@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 {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 {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},
}

@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},
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 ; 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 {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 {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 = {},
number = {},
pages = {118543},
doi = {10.1016/j.marpolbul.2025.118543},
pmid = {40774918},
issn = {1879-3363},
}

@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 = {},
number = {},
pages = {122524},
doi = {10.1016/j.envres.2025.122524},
pmid = {40774560},
issn = {1096-0953},
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 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.},
}

@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 {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 = {},
number = {},
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/ ; },
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.},
}

@article {pmid40770961,
year = {2025},
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 = {},
number = {},
pages = {},
doi = {10.1002/ijc.70076},
pmid = {40770961},
issn = {1097-0215},
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.},
}

@article {pmid40484397,
year = {2025},
author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y},
title = {Field dynamics of the root endosphere microbiome assembly in paddy rice cultivated under no fertilizer input.},
journal = {Plant & cell physiology},
volume = {66},
number = {7},
pages = {1086-1101},
doi = {10.1093/pcp/pcaf045},
pmid = {40484397},
issn = {1471-9053},
support = {18H02467//Ministry of Education, Culture, Sports, Science, and Technology of Japan/ ; 24K21870//Ministry of Education, Culture, Sports, Science, and Technology of Japan/ ; JPMJTR23UJ//Japan Science and Technology Agency/ ; JPMJSP2140//JST SPRING, Japan/ ; },
abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared with a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.},
}

@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 {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 {pmid40744438,
year = {2025},
author = {Posthuma, L and Price, T and Viljanen, M},
title = {Improving the Ecotoxicological Hazard Assessment of Chemicals by Pairwise Learning.},
journal = {Environmental science & technology},
volume = {59},
number = {31},
pages = {16250-16260},
doi = {10.1021/acs.est.5c01289},
pmid = {40744438},
issn = {1520-5851},
mesh = {*Ecotoxicology ; *Machine Learning ; Animals ; Risk Assessment ; Environmental Pollutants ; },
abstract = {This study demonstrates how machine learning techniques can bridge data gaps in the ecotoxicological hazard assessment of chemical pollutants and illustrates how the results can be used in practice. The innovation herein consists of the prediction of the sensitivity of all species that were tested for at least one chemical for all chemicals based on all available data. As proof of concept, pairwise learning was applied to 3295 × 1267 (chemical,species) pairs of Observed LC50 data, where only 0.5% of the pairs have experimental data. This yielded more than four million Predicted LC50s for separate exposure durations. These were used to create (1) a novel Hazard Heatmap of Predicted LC50s, (2) Species Sensitivity Distributions (SSD) for all chemicals based on 1267 species each, as well as (3) for taxonomic groups separately, and (4) newly defined Chemical Hazard Distributions (CHD) for all species based on 3295 chemicals each. Validation results and graphical examples illustrate the utility of the results and highlight species and compound selection biases in the input data. The results are broadly applicable, ranging from Safe and Sustainable by Design (SSbD) assessments and setting protective standards to Life Cycle Assessment of products and assessing and mitigating impacts of chemical pollution on biodiversity.},
}

*Ecotoxicology
*Machine Learning
Animals
Risk Assessment
Environmental Pollutants

@article {pmid40763572,
year = {2025},
author = {Sagawa, N and Ichikawa, K and Furukawa, K and Morita, H and Takahara, A and Hinata, H},
title = {Time-resolved fragmentation pathways of expanded polystyrene microplastics: Intrinsic pathway modulated by sand morphology and degradation state.},
journal = {The Science of the total environment},
volume = {997},
number = {},
pages = {180172},
doi = {10.1016/j.scitotenv.2025.180172},
pmid = {40763572},
issn = {1879-1026},
abstract = {Microplastic fragmentation, driven by ultraviolet exposure, mechanical forces, and sand properties, remains poorly understood in natural settings despite its ecological significance. This study investigates temporal variation (6-240 h) in the shape, size, and number of EPS fragments (size distribution) and their dependence on sand morphology and parent microplastic degradation state based on pot mill experiments. Two experimental setups were employed: Time-Resolved Fragmentation (TRF) experiments using virgin EPS (∼5000 μm) with beach sand (TRF-VB), and virgin or degraded EPS with river sand (TRF-VR/DR). In the TRF-VB, two dominant size classes were identified: size class 1 (5-100 μm), appearing early (6-12 h), and size class 2 (200-1000 μm), emerging at 48-72 h and plateauing at 120 h due to hardened surface layer exfoliation of the parent EPS. The steep slopes of the size distributions (<-3) are explained by a combination of continuous-cascading and leap-cascading fragmentation mechanisms. In the TRF-VR experiment, only size class 1 persisted, whereas in the TRF-DR experiment, degraded EPS produced both classes by 120 h. The fragmentation pathway was influenced by both sand morphology and the parent degradation state. Volume balance analysis revealed the dominance of fine fragments (<5 μm) in both experiments, indicating their environmental relevance. These findings provide a conceptual framework for modeling EPS fragmentation and highlight the ecological risks associated with the rapid generation of fine microplastics. In the future, the continued integration of experimental, numerical, and theoretical approaches will be essential for advancing our understanding of plastic fragmentation processes.},
}

@article {pmid40763003,
year = {2025},
author = {Chen, AT and Wang, LC and Pike, KC and Conway, M and Glass, JE},
title = {Comparing the Use Experiences, Contextual Factors, and Recovery Strategies Associated with Different Substances: An Analysis of Social Media Narratives.},
journal = {Substance use & misuse},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/10826084.2025.2540938},
pmid = {40763003},
issn = {1532-2491},
abstract = {BACKGROUND: Research on use experience and recovery has often focused on a single substance or polysubstance use. However, there can be substance-specific differences; understanding these can be critical to developing targeted interventions. We examined social media relating to alcohol, cannabis, and/or opioids to: 1) construct use profiles highlighting salient settings, actors, and contextual factors; and 2) characterize differences in recovery strategies depending on readiness to change.

METHODS: We constructed a dataset of Reddit posts from subreddits pertaining to alcohol, cannabis, and opioids, authored between January 2013 and December 2019. We leveraged computational techniques to sample posts containing stigma, logistic regression to compare substance use experiences, and content analysis to identify stages of change and recovery strategies.

RESULTS: We examined 748 posts (alcohol, n = 316; cannabis, n = 335; opioids, n = 135). Regression models indicated leisure settings, coworkers, health, and legal consequences were associated with alcohol versus other substances. Posts involving cannabis were more likely to include school, and heightened self-awareness, demonstrated through curiosity, disgust, and realization. Posts involving opioids were more likely to include anticipated stigma, anger, healthcare, medications, financial, and religious content; they were less likely to include home and leisure. With respect to recovery strategies, social support seeking and awareness of substance use consequences were more common in earlier stages of readiness. In the action and maintenance stages, there was greater use of recovery strategies overall.

