@article {pmid41673365,
year = {2026},
author = {Jena, R and Ramakrishnan, S and Sarma, A and Sinha, VSP and Jayaraman, A},
title = {Estimation of surface water susceptibility to pollution index of natural wetlands of North-East India using multi-criteria decision model.},
journal = {Environmental science and pollution research international},
volume = {33},
number = {8},
pages = {3360-3378},
pmid = {41673365},
issn = {1614-7499},
mesh = {*Wetlands ; India ; Water Quality ; *Environmental Monitoring/methods ; *Water Pollution/analysis ; Models, Theoretical ; Decision Support Techniques ; },
abstract = {This study aims to develop a comprehensive and spatially explicit Surface Water Susceptibility to Pollution (SWSP) index using a Multi-Criteria Decision-Making (MCDM) framework, integrated with spatial environmental considerations. The proposed SWSP model employs a data-driven modelling approach, incorporating eight independent watershed characteristics and 55 sub-factors into the index to assess the health and quality of the wetland landscape. Unlike conventional single-parameter or empirical assessments, it includes a holistic evaluation of determinants contributing to surface water pollution within a catchment. The study was conducted in the wetland-dominated area of northeast India to demonstrate the scalability and replicability of the model for larger applications. Meanwhile, the Water Quality Index (WQI) is scientifically important because it consolidates multiple water quality parameters into a single, standardised score that reflects the overall health of a wetland, which depends on watershed characteristics. Therefore, the WQI can be used to cross-validate the SWSP index by comparing predicted pollution vulnerability with actual water quality measurements. In the present study, the WQI was measured through in situ and laboratory tests of the physicochemical parameters of surface water in three natural wetlands: Deepor Beel, Chandubi Lake, and Digholi Bil. This measurement was used to validate the SWSP index. The water quality analysis reveals that 96% of the total geographical area (TGA) of Deepor Beel has a WQI above 200, characterised by high turbidity (73.6 NTU), rendering the water unsuitable for any use. High and very high SWSP index areas within the catchment of Deepor Beel (72% TGA), Digholi Bil (63% TGA), and Chandubi Lake (62% TGA) are encompassed by built-up areas, agricultural land, and hilly forested regions. Linear regression shows a significant correlation between the SWSP Index and the WQI in all three wetlands: Deepor Beel (R[2] = 0.72), Chandubi Lake (R[2] = 0.85), and Digholi Bil (R[2] = 0.68), with p < 0.05. A strong correlation between the two confirms the model's reliability, while discrepancies suggest the need for refinement. This cross-validation enhances the scientific credibility of the SWSP index, supporting policymakers in sustainable watershed management, public health protection, and ecological conservation.},
}

*Wetlands
India
Water Quality
*Environmental Monitoring/methods
*Water Pollution/analysis
Models, Theoretical
Decision Support Techniques

@article {pmid42254981,
year = {2026},
author = {Nwinyi, OC and Siyanbola, KF},
title = {Spatial Heterogeneity of CYP9K1 Gene Overexpression Driving Cross-Resistance to Insecticide in Anopheles Mosquitoes Across Sub-Saharan Africa: A Systematic Review and Meta-Analysis.},
journal = {Journal of parasitology research},
volume = {2026},
number = {},
pages = {7708566},
pmid = {42254981},
issn = {2090-0023},
abstract = {Insecticide resistance in Anopheles mosquitoes poses a growing challenge to malaria elimination efforts across sub-Saharan Africa, threatening the continued effectiveness of frontline interventions. Among the metabolic mechanisms driving resistance, the cytochrome P450 monooxygenase gene CYP9K1 has been increasingly associated with detoxification and cross-resistance to multiple insecticide classes, particularly pyrethroids. This review assessed spatial heterogeneity in CYP9K1 overexpression (log2 fold change) in cross-resistant Anopheles mosquito populations across sub-Saharan Africa. This systematic review was conducted in accordance with PRISMA guidelines, drawing data from PubMed, Scopus, Web of Science, ScienceDirect, BioMed Central, and Google Scholar (2015-2025). Random-effects models using restricted maximum likelihood (REML) estimation were applied in JASP, alongside subgroup, sensitivity, and publication bias analyses. Out of 17,163 retrieved records, 11 studies met the inclusion criteria, representing data from six sub-Saharan African countries. The pooled log2 fold change for CYP9K1 expression was 1.910 (95% CI: 1.274-2.545; p < 0.001), confirming significant upregulation in resistant mosquito populations. Subgroup analyses further revealed that CYP9K1 overexpression followed a similar trend across countries, with no statistically significant differences observed between the countries (p > 0.05). This consistency suggests that the same CYP9K1-linked resistance mechanism may be spreading across different ecological and geographic regions, possibly through gene flow or shared selection pressure from insecticide use. These findings highlight CYP9K1 as a key metabolic marker conferring cross-resistance among Anopheles mosquitoes. The integration of CYP9K1 molecular surveillance into national vector control programs will strengthen early detection of resistance hotspots, inform insecticide rotation policies, and support the development of next-generation long-lasting insecticidal nets (LLINs) incorporating synergists or nonpyrethroid active ingredients. This evidence-based approach could guide tailored resistance management strategies essential for sustaining malaria control gains across sub-Saharan Africa.},
}

@article {pmid42255360,
year = {2026},
author = {Falk, S and Grzywacz, A and , and , and , and , and , and , and , },
title = {The genome sequence of a muscid fly, Phaonia angelicae (Scopoli, 1763) (Diptera: Muscidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {236},
pmid = {42255360},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Phaonia angelicae (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The assembly contains two haplotypes with total lengths of 1 593.88 megabases and 1 575.57 megabases. Most of haplotype 1 (97.48%) is scaffolded into 5 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.82 kilobases. Gene annotation of this assembly on Ensembl identified 13 923 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid42258804,
year = {2026},
author = {Yeung, SK and Tong, ACY and Zhao, H and Mak, WWS},
title = {Using Ultra-Abridged Individual Difference Scales for Personalization in Digital Mental Health to Improve Uptake, Engagement, and Experiences: Three-Tiered Decision Framework for Scale Shortening.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e80662},
doi = {10.2196/80662},
pmid = {42258804},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; *Mental Health ; *Individuality ; Digital Media ; },
abstract = {Given the diversity of human characteristics and experiences, personalization in nudges, messages, choice presentations, interventions, and overall product design has been increasingly adopted in digital health to promote engagement. Past studies on moderators and personalization in digital health and mental health services generally focused on demographic and symptom variables, with generally inconsistent findings or null findings. Cognitive, motivational, and decisional psychological attributes are largely overlooked. Psychology often uses long self-report scales to measure various psychological attributes. Although they are useful in tapping into individuals' psychological profiles, when applied in real-life, everyday settings to assess individual differences, people are most likely unwilling to complete them. With the pressing need to personalize digital health platforms to enhance uptake, retention, and engagement, ultrashort versions of these psychological scales may be considered to allow assessment of multiple attributes at the same time. Scale shortening can be achieved through regression analyses of each item, factor analyses, item response theory, ant colony optimization, and machine learning methods, with each method having advantages, disadvantages, and conditions required to make it suitable. To illustrate, we provided examples of regression analyses of each item and factor analyses, with potential implications for personalizing narrative versus research-based messages in digital mental health contexts. We present a 3-tiered decision framework for scale shortening method selection depending on goals and possible constraints, with guidelines on validation methods for ultrashort scales. Moving forward, more validation studies and field studies in digital health platforms are needed to evaluate the ecological validity, reliability, and generalizability of these methods, bearing in mind the limitations and conditions where such shortening methods may not work well. Researchers may compare the effectiveness and limitations of personalization using ultrashort scales with other commonly adopted personalization methods (eg, based on longer scales, behavioral data, and large language models). Ethical concerns need to be considered and mitigated carefully, respecting diverse preferences, informed choices, and the privacy of service users. Our viewpoint piece is primarily intended for digital mental health researchers and practitioners, but may also be informative for the fields of digital health and medicine as well as personalization (eg, personalized health care, personalized nudging, and message matching) more broadly, given the common goal of boosting uptake and engagement as well as improving service users' experiences.},
}

Humans
Digital Health
*Mental Health
*Individuality
Digital Media

@article {pmid41654280,
year = {2026},
author = {Zhao, L and Liu, W},
title = {Metabolomics applications in lactic acid bacteria: Identification, classification, and functional analysis.},
journal = {Biotechnology advances},
volume = {88},
number = {},
pages = {108838},
doi = {10.1016/j.biotechadv.2026.108838},
pmid = {41654280},
issn = {1873-1899},
mesh = {*Metabolomics/methods ; *Lactobacillales/metabolism/classification/genetics ; Multiomics ; },
abstract = {BACKGROUND: Lactic acid bacteria (LAB) exhibit a limited correlation between genomic attributes and expressed metabolic traits, with their metabolic profiles being strongly influenced by ecological and environmental conditions. Recent advances in metabolomics have enabled high-resolution profiling of LAB-specific metabolic fingerprints and bioactive compounds. Nevertheless, challenges such as metabolite instability, incomplete annotation of LAB-derived metabolites, and environmental interference within complex fermentation matrices continue to hinder data standardization, reproducibility, and mechanistic interpretation.

SCOPE AND APPROACH: This review synthesizes recent advances in LAB metabolomics, highlighting how state-of-the-art analytical platforms, in combination with single-cell and metabolic flux-based approaches, improve strain identification, metabolic phenotyping, and functional metabolite discovery. It further addresses LAB-specific methodological challenges and observed discordance between phylogenetic relationships and metabolomic phenotypes, and discusses how the integration of metabolomics with genome-scale metabolic models (GSMMs) and multi-omics frameworks can improve functional prediction and provide deeper mechanistic insights.

KEY FINDINGS AND CONCLUSIONS: Overall, the integration of metabolomics is transforming functional studies in LAB by enabling strain-specific functional differentiation and the direct inference of adaptive traits from metabolic phenotypes. As metabolomics increasingly integrates with multi-omics datasets, GSMMs, and experimental validation approaches, a more unified framework for LAB functional analysis is emerging. This integrated approach provides a robust foundation for mechanistic elucidation, functional strain selection, and targeted applications in fermented food systems.},
}

*Metabolomics/methods
*Lactobacillales/metabolism/classification/genetics
Multiomics

@article {pmid41662579,
year = {2026},
author = {Monasterio, G and Fernández-López, MJ and Valero, E and Martin, U and Ayala-García, A},
title = {Digital Inequalities in the Use of eHealth Services in European Public Health Care Systems: Systematic Review of Observational Studies.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e81841},
pmid = {41662579},
issn = {1438-8871},
mesh = {Humans ; *Telemedicine/statistics & numerical data ; Europe ; Digital Health ; Socioeconomic Disparities in Health ; Observational Studies as Topic ; *Healthcare Disparities ; *Public Health ; Health Services Accessibility ; Socioeconomic Factors ; Social Determinants of Health ; },
abstract = {BACKGROUND: European public health care systems are expanding eHealth tools such as teleconsultations, online appointment bookings, and electronic health records to improve efficiency and access to health care. However, their use depends on factors such as digital skills and internet access, which are unequally distributed across socioeconomic and demographic determinants. Most existing evidence on these inequalities is qualitative or outside universal health care systems.

OBJECTIVE: This systematic review aims to synthesize quantitative evidence on social inequalities in access to and use of eHealth services within European public health care systems. Specifically, we sought to identify which social determinants were most consistently associated with unequal use of online appointment booking, teleconsultations, electronic health records, and eHealth portals, across major social determinants of health.

METHODS: A systematic search was conducted across PubMed, Scopus, Web of Science, and PsycINFO for studies published in English or Spanish between 2015 and October 2025. Eligible quantitative studies included adults (≥18 years) using public health care systems in European countries. The primary outcome was differential access to or use of eHealth tools by social determinants in any level of care. Screening and data extraction were independently performed by 3 reviewers using Rayyan, resolving disagreements through consensus. Data extracted covered study design, population, eHealth tools, social determinants, and outcomes. Risk of bias was evaluated using Joanna Briggs Institute tools. Due to study heterogeneity in digital tools and inequality dimensions, results were synthesized narratively by tool type and social inequality factors. Point estimates and 95% CIs were extracted when available.

RESULTS: Of the 2366 records retrieved, 18 observational studies met the inclusion criteria: 13 cross-sectional, 3 prevalence, 1 retrospective cohort, and 1 ecological cohort. Publication output increased from 2020 onward, mostly driven by cross-sectional studies from northern and western Europe. Findings revealed consistent social gradients in eHealth use: older adults, individuals with lower educational or socioeconomic level, ethnic minorities, and those with limited digital skills or poorer health were less likely to use eHealth tools. Most studies were rated as high quality (78%), and the remainder as moderate, heterogeneity in designs, outcomes, and populations may limit generalizability.

CONCLUSIONS: Digital transformation in European public health systems has not benefited all groups equally. This review highlights persistent social inequalities in the use of key digital health tools. While many included studies were of high quality, heterogeneity in study designs, populations, and outcomes, as well as risk of bias, limits causal inference and the direct translation of findings into policy and practice. The findings nonetheless reveal systematic patterns of exclusion that are highly relevant for policy. Emphasizing an intersectional approach and standardizing measures of digital access will be essential to develop effective, equity-focused policies that ensure inclusive digital health services for all.},
}

Humans
*Telemedicine/statistics & numerical data
Europe
Digital Health
Socioeconomic Disparities in Health
Observational Studies as Topic
*Healthcare Disparities
*Public Health
Health Services Accessibility
Socioeconomic Factors
Social Determinants of Health

@article {pmid41959181,
year = {2026},
author = {Yuan, H and Mandava, A and Samart, K and Ganz, J and Krishnan, A},
title = {Linking Genetic Risk to Disease-Relevant Cellular States via Metacell-Informed Modeling with ICePop.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.01.715877},
pmid = {41959181},
issn = {2692-8205},
abstract = {Genome-wide association studies (GWAS) have implicated thousands of loci in complex diseases, but translating these population-level signals into specific cellular contexts remains a central challenge. Integrating GWAS with single-cell transcriptomics data has enabled systematic identification of disease-relevant cell types, yet existing methods face a fundamental tradeoff: approaches like seismic that optimized for statistical power operate at the annotated cell-type level and miss heterogeneous disease signals concentrated in specific cellular states, while single-cell-resolution approaches like scDRS that capture such heterogeneity often lack sufficient power to detect subtle associations. Here we present ICePop (Informative Cell Populations), a framework that resolves this tradeoff by performing disease-cell type association at metacell resolution, thus achieving statistical power comparable to cell-type-level methods while detecting heterogeneous disease signals within cell types. In simulations against seismic and scDRS, ICePop maintains appropriate false positive rates and demonstrates superior power when disease effects are concentrated in cellular subpopulations. Applied to Tabula Muris across 81 traits and 120 cell types, ICePop identifies 1,684 disease-cell type associations, including the preferential vulnerability of differentiated gut epithelial cells in ulcerative colitis and loss of cell identity in immune-stressed lung capillary endothelial cells underlying their association with lung function. Clustering diseases by metacell association profiles reveals groupings that diverge from genetic risk-based clustering, including separation of blood cell count traits from immune diseases despite shared genetic architecture, reflecting differences in cellular rather than genetic etiology. In autism spectrum disorder, ICePop identifies preferential enrichment of genetic risk in specific enteric neuron subtypes, implicating dysfunction of the enteric nervous system in gastrointestinal comorbidities. ICePop's resolution of disease-relevant cell states within annotated cell types enables generation of testable, cell-state-specific hypotheses about disease mechanisms and therapeutic targets.},
}

@article {pmid42146430,
year = {2026},
author = {Ramola, R and De Paolis Kaluza, MC and Piovesan, D and Peng, Y and Joshi, P and Mehdiabadi, M and Quaglia, F and Pancsa, R and Chemes, LB and Ahmadi, M and Ahn, H and Altenhoff, AM and Asgari, E and Aspromonte, MC and Atalay, V and Babbi, G and Baldazzi, D and Barot, MM and Ben-Hur, A and Benso, A and Berenberg, D and Björne, J and Boecker, F and Boldi, P and Bonello, J and Bordin, N and Borole, P and Boroojeny, AE and Cao, R and Di Carlo, S and Casadio, R and Casiraghi, E and Chang, JM and Chen, C and Chen, TM and Cheng, J and Chiu, S and Dalkıran, A and Davidović, RS and Dessimoz, C and Diao, R and Djeddi, WE and Dogan, T and Flannery, ST and Fontana, P and Frasca, M and Freddolino, L and Gemović, B and Gillis, J and Ginter, F and Gligorijevic, V and Grossi, G and Heinzinger, M and Hippe, K and Hoehndorf, R and Holm, L and Hou, J and Hover, JR and Huang, YT and Ispano, E and Jabin, S and Jain, A and Jones, DT and Kaewphan, S and Kagaya, Y and Kanerva, J and Kihara, D and Kulmanov, M and Kumar, S and Kurgan, L and Lavezzo, E and Lees, J and Liao, WH and Lin, H and Linial, M and Littmann, M and Liu, L and Liu, T and Liu, YW and Makrodimitris, S and Manuto, L and Martelli, PL and Mchardy, AC and Merino, GA and Milone, DH and Mishra, S and Mofrad, MRK and Moi, D and Nakamura, T and Narsapuram, VK and Nugnes, MV and Obayashi, T and Ofer, D and Paccanaro, A and Perovic, VR and Petrini, A and Politano, G and Raimondi, D and Rappoport, N and Rehman, HU and Reijnders, MJMF and Reinders, MJT and Renfrew, PD and Rifaioglu, AS and Romero, AE and Saraswathi, A and Savojardo, C and Scholes, HM and Schoof, H and Shen, Y and Sillitoe, I and Stegmayer, G and Stern, A and Tiittanen, H and Toonsi, S and Toppo, S and Toronen, P and Torres, M and Trucco, G and Valentini, G and Veljkovic, N and Vesztrocy, AW and Vidulin, V and Villegas-Morcillo, A and Virtanen, A and Vranken, W and Vucetic, S and Wan, C and Wang, Z and Wass, MN and Waterhouse, RM and Ben Yahia, S and Yang, H and Yao, S and You, R and Yunes, J and Zhang, C and Zhang, Y and Zhao, C and Zhou, X and Zhu, YH and Zhu, S and Zhu, H and Özsari, G and Rost, B and Orengo, C and Robinson-Rechavi, M and Durand, D and Brenner, SE and Greene, CS and Mooney, SD and Tosatto, SCE and Friedberg, I and Radivojac, P},
title = {On the state of protein function prediction: a report on the fourth CAFA challenge.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42146430},
issn = {2692-8205},
abstract = {BACKGROUND: The Critical Assessment of Functional Annotation (CAFA) is a community effort held to understand the field of computational protein function prediction. Every three years, since 2010, the organizers initiate an experiment to collect function predictions on a large set of proteins and then evaluate the performance of predicting methods on a subset of proteins that have accumulated experimental annotations between the submission deadline and the evaluation time. CAFA provides an independent and rigorous assessment of the current state of the art, thus leveling the playing field, highlighting successes, revealing bottlenecks, and offering a forum for the exchange of ideas in protein science. Here, we report the results of the fourth CAFA experiment (CAFA4).

RESULTS: CAFA4 featured the participation of 148 methods from 70 research groups on a total of 46,205 unique proteins over a 5-year annotation accumulation phase, the longest in any CAFA. In a comparison across CAFA2-CAFA4 methods, the prediction of Gene Ontology (GO) terms has clearly improved across all three GO aspects and traditional evaluation settings. While not achieving the first rank, several CAFA2 and CAFA3 methods featured in the top ten methods in many evaluations, suggesting that earlier methods still hold relevance. The performance is weaker in the newly introduced "partial knowledge" evaluation category (proteins with experimental annotations before submission deadline that gained additional annotations in the same GO aspect during the annotation accumulation phase), highlighting the need for a new class of methods. The rankings of the methods were stable over the years in traditional evaluation settings, but less so in the new partial knowledge evaluation. Overall, the field continues to progress with some influx of new participants. Sustained efforts will be necessary to substantially advance it.},
}

@article {pmid42189907,
year = {2026},
author = {Wang, YJ and Schaal, KA and Nauta, J and Liaghat, A and De Domenico, M and Hall, JPJ and Pilosof, S},
title = {The interplay between ecological networks drives host-plasmid community dynamics.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014339},
pmid = {42189907},
issn = {1553-7358},
mesh = {*Plasmids/genetics/physiology ; *Models, Biological ; Computational Biology ; *Host-Pathogen Interactions/genetics ; },
abstract = {Plasmids drive evolution by transferring traits across microbial hosts. Transmission depends on both host-plasmid (infection) and plasmid-plasmid (compatibility) interactions, yet how the structure of these networks shapes transmission remains poorly understood. We hypothesized that these two ecological networks interact in non-additive ways to influence community outcomes. To test this, we developed a stochastic agent-based model that embeds both network structures and simulates coupled host-plasmid dynamics. We systematically varied the structure of each network, both individually and in combination, to isolate the effect of structure on host-plasmid dynamics. A modular (interactions organized into clusters) and hub (interactions concentrated on the highly connected) plasmid-plasmid compatibility network promoted transient host coexistence, while a modular host-plasmid infection network promoted plasmid diversity and stable host coexistence. Importantly, structured networks interacted non-additively, and their impact was most apparent when plasmid carriage imposed a moderate fitness cost on hosts. For example, combining a modular infection network with a hub compatibility network reversed the expected plasmid prevalence patterns, demonstrating that the structure of one network can counteract the effects of the other. We further re-parameterized our model to recapitulate empirical host-plasmid community dynamics, showing that infection network structure can strongly shape plasmid prevalence even in the presence of substantial biological heterogeneity. Our results highlight the necessity of jointly considering host-plasmid infection and plasmid-plasmid compatibility networks to understand host-plasmid community dynamics and their eco-evolutionary potential. More broadly, this work provides an initial mechanistic framework for generating testable hypotheses and underscores that systems involving multiple hosts and infectious agents require explicit consideration of how different ecological networks interact to shape community dynamics.},
}

*Plasmids/genetics/physiology
*Models, Biological
Computational Biology
*Host-Pathogen Interactions/genetics

@article {pmid42251245,
year = {2026},
author = {Kupika, OL and Zlotnikova, I},
title = {Biodiversity conservation informatics under anthropogenic climate change: an open and FAIR bibliometric review.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {42251245},
issn = {2676-8607},
abstract = {Informatics technologies are transforming biodiversity conservation by enabling large-scale data analysis, predictive modelling, and real-time monitoring in the face of anthropogenic climate change. This study presents a bibliometric analysis of global research on the application of informatics tools - such as machine learning, remote sensing, geographic information systems, and big data analytics - to biodiversity conservation and anthropogenic climate change. Using the Scopus database, we analysed 643 publications from 1993 to 2024 to identify research trends, collaboration networks, and emerging thematic areas. The results reveal a rapid increase in publications over the last decade, with developed countries and China leading research output, while contributions from Africa remain limited. Keyword co-occurrence analysis highlights key research themes, including species distribution modelling, climate change impacts, conservation technology, and ecological informatics. Co-authorship network mapping underscores the interdisciplinary and collaborative nature of biodiversity informatics and anthropogenic climate change research. This bibliometric review provides a quantitative synthesis of knowledge production in this field, offering insights into dominant research trajectories and identifying gaps in geographic representation and thematic coverage. Overall, the review reveals a large but geographically skewed scientific footprint whose future value depends on closing gaps in data-poor, biodiversity-rich regions and explicitly linking biodiversity informatics outputs to climate-resilient policy and practice. The findings inform future research and policy efforts aimed at leveraging informatics technologies for effective and inclusive biodiversity conservation strategies in a changing climate. This study is FAIR-aligned and accompanied by openly shared data and materials with ISO-aligned, machine-readable metadata.},
}

@article {pmid42252446,
year = {2026},
author = {Kim, Y and Lee, H and Lee, E and Kim, YH and Oh, CK},
title = {Oxidative aging facilitates biological barrier penetration of polyethylene microplastics, amplifying systemic lipotoxicity in aquatic species.},
journal = {Particle and fibre toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12989-026-00689-2},
pmid = {42252446},
issn = {1743-8977},
support = {RS-2025-02303107//National Research Foundation of Korea/ ; RS-2025-02214034//Korea Institute for Advancement of Technology/ ; },
abstract = {BACKGROUND: Environmental aging processes, such as oxidation, can substantially modify the physicochemical properties and toxicity of microplastics (MPs). Nevertheless, most studies have focused on pristine MPs, overlooking aged forms that more accurately represent environmental exposure conditions. Understanding the toxicological consequences of oxidative aging is essential for realistic ecological risk assessment.

