959},
mesh = {*Remote Sensing Technology ; *Environmental Monitoring/methods ; *Ecosystem ; China ; Tibet ; Spatio-Temporal Analysis ; Conservation of Natural Resources ; Geographic Information Systems ; },
abstract = {The Qinghai-Tibetan Plateau (QTP) serves as a vital ecological security barrier in China and globally. Evaluating changes in ecological quality on the QTP provides critical insights for regional conservation initiatives. This study, tailored to the unique characteristics of the region, develops an Improved Remote Sensing Ecological Index (IRSEI) framework by integrating Gross Primary Productivity (GPP) with the Normalized Difference Vegetation Index (NDVI), humidity (WET), Land Surface Temperature (LST), and the Negative Drought Index (NDBSI). This comprehensive index aims to provide a more precise assessment of the environmental quality of the alpine ecosystem. It investigates spatial and temporal variations in ecological quality across the QTP, as well as within individual geographic subregions from 2000 to 2020. The first principal component accounts for an average variance of 63.69%. Over the past 20 years, the spatial distribution pattern of IRSEI on the QTP has shown lower values in the northwest, higher values in the southeast, and predominantly poor grades throughout the region. The mean trend coefficient for IRSEI was 0.002, indicating a gradual improvement in ecological quality on the QTP over time. Among 11 influencing factors examined, NDVI and GPP exhibit significant positive correlation with ecological quality, with q statistics of 0.942 and 0.932, respectively, underscoring the substantial impact of vegetation cover on ecosystem quality. These findings provide a robust theoretical foundation for supporting ecological management, restoration efforts, and the evaluation of ecological restoration within the QTP, thereby promoting ecosystem balance.},
}

*Remote Sensing Technology
*Environmental Monitoring/methods
*Ecosystem
China
Tibet
Spatio-Temporal Analysis
Conservation of Natural Resources
Geographic Information Systems

@article {pmid40329811,
year = {2025},
author = {Yang, Y and Liu, X and Wu, J and Svenning, JC and Liu, J and Shrestha, N},
title = {A comprehensive county-level distribution database of alien and invasive plants in China.},
journal = {Ecology},
volume = {106},
number = {5},
pages = {e70084},
pmid = {40329811},
issn = {1939-9170},
support = {2022YFC2601100//National Key Research and Development Program of China/ ; DNRF173//Danmarks Grundforskningsfond/ ; },
mesh = {*Introduced Species ; China ; *Plants/classification ; *Databases, Factual ; Biodiversity ; },
abstract = {Over the past half century, international trade and exchange have continued to increase in China, resulting in the widespread introduction of alien plant species. The accumulation of these alien species has accelerated invasion events, posing serious threats to local ecological security and economic development. Comprehensive and accurate species distribution records are extremely important for early detection, understanding dispersal dynamics, and supporting various management strategies and research initiatives. However, biodiversity databases, both global and local, often lack comprehensive and high-resolution distribution data for alien invasive plant species (AIPs). This limitation is particularly evident in China, where local databases typically provide coarse spatial data, often restricted to the provincial level, leading to a substantial underestimation of the actual distribution of AIPs. Here, we fill this gap by creating the most comprehensive distribution database for AIPs in China at a much finer spatial resolution. By integrating 73,469 distribution records from China's online herbarium, biodiversity databases, flora, published literature, and 173,396 georeferenced records from GBIF, we built the county-level distribution database for 400 AIPs and report for the first time their presence in 2684 administrative counties in China (92.5% of the total counties). Notably, our database provides 2.58 times more distribution records than global biodiversity data repositories such as GBIF and also includes the earliest introduction dates for each AIP. The temporal range of the records spans from 1607 to 2023, capturing over 400 years of AIP presence in China. These rigorously quality-controlled georeferenced data can be used to examine the dynamics and influencing factors of plant invasions in China. They can also serve as the most updated data reference for policy makers in designing effective AIP management policies in China. We encourage users to cite this data paper when utilizing the data, and there are no restrictions on its use for non-commercial purposes.},
}

*Introduced Species
China
*Plants/classification
*Databases, Factual
Biodiversity

@article {pmid40294093,
year = {2025},
author = {Williams, B and Balvanera, SM and Sethi, SS and Lamont, TAC and Jompa, J and Prasetya, M and Richardson, L and Chapuis, L and Weschke, E and Hoey, A and Beldade, R and Mills, SC and Haguenauer, A and Zuberer, F and Simpson, SD and Curnick, D and Jones, KE},
title = {Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1013029},
pmid = {40294093},
issn = {1553-7358},
mesh = {*Coral Reefs ; Animals ; Acoustics ; *Unsupervised Machine Learning ; *Artificial Intelligence ; Ecosystem ; Algorithms ; Neural Networks, Computer ; Computational Biology ; Fishes/physiology ; Machine Learning ; Environmental Monitoring/methods ; },
abstract = {Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in contrast to detailed but time-consuming analysis of individual bioacoustic events. However, a lack of effective automated analysis for whole soundscape data has impeded progress in this field. Here, we show that machine learning (ML) can be used to unlock greater insights from reef soundscapes. We showcase this on a diverse set of tasks using three biogeographically independent datasets, each containing fish community (high or low), coral cover (high or low) or depth zone (shallow or mesophotic) classes. We show supervised learning can be used to train models that can identify ecological classes and individual sites from whole soundscapes. However, we report unsupervised clustering achieves this whilst providing a more detailed understanding of ecological and site groupings within soundscape data. We also compare three different approaches for extracting feature embeddings from soundscape recordings for input into ML algorithms: acoustic indices commonly used by soundscape ecologists, a pretrained convolutional neural network (P-CNN) trained on 5.2 million hrs of YouTube audio, and CNN's which were trained on each individual task (T-CNN). Although the T-CNN performs marginally better across tasks, we reveal that the P-CNN offers a powerful tool for generating insights from marine soundscape data as it requires orders of magnitude less computational resources whilst achieving near comparable performance to the T-CNN, with significant performance improvements over the acoustic indices. Our findings have implications for soundscape ecology in any habitat.},
}

*Coral Reefs
Animals
Acoustics
*Unsupervised Machine Learning
*Artificial Intelligence
Ecosystem
Algorithms
Neural Networks, Computer
Computational Biology
Fishes/physiology
Machine Learning
Environmental Monitoring/methods

@article {pmid40329386,
year = {2025},
author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y},
title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {114},
pmid = {40329386},
issn = {2049-2618},
support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; },
mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.

RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).

CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.},
}

*Snow/microbiology
Gammaproteobacteria/metabolism/genetics/classification
Metagenomics/methods
Metagenome
*Seawater/microbiology
*Microbiota
*Bacteria/classification/metabolism/genetics/isolation & purification
Phytoplankton/microbiology/metabolism
Multiomics

@article {pmid40328721,
year = {2025},
author = {Zhang, H and Wen, T and Wang, Z and Zhao, X and Wu, H and Xiang, P and Ma, Y},
title = {[Multi-omics analysis of hormesis effect of lanthanum chloride on carotenoid synthesis in Rhodotorula mucilaginosa].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {4},
pages = {1631-1648},
doi = {10.13345/j.cjb.240537},
pmid = {40328721},
issn = {1872-2075},
mesh = {*Lanthanum/pharmacology ; *Rhodotorula/metabolism/drug effects/genetics ; *Carotenoids/metabolism ; *Hormesis/drug effects ; Fermentation ; Multiomics ; },
abstract = {Hormesis effect has been observed in the secondary metabolite synthesis of microorganisms induced by rare earth elements. However, the underlying molecular mechanism remains unclear. To analyze the molecular mechanism of the regulatory effect of Rhodotorula mucilaginosa in the presence of lanthanum chloride, different concentrations of lanthanum chloride were added to the fermentation medium of Rhodotorula mucilaginosa, and the carotenoid content was subsequently measured. It was found that the concentrations of La[3+] exerting the promotional and inhibitory effects were 0-100 mg/L and 100-400 mg/L, respectively. Furthermore, the expression of 33 genes and the synthesis of 55 metabolites were observed to be up-regulated, while the expression of 85 genes and the synthesis of 123 metabolites were found to be down-regulated at the concentration range of the promotional effect. Notably, the expression of carotenoid synthesis-related genes except AL1 was up-regulated. Additionally, the content of β-carotene, lycopene, and astaxanthin demonstrated increases of 10.74%, 5.02%, and 3.22%, respectively. The expression of 5 genes and the synthesis of 91 metabolites were up-regulated, while the expression of 35 genes and the synthesis of 138 metabolites were down-regulated at the concentration range of the inhibitory effect. Meanwhile, the content of β-carotene, lycopene, and astaxanthin decreased by 21.73%, 34.81%, and 35.51%, respectively. In summary, appropriate concentrations of rare earth ions can regulate the synthesis of secondary metabolites by modulating the activities of various enzymes involved in metabolic pathways, thereby exerting the hormesis effect. The findings of this study not only contribute to our comprehension for the mechanism of rare earth elements in organisms but also offer a promising avenue for the utilization of rare earth elements in diverse fields, including agriculture, pharmaceuticals, and healthcare.},
}

*Lanthanum/pharmacology
*Rhodotorula/metabolism/drug effects/genetics
*Carotenoids/metabolism
*Hormesis/drug effects
Fermentation
Multiomics

@article {pmid40325107,
year = {2025},
author = {Pitogo, KME and Meneses, CG and Flores, ABA and Saavedra, AJL and Amarga, AKS and Angeles, MD and Lucañas, CC and Decena, SCP and Venturina, REL and Fidelino, JS and Pantinople, D and Cabañas, AJC and Herr, MW and Bernstein, JM and Chan, KO and Sanguila, MB and Mallari, NA and Brown, RM and Supsup, CE},
title = {Caught in statistical noise: pitfalls of a unidimensional approach to understanding biodiversity-conflict relationships.},
journal = {npj biodiversity},
volume = {4},
number = {1},
pages = {17},
pmid = {40325107},
issn = {2731-4243},
}

@article {pmid40324092,
year = {2025},
author = {Compton, ZT and Vincze, O and Mellon, W and Tollis, M and Abegglen, L and Schiffman, JD and Giraudeau, M and Boddy, AM and Maley, CC},
title = {Paradoxical indeed.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {19},
pages = {e2504512122},
doi = {10.1073/pnas.2504512122},
pmid = {40324092},
issn = {1091-6490},
support = {T32 CA272303/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; },
}

@article {pmid40323496,
year = {2025},
author = {Oyelayo, EA and Taiwo, TJ and Oyelude, SO and Alao, JO},
title = {The global impact of industrialisation and climate change on antimicrobial resistance: assessing the role of Eco-AMR Zones.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {6},
pages = {625},
pmid = {40323496},
issn = {1573-2959},
mesh = {*Industrial Development ; *Drug Resistance, Microbial/genetics ; *Climate Change ; Temperature ; Environmental Monitoring ; Genes, Microbial ; Computational Biology ; Anti-Bacterial Agents ; },
abstract = {This study examines the relationship between industrialisation, climate change, and antimicrobial resistance (AMR) gene prevalence. Data analysis from the top 20 highly industrialised and the top 20 least industrialised nations revealed that industrial activities significantly contribute to global warming, with temperature increases of up to 2 °C observed in highly industrialised regions. These environmental changes influence the distribution and evolution of AMR genes, as rising temperatures can affect bacterial resistance in a manner similar to antibiotics. Through a bioinformatics approach, a marked disparity in AMR gene frequencies was observed between highly industrialised and less industrialised nations, with developed countries reporting higher frequencies due to extensive antibiotic use and advanced monitoring systems. 'Eco-AMR Zones' is proposed as a solution to specialised areas by promoting sustainable industrial practices, enforcing pollution controls, and regulating antibiotic use to mitigate AMR's environmental and public health impacts. These zones, supported by collaboration across various sectors, offer a promising approach to preserving antibiotic effectiveness and reducing environmental degradation. The study emphasises the importance of integrated global strategies that address both the ecological and public health challenges posed by AMR, advocating for sustainable practices, international collaboration, and ongoing research to combat the evolving threats of climate change and antimicrobial resistance.},
}

*Industrial Development
*Drug Resistance, Microbial/genetics
*Climate Change
Temperature
Environmental Monitoring
Genes, Microbial
Computational Biology
Anti-Bacterial Agents

@article {pmid40112992,
year = {2025},
author = {Wei, L and Luo, Z and Wu, X and Liu, C and Shi, Y and Zhang, Q and Chen, M and Qin, W},
title = {Multi-omics analysis provided insights into the fruit softening of postharvest okra under carboxymethyl chitosan treatment.},
journal = {International journal of biological macromolecules},
volume = {307},
number = {Pt 3},
pages = {142149},
doi = {10.1016/j.ijbiomac.2025.142149},
pmid = {40112992},
issn = {1879-0003},
mesh = {*Chitosan/analogs & derivatives/pharmacology ; *Fruit/drug effects/metabolism/genetics ; *Abelmoschus/genetics/metabolism/drug effects ; Gene Expression Regulation, Plant/drug effects ; Transcriptome/drug effects ; *Metabolomics/methods ; Metabolome/drug effects ; Gene Expression Profiling ; Pectins/metabolism ; Multiomics ; },
abstract = {To understand the potential regulatory mechanism of carboxymethyl chitosan (CMCS) treatment on postharvest softening of okra, a joint analysis of physiologic index, transcriptome and metabolome was used. The results showed that CMCS could delay the deterioration of the apparent quality of okra and reduce the degradation of chlorophyll. CMCS can reduce the accumulation of WSP and CSP and the decrease of NSP, and inhibit the enzyme activities of pectin degradation (PE, PG, PL). The results of metabolic pathways related to quality and texture showed that CMCS could increase the metabolic level of pentose phosphate pathway (PPP), inhibit the expression of membrane lipid degradation-related genes, and balance the expression of antioxidant-related genes. Ethylene and abscisic acid (ABA) are two important phytohormones. CMCS down-regulates the biosynthesis of ethylene and increases the expression of ABA. The combined analysis of transcriptome and metabolome showed that CMCS could significantly up-regulate flavonoid biosynthesis metabolites and transcriptional expression levels. Cellulose and pectin are important polymers to maintain the rigidity of okra cell wall. CMCS treatment can slow down the accumulation of cellulose by regulating the expression of DEGs related to cellulose synthesis (CesA) and degradation (EGase). CMCS slowed down the degradation of pectin by down-regulating the expression of pectin degradation-related genes. These results indicate that the quality of okra is deteriorated and the fruit is softened during cold storage. CMCS treatment can improve the nutritional quality of okra and slow down its texture decline. In this study, the regulatory effect of CMCS on softening and quality deterioration of okra during cold storage was discussed at the molecular level, which provided a reference for improving the quality of postharvest okra.},
}

*Chitosan/analogs & derivatives/pharmacology
*Fruit/drug effects/metabolism/genetics
*Abelmoschus/genetics/metabolism/drug effects
Gene Expression Regulation, Plant/drug effects
Transcriptome/drug effects
*Metabolomics/methods
Metabolome/drug effects
Gene Expression Profiling
Pectins/metabolism
Multiomics

@article {pmid40089216,
year = {2025},
author = {Torres-Roman, JS and Quispe-Vicuña, C and Benavente-Casas, A and Julca-Marin, D and Rios-Garcia, W and Challapa-Mamani, MR and Rio-Muñiz, LD and Ybaseta-Medina, J},
title = {Trends in stroke mortality in Latin America and the Caribbean from 1997 to 2020 and predictions to 2035: An analysis of gender, and geographical disparities.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {34},
number = {6},
pages = {108286},
doi = {10.1016/j.jstrokecerebrovasdis.2025.108286},
pmid = {40089216},
issn = {1532-8511},
mesh = {Humans ; Latin America/epidemiology ; Female ; Male ; *Stroke/mortality/diagnosis ; Caribbean Region/epidemiology ; Risk Factors ; Sex Factors ; Middle Aged ; Sex Distribution ; Time Factors ; Databases, Factual ; Aged ; Adult ; *Health Status Disparities ; Age Distribution ; Forecasting ; Risk Assessment ; Age Factors ; Young Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Stroke is a leading cause of death and disability globally, with significant public health implications. In Latin America, while mortality rates have declined, the number of stroke cases has increased due to prevalent risk factors like high blood pressure and obesity. Unlike Europe, recent trends in stroke mortality in this region remain underreported.

OBJECTIVE: This study evaluates stroke mortality rates in Latin America Latin American and Caribbean (LAC) countries from 1997 to 2020 and predictions to 2035.

METHODS: This ecological observational study utilized mortality data from the World Health Organization database. Trends were analyzed using Joinpoint regression to evaluate the annual percent change (APC) by sex and country. Predicted mortality rates through 2035 were calculated using the Nordpred package in R. Changes in stroke mortality were assessed by disentangling the effects of population growth, aging, and risk factor modifications, based on age-specific rates and projections. Results were presented as absolute case numbers and relative percentages.

RESULTS: From 1997 to 2020, twelve countries presented significant reductions in stroke mortality rates for men in LAC, the main ones being Chile (-4.2 %), El Salvador (-4.2 %), and Puerto Rico (-4.0 %). Thirteen countries reported a reduction in their mortality for women, mainly in Puerto Rico (-4.3 %), Chile (-3.7 %), Argentina, El Salvador, and Uruguay (-3.5 %). By 2035, an increase in deaths among men and women is expected, mainly due to the increase in population structure and size. However, a decrease in the mortality rate will be reported, mainly due to the reduction of risk factors.