CONCLUSIONS: Substance-specific use profiles highlighted salient settings, actors, and contextual factors. Recovery strategies were also differentiated across stages of change, affording opportunities for treatment and intervention.},
}

@article {pmid40757428,
year = {2025},
author = {Callaway, RM and Pal, RW and Schaar, A and Hooper, D and Auge, H and Hensen, I and Kožić, K and Lekberg, Y and Nagy, DU and Selke, JA and Thoma, AE and Träger, S and Rosche, C},
title = {Exotic Invasive Plant Species Increase Primary Productivity, but Not in Their Native Ranges.},
journal = {Ecology letters},
volume = {28},
number = {8},
pages = {e70187},
doi = {10.1111/ele.70187},
pmid = {40757428},
issn = {1461-0248},
support = {//German Research Foundation/ ; //federal state of Saxony-Anhalt/ ; //German Academic Exchange Service London/ ; },
mesh = {*Introduced Species ; *Biomass ; *Ecosystem ; *Plants ; },
abstract = {Ecosystem net primary productivity is thought to occur near the maximum that abiotic constraints allow; but exotic invasive plants often correlate with increased productivity. However, field patterns and experimental evidence for this come only from the non-native ranges of exotic species. Thus, we do not know if this pattern is caused by exotic invasions per se or whether successful exotic species are disproportionately productive or colonise more productive microsites. We measured aboveground biomass in the field and in common gardens with five plant species in their native and non-native ranges. For all species combined, exotic invaders increased total plot productivity in their non-native ranges by 91% in the field, and by 107% in the common garden, but had much smaller or no such effects in their native ranges. Thus, exotic invaders appear to be a driver of increased productivity, not simply a passenger, but only in their non-native ranges.},
}

*Introduced Species
*Biomass
*Ecosystem
*Plants

@article {pmid40753432,
year = {2025},
author = {Sigrist, C and Bechdolf, A and Bertsch, K and Bullenkamp, R and Busse, M and Darrelmann, UG and Dempfle, A and Driessen, M and Frodl, T and Kersting, JM and Kesik, J and Matzke, B and Neukel, C and Niessen, E and Nückel, S and Oertel, V and Padberg, F and Philipsen, A and Pink, D and Reif, A and Reinhard, M and Steuwe, C and Wolkenstein, L and Herpertz, SC and Consortium, TM},
title = {A mechanism-based group psychotherapy approach to aggressive behavior (MAAP) in borderline personality disorder: a multicenter randomized controlled clinical trial.},
journal = {Trials},
volume = {26},
number = {1},
pages = {265},
pmid = {40753432},
issn = {1745-6215},
support = {462340798//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Borderline Personality Disorder/therapy/psychology/diagnosis ; *Aggression/psychology ; Treatment Outcome ; *Psychotherapy, Group/methods ; Germany ; Adult ; Multicenter Studies as Topic ; Female ; Male ; Randomized Controlled Trials as Topic ; Young Adult ; Time Factors ; },
abstract = {BACKGROUND: High levels of trait anger and aggressive behavior are common and problematic phenomena in patients with borderline personality disorder (BPD). In BPD, patterns of reactive aggression often lead to functional impairment affecting important areas of life. Despite the high burden on individuals and their social environment, there are no specific, cost-effective treatments to reduce aggression in BPD. In previous studies, we and others have been able to infer specific biobehavioral mechanisms underlying patterns of reactive aggression in BPD that can be used as potential treatment targets. To address this, we developed a mechanism-based anti-aggression psychotherapy (MAAP) for the group setting that specifically targets the biobehavioral mechanisms underlying outward-directed aggression in BPD. A previously conducted proof-of-concept study had suggested beneficial effects for this neglected group of patients.

METHODS: In this multicenter, confirmatory, randomized-controlled-clinical-trial, MAAP, which consists of multifaceted, evidence-based treatment elements adapted from other sophisticated treatment programs such as Dialectical Behavior Therapy and Mentalization-Based Treatment, is tested for efficacy against a non-specific supportive psychotherapy (NSSP) program focusing on non-specific general factors of psychotherapy at seven different sites in Germany. Both treatment arms, based on one individual and 13 group therapeutic sessions (1.5 h per session, twice a week), are delivered over a period of 7-10 weeks. A total of N = 186 patients will be recruited, half of whom will be cluster-randomized to MAAP. Outcomes are assessed at baseline, immediately, and 4, 12, 20, and 24 weeks post-treatment using ecological momentary assessment, clinical interviews, questionnaires, and online tasks.

DISCUSSION: If proven superior, MAAP can be incorporated into standard psychiatric care, filling a critical gap in the current therapeutic landscape by offering a structured, cost-effective, and evidence-based treatment that directly targets the biobehavioral mechanisms underlying reactive aggression in BPD. By potentially improving clinical outcomes and reducing the burden of reactive aggression in BPD, MAAP could be beneficial for both individuals and their social environments. The study's large, multicenter design enhances the generalizability of the results, making them more relevant for broader clinical applications.

TRIAL REGISTRATION: This study was registered in the German Clinical Trials Register DRKS (DRKS00031608) on 31.10.2023 (https://drks.de/search/de/trial/DRKS00031608).},
}

Humans
*Borderline Personality Disorder/therapy/psychology/diagnosis
*Aggression/psychology
Treatment Outcome
*Psychotherapy, Group/methods
Germany
Adult
Multicenter Studies as Topic
Female
Male
Randomized Controlled Trials as Topic
Young Adult
Time Factors

@article {pmid40743301,
year = {2025},
author = {Lu, Z and Chen, Z and Zhou, M and Lei, D and Chen, Y},
title = {Spatiotemporal patterns of water and vegetation in Poyang Lake from 2013 to 2021 using remote sensing data.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327579},
pmid = {40743301},
issn = {1932-6203},
mesh = {*Lakes ; *Remote Sensing Technology ; China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; Ecosystem ; Geographic Information Systems ; Support Vector Machine ; *Plants ; Water ; },
abstract = {Continuous monitoring and research on Poyang Lake is essential to understand its ecological dynamics and promote sustainable development. Spatial and temporal dynamic monitoring and analyses of vegetation changes in the water body of Poyang Lake are still limited. This study fills this gap by using remote sensing and GIS techniques for dynamic monitoring and analysing the changes of water bodies and vegetation in Poyang Lake from 2013 to 2021. We used a combination of Maximum Likelihood Classification (MLC) and Support Vector Machine (SVM) to preprocess and classify 42 Landsat 8 OLI images. The results showed that the stability of the water body and vegetation varied greatly, with the water body showing the obvious change pattern of water rises, vegetation recedes and water recedes, vegetation grows, and the high-frequency inundation area was concentrated in the northeastern part of the lake (accounting for 60% of the total inundation area). Vegetation frequency distribution showed a pattern of sparse in the north and dense in the south, with the middle frequency area being the most, accounting for 19.88%, and the low frequency area being the least, accounting for 16.09%. The results show that the spatial and temporal distribution characteristics of water body and vegetation in Poyang Lake show low stability, which is a highly dynamic ecosystem. This study relatively makes up for the missing analysis of the stability change of water body and vegetation in the cycle of Poyang Lake, and provides a solid scientific basis for the protection and sustainable management work.},
}

*Lakes
*Remote Sensing Technology
China
*Environmental Monitoring/methods
Spatio-Temporal Analysis
Ecosystem
Geographic Information Systems
Support Vector Machine
*Plants
Water

@article {pmid40736894,
year = {2025},
author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK},
title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {71-88},
doi = {10.1007/978-1-0716-4702-8_5},
pmid = {40736894},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; },
abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.},
}

*Metagenomics/methods
*Environmental Monitoring/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Gene Library