RESULTS: We investigated the toxicological effects of pristine polyethylene (PE) and oxidized polyethylene (OPE) microplastics using a dual-species aquatic model comprising Daphnia magna and zebrafish (Danio rerio) embryos. Physicochemical characterization revealed that OPE particles exhibited increased surface roughness, a more negative surface charge, and a higher proportion of oxygen-containing functional groups on the particle surface compared with PE. Exposure to OPE induced pronounced lipid accumulation and significantly reduced heart rate in both models. Transcriptomic analysis indicated that OPE downregulated key genes related to lipid transport and metabolism, including mttp, apoea, and apobb. These findings were further validated by quantitative PCR and Oil Red O staining. Notably, zebrafish embryos exposed to OPE displayed developmental impairment even with intact chorions, implying enhanced bioavailability and barrier penetration of oxidized particles.

CONCLUSIONS: Our findings demonstrate that oxidative aging amplifies the biological toxicity of polyethylene microplastics by disrupting lipid metabolism and developmental processes. This study underscores the importance of considering environmentally aged MPs in ecological risk evaluations, as pristine particles may underestimate their actual hazard potential in aquatic ecosystems.},
}

@article {pmid41609929,
year = {2026},
author = {Mo, Y and Ahlgren, N and Fuhrman, JA and Sun, F and Hou, S},
title = {A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets.},
journal = {Current protocols},
volume = {6},
number = {2},
pages = {e70310},
doi = {10.1002/cpz1.70310},
pmid = {41609929},
issn = {2691-1299},
support = {549943//Simons Foundation/ ; 42476109//National Natural Science Foundation of China/ ; 42276163//National Natural Science Foundation of China/ ; EF-2125142//National Science Foundation/ ; 3779//Gordon and Betty Moore Foundation/ ; },
mesh = {*Metagenomics/methods ; *Software ; *Deep Learning ; *Viruses/genetics ; Genome, Viral ; *Computational Biology/methods ; },
abstract = {Identifying viral sequences from metagenomic datasets is critical for investigating their origins, evolutionary patterns, and ecological functions. Previously, we developed a novel deep learning software, DeepVirFinder, to predict viral sequences from shotgun metagenomic assemblies. This method employs a twin convolutional neural network model to extract features from known viral and prokaryotic host genomic sequences for binary classification of input query sequences. With the rapid accumulation of environmental metagenomic data, this approach has accelerated the discovery of novel viruses from diverse environments through an alignment-free and reference-free deep learning strategy. To facilitate the rapid adoption of this software for beginning users, here we have further improved DeepVirFinder by optimizing its runtime performance, while maintaining the essential user interface of the original version. This comprehensive guide provides basic workflows for the most common use cases of DeepVirFinder. Additionally, to assist users in downstream analyses, supplementary scripts were provided in the software for extracting viral sequences and inspecting the results, thereby helping researchers more effectively mine viral information from metagenomic datasets. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Predicting viral sequences in metagenomic assemblies Basic Protocol 2: An integrated pipeline for viral sequence analysis: Prediction, extraction, and visualization Basic Protocol 3: Retraining the DeepVirFinder model using a customized dataset.},
}

*Metagenomics/methods
*Software
*Deep Learning
*Viruses/genetics
Genome, Viral
*Computational Biology/methods

@article {pmid41617485,
year = {2026},
author = {Chang, YH and Hong, TC and Lin, KT and Hsiao, YJ and Hsu, HE and Waniwan, JT and Silva, RE and Lai, IR and Lee, PC and Lin, MT and Shun, CT and Hsieh, MS and Chen, YJ and Wang, SW and Hsu, WH and Wu, IC and Wang, YK and Li, CC and Wang, JY and Hsu, YC and Fang, H and Lin, ZS and Chang, WH and Lin, JH and Chen, YS and Ko, YC and Shen, CY and Chen, YM and Wang, CY and Jheng, YT and Liu, WY and Wang, YT and Yeh, CW and Huang, PR and Liou, JM and Chen, LT and Han, CL and Wu, DC and Chen, HY and Yu, SL and Wu, MS and Chen, YJ and , },
title = {Integrative proteogenomics maps multifactorial aetiology, progression and therapeutic vulnerabilities in gastric cancer.},
journal = {Gut},
volume = {75},
number = {5},
pages = {886-904},
doi = {10.1136/gutjnl-2025-337247},
pmid = {41617485},
issn = {1468-3288},
mesh = {Humans ; *Stomach Neoplasms/microbiology/genetics/etiology/pathology/therapy ; *Proteogenomics/methods ; Male ; Female ; Disease Progression ; Multiomics ; Helicobacter pylori ; Helicobacter Infections/complications/microbiology ; Middle Aged ; Taiwan ; Gastrointestinal Microbiome ; Aged ; Microbiota ; },
abstract = {BACKGROUND: Gastric cancer, with disproportionately higher incidence in East Asia, arises from complex host-microbiome-environment interactions beyond Helicobacter pylori (HP) infection. However, the molecular architecture linking environmental carcinogens, microbial succession and host response remains unclear.

OBJECTIVE: To delineate multifactorial aetiologies and clinically actionable subtypes/biomarkers of gastric cancer through integrative proteogenomic, microbial and environmental exposure profiling.

DESIGN: We established a multiomics atlas of paired tumour, adjacent mucosa tissues and blood from 154 treatment-naïve Taiwanese patients, integrating whole-exome sequencing, RNA-seq, proteome and phosphoproteome profiling with carcinogen signatures, HP status, microbiome composition and refined anatomical mapping. Cell-based functional assays tested carcinogen effects. Microbial subtype was assessed in an independent cohort.

RESULTS: A polycyclic-aromatic-hydrocarbon signature, dibenz[a,h]acridine, emerged as a high-risk exposure promoting invasion, immune suppression and poor survival, significantly exceeding nitrosamine-linked risk in this cohort. Multilayer integration defined three initiation ecologies: HP-driven inflammatory, non-HP microbiome-enriched immune-silent and HP-free microbially depleted states. Among HP-negative tumours, a Streptococcus-enriched subtype associated with tight-junction (CLDN18.2/ZO-1/OCLN) disruption and epithelial-mesenchymal transition, whereas a subset of clinically aggressive cases retained CLDN18.2-high epithelial-stable subtype for therapeutic accessibility. An independent cohort revealed gastric juice-derived Streptococcus anginosus abundance inversely correlated with tight-junction proteins. Anatomical mapping reveals location-specific, sex-specific, subtype-specific oncogenic networks and kinase activity, including CDK4 activation in clinical biomarker-negative tumours. Decision-tree models combining exposure and proteome-immune states refined recurrence and survival prediction beyond stage.

CONCLUSION: This proteogenomic framework defines exposure-informed and microbiome-informed gastric cancer subtypes, providing a molecular schema for patient stratification, prevention and actionable therapeutic vulnerabilities.},
}

Humans
*Stomach Neoplasms/microbiology/genetics/etiology/pathology/therapy
*Proteogenomics/methods
Male
Female
Disease Progression
Multiomics
Helicobacter pylori
Helicobacter Infections/complications/microbiology
Middle Aged
Taiwan
Gastrointestinal Microbiome
Aged
Microbiota

@article {pmid41649858,
year = {2026},
author = {Lane, R and Millard, LAC and Salway, R and Stone, CJ and Skinner, AL and Brady, SM and Mariapun, J and Rajakumar, S and Ramadas, A and Rizal, H and Johnson, L and Su, TT and Armstrong, MEG},
title = {The Feasibility of Smartwatch Micro-Ecological Momentary Assessment for Tracking Eating Patterns of Malaysian Children and Adolescents in the South-East Asian Community Observatory Child Health Update 2020: Cross-Sectional Study.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e73435},
pmid = {41649858},
issn = {1438-8871},
mesh = {Humans ; Child ; Adolescent ; Male ; Malaysia ; *Ecological Momentary Assessment ; Female ; Cross-Sectional Studies ; Feasibility Studies ; *Feeding Behavior ; Cell Phone ; Digital Health ; },
abstract = {BACKGROUND: Mobile phone ecological momentary assessment (EMA) methods are a well-established measure of eating and drinking behaviors, but compliance can be poor. Micro-EMA (μEMA), which collects information with a single tap response to brief questions on smartwatches, offers a novel application that may improve response rates. To our knowledge, there is no data evaluating μEMA to measure eating habits in children or in low-to-middle-income countries.

OBJECTIVE: In this study, we investigated the feasibility of micro-EMA to measure eating patterns in Malaysian children and adolescents.

METHODS: We invited 100 children and adolescents aged 7-18 years in Segamat, Malaysia, to participate in 2021-2022. Smartwatches were distributed to 83 children and adolescents who agreed to participate. Participants were asked to wear the smartwatch for 8 days and respond to 12 prompts per day, hourly, from 9AM to 8PM, asking for information on their meals, snacks, and drinks consumed. A questionnaire captured their experiences using the smartwatch and μEMA interface. Response rate (proportion of prompts responded to) assessed participants' adherence. We explored associations between response rate with time of day, across days, age, and sex using multilevel binomial logistic regression modeling.

RESULTS: Eighty-two participants provided usable smartwatch data. The median number (IQR) of meals, drinks, and snacks per day was 2 (2-4), 3 (1-5), and 1 (0-2), respectively, on the first day of the study. The median response rate across the study was 68% (IQR 50-83). The response rate decreased across study days from 74% (68-78) on Day 1 to 40% (30-50) on Day 7 (odds ratio [OR] per study day 0.73, 95% CI 0.64-0.83). Response rate was lowest at the start of the day and highest between the hours of 12 PM and 2 PM. Female participants responded to more prompts than male participants (OR 1.72, 95% CI 1.03-2.86). There was no evidence of differential response by age (OR 0.73, 95% CI 0.41-1.28). Most participants (65%) rated their experience using the smartwatch positively, with 33% saying they were happy to participate in future studies using the smartwatch. For children that did not wear the smartwatch for the full study duration (n=22), discomfort was the most common complaint (41%).

CONCLUSIONS: In this study of the feasibility of μEMA on smartwatches to measure eating in Malaysian children, we found the method was acceptable. However, response rates declined across study days, resulting in substantial missingness. Future studies (eg, through focus groups) should explore approaches to improving response to event prompts, trial alternative devices to increase children's comfort, and evaluate revised protocols for reporting of intake events.},
}

Humans
Child
Adolescent
Male
Malaysia
*Ecological Momentary Assessment
Female
Cross-Sectional Studies
Feasibility Studies
*Feeding Behavior
Cell Phone
Digital Health

@article {pmid41596418,
year = {2026},
author = {Wang, J and Zeng, NK and Zhang, X},
title = {Tuber Inoculation Drives Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Corylus.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
pmid = {41596418},
issn = {1422-0067},
support = {2019RC185 and 320RC597//Natural Science Foundation of HainanProvince/ ; (2024)171//Project of Science and Technology Programs of Guizhou Province/ ; Gui(2024)TG12//Project of Central Government Financial Fund for Forest Reform and Development/ ; },
mesh = {*Rhizosphere ; *Microbiota ; *Corylus/microbiology/metabolism ; Symbiosis ; Multiomics ; Plant Roots/microbiology/metabolism ; Metabolic Reprogramming ; Mycorrhizae/physiology ; *Plant Tubers/microbiology/metabolism ; Metabolomics/methods ; Soil Microbiology ; },
abstract = {To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential "symbiosis-priority" strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as "ecosystem engineers" and providing a methodological framework for green agriculture research.},
}

*Rhizosphere
*Microbiota
*Corylus/microbiology/metabolism
Symbiosis
Multiomics
Plant Roots/microbiology/metabolism
Metabolic Reprogramming
Mycorrhizae/physiology
*Plant Tubers/microbiology/metabolism
Metabolomics/methods
Soil Microbiology

@article {pmid41603972,
year = {2026},
author = {Rossmann, C and Karnowski, V and Metag, J and Raupp, J and Reifegerste, D and Riesmeyer, C and Sawalha, N and Lux, A and Esser, AL and Kammerer, R and Singh, F and Rödel, N and Brill, J and Gerling, E and Wiedicke, A},
title = {The Role of Digital Media in Chronic Disease Self-Management: Protocol for a Multimethod Study of the DISELMA Research Consortium.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e77811},
pmid = {41603972},
issn = {1929-0748},
mesh = {Humans ; *Digital Media ; Chronic Disease/therapy/psychology ; *Self-Management/methods/psychology ; Focus Groups ; Surveys and Questionnaires ; Digital Health ; },
abstract = {BACKGROUND: Chronic diseases, such as type 1 and type 2 diabetes, asthma, and chronic obstructive pulmonary disease , demand long-term treatment and permanent adaptation. One important pillar in coping with these diseases is individuals' self-management, including support from digital media. Research on their effects confirms their potential. However, it is flawed by theoretical underdevelopment and methodological weaknesses, such as a focus on short-term effects, single digital features, and microlevel studies.

OBJECTIVE: The research unit (RU) DISELMA ("Digital Media in Chronic Disease Self-Management") aims to examine the continued use patterns and effects of the digital self-management of chronic diseases, as well as the role of the interpersonal, organizational, and societal levels to gain a comprehensive picture of the individual processes, their contextual embeddedness, and cross-level interactions.

METHODS: To fully capture the manifold multilevel influences, the RU comprises 6 individual projects (IPs), each of which conducts several studies. Two projects at the individual level analyze determinants of use, usage patterns, and effects of digital media, combining systematic reviews, experience sampling method studies, focus groups, panel surveys, and content analysis of apps used. Two projects examine the interpersonal context by analyzing the role of health care providers and the diffusion of digital media in informal networks, conducting a scoping review, online surveys with physicians, semistructured interviews, and participant observations of physician-patient dyads, patient focus groups, and interviews with peers. One project aims to analyze the role of organizations within the mobile health market by conducting a content analysis of organizational messages and a survey. Finally, one project analyzes journalistic and social media to gain insight into the discourses about digital chronic disease self-management on the societal level.

RESULTS: The RU received funding approval from the Deutsche Forschungsgemeinschaft (German Research Foundation; grant 456132969) in July 2023, and the 4-year funding period ranges from December 2023 to November 2027. IP1 is currently conducting its systematic reviews and experience sampling method studies, both to be finalized in 2026. IP2 is conducting its systematic review and meta-analysis alongside panel surveys until June 2026. IP3 has completed its online survey with physicians and is currently conducting observations until August 2026. IP4 is conducting its scoping review and peer interviews through 2026, while IP5 is working on its content analysis and survey, and IP6 on its manual content analysis. First publications of the results are expected in 2026.

CONCLUSIONS: The results will contribute to the existing research through a theoretically and methodologically comprehensive approach that improves our understanding of the processes within and between all levels. These insights will inform providers of digital health solutions and health care practitioners about users' needs, advance evidence-based disease self-management programs, and contribute to better coping with chronic diseases, improved well-being of affected individuals, and reduced health care costs.},
}

Humans
*Digital Media
Chronic Disease/therapy/psychology
*Self-Management/methods/psychology
Focus Groups
Surveys and Questionnaires
Digital Health

@article {pmid41617725,
year = {2026},
author = {Xu, X and Lin, J and Zhu, LT and Long, L and Duan, Y and Hayatov, J and Lin, L and Chen, H and Huang, Q},
title = {Extracellular vesicles as structured vectors of quorum sensing signals influence aquatic microbial communities.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41617725},
issn = {2055-5008},
support = {32161143016//National Natural Science Foundation of China/ ; NO. NBSDC-DB-21//National Basic Science Data Center "Environment Health DataBase"/ ; },
mesh = {*Quorum Sensing ; *Extracellular Vesicles/metabolism ; Acyl-Butyrolactones/metabolism ; *Microbiota ; *Bacteria/classification/metabolism/genetics ; Multiomics ; Signal Transduction ; *Water Microbiology ; Proteomics ; },
abstract = {Quorum sensing (QS) orchestrates collective microbial behaviors and functional acclimatization through chemical communication. However, QS in natural waters is challenged by dilution, alkaline hydrolysis, and enzymatic degradation of freely dissolved autoinducers. Here, we demonstrate that extracellular vesicles (EVs) act as selective, durable, and protective vectors for QS signal molecules under environmental stresses. Specifically, EVs preferentially package hydrophobic acyl‑homoserine lactones, concentrate them locally, and shield them from alkaline hydrolysis, and exhibiting long-distance transport. In addition, EVs possess specific affinity to recipients, thus influencing microbial community. Field investigation via multi-omics showed that EV abundance covaried with salinity, nutrients, chlorophyll a, and biomass, which were validated by culture experiments. Our statistical framework demonstrated that organisms producing moderate EV levels contributed significantly to maintaining community stability and ecosystem functions. Distinctively within this group, QS-active species (including Burkholderiaceae, Pseudomonadaceae, Rhodobacteraceae, Roseobacteraceae, Flavobacteriaceae etc.) emerge as key drivers facilitating these crucial ecological roles. Furthermore, metaproteomics of field EVs reveal QS receptor and synthesis proteins, suggesting coordinated transport of signals and proteins, which indicate new routes for QS crosstalk, particularly for taxa bearing luxR/I solos. Our results show that moderately generated EVs are the potentially important QS signal carriers and ecological regulation hubs in natural waters.},
}

*Quorum Sensing
*Extracellular Vesicles/metabolism
Acyl-Butyrolactones/metabolism
*Microbiota
*Bacteria/classification/metabolism/genetics
Multiomics
Signal Transduction
*Water Microbiology
Proteomics

@article {pmid41634036,
year = {2026},
author = {Huang, L and Pu, YT and Zhao, YH and Sun, XY and Zhu, Y and Lu, YP and Leng, HX and Feng, J and Jin, LR and Sun, KP},
title = {Diet and environmental factors jointly drive the gut microbiome, resistome, and virulome of urban bats.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41634036},
issn = {2055-5008},
support = {32430066//National Natural Science Foundation of China/ ; 32171525//National Natural Science Foundation of China,China/ ; },
mesh = {Animals ; *Chiroptera/microbiology ; *Diet ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Environment ; Gene Transfer, Horizontal ; Female ; Genes, Bacterial ; Multiomics ; Drug Resistance, Bacterial ; },
abstract = {The coexistence and horizontal transfer of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) carried by urban wildlife represent an emerging form of biological pollution, constituting a significant threat to public health. We employed meta-omic approaches to evaluate the effects of host traits (sex, age, etc.), environmental factors (including geographical location and time), and diet (including food composition and antibiotic residues) on the bacterial, ARG, and VFG profiles of Vespertilio sinensis, an urban-dwelling bat. Our results demonstrate that the feces of V. sinensis harbor diverse ARGs and VFGs, but their genomic evidence for horizontal mobility in bacterial communities is limited. Notably, environmental changes over time and across geographical locations are associated with the ARG and VFG profiles, potentially due to the influence of pollutants in specific habitats. Dietary factors are associated with their dynamics through the microbiome, with antibiotic residues exerting selective pressure on ARG profiles. No significant impacts of sex, age, body size, and reproductive status on the gut microbiota, resistome, or virulome were observed. This study provides valuable insights into the ecological drivers of the gut microbiome, resistome, and virulome in bats, thereby contributing to our understanding of the public health risks associated with urban wildlife.},
}

Animals
*Chiroptera/microbiology
*Diet
*Gastrointestinal Microbiome
Feces/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Environment
Gene Transfer, Horizontal
Female
Genes, Bacterial
Multiomics
Drug Resistance, Bacterial

@article {pmid41637624,
year = {2026},
author = {Kadirvelu, B and Bellido Bel, T and Freccero, A and Di Simplico, M and Nicholls, D and Faisal, AA},
title = {Digital Phenotyping for Adolescent Mental Health: Feasibility Study Using Machine Learning to Predict Mental Health Risk From Active and Passive Smartphone Data.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e72501},
pmid = {41637624},
issn = {1438-8871},
mesh = {Humans ; Adolescent ; Feasibility Studies ; *Smartphone ; Female ; *Machine Learning ; Male ; *Mental Health ; *Mental Disorders/diagnosis ; Digital Health ; *Phenotype ; Predictive Learning Models ; *Mobile Applications ; },
abstract = {BACKGROUND: Adolescents are particularly vulnerable to mental disorders, with over 75% of lifetime cases emerging before the age of 25 years. Yet most young people with significant symptoms do not seek support. Digital phenotyping, leveraging active (self-reported) and passive (sensor-based) data from smartphones, offers a scalable, low-burden approach for early risk detection. Despite this potential, its application in school-going adolescents from general (nonclinical) populations remains limited, leaving a critical gap in community-based prevention efforts.

OBJECTIVE: This study evaluated the feasibility of using a smartphone app to predict mental health risks in nonclinical adolescents by integrating active and passive data streams within a machine learning (ML) framework. We examined the utility of this approach for identifying risks related to internalizing and externalizing difficulties, eating disorders, insomnia, and suicidal ideation.

METHODS: Participants (n=103; mean age 16.1 years, SD 1.0) from 3 UK secondary schools used the Mindcraft app (Brain and Behaviour Lab) for 14 days, providing daily self-reports (eg, mood, sleep, and loneliness) and continuous passive sensor data (eg, location, step count, and app usage). We developed a deep learning model incorporating contrastive pretraining with triplet margin loss to stabilize user-specific behavioral patterns, followed by supervised fine-tuning for binary classification of 4 mental health outcomes, namely, the Strengths and Difficulties Questionnaire (SDQ)-high risk, insomnia, suicidal ideation, and eating disorder. Performance was assessed using leave-one-subject-out cross-validation (LOSO-CV), with balanced accuracy as the primary metric. Comparative analyses were conducted using CatBoost (Yandex) and multilayer perceptron (MLP) models without pretraining. Feature importance was assessed using Shapley Additive Explanations (SHAP) values, and associations between key digital features and clinical scales were analyzed.

RESULTS: Integration of active and passive data outperformed single-modality models, achieving mean balanced accuracies of 0.71 (0.03) for SDQ-high risk, 0.67 (0.04) for insomnia, 0.77 (0.03) for suicidal ideation, and 0.70 (0.03) for eating disorder. The contrastive learning approach improved representation stability and predictive robustness. SHAP analysis highlighted clinically relevant features, such as negative thinking and location entropy, underscoring the complementary value of combining subjective and objective data. Correlation analyses confirmed meaningful associations between key digital features and mental health outcomes. Performance in an independent external validation cohort (n=45) achieved balanced accuracies of 0.63-0.72 across outcomes, suggesting generalizability to new settings.

CONCLUSIONS: This study demonstrates the feasibility and utility of smartphone-based digital phenotyping for predicting mental health risks in nonclinical, school-going adolescents. By integrating active and passive data with advanced machine modeling techniques, this approach shows promise for early detection and scalable intervention strategies in community settings.},
}

Humans
Adolescent
Feasibility Studies
*Smartphone
Female
*Machine Learning
Male
*Mental Health
*Mental Disorders/diagnosis
Digital Health
*Phenotype
Predictive Learning Models
*Mobile Applications

@article {pmid41882511,
year = {2026},
author = {Yu, X and Hunt, BJ and Wang, S and Troczka, BJ and Shangguan, C and Zhu, W and Kuang, Y and Bass, C},
title = {A chromosome-level genome assembly and multi-omics analysis reveal fenpropathrin resistance mechanisms in the turnip aphid, Lipaphis erysimi.},
journal = {Pest management science},
volume = {82},
number = {7},
pages = {6564-6574},
doi = {10.1002/ps.70744},
pmid = {41882511},
issn = {1526-4998},
support = {20212ACB215001//Natural Science Foundation for Distinguished Young Scholars of Jiangxi Province/ ; 32160634//National Natural Science Foundation of China/ ; JXSQ2019101058//Double Thousand Plan of Jiangxi Province/ ; },
mesh = {Animals ; *Pyrethrins/pharmacology ; *Insecticide Resistance/genetics ; *Insecticides/pharmacology ; *Aphids/genetics/drug effects/metabolism ; Multiomics ; *Genome, Insect ; Insect Proteins/genetics/metabolism ; Cytochrome P-450 Enzyme System/genetics/metabolism ; },
abstract = {BACKGROUND: The turnip aphid Lipaphis erysimi is a cruciferous crop pest with the potential to reduce yields by up to 90%. Treatment of L. erysimi infestations using insecticides has resulted in numerous cases of resistance in field populations yet genomic resources are lacking for this species, limiting the ability of researchers to investigate the molecular basis of resistance and develop management strategies.