CONCLUSION: Our final findings show a reduction in stroke mortality trends in LAC countries between 1997 and 2020, due to creating public awareness about vascular risk factors by authorities and the implementation of effective health policies. By 2035, an overall increase in mortality is expected, mainly due to population change in each country.},
}

Humans
Latin America/epidemiology
Female
Male
*Stroke/mortality/diagnosis
Caribbean Region/epidemiology
Risk Factors
Sex Factors
Middle Aged
Sex Distribution
Time Factors
Databases, Factual
Aged
Adult
*Health Status Disparities
Age Distribution
Forecasting
Risk Assessment
Age Factors
Young Adult
Aged, 80 and over

@article {pmid40102961,
year = {2025},
author = {Hinojosa-Alvarez, S and Mendoza-Portillo, V and Chavez-Santoscoy, RA and Hernández-Pérez, J and Felix-Ceniceros, A and Magallón-Gayón, E and Mar-Silva, AF and Ochoa-Zavala, M and Díaz-Jaimes, P},
title = {The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {5},
pages = {},
doi = {10.1093/g3journal/jkaf059},
pmid = {40102961},
issn = {2160-1836},
support = {CF-2023-G-493//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {Animals ; *Genome ; Molecular Sequence Annotation ; *Genomics/methods ; *Perciformes/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; *Fishes/genetics ; Whole Genome Sequencing ; Computational Biology/methods ; },
abstract = {For the first time, the complete genome assembly of the dolphinfish (Coryphaena hippurus), a tropical cosmopolitan species with commercial fishing importance was sequenced. Using a combination of Illumina and Nanopore sequencing technologies, a draft genome of 497.8 Mb was assembled into 6,044 contigs, with an N50 of 200.9 kb and a BUSCO genome completeness score of 89%. This high-quality genome assembly provides a valuable resource to study adaptive evolutionary processes and supports conservation and management strategies for this ecologically and economically significant species.},
}

Animals
*Genome
Molecular Sequence Annotation
*Genomics/methods
*Perciformes/genetics
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing
*Fishes/genetics
Whole Genome Sequencing
Computational Biology/methods

@article {pmid40319413,
year = {2025},
author = {Wang, Y and Mao, Z and Yu, J and Feng, B and Zhang, Z and Zhong, L and Tang, Y},
title = {Construction of risk management system for polluted sites in coal industry clusters.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {6},
pages = {195},
pmid = {40319413},
issn = {1573-2983},
mesh = {*Coal Industry ; *Risk Management/methods ; China ; *Coal ; *Environmental Pollution/prevention & control/statistics & numerical data ; Soil/chemistry ; Groundwater/chemistry ; Environmental Restoration and Remediation ; Environmental Monitoring ; Risk Assessment ; Decision Making, Organizational ; *Coal Mining ; Decision Making, Computer-Assisted ; Algorithms ; *Environmental Pollutants/analysis ; },
abstract = {Coal has always been the main source of energy in China, accounting for more than 60% of primary energy production and consumption. As a result of coal mining, coal industry agglomerations such as mining, coal chemical industry, and so on have been gradually formed, and there are many types of industries in the agglomerations, complex sources of pollutants, and sensitive soil and water environments, and all kinds of industrial sites and solid waste dumps of coal-related industries may pollute the soil and groundwater, and have a certain impact on the ecological environment. However, at present, there is a lack of a targeted region-wide pollution risk management technology system for the polluted sites in the agglomeration area, therefore, it is particularly important to construct a scientific and complete soil-groundwater risk management system and propose more targeted and effective control strategies for the polluted sites in the coal industry agglomeration area. Based on the domestic and international experience and historical data, this paper takes the coal industry cluster area as the research object classifies the land in the area according to the land use type into construction land, agricultural land, and another ecological land, and carries out the risk zoning and grading based on the dosage-effect model and the potential ecological hazard index method respectively, assesses the appropriateness, feasibility, and necessity of the implementation of risk control for the polluted plots, and then designs and develops a risk control decision-making framework by using the hierarchical analysis method. Hierarchical analysis was used to design and develop a decision-making framework for risk management, and finally, the optimal risk management and remediation strategy was proposed based on the AHP + TOPSIS algorithm, which combined with the contaminated land conditions to propose a suitable solution.},
}

*Coal Industry
*Risk Management/methods
China
*Coal
*Environmental Pollution/prevention & control/statistics & numerical data
Soil/chemistry
Groundwater/chemistry
Environmental Restoration and Remediation
Environmental Monitoring
Risk Assessment
Decision Making, Organizational
*Coal Mining
Decision Making, Computer-Assisted
Algorithms
*Environmental Pollutants/analysis

@article {pmid40318965,
year = {2025},
author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C},
title = {Corrigendum to "Integrating 'nature' in the water-energy-food nexus: Current perspectives and future directions" [Science of The Total Environment, Volume 966, 2025, 178600].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {179482},
doi = {10.1016/j.scitotenv.2025.179482},
pmid = {40318965},
issn = {1879-1026},
}

@article {pmid40318638,
year = {2025},
author = {Aguilar-Gómez, D and Bejder, J and Graae, J and Ko, Y and Vaughn, A and Clement, K and Tristani-Firouzi, M and Lee, JY and Nordsborg, NB and Nielsen, R and Ilardo, M},
title = {Genetic and training adaptations in the Haenyeo divers of Jeju, Korea.},
journal = {Cell reports},
volume = {},
number = {},
pages = {115577},
doi = {10.1016/j.celrep.2025.115577},
pmid = {40318638},
issn = {2211-1247},
abstract = {Natural selection and relative isolation have shaped the genetics and physiology of unique human populations from Greenland to Tibet. Another such population is the Haenyeo, the all-female Korean divers renowned for their remarkable diving abilities in frigid waters. Apnea diving induces considerable physiological strain, particularly in females diving throughout pregnancy. In this study, we explore the hypothesis that breath-hold diving has shaped physiological and genetic traits in the Haenyeo. We identified pronounced bradycardia during diving, a likely training effect. We paired natural selection and genetic association analyses to investigate adaptive genetic variation that may mitigate the effects of diving on pregnancy through an associated reduction of diastolic blood pressure. Finally, we identified positively selected variation in a gene previously associated with cold water tolerance, which may contribute to reduced hypothermia susceptibility. These findings highlight the importance of traditional diving populations for understanding genetic and physiological adaptation.},
}

@article {pmid40318544,
year = {2025},
author = {Gomes, MLS and Cestari, VRF and Florêncio, RS and Yamamura, M and Santos, JO and Sales, LBF and Silva, RR and Oriá, MOB},
title = {Spatial-temporal analysis of cervical cancer screening and social and health indicators in Brazil.},
journal = {Public health},
volume = {243},
number = {},
pages = {105747},
doi = {10.1016/j.puhe.2025.105747},
pmid = {40318544},
issn = {1476-5616},
abstract = {OBJECTIVE: To identify the spatial-temporal patterns of cervical cancer (CC) screening in Brazil from 2013 to 2022 and its relationship with social and health indicators.

STUDY DESIGN: This ecological study uses data from the Cancer Information System (SISCAN) of the Brazilian Unified Health System's Department of Informatics.

METHODS: The study analyzed women aged 25 to 64 who underwent CC screening in 5570 municipalities across Brazil. Global Moran's I and the Local Index of Spatial Autocorrelation (LISA) were employed to investigate clustering. The purely spatial scan statistic technique was used for spatial cluster detection. Temporal trends were assessed using joinpoint regression. GeoDa, SaTScan, GWR, and QGIS software were used for the analysis.

RESULTS: The global clustering analysis of CC screening proportions revealed significant spatial autocorrelation (Moran's I = 0.530). Clusters of municipalities with low screening rates were significantly observed in the Northern (Amapá, Amazonas, Rondônia, Roraima) and Northeastern (Piauí, Pernambuco) regions. The Gini Index (β = -2.60), the Municipal Human Development Index (MHDI) (β = -10.5), and the Social Vulnerability Index (SVI) (β = -9.14) showed negative associations. Conversely, Family Health Strategy (FHS) coverage (β = 2.18) demonstrated a positive impact on screening rates. In terms of temporal trends, the screening proportion gradually increased from 5.4 % in 2014 to 10.5 % in 2022.

CONCLUSION: Areas with a high risk of low CC screening rates were identified in the Northern and Northeastern regions of Brazil, which are characterized by socioeconomic and demographic disparities, vulnerabilities, and inequalities.},
}

@article {pmid40317095,
year = {2025},
author = {Seizer, L and Pascher, A and Branz, S and Schmitt, N and Löchner, J and Schuller, BW and Rohleder, N and Renner, TJ},
title = {Bridging acute and chronic stress effects on inflammation: protocol for a mixed-methods intensive longitudinal study.},
journal = {BMC psychology},
volume = {13},
number = {1},
pages = {464},
pmid = {40317095},
issn = {2050-7283},
mesh = {Humans ; Longitudinal Studies ; *Stress, Psychological/metabolism/immunology/complications ; *Inflammation/metabolism/psychology/immunology ; Saliva/chemistry ; Male ; Female ; Young Adult ; Chronic Disease ; Adult ; Ecological Momentary Assessment ; Biomarkers/metabolism ; Cytokines/metabolism ; Research Design ; },
abstract = {Acute stress triggers adaptive physiological responses-including transient increases in inflammatory cytokines-while chronic stress is associated with sustained inflammatory activity that may underlie the development of various disorders. Despite extensive research on each stress type individually, the transition and interaction between them remain underexplored. This study aims to address this gap by employing an intensive longitudinal measurement burst design. Healthy university students will be recruited and monitored over three one-week assessment bursts, spaced by three-month breaks. Participants will complete ecological momentary assessments four times daily, recording their emotional states, stress experiences, and daily incidents. Simultaneously, saliva samples will be collected at matching time points to measure biomarkers of immune and stress system activity. In addition, daily audio diaries will provide qualitative context through advanced speech analysis techniques. Data will be analyzed using a multi-level modeling approach to differentiate within-person dynamics from between-person variability, accounting for potential moderators. The findings are expected to shed light on how repeated acute stressors transition into chronic stress and how chronic stress burden may influence acute stress responses.},
}

Humans
Longitudinal Studies
*Stress, Psychological/metabolism/immunology/complications
*Inflammation/metabolism/psychology/immunology
Saliva/chemistry
Male
Female
Young Adult
Chronic Disease
Adult
Ecological Momentary Assessment
Biomarkers/metabolism
Cytokines/metabolism
Research Design

@article {pmid39937595,
year = {2025},
author = {Royaux, C and Mihoub, JB and Jossé, M and Pelletier, D and Norvez, O and Reecht, Y and Fouilloux, A and Rasche, H and Hiltemann, S and Batut, B and Marc, E and Seguineau, P and Massé, G and Amossé, A and Bissery, C and Lorrilliere, R and Martin, A and Bas, Y and Virgoulay, T and Chambon, V and Arnaud, E and Michon, E and Urfer, C and Trigodet, E and Delannoy, M and Loïs, G and Julliard, R and Grüning, B and Le Bras, Y and , },
title = {Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {39937595},
issn = {2047-217X},
support = {2020-1-NL01-KA203-064717//European Union/ ; //Agence Nationale de la Recherche/ ; //Muséum National d'Histoire Naturelle/ ; //Ministry of Higher Education and Research/ ; },
mesh = {*Ecology/methods/standards ; *Software ; *Data Analysis ; Reproducibility of Results ; *Computational Biology/methods/standards ; },
abstract = {Numerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as "atoms" composing an analytical procedure. When generalized, "atoms" can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized.},
}

*Ecology/methods/standards
*Software
*Data Analysis
Reproducibility of Results
*Computational Biology/methods/standards

@article {pmid40316929,
year = {2025},
author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lembebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, G and Wedajo, LF and Purohit, S and Kalayou, MH},
title = {Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {647},
pmid = {40316929},
issn = {1471-2334},
mesh = {Humans ; Ethiopia/epidemiology ; Infant ; *Pneumonia/epidemiology/diagnosis ; *Machine Learning ; Female ; Male ; Algorithms ; Risk Factors ; },
abstract = {INTRODUCTION: Pneumonia is the leading cause of child morbidity and mortality and accounts for 5.6 million under-five child deaths. Pneumonia has a significant impact on the quality of life, the country's economy, and the survival of children. Therefore, this study aimed to develop data-driven predictive model using machine learning algorithms to predict pneumonia and stratify the determinant factors among children aged 6-23 months in Ethiopia.

METHODS: A total of 2035 samples of children were used from the 2016 Ethiopian Demographic and Health Survey dataset. Jupyter Notebook from Anaconda Navigators was used for data management and analysis. Important libraries such as Pandas, Seaborn, and Numpy were imported from Python. The data was pre-processed into a training and testing dataset with a 4:1 ratio, and tenfold cross-validation was used to reduce bias and enhance the models' performance. Six machine learning algorithms were used for model building and comparison, and confusion matrix elements were used to evaluate the performance of each algorithm. Principal component analysis and heatmap function were used for correlation detection between features. Feature importance score was used to identify and stratify the most important predictors of pneumonia.

RESULTS: From 2035 total samples, 16.6%, 20.1%, and 24.2% of children had short rapid breath, fever, and cough respectively. The overall magnitude of pneumonia among children aged 6-23 months was 31.3% based on the 2016 EDHS report. A random forest algorithm is the relatively best performance model to predict pneumonia and stratify its determinates with 91.3% accuracy. The health facility visits, child sex, initiation of breastfeeding, birth interval, birth weight, husbands' education, women's age, and region, are the top eight important predictors of pneumonia among children with important scores of more than 5% to 20% respectively.

CONCLUSIONS: Random forest is the best model to predict pneumonia and stratify its determinant factors. The implications of this study are profound for advanced research methodology, tailored to promote effective health interventions such as lifestyle modification and behavioral intervention, based on individuals' unique features, specifically for stakeholders to take proactive childcare interventions. The study would serve as pioneering evidence for future research, and researchers are recommended to use deep learning algorithms to enhance prediction accuracy.},
}

Humans
Ethiopia/epidemiology
Infant
*Pneumonia/epidemiology/diagnosis
*Machine Learning
Female
Male
Algorithms
Risk Factors

@article {pmid40307287,
year = {2025},
author = {Wu, J and He, D and Wang, Y and Liu, S and Du, Y and Wang, H and Tan, S and Zhang, D and Xie, J},
title = {An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {717},
pmid = {40307287},
issn = {2052-4463},
mesh = {*Metabolome ; *Microbiota ; Nutrients ; Plant Roots/microbiology/metabolism ; *Populus/microbiology/genetics/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Transcriptome ; Datasets as Topic ; },
abstract = {The rhizosphere microbiota recruited by plants contributes significantly to maintaining host productivity and resisting stress. However, the genetic mechanisms by which plants regulate this recruitment process remain largely unclear. Here, we generated a comprehensive dataset, including 27 root transcriptomes, 27 root metabolomes, and 54 bulk or rhizosphere soil 16S rRNA amplicons across nine poplar species from four sections grown in nutrient-poor natural soil, along with eleven growth phenotype data. We provided a thorough description of this dataset, followed by a comprehensive co-expression network analysis example that broke down the wall of the four-way relationship between plant gene-metabolite-microbe-phenotype, thus identifying the links between plant gene expression, metabolite accumulation, growth behavior, and rhizosphere microbiome variation under nutrient-poor conditions. Overall, this dataset enhances our understanding of plant and microbe interactions, offering valuable strategies and novel insights for resolving how plants regulate rhizosphere microbial compositions and functions, thereby improving host fitness, which will benefit future research.},
}

*Metabolome
*Microbiota
Nutrients
Plant Roots/microbiology/metabolism
*Populus/microbiology/genetics/metabolism
Rhizosphere
RNA, Ribosomal, 16S/genetics
Soil Microbiology
*Transcriptome
Datasets as Topic

@article {pmid40314555,
year = {2025},
author = {Yu, Z and Li, S and Yang, W and Chen, J and Rahman, MA and Wang, C and Ma, W and Yao, X and Xiong, J and Xu, C and Zhou, Y and Chen, J and Huang, K and Gao, X and Fensholt, R and Weng, Q and Zhou, W},
title = {Enhancing Climate-Driven Urban Tree Cooling with Targeted Nonclimatic Interventions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c14275},
pmid = {40314555},
issn = {1520-5851},
abstract = {Urban trees play a pivotal role in mitigating heat, yet the global determinants and patterns of their cooling efficiency (CE) remain elusive. Here, we quantify the diel CE of 229 cities across four climatic zones and employ a machine-learning model to assess the influence of variables on CE. We found that for every 10% increase in tree cover, surface temperatures are reduced by 0.25 °C during the day and 0.04 °C at night. Trees in humid regions exhibit the highest daytime CE, while those in arid zones demonstrate the greatest cooling effect at night. This can be explained by the difference in canopy density between the humid and arid zones. During the day, the high canopy density in the humid zone converts more solar radiation into latent heat flux. At night, the low canopy density in the arid zone intercepts less longwave radiation, which favors surface cooling. While climatic factors contribute nearly twice as much to CE as nonclimatic ones, our findings suggest that optimizing CE is possible by managing variables within specific thresholds due to their nonlinear effects. For instance, we revealed that in arid regions, an impervious surface coverage of approximately 60% is optimal, whereas in humid areas, reducing it to around 40% maximizes cooling benefits. These insights underscore the need for targeted management of nonclimatic factors to sustain tree cooling benefits and offer practical guidance for designing climate-resilient, nature-based urban strategies.},
}

@article {pmid40312707,
year = {2025},
author = {Ketchaji, A and Fokam, J and Assah, F and Ateba, F and Wandji, ML and Pamen, JNB and Djoko, GRP and Seugnou, CDN and Kah, E and Atangana, AF and Ateudjieu, J},
title = {The impact of short message service reminders or peer home visits on adherence to antiretroviral therapy and viral load suppression among HIV-Infected adolescents in Cameroon: a randomized controlled trial.},
journal = {AIDS research and therapy},
volume = {22},
number = {1},
pages = {49},
pmid = {40312707},
issn = {1742-6405},
mesh = {Humans ; *HIV Infections/drug therapy/virology ; Adolescent ; Female ; Cameroon/epidemiology ; Male ; *Viral Load/drug effects ; *Text Messaging ; *House Calls ; Young Adult ; *Medication Adherence ; *Anti-HIV Agents/therapeutic use ; *Reminder Systems ; Peer Group ; },
abstract = {BACKGROUND: Adherence to antiretroviral therapy (ART) and viral load suppression (VLS) constitute one of the key challenges to control human immunodeficiency virus (HIV), especially during adolescence. This trial aimed at assessing the impact of short message services (SMS) or peer home visits (PHV) on adherence to ART and VL suppression among adolescents living with HIV (ALWHIV) in Cameroon.