@article {pmid40663905,
year = {2025},
author = {Errea, P and Lasanta, T and Zabalza-Martínez, J and Cortijos-López, M and Nadal-Romero, E},
title = {Rethinking extensive livestock grazing to revive Mediterranean mountain landscapes.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126541},
doi = {10.1016/j.jenvman.2025.126541},
pmid = {40663905},
issn = {1095-8630},
mesh = {Mediterranean Region ; Altitude ; *Herbivory ; Ecosystem ; *Livestock ; Anthropogenic Effects ; *Animal Husbandry/methods ; Conservation of Natural Resources ; Geographic Information Systems ; Public Policy ; Agroecology/methods ; Climate ; Animals ; Animal Migration ; },
abstract = {Extensive livestock grazing is vital for the socio-economic resilience of Mediterranean mountains, providing key environmental benefits. Grazing patterns result from complex interactions between topographical, environmental, and anthropogenic factors, requiring an understanding of these dynamics to optimise land management. This study analyses spatio-temporal patterns of extensive livestock grazing in the Iberian System (north-eastern Spain), a representative Mediterranean mountain with a history of agricultural abandonment. Using GPS tracking, spatial analysis, and statistical modelling, this research evaluates how land use and land cover, environmental variables, public policy, and human infrastructure affect livestock movement. Three hypotheses are tested: (1) grazing distribution is influenced by both environmental and anthropogenic factors; (2) silvopastoral systems are key components of grazing; and (3) shrub cleared areas display heterogeneous levels of use. Results reveal diurnal and seasonal patterns, with peak grazing during early morning and late afternoon, and a decline in cattle presence during autumn and winter. Approximately 81 % of grazing occurs on land subsidised by the Common Agricultural Policy (CAP), whereas sheep dominate silvopastoral areas (non-subsidised). Shrub pastures and pastures are most frequently grazed, though wooded pastures exhibited the highest intensity. Species-specific preferences were evident: sheep prefer higher altitudes and steeper terrains, while cattle favour areas with higher NDVI values. Multiple regression analysis reveals that proximity to water, salt, and feed points and livestock sheds are key predictors of grazing distribution. Shrub clearing enhances grazing activity. These findings highlight the need for targeted grazing management strategies to improve the ecological and economic sustainability of Mediterranean mountains.},
}

Mediterranean Region
Altitude
*Herbivory
Ecosystem
*Livestock
Anthropogenic Effects
*Animal Husbandry/methods
Conservation of Natural Resources
Geographic Information Systems
Public Policy
Agroecology/methods
Climate
Animals
Animal Migration

@article {pmid40733364,
year = {2025},
author = {Onyeagoziri, CA and Minoarivelo, HO and Hui, C},
title = {Mutualism and Dispersal Heterogeneity Shape Stability, Biodiversity, and Structure of Theoretical Plant-Pollinator Meta-Networks.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40733364},
issn = {2223-7747},
support = {89967//National Research Foundation/ ; //PhD bursary of the Southern African Systems Analysis Centre (SASAC), with partial funding from the German Academic Exchange Service (DAAD - Deutscher Akademischer Austauschdienst)/ ; },
abstract = {Mutualistic interactions are crucial to the structure and functioning of ecological communities, playing a vital role in maintaining biodiversity amidst environmental perturbations. In studies of meta-networks, which are groups of local networks connected by dispersal, most research has focused on the effect of dispersal on interaction networks of competition and predation, without much attention given to mutualistic interactions. Consequently, the role of different dispersal rates (between local networks and across species) in stability and network structures is not well understood. We present a competition-mutualism model for meta-networks where mutualistic interactions follow a type II functional response, to investigate stability and species abundance dynamics under varying dispersal scenarios. We specifically assess the impact of mutualism and dispersal heterogeneity, both between local networks and across species, on the structure and stability of meta-networks. We find that mutualistic meta-networks exhibit greater stability, higher total abundance, lower species unevenness, and greater nestedness compared to meta-networks with only competition interactions. Although dispersal heterogeneity across species exerts some influence, dispersal heterogeneity between local networks mainly drives the patterns observed: it reduces total abundance, increases unevenness, and diminishes compositional similarity across the meta-network. These results highlight the pivotal role of both mutualism and spatial dispersal structure in shaping ecological networks. Our work advances understanding of how mutualistic interactions and dispersal dynamics interact to influence biodiversity and stability in complex ecosystems.},
}

@article {pmid40732512,
year = {2025},
author = {Adlou, B and Wilburn, C and Weimar, W},
title = {Motion Capture Technologies for Athletic Performance Enhancement and Injury Risk Assessment: A Review for Multi-Sport Organizations.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {14},
pages = {},
pmid = {40732512},
issn = {1424-8220},
mesh = {Humans ; *Athletic Performance/physiology ; Risk Assessment ; *Athletic Injuries/prevention & control ; *Sports ; Geographic Information Systems ; Movement/physiology ; Motion Capture ; },
abstract = {Background: Motion capture (MoCap) technologies have transformed athlete monitoring, yet athletic departments face complex decisions when selecting systems for multiple sports. Methods: We conducted a narrative review of peer-reviewed studies (2015-2025) examining optical marker-based, inertial measurement unit (IMU) systems, including Global Navigation Satellite System (GNSS)-integrated systems, and markerless computer vision systems. Studies were evaluated for validated accuracy metrics across indoor court, aquatic, and outdoor field environments. Results: Optical systems maintain sub-millimeter accuracy in controlled environments but face field limitations. IMU systems demonstrate an angular accuracy of 2-8° depending on movement complexity. Markerless systems show variable accuracy (sagittal: 3-15°, transverse: 3-57°). Environmental factors substantially impact system performance, with aquatic settings introducing an additional orientation error of 2° versus terrestrial applications. Outdoor environments challenge GNSS-based tracking (±0.3-3 m positional accuracy). Critical gaps include limited gender-specific validation and insufficient long-term reliability data. Conclusions: This review proposes a tiered implementation framework combining foundation-level team monitoring with specialized assessment tools. This evidence-based approach guides the selection of technology aligned with organizational priorities, sport-specific requirements, and resource constraints.},
}

Humans
*Athletic Performance/physiology
Risk Assessment
*Athletic Injuries/prevention & control
*Sports
Geographic Information Systems
Movement/physiology
Motion Capture

@article {pmid40732191,
year = {2025},
author = {Eaton, WD and Hamilton, DA and Lemenze, A and Soteropoulos, P},
title = {Initial Analysis of Plant Soil for Evidence of Pathogens Associated with a Disease of Seedling Ocotea monteverdensis.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40732191},
issn = {2076-2607},
support = {no number//Fundacion Conservacionista Costarricense Fundacion/ ; 2022-10//Fondation Franklinia/ ; no number//Pace University Dyson College Deans Office/ ; no number//Pace University Dyson College Faculty Research Grant Committee/ ; no number//Pace University Provost Office for Research and Support/ ; },
abstract = {Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and bulk soils were analyzed for various carbon and nitrogen (N) metrics and respiration levels, and DNA sequence-based bacterial and fungal community compositions. All nitrogen metric levels were greater in diseased vs. healthy plant root soils, which could enhance pathogen growth and pathogenic mechanisms. Greater DNA percentages from several potential pathogens were found in diseased vs. healthy plant root soils, suggesting this disease may be associated with a root pathogen. The DNA of the fungus Mycosphaerella was at greater levels in diseased vs. healthy plant root soils than other potential pathogens. Mycosphaerella causes similar diseases in other plants, including coffee, after onset of the wet season. The O. monteverdensis disease also occurs in seedlings planted within or near former coffee plantations at wet season onset. Distance-based linear model analyses indicated that NO3[-] levels best predicted the pattern of fungal pathogens in the soils, and Mycosphaerella and Tremella best predicted the patterns of the different N metrics in the soils, supporting their possible roles in this disease.},
}