RESULTS: Here we describe the creation of a chromosome scale genome assembly for L. erysimi and the characterization of fenpropathrin resistance in this species using multi-omics analysis. A 409 Mb genome was assembled for L. erysimi, with an N50 of 95.2 Mb and 90% of assembled content contained within four chromosome-scale scaffolds. We identified a key M903L mutation in a voltage-gated sodium channel gene that is targeted by fenpropathrin and the accompanying up-regulation of cytochrome P450 and UDP-glycosyltransferase detoxification genes. Using transgenic flies, we further confirmed the ability of L. erysimi CYP4CJ1 to confer fenpropathrin resistance in vivo.

CONCLUSION: Mechanisms for fenpropathrin resistance in L. erysimi were identified through multi-omics analysis and functional characterization. Collectively, this study provides valuable genomic resources for molecular investigations of L. erysimi and establishes a foundation for developing novel strategies to enhance pyrethroid efficacy in this species. © 2026 Society of Chemical Industry.},
}

Animals
*Pyrethrins/pharmacology
*Insecticide Resistance/genetics
*Insecticides/pharmacology
*Aphids/genetics/drug effects/metabolism
Multiomics
*Genome, Insect
Insect Proteins/genetics/metabolism
Cytochrome P-450 Enzyme System/genetics/metabolism

@article {pmid41926903,
year = {2026},
author = {Lin, C and Gao, M and Chen, H and Guo, J and Zhang, B and Lin, J and Zhao, C},
title = {Multi-omics analysis reveals polyethylene microplastics-induced gill damage, metabolic disruption and immune dysregulation in Lateolabrax maculatus.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101815},
doi = {10.1016/j.cbd.2026.101815},
pmid = {41926903},
issn = {1878-0407},
mesh = {Animals ; *Microplastics/toxicity ; *Gills/drug effects/metabolism/pathology ; *Polyethylene/toxicity ; *Water Pollutants, Chemical/toxicity ; Multiomics ; Oxidative Stress/drug effects ; Transcriptome/drug effects ; },
abstract = {Microplastics (MPs) are emerging environmental pollutants that can induce physiological toxicity in aquatic organisms. This study investigated the toxicological effects of dietary exposure to polyethylene microplastics (PE-MPs) on gill tissues of Lateolabrax maculatus, using diets containing 0%, 4%, and 8% (w/w) PE-MPs. Histological, transcriptomic, and biochemical analyses were performed to assess structural damage, alterations in gene expression, and changes in antioxidant and immune parameters. Histological examination revealed structural abnormalities, including bending of gill lamellae and epithelial cell swelling, suggesting that gills may be sensitive to MP exposure. Transcriptomic analysis indicated that differentially expressed genes were enriched in pathways related to energy metabolism and immune response, including glycolysis/gluconeogenesis, oxidative phosphorylation, and phagosome. Key glycolytic enzymes (HK, PFK, PK) were upregulated, and the PPAR signaling pathway was activated, suggesting enhanced energy demands under stress conditions. Biochemical assays showed dynamic changes in antioxidant enzyme activities, with increased malondialdehyde (MDA) content in the high-concentration group, indicating oxidative stress. Immune-related genes associated with the NF-κB pathway (e.g., IL-1β, TNF-α) were upregulated, while TGF-β expression showed no significant changes. Following a 14-day depuration period without MP exposure, most antioxidant and immune parameters showed a trend toward recovery, indicating that the observed effects may be partially reversible. These findings suggest that MP exposure can contribute to gill structural impairment and perturbations in energy metabolism, redox homeostasis, and immune regulation in Lateolabrax maculatus, providing insights into the potential ecological risks of microplastic pollution in aquaculture environments.},
}

Animals
*Microplastics/toxicity
*Gills/drug effects/metabolism/pathology
*Polyethylene/toxicity
*Water Pollutants, Chemical/toxicity
Multiomics
Oxidative Stress/drug effects
Transcriptome/drug effects

@article {pmid42118777,
year = {2026},
author = {Wang, Z and Fu, Y and Goyal, A and Maslov, S},
title = {Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014277},
pmid = {42118777},
issn = {1553-7358},
mesh = {*Models, Biological ; Proteome/metabolism ; Biomass ; Ecosystem ; Computational Biology ; *Microbial Interactions/physiology ; },
abstract = {Microbes growing in fluctuating environments employ two key metabolic strategies: sequential (diauxic) utilization and co-utilization of nutrients. Most work has focused on understanding and comparing these strategies physiologically for the growth of single species, rather than ecologically for the assembly of complex natural communities. This is in part because of the lack of a framework for directly comparing the fitness of these strategies in an ecological context. Here, we present a new consumer-resource framework that incorporates dynamic proteome reallocation, and use it to compare the fitness of metabolic strategies during community assembly. We introduce two notions of fitness of a strategy in fluctuating environments: the time-averaged growth rate and the biomass-weighted prevalence of microbes using a given strategy. We find that sequential utilizers, although disadvantaged in pairwise competitions, gain a significant edge during community assembly - an advantage that becomes more pronounced with increasing community diversity and the size of the species pool from which they are assembled. Low diversity communities resemble pairwise competitions and are dominated by co-utilizers, whereas high diversity, mature communities (i.e., those assembled from a larger species pool) are dominated by the sequential utilizers. This shift is driven by two factors: the difference in lag times and the increased structural stability conferred by sequential strategies. Overall, our work provides several testable predictions about the co-occurrence patterns of microbes using different metabolic strategies.},
}

*Models, Biological
Proteome/metabolism
Biomass
Ecosystem
Computational Biology
*Microbial Interactions/physiology

@article {pmid42250063,
year = {2026},
author = {Boxrud, B and Siegle, E and Shankman, SA and Reddy, M and Griffith, JW and Ashaie, SA},
title = {Measuring affective symptoms of depression in aphasia: development of an accessible ecological momentary assessment tool.},
journal = {Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation},
volume = {35},
number = {7},
pages = {},
pmid = {42250063},
issn = {1573-2649},
support = {K23DC020757/DC/NIDCD NIH HHS/United States ; },
abstract = {PURPOSE: Post-stroke depression is highly prevalent in aphasia, yet existing depression measures rely heavily on language and lack sufficient validity for this population. The aim of this study was to develop an aphasia-accessible Ecological Momentary Assessment (EMA) of depression based on the input of people with aphasia, their care partners, and speech-language pathologists (SLPs).

METHODS: Nine focus groups were conducted with people with aphasia (n = 15), care partners (n = 13), and SLPs (n = 13) to identify relevant depression symptoms. Items were selected based on factors such as endorsement ratings and qualitative feedback across stakeholder groups. Participants with aphasia also took part in individual cognitive interviews to ensure comprehensibility and accessibility of the final items, corresponding pictures, and pictorial rating scale.

RESULTS: The final set of items to be included in the EMA consisted of three positive affect items (determined, proud, interested) and three negative affect items (sad, like a failure, angry). Cognitive interviews confirmed comprehensibility and accessibility of the items, though the picture for interested required revision. Additionally, participants found 3-4 daily assessments feasible.

CONCLUSION: Stakeholder engagement revealed that positive affect dysregulation (e.g., reduced interest in previously rewarding activities) may be particularly salient for depression in aphasia in addition to negative affect dysregulation (e.g., increased feelings of failure and anger). The resulting six-item EMA uses multimodal supports (e.g., text, pictures, pictorial rating scale, audio recordings) to capture both valence systems.},
}

@article {pmid41586531,
year = {2026},
author = {Han, J-R and Li, S and Lian, W-H and Xu, L and Duan, L and Li, J-L and Shi, G-Y and Wei, Q-C and Ali, M and Li, W-J and Dong, L},
title = {Fermentation conditions outweigh phylogeny in shaping the metabolome of novel Micromonospora strains: an integrated genomics-metabolomics analysis.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {2},
pages = {e0223525},
pmid = {41586531},
issn = {1098-5336},
support = {2024CXTD04//Guangdong Province Modern Agricultural Industry Technology System Innovation Team Construction Project Focused on Agricultural Products (Agricultural Microorganisms)/ ; 2025A04J3495//Guangzhou Basic and Applied Basic Research Foundation, China/ ; 32270076//National Natural Science Foundation of China/ ; },
mesh = {*Micromonospora/genetics/metabolism/classification/isolation & purification ; Phylogeny ; *Metabolome ; Genomics ; Metabolomics ; Fermentation ; Multiomics ; Genome, Bacterial ; Geologic Sediments/microbiology ; Soil Microbiology ; Terpenes/metabolism ; Polyketides/metabolism ; },
abstract = {The genus Micromonospora, a key member of the actinomycetes, has demonstrated considerable potential for natural product biosynthesis. In this study, we isolated 15 Micromonospora spp. strains from desert soil and marine sediment samples, eight of which represent four novel species. To explore the biosynthetic capacity of this genus, we performed an integrated analysis of Micromonospora reference genomes. Pan-genomic analysis further unveiled the core biosynthetic characteristics of the genus responsible for producing terpenes and polyketides. Further multi-omics investigation, combining genomic and metabolomic data, uncovered a positive correlation between phylogenetic relationships and biosynthetic potential, alongside a decoupling of metabolic profiles. Notably, metabolomic findings emphasized the dominant influence of culture conditions on the expression of biosynthetic capabilities. Overall, our study provides a comprehensive elucidation of the biosynthetic potential of the genus Micromonospora and highlights the value of investigating novel strains and applying diverse cultivation strategies in natural product discovery.IMPORTANCEOur study provides a comprehensive genomic and metabolomic elucidation of the significant biosynthetic potential within the genus Micromonospora. It reveals a core biosynthetic capacity for terpenes and polyketides that is phylogenetically linked, whereas the resulting natural product repertoire is subject to strong modulation by cultivation conditions. These findings underscore the critical importance of exploring novel species and employing diverse cultivation strategies to unlock the full potential of microbial resources for natural product discovery.},
}

*Micromonospora/genetics/metabolism/classification/isolation & purification
Phylogeny
*Metabolome
Genomics
Metabolomics
Fermentation
Multiomics
Genome, Bacterial
Geologic Sediments/microbiology
Soil Microbiology
Terpenes/metabolism
Polyketides/metabolism

@article {pmid42146349,
year = {2026},
author = {Wagner, J and Keskus, AG and Oshima, KK and Ranallo-Benavidez, TR and McDaniel, J and Sikic, M and Lin, D and Paulin, LF and English, AC and Sedlazeck, FJ and Munding, EM and Sanborn, JZ and Carroll, A and Chang, PC and Cook, DE and Shafin, K and de Ligt, J and Hassaine, R and Cameron, D and Catreux, S and Lee, Y and Murray, L and Truong, S and Brueffer, C and Zimin, AV and Cross, E and McGowan, M and Vernich, M and Liss, AS and Kocher, JP and Stephens, Z and Ahmad, T and Bryant, A and Dwarshuis, N and He, HJ and He, Z and Olson, ND and Thibaud-Nissen, F and Antipov, D and Koren, S and Phillippy, A and Musunuri, RL and Narzisi, G and Jain, M and Wenger, AM and Eacker, S and Sahraeian, SME and Boutros, PC and Patel, Y and Yamaguchi, TN and McConnell, J and Borchers, M and Gerton, JL and Kostos, P and Guarracino, A and Jehangir, M and Benjamin, H and Mootor, MFE and Xu, Y and Asri, M and Miga, KH and Park, J and Paten, B and Luo, R and Zheng, Z and Choi, JY and Nguyen, L and Vats, P and Robinson, DR and Vo, JN and Gao, S and Murtaza, G and Mason, CE and Cheng, H and Barthel, FP and Xiao, C and Logsdon, GA and Kolmogorov, M and Zook, JM},
title = {A complete human pancreatic cancer genome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42146349},
issn = {2692-8205},
support = {U54 CA302435/CA/NCI NIH HHS/United States ; },
abstract = {Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine.[1] However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions.[1-3] It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres.[4] To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.},
}

@article {pmid42233158,
year = {2026},
author = {Zhong, S and Xing, L and Li, H and Wang, L and Zhu, X and Wang, C},
title = {Genomic characterization and niche adaptive analysis of Pseudomonas promysalinigenes W2469: the first clinical isolate from a human bile specimen.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1825480},
pmid = {42233158},
issn = {2235-2988},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Pseudomonas/genetics/isolation & purification/classification/drug effects/physiology ; *Genome, Bacterial ; *Bile/microbiology ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; *Pseudomonas Infections/microbiology ; Phylogeny ; Genomics ; Microbial Sensitivity Tests ; DNA, Bacterial/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Computational Biology ; Lipopeptides ; },
abstract = {BACKGROUND: Pseudomonas promysalinigenes is a newly described bacterial species renowned for producing promysalin, a species-selective lipopeptide antibiotic. All previously reported strains of this species are derived from environmental niches such as plant rhizospheres, and no clinical infection cases associated with this bacterium have been documented to date. Thus, the clinical microbiology relevance, genomic features, and adaptive potential of P. promysalinigenes remain largely unexplored, and current reference databases have limited coverage of this rare species.

METHODS: A bacterial strain designated W2469 was isolated from the bile specimen of a patient with acute suppurative cholecystitis and cholecystolithiasis. Conventional phenotypic and molecular identification [matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), VITEK 2 biochemical assay, 16S ribosomal RNA (rRNA), and whole-genome sequencing (WGS)] was performed. Bioinformatics analyses, including average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), core genome single-nucleotide polymorphism (cgSNP), pan-genome analysis, and functional annotation against COG, KEGG, CAZy, VFDB, and CARD databases, were conducted to characterize the strain.

RESULTS: Conventional methods yielded consistent misidentification of the strain, while WGS definitively assigned it to P. promysalinigenes (ANI = 98.8%, dDDH = 91.1% against the type strain RW10S1). The strain exhibited a narrow-spectrum resistance phenotype, with resistance to aztreonam and ticarcillin/clavulanic acid, intermediate susceptibility to meropenem, and susceptibility to most clinically used antibiotics. Genomic annotation identified 25 antimicrobial resistance genes and 139 niche adaptation-related factors, most of which are low-identity homologs (<80%) of canonical reference sequences. Pan-genome analysis identified 571 clinical-specific genes associated with host adaptation, with complete loss of the environmental promysalin biosynthetic gene cluster.

CONCLUSION: This study provides the first documentation of P. promysalinigenes as a clinical isolate from human bile, expanding the known ecological niche of this species to the clinical setting. Conventional methods are prone to misidentifying this rare species, and WGS is critical for accurate taxonomic identification. Importantly, the strain exhibits clear adaptive phenotypes despite low sequence identity to known functional elements, highlighting profound knowledge gaps in the genomic diversity and uncharacterized adaptive mechanisms of this rare Pseudomonas species. This work provides a foundational genomic resource for future investigations into this emerging opportunistic pathogen.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Pseudomonas/genetics/isolation & purification/classification/drug effects/physiology
*Genome, Bacterial
*Bile/microbiology
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
*Pseudomonas Infections/microbiology
Phylogeny
Genomics
Microbial Sensitivity Tests
DNA, Bacterial/genetics
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Computational Biology
Lipopeptides

@article {pmid42246990,
year = {2026},
author = {Rajan, DK and Rajan, DK and Li, H and Yang, W and Wu, J and Zhang, S and Jiang, H and Zhang, S},
title = {One-pot fabrication and characterization of ZnO nanoflowers using Zanthoxylum simulans and evaluating their biomedical claims.},
journal = {Mikrochimica acta},
volume = {193},
number = {7},
pages = {},
pmid = {42246990},
issn = {1436-5073},
support = {(2025M782323)//China Postdoctoral Science Foundation/ ; (2025JJ80166)//Natural Science Foundation of Hunan Province of China/ ; },
abstract = {Novel zinc oxide nanoflowers (ZnO NFs) were synthesized using the aqueous extract of Zanthoxylum simulans. The green synthesized Zs-ZnO NFs were characterized using FT-IR, XPS, XRD, HR-TEM, EDAX, DLS, and zeta potential (ZP) analysis to confirm the physicochemical properties. HR-TEM analysis exposed the flower-like morphology with uniform size. The XPS analysis exposed the elements present in the Zs-ZnO NFs. Further, the Zn element exhibited two binding energy peaks at 1021.41 and 1044.50 eV. The purity of Zs-ZnO NFs was confirmed using EDAX analysis. The Zs-ZnO NFs displayed bactericidal properties against the tested pathogens. To evaluate the effectiveness of Zs-ZnO NFs against dental pathogens via MIC, antibacterial, biofilm ring formation, and TTC assays were performed. A concentration-dependent biofilm inhibition was also observed against Staphylococcus aureus and Streptococcus mutans upon treatment with Zs-ZnO NFs, and it was confirmed using a 2.5D fluorescence imaging technique. A 100 µg/mL of Zs-ZnO NFs treatment displayed bacterial cell death, which was confirmed via dual staining. Furthermore, Zs-ZnO NFs induced protein leakage was observed upon treatment with 100 µg/mL concentration against the pathogens. Cytotoxicity of Zs-ZnO NFs was confirmed using HUVECs cells. Overall, the synthesized Zs-ZnO NFs exhibits efficient bactericidal, antibiofilm and biocompatible properties.},
}

@article {pmid42247603,
year = {2026},
author = {Haberkorn, C and Gettle, N and Elsen, J and Medina Chavez, NO and Sivigny, J and Baselga-Cervera, B and Greig, D and Travisano, M and Saxer, G and Stelkens, R},
title = {Adaptive Benefits of Hybridization in Saccharomyces Yeast are Constrained by Genomic Background and Depend on Temperature.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpag108},
pmid = {42247603},
issn = {1558-5646},
abstract = {Climate change urges us to better understand and predict evolutionary responses to temperature shifts. Hybridization, by increasing genetic variation, can widen the range of adaptive responses and genetic mechanisms available to survive temperature changes. However, genomic data on the long-term effect of hybridization on adaptation is rare, and the molecular mechanisms usually remain unclear. Here, we hybridized two divergent species of Saccharomyces yeast. We experimentally evolved both hybrid and parental populations for 200 generations under hot (30°C), cold (16°C), and fluctuating (16-30°C) temperature regimes. Most hybrids showed intermediate growth but the large variance produced by hybridization also led to thermally transgressive hybrids with high performance. Across regimes, response to selection scaled negatively with ancestral growth, consistent with diminishing-returns epistasis. Analysis of genes with identified mutations revealed enrichment in multiple shared annotation terms between populations evolved in cold and fluctuating environments, such as cell wall functions. Evolved hybrid populations, across all evolution regimes, accumulated significantly more de novo copy number variants (CNVs) than both parental species, indicating extensive genome restructuring in hybrids. This increased structural variation may provide a substrate for selection and adaptive divergence among hybrid lineages. Our results suggest that hybridization can lead to increased growth, especially in hot and thermally unstable environments, by capitalizing on the genomic content inherited from one or the other parental species.},
}

@article {pmid41538705,
year = {2026},
author = {Li, R and Xu, X and Li, Q and Liu, H and Zhou, TT and Amhare, AF and Liu, P and Tang, J and Wang, W and Zheng, F and Han, J},
title = {Internet Health Care Service Use Behavioral Pattern Among Older Adults and the Role of the Technology Acceptance and Social Ecological Theory Model: Cross-Sectional Survey.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e78037},
pmid = {41538705},
issn = {1438-8871},
mesh = {Humans ; Cross-Sectional Studies ; Male ; Aged ; Middle Aged ; Digital Health ; *Internet ; Female ; China ; Surveys and Questionnaires ; *Telemedicine/statistics & numerical data ; *Patient Acceptance of Health Care ; Models, Theoretical ; Digital Media ; },
abstract = {BACKGROUND: The rapid growth of internet health care (IH) offers older adults convenient medical services like remote consultations and health monitoring. However, its adoption among this group remains low, highlighting a significant digital divide. Understanding the behavioral patterns and determinants of IH use in the older population is crucial for optimizing digital health design and improving service accessibility.

OBJECTIVE: This study aimed to analyze the multidimensional influencing factors of Chinese older adults' use of IH services based on the integrated framework of the technology acceptance model and social ecological model, and explore their behavioral patterns and key driving factors.

METHODS: A cross-sectional study design was adopted to conduct a multistage stratified cluster random sampling survey in 3 cities in Shandong Province from May 2024 to July 2024, with a total of 1828 older adults aged 60 to 75 years included. The study uses latent category analysis to classify the use of IH service behaviors and employs multiple logistic regression, decision tree models, and structural equation modeling to analyze influencing factors and mediating pathways.

RESULTS: Five distinct user groups were identified: nonusers (n=911), registration-dominant users (n=286), low-activity users (n=320), moderate comprehensive users (n=288), and full-service users (n=23). Multinomial logistic regression with nonusers as the reference group identified key determinants: individuals with below primary education had 96% lower odds of membership (odds ratios [OR] 0.039, 95% CI 0.012-0.084) compared to the reference group with junior college education or above in moderate comprehensive users, while male participants had higher odds of being full-service (OR 1.980, 95% CI 1.126-3.514) or moderate comprehensive (OR 1.310, 95% CI 1.012-1.705) users. Older age was consistently associated with lower adoption across all classes. Full-service users exhibited exceptionally high social support (OR 4.502, 95% CI 3.601-5.627), while moderate comprehensive users showed the highest technology acceptance (OR 2.803, 95% CI 2.355-3.342). The decision tree model (area under the curve of 0.94) found the optimal path: sufficient social support (≥2), good health status (>5), and high technical acceptance (≥30) yield the highest use probability (92%→96%). Mediation analysis indicated that social support influences usage willingness through both direct and indirect pathways. The direct effect was 0.712 (95% CI 0.552-0.972; P<.001). Among indirect pathways, technology availability and practicality accounted for the largest proportion of mediation (19.7%, 95% CI 16.8%-22.6%), followed by technology acceptance (13.7%, 95% CI 11.1%-16.3%) and social influence (8.9%, 95% CI 6.9%-10.9%).

CONCLUSIONS: Optimizing age-friendly design, strengthening social support networks, and improving technological usability are keys to increasing the adoption of IH services among the older population. Future policies should develop targeted intervention strategies for different user groups to narrow the digital health divide.},
}

Humans
Cross-Sectional Studies
Male
Aged
Middle Aged
Digital Health
*Internet
Female
China
Surveys and Questionnaires
*Telemedicine/statistics & numerical data
*Patient Acceptance of Health Care
Models, Theoretical
Digital Media

@article {pmid41649265,
year = {2026},
author = {Gu, C and Han, M and Chen, X and Liu, Y and Jian, G and Qin, Q and Yin, H and Zhou, L and Cai, D and Zhang, L and Wang, D and Li, P},
title = {Gut microbiota and metabolomic changes across preterm stages: potential associations with bronchopulmonary dysplasia.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0274025},
pmid = {41649265},
issn = {2165-0497},
support = {823RC606//Hainan Provincial Natural Science Foundation of China/ ; },
mesh = {Humans ; *Bronchopulmonary Dysplasia/microbiology/metabolism ; *Infant, Premature/metabolism ; Infant, Newborn ; *Metabolome ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Female ; Male ; Streptococcus/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metabolomics ; Biomarkers ; Oxidative Stress ; },
abstract = {UNLABELLED: The coordinated post-natal development of the gut microbiome and metabolome is essential for preterm infant health, yet its disruption is increasingly linked to adverse outcomes such as bronchopulmonary dysplasia (BPD). In this study, we performed an integrated multiomics analysis of fecal samples collected from preterm infants to characterize temporal changes in gut microbial and metabolic profiles and explore their potential associations with BPD development. This study observed a distinct trajectory of the phylum Bacteroidota as a hallmark of normal gut maturation, with its abundance progressively declining across non-BPD infants. In contrast, infants who later developed BPD exhibited early depletion followed by irregular enrichment of Bacteroidota. Correlation analysis revealed that Streptococcus abundance was positively associated with elevated cysteic acid, a metabolite linked to oxidative stress. Together, these findings suggest that altered Bacteroidota succession and Streptococcus-associated oxidative imbalance may reflect early microbial-metabolic perturbations in infants at risk of BPD. This work provides preliminary, hypothesis-generating insights into gut-associated signatures potentially relevant to BPD pathogenesis.