METHODS: A randomized controlled trial (RCT) was conducted from July 2018 to February 2019 at the Mother and Child Center of the Chantal Biya Foundation in Yaounde. Eligible ALWHIV (15-19 years), with a fully disclosed HIV status, with availability of phone and guardian's consent, were randomly assigned to receive either daily SMS or bi-weekly PHV for a six-months period. The control-group received standard of care according to the national guidelines. Study investigators and participants were not blinded to the interventions group allocation, and no adverse events or side effects were observed. Adjusted logistic regression was used to assess the impact of interventions on outcomes. The study was approved by The Pan-African Clinical Trials Registry with PACTR201904582515723 at (www.pactr.org).

RESULTS: Adherence to ART increased in the PHV (aRR: 4.3; 95% CI: 2.2-8.3; p < 0.001) and SMS (aRR: 3.1, 95% CI: 2.1-5.3; p < 0.001) groups compared to the control-group. Likewise, VL suppression was higher in PHV (aRR: 2.1; 95% CI: 1.9-7.5 p < 0.001) and SMS (aRR: 3.2; 95% CI: 1.8-5.4; p < 0.001) groups compared to the control-group. Based on CI, both interventions showed similar benefits on improving adherence and VLS.

CONCLUSIONS: Among ALHIV, SMS or PHV contribute substantially to improving adherence and VL suppression among ALWHIV. Implementing such strategies would support efforts in eliminating pediatric AIDS in low- and middle-income countries.},
}

Humans
*HIV Infections/drug therapy/virology
Adolescent
Female
Cameroon/epidemiology
Male
*Viral Load/drug effects
*Text Messaging
*House Calls
Young Adult
*Medication Adherence
*Anti-HIV Agents/therapeutic use
*Reminder Systems
Peer Group

@article {pmid40120189,
year = {2025},
author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y},
title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.},
journal = {Water research},
volume = {279},
number = {},
pages = {123497},
doi = {10.1016/j.watres.2025.123497},
pmid = {40120189},
issn = {1879-2448},
mesh = {*Sewage ; *Ammonia ; Anaerobiosis ; Iron/chemistry ; Methane ; *Peracetic Acid/chemistry ; Multiomics ; },
abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.},
}

*Sewage
*Ammonia
Anaerobiosis
Iron/chemistry
Methane
*Peracetic Acid/chemistry
Multiomics

@article {pmid39871222,
year = {2025},
author = {Diongue, FB and Faye, A and Loucoubar, C and Sougou, NM and Sy, I and Tall, A and Ndiaye, Y and Sarr, SC},
title = {Situational analysis of the quality of maternal, child, and adolescent health data in the health districts of Thiès, Mbour, Kédougou, and Saraya in Senegal.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {337},
pmid = {39871222},
issn = {1471-2458},
mesh = {Senegal ; Humans ; Adolescent ; Female ; *Data Accuracy ; Child ; *Health Information Systems/standards ; *Child Health/statistics & numerical data ; *Adolescent Health/statistics & numerical data ; Qualitative Research ; Lot Quality Assurance Sampling ; *Maternal Health ; },
abstract = {INTRODUCTION: In Senegal, the Routine Health Information System (RHIS) captures the majority of data from the Ministry of Health and Social Action (MHSA) public structures and very little health data from the private sector and other ministerial departments. Quality data strengthens the validity and reliability of research results. Common areas of data quality include accuracy, completeness, consistency, credibility, and timeliness. The work aims to assess the quality of routine maternal, child, and adolescent health data in Senegal.

MATERIALS AND METHODS: A mixed quantitative and qualitative design was chosen in four health districts, including Thiès, Mbour, Kédougou, and Saraya. The study included functional health structures that produce maternal, child, and adolescent health data. For the quantitative part, a descriptive and analytical study was carried out. Lot Quality Assurance Sampling (LQAS) was used as the sampling method. Data were collected using Performance of Routine Information Systems Management (PRISM) data collection tools and the ODK application and analyzed (univariate and bivariate) using R and Stata with an alpha risk of 5%. The following data quality indicators (accuracy, completeness, and promptness) were estimated. An exploratory case study and purposive sampling supported the qualitative part by implementing individual interviews.

RESULTS: The study showed an accuracy ratio of 1 in the intervention districts, a difference in the control districts, and a disparity in the transmission of guidelines between districts (inter- and intra-region). The average level of completeness was 0.64 (+/- 0.44) for all regions combined, with no significant difference between districts. The promptness rate for Kédougou, Saraya, Thiès, and Mbour districts was 81%, 75.9%, 72.2%, and 86.7%, respectively. Between 40% and 60% of facilities in each district carried out self-assessments. Data collection tools were considered to be numerous. A large number of tools were easy to use. The recording space was appreciated. On the other hand, the length of the forms was little or not appreciated by the providers. Few of the providers in the 4 districts had been trained to record data in DHIS2.

CONCLUSION: Assessment of data quality in the districts studied shows shortcomings in terms of completeness and timeliness. Many factors influence the SMEA data quality situation, including knowledge or application of RHIS policies, standards, and protocols, perception of the importance of RHIS, ease of use of data collection tools, training of providers, and diversity of data production sources.},
}

Senegal
Humans
Adolescent
Female
*Data Accuracy
Child
*Health Information Systems/standards
*Child Health/statistics & numerical data
*Adolescent Health/statistics & numerical data
Qualitative Research
Lot Quality Assurance Sampling
*Maternal Health

@article {pmid40307720,
year = {2025},
author = {Moreau, SJM and Marchal, L and Boulain, H and Musset, K and Labas, V and Tomas, D and Gauthier, J and Drezen, JM},
title = {Multi-omic approach to characterize the venom of the parasitic wasp Cotesia congregata (Hymenoptera: Braconidae).},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {431},
pmid = {40307720},
issn = {1471-2164},
support = {ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; SMHART project 35069//European Regional Development Fund/ ; SMHART project 35069//European Regional Development Fund/ ; },
mesh = {Animals ; *Wasps/genetics/virology/metabolism ; *Wasp Venoms/genetics/metabolism/chemistry ; Female ; *Proteomics/methods ; Insect Proteins/genetics/metabolism/chemistry ; Multiomics ; },
abstract = {BACKGROUND: Cotesia congregata is a parasitoid Hymenoptera belonging to the Braconidae family and carrying CCBV (Cotesia congregata Bracovirus), an endosymbiotic polydnavirus. CCBV virus is considered as the main virulence factor of this species, which has raised questions, over the past thirty years, about the potential roles of venom in the parasitic interaction between C. congregata and its host, Manduca sexta (Lepidoptera: Sphingidae). To investigate C. congregata venom composition, we identified genes overexpressed in the venom glands (VGs) compared to ovaries, analyzed the protein composition of this fluid and performed a detailed analysis of conserved domains of these proteins.

RESULTS: Of the 14 140 known genes of the C. congregata genome, 659 genes were significantly over-expressed (with 10-fold or higher changes in expression) in the VGs of female C. congregata, compared with the ovaries. We identified 30 proteins whose presence was confirmed in venom extracts by proteomic analyses. Twenty-four of these were produced as precursor molecules containing a predicted signal peptide. Six of the proteins lacked a predicted signal peptide, suggesting that venom production in C. congregata also involves non-canonical secretion mechanisms. We have also analysed 18 additional proteins and peptides of interest whose presence in venom remains uncertain, but which could play a role in VG function.

CONCLUSIONS: Our results show that the venom of C. congregata not only contains proteins (including several enzymes) homologous to well-known venomous compounds, but also original proteins that appear to be specific to this species. This exhaustive study sheds a new light on this venom composition, the molecular diversity of which was unexpected. These data pave the way for targeted functional analyses and to better understand the evolutionary mechanisms that have led to the formation of the venomous arsenals we observe today in parasitoid insects.},
}

Animals
*Wasps/genetics/virology/metabolism
*Wasp Venoms/genetics/metabolism/chemistry
Female
*Proteomics/methods
Insect Proteins/genetics/metabolism/chemistry
Multiomics

@article {pmid39849009,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K},
title = {The influence of depth on the global deep-sea plasmidome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2959},
pmid = {39849009},
issn = {2045-2322},
support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; },
mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; },
abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.},
}

*Plasmids/genetics
*Metagenome
*Seawater/microbiology
Ecosystem
Gammaproteobacteria/genetics
Alphaproteobacteria/genetics
Oceans and Seas
Bacteria/genetics
Computational Biology/methods
Indian Ocean

@article {pmid40306212,
year = {2025},
author = {Nica, I and Georgescu, I},
title = {The ecological impact of agricultural production on CO2 emissions in India: Pathways to sustainable agriculture.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125548},
doi = {10.1016/j.jenvman.2025.125548},
pmid = {40306212},
issn = {1095-8630},
abstract = {This study examines the relationship between CO2 emissions and agricultural production in India from 1990 to 2023, using an Autoregressive Distributed Lag (ARDL) model. Key agricultural indicators analyzed include the Food Production Index (FPI), Cereal Production (CP), Livestock Production Index (LPI), and the value added by Agriculture, Forestry, and Fishing (AFF). The results show that on the long run, a 1 % increase in FPI leads to a 7.86 unit increase in CO2 emissions per capita, while a 1 % increase in livestock production results in a 3.28 unit decrease in CO2 emissions per capita. In the short run, a similar increase in food production and livestock production also influences CO2 emissions, with notable but varying impacts over time. These findings underline the environmental trade-offs between food security and CO2 emissions, emphasizing the need for sustainable agricultural practices. This research contributes to existing literature by utilizing a broad set of agricultural indicators and robust ARDL analysis to examine both short- and long-term effects, providing a more comprehensive understanding of agricultural sustainability. The study was prompted by India's rapid agricultural growth, driven by its growing population and economic expansion, which has raised significant environmental concerns. Unlike prior research that often takes a generalized or global approach, this study offers an India-specific analysis that captures the country's distinct socio-economic and ecological conditions. By focusing on nationally relevant agricultural indicators and sustainability challenges, the research provides context-sensitive insights that can support effective and targeted policy design. The findings highlight the importance of policies that align agricultural productivity with sustainability, supporting the UN Sustainable Development Goals on climate action and food security.},
}

@article {pmid40305182,
year = {2025},
author = {Uemura, NA and Nakane, D},
title = {Type IV Pili in Thermophilic Bacteria: Mechanisms and Ecological Implications.},
journal = {Biomolecules},
volume = {15},
number = {4},
pages = {},
pmid = {40305182},
issn = {2218-273X},
support = {24KJ1131//Japan Society for the Promotion of Science/ ; 21K07020//Japan Society for the Promotion of Science/ ; 22H05066//Japan Society for the Promotion of Science/ ; },
mesh = {*Fimbriae, Bacterial/metabolism/physiology ; *Thermus thermophilus/metabolism/physiology/genetics ; },
abstract = {Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables bacteria to move over two-dimensional surfaces through repeated cycles of extension and retraction of pilus filaments. Notably, T. thermophilus exhibits upstream-directed migration under shear stress, known as rheotaxis, which appears to represent an adaptive strategy unique to thermophilic bacteria thriving in rapid water flows. Furthermore, T4P contributes to the capture of DNA and phages, indicating their multifunctionality in natural environments. Understanding the T4P dynamics provides insights into bacterial survival and evolution in extreme habitats.},
}

*Fimbriae, Bacterial/metabolism/physiology
*Thermus thermophilus/metabolism/physiology/genetics

@article {pmid40303041,
year = {2024},
author = {McDuie, F and T Overton, C and A Lorenz, A and L Matchett, E and L Mott, A and A Mackell, D and T Ackerman, J and De La Cruz, SEW and Patil, VP and Prosser, DJ and Takekawa, JY and Orthmeyer, DL and Pitesky, ME and Díaz-Muñoz, SL and Riggs, BM and Gendreau, J and Reed, ET and Petrie, MJ and Williams, CK and Buler, JJ and Hardy, MJ and Ladman, BS and Legagneux, P and Bêty, J and Thomas, PJ and Rodrigue, J and Lefebvre, J and Casazza, ML},
title = {Mitigating Risk: Predicting H5N1 Avian Influenza Spread with an Empirical Model of Bird Movement.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {5525298},
pmid = {40303041},
issn = {1865-1682},
mesh = {Animals ; *Influenza in Birds/epidemiology/virology/transmission/prevention & control ; *Influenza A Virus, H5N1 Subtype/physiology ; *Animal Migration ; Birds ; Geographic Information Systems ; Disease Outbreaks/veterinary ; Animals, Wild ; },
abstract = {Understanding timing and distribution of virus spread is critical to global commercial and wildlife biosecurity management. A highly pathogenic avian influenza virus (HPAIv) global panzootic, affecting ~600 bird and mammal species globally and over 83 million birds across North America (December 2023), poses a serious global threat to animals and public health. We combined a large, long-term waterfowl GPS tracking dataset (16 species) with on-ground disease surveillance data (county-level HPAIv detections) to create a novel empirical model that evaluated spatiotemporal exposure and predicted future spread and potential arrival of HPAIv via GPS tracked migratory waterfowl through 2022. Our model was effective for wild waterfowl, but predictions lagged HPAIv detections in poultry facilities and among some highly impacted nonmigratory species. Our results offer critical advance warning for applied biosecurity management and planning and demonstrate the importance and utility of extensive multispecies tracking to highlight potential high-risk disease spread locations and more effectively manage outbreaks.},
}

Animals
*Influenza in Birds/epidemiology/virology/transmission/prevention & control
*Influenza A Virus, H5N1 Subtype/physiology
*Animal Migration
Birds
Geographic Information Systems
Disease Outbreaks/veterinary
Animals, Wild

@article {pmid39852552,
year = {2025},
author = {Yang, H and Luo, X and Shang, Z and Li, K and Cai, J and Chen, Y and Xin, L and Ju, J},
title = {Metabolic Blockade-Based Genome Mining of Malbranchea circinata SDU050: Discovery of Diverse Secondary Metabolites.},
journal = {Marine drugs},
volume = {23},
number = {1},
pages = {},
pmid = {39852552},
issn = {1660-3397},
support = {U2106207//National Natural Science Foundation of China/ ; 2022YFC2804100//National Key Research and Development Program of China/ ; 22037006//National Natural Science Foundation of China/ ; SYS202205//Shandong Laboratory Program/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology/isolation & purification ; *Secondary Metabolism/genetics ; Multigene Family ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Genome, Fungal ; Microbial Sensitivity Tests ; Gram-Positive Bacteria/drug effects ; Staphylococcus aureus/drug effects ; Bacillus subtilis/drug effects ; *Ascomycota/genetics/metabolism ; Isocoumarins/pharmacology ; Computational Biology ; Geologic Sediments/microbiology ; },
abstract = {Malbranchea circinata SDU050, a fungus derived from deep-sea sediment, is a prolific producer of diverse secondary metabolites. Genome sequencing revealed the presence of at least 69 biosynthetic gene clusters (BGCs), including 30 encoding type I polyketide synthases (PKSs). This study reports the isolation and identification of four classes of secondary metabolites from wild-type M. circinata SDU050, alongside five additional metabolite classes, including three novel cytochalasins (7-9), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (1) enabled the deduction of its biosynthetic pathway based on gene function predictions. Bioactivity assays demonstrated that sclerin (1) and (-)-mycousnine (10) exhibited weak antibacterial activity against Gram-positive bacteria such as Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Bacillus subtilis. These findings underscore the chemical diversity and biosynthetic potential of M. circinata SDU050 and highlight an effective strategy for exploring marine fungal metabolites.},
}

*Anti-Bacterial Agents/pharmacology/isolation & purification
*Secondary Metabolism/genetics
Multigene Family
Polyketide Synthases/genetics/metabolism
Biosynthetic Pathways/genetics
Methicillin-Resistant Staphylococcus aureus/drug effects
Genome, Fungal
Microbial Sensitivity Tests
Gram-Positive Bacteria/drug effects
Staphylococcus aureus/drug effects
Bacillus subtilis/drug effects
*Ascomycota/genetics/metabolism
Isocoumarins/pharmacology
Computational Biology
Geologic Sediments/microbiology

@article {pmid40303815,
year = {2023},
author = {Wielgus, E and Klamm, A and Conraths, FJ and Dormann, CF and Henrich, M and Kronthaler, F and Heurich, M},
title = {First-Passage Time Analysis Based on GPS Data Offers a New Approach to Estimate Restricted Zones for the Management of Infectious Diseases in Wildlife: A Case Study Using the Example of African Swine Fever.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {4024083},
pmid = {40303815},
issn = {1865-1682},
mesh = {Animals ; *African Swine Fever/prevention & control/epidemiology/transmission ; *Geographic Information Systems ; Swine ; Animals, Wild ; *Sus scrofa ; Germany/epidemiology ; Female ; Disease Outbreaks/veterinary/prevention & control ; Male ; African Swine Fever Virus ; },
abstract = {An essential part of any disease containment and eradication policy is the implementation of restricted zones, but determining the appropriate size of these zones can be challenging for managers. We designed a new method, based on animal movement, to help assess how large restricted zones should be after a spontaneous outbreak to successfully control infectious diseases in wildlife. Our approach uses first-passage time (FPT) analysis and Cox proportional hazard (CPH) models to calculate and compare the risk of an animal leaving different-sized areas. We illustrate our approach using the example of the African swine fever (ASF) virus and its wild pig reservoir host species, the wild boar (Sus scrofa), and we investigate the feasibility of applying this method to other systems. Using GPS data from 57 wild boar living in the Hainich National Park, Germany, we calculate the time spent by each individual in areas of different sizes using FPT analysis. We apply CPH models on the derived data to compare the risk of leaving areas of different sizes and to assess the effects of season and the sex of the wild boar on the risk of leaving. We conduct survival analyses to estimate the risk of leaving an area over time. Our results indicate that the risk of leaving an area decreases exponentially by 10% for each 100 m increase in radius size so that the differences were more pronounced for small sizes. Furthermore, the probability of leaving increases exponentially with time. Wild boar had a similar risk of leaving an area of a given size throughout the year, except in spring and winter, when females had a much lower risk of leaving. Our findings are in agreement with the literature on wild boar movement, further validating our method, and repeated analyses with location data resampled at different rates gave similar results. Our results may be applicable only to our study area, but they demonstrate the applicability of the proposed method to any ecosystem where wild boar populations are likely to be infected with ASF and where restricted zones should be established accordingly. The outlined approach relies solely on the analysis of movement data and provides a useful tool to determine the optimal size of restricted zones. It can also be applied to future outbreaks of other diseases.},
}