@article {pmid40731321,
year = {2025},
author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M},
title = {The BeeBiome data portal provides easy access to bee microbiome information.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {198},
pmid = {40731321},
issn = {1471-2105},
mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; },
abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.},
}

Bees/microbiology
Animals
*Microbiota/genetics
Metagenomics/methods
*Databases, Genetic
Metagenome

@article {pmid40730013,
year = {2025},
author = {Chen, CF and Zhou, Z and Li, C and Liu, W},
title = {Ecological compensation and breakthrough innovation: Evidence from heavily polluting firms.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126682},
doi = {10.1016/j.jenvman.2025.126682},
pmid = {40730013},
issn = {1095-8630},
abstract = {The continuous deepening of the concept of green development and the increasing pressure of environmental governance leads great theoretical significance and practical value to explore the impact of the ecological compensation (eco-compensation) policy on the innovation behavior of enterprises. Taking the implementation of China's ecological compensation policy as an exogenous shock, this paper adopts a multi-period difference-in-differences (DID) model to systematically assess the impact of eco-compensation on corporate breakthrough innovation based on the data of A-share listed companies in the heavy pollution industry from 2014 to 2023. The findings indicate that eco-compensation significantly promotes breakthrough innovation activities of heavy polluting firms. Mechanism analysis further reveals that the policy indirectly drives the enhancement of firms' breakthrough innovation capability mainly by improving the level of data asset disclosure, reducing innovation risk and enhancing R&D activity. The heterogeneity analysis reveals that the eco-compensation policy promotes breakthrough innovation more significantly in firms located in regions where big data management institutions remain unreformed, data factor utilization is low, or industry-university-research collaboration is absent. This study theoretically expands the understanding of the impact mechanism of environmental regulation on enterprises' green innovation and enriches the research framework of incentives for breakthrough innovation; in practice, it provides policy references for optimizing the design of eco-compensation policies and guiding heavily polluting enterprises to achieve green transformation and high-quality development.},
}

@article {pmid40728939,
year = {2025},
author = {Franco, ME and Araújo, CVM and Cerveny, D and Koubová, A and Danneels, B and Goksøyr, A and Bertram, MG},
title = {The extended chemical defensome: emphasizing mechanisms of defense as key research avenues to tackle priority questions in environmental toxicology.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/etojnl/vgaf190},
pmid = {40728939},
issn = {1552-8618},
abstract = {Chemical pollution threatens organismal integrity, affecting growth, reproduction, behavior, and overall fitness, ultimately leading to shifts in biodiversity and the provisioning of ecosystem services. In response to chemical exposure, organisms use specific regions of their genome coding for different defense mechanisms-this collection of genes is termed the "chemical defensome". Specifically, genes associated with efflux transporters, transcription factors, antioxidant systems, and biotransformation pathways, among others, are expressed to reduce toxicity. These sub-individual processes are, for the most part, widely conserved across taxa and play a critical role in enabling organisms to cope with polluted environments. Additionally, we argue that behavioral responses-particularly spatial avoidance-should be recognized as an individual-level defense mechanism and incorporated into an extended chemical defensome framework. Expanding and reinforcing the concept of the chemical defensome beyond traditional studies at the genome level, as well as developing strategies to synthesize existing data, offers a valuable opportunity to link gene composition to physiological and behavioral responses, thereby addressing key research needs in environmental toxicology. These include: estimating the impact of chemical mixtures across different exposure scenarios, identifying the main drivers of intra- and interspecific sensitivity to pollution, and assessing large-scale ecological processes, such as biodiversity losses, in polluted habitats in a more integrated manner. In ecotoxicology and environmental risk assessment, understanding not only how chemical pollutants exert toxicity but also how organisms counteract these effects is essential. Indeed, investigating chemical-induced shifts in defense mechanisms can improve predictions of adverse outcomes at higher levels of biological organization and can inform more effective chemical management and regulatory strategies.},
}

@article {pmid40681316,
year = {2025},
author = {Nekrakalaya, B and Kotimoole, CN and Arefian, M and Prasad, TSK and Palliyath, GK and Veerappa Hanumanthappa, P and Pandian Ramasubramania, TP and Bangalore Jayaseelan, NK and Muddumadiah, C and Santhappan, P and Muliyar Krishna, R},
title = {A Gel-Free Genome Annotation Provides Insights into the Proteome of the Oomycete Phytophthora meadii, a Disease-Causing Pathogen in Economically Important Crops.},
journal = {Omics : a journal of integrative biology},
volume = {29},
number = {8},
pages = {384-393},
doi = {10.1177/15578100251359566},
pmid = {40681316},
issn = {1557-8100},
mesh = {*Phytophthora/genetics/metabolism/pathogenicity ; *Proteome/genetics/metabolism ; *Plant Diseases/microbiology/parasitology ; Molecular Sequence Annotation ; *Crops, Agricultural/microbiology/parasitology ; Proteomics/methods ; Computational Biology/methods ; Tandem Mass Spectrometry ; Gene Ontology ; Chromatography, Liquid ; },
abstract = {Phytophthora meadii is a polyphagous oomycete causing fatal diseases in economically important cash crops such as rubber, arecanut, cardamom, and other crops and plants of economic significance. Although information on the proteogenomic and proteomic analysis is available for several Phytophthora species, no information on the proteome repertoire of P. meadii is available. In the present study, a gel-free protein annotation was performed using liquid chromatography with tandem mass spectrometry analysis of the P. meadii hyphae, followed by bioinformatics analysis. The results were compared with a global Phytophthora proteome database-based search and an in-house P. meadii genome database, along with RefSeq proteome databases of other selected species of Phytophthora. A total of 7725 and 3979 proteins were exclusively matched with global and in-house databases, respectively. Basic Local Alignment Search Tool analysis showed 209 unique peptide sequences belonging to 85 proteins of P. meadii. Gene Ontology-based functional analysis of the P. meadii mycelial proteome categorized the proteins based on their role in cellular components, molecular functions, and biological processes. Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein network analysis further revealed the role of these proteins in growth and development functions. In addition, proteins potentially involved in virulence, infections in the host system, and several signaling mechanisms were deduced. The current study is the first report on the P. meadii mycelial proteins under optimum growth conditions. These omics data also have socioeconomic implications since Phytophthora causes disease in a wide range of economically noteworthy crops and forest ecosystems.},
}

*Phytophthora/genetics/metabolism/pathogenicity
*Proteome/genetics/metabolism
*Plant Diseases/microbiology/parasitology
Molecular Sequence Annotation
*Crops, Agricultural/microbiology/parasitology
Proteomics/methods
Computational Biology/methods
Tandem Mass Spectrometry
Gene Ontology
Chromatography, Liquid