IMPORTANCE: Bronchopulmonary dysplasia (BPD) remains a leading cause of morbidity in preterm infants, yet early biomarkers and targeted preventive strategies are limited. By integrating microbiome and metabolome data from a pilot cohort, this study identified patterns of disrupted Bacteroidota succession and Streptococcus-associated oxidative stress that are associated with BPD risk. These findings highlight the gut as a potential extrapulmonary contributor to disease susceptibility and support early risk assessment and guide future microbiome-targeted interventions in preterm infants.},
}

Humans
*Bronchopulmonary Dysplasia/microbiology/metabolism
*Infant, Premature/metabolism
Infant, Newborn
*Metabolome
Feces/microbiology
*Gastrointestinal Microbiome/physiology
Multiomics
Female
Male
Streptococcus/isolation & purification/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
Metabolomics
Biomarkers
Oxidative Stress

@article {pmid42105545,
year = {2026},
author = {Shan, X and Wang, H and Liu, X and Li, P and Zhang, F and Wang, R and Xue, M and Li, F},
title = {Remodeling distinct rhizosphere interactions of plant-microbiome by legacy and alternative PFASs: A multi-omics insight and biphasic role of iron plaque.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142313},
doi = {10.1016/j.jhazmat.2026.142313},
pmid = {42105545},
issn = {1873-3336},
mesh = {*Rhizosphere ; Plant Roots/microbiology/metabolism ; *Microbiota/drug effects ; *Iron ; Multiomics ; Soil Microbiology ; *Soil Pollutants/toxicity/metabolism ; Photosynthesis/drug effects ; Molecular Docking Simulation ; Oxidative Stress ; },
abstract = {Rhizosphere microhabitat as a dominant sink for per(poly)fluoroalkyl substances (PFASs) and hotspot for redox reactions and root iron plaque (IP) forming is largely affected by the interactions between plants and bacteria. However, whether PFOA and its substitute (HFPO-DA) modulated distinct rhizosphere symbiotic patterns and what roles IP played remain unclear. This study integrated plant physiology, metabolism and rhizosphere microbiome to systematically elucidate their differences in remodulating plant-microbiome interactions and IP roles. Results showed that PFOA preferred to accumulate in roots and induced serious oxidative stress, while HFPO-DA was more easily transported to shoots directly affecting photosynthesis. Molecular docking suggested higher proteinic affinity of HFPO-DA, inhibiting superoxide dismutase activity. PFOA and HFPO-DA increased organic acids and sugars in root exudates recruiting differential beneficial bacteria. However, HFPO-DA downregulated the glycerophospholipid metabolism, shaped a more vulnerable and simpler bacterial network. Remarkably, PFASs concentration determined the double-edged roles of IP. At environmental levels, IP promoted glycerophospholipids and small peptides release facilitating azotobacter recruitment and photosynthesis. But under high-dose stress, it induced accelerated pollutant migration especially HFPO-DA, thereby exacerbating phytotoxicity. Partial least squares path modeling revealed that PFOA indirectly influenced plant phenotypes via shaping bacterial community, while HFPO-DA not only modified that but also altered root exudates. This work unveils distinct rhizosphere symbiotic patterns and IP biphasic role remodulated by legacy and alternative PFASs, and provides a reference for their risk assessment and control through nature-based solutions.},
}

*Rhizosphere
Plant Roots/microbiology/metabolism
*Microbiota/drug effects
*Iron
Multiomics
Soil Microbiology
*Soil Pollutants/toxicity/metabolism
Photosynthesis/drug effects
Molecular Docking Simulation
Oxidative Stress

@article {pmid42150507,
year = {2026},
author = {Xu, L and Cheng, C and Xie, S and Pu, E and Zeng, Y and Pu, R and Xie, H and Liu, Y and He, Y and Chen, X and Zhang, Z and Liu, Q},
title = {Advancing safe and value-added Hydrilla verticillata silage: multi-omics deciphering of Lactiplantibacillus plantarum mediated pesticide detoxification and antibiotic resistance genes attenuation based on AI-autonomous learning.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142265},
doi = {10.1016/j.jhazmat.2026.142265},
pmid = {42150507},
issn = {1873-3336},
mesh = {*Lactiplantibacillus plantarum/metabolism/genetics ; *Drug Resistance, Microbial/genetics ; *Hydrocharitaceae/metabolism ; *Silage/microbiology ; Multiomics ; Genes, Bacterial ; Pyrethrins/metabolism ; *Pesticide Residues/metabolism ; *Pesticides/metabolism ; Animals ; },
abstract = {Water-purifying Hydrilla verticillata (SXY) in crab ponds paradoxically poses pollution risks. It accumulates pesticide residues (PRs) and antibiotic resistance genes (ARGs), which leach back into water after fished out and left on pond ridges to deteriorate, triggering cyclic pollution. Objectives of this study were to address this pollution: PRs and ARGs in SXY were first characterized. Correspondingly, two anti-pesticide Lactiplantibacillus plantarum strains (L1 and L3) were screened. Traditional mixture of SXY and wheat bran (HXY) was inoculated without (the control, WCON) or with L1 (WL1), L3 (WL3), and L. pentosus h (WLh) for ensiling 60 days to pesticide detoxification and ARGs attenuation. SXY ensiled alone as the negative control (CON). Results showed that 35 kinds of PRs and 11 types of ARGs were identified. SXY ensiling alone increased abundances of coumafuryl, mepanipyrim, and dinoterb, and ARGs of multidrug, fluoroquinolone, and beta-lactam, but they were lowered in the WCON and inoculation groups. Furthermore, WL1 enhanced averaged degradation rates of organochlorine, fenvalerate, and deltamethrin, reduced abundances of hazardous etoxazole and benomyl, and improved fermentation quality and levels of value-added antioxidants and peptides. WL3 increased bioavailable phosphorus content compared with WCON. L. plantarum acted as leader and keystone species, interacting with 2 outstanding contributing and 4 keystone species through 3 critical KEGG pathways and 3 metabolites to construct a pesticide-degradation causal network, according to AI autonomously learned from authors' inspiration. This study offered an effective approach to turn SXY into safe and value-added feed for eliminating cyclic pollution in crab farming.},
}

*Lactiplantibacillus plantarum/metabolism/genetics
*Drug Resistance, Microbial/genetics
*Hydrocharitaceae/metabolism
*Silage/microbiology
Multiomics
Genes, Bacterial
Pyrethrins/metabolism
*Pesticide Residues/metabolism
*Pesticides/metabolism
Animals

@article {pmid42228842,
year = {2026},
author = {Astill Wright, L and Rawsthorne, M and Nixon, N and Guo, B and Morriss, R},
title = {Recommendations for Research and Clinical Implementation of Ambulatory Assessment, Mood Monitoring, Digital Phenotyping, and Remote Measurement Technology in Mood Disorders: Synthesis of Systematic Review Findings.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e79501},
pmid = {42228842},
issn = {2368-7959},
abstract = {BACKGROUND: Ambulatory assessment and active and passive monitoring all offer a real-time, flexible approach to assessing mood and behavior in mood disorders. Despite their potential, concerns remain regarding the performance, usability, adherence, and potential safety of these tools.

OBJECTIVE: This study synthesizes the findings from 7 systematic reviews, integrating quantitative and qualitative data from randomized trials, observational studies, and user experience research to evaluate the performance, feasibility, acceptability, and clinical impact of ambulatory assessment and mood monitoring in people with depression and bipolar disorder. We assessed studies over the medium or long term (3 months or more).

METHODS: A summary of a series of systematic reviews was carried out by the authors-including meta-analyses (for quantitative data) and meta-syntheses (for qualitative data). Eight electronic databases were searched, and mixed methods studies were included. Studies were assessed for risk of bias. The results were checked for coherence, and recommendations were made by individuals with lived experience, methodologists, and psychiatrists. GRADE (Grading of Recommendations Assessment, Development, and Evaluation) was used to assess the quality and strength of the evidence.

RESULTS: The 111 included studies included 19,945 participants and used 69 different ambulatory assessment protocols or mood-monitoring interventions. Key barriers to implementation were identified, including performance inconsistency, adverse effects, and user disengagement. Evidence-based recommendations are provided to guide future clinical and research applications.

CONCLUSIONS: Ambulatory assessment and mood monitoring hold promise in research and clinical practice, yet their implementation requires more rigorous evaluation, greater personalization, and responsible, user-centered design. Crucially, these measures can add granularity and confirmation, but additional context is often required, and none of these measures are robust enough yet to replace current outcomes.},
}

@article {pmid42237540,
year = {2026},
author = {Banik, P and Zimmann, F and Thakur, PK and Dudakova, L and Večerková, K and Kostov, O and Caruthers, MH and Kolář, M and Krejčířová, I and Vajter, M and Liskova, P and Bárta, T and Staněk, D},
title = {Targeted antisense oligonucleotide therapy rescues PRPF31 expression in retinitis pigmentosa caused by a splicing mutation.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2026.05.033},
pmid = {42237540},
issn = {1525-0024},
abstract = {Pathogenic variants in splicing factors are the second most common cause of autosomal dominant retinitis pigmentosa (RP), with mutations in PRPF31 being the most prevalent. Here, we characterize a novel intronic variant in PRPF31 (c.1074-11C>G) that creates a cryptic 3' splice site, resulting in an aberrantly spliced transcript predicted to encode a protein with an altered C-terminus. However, the pathogenic protein is unstable and undetectable in patient-derived induced pluripotent stem cells (iPSCs). In addition, expression of the full-length PRPF31 protein was reduced in patient-derived retinal pigment epithelium (RPE). To correct the splicing defect, we designed a panel of antisense oligonucleotides (ASOs) targeting putative RNA-binding sites in exon 10 and intron 10 and identified a candidate that corrects PRPF31 splicing in a minigene reporter system as well as in patient-derived iPSCs and RPE. We further showed that ASO treatment enhances PRPF31 protein expression in patient-derived iPSC and RPE carrying the intronic mutation, supporting the potential of the ASO-based approach to restore PRPF31 expression in patients with the same or similar splicing defects.},
}

@article {pmid42241802,
year = {2026},
author = {Ye, JF and Lai, YK and Kim, N and Liu, PL},
title = {Discussing diseases in everyday talk: Examining the roles of medical and phatic patient-provider communication in promoting Chinese patients' healthy lifestyle behaviors.},
journal = {Patient education and counseling},
volume = {150},
number = {},
pages = {109727},
doi = {10.1016/j.pec.2026.109727},
pmid = {42241802},
issn = {1873-5134},
abstract = {OBJECTIVE: Previous patient-provider communication (PPC) research has focused on treatment or illness-centered medical PPC but has overlooked phatic PPC. Based on the ecological model of communication in medical encounters, this study examines how medical PPC and phatic PPC relate to patients' healthy lifestyle behaviors through perceived patient-centeredness and patient activation.

METHODS: Cross-sectional data from one representative sample of Chinese patients (N = 5000) were analyzed.

RESULTS: Medical PPC was positively associated with perceived patient-centeredness (β =.204, p < .001), which in turn was positively associated with patient activation (β =.405, p < .001) and healthier lifestyle behaviors. Phatic PPC showed a small negative direct association with patient-centeredness (β = -.056, p < .05), but it positively moderated the relationship between medical PPC and patient-centeredness (b =.030, p < .01).

CONCLUSION: By testing a moderated mediation model, the study demonstrates the complementary role of phatic PPC for medical PPC and elucidates how these two functionally distinct forms of PPC jointly promote healthy lifestyle behaviors.

PRACTICAL IMPLICATIONS: Healthcare providers should be trained to strategically integrate medical and phatic PPC, using brief relational cues to build supportive patient-centered care without compromising the efficiency of medical communication.},
}

@article {pmid42242207,
year = {2026},
author = {Yasuma-Mitobe, K and Liao, C and Németh, T and Byrne, K and Billips, A and Faustino Ramos, RJJ and Salinas, CN and Chan, E and Perissinoto, M and Adami-Sampson, S and Salman, A and Sidebottom, AM and Plitas, G and Butler, G and Cross, JR and Pamer, EG and Gácser, A and Xavier, JB and Hohl, TM},
title = {Intracellular acidification by microbiota-derived valeric acid facilitates trans-kingdom ecology limiting Candida parapsilosis colonization.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.008},
pmid = {42242207},
issn = {1934-6069},
abstract = {In hematopoietic cell transplant (HCT) patients, intestinal Candida parapsilosis expansion and translocation can cause life-threatening candidemia, yet whether commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of Lachnospiraceae to identify bacteria-derived inhibitors of fungal growth, identifying valeric and butyric acids as top hits. Fecal samples from HCT patients supported this association, with valeric and butyric acid levels inversely correlating with C. parapsilosis growth. In cell culture and mice, valeric acid inhibited C. parapsilosis growth by increasing intracellular acidification. Administration of glycerol valerate, or free or microencapsulated valeric acid, to release valeric acid along the entire intestinal tract blunted C. parapsilosis growth at murine intestinal sites where valeric acid was detected. Thus, machine learning identified a mechanistic driver of trans-kingdom ecology limiting C. parapsilosis intestinal expansion and may inform strategies to reduce patient risk of candidiasis.},
}

@article {pmid41538056,
year = {2026},
author = {Rehman, U and Sarfraz, M and Bibi, F and Noor, A and Ullah, M and Tarafder, E and Shinwari, ZK},
title = {DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {2},
pages = {40},
pmid = {41538056},
issn = {1572-9699},
mesh = {*DNA Barcoding, Taxonomic/methods/trends ; *Agaricales/genetics/classification ; Multiomics ; *Phylogeny ; Genomics/methods ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; },
abstract = {Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.},
}

*DNA Barcoding, Taxonomic/methods/trends
*Agaricales/genetics/classification
Multiomics
*Phylogeny
Genomics/methods
Genome, Fungal
High-Throughput Nucleotide Sequencing

@article {pmid41538613,
year = {2025},
author = {Soares Filho, AM and Vasconcelos, CH and Vasconcelos, NM and Lima, CM and Souza, MFM and Pinto, IV and Cardoso, LO and Malta, DC},
title = {Mapping of underreporting of interpersonal violence based on the occurrence of homicides in Brazilian municipalities, 2016-2018.},
journal = {Ciencia & saude coletiva},
volume = {30},
number = {12},
pages = {e08432024},
doi = {10.1590/1413-812320253012.08432024},
pmid = {41538613},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; *Homicide/statistics & numerical data ; Female ; *Violence/statistics & numerical data ; Adult ; Cities ; Middle Aged ; Young Adult ; *Information Systems/statistics & numerical data ; },
abstract = {Identify municipalities with underreporting of interpersonal violence based on homicide in Brazil, 2016 to 2018. Ecological study with rate on violence from the Notifiable Diseases Information System and homicide estimates from the Global Burden of Disease concerning < 20 years, women of 20 to 59 years, ≥ 60 years and the total of these subgroups. Bivariate Local Moran identified clusters of critical areas of low reporting rates and high homicide rates (p < 0.05). Municipalities in the North, Northeast, and Midwest of Brazil represented 29% of all reports of violence and 58% of homicides. The majority of these municipalities were concentrated in low reporting rates (≤ 0.8/10,000) and high homicide rates (≥ 13.7/100,000); and 31.4% of municipalities with high homicide rate reported zero cases. Reports of violence and homicide rates showed a negative spatial correlation (I<20 = -0.083; Iwomen20-59 = -0.023; I≥60 = -0.086; Itotal = -0.085), showing that nearby places have inverse values. Critical municipalities for underreporting of violence reach 16% of < 20 years, 12% of women, 23% of the elderly, and 18% in total. The low reporting in seriously violent areas provides evidence of underreporting. The findings can provide management with tools for initiatives to improve violence surveillance and access to the protection network.},
}

Brazil/epidemiology
Humans
*Homicide/statistics & numerical data
Female
*Violence/statistics & numerical data
Adult
Cities
Middle Aged
Young Adult
*Information Systems/statistics & numerical data

@article {pmid42166940,
year = {2026},
author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM},
title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.},
journal = {Pathology, research and practice},
volume = {285},
number = {},
pages = {156543},
doi = {10.1016/j.prp.2026.156543},
pmid = {42166940},
issn = {1618-0631},
mesh = {Humans ; *Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; *Tumor Microenvironment/genetics ; Multiomics ; Animals ; },
abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.},
}

Humans
*Neoplasms/microbiology/genetics
*Microbiota/genetics
*Metagenomics/methods
*Tumor Microenvironment/genetics
Multiomics
Animals

@article {pmid42235263,
year = {2026},
author = {Kim, J and Müller, F and Ribeiro, CC and Dietz, C and Hero, D and Witayakran, S and Gallei, M},
title = {Cyclodextrin-modified core-shell particle synthesis and photonic crystal film formation for redox-mediated surface interaction.},
journal = {Journal of colloid and interface science},
volume = {722},
number = {},
pages = {140824},
doi = {10.1016/j.jcis.2026.140824},
pmid = {42235263},
issn = {1095-7103},
abstract = {In recent years, extensive efforts have been made to develop and utilize smart optical materials. Carbohydrate-based materials are abundant, readily accessible, and essential for advancing sustainable science and ecological cycles. Carbohydrates containing α-glycosidic linkages are naturally generated, and cyclodextrin represents a typical oligosaccharide with such a structure. The ring-shaped architecture of cyclodextrin has been widely studied because, unlike conventional chemical bonds, it enables host-guest interactions based on noncovalent binding. Incorporating cyclodextrin into nanosized, highly uniform core-shell particles could enable the production of photonic crystal films. A synthesis route for the preparation of β-cyclodextrin-modified core-shell particles with host functionality has been reported and characterized at the molecular and material levels. The molecular structures and particle-based optical film formation were validated by spectroscopic and microscopic analysis. The resulting photonic crystal films displayed vivid structural colors. Their capture property was demonstrated by a decrease in the electrochemical redox signal arising from host-guest interactions with ferrocene, while maintaining structural coloration after capture. These findings highlight the potential of the developed system for applications involving selective particle-surface interactions that can be triggered by an electrochemical response. This method will pave the way to new capturing and separation strategies and optical anti-counterfeiting technologies.},
}

@article {pmid40764303,
year = {2025},
author = {Xu, Y and Gkoutos, GV},
title = {A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {87},
pmid = {40764303},
issn = {2056-7189},
support = {101095480//HYPERMARKER/ ; 101095480//HYPERMARKER/ ; 731032//Nanocommons H2020-EU/ ; 965286//MAESTRIA/ ; 101057014//PARC/ ; HDRUK/CFC/01//MRC Heath Data Research UK/ ; },
mesh = {Animals ; *Computational Biology/methods ; Mice ; Humans ; *Microbiota ; Computer Simulation ; Machine Learning ; Gastrointestinal Microbiome ; *Ecology/methods ; Ecosystem ; Clostridioides difficile ; Clostridium Infections/microbiology ; Models, Biological ; Microbial Interactions ; },
abstract = {We present MBPert, a generic computational framework for inferring species interactions and predicting dynamics in time-evolving ecosystems from perturbation and time-series data. In this work, we contextualize the framework in microbial ecosystem modeling by coupling a modified generalized Lotka-Volterra formulation with machine learning optimization. Unlike traditional methods that rely on gradient matching, MBPert leverages numerical solutions of differential equations and iterative parameter estimation to robustly capture microbial dynamics. The framework is assessed within the context of two experimental scenarios: (i) paired before-and-after measurements under targeted perturbations, and (ii) longitudinal time-series data with time-dependent perturbations. Extensive simulation studies, benchmarking on standardized MTIST datasets, and application to Clostridium difficile infection in mice and repeated antibiotic perturbations of human gut micribiota, demonstrate that MBPert accurately recapitulates species interactions and predicts system dynamics. Our results highlight MBPert as a powerful and flexible tool for mechanistic insight into microbiota ecology, with broad potential applicability to other complex dynamical systems.},
}

Animals
*Computational Biology/methods
Mice
Humans
*Microbiota
Computer Simulation
Machine Learning
Gastrointestinal Microbiome
*Ecology/methods
Ecosystem
Clostridioides difficile
Clostridium Infections/microbiology
Models, Biological
Microbial Interactions

@article {pmid40770074,
year = {2025},
author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A},
title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1159},
pmid = {40770074},
issn = {2399-3642},
mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; },
abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.},
}

Humans
*Aging
*Biometry/methods
*Deep Learning
*Gastrointestinal Microbiome
*Principal Component Analysis/methods
*Skin Microbiome
Software Validation

@article {pmid40770961,
year = {2026},
author = {Lopes-Araujo, HF and Guimarães, RL and Carvalho-Silva, WHV},
title = {Correlations between new HIV infections and hospital admissions for non-Hodgkin lymphoma in Brazil.},
journal = {International journal of cancer},
volume = {158},
number = {1},
pages = {84-93},
doi = {10.1002/ijc.70076},
pmid = {40770961},
issn = {1097-0215},
mesh = {Humans ; Brazil/epidemiology ; Male ; *HIV Infections/epidemiology/complications ; Female ; *Lymphoma, Non-Hodgkin/epidemiology/virology ; Adult ; Middle Aged ; *Hospitalization/statistics & numerical data ; Adolescent ; Incidence ; Young Adult ; Aged ; Child ; },
abstract = {Despite advancements in antiretroviral therapy, human immunodeficiency virus (HIV) infections remain a significant global health challenge. With increasing life expectancy among people living with HIV, the emergence of HIV-related malignancies, notably non-Hodgkin lymphoma (NHL), has become a prominent concern. This study aims to investigate the correlation between new HIV infections and NHL hospitalizations in Brazil from 2010 to 2022. Using an ecological time series design, data from authoritative sources, including the Notifiable Diseases Information System and the Department of Unified Health System Informatics, were analyzed. The study cohort comprised individuals admitted to the Brazilian Unified Health System, categorized by geographical region, sex, and age cohorts. Pearson's and Spearman's correlation coefficients were utilized to examine the correlation between new HIV infections and NHL hospitalizations. Our analysis revealed a strong positive and statistically significant correlation between the incidence of new HIV cases and NHL hospitalizations in Brazil (r = 0.8901; p = .0001) and in most regions (r > 0.80; p < .001). Moreover, our findings indicate that this correlation becomes evident from the age of 15 onward, with a discernible tendency to escalate with advancing age from moderate to very strong (r > 0.62; p < .02). Regarding sex, the observed correlations were strong positive for male (r = 0.8681; p = .0003) and female (r = 0.7912; p = .0020). These results underscore the importance of vigilant monitoring for individuals living with HIV. Furthermore, we emphasize the importance of rigorous screening practices and adherence to antiretroviral therapy, which may hold promising implications for managing neoplastic conditions.},
}

Humans
Brazil/epidemiology
Male
*HIV Infections/epidemiology/complications
Female
*Lymphoma, Non-Hodgkin/epidemiology/virology
Adult
Middle Aged
*Hospitalization/statistics & numerical data
Adolescent
Incidence
Young Adult
Aged
Child