Animals
*African Swine Fever/prevention & control/epidemiology/transmission
*Geographic Information Systems
Swine
Animals, Wild
*Sus scrofa
Germany/epidemiology
Female
Disease Outbreaks/veterinary/prevention & control
Male
African Swine Fever Virus

@article {pmid40298711,
year = {2025},
author = {Prado, SI and Novais, MAP},
title = {Acute viral bronchiolitis in Brazil: characteristics of length of stay and hospital costs.},
journal = {Ciencia & saude coletiva},
volume = {30},
number = {4},
pages = {e07402023},
doi = {10.1590/1413-81232025304.07402023},
pmid = {40298711},
issn = {1678-4561},
mesh = {Humans ; Brazil ; Infant ; Retrospective Studies ; *Length of Stay/statistics & numerical data/economics ; Acute Disease ; Child, Preschool ; *Hospitalization/economics/statistics & numerical data ; *Bronchiolitis, Viral/economics/therapy/epidemiology ; *Hospital Costs/statistics & numerical data ; Longitudinal Studies ; Male ; Female ; National Health Programs/economics ; },
abstract = {The objective of the study was to evaluate the length of stay in pediatric hospitalizations for acute viral bronchiolitis in the Brazilian Health System (SUS) and the costs of hospitalizations. This was a quantitative, observational, and ecological study, based on a retrospective and longitudinal analysis of data from the Department of Informatics of the Unified Health System (DATASUS; 2012-2021) using descriptive statistics and Tukey's paired test. Regarding the mean value of AIH/HAA Hospital Admission Authorization, among the regions, the high costs of hospitalizations are located more frequent in the Southeast region and the lowest proportion is directed to the corresponds to the North region. In the length of hospital stay among the regions, the shortest mean stay was identified in the Central West region (2.5 days) and the greatest stay in the Northeast region (3.1 days). Considering the age group of one year of life, its representativeness was 57% when compared to the age group of 1-4 years (43%). The fragility of the implementation of primary public policies in the prevention of bronchiolitis contributes to high hospital costs and significant economic impacts on the national healthcare system.},
}

Humans
Brazil
Infant
Retrospective Studies
*Length of Stay/statistics & numerical data/economics
Acute Disease
Child, Preschool
*Hospitalization/economics/statistics & numerical data
*Bronchiolitis, Viral/economics/therapy/epidemiology
*Hospital Costs/statistics & numerical data
Longitudinal Studies
Male
Female
National Health Programs/economics

@article {pmid39969985,
year = {2025},
author = {Zhang, J and Gao, X and Liang, C and Zhang, M and Zhang, S},
title = {Spatiotemporal pattern evolution analysis of ecological networks based on morphological spatial pattern analysis: a case study of Ningbo City, China.},
journal = {Integrated environmental assessment and management},
volume = {21},
number = {3},
pages = {540-554},
doi = {10.1093/inteam/vjaf027},
pmid = {39969985},
issn = {1551-3793},
support = {202148/WT_/Wellcome Trust/United Kingdom ; },
mesh = {China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; *Ecosystem ; Cities ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Biodiversity ; Urbanization ; },
abstract = {The exponential expansion of urban areas has precipitated a concomitant deterioration in the natural environment. Constructing ecological networks is vital in improving landscape connectivity, protecting biodiversity, and maintaining regional sustainable development. Ningbo, China, was set as the research area. Geographic information system and morphological spatial pattern analysis (MSPA) were used to determine the ecological source area. Subsequently, the corridor design model Linkage Mapper was used to ascertain and assess the linkages between the designated ecological source areas. The results showed that from 2000-2020, there was a large-scale change in land use type in Ningbo, with increasing complexity of patches and landscape fragmentation. The ecological sources of the three periods in Ningbo were primarily situated in the western, southern, and Hangzhou Bay coastal regions, exhibiting an uneven distribution in the eastern and western areas. The number of primary ecological corridors in Ningbo underwent a significant reduction, from 26 to 17, between the years 2000-2020. In terms of the distribution of ecological corridors, the primary corridors were concentrated in the central, southern, and western regions of the study area in 2000. By 2020, however, the primary ecological corridors within the study region were distributed mainly in a southerly direction. The interaction between north and south ecological sources was weakened, which adversely affected the species spread and ecosystem stability. After optimization, 12 ecological corridors and four ecological nodes were incorporated into Ningbo, 67 ecological breakpoints were identified, and four stepping stone patches were added. The study used spatiotemporal change trends, including land use type and landscape pattern, to examine the ecological network of Ningbo. In conclusion, the proposed optimization strategy is aligned with the current urban development context, offering a particularly pertinent reference point for Ningbo's ecological protection initiatives.},
}

China
*Environmental Monitoring/methods
Spatio-Temporal Analysis
*Ecosystem
Cities
*Conservation of Natural Resources/methods
Geographic Information Systems
Biodiversity
Urbanization

@article {pmid40297776,
year = {2025},
author = {Schwarzerova, J and Olesova, D and Jureckova, K and Kvasnicka, A and Kostoval, A and Friedecky, D and Sekora, J and Pomenkova, J and Provaznik, V and Popelinsky, L and Weckwerth, W},
title = {Enhanced metabolomic predictions using concept drift analysis: identification and correction of confounding factors.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf073},
pmid = {40297776},
issn = {2635-0041},
abstract = {MOTIVATION: The increasing use of big data and optimized prediction methods in metabolomics requires techniques aligned with biological assumptions to improve early symptom diagnosis. One major challenge in predictive data analysis is handling confounding factors-variables influencing predictions but not directly included in the analysis.

RESULTS: Detecting and correcting confounding factors enhances prediction accuracy, reducing false negatives that contribute to diagnostic errors. This study reviews concept drift detection methods in metabolomic predictions and selects the most appropriate ones. We introduce a new implementation of concept drift analysis in predictive classifiers using metabolomics data. Known confounding factors were confirmed, validating our approach and aligning it with conventional methods. Additionally, we identified potential confounding factors that may influence biomarker analysis, which could introduce bias and impact model performance.

Based on biological assumptions supported by detected concept drift, these confounding factors were incorporated into correction of prediction algorithms to enhance their accuracy. The proposed methodology has been implemented in Semi-Automated Pipeline using Concept Drift Analysis for improving Metabolomic Predictions (SAPCDAMP), an open-source workflow available at https://github.com/JanaSchwarzerova/SAPCDAMP.},
}

@article {pmid40295976,
year = {2025},
author = {Liberati, F and Pose Marino, TM and Bottoni, P and Canestrelli, D and Castrignanò, T},
title = {HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {113},
pmid = {40295976},
issn = {1471-2105},
mesh = {*Software ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Computational Biology/methods ; Databases, Genetic ; RNA-Seq/methods ; },
abstract = {BACKGROUND: Recent years have seen a substantial increase in RNA-seq data production, with this technique becoming the primary approach for gene expression studies across a wide range of non-model organisms. The majority of these organisms lack a well-annotated reference genome to serve as a basis for studying differentially expressed genes (DEGs). As an alternative cost-effective protocol to using a reference genome, the assembly of RNA-seq raw reads is performed to produce what is referred to as a 'de novo transcriptome,' serving as a reference for subsequent DEGs' analysis. This assembly step for conventional DEGs analysis pipelines for non-model organisms is a computationally expensive task. Furthermore, the complexity of the de novo transcriptome assembly workflows poses a challenge for researchers in implementing best-practice techniques and the most recent software versions, particularly when applied to various organisms of interest.

RESULTS: To address computational challenges in transcriptomic analyses of non-model organisms, we present HPC-T-Assembly, a tool for de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures. It is designed for straightforward setup via a Web-oriented interface, allowing analysis configuration for several species. Once configuration data is provided, the entire parallel computing software for assembly is automatically generated and can be launched on a supercomputer with a simple command line. Intermediate and final outputs of the assembly pipeline include additional post-processing steps, such as assembly quality control, ORF prediction, and transcript count matrix construction.

CONCLUSION: HPC-T-Assembly allows users, through a user-friendly Web-oriented interface, to configure a run for simultaneous assemblies of RNA-seq data from multiple species. The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.},
}

*Software
*Transcriptome
*Gene Expression Profiling/methods
Sequence Analysis, RNA/methods
Computational Biology/methods
Databases, Genetic
RNA-Seq/methods

@article {pmid40295704,
year = {2024},
author = {Grunnill, M and Eshaghi, A and Damodaran, L and Nagra, S and Gharouni, A and Braukmann, T and Clark, S and Peci, A and Isabel, S and Banh, P and Plessis, LD and Murall, CL and Colijn, C and Mubareka, S and Hasso, M and Bahl, J and Mostafa, HH and Gubbay, JB and Patel, SN and Wu, J and Duvvuri, VR},
title = {Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks.},
journal = {Npj viruses},
volume = {2},
number = {1},
pages = {34},
pmid = {40295704},
issn = {2948-1767},
abstract = {Enterovirus D68 (EV-D68) has emerged as a significant cause of acute respiratory illness in children globally, notably following its extensive outbreak in North America in 2014. A recent outbreak of EV-D68 was observed in Ontario, Canada, from August to October 2022. Our phylogenetic analysis revealed a notable genetic similarity between the Ontario outbreak and a concurrent outbreak in Maryland, USA. Utilizing Bayesian phylodynamic modeling on whole genome sequences (WGS) from both outbreaks, we determined the median peak time-varying reproduction number (Rt) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The Rt trends in Ontario closely matched those derived via EpiEstim using reported case numbers. Our study also provides new insights into the median infection duration of EV-D68, estimated at 7.94 days, 95% HPD (4.55, 12.8) in Ontario and 10.8 days, 95% HPD (5.85, 18.6) in Maryland, addressing the gap in the existing literature surrounding EV-D68's infection period. We observed that the estimated Time since the Most Recent Common Ancestor (TMRCA) and the epidemic's origin coincided with the easing of COVID-19 related social contact restrictions in both areas. This suggests that the relaxation of non-pharmaceutical interventions, initially implemented to control COVID-19, may have inadvertently facilitated the spread of EV-D68. These findings underscore the effectiveness of phylodynamic methods in public health, demonstrating their broad application from local to global scales and underscoring the critical role of pathogen genomic data in enhancing public health surveillance and outbreak characterization.},
}

@article {pmid40245036,
year = {2025},
author = {Hu, J and Weber, JN and Fuess, LE and Steinel, NC and Bolnick, DI and Wang, M},
title = {A spectral framework to map QTLs affecting joint differential networks of gene co-expression.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012953},
pmid = {40245036},
issn = {1553-7358},
mesh = {*Quantitative Trait Loci/genetics ; *Gene Regulatory Networks/genetics ; Animals ; Computational Biology/methods ; *Chromosome Mapping/methods ; Phenotype ; Genotype ; Models, Genetic ; Gene Expression Profiling/methods ; },
abstract = {Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype → expression → phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype → network → phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.},
}

*Quantitative Trait Loci/genetics
*Gene Regulatory Networks/genetics
Animals
Computational Biology/methods
*Chromosome Mapping/methods
Phenotype
Genotype
Models, Genetic
Gene Expression Profiling/methods

@article {pmid39808116,
year = {2024},
author = {Zárate, A and Díaz-González, L and Taboada, B},
title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39808116},
issn = {1477-4054},
mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Viral Proteins/genetics ; Humans ; *Eukaryota/virology ; *Viruses/genetics ; Genome, Viral ; Artificial Intelligence ; Computational Biology/methods ; Metagenome ; Convolutional Neural Networks ; },
abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.},
}

*Metagenomics/methods
*Neural Networks, Computer
*Viral Proteins/genetics
Humans
*Eukaryota/virology
*Viruses/genetics
Genome, Viral
Artificial Intelligence
Computational Biology/methods
Metagenome
Convolutional Neural Networks

@article {pmid40293859,
year = {2025},
author = {Wastler, HM and Cowan, HR and Breitborde, NJK and Tabares, JV and Yu, M and Pan, X and Boettner, B and Browning, C and Bryan, CJ},
title = {Ecological Momentary Assessment of Emotion Regulation and Suicidal Ideation in First-Episode Psychosis.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf042},
pmid = {40293859},
issn = {1745-1701},
support = {YIG-0-184-20//American Foundation for Suicide Prevention/ ; },
abstract = {Individuals with first-episode psychosis (FEP) are at increased risk for suicide, though few studies have examined the extent to which emotion regulation abnormalities contribute to this risk. The current study sought to address this gap by examining which stages of emotion regulation (ie, identification, selection, implementation) are related to suicidal ideation among individuals with FEP. Forty-one participants completed 28 days of ecological momentary assessment to assess suicidal ideation, negative affect, and emotion regulation in real-time. Results indicated that all 3 stages of emotion regulation were related to suicidal ideation in FEP. Specifically, within-person emotion regulation interacted with between-person negative affect to predict concurrent suicidal ideation (identification stage). Additionally, decreased use of adaptive strategies and increased use of maladaptive strategies were associated with more severe suicidal ideation (selection stage). Finally, decreased emotion regulation effectiveness was associated with more severe suicidal ideation (implementation stage). These findings suggest that emotion regulation difficulties might contribute to the high rates of suicide risk among individuals with FEP. Additional research is needed to determine whether these emotion regulation difficulties are unique to FEP or if they also appear in other high-risk groups.},
}

@article {pmid40292360,
year = {2025},
author = {Andersen, ZJ and Badyda, A and Tzivian, L and Dzhambov, AM and Paunovic, K and Savic, S and Jacquemin, B and Dragic, N},
title = {Air pollution inequalities in Europe: A deeper understating of challenges in Eastern Europe and pathways forward towards closing the gap between East and West.},
journal = {Environmental epidemiology (Philadelphia, Pa.)},
volume = {9},
number = {3},
pages = {e383},
pmid = {40292360},
issn = {2474-7882},
}

@article {pmid40292044,
year = {2025},
author = {Edelson, JB and Huang, J and Wang, Z and Tam, V and Lefktowitz, D and O'Connor, MJ and White, R and Ha, L and Wittlieb-Weber, CA and Rossano, JW and Lin, K and Cousino, MK and Lane-Fall, M and O'Byrne, ML},
title = {Identifying the determinants of health-related quality of life in children after heart transplant.},
journal = {JHLT open},
volume = {8},
number = {},
pages = {100250},
pmid = {40292044},
issn = {2950-1334},
abstract = {BACKGROUND: Pediatric heart transplant (PHT) recipients have impaired health-related quality of life (HRQOL) that is not fully explained by cardiac limitations. Environment is known to influence HRQOL in other chronic disease populations but is less understood in PHT. Understanding the determinants of HRQOL is a necessary step in identifying high-risk groups and designing actionable interventions.

METHODS: This cross-sectional study includes 8- to 18-year heart transplant (HT) recipients and their families. Generalized estimating equations were used to evaluate the associations of individual characteristics (diagnosis, pulmonary capillary wedge pressure [PCWP], cardiac index [CI]), microenvironment (parent education level, financial security, parental stress [PSI], assessment of child anxiety) and macroenvironment [Child Opportunity Index (COI)] with HRQOL.

RESULTS: Of 31 participants, 32% self-identified as Black, and 40% had congenital heart disease. On cardiac catheterization, 61% had a CI ≥3 liter/min/m[2] and PCWP ≤10 mm Hg. Most households had ≥1 parent who had completed college (58%); 28% of households expressed difficulty paying bills. The PSI showed elevated parental stress [64.5 (interquartile range [IQR] 52.0, 77.8)], while the COI was low [73.0 (IQR 44.5, 89.0)] as was HRQOL [Pediatric Quality of Life 4.0 Core Scales 71.7 (IQR 64.2-82.5), Pediatric Cardiac Quality of Life Index 61.8 (IQR 55.7-74.8)]. Higher parental stress (p = 0.036), higher parental perception of child anxiety (p = 0.058), lower Max VO2 (p = 0.059), and higher PCWP (p = 0.006) were independently associated with worse quality of life.

CONCLUSIONS: HRQOL in children after heart transplant is reduced and determined not only by traditional measures of cardiovascular function, but also by patient psychology and their household environment, highlighting the utility of using an adapted ecological systems framework to understand HRQOL.},
}

@article {pmid40287834,
year = {2025},
author = {Mohanty, A and Srinivasan, A and Udupaa, P and Catchpoole, D},
title = {Multiomics and tumor banking: comprehensive plaforms- integrating cancer diversity, biomarker discovery and personalised cancer care in India.},
journal = {Human molecular genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/hmg/ddaf033},
pmid = {40287834},
issn = {1460-2083},
abstract = {Biobanks are innovative biomedical research infrastructures that play a crucial role in advancing cancer research by supporting investigations into the etiology, progression, and therapeutic interventions of the disease. Biobanks have significantly contributed to personalized medicine by providing high-quality bio specimen resources and expertise in tissue handling, essential for understanding the interplay of genetic, ecological, and lifestyle factors on cancer biology, human health, and mortality. By linking bio specimens with clinical, pathological, and epidemiological data, biobanks are central in the discovery and development of cancer therapeutics through biomarkers. In this review, the importance of managing biobanks as integral parts of data generation and analytics continuum driving precision medicine is pointed out. The advent of multi-OMICS analytics, combined with artificial intelligence, systems biology, and deep machine learning, has elevated the importance of bio banking human bio specimens as not only a biological resource but also an informatics asset. Here, we examine the impact of bio banking in facilitating translational, bench-to-bedside cancer research, with a focus on multi-OMICS data-driven biomarker discovery and precision oncology. In addition, we discuss one of the major innovations in biobank management: the hub-and-spoke model. This centralized system leverages core expertise and resources while collecting bio specimens from diverse geographic regions, thereby capturing the heterogeneity of cancer biology. The hub-and-spoke approach is particularly advantageous for countries like India, characterized by vast geographic and demographic diversity. It ensures complete coverage of the different types of cancers, disease stages, and population groups in addressing the complexity and diversity of cancer biology.},
}

@article {pmid39724139,
year = {2024},
author = {Stephens, JL and Fraga, LAO and Ferreira, JA and De Mondesert, L and Kitron, U and Clennon, JA and Fairley, JK},
title = {Spatial associations of Hansen's disease and schistosomiasis in endemic regions of Minas Gerais, Brazil.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {12},
pages = {e0012682},
pmid = {39724139},
issn = {1935-2735},
mesh = {Humans ; Brazil/epidemiology ; *Leprosy/epidemiology ; *Endemic Diseases ; Female ; Male ; Spatial Analysis ; Adult ; Incidence ; Adolescent ; Middle Aged ; Young Adult ; Child ; Geographic Information Systems ; Animals ; *Schistosomiasis mansoni/epidemiology ; *Schistosomiasis/epidemiology ; Child, Preschool ; Aged ; },
abstract = {BACKGROUND: Brazil has the second highest case count of Hansen's disease (leprosy, HD), but factors contributing to transmission in highly endemic areas of the country remain unclear. Recent studies have shown associations of helminth infection and leprosy, supporting a biological plausibility for increased leprosy transmission in areas with helminths. However, spatial analyses of the overlap of these infections are limited. Therefore, we aimed to spatially analyze these two diseases in a co-endemic area of Minas Gerais, Brazil, in order to identify potential epidemiologic associations.