@article {pmid40646315,
year = {2025},
author = {Tsimpida, D and Piroddi, R and Daras, K and Melis, G},
title = {Assessing hearing health inequalities using routine health information systems.},
journal = {Journal of public health policy},
volume = {46},
number = {3},
pages = {630-644},
doi = {10.1057/s41271-025-00584-8},
pmid = {40646315},
issn = {1745-655X},
support = {MHF106//National Institute for Health and Care Research/ ; NIHR200182//National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care North West Coast/ ; 177946//Research England/ ; },
mesh = {Humans ; *Hearing Loss/epidemiology ; England/epidemiology ; Male ; Middle Aged ; Female ; *Health Status Disparities ; Adult ; Aged ; *Health Information Systems/statistics & numerical data ; Prevalence ; Adolescent ; Young Adult ; Primary Health Care/statistics & numerical data ; Socioeconomic Factors ; Child ; },
abstract = {Hearing loss is a significant public health challenge, with prevalence estimates based on projected age demographics rather than actual public health needs. This study aimed to quantify hearing loss using real-world data from primary care and explore local patterns and trends from 2013 to 2022 in Cheshire and Merseyside counties of Northwest England. Annual hearing loss prevalence was measured using an ecological space-time analysis of 2.7 million primary care records from Cheshire and Merseyside Integrated Care System. We applied cluster and outlier analysis with geographically weighted regression to examine local deprivation effects. We detected spatial clusters of high prevalence of hearing loss in Cheshire and an increasing trend in hearing loss prevalence in Halton. Deprivation accounted for up to 35% of hearing loss variance in 2020. Monitoring spatial patterns of hearing loss is crucial for addressing health inequalities and guiding targeted prevention and intervention strategies.},
}

Humans
*Hearing Loss/epidemiology
England/epidemiology
Male
Middle Aged
Female
*Health Status Disparities
Adult
Aged
*Health Information Systems/statistics & numerical data
Prevalence
Adolescent
Young Adult
Primary Health Care/statistics & numerical data
Socioeconomic Factors
Child

@article {pmid40459864,
year = {2025},
author = {Shilenok, VV and Shilenok, IV and Soldatov, VO and Orlov, YL and Kobzeva, KA and Deykin, AV and Bushueva, OY},
title = {Bioinformatic analysis of the regulatory potential of tagging SNPs provides evidence of the involvement of genes encoding the heat-resistant obscure (Hero) proteins in the pathogenesis of cardiovascular diseases.},
journal = {Journal of integrative bioinformatics},
volume = {22},
number = {1},
pages = {},
pmid = {40459864},
issn = {1613-4516},
mesh = {*Polymorphism, Single Nucleotide ; Humans ; *Computational Biology/methods ; *Cardiovascular Diseases/genetics/pathology/metabolism ; *Genetic Predisposition to Disease ; Quantitative Trait Loci ; },
abstract = {Although multiple aspects of molecular pathology underlying cardiovascular diseases (CVDs) have been revealed, the complete picture has yet to be elucidated. In this respect, annotation of the novel links between genes and atherosclerosis is of great importance for cardiovascular medicine. Aligning with our previous research, we aimed to analyze the cardiovascular predisposition contribution of the genes encoding Hero-proteins, polypeptides with chaperone activity. Following bioinformatic sources were utilized to annotate data regarding the cardiovascular contribution of Hero-proteins and their genes: SNPinfo Web Server, The Cardiovascular Disease Knowledge Portal, GTEx Portal, HaploReg, rSNPBase, RegulomeDB, atSNP, Gene Ontology, QTLbase, and the Blood eQTL browser. Almost all analyzed genes were characterized by a very high regulatory potential of tag SNPs (except BEX3). Multiple substantial impacts of the analyzed SNPs on histone modifications, eQTL effects on CVD-related genes, and binding to transcription factors involved in biological processes pathogenetically significant for CVDs have been discovered. Here we provide in silico evidence of the involvement of genes C9orf16 (BBLN), C11orf58, SERBP1, SERF2, and C19orf53 in CVDs and their risk factors (high blood pressure, dyslipidemia, obesity, arrhythmias, etc.), thus revealing Hero-proteins as putative actors in the pathobiology of the heart and vessels.},
}

*Polymorphism, Single Nucleotide
Humans
*Computational Biology/methods
*Cardiovascular Diseases/genetics/pathology/metabolism
*Genetic Predisposition to Disease
Quantitative Trait Loci

@article {pmid40724857,
year = {2025},
author = {Piotrowski, M and Pawlaczyk, A and Szynkowska-Jóźwik, MI and Maras, P and Kozicki, M},
title = {Radiation-Sensitive Nano-, Micro-, and Macro-Gels and Polymer Capsules for Use in Radiotherapy Dosimetry.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40724857},
issn = {1422-0067},
mesh = {*Polymers/chemistry ; *Radiometry/methods ; Alginates/chemistry ; Capsules/chemistry ; *Hydrogels/chemistry ; Humans ; Iron/chemistry ; *Radiotherapy/methods ; Gels/chemistry ; Radiation, Ionizing ; },
abstract = {This work introduces an original approach to the manufacturing of ionizing radiation-sensitive systems for radiotherapy applications-dosimetry. They are based on the Fricke dosimetric solution and the formation of macro-gels and capsules, and nano- and micro-gels. The reaction of ionic polymers, such as sodium alginate, with Fe and Ca metal ions is employed. Critical polymer concentration (c*) is taken as the criterion. Reaction of ionic polymers with metal ions leads to products related to c*. Well below c*, nano- and micro-gels may form. Above c*, macro-gels and capsules can be prepared. Nano- and micro-gels containing Fe in the composition can be used for infusion of a physical gel matrix to prepare 2D or 3D dosimeters. In turn, macro-gels can be formed with Fe ions crosslinking polymer chains to obtain radiation-sensitive hydrogels, so-called from wall-to-wall, serving as 3D dosimeters. The encapsulation process can lead to capsules with Fe ions serving as 1D dosimeters. This work presents the concept of manufacturing various gel structures, their main features and manufacturing challenges. It proposes new directions of research towards novel dosimeters.},
}

*Polymers/chemistry
*Radiometry/methods
Alginates/chemistry
Capsules/chemistry
*Hydrogels/chemistry
Humans
Iron/chemistry
*Radiotherapy/methods
Gels/chemistry
Radiation, Ionizing

@article {pmid40724441,
year = {2025},
author = {Hunyadi, ID and Cismaș, C},
title = {Mining Complex Ecological Patterns in Protected Areas: An FP-Growth Approach to Conservation Rule Discovery.},
journal = {Entropy (Basel, Switzerland)},
volume = {27},
number = {7},
pages = {},
pmid = {40724441},
issn = {1099-4300},
support = {LBUS-IRG-10-2024//Lucian Blaga University of Sibiu/ ; },
abstract = {This study introduces a data-driven framework for enhancing the sustainable management of fish species in Romania's Natura 2000 protected areas through ecosystem modeling and association rule mining (ARM). Drawing on seven years of ecological monitoring data for 13 fish species of ecological and socio-economic importance, we apply the FP-Growth algorithm to extract high-confidence co-occurrence patterns among 19 codified conservation measures. By encoding expert habitat assessments into binary transactions, the analysis revealed 44 robust association rules, highlighting interdependent management actions that collectively improve species resilience and habitat conditions. These results provide actionable insights for integrated, evidence-based conservation planning. The approach demonstrates the interpretability, scalability, and practical relevance of ARM in biodiversity management, offering a replicable method for supporting adaptive ecological decision making across complex protected area networks.},
}