@article {pmid40772542,
year = {2025},
author = {Reddy, S and Wacker, K and Fahmy, M and Hekkala, E and Bates, JM and Goodman, SM and Hackett, SJ and Raherilalao, MJ and Maddox, JD},
title = {VoronaGasyCodes: A Public Database of Mitochondrial Barcodes for Malagasy Birds.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70027},
pmid = {40772542},
issn = {1755-0998},
mesh = {Animals ; Madagascar ; *Birds/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA, Mitochondrial/genetics/chemistry ; Biodiversity ; *Databases, Genetic ; },
abstract = {Molecular tools are increasingly being used to survey the presence of biodiversity and their interactions within ecosystems. Indirect methods, like environmental DNA (eDNA) and invertebrate-derived DNA (iDNA), are dependent on sequence databases with accurate and sufficient taxonomic representation. These methods are increasingly being used in regions and habitats where direct detection or observations can be difficult for a variety of reasons. Madagascar is a biodiversity hotspot with a high proportion of endemic species, many of which are threatened or endangered. Here we describe a new resource, VoronaGasyCodes, a curated database of newly published genetic sequences from Malagasy birds. Our database is currently populated with six mitochondrial genes or DNA barcodes for 142 species including 70% of the birds endemic to the island and will be periodically updated as new data become available. We demonstrate the utility of our database with an iDNA study of leech blood meals where we successfully identified 77% of the hosts to species. These types of resources for characterising biodiversity are critical for insights into species distribution, discovery of new taxa, novel ecological connections and advancing conservation and restoration measures.},
}

Animals
Madagascar
*Birds/genetics/classification
*DNA Barcoding, Taxonomic/methods
*DNA, Mitochondrial/genetics/chemistry
Biodiversity
*Databases, Genetic

@article {pmid40772610,
year = {2025},
author = {Tsuji, S and Kunimatsu, S and Watanabe, K},
title = {Environmental DNA Comparative Phylogeography: Simultaneous Estimation of Population Structures Within a Species-Rich Group of Freshwater Gobies.},
journal = {Molecular ecology},
volume = {34},
number = {18},
pages = {e70059},
doi = {10.1111/mec.70059},
pmid = {40772610},
issn = {1365-294X},
support = {23K13967//Japan Society for the Promotion of Science/ ; //ESPEC Foundation for Global Environment Research and Technology/ ; },
mesh = {Phylogeography ; Animals ; *DNA, Environmental/genetics ; Fresh Water ; Japan ; *Genetics, Population ; Haplotypes ; *Perciformes/genetics/classification ; Cytochromes b/genetics ; Phylogeny ; Biodiversity ; DNA, Mitochondrial/genetics ; Genetic Variation ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; },
abstract = {Comparative phylogeography provides crucial insights into evolutionary processes shaping biodiversity patterns by analysing spatial genetic variations across multiple species. However, conventional capture-based methods are often labour-intensive, particularly for multi-species analyses. Environmental DNA (eDNA) analysis has significant advantages in comparative phylogeography, including simplified field surveys requiring only water collection and the potential to simultaneously analyse multiple species from a single sample. To further expand the eDNA application and demonstrate its utility in comparative phylogeographic studies, this study employed eDNA analysis to simultaneously analyse the phylogeographic patterns in a species-rich freshwater goby group (Rhinogobius) in the Japanese Archipelago. DNA amplification was performed on eDNA samples collected from 573 sites across the archipelago using newly designed group-specific primers targeting the mitochondrial cytochrome b region of Rhinogobius. High-throughput sequencing detected haplotypes of all nine known species (or species groups) occurring in this region, followed by phylogenetic and network analyses. The eDNA analysis successfully revealed the genetic population structures across multiple species. A landlocked species, R. flumineus, exhibited fine-scale population differentiation shaped by geomorphological barriers, while amphidromous species showed broader genetic patterns likely influenced by ocean currents and their ecological traits. The phylogenetic and phylogeographic patterns reconstructed by the eDNA analysis were almost completely concordant with previously identified patterns of limited groups based on conventional methods, demonstrating the reliability of eDNA-based comparative phylogeography. This study highlights the potential of eDNA to complement and partially replace conventional methods, facilitating large-scale comparative phylogeographic research to gain new insights into spatial patterns and evolutionary processes of biodiversity.},
}

Phylogeography
Animals
*DNA, Environmental/genetics
Fresh Water
Japan
*Genetics, Population
Haplotypes
*Perciformes/genetics/classification
Cytochromes b/genetics
Phylogeny
Biodiversity
DNA, Mitochondrial/genetics
Genetic Variation
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing

@article {pmid40774342,
year = {2025},
author = {Cao, W and Cao, X and Sutherland, AD},
title = {Planning for the Unexpected and Unintended Effects of mHealth Interventions: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e68909},
pmid = {40774342},
issn = {1438-8871},
mesh = {*Telemedicine ; Humans ; },
abstract = {BACKGROUND: Mobile health (mHealth) interventions can produce both intended and unintended effects. Examining these unintended effects helps create a more complete and objective understanding of mHealth interventions and can reduce potential harm to participants. Existing studies on the unintended effects, which were published several years ago, tend to have either a general focus on health IT or a specific focus on health care providers, thereby excluding other key stakeholders (eg, patients and community health workers). Additionally, these studies did not systematically outline the causes of the unintended effects or strategies for their prevention.

OBJECTIVE: To address this gap, this systematic review, guided by the ecological framework, aims to systematically identify the unintended effects of mHealth interventions, create a typology for them, investigate the reasons for their occurrence, describe how they were detected, and propose ways to prevent or lessen them.

METHODS: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, a systematic review was performed to examine the unintended effects of health interventions that use mobile technology.

RESULTS: A total of 15 papers were included in the review. An ecological typology of mHealth intervention unintended effects (mHUE) was developed, which includes 26 distinct effects (eg, silencing and boomerang). The majority of these unintended effects (n=20) occur at the individual level and span physical or behavioral (n=7), psychological (n=8), cognitive (n=4), and financial (n=1) domains. Three effects occur at the interpersonal level and another 3 at the community or institutional level. Most of the identified effects (n=22) were negative. Potential causes for these effects include the improper use of mHealth technology, poorly designed interventions, the application of unsuitable intervention mechanisms, or a misalignment between the intended outcomes and the sociocultural context. Strategies and recommendations (eg, considering the context such as cultural norms) were suggested to help prevent or reduce the unintended effects.

CONCLUSIONS: The unintended effects detailed in the mHUE typology were heterogenous and context-dependent. These effects can influence individuals across different domains and also affect unintended people within the ecological system. As most of the unintended effects are negative, if they are not monitored, mHealth interventions designed to empower participants could paradoxically disempower them (eg, decreasing self-efficacy for disease management, undermining patient control, and engagement). The mHUE typology, together with the proposed recommendations and strategies, can be used as a guide to enhance the planning, design, implementation, and postimplementation evaluation on mHealth interventions. Future research should concentrate on understanding the specific mechanisms behind these unintended effects.},
}

*Telemedicine
Humans

@article {pmid40774411,
year = {2025},
author = {Zhang, L and Liu, Y and Chen, K and Yue, Q and Wang, C and Xie, L and Molnár, I and Xu, Y},
title = {Genome mining of tailoring enzymes from biosynthetic gene clusters for synthetic biology: A case study with fungal methyltransferases.},
journal = {Metabolic engineering},
volume = {92},
number = {},
pages = {125-135},
doi = {10.1016/j.ymben.2025.08.001},
pmid = {40774411},
issn = {1096-7184},
mesh = {*Methyltransferases/genetics/metabolism ; *Multigene Family ; *Genome, Fungal ; *Fungal Proteins/genetics/metabolism ; *Synthetic Biology/methods ; *Fungi/genetics/enzymology ; *Data Mining/methods ; Biosynthetic Pathways/genetics ; Biological Products/metabolism ; },
abstract = {Harnessing the potential of tailoring enzymes within fungal natural product (NP) biosynthetic gene clusters (BGCs) can significantly enhance NP diversity and production efficiency via artificially constructed microbial cell factories. To achieve this, an efficient genome mining method is crucial, especially since the functions of many putative enzymes in databases are unknown. As a test case, we aimed to identify methyltransferases (MTs) that modify a polyketide substrate without a known cognate MT. 16,748 putative MTs were annotated in 101,321 fungal BGCs and grouped into orthologous families. Three methods were explored to prioritize suitable enzymes. Among these, the machine learning method proved superior, with 11 out of 15 tested MTs successfully methylating the test substrate. This demonstrates the effectiveness of machine learning to mine tailoring enzymes that modify selected compounds, aiding synthetic biology in optimizing NP biosynthesis and facilitating the production of "unnatural products" for pharmaceutical or other bioindustrial applications.},
}

*Methyltransferases/genetics/metabolism
*Multigene Family
*Genome, Fungal
*Fungal Proteins/genetics/metabolism
*Synthetic Biology/methods
*Fungi/genetics/enzymology
*Data Mining/methods
Biosynthetic Pathways/genetics
Biological Products/metabolism

@article {pmid40774560,
year = {2025},
author = {Guo, J and Lei, W and Liang, X and Wang, H and Qi, W and Huang, S and Chen, X and He, S},
title = {Three-dimensional distribution and key drivers of neonicotinoid residues in hilly agricultural areas.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122524},
doi = {10.1016/j.envres.2025.122524},
pmid = {40774560},
issn = {1096-0953},
mesh = {*Neonicotinoids/analysis ; *Soil Pollutants/analysis ; *Insecticides/analysis ; *Environmental Monitoring ; Agriculture ; *Pesticide Residues/analysis ; Soil/chemistry ; China ; Nitro Compounds/analysis ; Guanidines/analysis ; Thiazoles ; },
abstract = {Neonicotinoids (NNIs) raise global concern due to their substantial soil residues and potential health risks to animal and human health. High water solubility and low soil adsorption enhanced vertical and horizontal migration of NNIs. However, understanding of NNIs' three-dimensional distribution in soils and influencing factors remains limited, limiting accurate risk assessment and remediation strategies for agriculture ecosystems. This study selected typical mountainous farmland soil to investigate the three-dimensional distribution of NNIs contents and composition. The findings indicated that the average detection rate of imidacloprid (IMI) in the 0-20 cm layer was 33 % higher than that in the 30-40 cm layer, whereas clothianidin (CLO) detection rates remained consistent across 0-40 cm layer. The contents of eight NNIs (∑8NNIs) in the study area ranged from 0.09 to 37.08 ng/g, with the 6.58 ± 8.65 ng/g in the 0-10 cm and 2.60 ± 7.78 ng/g in the 30-40 cm layer. The contents of ∑8NNIs, IMI, and CLO decreased by 60 %, 62 %, and 75 %, respectively, with increasing depth. The proportion of IMI and CLO to ∑8NNIs decreased and increased by 35 % and 12 %, respectively, in the 0-40 cm soil, leading to IMI predominance in the topsoil (60 %) and CLO in the deeper soil (29 %). Correlation analysis revealed that soil particle size, slope, and elevation were significantly associated with both the ∑8NNIs and the proportions of IMI and CLO. These results highlighted the substantial influence of topography and soil structure on the vertical distribution of NNIs. Additionally, the ∑8NNIs content in stem mustard soil was higher than in sweet potato, rice, corn, and forest. Overall, the study found very low health risks to humans (hazard index, HI < 1) and no overall potential ecological risk in the study area, though localized sublethal risks to non-target organisms were identified. Furthermore, the spatial correlation between IMI and CLO health risk regions identified overlapping high-risk areas.},
}

*Neonicotinoids/analysis
*Soil Pollutants/analysis
*Insecticides/analysis
*Environmental Monitoring
Agriculture
*Pesticide Residues/analysis
Soil/chemistry
China
Nitro Compounds/analysis
Guanidines/analysis
Thiazoles

@article {pmid40774918,
year = {2025},
author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santsch, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY},
title = {Corrigendum to "Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050" [Mar. Pollut. Bull. 206 (2024) 116664].},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118543},
doi = {10.1016/j.marpolbul.2025.118543},
pmid = {40774918},
issn = {1879-3363},
}

@article {pmid40776104,
year = {2025},
author = {Bauberg, H and Tachnai, N and Hanan, G and Nehama, D and Tamburis, O and Darmoni, S and Grosjean, J and Benis, A},
title = {Automated Elicitation of Human and Ecological Health Indicators: An LLM-Based Practical Implementation for One Digital Health.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1488-1492},
doi = {10.3233/SHTI251086},
pmid = {40776104},
issn = {1879-8365},
mesh = {Humans ; *One Health ; *Health Status Indicators ; *Environmental Health/methods ; Digital Health ; },
abstract = {This paper presents a new method for automating the identification of human and ecological health indicators using the One Digital Health framework, which combines One Health and Digital Health principles. By applying mainly Large Language Models, we conduct a systematic literature review on urban freshwater environments. This automation streamlines the process of finding and analyzing relevant research, allowing us to extract vital health indicators related to urban aquatic ecosystems and human wellness. The findings support the OneAquaHealth project's goals, enhancing environmental monitoring and linking human, animal, and environmental health in a digital context.},
}

Humans
*One Health
*Health Status Indicators
*Environmental Health/methods
Digital Health

@article {pmid40777262,
year = {2025},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40777262},
issn = {2692-8205},
support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; },
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes including colony morphology, cell elongation, and cell chaining in C. difficile. Here we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state leading to chaining and a rough colony morphology. This phenomenon preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.},
}

@article {pmid40778113,
year = {2025},
author = {Sprint, G and Schmitter-Edgecombe, M and Weaver, R and Wiese, L and Cook, DJ},
title = {CogProg: Utilizing Large Language Models to Forecast In-the-moment Health Assessment.},
journal = {ACM transactions on computing for healthcare},
volume = {6},
number = {2},
pages = {},
pmid = {40778113},
issn = {2637-8051},
support = {R01 AG066748/AG/NIA NIH HHS/United States ; R01 AG083925/AG/NIA NIH HHS/United States ; R25 AG046114/AG/NIA NIH HHS/United States ; R01 AG065218/AG/NIA NIH HHS/United States ; R35 AG071451/AG/NIA NIH HHS/United States ; R01 EB009675/EB/NIBIB NIH HHS/United States ; },
abstract = {Forecasting future health status is beneficial for understanding health patterns and providing anticipatory support for cognitive and physical health difficulties. In recent years, generative large language models (LLMs) have shown promise as forecasters. Though not traditionally considered strong candidates for numeric tasks, LLMs demonstrate emerging abilities to address various forecasting problems. They also provide the ability to incorporate unstructured information and explain their reasoning process. In this paper, we explore whether LLMs can effectively forecast future self-reported health state. To do this, we utilized in-the-moment assessments of mental sharpness, fatigue, and stress from multiple studies, utilizing daily responses (N=106 participants) and responses that are accompanied by text descriptions of activities (N=32 participants). With these data, we constructed prompt/response pairs to predict a participant's next answer. We fine-tuned several LLMs and applied chain-of-thought prompting evaluating forecasting accuracy and prediction explainability. Notably, we found that LLMs achieved the lowest mean absolute error (MAE) overall (0.851), while gradient boosting achieved the lowest overall root mean squared error (RMSE) (1.356). When additional text context was provided, LLM forecasts achieved the lowest MAE for predicting mental sharpness (0.862), fatigue (1.000), and stress (0.414). These multimodal LLMs further outperformed the numeric baselines in terms of RMSE when predicting stress (0.947), although numeric algorithms achieved the best RMSE results for mental sharpness (1.246) and fatigue (1.587). This study offers valuable insights for future applications of LLMs in health-based forecasting. The findings suggest that LLMs, when supplemented with additional text information, can be effective tools for improving health forecasting accuracy.},
}

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

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

@article {pmid40781089,
year = {2025},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1385},
doi = {10.1038/s41597-025-05752-9},
pmid = {40781089},
issn = {2052-4463},
support = {R44 CA278140/CA/NCI NIH HHS/United States ; R44 HD104323/HD/NICHD NIH HHS/United States ; },
}

@article {pmid40781446,
year = {2025},
author = {Rauniyar, S and Samanta, D and Thakur, P and Saxena, P and Singh, RN and Bazin, A and Bomgni, A and Fotseu, E and Etienne, GZ and Gadhamshetty, V and Peyton, BM and Fields, M and Subramaniam, M and Sani, RK},
title = {Mapping the pangenome of sulfate reducing bacteria: core genes, plasticity, and novel functions in Desulfovibrio spp.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {305},
pmid = {40781446},
issn = {1573-0972},
support = {5P20GM103443-20/NH/NIH HHS/United States ; 1736255//National Science Foundation/ ; },
mesh = {*Desulfovibrio/genetics/metabolism/classification ; *Genome, Bacterial ; *Sulfates/metabolism ; Phylogeny ; Multigene Family ; Gene Regulatory Networks ; Genes, Bacterial ; Gene Ontology ; },
abstract = {The pangenome of sulfate reducing bacteria represents a genetic reservoir that deciphers the intricate interplay of conserved and variable elements driving their ecological dominance, evolutionary adaptability, and industrial relevance. This study introduces the most comprehensive pangenome analysis of the genus Desulfovibrio till date, incorporating 63 complete and high-quality genomes using the Partitioned Pangenome Graph of Linked Neighbors (PPanGGOLiN) pipeline. The structure and dynamics of core gene families were investigated through gene ontology, KEGG pathway mapping, and gene network analyses, shedding light on the functional organization of the Desulfovibrio genomes. The analysis categorized 799, 4053, and 43,581 gene families into persistent, shell, and cloud groups, respectively. A core set of 326 gene families, conserved across Desulfovibrio genomes, highlights their essential role in community functionality. Genome plasticity analysis identified 4,576 regions of genome plasticity, with 1,322 hotspots enriched in horizontally acquired genes (89% in the cloud partition). Key gene families in these regions included glpE, fdhD, petC, and cooF, linked to sulfur metabolism. Out of 29 hypothetical genes, one was linked to actin nucleation, another contained a TRASH domain, while the other regulates filopodium assembly. Other predicted functions included lnrL, folE, RNA binding, and pyrG/pyrH involvement in CTP biosynthesis. Additionally, genomic islands revealed evolutionary events, such as cheY acquisition in Oleidesulfovibrio alaskensis G20. This study provides a genus-wide view of Desulfovibrio, emphasizing genome plasticity, hypothetical gene functions, and adaptation mechanisms.},
}

*Desulfovibrio/genetics/metabolism/classification
*Genome, Bacterial
*Sulfates/metabolism
Phylogeny
Multigene Family
Gene Regulatory Networks
Genes, Bacterial
Gene Ontology

@article {pmid40782603,
year = {2025},
author = {Benvenuti, MC and Merkle, EC and McCarthy, DM},
title = {Physical context of alcohol use and craving: An EMA exploratory study.},
journal = {Addictive behaviors},
volume = {170},
number = {},
pages = {108450},
pmid = {40782603},
issn = {1873-6327},
support = {R01 AA019546/AA/NIAAA NIH HHS/United States ; T32 AA013526/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Craving ; Male ; Female ; *Ecological Momentary Assessment ; *Alcohol Drinking/psychology/epidemiology ; Adult ; Young Adult ; Adolescent ; Geographic Information Systems ; Self Report ; },
abstract = {While environmental and physical contextual factors play an important role in alcohol use and motivation for use, assessment of the physical context of use, even when using ecological momentary assessments (EMA), has been limited. While EMA research has examined drinking locations at the event level using categories of drinking locations, there is considerable within-category variability in the attributes of drinking locations. Using data from a 6-week EMA study (N = 207), this exploratory study sought to determine drinking locations through the combination of EMA self-report and GPS coordinates. Through multilevel modeling, we also tested whether specific locations were associated with variability in drinking (self-reported drinking and breathalyzer readings) and craving for alcohol. Results indicated significant differences in both alcohol consumption and craving between home, friend's houses, and on-premises drinking locations. Our results offer proof of concept for using mobile and geospatial data to passively identify on-premise drinking locations. This approach has the potential to aid in the development of targeted intervention strategies that identify and mitigate risks associated with specific drinking environments.},
}

Humans
*Craving
Male
Female
*Ecological Momentary Assessment
*Alcohol Drinking/psychology/epidemiology
Adult
Young Adult
Adolescent
Geographic Information Systems
Self Report

@article {pmid40786600,
year = {2025},
author = {Boyes, D and Gardiner, A and , and , and , and , and , and , and , and , },
title = {The genome sequence of the V-Pug moth, Chloroclystis v-ata (Haworth, 1809).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {197},
pmid = {40786600},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Chloroclystis v-ata (V-Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 275.35 megabases. Most of the assembly (99.95%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.49 kilobases.},
}

@article {pmid40788461,
year = {2025},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM},
title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {816},
pmid = {40788461},
issn = {1573-4978},
support = {408693/2022-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico,Brazil/ ; },
mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.},
}

Swine
*Wastewater/microbiology
Animals
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Metagenome/genetics
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Computational Biology/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {967},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
mesh = {*Metagenomics/methods ; *Ecosystem ; Microbiota/genetics ; *Water Microbiology ; Environmental Monitoring/methods ; Computational Biology/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples such as soil, water, air, and the human body. Metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the broad applications of metagenomics in environmental monitoring, encompassing sample collection, high-throughput sequencing, data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will become crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}

*Metagenomics/methods
*Ecosystem
Microbiota/genetics
*Water Microbiology
Environmental Monitoring/methods
Computational Biology/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Metagenome

@article {pmid40794746,
year = {2025},
author = {Alkhatib, SA and Arya, S and Islayem, D and Nyadzayo, RM and Mohamed, S and Yousef, AF and Hernandez, HH and Pappa, AM},
title = {Revealing bioremediation potential of novel indigenous bacteria from oil-contaminated sites in the UAE: A combined bioinformatics and experimental validation.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329515},
pmid = {40794746},
issn = {1932-6203},
mesh = {*Biodegradation, Environmental ; *Computational Biology/methods ; United Arab Emirates ; Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteria/metabolism/genetics/isolation & purification ; Phenols/metabolism ; *Soil Pollutants/metabolism ; },
abstract = {Microbial biodegradation of recalcitrant aromatic hydrocarbon pollutants represents an environmentally sustainable strategy for remediating contaminated sites. However, elucidating the metabolic capabilities and genetic determinants of biodegrading strains is crucial for optimizing bioremediation strategies. In this study, we comprehensively characterize the aromatic catabolic potential of two indigenous bacterial isolates, A. xylosoxidans C2 (A. x. C2) and A. xylosoxidans KW38 (A. x. KW38), obtained from hydrocarbon-impacted environments in the United Arab Emirates (UAE). Experimental validation through aromatic hydrocarbons supplemented growth studies confirmed the capability of the isolated bacteria to mineralize bisphenol A, 4-hydroxybenzoic acid, 1-naphthalenemethanol, and the high molecular weight polycyclic aromatic hydrocarbon (PAH), pyrene, in the presence of glucose. Their degradation efficiencies were comparable to or greater than those of Pseudomonas paraeruginosa, a well-characterized model organism for aromatic compound degradation. Integrated bioinformatic analyses uncovered fundamental aromatic catabolic pathways conserved across Achromobacter species, along with strain-specific genes that potentially confer specialized degradative capacities, highlighting the genomic basis of the observed metabolic versatility. Further, protein modeling based on the curated sequences revealed unique features of individual catabolic enzymes and their interaction networks. Notably, a dehydrogenase enzyme involved in aromatic ring cleavage was identified exclusively in these UAE isolates. These findings establish A. x. C2 and A. x. KW38 as promising bioremediators of diverse aromatic pollutants. Overall, the study exemplifies a powerful and comprehensive methodological framework that bridges bioinformatic analysis and experimental research to further optimize the effectiveness of experimental design. We achieved a substantial reduction in the number of unknown genetic and metabolic determinants of aromatic hydrocarbon degradation in the strains, reducing uncertainty by 99.3%, thereby enhancing the overall process and outcomes for systematic biodiscovery of pollutant-degrading environmental microbes to address ecological challenges.},
}

*Biodegradation, Environmental
*Computational Biology/methods
United Arab Emirates
Polycyclic Aromatic Hydrocarbons/metabolism
*Bacteria/metabolism/genetics/isolation & purification
Phenols/metabolism
*Soil Pollutants/metabolism