METHODS: An ecological study using public health surveillance records and census data was conducted to investigate whether the occurrence of HD -and specifically multibacillary (MB) disease- was associated with the presence of schistosomiasis in a community of 41 municipalities in eastern Minas Gerais, Brazil from 2011 to 2015. Multivariate logistic regression and spatial cluster analyses using geographic information systems (GIS) were performed.

RESULTS: The average annual incidence of HD in the study area was 35.3 per 100,000 while Schistosoma mansoni average annual incidence was 26 per 100,000. Both HD and schistosomiasis were spatially distributed showing significant clustering across the study area. Schistosomiasis was present in 10.4% of the tracts with HD and thirteen high-high clusters of local bivariate autocorrelation for HD and schistosomiasis cases were identified. A multivariate non-spatial analysis found that census tracts with MB disease were more likely to have schistosomiasis when adjusted for population density, household density, and household income (aOR = 1.7, 95% CI 1.0, 2.7). This remained significant when accounting for spatial correlation (aOR = 1.1, 95% CI (1.0, 1.2)).

CONCLUSION: We found clustering of both HD and schistosomiasis in this area with some statistically significant overlap of multibacillary HD with S. mansoni infection. Not only did we provide an effective approach to study the epidemiology of two endemic neglected tropical diseases with geographic spatial analyses, we highlight the need for further clinical and translational studies to study the potential epidemiologic associations uncovered.},
}

Humans
Brazil/epidemiology
*Leprosy/epidemiology
*Endemic Diseases
Female
Male
Spatial Analysis
Adult
Incidence
Adolescent
Middle Aged
Young Adult
Child
Geographic Information Systems
Animals
*Schistosomiasis mansoni/epidemiology
*Schistosomiasis/epidemiology
Child, Preschool
Aged

@article {pmid40287826,
year = {2025},
author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
pmid = {40287826},
issn = {1362-4962},
support = {DBI1356288NSF//NSF/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; },
abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.},
}

Phylogeny
*Genome, Bacterial
*Software
*Bacteria/genetics/classification
*Amino Acids/genetics
*Computational Biology/methods

@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {Workflow ; *Software ; *Gene Expression Profiling/methods ; *Computational Biology/methods ; *Transcriptome ; Microbiota/genetics ; Humans ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}

Workflow
*Software
*Gene Expression Profiling/methods
*Computational Biology/methods
*Transcriptome
Microbiota/genetics
Humans

@article {pmid40286849,
year = {2025},
author = {Bartas, M and Petrovič, M and Brázda, V and Trenz, O and Ďurčanský, A and Štastný, J},
title = {CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {108537},
doi = {10.1016/j.jbc.2025.108537},
pmid = {40286849},
issn = {1083-351X},
abstract = {With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation; with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/#/analyse/cpg.},
}

@article {pmid40286830,
year = {2025},
author = {Yu, X and Yao, R and Yao, R and Jin, X and Huang, J and Liang, Q and Jin, LN and Sun, J},
title = {Mechanistic understanding of the toxic effects of tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP) to Escherichia coli: Evidence from alterations in biomarker expression and perturbations of the metabolic network.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110211},
doi = {10.1016/j.cbpc.2025.110211},
pmid = {40286830},
issn = {1532-0456},
abstract = {Tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP), emerging flame retardants and plasticizers, have garnered increasing attention due to their potential risks to ecosystem. A few researches regarding the toxicological mechanisms of TnBP and TCP had been performed, while molecular-level toxic effects of them and metabolic response using microbial models are the lack of relevant investigation. Thus, we investigated the cytotoxicity, oxidative stress response, and metabolic response in E. coli exposed to TnBP and TCP. Exposure to them significantly increased the activities of antioxidant enzymes, indicating activation of the antioxidant defense system. Excessive accumulation of reactive oxygen species (ROS) triggered various biological events, including a reduction in membrane potential (MP), decrease of adenosine triphosphatase (ATPase) activity, and increased malondialdehyde (MDA) content. These findings suggested that oxidative damage compromised membrane proteins function, membrane stability, and intracellular homeostasis. GC-MS and LC-MS-based metabolomics analyses revealed that TnBP and TCP strongly disrupted multiple metabolic pathways, including carbohydrate metabolism, nucleotide metabolism, lipid metabolism, beta-alanine metabolism, pyruvate metabolism and oxidative phosphorylation. These disruptions highlighted the inhibitory effects on molecular functions and metabolic processes. Notably, lipids biomarkers e.g., PC(11:0/16:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(17:0/14:1(9Z)), and LysoPE(0:0/18:1(11Z)) were significantly altered, verifying that the regulation of lipid-associated metabolite synthesis plays a protective role in maintaining cellular membrane function. In summary, this study enhances our understanding of TnBP and TCP toxicity in E. coli, providing novel insights into their toxicological mechanisms at molecular and network levels. These findings underscore the ecological risks posed by organophosphate flame retardants in aquatic ecosystem.},
}

@article {pmid38163964,
year = {2025},
author = {Bhardwaj, N and S, S and Tripathi, N and Kumar, S and Lal, UR and G, R and Guru, SK and Jain, SK},
title = {Mahamanalactone A, a new triterpenoid from Dysoxylum malabaricum bark: a case study for rapid identification of new metabolites via LC-HRMS profiling and database mining strategy.},
journal = {Natural product research},
volume = {39},
number = {9},
pages = {2438-2443},
doi = {10.1080/14786419.2023.2298721},
pmid = {38163964},
issn = {1478-6427},
mesh = {Humans ; *Triterpenes/chemistry/isolation & purification/pharmacology ; *Plant Bark/chemistry ; Cell Line, Tumor ; *Antineoplastic Agents, Phytogenic/chemistry/pharmacology/isolation & purification ; Chromatography, Liquid ; Molecular Structure ; Mass Spectrometry ; *Meliaceae/chemistry ; Data Mining ; Plant Extracts/chemistry ; },
abstract = {In this recent investigation, the focus centred on exploring the potential phytoconstituents within the bark of Dysoxylum malabaricum. A profiling strategy employing LC-HRMS (Liquid Chromatography-High Resolution Mass Spectrometry) was implemented for the rapid identification of compounds from the bark extract. The crude extract underwent fractionation, resulting in the isolation of four previously known compounds (1-4) and a novel cycloartane triterpenoid named Mahamanalactone A (5). Compound 5 represents a cycloartane triterpenoid with a modified ring-A, featuring £-caprolactone fusion at positions 4 and 5, distinguishing it from other reported compounds where £-caprolactone is typically fused at positions 3 and 4. Cytotoxicity assessment revealed that the newly identified compound 5 exhibited a moderate cytotoxic profile (IC50 29 to 78 µM) against a panel of cancer cell lines.},
}

Humans
*Triterpenes/chemistry/isolation & purification/pharmacology
*Plant Bark/chemistry
Cell Line, Tumor
*Antineoplastic Agents, Phytogenic/chemistry/pharmacology/isolation & purification
Chromatography, Liquid
Molecular Structure
Mass Spectrometry
*Meliaceae/chemistry
Data Mining
Plant Extracts/chemistry

@article {pmid40284070,
year = {2025},
author = {Lu, F and Yi, B and Qin, K and Bu, ZJ},
title = {Long-Term Nitrogen Addition Eliminates the Cooling Effect on Climate in a Temperate Peatland.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {40284070},
issn = {2223-7747},
support = {U23A2003//National Natural Science Foundation of China/ ; 42407354//National Natural Science Foundation of China/ ; 42371050//National Natural Science Foundation of China/ ; 20210402032GH//Jilin Provincial Science and Technology Development Pro-ject/ ; 20230203002SF//Jilin Provincial Science and Technology Development Pro-ject/ ; JP230021//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Peatlands play a crucial role in global carbon (C) sequestration, but their response to long-term nitrogen (N) deposition remains uncertain. This study investigates the effects of 12 years of simulated N addition on CO2 and CH4 fluxes in a temperate peatland through in situ monitoring. The results demonstrate that long-term N addition significantly reduces net ecosystem exchange (NEE), shifting the peatland from a C sink to a C source. This transition is primarily driven by a decline in aboveground plant productivity, as Sphagnum mosses were suppressed and even experienced mortality, while graminoid plants thrived under elevated N conditions. Although graminoid cover increased, it did not compensate for the GPP loss caused by Sphagnum decline. Instead, it further increased CH4 emissions. These findings suggest that sustained N input may diminish the C sequestration function of peatlands, significantly weakening their global cooling effect.},
}

@article {pmid40278529,
year = {2025},
author = {Fabio, RA and Semino, M and Perina, M and Martini, M and Riccio, E and Pili, G and Pani, D and Chessa, M},
title = {Virtual Reality as a Tool for Upper Limb Rehabilitation in Rett Syndrome: Reducing Stereotypies and Improving Motor Skills.},
journal = {Pediatric reports},
volume = {17},
number = {2},
pages = {},
pmid = {40278529},
issn = {2036-749X},
abstract = {BACKGROUND/OBJECTIVES: Rett Syndrome (RTT) is a rare neurodevelopmental disorder that causes the loss of motor, communicative, and cognitive skills. While no cure exists, rehabilitation plays a crucial role in improving quality of life. Virtual Reality (VR) has shown promise in enhancing motor function and reducing stereotypic behaviors in RTT. This study aims to assess the impact of VR training on upper limb motor skills in RTT patients, focusing on reaching and hand-opening tasks, as well as examining its role in motivation and engagement during rehabilitation.

METHODS: Twenty RTT patients (aged 5-33) were randomly assigned to an experimental group (VR training) and a control group (standard rehabilitation). Pre- and post-tests evaluated motor skills and motivation in both VR and real-world contexts. The VR training involved 40 sessions over 8 weeks, focusing on fine motor tasks. Non-parametric statistical methods were used to analyze the data.

RESULTS: Results indicated significant improvements in the experimental group for motor parameters, including reduced stereotypy intensity and frequency, faster response times, and increased correct performance. These improvements were consistent across VR and ecological conditions. Moreover, attention time increased, while the number of aids required decreased, highlighting enhanced engagement and independence. However, motivation levels remained stable throughout the sessions.

CONCLUSIONS: This study demonstrates the potential of VR as a tool for RTT rehabilitation, addressing both motor and engagement challenges. Future research should explore the customization of VR environments to maximize the generalization of skills and sustain motivation over extended training periods.},
}

@article {pmid40277515,
year = {2025},
author = {Kargarandehkordi, A and Li, S and Lin, K and Phillips, KT and Benzo, RM and Washington, P},
title = {Fusing Wearable Biosensors with Artificial Intelligence for Mental Health Monitoring: A Systematic Review.},
journal = {Biosensors},
volume = {15},
number = {4},
pages = {},
pmid = {40277515},
issn = {2079-6374},
support = {MedRes_2023_00002689//Hawai'i Community Foundation/ ; 2406251//U.S. National Science Foundation/ ; 1U54GM138062-02A1/NH/NIH HHS/United States ; U54 GM138062/GM/NIGMS NIH HHS/United States ; U54GM138062/GM/NIGMS NIH HHS/United States ; },
mesh = {*Wearable Electronic Devices ; *Biosensing Techniques ; Humans ; *Artificial Intelligence ; *Mental Health ; Monitoring, Physiologic ; Heart Rate ; },
abstract = {The development of digital instruments for mental health monitoring using biosensor data from wearable devices can enable remote, longitudinal, and objective quantitative benchmarks. To survey developments and trends in this field, we conducted a systematic review of artificial intelligence (AI) models using data from wearable biosensors to predict mental health conditions and symptoms. Following PRISMA guidelines, we identified 48 studies using a variety of wearable and smartphone biosensors including heart rate, heart rate variability (HRV), electrodermal activity/galvanic skin response (EDA/GSR), and digital proxies for biosignals such as accelerometry, location, audio, and usage metadata. We observed several technical and methodological challenges across studies in this field, including lack of ecological validity, data heterogeneity, small sample sizes, and battery drainage issues. We outline several corresponding opportunities for advancement in the field of AI-driven biosensing for mental health.},
}

*Wearable Electronic Devices
*Biosensing Techniques
Humans
*Artificial Intelligence
*Mental Health
Monitoring, Physiologic
Heart Rate

@article {pmid40276974,
year = {2025},
author = {Blin, K and Shaw, S and Vader, L and Szenei, J and Reitz, ZL and Augustijn, HE and Cediel-Becerra, JDD and de Crécy-Lagard, V and Koetsier, RA and Williams, SE and Cruz-Morales, P and Wongwas, S and Segurado Luchsinger, AE and Biermann, F and Korenskaia, A and Zdouc, MM and Meijer, D and Terlouw, BR and van der Hooft, JJJ and Ziemert, N and Helfrich, EJN and Masschelein, J and Corre, C and Chevrette, MG and van Wezel, GP and Medema, MH and Weber, T},
title = {antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf334},
pmid = {40276974},
issn = {1362-4962},
support = {NNF20CC0035580//Novo Nordisk Foundation/ ; //Microbial Secondary Metabolites/ ; DNRF137//Danish National Research Foundation/ ; MSC 101072485//Horizon Europe Programme/ ; 101000392//Horizon 2020/ ; KICH1.LWV04.21.013//NWO/ ; 101055020//ERC/ ; RM1GM145426/NH/NIH HHS/United States ; TTU09.716//German Center for Infection Research/ ; //The Royal Thai Government/ ; 504947087//German Research Foundation/ ; //Hessian Ministry for Science and the Arts/ ; //Translational Biodiversity Genomics/ ; I008520N//FWO/ ; },
abstract = {Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in microbial interactions and soil health, but are also crucial for the development of pharmaceuticals or agrochemicals. Over the past decades, advancements in genome sequencing have enabled the identification of large numbers of biosynthetic gene clusters directly from microbial genomes. Since its inception in 2011, antiSMASH (https://antismash.secondarymetabolites.org/), has become the leading tool for detecting and characterizing these gene clusters in bacteria and fungi. This paper introduces version 8 of antiSMASH, which has increased the number of detectable cluster types from 81 to 101, and has improved analysis support for terpenoids and tailoring enzymes, as well as improvements in the analysis of modular enzymes like polyketide synthases and nonribosomal peptide synthetases. These modifications keep antiSMASH up-to-date with developments in the field and extend its overall predictive capabilities for natural product genome mining.},
}

@article {pmid40275196,
year = {2025},
author = {Li, Q},
title = {Assessing and adjusting for bias in ecological analysis using multiple sample datasets.},
journal = {BMC medical research methodology},
volume = {25},
number = {1},
pages = {112},
pmid = {40275196},
issn = {1471-2288},
mesh = {Humans ; Bias ; Kenya ; *Ecology/methods ; *Datasets as Topic ; Health Surveys ; Models, Statistical ; Data Interpretation, Statistical ; Computer Simulation ; },
abstract = {BACKGROUND: Ecological analysis utilizes group-level aggregate measures to investigate the complex relationships between individuals or groups and their environment. Despite its extensive applications across various disciplines, this approach remains susceptible to several biases, including ecological fallacy.

METHODS: Our study identified another significant source of bias in ecological analysis when using multiple sample datasets, a common practice in fields such as public health and medical research. We show this bias is proportional to the sampling fraction used during data collection. We propose two adjustment methods to address this bias: one that directly accounts for the sampling fraction and another based on measurement error models. The effectiveness of these adjustments is evaluated through formal mathematical derivations, simulations, and empirical analysis using data from the 2014 Kenya Demographic and Health Survey.

RESULTS: Our findings reveal that the sampling fraction bias can lead to significant underestimation of true relationships when using aggregate measures from multiple sample datasets. Both adjustment methods effectively mitigate this bias, with the measurement-error-adjusted estimator showing particular robustness in real-world applications. The results highlight the importance of accounting for sampling fraction bias in ecological analyses to ensure accurate inference.