@article {pmid40715537,
year = {2025},
author = {Zhang, F and Guo, A and Hu, Z and Liang, Y},
title = {A novel image fusion method based on UAV and Sentinel-2 for environmental monitoring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27256},
pmid = {40715537},
issn = {2045-2322},
support = {2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; },
abstract = {In recent years, with the rapid development of remote sensing technology, environmental monitoring in mining areas using remote sensing imagery has gained increasing attention. Due to the small scale of mining areas, the resolution of satellite remote sensing imagery is insufficient for detailed monitoring needs. UAV remote sensing imagery provides high resolution, but its monitoring range is limited and lacks access to historical data. Furthermore, effectively fusing multi-source data with disparate spatial-temporal characteristics to accurately capture the complex dynamic changes in mining areas remains a key methodological challenge.To address this, this study, utilizing UAV remote sensing imagery and Sentinel-2 satellite imagery acquired on September 5, 2023, from the Erlintu mining area, proposes a novel fusion method aimed at achieving small-scale, long-term environmental monitoring in mining areas.First, the spatial resolution of both UAV and Sentinel-2 imagery is resampled to 0.1 m. Second, a two-layer preprocessing approach is applied to enhance data quality. Third, a stacked inversion model based on an ensemble learning framework is developed. Finally, using high-resolution UAV imagery as the reference, and original, resampled, and model-inverted Sentinel-2 imagery as experimental values, accuracy is assessed and analyzed with Mean Absolute Percentage Error (MAPE) as the metric. Results demonstrate that the stacked learning model, combined with cubic convolution resampling, reduces the MAPE of NDVI values between Sentinel-2 and UAV imagery from 54.31 to 10.01%, markedly improving accuracy. This study further uncovers the synergistic effect of resampling techniques and model architecture, offering reliable data support for small-scale, long-term environmental monitoring in mining areas.},
}

@article {pmid40321106,
year = {2025},
author = {Brazier, T and Stetsenko, R and Roze, D and Glémin, S},
title = {Mating system and the evolution of recombination rates in seed plants.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {7},
pages = {920-929},
doi = {10.1093/jeb/voaf008},
pmid = {40321106},
issn = {1420-9101},
support = {ANR-19-CE12472//Agence Nationale de la Recherche/ ; },
mesh = {*Magnoliopsida/genetics ; Genome, Plant ; Chromosomes, Plant ; Genome Size ; *Recombination, Genetic ; *Biological Evolution ; *Self-Fertilization/genetics ; Pollination ; Life History Traits ; Datasets as Topic ; Longevity ; Selection, Genetic ; },
abstract = {Meiotic recombination is a central mechanism underlying sexual reproduction among eukaryotes. In many species, the recombination rate is strongly constrained by chromosome size, as the number of crossovers per chromosome generally ranges between one and no more than a few (around three to five). Yet, recombination rates are variable and can evolve between species, in particular when they differ in their reproductive system. According to theory, indirect selection towards higher recombination rates is expected to be stronger in inbred populations, such as selfing species compared with randomly mating species. To test for the impact of the mating system on the evolution of recombination rates, we leveraged a dataset with genetic maps, genome sizes, chromosome numbers, and life history traits in 200 seed plant species. After controlling for the chromosome size effect, the phylogeny, and map quality, we found a joint positive effect of the mating system and longevity on recombination rates, with higher recombination rates in mixed-mating and selfing species. We also found that mixed-mating and selfing species had a significantly higher number of crossovers in larger chromosomes than outcrossing species, suggesting selection for relaxed crossover interference in these former species. Our results point to the mating system as an important factor potentially shaping the evolution of recombination despite mechanical constraints acting on the number of crossovers per chromosome.},
}

*Magnoliopsida/genetics
Genome, Plant
Chromosomes, Plant
Genome Size
*Recombination, Genetic
*Biological Evolution
*Self-Fertilization/genetics
Pollination
Life History Traits
Datasets as Topic
Longevity
Selection, Genetic

@article {pmid40715152,
year = {2025},
author = {Aubouin, L and Genoud, D and Givord-Coupeau, B and Tercerie, S and Gargominy, O and Geslin, B and Schatz, B},
title = {BeeFunc, a comprehensive trait database for French bees.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1302},
pmid = {40715152},
issn = {2052-4463},
mesh = {Bees/classification/anatomy & histology ; Animals ; France ; *Databases, Factual ; },
abstract = {Given pollinator's reported decline, it is of utmost importance to better understand the vulnerability of wild bees to human pressures. One way to achieve this goal is to explore how their traits are associated with exposure to anthropogenic perturbations. To date, there is no database synthesizing traits of bees at the species level in France, limiting the functional interpretation of inventories. We present BeeFunc 1.0, the first database on traits for the entire fauna of French wild bees. Based on extensive literature research and expert knowledge, the database is structured according to the French taxonomic register (TAXREF) and its associated knowledge base. The base gathers 26,176 trait information from 483 sources, describing 932 species for 20 features related to morphology, ecology, biogeography, and conservation. BeeFunc is intended to be collaborative and regularly updated. Bees can finally be better considered from a functional perspective. We expect this database to be widely used by researchers, conservationists, naturalists, and stakeholders, stimulating future research on wild bees.},
}

Bees/classification/anatomy & histology
Animals
France
*Databases, Factual

@article {pmid40713811,
year = {2025},
author = {Sun, B and Yuan, J and Zhang, X and Ma, X and Hao, Z and Wang, L and Li, Y and Zhang, L and Li, L},
title = {Metaproteomics Reveals Community Coalescence Outcomes in Co-Cultured Human Gut Microbiota.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e70009},
doi = {10.1002/pmic.70009},
pmid = {40713811},
issn = {1615-9861},
support = {32370050//National Natural Science Foundation of China/ ; 82371559//National Natural Science Foundation of China/ ; },
abstract = {The human gut microbiome exhibits characteristics of complex ecosystems, including the ability to resist and compete with exogenous species or communities. Understanding the microbiome response that emerges from such competitive interactions is crucial, particularly for applications like fecal microbiota transplantation (FMT), where the success of treatment largely depends on the outcome of these microbial competitions. During these processes, microbial communities undergo coalescence, a phenomenon where distinct microbial communities combine and interact, leading to complex ecological outcomes that are still being uncovered. In this study, we examined the coalescent dynamics of 10 different pairs of human gut microbiota by co-culturing the plateau-phase communities of individual samples in vitro, and highlighted the critical role of metaproteomics in elucidating the competitive dynamics of co-cultured human fecal samples. Results showed that microbiome changes observed after coalescent co-culture were not straightforwardly an approximate average of the initial taxonomic or functional compositions of the two samples. Instead, both coalescent microbiotas behaved as cohesive structures, influencing the competitive outcome toward one of them. Although co-cultured communities usually exhibited high degrees of taxonomic similarities to one of its parental samples, we found that 23% of the observed proteins still showed differential expression or abundance at the metaproteomic level. Interestingly, and somewhat counterintuitively, no specific microbial ecological characteristic could linearly determine which of the two initial microbiotas would act as the driving microbiota. Instead, we observed that the outcomes of the microbial co-cultures resembled a "rock-paper-scissors"-like dynamic. Through an analysis of co-colonizing species in such "rock-paper-scissors"-like triangle, we discovered that co-colonizing species that contributed to winning each between-community competition differed from one community pair to another. This suggests that no single species or function consistently dominates across all situations; instead, this involves more complex mechanisms, which require further in-depth investigation in future studies. Our findings demonstrate that the complex competitive interactions between microbial communities make predicting success through a single parameter challenging, whereas pre-co-culturing shows promise as an effective method for predicting outcomes in ecological therapies such as FMT. SUMMARY: This study underscores the critical importance of integrating metaproteomics with microbial systems ecology to gain a functional understanding of microbial coalescence. By addressing the ecological question of how two communities compete when they are brought into contact, we investigated the metaproteomic responses of pairs of coalescent co-cultured human gut microbiotas. Our results revealed significant insights: post-co-culture microbiota changes were not merely a simple average of the initial compositions but instead exhibited distinct shifts toward one of the original samples. Notably, due to the observed rock-paper-scissors-like cycle of winning, we argue that no single microbial ecological characteristic could straightforwardly predict which of the two samples would dominate as the driving microbiota. Overall, our findings suggest that during coalescence, microbial communities behave as cohesive structures both taxonomically and functionally, influencing competitive dynamics and ecosystem complexity, indicating that an in vitro coalescence pretest may help predict the success of therapies like FMT.},
}