@article {pmid40796553,
year = {2025},
author = {Arehart, CH and Lin, M and Gibson, RA and , and Raghavan, S and Gignoux, CR and Stanislawski, MA and Grotzinger, AD and Evans, LM},
title = {Modeling the genomic architecture of adiposity and anthropometrics across the lifespan.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7494},
pmid = {40796553},
issn = {2041-1723},
support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 AG046938/AG/NIA NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; RF1 AG073593/AG/NIA NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 MH120219/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Adiposity/genetics ; Male ; Female ; Genome-Wide Association Study ; *Obesity/genetics ; Multifactorial Inheritance ; Adult ; Middle Aged ; Anthropometry ; *Longevity/genetics ; Genomics ; Polymorphism, Single Nucleotide ; Aged ; Body Size/genetics ; },
abstract = {Obesity-related conditions are among the leading causes of preventable death and are increasing in prevalence worldwide. Body size and composition are complex traits that are challenging to characterize due to environmental and genetic influences, longitudinal variation, heterogeneity between sexes, and differing health risks based on adipose distribution. Here, we construct a 4-factor genomic structural equation model using 18 measures, unveiling shared and distinct genetic architectures underlying birth size, abdominal size, adipose distribution, and adiposity. Multivariate genome-wide associations reveal the adiposity factor is enriched specifically in neural tissues and pathways, while adipose distribution is enriched more broadly across physiological systems. In addition, polygenic scores for the adiposity factor predict many adverse health outcomes, while those for body size and composition predict a more limited subset. Finally, we characterize the factors' genetic correlations with obesity-related traits and examine the druggable genome by constructing a bipartite drug-gene network to identify potential therapeutic targets.},
}

Humans
*Adiposity/genetics
Male
Female
Genome-Wide Association Study
*Obesity/genetics
Multifactorial Inheritance
Adult
Middle Aged
Anthropometry
*Longevity/genetics
Genomics
Polymorphism, Single Nucleotide
Aged
Body Size/genetics

@article {pmid40796641,
year = {2025},
author = {Sanad, H and Moussadek, R and Mouhir, L and Lhaj, MO and Dakak, H and Manhou, K and Zouahri, A},
title = {Monte carlo simulation for evaluating spatial dynamics of toxic metals and potential health hazards in sebou basin surface water.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29471},
pmid = {40796641},
issn = {2045-2322},
mesh = {Monte Carlo Method ; Humans ; *Metals, Heavy/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; Risk Assessment ; *Environmental Monitoring/methods ; Morocco ; Geographic Information Systems ; Principal Component Analysis ; },
abstract = {Surface water is vital for environmental sustainability and agricultural productivity but is highly vulnerable to heavy metals (HMs) pollution from human activities. The focus of this research is to provide an analysis of ecological and human exposure to HMs in the Sebou Basin, an agriculturally significant region within Morocco's Gharb Plain. Using a multi-index integration approach, encompassing HM pollution indices, Human Health Risk Assessment (HHRA), Monte Carlo Simulation (MCS), multivariate statistical analysis (MSA), and Geographic Information Systems (GIS), twenty samples of surface water were taken and subjected to analysis. The results demonstrated notable spatial variability, with the northwestern, southwestern, and western parts of the Sebou Basin showing higher contamination levels. Cu exhibited the highest hazard quotient for ingestion, while Cr exceeded the hazard index (HI) threshold in both age categories. Statistical analysis uncovered strong associations, particularly between As and Cr, while principal component analysis (PCA) detected two key factors explaining 74.44% of the overall variability. Pollution indices classified all samples as highly contaminated (HPI > 30), with 65% categorized as "seriously affected" (MI > 6). The HHRA results indicated a heightened non-carcinogenic risk for children and carcinogenic risks exceeding acceptable thresholds (TCR > 10[-4]), with Ni presenting the highest risk (TCR = 2.32 × 10[-3] for children). MCS results revealed that Cu and Cr pose potential risks, with Cu exceeding the safety threshold for ingestion in both adults and children. These results emphasize the urgent necessity for tailored strategies to reduce contamination and foster sustainable agricultural and environmental management practices.},
}

Monte Carlo Method
Humans
*Metals, Heavy/analysis/toxicity
*Water Pollutants, Chemical/analysis/toxicity
Risk Assessment
*Environmental Monitoring/methods
Morocco
Geographic Information Systems
Principal Component Analysis

@article {pmid40797121,
year = {2025},
author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA},
title = {Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.},
journal = {Behavior research methods},
volume = {57},
number = {9},
pages = {257},
pmid = {40797121},
issn = {1554-3528},
support = {UL1 TR002378/TR/NCATS NIH HHS/United States ; UL1TR002378/NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Adult ; *Voice ; Young Adult ; *Mobile Applications ; *Speech ; Middle Aged ; Adolescent ; },
abstract = {This article reports on the validation of Fabla, a researcher-developed and university-hosted smartphone app that facilitates naturalistic and secure collection of participants' spoken responses to researcher questions. Fabla was developed to meet the need for tools that (a) collect longitudinal qualitative data and (b) capture speech biomarkers from participants' natural environments. This study put Fabla to its first empirical test using a repeated-measures experimental design in which participants (n = 87) completed a 1-week voice daily diary via the Fabla app, and an identical 1-week text-entry daily diary administered via Qualtrics, with diary method order counterbalanced and randomized. A preregistered analysis plan investigated (1) adherence, usability, and acceptability of Fabla, (2) concurrent validity of voice diaries (vs. text-entry diaries) by comparing linguistic features obtained via each diary method, and (3) differences in the strength of the association between linguistic features and their known psychological correlates when assessed by voice versus text-entry diary. Voice diaries yielded more than double the mean daily language volume (word count) compared to text-entry diaries and received high usability and acceptability ratings. Linguistic markers consistently associated with depression in prior research were significantly associated with depression symptoms when assessed via voice but not text-entry diaries, and the difference in correlation magnitude was significant. Word-count-adjusted linguistic patterns were highly correlated between diary methods, with statistically significant mean differences observed for some linguistic dimensions in the presence of these associations. Fabla is a promising tool for collecting high-quality speech data from participants' naturalistic environments, overcoming multiple limitations of text-entry responding.},
}

Humans
Female
Male
Adult
*Voice
Young Adult
*Mobile Applications
*Speech
Middle Aged
Adolescent

@article {pmid40798830,
year = {2025},
author = {Abraham, AJ and Clauss, M and Bailey, MA and Duvall, ES},
title = {Body Mass Scaling of Sodium Regulation in Mammals.},
journal = {Acta physiologica (Oxford, England)},
volume = {241},
number = {9},
pages = {e70090},
doi = {10.1111/apha.70090},
pmid = {40798830},
issn = {1748-1716},
}

@article {pmid40800427,
year = {2024},
author = {Merritt, H and Faskowitz, J and Gonzalez, MZ and Betzel, RF},
title = {Stability and variation of brain-behavior correlation patterns across measures of social support.},
journal = {Imaging neuroscience (Cambridge, Mass.)},
volume = {2},
number = {},
pages = {},
pmid = {40800427},
issn = {2837-6056},
abstract = {The social environment has a critical influence on human development, cognition, and health. Research in health psychology and social neuroscience indicate an urgent need to understand how social relationships are associated with brain function and organization. To address this, we apply multilayer modeling and modularity maximization-both established tools in network neuroscience-to jointly cluster patterns of brain-behavior associations for seven social support measures. By using network approaches to map and analyze the connectivity between all pairs of brain regions simultaneously, we can clarify how relationships between brain regions (e.g. connectivity) change as a function of social relationships. This multilayer approach enables direct comparison of brain-behavior associations across social contexts for all brain regions and builds on both ecological and developmental neuroscientific findings and network neuroscientific approaches. In particular, we find that subcortical and control systems are especially sensitive to different constructs of perceived social support. Network nodes in these systems are highly flexible; their community affiliations, which reflect groups of nodes with similar patterns of brain-behavior associations, differ across social support measures. Additionally, our application of multilayer modeling to patterns of brain-behavior correlations, as opposed to just functional connectivity, represents an innovation in how multilayer models are used in human neuroscience. More than that, it offers a generalizable technique for studying the stability and variation of brain-behavior associations.},
}

@article {pmid40801436,
year = {2025},
author = {Karaman, MZ and Yetiman, AE and Zhan, J and Fidan, O},
title = {Biochemical Characterization and Genome Analysis of Pseudomonas loganensis sp. nov., a Novel Endophytic Bacterium.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70051},
pmid = {40801436},
issn = {2045-8827},
support = {//This study was financially supported by The Scientific and Technological Research Council of Turkiye (TUBITAK) (Grant No: 221Z280)./ ; },
mesh = {*Pseudomonas/genetics/classification/isolation & purification/drug effects/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics/chemistry ; *Endophytes/genetics/classification/isolation & purification ; Multigene Family ; Microbial Sensitivity Tests ; Carotenoids/metabolism ; Sequence Analysis, DNA ; Computational Biology ; },
abstract = {Pseudomonas species are highly adaptable, thriving in diverse environments and exhibiting remarkable genetic and metabolic diversity. While some strains are pathogenic, others have significant ecological and industrial applications. Bioinformatics and biochemical analyses, including antibiotic sensitivity testing, revealed that Pseudomonas loganensis sp. nov. can tolerate NaCl concentrations up to 5% and pH ranges between 5 and 9. Antibiogram results corroborated genome data, demonstrating resistance to vancomycin, ampicillin, methicillin, oxacillin, and penicillin G. Phylogenetic analysis based on 16S rRNA, rpoB, rpoD, and gyrB genes, combined with average nucleotide identity (ANI) comparisons, confirmed P. loganensis sp. nov. as a novel species within the Pseudomonas genus. Genome analysis further revealed the presence of turnerbactin and carotenoid gene clusters. Turnerbactin, known to contribute to nitrogen fixation in plants, highlights the strain's potential as a biofertilizer. Additionally, the carotenoid gene cluster suggests potential applications in industrial carotenoid production. The discovery of a trehalose synthase (treS) gene indicates the capability for one-step conversion of maltose into trehalose, underscoring its potential utility in trehalose production.},
}

*Pseudomonas/genetics/classification/isolation & purification/drug effects/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
*Genome, Bacterial
Anti-Bacterial Agents/pharmacology
DNA, Bacterial/genetics/chemistry
*Endophytes/genetics/classification/isolation & purification
Multigene Family
Microbial Sensitivity Tests
Carotenoids/metabolism
Sequence Analysis, DNA
Computational Biology

@article {pmid40803399,
year = {2025},
author = {Jin, L and Lu, Y and Huang, J and Liu, J and Wei, X and Ma, G and Yu, H},
title = {Metabolism exploration of disinfection byproducts halonitromethanes (HNMs) by cytochrome P450 enzymes and toxicity evaluation.},
journal = {Environmental research},
volume = {285},
number = {Pt 4},
pages = {122575},
doi = {10.1016/j.envres.2025.122575},
pmid = {40803399},
issn = {1096-0953},
mesh = {*Cytochrome P-450 Enzyme System/metabolism ; *Disinfectants/toxicity/metabolism ; Animals ; Humans ; Rats ; *Nitroparaffins/toxicity/metabolism ; Disinfection ; Microsomes, Liver/metabolism ; },
abstract = {The nitrogen-contained disinfection by-products, halonitromethanes (HNMs), are known for their high cytotoxicity and genotoxicity. Although HNMs can be metabolized by cytochrome P450 enzymes (P450s), the specific mechanism has remained unclear. To shed light on this, density functional theory (DFT) calculations were performed to elucidate the potential oxidative P450-catalytic activation of the nine HNMs. Our findings reveal that active species of P450s (Cpd I) predominantly react with halogen-substituted nitromethanes via hydrogen abstraction and bromine atom abstraction, rather than chlorosylation. As a result of these reactions, oxidized HNMs are produced and can undergo further hydrolysis, leading to nitro-formaldehyde, nitro formyl halogen, halogen hydride, hypobromous acid, and nitroformic acid. To experimentally validate the computational predictions, in vitro experiments were conducted on five typical nitromethanes using human liver microsomes and the results reveal that DCNM, BCNM and DBCNM form nitroformyl chlorine (NO2CClO), while BCNM, DBNM and TBNM are transferred into nitroformyl bromide (NO2CBrO). Nitroformic acid is also identified as a metabolite in the TBNM metabolism reaction. Toxicity assessment reveals that metabolic transformation leads to an overall reduction in the ecological toxicity. However, metabolites showed similar toxicity to Fathead minnow and even higher acute toxicity to rat, as well as larger probability of hERG inhibition effects than HNMs, underscoring the need for caution in health risk assessment. By integrating in silico and in vitro approaches, this work has provided a comprehensive understanding of the metabolism of HNMs and offered potential toxicity data basis of these compounds.},
}

*Cytochrome P-450 Enzyme System/metabolism
*Disinfectants/toxicity/metabolism
Animals
Humans
Rats
*Nitroparaffins/toxicity/metabolism
Disinfection
Microsomes, Liver/metabolism

@article {pmid40805736,
year = {2025},
author = {Lu, F and Yi, B and Ma, JX and Wang, SN and Feng, YJ and Qin, K and Tu, Q and Bu, ZJ},
title = {Drought and Shrub Encroachment Accelerate Peatland Carbon Loss Under Climate Warming.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40805736},
issn = {2223-7747},
support = {U23A2003//The National Nature Science Foundation of China/ ; 42407354//The National Nature Science Foundation of China/ ; 42371050//The National Nature Science Foundation of China/ ; 20230203002SF and 20210402032GH//Jilin Provincial Science and Technology Development Project/ ; 2024QN1081//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Peatlands store substantial amounts of carbon (C) in the form of peat, but are increasingly threatened by drought and shrub encroachment under climate warming. However, how peat decomposition and its temperature sensitivity (Q10) vary with depth and plant litter input under these stressors remains poorly understood. We incubated peat from two depths with different degrees of decomposition, either alone or incubated with Sphagnum divinum shoots or Betula ovalifolia leaves, under five temperature levels and two moisture conditions in growth chambers. We found that drought and Betula addition increased CO2 emissions in both peat layers, while Sphagnum affected only shallow peat. Deep peat alone or with Betula exhibited higher Q10 than pure shallow peat. Drought increased the Q10 of both depths' peat, but this effect disappeared with fresh litter addition. The CO2 production rate showed a positive but marginal correlation with microbial biomass carbon, and it displayed a rather similar responsive trend to warming as the microbial metabolism quotient. These results indicate that both deep and dry peat are more sensitive to warming, highlighting the importance of keeping deep peat buried and waterlogged to conserve existing carbon storage. Additionally, they further emphasize the necessity of Sphagnum moss recovery following vascular plant encroachment in restoring carbon sink function in peatlands.},
}

@article {pmid40807726,
year = {2025},
author = {Ye, G and Yu, R},
title = {Spatiotemporal Mapping of Grazing Livestock Behaviours Using Machine Learning Algorithms.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {15},
pages = {},
pmid = {40807726},
issn = {1424-8220},
support = {Project No. 72104065//National Natural Science Foundation of China/ ; Project No. NHXXRCXM202303//Hainan New Star Projects/ ; Project No. KC20230018//Natural Resources Comprehensive Survey Command Centre Science and Technology Innovation Fund/ ; Project No. 2022KJCX04//Sanya Science and Technology Special Fund/ ; },
mesh = {Animals ; *Machine Learning ; *Livestock/physiology ; China ; Grassland ; Spatio-Temporal Analysis ; Algorithms ; Geographic Information Systems ; *Behavior, Animal/physiology ; *Herbivory/physiology ; Ecosystem ; },
abstract = {Grassland ecosystems are fundamentally shaped by the complex behaviours of livestock. While most previous studies have monitored grassland health using vegetation indices, such as NDVI and LAI, fewer have investigated livestock behaviours as direct drivers of grassland degradation. In particular, the spatial clustering and temporal concentration patterns of livestock behaviours are critical yet underexplored factors that significantly influence grassland ecosystems. This study investigated the spatiotemporal patterns of livestock behaviours under different grazing management systems and grazing-intensity gradients (GIGs) in Wenchang, China, using high-resolution GPS tracking data and machine learning classification. the K-Nearest Neighbours (KNN) model combined with SMOTE-ENN resampling achieved the highest accuracy, with F1-scores of 0.960 and 0.956 for continuous and rotational grazing datasets. The results showed that the continuous grazing system failed to mitigate grazing pressure when grazing intensity was reduced, as the spatial clustering of livestock behaviours did not decrease accordingly, and the frequency of temporal peaks in grazing behaviour even showed an increasing trend. Conversely, the rotational grazing system responded more effectively, as reduced GIGs led to more evenly distributed temporal activity patterns and lower spatial clustering. These findings highlight the importance of incorporating livestock behavioural patterns into grassland monitoring and offer data-driven insights for sustainable grazing management.},
}

Animals
*Machine Learning
*Livestock/physiology
China
Grassland
Spatio-Temporal Analysis
Algorithms
Geographic Information Systems
*Behavior, Animal/physiology
*Herbivory/physiology
Ecosystem

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

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

@article {pmid40808315,
year = {2025},
author = {Navratilova, HF and Whetton, AD and Geifman, N},
title = {Integrating Food Preference Profiling, Behavior Change Strategies, and Machine Learning for Cardiovascular Disease Prevention in a Personalized Nutrition Digital Health Intervention: Conceptual Pipeline Development and Proof-of-Principle Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e75106},
pmid = {40808315},
issn = {1438-8871},
mesh = {Humans ; *Cardiovascular Diseases/prevention & control ; *Machine Learning ; *Food Preferences ; Female ; Male ; *Precision Medicine ; Middle Aged ; United Kingdom ; Digital Health ; },
abstract = {BACKGROUND: Personalized dietary advice needs to consider the individual's health risks as well as specific food preferences, offering healthier options aligned with personal tastes.

OBJECTIVE: This study aimed to develop a digital health intervention (DHI) that provides personalized nutrition recommendations based on individual food preference profiles (FPP), using data from the UK Biobank.

METHODS: Data from 61,229 UK Biobank participants were used to develop a conceptual pipeline for a DHIs. The pipeline included three steps: (1) developing a simplified food preference profiling tool, (2) creating a cardiovascular disease (CVD) prediction model using the subsequent profiles, and (3) selecting intervention features. The CVD prediction model was created using 3 different predictor sets (Framingham set, diet set, and FPP set) across 4 machine learning models: logistic regression, linear discriminant analysis, random forest, and support vector machine. Intervention functions were designed using the Behavior Change Wheel, and behavior change techniques were selected for the DHI features.

RESULTS: The feature selection process identified 14 food items out of 140 that effectively classify FPPs. The food preference profile prediction set, which did not include blood measurements or detailed nutrient intake, demonstrated comparable accuracy (across the 4 models: 0.721-0.725) to the Framingham set (0.724-0.727) and diet set (0.722-0.725). Linear discriminant analysis was chosen as the best-performing model. Four key features of the DHI were identified: food source and portion information, recipes, a dietary recommendation system, and community exchange platforms. The FPP and CVD risk prediction model serve as inputs for the dietary recommendation system. Two levels of personalized nutrition advice were proposed: level 1-based on food portion intake and FPP; and level 2-based on nutrient intake, FPP, and CVD risk probability.

CONCLUSIONS: This study presents proof of principle for a conceptual pipeline for a DHI that empowers users to make informed dietary choices and reduce CVD risk by catering to person-specific needs and preferences. By making healthy eating more accessible and sustainable, the DHI has the potential to significantly impact public health outcomes.},
}

Humans
*Cardiovascular Diseases/prevention & control
*Machine Learning
*Food Preferences
Female
Male
*Precision Medicine
Middle Aged
United Kingdom
Digital Health

@article {pmid40811794,
year = {2025},
author = {Shen, S and Qi, W and Zeng, J and Li, S and Liu, X and Zhu, X and Dong, C and Wang, B and Shi, Y and Yao, J and Wang, B and Lou, X and Gu, S and Li, P and Wang, J and Jiang, G and Cao, S},
title = {Passive Sensing for Mental Health Monitoring Using Machine Learning With Wearables and Smartphones: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e77066},
pmid = {40811794},
issn = {1438-8871},
mesh = {*Wearable Electronic Devices ; Humans ; *Machine Learning ; *Smartphone ; *Mental Health ; *Mental Disorders/diagnosis ; Monitoring, Physiologic ; },
abstract = {BACKGROUND: Mental health issues have become a significant global public health challenge. Traditional assessments rely on subjective methods with limited ecological validity. Passive sensing via wearable devices and smartphones, combined with machine learning (ML), enables objective, continuous, and noninvasive mental health monitoring.

OBJECTIVE: This study aimed to provide a comprehensive review of the current state of passive sensing-based and ML technologies for mental health monitoring. We summarized the technical approaches, revealed the association patterns between behavioral features and mental disorders, and explored potential directions for future advancements.

METHODS: This scoping review adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines and was prospectively registered on the Open Science Framework. We systematically searched 7 databases (Web of Science, PubMed, IEEE Xplore, Embase, PsycINFO, Scopus, and ACM Digital Library) for studies published between January 2015 and February 2025. We included 42 peer-reviewed studies that used passive sensing from wearables or smartphones with ML to monitor clinically diagnosed mental disorders, such as depression and anxiety. Data were synthesized across technical dimensions (data collection, preprocessing, feature engineering, and ML models) and clinical associations, with behavioral features categorized into 8 domains.

RESULTS: The 42 included studies were predominantly cohort designs (23/42, 55%), with a median sample size of 60.5 (IQR 54-99). Most studies focused on depression (23/42, 55%) and anxiety (9/42, 21%) using primarily wrist-worn devices (32/42, 76%) collecting heart rate (28/42, 67%), movement index (25/42, 60%), and step count (17/42, 40%) as key biomarkers. Deep learning models (eg, convolutional neural networks and long short-term memory) showed high accuracy, while traditional ML (eg, random forest) remained prevalent due to better interpretability. We identified critical limitations, including small samples (32/42, 76% with N<100), short monitoring periods (19/42, 45% <7 days), scarce external validation (1/42, 2%), and limited reporting on data anonymization (6/42, 14%).

CONCLUSIONS: While passive sensing and ML demonstrate promising accuracy (eg, convolutional neural network-long short-term memory achieving 92.16% in anxiety detection), the evidence remains constrained by three key limitations: (1) methodological heterogeneity (32/42, 76% single-device studies; 19/42, 45% with <7-day monitoring), (2) high risk of bias from small samples (median 60.5, IQR 54-99 participants) and scarce external validation (1/42, 2%), and (3) ethical gaps (only 6/42, 14% addressing anonymization). These findings underscore the technology's potential to transform mental health care through objective, continuous monitoring-particularly for depression (heart rate and step count biomarkers) and anxiety (sleep and social interaction patterns). However, clinical translation requires standardized protocols, larger longitudinal studies (≥3 months), and ethical frameworks for data privacy. Future work should prioritize multimodal sensor fusion and explainable artificial intelligence to bridge the gap between technical performance and clinical deployability.},
}

*Wearable Electronic Devices
Humans
*Machine Learning
*Smartphone
*Mental Health
*Mental Disorders/diagnosis
Monitoring, Physiologic

@article {pmid40812171,
year = {2025},
author = {Lundberg, DS and Bergelson, J and Roux, F and Weigel, D and Karasov, TL},
title = {Lab to field: Challenges and opportunities for plant biology.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1212-1216},
doi = {10.1016/j.chom.2025.05.027},
pmid = {40812171},
issn = {1934-6069},
mesh = {*Plants/microbiology ; Plant Diseases/microbiology ; *Plant Physiological Phenomena ; },
abstract = {Plant-microbe research offers many choices of model and strain and whether a field-first or lab-first approach is best. However, differences between laboratory studies, offering control and repeatability, versus field experiments, revealing ecological relevance and environmental effects, should not be seen as failure but motivate further inquiry and allow complementary discovery.},
}

*Plants/microbiology
Plant Diseases/microbiology
*Plant Physiological Phenomena

@article {pmid40814786,
year = {2026},
author = {Misono, S and Nguyen-Feng, VN and Lei, X and Feddema, E and Tella, A and Stockness, A and Frazier, PA and Kummerfeld, E and Lim, KO},
title = {Ecological Momentary Assessment of Voice & Psychological Factors: Group & Individual Mechanisms.},
journal = {The Laryngoscope},
volume = {136},
number = {1},
pages = {324-331},
pmid = {40814786},
issn = {1531-4995},
support = {K23DC016335/DC/NIDCD NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002494/TR/NCATS NIH HHS/United States ; KL2 TR000113/TR/NCATS NIH HHS/United States ; K23 DC016335/DC/NIDCD NIH HHS/United States ; KL2TR000113/TR/NCATS NIH HHS/United States ; //American College of Surgeons, Triological Society: Clinical Scientist Development Award/ ; },
mesh = {Humans ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; *Dysphonia/psychology/physiopathology ; *Voice Quality ; Cross-Sectional Studies ; Anxiety/psychology ; Stress, Psychological ; Aged ; },
abstract = {OBJECTIVES: Cross-sectional associations between voice and psychological factors are known, but changes over time offer opportunities to refine our understanding of their interactions and consider customized treatment options. Study objectives were to measure relationships between voice and psychological factors using ecological momentary assessment and applying (1) group-level time series analysis and (2) group and (3) individual causal modeling to identify key psychological factors relevant for voice outcomes.