CONCLUSION: Beyond the ecological fallacy uncovered by Robinson's seminar work, our research identified another critical bias in ecological analysis that is likely just as prevalent and consequential. The proposed adjustment methods provide potential tools for researchers to adjust for this bias, thereby improving the validity of ecological inferences. This study underscores the need for caution when pooling aggregate measures from multiple sample datasets and offers potential solutions to enhance the reliability of ecological analyses in various research domains.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Bias
Kenya
*Ecology/methods
*Datasets as Topic
Health Surveys
Models, Statistical
Data Interpretation, Statistical
Computer Simulation

@article {pmid40275133,
year = {2025},
author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A},
title = {Correction: High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {517},
doi = {10.1186/s12870-025-06560-4},
pmid = {40275133},
issn = {1471-2229},
}

@article {pmid40273274,
year = {2025},
author = {Chen, N},
title = {The impact of the rural digital economy on China's new-type urbanization.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321663},
doi = {10.1371/journal.pone.0321663},
pmid = {40273274},
issn = {1932-6203},
mesh = {China ; *Urbanization/trends ; *Rural Population ; Humans ; *Economic Development/trends ; Agriculture ; },
abstract = {The Chinese government is vigorously implementing the rural revitalization strategy and accelerating the process of new-type urbanization. The rapid development of the rural digital economy has emerged as a new driving force for new-type urbanization. This study aims to explore how the rural digital economy impacts China's new-type urbanization from direct, heterogeneous, and indirect perspectives. Using the provincial-level panel data in China from 2014 to 2022, a mixed-methods approach is employed for the empirical research. The CRITIC and Entropy TOPSIS are used to assess the comprehensive development level and temporal characteristics of the rural digital economy and new-type urbanization. Moreover, a global-local auto-correlation analysis is carried out to depict the spatial distribution of the two variables. Subsequently, a two-way fixed effects model is constructed to verify the direct impact of the rural digital economy on new-type urbanization, as well as its structural and spatial heterogeneity characteristics. Finally, an mediating effect model is established to explore the impact paths through which the rural digital economy impacts new-type urbanization. The results show that the rural digital economy has significantly promoted new-type urbanization. Specifically, rural digital infrastructure, digital transformation of agriculture, agricultural production service informatization have a significant positive effect, while the role of rural life digitization is not significant. The rural digital economy has more significant positive impact on population agglomeration and economic growth, followed by social public service, but has no significant impact on ecological environmental protection and urban-rural coordination. Additionally, the qualitative analysis identifies geographical region, poverty, demographic structure and social equality as notable influencing factors in this impact. Further mechanism analysis result indicates that the rural digital economy impacts new-type urbanization through rural human capital improvement, agricultural economic growth and rural industrial structure upgrading. This research contributes to the existing body of knowledge by providing the practical path of rural development to promote new-type urbanization in the context of the digital economy, also clarifies the weak points and key links in this process. It also highlights the need for further research into the institutional factors that influence this relationship to enhances the policy applicability.},
}

China
*Urbanization/trends
*Rural Population
Humans
*Economic Development/trends
Agriculture

@article {pmid39475336,
year = {2025},
author = {Menssen, M and Dammann, M and Fneish, F and Ellenberger, D and Schaarschmidt, F},
title = {Prediction Intervals for Overdispersed Poisson Data and Their Application in Medical and Pre-Clinical Quality Control.},
journal = {Pharmaceutical statistics},
volume = {24},
number = {2},
pages = {e2447},
pmid = {39475336},
issn = {1539-1612},
mesh = {Humans ; *Quality Control ; Poisson Distribution ; Monte Carlo Method ; Algorithms ; Computer Simulation ; Models, Statistical ; Multiple Sclerosis ; Data Interpretation, Statistical ; },
abstract = {In pre-clinical and medical quality control, it is of interest to assess the stability of the process under monitoring or to validate a current observation using historical control data. Classically, this is done by the application of historical control limits (HCL) graphically displayed in control charts. In many applications, HCL are applied to count data, for example, the number of revertant colonies (Ames assay) or the number of relapses per multiple sclerosis patient. Count data may be overdispersed, can be heavily right-skewed and clusters may differ in cluster size or other baseline quantities (e.g., number of petri dishes per control group or different length of monitoring times per patient). Based on the quasi-Poisson assumption or the negative-binomial distribution, we propose prediction intervals for overdispersed count data to be used as HCL. Variable baseline quantities are accounted for by offsets. Furthermore, we provide a bootstrap calibration algorithm that accounts for the skewed distribution and achieves equal tail probabilities. Comprehensive Monte-Carlo simulations assessing the coverage probabilities of eight different methods for HCL calculation reveal, that the bootstrap calibrated prediction intervals control the type-1-error best. Heuristics traditionally used in control charts (e.g., the limits in Shewhart c- or u-charts or the mean ± 2 SD) fail to control a pre-specified coverage probability. The application of HCL is demonstrated based on data from the Ames assay and for numbers of relapses of multiple sclerosis patients. The proposed prediction intervals and the algorithm for bootstrap calibration are publicly available via the R package predint.},
}

Humans
*Quality Control
Poisson Distribution
Monte Carlo Method
Algorithms
Computer Simulation
Models, Statistical
Multiple Sclerosis
Data Interpretation, Statistical

@article {pmid40273037,
year = {2025},
author = {Wu, KC and Belza, B and Berry, D and Lewis, F and Zaslavsky, O and Hartzler, A},
title = {UTI risk factors in older people living with dementia: A conceptual framework and a scoping review.},
journal = {Dementia (London, England)},
volume = {},
number = {},
pages = {14713012251326129},
doi = {10.1177/14713012251326129},
pmid = {40273037},
issn = {1741-2684},
abstract = {Background and Aims: UTIs greatly impact hospitalization rates for people living with dementia. This study aims to craft a framework through a scoping review, assessing UTI symptoms, risk factors, and non-pharmacological prevention strategies in older people living with dementia. Research Design and Methods: Our scoping review followed PRISMA-ScR guidelines, exploring databases (PubMed, CINAHL, Embase, Web of Science) for topics like geriatric care, urinary tract issues published from January 1977 to April 2023. Two reviewers assessed data, organizing it using the Social-Ecological Model to construct the UTI Prevention (UTIP) framework. Results: The literature review scrutinized 1394 articles, selecting 14 through rigorous evaluation. It detailed demographic characteristics, synthesized UTI symptoms, 14 risk factors, and seven outcomes for older people living with dementia. Moreover, it outlined ten preventive domains and proposed a comprehensive UTI Prevention (UTIP) framework spanning individual, relational, community, and societal levels. This framework aims to prevent UTIs among older people living with dementia, integrating risk factors and outcomes to bolster effective prevention strategies for this population. Discussion and Implications: The review introduced a UTIP framework, and non-pharmacological preventive measures tailored for elderly people living with dementia. However, some factors in the framework require further validation to strengthen their associations with outcomes. Preventive measures from studies had limitations like small sample sizes, bias risks, and inconsistent findings. Future research should prioritize robust randomized trials with strong statistical power, strict criteria, and consistent individual-level interventions to boost outcome reliability and validity. Such efforts will enhance the credibility of findings and contribute significantly to refining preventive strategies for this vulnerable population.},
}

@article {pmid40266389,
year = {2025},
author = {Xinyi, B and Qingbiao, G and Songbo, W and Jin, L and Jiren, X},
title = {Identifying the spatio-temporal evolution and driving mechanisms of ecosystem service value in high groundwater table coal mining areas.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {5},
pages = {581},
pmid = {40266389},
issn = {1573-2959},
support = {No. 2024cx2152//the Graduate Innovation Fund Project of Anhui University of Science and Technology/ ; 2024cxcysj094//the Provincial graduate student innovation and entrepreneurship practice project/ ; NO. KSXTJC202401//Engineering Research Center of Mining Area Environmental And Disaster Cooperative Monitoring (Anhui University of Science and Technology)/ ; No. 52274164//the Natural Science Foundation of China/ ; No. 2308085Y31//the Anhui Provincial Natural Science Foundation/ ; No. 2022QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; No. GJNY-21-41-15//the Open Fund of State Key Laboratory of Water Resource Protection and Utilization in Coal Mining/ ; },
mesh = {*Coal Mining ; *Environmental Monitoring ; *Ecosystem ; *Groundwater/chemistry ; *Conservation of Natural Resources/methods ; Spatio-Temporal Analysis ; China ; },
abstract = {In coal mining areas with high groundwater tables, surface subsidence has emerged as a non-negligible phenomenon, stemming from long-term coal mining activities. Employing the Huainan mining area as an exemplar, this research meticulously examines the temporal and spatial attributes of ecosystem service value (ESV) across distinct timeframes of 2005, 2010, 2015, and 2020, utilizing the refined equivalent factor approach in conjunction with spatial analysis methodologies. To delve into the primary forces driving the observed changes, the optimal parameter-based geographical detector (OPGD) model is subsequently utilized as a tool for analysis. Lastly, the study delves into the trade-offs and synergies existing between four exemplary services at the grid level, utilizing Spearman correlation coefficient and bivariate spatial autocorrelation. The findings suggest that: (1) From 2005 to 2020, the total ESV in the Huainan mining area demonstrated a general increasing tendency, primarily attributed to the increase in waters. (2) Throughout the research period, the ecosystem service functions in the coal mining area all exhibited relatively significant hydrological regulation and waste treatment capabilities. (3) Vegetation factors significantly influenced the ESV in the Huainan mining area. (4) The Huainan mining area predominantly exhibited synergistic effects among ecosystem services, with the most pronounced synergy occurring between cultural services (CS) and regulating services (RS). All services were transitioning towards an enhanced trend of synergistic effects. (5) Significant spatial variations are present in the observed trade-offs and synergies among diverse ecosystem services. The aforementioned research findings will provide scientific theoretical guidance for rational mining activities and ecological environmental governance in coal mining areas.},
}

*Coal Mining
*Environmental Monitoring
*Ecosystem
*Groundwater/chemistry
*Conservation of Natural Resources/methods
Spatio-Temporal Analysis
China

@article {pmid40263346,
year = {2025},
author = {Yamamoto, PK and Takasuka, K and Mori, M and Masuda, T and Kono, N},
title = {Non-invasive molecular species identification using spider silk proteomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13844},
pmid = {40263346},
issn = {2045-2322},
support = {23K21203//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Spiders/genetics/classification/metabolism ; *Proteomics/methods ; *Silk/chemistry/genetics/metabolism ; Species Specificity ; Amino Acid Sequence ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.},
}

Animals
*Spiders/genetics/classification/metabolism
*Proteomics/methods
*Silk/chemistry/genetics/metabolism
Species Specificity
Amino Acid Sequence
Computational Biology/methods
DNA Barcoding, Taxonomic/methods

@article {pmid40259303,
year = {2025},
author = {Yano, KM and Zucchi, P and Novais, MAP},
title = {Psychiatric hospitalizations in the Unified Health System: an observational study on hospitalization rates from 2012 to 2023.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {1463},
pmid = {40259303},
issn = {1471-2458},
support = {2022/10716-2//São Paulo State Research Foundation (FAPESP)/ ; },
mesh = {Humans ; *Hospitalization/trends/statistics & numerical data ; Brazil/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; *Mental Disorders/therapy/epidemiology ; Aged ; Young Adult ; Aged, 80 and over ; Child ; Infant ; Child, Preschool ; *National Health Programs/statistics & numerical data ; Infant, Newborn ; },
abstract = {BACKGROUND: Psychiatric care in Brazil is based on the National Mental Health Policy and is aligned with the guidelines of the Brazilian Unified Health System. It is based on the preeminence of care in the extra-hospital context over the hospital context. Hospital admissions should occur solely when extra-hospital resources prove insufficient for the proper management of the mental health condition.

METHOD: It refers to a time series investigation of a descriptive, ecological, and observational nature. We used publicly available hospital admissions data from the Brazilian Unified Health System's Department of Informatics. The study looked at information on diseases in ICD-10 group V that affected both men and women aged 0 to 80 or older, from 2012 to 2023. The information was analyzed using the statistical software SPSS 20.0, as well as Jointpoint, through permutation tests, with the aim of evaluating the temporal trend of hospitalization and mortality rates. The joinpoint regression model used a log-linear method to set up a series of connected lines on a logarithmic scale and the Monte Carlo permutation method to figure out the direction or statistical significance. A significance level of 5% was established for the execution of all statistical tests.

RESULTS: Overall, a trend of reduction in psychiatric hospitalization rates was observed. However, these trends exhibited fluctuations when analyzed in isolation with respect to the type of disorder, gender, and age group. In contrast to the general trend, the number of hospitalizations for affective disorders and disorders linked to stress and somatization went up. This was especially true between 2021 and 2023, when the number of hospitalizations for other disorders went down more significantly. The predominance of hospitalizations in the male gender was significant. However, the trends of decrease were less pronounced in the male group, especially regarding hospitalizations associated with alcohol and other substance use, which draws attention to the hospitalization rates of the female sex. As it relates to dementias, the national picture shows that hospitalizations are going down, and most of the patients are women and older adults or people who are very old. However, an analysis of the state scenario showed that hospitalizations went up for adults, more than for the elderly combined, with more men than women.

CONCLUSION: the results achieved in this research confirm the findings, both nationally and internationally. Studies have shown that investments made through the National Mental Health Policy and the effects of Covid-19 led to a drop in the number of people admitted to psychiatric hospitals. This was because of the restructuring of the care model, which meant that hospitalizations had to be prioritized to meet the needs of Covid-19, which hurt people with mental disorders.},
}

Humans
*Hospitalization/trends/statistics & numerical data
Brazil/epidemiology
Female
Male
Adult
Middle Aged
Adolescent
*Mental Disorders/therapy/epidemiology
Aged
Young Adult
Aged, 80 and over
Child
Infant
Child, Preschool
*National Health Programs/statistics & numerical data
Infant, Newborn

@article {pmid40208899,
year = {2025},
author = {Minier, L and Rouch, J and Sabbagh, B and Bertucci, F and Parmentier, E and Lecchini, D and Sèbe, F and Mathevon, N and Emonet, R},
title = {Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012050},
doi = {10.1371/journal.pcbi.1012050},
pmid = {40208899},
issn = {1553-7358},
mesh = {*Coral Reefs ; *Software ; Animals ; Acoustics ; Anthozoa/physiology ; Sound ; Machine Learning ; Computational Biology ; Polynesia ; Ecosystem ; *Environmental Monitoring/methods ; },
abstract = {Despite hosting some of the highest concentrations of biodiversity and providing invaluable goods and services in the oceans, coral reefs are under threat from global change and other local human impacts. Changes in living ecosystems often induce changes in their acoustic characteristics, but despite recent efforts in passive acoustic monitoring of coral reefs, rapid measurement and identification of changes in their soundscapes remains a challenge. Here we present the new open-source software CoralSoundExplorer, which is designed to study and monitor coral reef soundscapes. CoralSoundExplorer uses machine learning approaches and is designed to eliminate the need to extract conventional acoustic indices. To demonstrate CoralSoundExplorer's functionalities, we use and analyze a set of recordings from three coral reef sites, each with different purposes (undisturbed site, tourist site and boat site), located on the island of Bora-Bora in French Polynesia. We explain the CoralSoundExplorer analysis workflow, from raw sounds to ecological results, detailing and justifying each processing step. We detail the software settings, the graphical representations used for visual exploration of soundscapes and their temporal dynamics, along with the analysis methods and metrics proposed. We demonstrate that CoralSoundExplorer is a powerful tool for identifying disturbances affecting coral reef soundscapes, combining visualizations of the spatio-temporal distribution of sound recordings with new quantification methods to characterize soundscapes at different temporal scales.},
}

*Coral Reefs
*Software
Animals
Acoustics
Anthozoa/physiology
Sound
Machine Learning
Computational Biology
Polynesia
Ecosystem
*Environmental Monitoring/methods

@article {pmid40173380,
year = {2025},
author = {Zagorščak, M and Abdelhakim, L and Rodriguez-Granados, NY and Široká, J and Ghatak, A and Bleker, C and Blejec, A and Zrimec, J and Novák, O and Pěnčík, A and Baebler, Š and Perez Borroto, L and Schuy, C and Županič, A and Afjehi-Sadat, L and Wurzinger, B and Weckwerth, W and Pompe Novak, M and Knight, MR and Strnad, M and Bachem, C and Chaturvedi, P and Sonnewald, S and Sasidharan, R and Panzarová, K and Gruden, K and Teige, M},
title = {Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.},
journal = {Plant physiology},
volume = {197},
number = {4},
pages = {},
doi = {10.1093/plphys/kiaf126},
pmid = {40173380},
issn = {1532-2548},
support = {//H2020-SFS-2019-2/ ; P4-0165//Slovenian Research Agency/ ; //Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_026/0008446//European Regional Development Fund-Project/ ; },
mesh = {*Solanum tuberosum/physiology/genetics/metabolism ; *Stress, Physiological/genetics ; Phenotype ; Droughts ; Proteomics ; Metabolomics ; Gene Expression Regulation, Plant ; Transcriptome ; Plant Leaves/physiology ; Plant Tubers ; Multiomics ; },
abstract = {Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.},
}

*Solanum tuberosum/physiology/genetics/metabolism
*Stress, Physiological/genetics
Phenotype
Droughts
Proteomics
Metabolomics
Gene Expression Regulation, Plant
Transcriptome
Plant Leaves/physiology
Plant Tubers
Multiomics

@article {pmid40253432,
year = {2025},
author = {Kelliher, JM and Aljumaah, M and Bordenstein, SR and Brister, JR and Chain, PSG and Dundore-Arias, JP and Emerson, JB and Fernandes, VMC and Flores, R and Gonzalez, A and Hansen, ZA and Hatcher, EL and Jackson, SA and Kellogg, CA and Madupu, R and Miller, CML and Mirzayi, C and Moustafa, AM and Mungall, C and Oliver, A and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and Eloe-Fadrosh, EA},
title = {Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {40},
pmid = {40253432},
issn = {2524-6372},
support = {2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; },
abstract = {Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12-13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.},
}

@article {pmid40249863,
year = {2025},
author = {Wu, Q and Cheng, S and Zhang, W and Zhao, J and Zhang, L and Lv, M and Ma, J and Ding, J and Wang, S and Zheng, X and Gao, J and Liu, R and Yin, Y and Shi, J and Qu, G and Jiang, G},
title = {Heterogeneous Single-Cell Distribution of Trace-Level Metal Mixtures in Tetrahymena thermophila Using Mass Cytometry.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12818},
pmid = {40249863},
issn = {1520-5851},
abstract = {The uptake of heavy metals by unicellular organisms can lead to the bioaccumulation of these metals in higher organisms, detrimentally affecting organismal health and ultimately impacts the ecosystems. By studying the uptake and accumulation of heavy metals in unicellular organisms, we gain insights into potential risks associated with low-dose heavy metal exposure in aquatic environments. Thus, to investigate the accumulation characteristics of Mo, Ag, Cd, Sn, Sb, Hg, Tl, and Pb mixtures in single Tetrahymena thermophila cells, we developed a label-free approach for the simultaneous absolute quantification of multiple metals in a single cell using mass cytometry. Our results demonstrated the dynamic changes in metal concentrations in T. thermophila, and the competition between metals in uptake and excretory pathways resulted in heterogeneous accumulation and bioconcentration of these metals. Additionally, our findings revealed the limited capacity of T. thermophila to excrete Cd and Hg, suggesting a higher risk for T. thermophila cells when exposed to Cd and Hg over an extended period. Therefore, the current study provides valuable data for a more comprehensive understanding of the impact of low-dose heavy metals on aquatic ecosystems.},
}