@article {pmid40171777,
year = {2025},
author = {Zhao, W and Han, Q and Yang, F and Zhao, Y},
title = {Enhancing Enzyme Commission Number Prediction With Contrastive Learning and Agent Attention.},
journal = {Proteins},
volume = {93},
number = {9},
pages = {1507-1517},
doi = {10.1002/prot.26822},
pmid = {40171777},
issn = {1097-0134},
support = {32101590//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; 32071838//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
mesh = {*Enzymes/chemistry/metabolism/classification ; Databases, Protein ; *Machine Learning ; *Computational Biology/methods ; Algorithms ; Software ; Data Mining ; Proteins/chemistry ; },
abstract = {The accurate prediction of enzyme function is crucial for elucidating disease mechanisms and identifying drug targets. Nevertheless, existing enzyme commission (EC) number prediction methods are limited by database coverage and the depth of sequence information mining, hindering the efficiency and precision of enzyme function annotation. Therefore, this study introduces ProteEC-CLA (Protein EC number prediction model with Contrastive Learning and Agent Attention). ProteEC-CLA utilizes contrastive learning to construct positive and negative sample pairs, which not only enhances sequence feature extraction but also improves the utilization of unlabeled data. This process helps the model learn the differences in sequence features, thereby enhancing its ability to predict enzyme function. Integrating the pre-trained protein language model ESM2, the model generates informative sequence embeddings for deep functional correlation analysis, significantly enhancing prediction accuracy. With the incorporation of the Agent Attention mechanism, ProteEC-CLA's ability to comprehensively capture local details and global features is enhanced, ensuring high-accuracy predictions on complex sequences. The results demonstrate that ProteEC-CLA performs exceptionally well on two independent and representative datasets. In the standard dataset, it achieves 98.92% accuracy at the EC4 level. In the more challenging clustered split dataset, ProteEC-CLA achieves 93.34% accuracy and an F1-score of 94.72%. With only enzyme sequences as input, ProteEC-CLA can accurately predict EC numbers up to the fourth level, significantly enhancing annotation efficiency and accuracy, which makes it a highly efficient and precise functional annotation tool for enzymology research and applications.},
}

*Enzymes/chemistry/metabolism/classification
Databases, Protein
*Machine Learning
*Computational Biology/methods
Algorithms
Software
Data Mining
Proteins/chemistry

@article {pmid40705801,
year = {2025},
author = {Solowiej-Wedderburn, J and Pentz, JT and Lizana, L and Schroeder, BO and Lind, PA and Libby, E},
title = {Competition and cooperation: The plasticity of bacterial interactions across environments.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013213},
pmid = {40705801},
issn = {1553-7358},
mesh = {*Microbial Interactions/physiology ; *Models, Biological ; *Bacteria/genetics/metabolism ; Computational Biology ; Computer Simulation ; *Bacterial Physiological Phenomena ; Metabolic Networks and Pathways/genetics ; Ecosystem ; Environment ; },
abstract = {Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By computationally simulating thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This modeling approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions in response to the availability of environmental resources.},
}

*Microbial Interactions/physiology
*Models, Biological
*Bacteria/genetics/metabolism
Computational Biology
Computer Simulation
*Bacterial Physiological Phenomena
Metabolic Networks and Pathways/genetics
Ecosystem
Environment

@article {pmid40705402,
year = {2025},
author = {Oba, T and Takano, K and Sugawara, D and Kimura, K},
title = {Just-in-Time Delivery of Cognitive Behavioral Therapy-Based Exercises: Single-Case Experimental Design With Random Multiple Baselines.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e69556},
pmid = {40705402},
issn = {2561-326X},
mesh = {Humans ; *Cognitive Behavioral Therapy/methods ; Female ; Adult ; Male ; Middle Aged ; *Stress, Psychological/therapy/psychology ; *Mobile Applications ; Smartphone ; Single-Case Studies as Topic ; Feasibility Studies ; Japan ; },
abstract = {BACKGROUND: Just-in-time adaptive interventions (JITAIs) are a promising approach in mental health care given the potential scalability (ie, interventions are offered automatically and remotely) and preciseness (ie, the right interventions are offered at the right moments). Typically, a smartphone app is programmed to assess users' psychological states in daily life; when a particular state is detected, the app prompts users to engage in specific behaviors. Conceptually, JITAIs hold significant potential for precision health, although there is currently limited evidence in the literature.

OBJECTIVE: We implemented this scheme as a smartphone intervention for daily stress management, based on cognitive behavioral therapy (CBT), and evaluated its feasibility and efficacy using a single-case experimental design.

METHODS: A total of 8 Japanese adults (community sample: 4 women; mean 37.6, SD 13.1 y) were recruited. An AB phase design with multiple random baselines was used, where "A" represents the baseline phase and "B" represents the intervention phase. Throughout the study period (28 d), participants were prompted to indicate their momentary levels of stress (range 0-100) using a smartphone thrice a day. The baseline phase duration was randomly varied among participants, lasting between 7 and 14 days. The remaining period was used as the intervention phase (14-21 d), where 6 CBT-based exercises (ie, breath control, mindfulness, relaxation, self-talk, cognitive defusion, and cognitive restructuring) were offered depending on the reported levels of stress.

RESULTS: Approximately 70% (6/8) of the participants perceived the intervention to be useful and helpful. A randomization test detected a statistically significant decrease in reported stress levels after the intervention began (P=.005), though this effect was less pronounced when analyzed individually for each participant. Multilevel model analysis detected a significant acute reduction in the momentary level of stress right after completing a CBT-based exercise (pre-exercise: mean 47.98, SD 21.65; post exercise: mean 42.13, SD 19.88; P=.03; Cohen dz=0.58). Also, a significant reduction in depressive rumination was observed in the postintervention assessment (preintervention: mean 13.00, SD 3.21; post intervention: mean 9.25, SD 2.60; P=.01, Cohen dz=1.17).