METHODS: Adults (N = 32) with primary muscle tension dysphonia completed multiple assessments daily for 10 days. Measures included items from the Voice Handicap Index-10, voice-adapted perceived present control scale, items from NIH PROMIS and the NIH Toolkit to assess distress, and the Positive and Negative Affect Scale. Group-level time series analysis was conducted using dynamic structural equation modeling; causal analysis utilized the Greedy Fast Causal Inference algorithm.

RESULTS: In group-level time series analyses, neither perceived control nor distress predicted subsequent timepoint voice handicap scores. In group-level causal modeling, anxiety was causal for voice handicap, but perceived control was not. Individual-level analyses identified various causal factors for voice handicap including perceived control and negative affect, and to a lesser extent, serenity, anxiety, somatic arousal, and stress.

CONCLUSIONS: Group-level analyses may obscure important heterogeneity that is identifiable using individual-level causal analyses. For example, perceived control was not identified as predictive or causal for voice handicap at the group level; but was a salient causal factor for voice handicap in some individuals. Causal modeling using intensive longitudinal datasets offers a potential avenue for individualized treatment approaches.},
}

Humans
Male
Female
Adult
*Ecological Momentary Assessment
Middle Aged
*Dysphonia/psychology/physiopathology
*Voice Quality
Cross-Sectional Studies
Anxiety/psychology
Stress, Psychological
Aged

@article {pmid40816181,
year = {2025},
author = {Xu, Z and Xu, D and Ma, J and Wang, J and Yan, S and Fu, R and Cui, Y},
title = {The risk assessment for metal(loid)s in soil-slag mixing systems: Coupling sequential extraction, leaching tests, and in vitro bioaccessibility assays.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139544},
doi = {10.1016/j.jhazmat.2025.139544},
pmid = {40816181},
issn = {1873-3336},
mesh = {Risk Assessment ; *Soil Pollutants/analysis/toxicity ; *Metalloids/analysis/toxicity ; Biological Availability ; Humans ; *Industrial Waste/analysis ; Soil/chemistry ; *Metals, Heavy/analysis ; *Metals/analysis ; Arsenic ; Metallurgy ; },
abstract = {The metals and metalloids (metal[loid]s) in the newly formed soil-slag mixing systems (SSMS), formed by the invasion of smelting slag into contaminated soils, may pose potential risks to environment and residents near the smelter sites. In this study, sequential extraction, leaching tests and in vitro bioaccessibility assays were conducted to assess the ecological and human health risk of metal(loid)s in SSMS. The results indicated that the contaminated soils and smelting slags were composed of more than 80 % silicate and oxide minerals, which served as the host phases for metal(loid)s in SSMS. Cd exhibited high mobility and availability, with its exchangeable fraction ranging from 0.15 % to 69.23 %. Leaching tests revealed high leachability and bioavailability of Cd, Mn and Zn. Moreover, metal(loid)s bioaccessibility varied amongst samples: 2.78-46.63 % of As, 11.87-95.25 % of Cd, 37.35-93.88 % of Mn, 1.97-87.84 % of Pb and 0-57.98 % of Zn. Risk assessment calculation results indicated potentially ecological risks posed by Cd, Mn, Pb, and Zn, and unfavorable carcinogenic risks associated with As and Cd, suggesting that remediation efforts were warranted. Overall, this study highlighted how the invasion of smelting slags can affect the accuracy of risk assessments, providing new guidance for risk control and environmental management at slag dumping sites.},
}

Risk Assessment
*Soil Pollutants/analysis/toxicity
*Metalloids/analysis/toxicity
Biological Availability
Humans
*Industrial Waste/analysis
Soil/chemistry
*Metals, Heavy/analysis
*Metals/analysis
Arsenic
Metallurgy

@article {pmid40817347,
year = {2025},
author = {Rajpal, H and Stengel, CV and Mediano, PAM and Rosas, FE and Viegas, E and Marquet, PA and Jensen, HJ},
title = {Information dynamics and the emergence of high-order individuality in ecosystems.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1231},
pmid = {40817347},
issn = {2399-3642},
support = {EP/W024020/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/X03870X/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/W007142/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; ES/T005319/2//RCUK | Economic and Social Research Council (ESRC)/ ; },
mesh = {*Ecosystem ; *Biological Evolution ; *Selection, Genetic ; Mutation ; Population Dynamics ; *Information Theory ; },
abstract = {At what level does natural selection occur? When considering the reproductive dynamics of interacting and mutating agents, it has long been debated whether selection is better understood by focusing on the individual or if hierarchical selection emerges as a consequence of joint adaptation. Despite longstanding efforts in theoretical ecology, there is still no consensus on this fundamental issue, most likely due to the difficulty in obtaining adequate data spanning a sufficient number of generations and the lack of adequate tools to quantify the effect of hierarchical selection. Here, we capitalise on recent advances in information-theoretic data analysis to advance this state of affairs by investigating the emergence of high-order structures- such as groups of species- in the collective dynamics of the Tangled Nature model of evolutionary ecology. Our results show that evolutionary dynamics can lead to clusters of species that act as a self-perpetuating group that exhibits greater information-theoretic agency than a single species for a broad range of stable mutation rates. However, this higher-order organization breaks down for mutation rates close to the error threshold, where increased information processing is observed at the level of a single species. For mutation rates higher than the error threshold, no stable population of species are observed in time, and all individuality is lost in the ecosystem. Overall, our findings provide quantitative evidence supporting the emergence of higher-order structures in evolutionary ecology from relatively simple processes of adaptation and reproduction.},
}

*Ecosystem
*Biological Evolution
*Selection, Genetic
Mutation
Population Dynamics
*Information Theory

@article {pmid40818234,
year = {2025},
author = {Poudel, B and Xie, J and Guo, C and Watt, OE and Pulster, EL and Patel, RJ and Steevens, JA and Xu, D},
title = {Real-time oil spill concentration assessment through fluorescence imaging and deep learning.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139374},
doi = {10.1016/j.jhazmat.2025.139374},
pmid = {40818234},
issn = {1873-3336},
abstract = {Oil spills may pose severe ecological and socioeconomic threats, necessitating rapid and accurate environmental assessment. Traditional assessment methods used to determine the extent of a spill including gas chromatography-mass spectrometry, satellite imaging, and visual surveys, are often time-consuming, expensive, and limited by weather conditions or sampling constraints. Furthermore, these methods frequently struggle to provide real-time data crucial for prompt decision-making during spill emergencies. This study addresses these limitations by combining fluorescence imaging, deep learning, a mobile application, and a data management system for automated and real-time oil spill assessment. Our approach leverages a convolutional neural network architecture for feature extraction coupled with a custom regression model, trained and evaluated on a self-curated comprehensive dataset of 1530 fluorescence images from two distinct oil types, a napthalenic crude oil and an aromatic-napthalenic crude oil, at concentrations ranging from 0 to 500 mg/L. The proposed approach demonstrates superior performance compared to both traditional machine learning models and more complex deep learning architectures, achieving an R[2] score of 0.9958 and RMSE of 9.28. The application enables rapid, cost-effective field measurements with robust data tracking and analysis capabilities. This research advances oil spill monitoring technology with a scalable solution that balances accuracy, speed, and accessibility for real-time environmental assessment and emergency response.},
}

@article {pmid40819189,
year = {2025},
author = {Alhashmi, AA and Elhessewi, GMS and Ghaleb, M and Ahmad, N and Aljehane, NO and Alkhaldi, TM and Almansour, H and Al Zanin, S},
title = {Enhancing medical response efficiency in real-time large crowd environments via smart coverage and deep learning for stable ecological health monitoring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30000},
pmid = {40819189},
issn = {2045-2322},
mesh = {*Deep Learning ; Humans ; Geographic Information Systems ; *Crowding ; Algorithms ; },
abstract = {Festivals and city-wide mass events are prevalent in human societies worldwide, drawing large crowds. Such events range from concerts with a dozen attendees to large-scale actions with thousands of viewers. It is the highest priority for each organizer of such an occasion to be capable of upholding a higher standard of safety and minimizing the danger of events, especially medical emergencies. Therefore, establishing sufficient safety measures is significant. There is a requirement for event organizers and emergency response personnel to identify developing, potentially critical crowd situations at an early stage during city-wide mass assemblies. In general, the localization of the global positioning system (GPS) and proximity-based tracking is employed to capture intricate crowd dynamics throughout an event. Recently, technology has been used in numerous diverse ways to achieve these large crowds. For example, computer vision-based models are employed to observe the flexibility and behaviour of crowds. In this manuscript, a model for Medical Response Efficiency in Real-Time Large Crowd Environments via Smart Coverage and Hiking Optimisation (MRELC-SCHO) is presented, aiming to maintain stable ecological health. The primary objective of this paper is to propose an effective method for enhancing medical response efficiency in large crowd environments by utilizing advanced optimization algorithms. Initially, the MRELC-SCHO model utilizes min-max normalization to transform the input data into a structured format. Furthermore, the Chimp Optimisation Algorithm (CHOA) model is employed for the feature selection (FS) process to select the most significant features from the dataset. Additionally, the MRELC-SCHO technique utilizes the bidirectional long short-term memory with an auto-encoder (BiLSTM-AE) method for classification. Finally, the parameter selection for the BiLSTM-AE model is performed by using the Hiking Optimisation Algorithm (HOA) model. The experimentation of the MRELC-SCHO approach is accomplished under the Ecological Health dataset. The comparison analysis of the MRELC-SCHO approach revealed a superior accuracy value of 98.56% compared to existing models.},
}

*Deep Learning
Humans
Geographic Information Systems
*Crowding
Algorithms

@article {pmid40820130,
year = {2025},
author = {Sehi, GT and Birhanie, SK and Hans, J and Brown, MQ and Parker, DM},
title = {Environmental correlates of Aedes aegypti abundance in the West Valley region of San Bernardino County, California, USA, from 2017 to 2023: an ecological modeling study.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {349},
pmid = {40820130},
issn = {1756-3305},
support = {U01 CK000649/CK/NCEZID CDC HHS/United States ; U01CK000649/ACL/ACL HHS/United States ; },
mesh = {Animals ; *Aedes/physiology/virology ; California/epidemiology ; *Mosquito Vectors/physiology/virology ; Geographic Information Systems ; Temperature ; *Environment ; Ecosystem ; Dengue/transmission ; Mosquito Control ; Humans ; },
abstract = {BACKGROUND: Aedes mosquitoes, particularly Aedes aegypti and Ae. albopictus, are major vectors of globally significant diseases such as dengue, Zika, and chikungunya. Since 2013, Ae. aegypti populations have rapidly expanded in California, making control efforts difficult due to their widespread, small-scale breeding sites and strong adaptation to urban environments.

METHODS: Remote sensing technologies, coupled with Geographic Information Systems (GIS), offer innovative solutions for mosquito surveillance and control. However, understanding the environmental drivers of mosquito abundance, particularly in California's diverse ecological settings, remains an important gap. To address this gap, we analyzed Ae. aegypti abundance (2017 to 2023) in relation to environmental variables, such as temperature, precipitation, surface water, elevation, and built environment. We applied hotspot analysis to identify spatial clusters of high mosquito abundance and used a generalized additive model (GAM) with a negative binomial distribution to assess environmental and meteorological influences on mosquito counts.

RESULTS: Hotspot analyses revealed clusters of Ae. aegypti hotspots near residential areas. Aedes aegypti counts increased with higher surface water availability and temperature.

CONCLUSIONS: Our study characterizes the spatial and temporal dynamics of Ae. aegypti mosquito abundance in the West Valley region of San Bernardino County from 2017 to 2023, shedding light on the influence of environmental factors and human activities on temporal trends. Our findings emphasize the critical role of temperature and water availability in shaping mosquito population dynamics, highlighting the need for proactive vector control strategies in response to environmental changes.},
}

Animals
*Aedes/physiology/virology
California/epidemiology
*Mosquito Vectors/physiology/virology
Geographic Information Systems
Temperature
*Environment
Ecosystem
Dengue/transmission
Mosquito Control
Humans

@article {pmid40820776,
year = {2025},
author = {Stansberry, TT and Myers, CR and Tran, L and Roberson, PNE and Ahn, S},
title = {Impacts of Access to Hospital and Emergency Care on Rural Mortality in Tennessee, 2010-2019: A GIS-Informed Study.},
journal = {Journal of health care for the poor and underserved},
volume = {36},
number = {3},
pages = {787-814},
doi = {10.1353/hpu.2025.a967333},
pmid = {40820776},
issn = {1548-6869},
mesh = {Humans ; Tennessee/epidemiology ; *Health Services Accessibility/statistics & numerical data ; Retrospective Studies ; *Rural Population/statistics & numerical data ; Cross-Sectional Studies ; Middle Aged ; Geographic Information Systems ; Female ; Male ; COVID-19/epidemiology ; Adult ; Aged ; *Mortality/trends ; *Emergency Medical Services/statistics & numerical data ; },
abstract = {Rural Tennessee's health and economic disparities have worsened since 2010 (while the state led the nation in hospital closures per capita). Guided by the Vulnerable Populations Conceptual Model, we examined the relationship between Tennessee's county-level rural mortality rates and declining access to hospital and emergency care in the decade preceding the COVID-19 pandemic (avoiding pandemic-related delayed data releases and potential statistical modeling issues). We conducted a retrospective, ecological correlational study using geographic information systems and annual cross-sectional secondary data, employing aspatial and spatial negative binomial generalized linear mixed-effects models (GLMMs). Our bivariate models revealed significant correlations between hospital and emergency care access and mortality rates, but the effect decreased when adjusted for rurality, median household income, age, and other covariates. While access to hospital and emergency care influences mortality, our findings indicate that socioeconomic and demographic factors have a greater impact, underscoring the strong health-wealth connection in rural Tennessee.},
}

Humans
Tennessee/epidemiology
*Health Services Accessibility/statistics & numerical data
Retrospective Studies
*Rural Population/statistics & numerical data
Cross-Sectional Studies
Middle Aged
Geographic Information Systems
Female
Male
COVID-19/epidemiology
Adult
Aged
*Mortality/trends
*Emergency Medical Services/statistics & numerical data

@article {pmid40821442,
year = {2025},
author = {Motlagh, SH and Momtazi, F and Saeedi, H},
title = {Senckenberg dogger bank long-term monitoring: First dataset on amphipods.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {111931},
pmid = {40821442},
issn = {2352-3409},
abstract = {This dataset includes unique occurrence records of amphipod specimens collected during the 2024 annual Senckenberg Long-Term Monitoring Project in Dogger Bank (a shallow sand bank in the central North Sea), Cruise DOG24. This cruise was part of an ongoing effort to monitor biodiversity, which has occurred annually from 1991 to 2024 by the Marine Zoology Department at the Senckenberg Research Institute and Natural History Museum. Amphipods, key components of marine benthic ecosystems, were sampled by beam trawl over the Dogger Bank's stable sandy substrate. A total of 8444 specimens of ten species belonging to 13 families and 14 genera were identified using morphological methods with Leica M60 and DM750 microscopes. This study presents the first species-level identification of benthic amphipods in the Dagger Bank, providing a taxonomically resolved dataset that serves as a reliable identification key for future monitoring efforts in the area. Data were structured and published to the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF) following the Darwin Core (DwC) standard. This dataset is the first-hand data ever published open-access from the Senckenberg Long Term Monitoring Project since 1991. This dataset also supports a broader research project aimed at (i) revealing the distribution pattern of amphipods in the North Sea, (ii) identifying environmental drivers of species distribution and diversity, and (iii) evaluating the response of the amphipod community to ecosystem changes.},
}

@article {pmid40822726,
year = {2025},
author = {Piršelová, B and Jakubčinová, J},
title = {Plant cyanogenic glycosides: from structure to properties and potential applications.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1612132},
pmid = {40822726},
issn = {1664-462X},
abstract = {Cyanogenic glycosides (CGs) represent an important group of secondary metabolites predominantly of plant origin, characterized by their ability to release hydrogen cyanide upon enzymatic hydrolysis. These compounds are widely distributed across the plant kingdom, where they play a crucial role in defense against herbivores and pathogens. In recent years, advanced analytical tools have greatly expanded our knowledge of CGs by enabling the identification of less abundant forms. Based on the latest data from published scientific studies, this review presents a comprehensive overview of CGs, with a focus on their structural variability, biosynthetic pathways, ecological functions, and inherent toxicity. Special attention is given to the quantity and distribution of significant CGs in plants, as the available data is often heterogeneous, fragmented, and dispersed across the literature. Furthermore, the review explores emerging evidence regarding the biomedical relevance of selected CGs, including their putative anticancer properties and broader therapeutic potential. The findings presented in this review may be applied in fields such as pharmacology, toxicology, food safety, and plant biotechnology - either to enhance CG content for crop protection or, conversely, to eliminate such content in order to improve food safety.},
}

@article {pmid40824055,
year = {2025},
author = {Grigson, SR and Bouras, G and Dutilh, BE and Olson, RD and Edwards, RA},
title = {Computational function prediction of bacteria and phage proteins.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {3},
pages = {e0002225},
pmid = {40824055},
issn = {1098-5557},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; DP250103825//Australian Research Council/ ; 865694/ERC_/European Research Council/International ; RC2DK116713/DK/NIDDK NIH HHS/United States ; 390713860//Deutsche Forschungsgemeinschaft/ ; DP220102915//Australian Research Council/ ; FL250100019//Australian Research Council/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Computational Biology/methods ; *Viral Proteins/genetics/metabolism/chemistry ; *Bacteria/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; Machine Learning ; Molecular Sequence Annotation/methods ; },
abstract = {SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial and ~65% of all bacteriophage (phage) protein sequences cannot be confidently annotated. In this review, we examine state-of-the-art bioinformatics tools and methodologies for annotating bacterial and phage proteins, particularly those of unknown or poorly characterized function. We describe the process of identifying protein-coding regions and the systems to classify protein functionalities. Additionally, we explore a range of protein annotation methods, from traditional homology-based methods to cutting-edge machine learning models. In doing so, we provide a toolbox for confidently annotating previously unknown bacterial and phage proteins, advancing the discovery of novel functions and our understanding of microbial systems.},
}

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

@article {pmid40825407,
year = {2025},
author = {Tarandek, A and Boštjančić, LL and Francesconi, C and Bonassin, L and Schardt, L and Jussila, J and Kokko, H and Schwenk, K and Hudina, S and Lecompte, O and Theissinger, K},
title = {Characterisation of the noble crayfish immune response to oomycete-derived immunostimulants.},
journal = {Fish & shellfish immunology},
volume = {166},
number = {},
pages = {110666},
doi = {10.1016/j.fsi.2025.110666},
pmid = {40825407},
issn = {1095-9947},
mesh = {Animals ; *Astacoidea/immunology/genetics/microbiology ; *Aphanomyces/chemistry/physiology/immunology ; *Adjuvants, Immunologic/pharmacology ; *Glucans/pharmacology ; *Immunity, Innate ; Hemocytes/immunology ; },
abstract = {The invasive oomycete pathogen Aphanomyces astaci significantly threatens native European crayfish populations, prompting investigations towards the effects of protective immunostimulation on the immune response of the vulnerable noble crayfish (Astacus astacus). Here, we evaluate the effect of three oomycete-derived immunostimulant treatments: laminarin (β-1,3-glucan found within the Ap. astaci cell wall), inactivated Ap. astaci spores and Ap. astaci hyphal homogenate. Our findings reveal immediate changes in the noble crayfish total haemocyte count (THC), differential haemocyte count (DHC), and gene expression. A short-term increase in the THC was observed in all treatments, with a gradual return to normal values 8 h post immunostimulation. Granular haemocytes seem to be involved in response to immunostimulation with inactivated Ap. astaci spores, while the number of semi-granular and hyaline haemocytes increased in response to laminarin and Ap. astaci hyphal homogenate. Analysis of the differentially expressed genes showed that the Prophenoloxidase pathway genes and Toll pathway genes are involved in the response to oomycete-derived immunostimulants. Prolonged effects of immunostimulation were reflected in the decreased C/EBP and Kr-h1 gene expression in the hyphal homogenate group as well as decreased Kr-h1 expression in the spore group. Taken together, our results indicate that immunostimulation causes a dynamic change in the noble crayfish immune system response, with similarities in the gene expression patterns between immunostimulated and Ap. astaci infected noble crayfish. As a future research focus, we highlight the importance of molecular characterisation of the genes involved in the anti-oomycete response which could provide valuable insights into pathogen resistance in freshwater crayfish. In the context of the Ap. astaci mediated downfall of the noble crayfish stocks across Europe, further exploration is needed regarding the benefits of the oomycete-derived immunostimulation that can potentially support conservation and aquacultural efforts.},
}

Animals
*Astacoidea/immunology/genetics/microbiology
*Aphanomyces/chemistry/physiology/immunology
*Adjuvants, Immunologic/pharmacology
*Glucans/pharmacology
*Immunity, Innate
Hemocytes/immunology

@article {pmid40826054,
year = {2025},
author = {Quintanilha, D and Moura, E and Xavier, D},
title = {Hospitalisations in Brazil: an ecological time series analysis of the impact of medical decision support data as an exogenous variable.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {2827},
pmid = {40826054},
issn = {1471-2458},
mesh = {Brazil/epidemiology ; Humans ; *Hospitalization/statistics & numerical data ; *Decision Support Systems, Clinical/statistics & numerical data ; *Public Health Surveillance/methods ; },
abstract = {PURPOSE: Public health surveillance depends on continuous monitoring to guide interventions and allocate resources effectively. This study aimed to evaluate whether structured medical search data from the Afya Whitebook®, a clinical decision-support platform, can serve as exogenous variables to enhance the explanatory capacity of time series models characterising hospitalisation patterns within Brazil's public health system.

METHODS: An ecological time series analysis was conducted using hospitalisation data (SIH/SUS) and Afya Whitebook® search volumes from 2021 to 2024. SARIMAX models assessed temporal associations between search activity and hospital admissions across Brazilian states, compared to univariate SARIMA models to evaluate the added value of search data.

RESULTS: In 278 of the 478 time series, SARIMAX models provided a better fit than univariate SARIMA models, particularly for conditions such as chronic obstructive pulmonary disease, dengue, urinary tract infections, type 2 diabetes, asthma, depression, and chronic kidney disease. Model fit varied by disease and region, underscoring the influence of contextual factors in the association between search behaviour and hospital admissions.