@article {pmid40188731,
year = {2025},
author = {Li, Y and Huang, S and Jiang, S and Yang, L and Huang, J and Yang, Q and Jiang, Z and Shi, J and Ma, Z and Li, E and Zhou, F},
title = {Multi-omics insights into antioxidant and immune responses in Penaeus monodon under ammonia-N, low salinity, and combined stress.},
journal = {Ecotoxicology and environmental safety},
volume = {295},
number = {},
pages = {118156},
doi = {10.1016/j.ecoenv.2025.118156},
pmid = {40188731},
issn = {1090-2414},
mesh = {Animals ; *Penaeidae/immunology/physiology/drug effects ; *Ammonia/toxicity ; Salinity ; *Antioxidants/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Stress, Physiological ; Transcriptome ; Nitrogen/toxicity ; Multiomics ; },
abstract = {Ammonia nitrogen and salinity are critical environmental factors that significantly impact marine organisms and present substantial threats to Penaeus monodon species within aquaculture systems. This study utilized a comprehensive multi-omics approach, encompassing transcriptomics, metabolomics, and gut microbiome analysis, to systematically examine the biological responses of shrimp subjected to low salinity, ammonia nitrogen stress, and their combined conditions. Metabolomic analysis demonstrated that exposure to ammonia nitrogen stress markedly influenced the concentrations of antioxidant-related metabolites, such as glutathione, suggesting that shrimp mitigate oxidative stress by augmenting their antioxidant capacity. The transcriptomic analysis revealed an upregulation of genes linked to energy metabolism and immune responses and antioxidant enzymes. Concurrently, gut microbiome analysis demonstrated that ammonia nitrogen stress resulted in a marked increase in Vibrio populations and a significant decrease in Photobacterium, indicating that alterations in microbial community structure are intricately associated with the shrimp stress response. A comprehensive analysis further indicated that the combined stressors of ammonia nitrogen and salinity exert a synergistic effect on the immune function and physiological homeostasis of shrimp by modulating antioxidant metabolic pathways and gut microbial communities. These findings provide critical systematic data for elucidating the mechanisms through which ammonia nitrogen and salinity influence marine ecosystems, offering substantial implications for environmental protection and ecological management.},
}

Animals
*Penaeidae/immunology/physiology/drug effects
*Ammonia/toxicity
Salinity
*Antioxidants/metabolism
*Water Pollutants, Chemical/toxicity
Oxidative Stress
Gastrointestinal Microbiome/drug effects
Metabolomics
Stress, Physiological
Transcriptome
Nitrogen/toxicity
Multiomics

@article {pmid40248649,
year = {2025},
author = {Boyes, D and Januszczak, I and , and , and , and , and , and , and , and , and Mitchell, R},
title = {The genome sequence of the Warted Knot-Horn moth, Acrobasis repandana Fabricius, 1798.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {50},
pmid = {40248649},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female specimen of Acrobasis repandana (Warted Knot-Horn moth; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence has a total length of 620.40 megabases. Most of the assembly (99.78%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,522 protein-coding genes.},
}

@article {pmid40247661,
year = {2025},
author = {Abraham, AJ and Duvall, ES and Doughty, CE and Riond, B and Ortmann, S and Terranova, M and le Roux, E and Clauss, M},
title = {Sodium Retention in Large Herbivores: Physiological Insights and Zoogeochemical Consequences.},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.2924},
pmid = {40247661},
issn = {2471-5646},
support = {//A.J.A. acknowledges Horizon Europe Marie Skłodowska-Curie Actions Grant Agreement No. 101062339./ ; },
abstract = {The assimilation, retention, and release of nutrients by animals fundamentally shapes their physiology and contributions to ecological processes (e.g., zoogeochemistry). Yet, information on the transit of nutrients through the bodies of large mammals remains scarce. Here, we examined how sodium (Na), a key element for animal health and ecosystem functioning, travels differently through fecal and urinary systems of cows (Bos taurus) and horses (Equus ferus caballus). We provided a large dose of Na and compared its timing of release in feces and urine to that of nonabsorbable markers. Na excretion by urine occurred approximately twice as fast as excretion by feces, yet both were shorter than indigestible particle markers. These differences correspond to rapid absorption of Na in the upper gastrointestinal tract and transport by blood to the kidneys (urine Na excretion) or resecretion of Na into the lower intestinal tract (fecal Na excretion). Interestingly, for cows, we found a second peak of Na excretion in urine and feces > 96 h after dosage. This result may indicate that surplus Na can be rapidly absorbed and stored in specific body cells (e.g., skin), from which it is later released. Using a propagule dispersal model, we found that the distance of cattle- and horse-driven nutrient dispersal by urine was 31% and 36% less than the fecal pathway and 60% and 41% less than the particle marker pathway, which is commonly used to estimate nutrient dispersal. Future physiological and zoogeochemical studies should resolve different pathways of nutrient retention and release from large mammals.},
}

@article {pmid40247093,
year = {2025},
author = {Yang, J and Chen, YN and Fang, CY and Li, Y and Ke, HQ and Guo, RQ and Xiang, P and Xiao, YL and Zhang, LW and Liu, H},
title = {Investigating immune cell infiltration and gene expression features in pterygium pathogenesis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13352},
pmid = {40247093},
issn = {2045-2322},
support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 202208535051//China Scholarship Council/ ; 81860171//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202205AC160016//Yunnan Young and middle-aged Academic and technical leader Project/ ; L2019029//Yunnan Provincial Health Committee Training program for leading medical talents/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; },
mesh = {Humans ; *Pterygium/genetics/immunology/pathology ; Gene Expression Profiling ; Computational Biology/methods ; Conjunctiva/pathology/metabolism/immunology ; Transcriptome ; *Gene Expression Regulation ; Biomarkers/metabolism ; },
abstract = {Pterygium is a prevalent ocular disease characterized by abnormal conjunctival tissue proliferation, significantly impacting patients' quality of life. However, the underlying molecular mechanisms driving pterygium pathogenesis remain inadequately understood. This study aimed to investigate gene expression changes following pterygium excision and their association with immune cell infiltration. Clinical samples of pterygium and adjacent relaxed conjunctival tissue were collected for transcriptomic analysis using RNA sequencing combined with bioinformatics approaches. Machine learning algorithms, including LASSO, SVM-RFE, and Random Forest, were employed to identify potential diagnostic biomarkers. GO, KEGG, GSEA, and GSVA were utilized for enrichment analysis. Single-sample GSEA was employed to analyze immune infiltration. The GSE2513 and GSE51995 datasets from the GEO database, along with clinical samples, were selected for validation analysis. Differentially expressed genes (DEGs) were identified from the PRJNA1147595 and GSE2513 datasets, revealing 2437 DEGs and 172 differentially regulated genes (DRGs), respectively. There were 52 co-DEGs shared by both datasets, and four candidate biomarkers (FN1, SPRR1B, SERPINB13, EGR2) with potential diagnostic value were identified through machine learning algorithms. Single-sample GSEA demonstrated increased Th2 cell infiltration and decreased CD8 + T cell presence in pterygium tissues, suggesting a crucial role of the immune microenvironment in pterygium pathogenesis. Analysis of the GSE51995 dataset and qPCR results revealed significantly higher expression levels of FN1 and SPRR1B in pterygium tissues compared to conjunctival tissues, but SERPINB13 and EGR2 expression levels were not statistically significant. Furthermore, we identified four candidate drugs targeting the two feature genes FN1 and SPRR1B. This study provides valuable insights into the molecular characteristics and immune microenvironment of pterygium. The identification of potential biomarkers FN1 and SPRR1B highlights their significance in pterygium pathogenesis and lays a foundation for further exploration aimed at integrating these findings into clinical practice.},
}

Humans
*Pterygium/genetics/immunology/pathology
Gene Expression Profiling
Computational Biology/methods
Conjunctiva/pathology/metabolism/immunology
Transcriptome
*Gene Expression Regulation
Biomarkers/metabolism

@article {pmid40163742,
year = {2025},
author = {Ghassemi Nedjad, C and Bolteau, M and Bourneuf, L and Paulevé, L and Frioux, C},
title = {Seed2LP: seed inference in metabolic networks for reverse ecology applications.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
doi = {10.1093/bioinformatics/btaf140},
pmid = {40163742},
issn = {1367-4811},
support = {//French National Research Agency/ ; },
mesh = {*Metabolic Networks and Pathways ; *Software ; *Computational Biology/methods ; Models, Biological ; Algorithms ; },
abstract = {MOTIVATION: A challenging problem in microbiology is to determine nutritional requirements of microorganisms and culture them, especially for the microbial dark matter detected solely with culture-independent methods. The latter foster an increasing amount of genomic sequences that can be explored with reverse ecology approaches to raise hypotheses on the corresponding populations. Building upon genome-scale metabolic networks (GSMNs) obtained from genome annotations, metabolic models predict contextualized phenotypes using nutrient information.

RESULTS: We developed the tool Seed2LP, addressing the inverse problem of predicting source nutrients, or seeds, from a GSMN and a metabolic objective. The originality of Seed2LP is its hybrid model, combining a scalable and discrete Boolean approximation of metabolic activity, with the numerically accurate flux balance analysis (FBA). Seed inference is highly customizable, with multiple search and solving modes, exploring the search space of external and internal metabolites combinations. Application to a benchmark of 107 curated GSMNs highlights the usefulness of a logic modelling method over a graph-based approach to predict seeds, and the relevance of hybrid solving to satisfy FBA constraints. Focusing on the dependency between metabolism and environment, Seed2LP is a computational support contributing to address the multifactorial challenge of culturing possibly uncultured microorganisms.

Seed2LP is available on https://github.com/bioasp/seed2lp.},
}

*Metabolic Networks and Pathways
*Software
*Computational Biology/methods
Models, Biological
Algorithms

@article {pmid40246854,
year = {2025},
author = {He, B and Zhang, H and Qin, T and Shi, B and Wang, Q and Dong, W},
title = {A simultaneous EEG and eye-tracking dataset for remote sensing object detection.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {651},
pmid = {40246854},
issn = {2052-4463},
support = {42230103//National Science Foundation of China | Key Programme/ ; },
mesh = {*Electroencephalography ; Humans ; *Eye-Tracking Technology ; *Remote Sensing Technology ; Artificial Intelligence ; },
abstract = {We introduce the EEGET-RSOD, a simultaneous electroencephalography (EEG) and eye-tracking dataset for remote sensing object detection. This dataset contains EEG and eye-tracking data when 38 remote sensing experts located specific objects in 1,000 remote sensing images within a limited time frame. This task reflects the typical cognitive processes associated with human visual search and object identification in remote sensing imagery. To our knowledge, EEGET-RSOD is the first publicly available dataset to offer synchronized eye-tracking and EEG data for remote sensing images. This dataset will not only advance the study of human visual cognition in real-world environment, but also bridge the gap between human cognition and artificial intelligence, enhancing the interpretability and reliability of AI models in geospatial applications.},
}

*Electroencephalography
Humans
*Eye-Tracking Technology
*Remote Sensing Technology
Artificial Intelligence

@article {pmid40245396,
year = {2025},
author = {Melia, R and Musacchio Schafer, K and Rogers, ML and Wilson-Lemoine, E and Joiner, TE},
title = {The Application of AI to Ecological Momentary Assessment Data in Suicide Research: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e63192},
doi = {10.2196/63192},
pmid = {40245396},
issn = {1438-8871},
mesh = {Humans ; *Ecological Momentary Assessment ; *Artificial Intelligence ; *Suicide ; *Suicidal Ideation ; },
abstract = {BACKGROUND: Ecological momentary assessment (EMA) captures dynamic processes suitable to the study of suicidal ideation and behaviors. Artificial intelligence (AI) has increasingly been applied to EMA data in the study of suicidal processes.

OBJECTIVE: This review aims to (1) synthesize empirical research applying AI strategies to EMA data in the study of suicidal ideation and behaviors; (2) identify methodologies and data collection procedures used, suicide outcomes studied, AI applied, and results reported; and (3) develop a standardized reporting framework for researchers applying AI to EMA data in the future.

METHODS: PsycINFO, PubMed, Scopus, and Embase were searched for published articles applying AI to EMA data in the investigation of suicide outcomes. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines were used to identify studies while minimizing bias. Quality appraisal was performed using CREMAS (adapted STROBE [Strengthening the Reporting of Observational Studies in Epidemiology] Checklist for Reporting Ecological Momentary Assessment Studies).

RESULTS: In total, 1201 records were identified across databases. After a full-text review, 12 (1%) articles, comprising 4398 participants, were included. In the application of AI to EMA data to predict suicidal ideation, studies reported mean area under the curve (0.74-0.86), sensitivity (0.64-0.81), specificity (0.73-0.86), and positive predictive values (0.72-0.77). Studies met between 4 and 13 of the 16 recommended CREMAS reporting standards, with an average of 7 items met across studies. Studies performed poorly in reporting EMA training procedures and treatment of missing data.

CONCLUSIONS: Findings indicate the promise of AI applied to self-report EMA in the prediction of near-term suicidal ideation. The application of AI to EMA data within suicide research is a burgeoning area hampered by variations in data collection and reporting procedures. The development of an adapted reporting framework by the research team aims to address this.

TRIAL REGISTRATION: Open Science Framework (OSF); https://doi.org/10.17605/OSF.IO/NZWUJ and PROSPERO CRD42023440218; https://www.crd.york.ac.uk/PROSPERO/view/CRD42023440218.},
}

Humans
*Ecological Momentary Assessment
*Artificial Intelligence
*Suicide
*Suicidal Ideation

@article {pmid40240877,
year = {2025},
author = {Li, W and Chu, C and Zhang, T and Sun, H and Wang, S and Liu, Z and Wang, Z and Li, H and Li, Y and Zhang, X and Geng, Z and Wang, Y and Li, Y and Zhang, H and Fan, W and Wang, Y and Xu, X and Cheng, L and Zhang, D and Xiong, Y and Li, H and Zhou, B and Guan, Q and Deng, CH and Han, Y and Ma, H and Han, Z},
title = {Pan-genome analysis reveals the evolution and diversity of Malus.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40240877},
issn = {1546-1718},
support = {CARS-27//Earmarked Fund for China Agriculture Research System/ ; 32172522//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32422077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2019M661344//China Postdoctoral Science Foundation/ ; },
abstract = {Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.},
}

@article {pmid40179878,
year = {2025},
author = {Li, Y and Liu, X and Guo, L and Han, K and Fang, S and Wan, X and Wang, D and Xu, X and Jiang, L and Fan, G and Xu, M},
title = {SpaGRN: Investigating spatially informed regulatory paths for spatially resolved transcriptomics data.},
journal = {Cell systems},
volume = {16},
number = {4},
pages = {101243},
doi = {10.1016/j.cels.2025.101243},
pmid = {40179878},
issn = {2405-4720},
mesh = {Animals ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; Humans ; *Gene Regulatory Networks/genetics ; Drosophila/genetics ; Computational Biology/methods ; },
abstract = {Cells spatially organize into distinct cell types or functional domains through localized gene regulatory networks. However, current spatially resolved transcriptomics analyses fail to integrate spatial constraints and proximal cell influences, limiting the mechanistic understanding of tissue organization. Here, we introduce SpaGRN, a statistical framework that reconstructs cell-type- or functional-domain-specific, dynamic, and spatial regulons by coupling intracellular spatial regulatory causality with extracellular signaling path information. Benchmarking across synthetic and real datasets demonstrates SpaGRN's superior precision over state-of-the-art tools in identifying context-dependent regulons. Applied to diverse spatially resolved transcriptomics platforms (Stereo-seq, STARmap, MERFISH, CosMx, Slide-seq, and 10x Visium), complex cancerous samples, and 3D datasets of developing Drosophila embryos and larvae, SpaGRN not only provides a versatile toolkit for decoding receptor-mediated spatial regulons but also reveals spatiotemporal regulatory mechanisms underlying organogenesis and inflammation.},
}

Animals
*Transcriptome/genetics
*Gene Expression Profiling/methods
Humans
*Gene Regulatory Networks/genetics
Drosophila/genetics
Computational Biology/methods

@article {pmid40238767,
year = {2025},
author = {Rodrigues, RDS and Cionek, VM and Barreto, AS and Branco, JO},
title = {Seabird strandings on the Brazilian coast: What influences spatial and temporal patterns?.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0317335},
doi = {10.1371/journal.pone.0317335},
pmid = {40238767},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *Animal Migration/physiology ; *Birds/physiology ; Seasons ; Spatio-Temporal Analysis ; Ecosystem ; Biodiversity ; },
abstract = {Seabirds exhibit physiological adaptations that allow them to forage in the marine environment and undertake long-distance migrations during non-reproductive periods. As a result, they face various natural and anthropogenic pressures, which can lead to extreme fatigue and even death. Stranded bodies that float in the sea can wash ashore, providing valuable ecological information. This study aimed to analyze seabird strandings along the south and southeast coasts of Brazil between 2016 and 2019, focusing on spatiotemporal and potential environmental and anthropogenic influences. Using data from the Santos Basin Beach Monitoring Project, we calculated ecological indices of abundance, richness, and diversity for the entire seabird community and separately by migratory behavior (resident, southern migratory, northern migratory). Statistical modeling revealed a strong decreasing trend in strandings from south to north, with higher events on the southern coast (Santa Catarina and Paraná) and lower on the southeast coast (São Paulo). Resident species and northern migratory species showed peak strandings in spring, while southern migratory peaked in winter. These spatial and temporal patterns reflected birds' home ranges, reproductive cycles, and migratory behaviors. Environmental variables influenced strandings differently depending on species migration behavior and ecological indices, highlighting the role of oceanographic processes in carcass drift and the impact of climatic events on species mortality. This study is the first to demonstrate a spatiotemporal pattern of seabird strandings on the Brazilian coast, providing valuable insights into seabird dynamics in the Santos Basin and offering important data for conservation efforts.},
}

Animals
Brazil
*Animal Migration/physiology
*Birds/physiology
Seasons
Spatio-Temporal Analysis
Ecosystem
Biodiversity

@article {pmid40238239,
year = {2025},
author = {Sutori, S and Eliasson, ET and Mura, F and Ortiz, V and Catrambonephd, V and Hadlaczky, G and Todorov, I and Alfeo, AL and Cardi, V and Cimino, MGCA and Mioni, G and Raya, MA and Valenza, G and Carli, V and Gentili, C},
title = {Acceptability, Usability, and Insights Into Cybersickness Levels of a Novel Virtual Reality Environment for the Evaluation of Depressive Symptoms: Exploratory Observational Study.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e68132},
doi = {10.2196/68132},
pmid = {40238239},
issn = {2561-326X},
mesh = {Humans ; *Virtual Reality ; Male ; Female ; Adult ; *Depression/diagnosis/psychology ; Young Adult ; Italy ; Surveys and Questionnaires ; User-Computer Interface ; Pilot Projects ; Self Report ; },
abstract = {BACKGROUND: There is a clear need for enhanced mental health assessment, depressive symptom (DS) evaluation being no exception. A promising approach to this aim is using virtual reality (VR), which entails the potential of adding a wider set of assessment domains with enhanced ecological validity. However, whilst several studies have used VR for both diagnostic and treatment purposes, its acceptance, in particular how exposure to virtual environments affects populations with psychiatric conditions remains unknown.

OBJECTIVE: This study aims to report on the acceptability, usability, and cybersickness levels of a pilot VR environment designed for the purpose of differentiating between individuals with DSs.

METHODS: The exploratory study, conducted in Italy, included 50 healthy controls and 50 young adults with mild-to-moderate DSs (without the need for a formal diagnosis). The study used an observational design with approximately 30 minutes of VR exposure followed by a self-report questionnaire battery. The battery included a questionnaire based on the Theoretical Framework of Acceptability, the System Usability Scale as well as the Simulator Sickness Questionnaire.

RESULTS: Results indicate that the majority found VR acceptable for the purposes of mental health screening and treatment. However, for diagnostics, there was a clear preference for VR to be used by mental health professionals as a supplementary tool, as opposed to a stand-alone solution. In practice, following exposure to the pilot VR environment, generally, good levels of acceptability and usability were reported, but areas in need of improvement were identified (such as self-efficacy). Self-reported cybersickness levels were comparable to literature averages but were considerably higher among those with DSs.

CONCLUSIONS: These findings raise questions about the potential interplay between underlying somatic symptoms of depression and VR-induced cybersickness and call for more attention from the scientific community both in terms of methodology as well as potential clinical and theoretical implications. Conclusively, user support indicates a potential for VR to aid mental health assessment, but further research is needed to understand how exposure to virtual environments might affect populations with varying severity and other forms of psychiatric symptoms.

RR2-10.1186/ISRCTN16396369.},
}

Humans
*Virtual Reality
Male
Female
Adult
*Depression/diagnosis/psychology
Young Adult
Italy
Surveys and Questionnaires
User-Computer Interface
Pilot Projects
Self Report

@article {pmid40235568,
year = {2025},
author = {Davies, H and Noble, PJ and Fins, IS and Pinchbeck, G and Singleton, D and Pirmohamed, M and Killick, D},
title = {Developing electronic health records as a source of real-world data for veterinary pharmacoepidemiology.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1550468},
pmid = {40235568},
issn = {2297-1769},
abstract = {Spontaneous reporting of adverse events (AEs) by veterinary professionals and the public is the cornerstone of post-marketing safety surveillance for veterinary medicinal products (VMPs). However, studies suggest that most veterinary AEs remain unreported. Veterinary medicine regulators, including the United Kingdom Veterinary Medicines Directorate and the European Medicines Agency, have included the exploration of big data utilization to support pharmacovigilance efforts in their regulatory strategies. In this study, we describe the application of veterinary electronic healthcare records (EHRs) from the SAVSNET veterinary first opinion informatics system to conduct pharmacoepidemiological analyses. Five VMP-AE pairs were selected for investigation in a proof-of-concept study, where drug exposure was identified from semi-structured treatment data and AEs from the unstructured free-text clinical narrative. Dictionaries were developed to identify AEs based on standard terminology. The precision of these dictionaries improved when they were expanded using word vectorization and expert opinion. A key strength of first-opinion EHR datasets is their ability to enable cohort studies and facilitate calculations of absolute incidence and relative risk. Thus, we demonstrate that unstructured free-text clinical narratives can be used to identify outcomes for veterinary pharmacoepidemiological studies and, consequently, support and expand pharmacovigilance efforts based on spontaneous AE reports.},
}

@article {pmid40232549,
year = {2025},
author = {Xu, F and Jiang, C and Liu, Q and Yang, R and Li, W and Wei, Y and Bao, L and Tong, H},
title = {Source identification of polycyclic aromatic hydrocarbons (PAHs) in river sediments within a hilly agricultural watershed of Southwestern China: an integrated study based on Pb isotopes and PMF method.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {5},
pages = {174},
pmid = {40232549},
issn = {1573-2983},
support = {NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 41977169//National Natural Science Foundation of China/ ; NO. 41977169//National Natural Science Foundation of China/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; },
mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Geologic Sediments/chemistry/analysis ; *Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring/methods ; *Lead/analysis ; Agriculture ; Isotopes/analysis ; Geographic Information Systems ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) in sediments represent a pervasive environmental issue that poses significant ecological risks. This study employed a combination of geographic information systems, diagnostic ratios, correlation analysis, Pb isotope ratios, and positive matrix factorization (PMF) to elucidate the potential sources of 16 priority PAHs in river sediments from a hilly agricultural watershed in Southwestern China. The results indicated that PAHs concentrations ranged from 55.9 to 6083.5 ng/g, with a mean value of 1582.1 ± 1528.9 ng/g, reflecting high levels of contamination throughout the watershed. The predominant class of PAHs identified was high molecular weight (HMW) PAHs. Diagnostic ratios and correlation analysis suggested that the presence of PHAs is likely attributed primarily to emissions from industrial dust and combustion of coal and petroleum. Furthermore, correlation analysis revealed a significant association between Pb and PAHs, indicating potential shared sources for both pollutants. Additionally, Pb isotopic analysis demonstrated that aerosols may be the primary contributor to Pb accumulation within this environment. Given the similarity in origins between Pb and PAHs, it can be inferred that PAHs predominantly originate from aerosols associated with coal combustion, industrial dust emissions, and vehicle exhaust. This inference is further supported by PMF results which yielded consistent findings with those derived from Pb isotopes analysis. Moreover, PMF estimated three major sources contributing 57.63%, 23.57%, and 18.80%, respectively. These findings provide novel insights into identifying the sources of PAHs in river sediments within hilly agricultural watersheds in Southwest China, thereby establishing a scientific foundation for enhancing environmental quality in agricultural regions.},
}

China
*Polycyclic Aromatic Hydrocarbons/analysis
*Geologic Sediments/chemistry/analysis
*Rivers/chemistry
*Water Pollutants, Chemical/analysis
*Environmental Monitoring/methods
*Lead/analysis
Agriculture
Isotopes/analysis
Geographic Information Systems

@article {pmid40198742,
year = {2025},
author = {Choi, H and Lee, CH},
title = {The impact of climate change on ecology of tick associated with tick-borne diseases.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012903},
doi = {10.1371/journal.pcbi.1012903},
pmid = {40198742},
issn = {1553-7358},
mesh = {*Climate Change ; *Tick-Borne Diseases/transmission/epidemiology/prevention & control ; Animals ; *Ticks/physiology ; Humans ; *Models, Biological ; Population Dynamics ; Computational Biology ; },
abstract = {Infectious diseases have caused significant economic and human losses worldwide. Growing concerns exist regarding climate change potentially exacerbating the spread of these diseases, particularly those transmitted by vectors such as ticks and mosquitoes. Tick-borne diseases, such as Severe Fever with Thrombocytopenia Syndrome (SFTS), can be particularly detrimental to elderly and immunocompromised individuals. This study utilizes a mathematical modeling approach to predict changes in tick populations under climate change scenarios, incorporating tick ecology and climate-sensitive parameters. Sensitivity analysis is performed to investigate the factors influencing tick population dynamics. The study further explores effective tick control strategies and their cost-effectiveness in the context of climate change. The findings indicate that the efficacy of tick population reduction varies greatly depending on the timing of control measure implementation and the effectiveness of the control strategies exhibits a strong dependence on the duration of implementation. Furthermore, as climate change intensifies, tick populations are projected to increase, leading to a rise in control costs and SFTS cases. In light of these findings, identifying and implementing appropriate control measures to manage tick populations under climate change will be increasingly crucial.},
}

*Climate Change
*Tick-Borne Diseases/transmission/epidemiology/prevention & control
Animals
*Ticks/physiology
Humans
*Models, Biological
Population Dynamics
Computational Biology

@article {pmid40229317,
year = {2025},
author = {Sabadel, AJM and Riekenberg, P and Ayala-Diaz, M and Belk, MC and Bennett, J and Bode, A and Bury, SJ and Dabouineau, L and Delgado, J and Finucci, B and García-Seoane, R and Giari, L and Henkens, J and IJsseldijk, LL and Joling, T and Kerr-Hislop, O and MacLeod, CD and Meyer, L and McGill, RAR and Negro, E and Quillfeldt, P and Reed, C and Roberts, C and Sayyaf Dezfuli, B and Schmidt, O and Sturbois, A and Suchomel, AD and Thieltges, DW and van der Lingen, CD and van der Meer, MTJ and Viana, IG and Weston, M and Willis, TJ and Filion, A},
title = {Establishing a comprehensive host-parasite stable isotope database to unravel trophic relationships.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {623},
pmid = {40229317},
issn = {2052-4463},
support = {CAWX2207//Ministry of Business, Innovation and Employment (MBIE)/ ; },
mesh = {*Host-Parasite Interactions ; Animals ; Nitrogen Isotopes/analysis ; Carbon Isotopes ; *Databases, Factual ; Sulfur Isotopes/analysis ; *Parasites ; },
abstract = {Over the past decades, stable isotopes have been infrequently used to characterise host-parasite trophic relationships. This is because we have not yet identified consistent patterns in stable isotope values between parasites and their host tissues across species, which are crucial for understanding host-parasite dynamics. To address this, we initiated a worldwide collaboration to establish a unique database of stable isotope values of novel host-parasite pairs, effectively doubling the existing data in published literature. This database includes nitrogen, carbon, and sulphur stable isotope values. We present 3213 stable isotope data entries, representing 586 previously unpublished host-parasite pairs. Additionally, while existing literature was particularly limited in sulphur isotope values, we tripled information on this crucial element. By publishing unreported host-parasite pairs from previously unsampled areas of the world and using appropriate host tissues, our dataset stands unparalleled. We anticipate that end-users will utilise our database to uncover generalisable patterns, deepening our understanding of the complexities of parasite-host relationships and driving future research efforts in stable isotope parasitology.},
}

*Host-Parasite Interactions
Animals
Nitrogen Isotopes/analysis
Carbon Isotopes
*Databases, Factual
Sulfur Isotopes/analysis
*Parasites

@article {pmid40229216,
year = {2025},
author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Wang, C and Tai, J and Li, D and Chen, J},
title = {Emission Dynamics and Public Health Implications of Airborne Pathogens and Antimicrobial Resistance from Urban Waste Collection Facilities.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12108},
pmid = {40229216},
issn = {1520-5851},
abstract = {Airborne pathogens and antimicrobial resistance (AMR) present significant global health threats. Household waste collection facilities (WCFs), crucial initial nodes in urban waste management systems, have been understudied in regards to their role in emitting these hazards. This study investigated the abundance, composition, sources, driving mechanisms, and health risks associated with pathogens and AMR originating from WCFs in a major city, using culture-based analysis, high-throughput sequencing, and health risk modeling, respectively. The atmospheric escape rates of culturable bacteria (43.4%), fungi (71.7%), and antibiotic-resistant bacteria (ARB) (43.7%) were estimated based on the concentration differences between the interior and exterior of the WCFs by using SourceTracker2 analysis. Health risk assessments showed that annual infection risks for waste-handling workers ranged from 0.194 to 0.489, far exceeding the World Health Organization's acceptable limit of 10[-4]. Community exposure risks were notable up to 220 m downwind from WCFs, marking the maximum extent of pathogen dispersion. Our analysis suggests that approximately 6.3% of the megacity's area (equivalent to 400 km[2]) is within potential risk zones influenced by WCF emissions. These results underscore the critical need to evaluate and mitigate the public health risks posed by airborne pathogens and AMR emitted from WCFs in megacities globally.},
}

@article {pmid40227267,
year = {2025},
author = {Cassaro, A and Pacelli, C and Fanelli, G and Baqué, M and Maturilli, A and Leo, P and Lelli, V and de Vera, JP and Onofri, S and Timperio, A},
title = {Biomarker Preservation in Antarctic Sandstones after Prolonged Space Exposure Outside the International Space Station During the ESA EXPOSE-E Lichens and Fungi Experiment.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2024.0068},
pmid = {40227267},
issn = {1557-8070},
abstract = {A primary aim of current and future space exploration missions is the detection and identification of chemical and biological indicators of life, namely biomarkers, on Mars. The Mars Sample Return NASA-ESA program will bring to Earth samples of martian soil, acquired from up to 7 cm depth. The ESA Rosalind Franklin rover will search for signs of life in the subsurface (down to a depth of 2 meters), given the highly radioactive conditions on Mars' surface, which are not ideal for life as we know it and for the preservation of its traces. In the frame of the Lichens and Fungi Experiment, small fragments of Antarctic sandstones colonized by cryptoendolithic microbial communities were exposed to space and simulated martian conditions in low Earth orbit for 18 months, aboard the EXPOSE-E payload. Through the use of Raman and infrared spectroscopies, as well as a metabolomic approach, we aimed to detect organic compounds in a quartz mineral matrix. The results show that pigments, such as melanin, carotenoids, and chlorophyll, lipids, and amino acids, maintained their stability within minerals under simulated martian conditions in space, which makes them ideal biomarkers for the exploration of putative life on Mars.},
}

@article {pmid40226649,
year = {2024},
author = {Tamm, J and Takano, K and Just, L and Ehring, T and Rosenkranz, T and Kopf-Beck, J},
title = {Ecological Momentary Assessment versus Weekly Questionnaire Assessment of Change in Depression.},
journal = {Depression and anxiety},
volume = {2024},
number = {},
pages = {9191823},
pmid = {40226649},
issn = {1520-6394},
mesh = {Humans ; *Ecological Momentary Assessment ; Male ; Female ; Adult ; Middle Aged ; Surveys and Questionnaires/standards ; *Depression/diagnosis/therapy ; *Outcome Assessment, Health Care/methods ; Reproducibility of Results ; Pessimism/psychology ; Psychiatric Status Rating Scales ; Rumination, Cognitive ; },
abstract = {OBJECTIVE: Ecological momentary assessment (EMA) is increasingly used to monitor depressive symptoms in clinical trials, but little is known about the comparability of its outcomes to those of clinical interviews and questionnaires. In our study, we administered EMA and questionnaires to measure change in depressive symptoms and repetitive negative thinking (RNT) in a clinical trial and investigated (a) the size of intervention effects associated with both techniques and (b) their validity in predicting clinical interview outcomes (i.e., global functioning).

MATERIALS AND METHODS: Seventy-one depressed patients were randomly assigned to one of three psychological interventions. The EMA comprised a concise item set (four items per scale) and was administered three times per day during a 7-week intervention period. Conversely, questionnaires were assessed weekly (WQA), encompassing their full sets of items of depressive symptoms and RNT.

RESULTS: While EMA excelled in detecting significant intervention effects, WQA demonstrated greater strength in predicting clinician ratings of global functioning. Additionally, we observed significant differences in time effects (slopes) between the two techniques. WQA scores decreased steeper over time and were more extreme, e.g., higher at baseline and lower postintervention, than EMA scores.

CONCLUSIONS: Although clinical interviews, questionnaires, and EMA outcomes are related, they assess changes in depression differently. EMA may be more sensitive to intervention effects, but all three methods harbor potential bias, raising validity and reliability questions. Therefore, to enhance the validity and reliability of clinical trial assessments, we emphasize the importance of EMA approaches that combine subjective self-reports with objectively measured behavioral markers. This trial is registered with osf.io/9fuhn.},
}

Humans
*Ecological Momentary Assessment
Male
Female
Adult
Middle Aged
Surveys and Questionnaires/standards
*Depression/diagnosis/therapy
*Outcome Assessment, Health Care/methods
Reproducibility of Results
Pessimism/psychology
Psychiatric Status Rating Scales
Rumination, Cognitive

@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods/trends
*Metabolomics/methods
*Genomics/methods
Proteomics/methods
Precision Medicine
Host Microbial Interactions
Multiomics

@article {pmid40222989,
year = {2025},
author = {Mu, K and Wang, Z and Tang, J and Zhang, J and Han, W},
title = {The satisfaction of ecological environment in sports public services by artificial intelligence and big data.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12748},
pmid = {40222989},
issn = {2045-2322},
mesh = {Humans ; *Artificial Intelligence ; *Big Data ; *Sports ; Surveys and Questionnaires ; Neural Networks, Computer ; *Personal Satisfaction ; },
abstract = {In order to gain a more accurate understanding and enhance the relationship between the fitness ecological environment and artificial intelligence (AI)-driven sports public services, this study combines a Convolutional Neural Network (CNN) approach based on residual modules and attention mechanisms with the SERVQUAL evaluation model. The method employed involves the analysis of big data collected from questionnaire surveys, literature reviews, and interviews. This study critically examines the impact of advanced AI technologies on residents' satisfaction with the fitness ecological environment in sports public services and conducts theoretical analysis of the obtained data. The results show that the quality of sports public services empowered by AI significantly influences residents' satisfaction with the fitness ecological environment, such as running, swimming, ball games and other sports with high requirements for sports service quality and ecological environment. Only the good public sports service quality matching with them can meet the needs of the ecological environment for fitness, and stimulate the enthusiasm of the people for fitness. The study also shows that swimming, running and all kinds of ball games account for the largest proportion of all sports. To sum up, the satisfaction of residents' fitness ecological environment is greatly affected by the quality of public sports services, which is mainly reflected in the good and perfect sports environment and facilities that can provide residents with a wealth of fitness options, greatly improving the sports ecological environment. This study is helpful to realize the relationship between sports public service and sports ecological environment. It contributes to understanding the role of AI and deep learning in enhancing the correlation between sports public service and the ecological environment of sports.},
}

Humans
*Artificial Intelligence
*Big Data
*Sports
Surveys and Questionnaires
Neural Networks, Computer
*Personal Satisfaction