CONCLUSION: This study demonstrates that structured medical search data can serve as exogenous variables to improve the explanatory capacity of time series models of hospitalisation patterns. Despite variation between diseases and regions, this approach shows promise in supporting public health surveillance and could be strengthened by incorporating contextual data in future studies.},
}

Brazil/epidemiology
Humans
*Hospitalization/statistics & numerical data
*Decision Support Systems, Clinical/statistics & numerical data
*Public Health Surveillance/methods

@article {pmid40827702,
year = {2025},
author = {Chung, J and Moloney, ME and Seixas, AA and Jackson, CL},
title = {The environment around the sleeper is changing: a perspective.},
journal = {Sleep},
volume = {48},
number = {11},
pages = {},
pmid = {40827702},
issn = {1550-9109},
support = {5R01HL152453-05/GF/NIH HHS/United States ; },
mesh = {Humans ; *Sleep/physiology ; Weather ; *Environmental Exposure/adverse effects ; *Environment ; Circadian Rhythm/physiology ; Temperature ; },
abstract = {Sleep is shaped by a complex interplay of biological, behavioral, and environmental factors. While substantial attention has been paid to the first two factors, the role of environmental exposures, particularly weather patterns, ambient temperature variability, and other dynamic atmospheric conditions, remains relatively underexplored in sleep research. This gap is notable given the increasing availability of high-resolution environmental data and growing evidence that ambient conditions can influence circadian regulation, thermal comfort, and sleep continuity. This perspective paper reviews emerging evidence linking environmental factors to sleep patterns, highlighting both direct effects (e.g. thermal disruptions) and indirect pathways (e.g., displacement or stress from extreme weather events). Recent advances in environmental sensing, geospatial data, and real-time monitoring offer new opportunities to capture high-resolution environmental data relevant to sleep. This perspective highlights the need for data infrastructure capable of integrating these dynamic environmental inputs with sleep metrics from, for instance, wearables, surveys, and clinical records. We also examine the methodological and informatics challenges of integrating environmental data with sleep measures and suggest directions for future research. As environmental conditions evolve, understanding their influence on sleep holds promise for advancing both scientific knowledge and public health relevance, particularly in identifying affected populations, designing responsive interventions, and contextualizing sleep within broader ecological systems.},
}

Humans
*Sleep/physiology
Weather
*Environmental Exposure/adverse effects
*Environment
Circadian Rhythm/physiology
Temperature

@article {pmid40828274,
year = {2025},
author = {Ramos-Onsins, SE and Guirao-Rico, S and Hafez, A and Ferretti, L},
title = {npstat: An Efficient Tool to Explore the Population Genome Variability and Divergence Using Pool Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {51-66},
pmid = {40828274},
issn = {1940-6029},
mesh = {*Software ; *Genetic Variation ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Computational Biology/methods ; },
abstract = {Pool sequencing has emerged as a valuable approach in ecological studies, particularly when dealing with very small organisms (with limited amount of DNA available), when distinguishing individual organisms is a challenge (e.g., in colonies, microbiome), when there is a trade-off between the sequencing cost and the number of individuals to sequence, when the main goal is to estimate nucleotide variability and variant frequency patterns at the population level (that is, when individual information is not required). Estimates of variability can be efficiently explored by analyzing sequences of pooled individuals sampled from the population. When using this approach, the number of pooled individuals and the mean read depth are key choices in the experimental design.The software npstat calculates different estimates of nucleotide variability and neutrality tests.It also calculates the number of synonymous and nonsynonymous variants and the proportion of beneficial substitutions (alpha) using the MKT approach when GTF annotation file and an outgroup is provided.},
}

*Software
*Genetic Variation
*Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
*Genetics, Population/methods
*Computational Biology/methods

@article {pmid40828279,
year = {2025},
author = {Vizueta, J and Pisarenco, VA and Rozas, J},
title = {Evolutionary Genomics of Gene Families: A Case Study of Insect Gustatory Receptors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {179-209},
pmid = {40828279},
issn = {1940-6029},
mesh = {Animals ; *Genomics/methods ; *Evolution, Molecular ; *Multigene Family ; Phylogeny ; *Receptors, Cell Surface/genetics ; *Ants/genetics ; Computational Biology/methods ; *Insect Proteins/genetics ; Molecular Sequence Annotation ; },
abstract = {Gene families, which are groups of genes that share common ancestry and are often functionally related, constitute a substantial proportion of the protein-coding sequences within eukaryotic genomes. In insects, genes involved in chemoperception belong to gene families characterized by numerous copies that arise from episodic bursts of gene duplication. This biological process is crucial for insect survival, as it enables the perception of environmental chemical cues. In this chapter, we analyze the gustatory receptors in the fire ant Solenopsis invicta and present a protocol for bioinformatic analyses. First, we employ BITACORA to identify and annotate gene family members in the genome assembly, providing tools for the annotation and subsequent validation. Then, we use GALEON to explore the genomic arrangement of gene family members in the chromosome-level assembly and visualize the distribution of gene clusters. To gain insights into the evolution and function of these genes, we conduct multiple-sequence alignment and reconstruct the phylogeny, incorporating data from two other insects. Finally, we integrate physical and evolutionary distances of the gustatory receptors to further understand the dynamics of this gene family.},
}

Animals
*Genomics/methods
*Evolution, Molecular
*Multigene Family
Phylogeny
*Receptors, Cell Surface/genetics
*Ants/genetics
Computational Biology/methods
*Insect Proteins/genetics
Molecular Sequence Annotation

@article {pmid40828283,
year = {2025},
author = {Aceto, S and Perrini, S and Varone, M and Lucibelli, F and Volpe, G and Di Lillo, P and Carfora, A and Mazzucchiello, SM and Saccone, G and Salvemini, M},
title = {Identification of Sex-Specific and Sex-Biased Transcripts for Genetic Sexing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {273-298},
pmid = {40828283},
issn = {1940-6029},
mesh = {Animals ; Male ; Female ; *Computational Biology/methods ; *Sex Determination Analysis/methods ; *Transcriptome ; },
abstract = {Sex-specific transcripts are RNA molecules expressed predominantly or exclusively in one sex, providing insights into molecular and physiological differences between males and females. This knowledge underpins the development of precise and efficient genetic sexing methods applicable in various contexts. In agriculture and livestock management, early sex determination could enhance resource management and productivity. In ecology and conservation, genetic sexing informs population monitoring and species management. In applied entomology, it could improve biological control strategies, such as the sterile insect technique. Here, we describe a bioinformatic framework to identify sex-specific transcripts using RNA-seq sequencing data in eukaryotic species with or without a sequenced reference genome.},
}

Animals
Male
Female
*Computational Biology/methods
*Sex Determination Analysis/methods
*Transcriptome

@article {pmid40828862,
year = {2025},
author = {Kubota, Y and Fukiage, T},
title = {Human-like monocular depth biases in deep neural networks.},
journal = {PLoS computational biology},
volume = {21},
number = {8},
pages = {e1013020},
pmid = {40828862},
issn = {1553-7358},
mesh = {Humans ; *Neural Networks, Computer ; *Depth Perception/physiology ; *Vision, Monocular/physiology ; Computational Biology ; Male ; Female ; Adult ; },
abstract = {Human depth perception from 2D images is systematically distorted, yet the nature of these distortions is not fully understood. By examining error patterns in depth estimation for both humans and deep neural networks (DNNs), which have shown remarkable abilities in monocular depth estimation, we can gain insights into constructing functional models of this human 3D vision and designing artificial models with improved interpretability. Here, we propose a comprehensive human-DNN comparison framework for a monocular depth judgment task. Using a novel human-annotated dataset of natural indoor scenes and a systematic analysis of absolute depth judgments, we investigate error patterns in both humans and DNNs. Employing exponential-affine fitting, we decompose depth estimation errors into depth compression, per-image affine transformations (including scaling, shearing, and translation), and residual errors. Our analysis reveals that human depth judgments exhibit systematic and consistent biases, including depth compression, a vertical bias (perceiving objects in the lower visual field as closer), and consistent per-image affine distortions across participants. Intriguingly, we find that DNNs with higher accuracy partially recapitulate these human biases, demonstrating greater similarity in affine parameters and residual error patterns. This suggests that these seemingly suboptimal human biases may reflect efficient, ecologically adapted strategies for depth inference from inherently ambiguous monocular images. However, while DNNs capture metric-level residual error patterns similar to humans, they fail to reproduce human-level accuracy in ordinal depth perception within the affine-invariant space. These findings underscore the importance of evaluating error patterns beyond raw accuracy, providing new insights into how humans and computational models resolve depth ambiguity. Our dataset and methodology provide a framework for evaluating the alignment between computational models and human perceptual biases, thereby advancing our understanding of visual space representation and guiding the development of models that more faithfully capture human depth perception.},
}

Humans
*Neural Networks, Computer
*Depth Perception/physiology
*Vision, Monocular/physiology
Computational Biology
Male
Female
Adult

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

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

@article {pmid40829560,
year = {2025},
author = {McKnight, JC and Solms, B and Jensen, M and Turnbull, J and Balfour, S and Laagland, M and Bronkhorst, M and Lee, HJ and Kang, G and Lee, JY and Bell, A and Hastie, G and Ilardo, M},
title = {Diving behaviour and physiology of the Korean Haenyeo.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R797-R798},
doi = {10.1016/j.cub.2025.06.066},
pmid = {40829560},
issn = {1879-0445},
mesh = {Adult ; Female ; Humans ; *Diving/physiology ; Republic of Korea ; *Breath Holding ; },
abstract = {There is a long history of breath-hold diving cultures in East Asia, with references in Japanese chronicles as early as the third century BC. Given evidence of genetic adaptations for phenotypes associated with enhanced diving capacity within such populations[1], it is likely they hold the most prodigious human diving abilities - abilities that may be akin to semi-aquatic mammals, and even some marine mammals. Yet, a dearth of fine-scale information exists on the combined natural diving behaviour and physiological responses within these diving populations. One such extraordinary population is the all-female Haenyeo. Here, we assess the fine-scale diving behaviours and physiological responses of these women during natural harvest diving. Our results show that Haenyeo divers demonstrate the highest proportions of time underwater of any humans, also exceeding those of semi-aquatic mammals and being comparable with some marine mammals. Additionally, they do not exhibit an overt cardiovascular depression, or 'dive response', classically associated with consummate diving mammals.},
}

Adult
Female
Humans
*Diving/physiology
Republic of Korea
*Breath Holding

@article {pmid40833038,
year = {2026},
author = {De Neef, E and Velásquez-Zapata, V and Gordon, ERL and Narva, K and Mc Cahon, P and Mézin, L and Lester, PJ and Romeis, J and Fletcher, S and Mitter, N and Devisetty, UK and Sridharan, K},
title = {A bioinformatic ecological risk assessment framework for externally applied double-stranded RNA-based biopesticides.},
journal = {Integrated environmental assessment and management},
volume = {22},
number = {1},
pages = {116-131},
doi = {10.1093/inteam/vjaf116},
pmid = {40833038},
issn = {1551-3793},
mesh = {*RNA, Double-Stranded/toxicity ; Risk Assessment/methods ; *Computational Biology/methods ; *Biological Control Agents/toxicity ; *Pest Control, Biological/methods ; Animals ; *Pesticides/toxicity ; },
abstract = {Double-stranded RNA (dsRNA)-based biopesticides are a promising new method of pest management. These biopesticides leverage the endogenous RNA interference pathway to selectively regulate expression of key genes involved in growth and development in pests, providing the potential to minimize harmful environmental effects by highly specific targeting. As dsRNA-based biopesticides are presented for regulatory review, evaluating potential off-target effects on nontarget organisms (NTOs) in a manner that may be unique to this novel sequence-specific mode of action is crucial. To address this, we propose here a bioinformatics framework for consideration of sequence-specific off-target effects in NTOs. This framework includes careful consideration of NTOs based on potential exposure and susceptibility and recommends standardizing analyses to search for 21-nucleotide stretches of perfect identity and 80% overall identity between the dsRNA and off-target transcripts. We recommend a three-pronged approach to ensure a comprehensive risk assessment: (a) phylogenetic analysis of gene orthologs that defines the taxonomic scope of sequence similarity, (b) broad searches of large databases to identify potential unexpected similarity in distantly related species, and (c) full transcriptome analyses in NTO species of particular concern for a thorough understanding of all potential hazards. Finally, we recommend considering the results of bioinformatic analyses in the context of risk characterization, which means considering likely exposure to the dsRNA-based pesticide and potential susceptibility or barriers to dsRNA uptake. This approach enables a robust ecological risk assessment for dsRNA-based biopesticides and a regulatory path forward for this promising new pest management tool.},
}

*RNA, Double-Stranded/toxicity
Risk Assessment/methods
*Computational Biology/methods
*Biological Control Agents/toxicity
*Pest Control, Biological/methods
Animals
*Pesticides/toxicity

@article {pmid40838167,
year = {2025},
author = {Boyes, D and Fletcher, C and Phillips, D and Sivess, L and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Tortix moth, Archips podanus (Scopoli, 1763).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {189},
pmid = {40838167},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Archips podanus (Tortix moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 549.00 megabases. Most of the assembly (99.72%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.45 kilobases.},
}

@article {pmid40840423,
year = {2025},
author = {Bozeman, BB and Matson, PG and DeRolph, CR and DeNeale, ST},
title = {The HydroBio Dataset: a new data resource for evaluating existing and potential hydropower capacity and freshwater biodiversity in the conterminous United States.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127042},
doi = {10.1016/j.jenvman.2025.127042},
pmid = {40840423},
issn = {1095-8630},
mesh = {*Biodiversity ; Conservation of Natural Resources ; Ecosystem ; *Fresh Water ; *Power Plants ; Rivers ; United States ; *Datasets as Topic ; },
abstract = {Hydropower is a critical source of affordable and reliable electricity and energy system stability services in the United States. Opportunities to expand US hydropower production include retrofitting existing non-powered dams to produce power, retrofitting existing hydropower dams to improve efficiency or increase capacity, or constructing new hydropower infrastructure on currently unregulated river reaches. We created the HydroBio Dataset, which summarizes existing and potential hydropower capacity and freshwater biodiversity at the sub-basin scale in the conterminous US to contextualize existing and potential grid contributions with the freshwater ecosystems in which dams are situated. We demonstrate a use-case of this dataset by rescaling and comparing potential non-powered dam nominal capacity to rarity-threat-weighted freshwater species richness for sub-basins where both types of data exist. On average, normalized freshwater biodiversity exceeded normalized potential non-powered dam nominal capacity in these sub-basins. Potential non-powered dam nominal capacity was concentrated in sub-basins in the Upper Mississippi and Ohio hydrologic regions while freshwater biodiversity was concentrated in the South Atlantic-Gulf, Ohio, and Tennessee hydrologic regions. Additionally, non-powered dams and existing hydropower dams are located in sub-basins with similar indices of freshwater biodiversity. The HydroBio Dataset adds an additional ecological dimension of context to our understanding of current and potential future US hydropower capabilities and is a valuable decision support tool for stakeholders tasked with balancing gains in services to the US power grid with the public and environmental benefits of freshwater ecosystems.},
}

*Biodiversity
Conservation of Natural Resources
Ecosystem
*Fresh Water
*Power Plants
Rivers
United States
*Datasets as Topic

@article {pmid40840460,
year = {2025},
author = {Carlozzi, NE and Troost, J and Lombard, WL and Miner, JA and Graves, CM and Choi, SW and Wu, Z and Sen, S and Sander, AM},
title = {Completion and Compliance Rates for an Intensive mHealth Study Design to Promote Self-Awareness and Self-Care Among Care Partners of Individuals With Traumatic Brain Injury: Secondary Analysis of a Randomized Controlled Trial.},
journal = {JMIR mHealth and uHealth},
volume = {13},
number = {},
pages = {e73772},
pmid = {40840460},
issn = {2291-5222},
support = {K24 HL156896/HL/NHLBI NIH HHS/United States ; R01 HL146354/HL/NHLBI NIH HHS/United States ; R01 NR013658/NR/NINR NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Awareness ; *Brain Injuries, Traumatic/psychology/therapy ; *Caregivers/psychology/statistics & numerical data ; Mobile Applications/statistics & numerical data/standards ; *Patient Compliance/statistics & numerical data/psychology ; *Self Care/methods/psychology/standards/statistics & numerical data ; Surveys and Questionnaires ; Telemedicine/standards/statistics & numerical data ; *Treatment Adherence and Compliance/statistics & numerical data/psychology ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Compliance rates for mobile health (mHealth) studies that involve intensive study designs are highly variable. Both person- and study-specific factors likely contribute to this variability. We were interested in understanding the impact that care partner characteristics and demographics have on study engagement, given that engagement is critical to the success of mHealth interventions.

OBJECTIVE: The primary objective of this report was to analyze the overall and component-specific completion and compliance rates for an intensive 6-month mHealth intervention (CareQOL app) designed to promote self-awareness and self-care among care partners of individuals with traumatic brain injury.

METHODS: This randomized controlled trial was designed to test the CareQOL app, an mHealth app designed to promote care partner self-awareness (through self-monitoring) and self-care (through personalized self-care push notifications). The study design consisted of a baseline assessment, a 6-month home-monitoring period that included 3 daily ecological momentary assessment (EMA) questions, monthly patient-reported outcome (PRO) surveys, continuous activity and sleep monitoring using a Fitbit, and 2 follow-up PRO surveys at 3 and 6 months posthome monitoring. Three participants withdrew prior to the initiation of the home-monitoring period, resulting in a final analytical sample size of 254. All participants had access to a self-monitoring dashboard (CareQOL app) that included graphical displays of the daily survey scores, as well as daily steps and sleep data from the Fitbit.

RESULTS: Overall compliance for the different aspects of the study was high. On average, the full-sample daily EMA PRO completion rate was 84% (SD 19%), Fitbit-based step count compliance was 90% (SD 21%), and Fitbit-based sleep duration compliance was 75% (SD 32%); there was no difference between the study arms for daily EMA PROs and Fitbit compliance rates. Completion rates for monthly and follow-up PRO surveys were even higher, with average end-of-month completion rates ranging from 97% to 100%, and follow-up completion rates of 95% for both time points. Again, these rates did not differ by study arm. The data were represented by 3 engagement groups: high-compliance-all data; high-compliance-PROs and steps only; and moderate PRO compliance-low Fitbit compliance. Group membership was predicted by both race (P<.001) and relationship to the care recipient (P=.001), but not by the other person-specific variables.

CONCLUSIONS: The compliance rates for this intensive study design are consistent, but at the high end, with what has been reported previously in the literature for studies with shorter time durations. Except for race and relationship to the care recipient, person-specific factors did not appear to be significantly associated with the engagement group. As such, we anticipate that the high compliance rates observed in this study are likely due to several study-specific design elements that were used to encourage study engagement.},
}

Adult
Female
Humans
Male
Middle Aged
*Awareness
*Brain Injuries, Traumatic/psychology/therapy
*Caregivers/psychology/statistics & numerical data
Mobile Applications/statistics & numerical data/standards
*Patient Compliance/statistics & numerical data/psychology
*Self Care/methods/psychology/standards/statistics & numerical data
Surveys and Questionnaires
Telemedicine/standards/statistics & numerical data
*Treatment Adherence and Compliance/statistics & numerical data/psychology
Secondary Data Analysis

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

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

@article {pmid40841201,
year = {2025},
author = {Sena, AVDS and Telles, L and Melo, PHM and Salomão, SL and Uzeda, TS and Pereira Lima, BL and Kratky, L and Mooney, DP and Bustorff-Silva, J},
title = {The management of cryptorchidism in Brazil: An ecological overview.},
journal = {Journal of pediatric urology},
volume = {21},
number = {6},
pages = {1813-1819},
doi = {10.1016/j.jpurol.2025.07.025},
pmid = {40841201},
issn = {1873-4898},
mesh = {Humans ; *Cryptorchidism/surgery/epidemiology ; Male ; Brazil/epidemiology ; *COVID-19/epidemiology ; Child ; Child, Preschool ; *Orchiopexy/statistics & numerical data ; Infant ; Adolescent ; Infant, Newborn ; },
abstract = {INTRODUCTION: Cryptorchidism refers to the extra-scrotal location of the testicle and is the most common male genital anomaly. Although the recommended age ranges for both hormonal and surgical treatments are well-established, within the Brazilian Unified Health System (SUS), children with cryptorchidism undergo surgery at varying ages across the country. As a time-sensitive procedure, delayed orchidopexy has consequences such as an increased risk of infertility or even testicular cancer. Correlating data on cryptorchidism treatment in SUS with geographic and socioeconomic indicators may help to understand how a population's profile influences the public healthcare system. This study explores the potential relationship between the age at which orchiopexy is performed and the quality of public healthcare services in Brazil while also assessing the impact of the COVID-19 pandemic on this surgery's backlog.

METHODS: To achieve this, we collected data from the Department of Informatics of the Brazilian Public Health System (DATASUS) and indicators provided by the Brazilian Institute of Geography (IBGE) and the Institute for Applied Economic Research (IPEA). We cataloged and compiled the data for comprehensive analysis.

RESULTS: Between 2008 and 2022, 94,237 orchiopexies were performed in SUS in patients aged 0-15. Nationwide, this represents only 47.6 % of the expected procedures, ranging from 22.75 % in the North to 68.18 % in the South. The proportion of surgeries performed before age 2 was very low, ranging from 12 % in the North and Northeast to 24 % in the South. Most orchiopexies in Brazil were performed after the age of five. The COVID-19 pandemic significantly worsened this situation, causing a 44.45 % decline in surgeries in 2020 compared to 2019, disproportionately affecting all age groups and exacerbating the backlog of surgeries.

CONCLUSION: Our study indicates that many children with cryptorchidism remain undiagnosed or receive delayed treatment. The COVID-19 pandemic further worsened this scenario, temporarily reducing the number of operations. These findings underscore the urgent need for comprehensive public policies to improve healthcare access and prevent complications associated with untreated cryptorchism.},
}

Humans
*Cryptorchidism/surgery/epidemiology
Male
Brazil/epidemiology
*COVID-19/epidemiology
Child
Child, Preschool
*Orchiopexy/statistics & numerical data
Infant
Adolescent
Infant, Newborn

@article {pmid40841825,
year = {2025},
author = {De Rovere, F and Mastropierro, M and Jungclaus, JH and Khodri, M and Rubino, A and Zanchettin, D},
title = {Future Atlantification of the European Arctic limited under sustained global warming.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30802},
pmid = {40841825},
issn = {2045-2322},
support = {2022CCRN7R, "ATTRACTION - ATlantificaTion dRiven by polAr-subpolar ConnecTIONs", CUP: H53D23001550006//Next-GenerationEU - PNRR - M.4 C.2, INVESTIMENTO 1.1 - PRIN22/ ; },
abstract = {Atlantification is an ongoing oceanic phenomenon characterised by the expansion of the typical Atlantic domain towards the Arctic, driving rapid oceanic and ecological changes in the European Arctic. Using reanalyses and a multi-model ensemble of unperturbed and transient preindustrial, historical and future-scenario simulations, this study shows that modern Atlantification possibly initiated in the late nineteenth century, preceded by several "Arctification" episodes in the preindustrial millennium. In the historical period, Atlantification and pan-Arctic warming superposed constructively to drive upper-ocean warming and salinification in the Barents Sea. Modern Atlantification is projected to continue in the next few decades, fully revealing its exceptional character in the context of the past millennium. However, Atlantification halts during the second half of the twenty-first century, decoupling from pan-Arctic warming. The northward expansion of the Atlantic domain is hindered by the onset of a damping mechanism where the Atlantic-Arctic density gradient increases progressively, which sustains a countercurrent by baroclinic adjustment pushing the Arctic polar front southward. As the evolution of this density gradient is intertwined with the retreat of the sea-ice edge, a late-summer ice-free Barents Sea may mark the end of modern Atlantification.},
}

@article {pmid40843346,
year = {2025},
author = {Xia, K and Hu, Y and Cai, S and Lin, M and Lu, M and Lu, H and Ye, Y and Lin, F and Gao, L and Xia, Q and Tian, R and Lin, W and Xie, L and Tan, D and Lu, Y and Lin, X and Yang, X and Zhong, L and Xu, L and Zhang, Z and Wang, L and Ren, J and Xu, H},
title = {GastritisMIL: An interpretable deep learning model for the comprehensive histological assessment of chronic gastritis.},
journal = {Patterns (New York, N.Y.)},
volume = {6},
number = {8},
pages = {101286},
pmid = {40843346},
issn = {2666-3899},
abstract = {The comprehensive histological assessment of chronic gastritis is imperative for guiding endoscopic follow-up strategies and surveillance of early-stage gastric cancer, yet rapid and objective assessment remains challenging in clinical workflows. We propose a powerful deep learning model (GastritisMIL) to effectively identify pathological alterations on H&E-stained biopsy slides, thereby expediting pathologists' evaluation and improving decision-making regarding follow-up intervals. We have trained and tested GastritisMIL by using retrospective data from 2,744 patients and evaluated discriminative performance across three medical centers (467 patients). GastritisMIL attained areas under the receiver operating curve greater than 0.971 in four tasks (inflammation, activity, atrophy, and intestinal metaplasia) and superior performance comparable to that of two senior pathologists. Specifically, interpretable attention heatmaps generated by GastritisMIL effectively assist junior pathologists in locating suspicious lesion regions across the entire field and minimizing missed diagnosis risk. Moreover, the high generalizability of this developed model across multiple external cohorts demonstrates its potential translational value.},
}