CONCLUSIONS: The intervention was feasible and effective in reducing subjective stress (and rumination) in the study sample. The small sample size and the nonclinical nature of the sample may limit the generalizability and implications of the study findings for clinical practice. More evidence should be collected to draw solid conclusions for technical and technological as well as clinical aspects of mobile interventions. Accumulating exemplars with different implementations will clarify how a JITAI can be designed and developed on a mobile platform and how the program can be delivered in the prevention and treatment of mental ill health.},
}

Humans
*Cognitive Behavioral Therapy/methods
Female
Adult
Male
Middle Aged
*Stress, Psychological/therapy/psychology
*Mobile Applications
Smartphone
Single-Case Studies as Topic
Feasibility Studies
Japan

@article {pmid40703330,
year = {2025},
author = {Boyes, D and Crowley, LM and Adewumi, T and , and , and , and , and , and , and , },
title = {The genome sequence of the Small Dotted Buff moth, Photedes minima Haworth, 1809.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {299},
pmid = {40703330},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Photedes minima (Small Dotted Buff; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 694.66 megabases. Most of the assembly (99.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.38 kilobases.},
}

@article {pmid40702785,
year = {2025},
author = {Lee, TY and Chen, CH and Liu, CM and Chen, IM and Chen, HC and Wu, SI and Hsiao, CK and Kuo, PH},
title = {Fourier Transform Analysis of GPS-Derived Mobility Patterns for Diagnosis and Mood Monitoring of Bipolar and Major Depressive Disorders: Prospective Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e71658},
pmid = {40702785},
issn = {1438-8871},
mesh = {Humans ; *Depressive Disorder, Major/diagnosis ; *Bipolar Disorder/diagnosis ; *Geographic Information Systems ; Female ; Male ; Adult ; Prospective Studies ; *Fourier Analysis ; Middle Aged ; Affect ; },
abstract = {BACKGROUND: Mood disorders, including bipolar disorder (BP) and major depressive disorder (MDD), are characterized by significant psychological and behavioral fluctuations, with mobility patterns serving as potential markers of emotional states.

OBJECTIVE: This study explores the diagnostic and monitoring capabilities of Fourier transform, a frequency-domain analysis method, in mood disorders by leveraging GPS data as an objective measure.

METHODS: A total of 62 participants (BP: n=20, MDD: n=27, and healthy controls: n=15) contributed 5177 person-days of data over observation periods ranging from 5 days to 6 months. Key GPS indicators-location variance (LV), transition time (TT), and entropy-were identified as reflective of mood fluctuations and diagnostic differences between BP and MDD.

RESULTS: Fourier transform analysis revealed that the maximum power spectra of LV and entropy differed significantly between BP and MDD groups, with patients with BP exhibiting greater periodicity and intensity in mobility patterns. Notably, participants with BP demonstrated consistent periodic waves (eg, 1-d, 4-d, and 9-d cycles), while such patterns were absent in those with MDD. In addition, after adjusting for age, gender, and employment status, only the power spectrum of LV remained a significant predictor of depressed mood (odds ratio [OR] 0.9976, 95% CI 0.9956-0.9996; P=.02). Daily GPS data showed stronger correlations with ecological momentary assessment (EMA)-reported mood states compared to weekly or monthly aggregations, emphasizing the importance of day-to-day monitoring. Depressive states were associated with reduced LV (OR 0.975, 95% CI 0.957-0.993; P=.008) and TT (OR 0.048, 95% CI 0.012-0.200; P<.001) on weekdays, and lower entropy (OR 0.662, 95% CI 0.520-0.842; P=.001) on weekends, indicating that mobility features vary with social and temporal contexts.

CONCLUSIONS: This study underscores the potential of GPS-derived mobility data, analyzed through Fourier transform, as a noninvasive and real-time diagnostic and monitoring tool for mood disorders. The findings suggest that the intensity of mobility patterns, rather than their frequency, may better differentiate BP from MDD. Integrating GPS data with EMAs could enhance the precision of clinical assessments, provide early warnings for mood episodes, and support personalized interventions, ultimately improving mental health outcomes. This approach represents a promising step toward digital phenotyping and advanced mental health monitoring strategies.},
}

Humans
*Depressive Disorder, Major/diagnosis
*Bipolar Disorder/diagnosis
*Geographic Information Systems
Female
Male
Adult
Prospective Studies
*Fourier Analysis
Middle Aged
Affect

@article {pmid40702703,
year = {2025},
author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M},
title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40702703},
issn = {1477-4054},
support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; },
abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.},
}

*Genome, Viral
*RNA Viruses/genetics
Animals
*Computational Biology/methods
Metagenomics/methods
*Software
RNA, Viral/genetics

@article {pmid40700599,
year = {2025},
author = {Mofidifar, S and Tefagh, M},
title = {Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {7},
pages = {},
pmid = {40700599},
issn = {1367-4811},
mesh = {*Phylogeny ; *Models, Biological ; *Microbiota ; *Metagenomics/methods ; *Computational Biology/methods ; Computer Simulation ; },
abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.

RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.

PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.},
}

*Phylogeny
*Models, Biological
*Microbiota
*Metagenomics/methods
*Computational Biology/methods
Computer Simulation

@article {pmid40522165,
year = {2025},
author = {Huang, JN and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ},
title = {Microplastics Change the Food Utilization of Filter-Feeding Fish via Gut Microbiota.},
journal = {Environmental science & technology},
volume = {59},
number = {29},
pages = {15353-15363},
doi = {10.1021/acs.est.5c02067},
pmid = {40522165},
issn = {1520-5851},
mesh = {Animals ; *Carps/growth & development/microbiology/parasitology ; *Environmental Pollutants/toxicity ; Fecal Microbiota Transplantation ; *Feeding Behavior/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Multiomics ; Zebrafish ; Phytoplankton ; Zooplankton ; Food Chain ; },
abstract = {Microplastics (MPs) are ubiquitous in aquatic environments, while their effects on filter-feeding fish are poorly understood. This study aims to explore how MPs change the feeding of planktivorous silver carp. After exposure to MPs, the utilization efficiency of zooplankton by carp increased from 28.45% to 38.63-40.20%, while that of phytoplankton decreased from 50.64% to 40.47-43.32%. MPs did not cause changes in the phytoplankton and zooplankton communities that carp consumed but altered its gut microbiota, leading to increased abundance of genes encoding proteases but decreased carbohydrase genes. Gut metabolomics further showed corresponding metabolic changes especially with increased levels of l-tyrosine, citrulline, succinic acid, and propionic acid, which are significantly correlated with the isotopic signatures of carp utilizing zooplankton. Germ-free zebrafish transplanted with feces of MPs-exposed carp showed metabolic changes like those of carp, verifying that the gut microbiota mediated the effects induced by MPs, while silver carp transplanted with feces of MPs-exposed carp exhibited increased protease activity and enhanced zooplankton utilization efficiency, confirming that MPs could alter its food utilization via gut microbiota. Our findings fill a knowledge gap regarding the ecological risk of MPs to the feeding of planktivorous fish, with potential cascading effects on aquatic ecosystems.},
}

Animals
*Carps/growth & development/microbiology/parasitology
*Environmental Pollutants/toxicity
Fecal Microbiota Transplantation
*Feeding Behavior/drug effects
*Gastrointestinal Microbiome/drug effects
*Microplastics/toxicity
Multiomics
Zebrafish
Phytoplankton
Zooplankton
Food Chain

@article {pmid40699651,
year = {2025},
author = {Wang, H and Zhou, H and Yao, X},
title = {Different Species of Bats: Genomics, Transcriptome, and Immune Repertoire.},
journal = {Current issues in molecular biology},
volume = {47},
number = {4},
pages = {},
pmid = {40699651},
issn = {1467-3045},
support = {82160279//National Natural Science Foundation of China/ ; No. (2018)5637//Guizhou Provincial Hundred level Talent Fund/ ; },
abstract = {Bats are the only mammals with the ability to fly and are the second largest order after rodents, with 20 families and 1213 species (over 3000 subspecies) and are widely distributed in regions around the world except for Antarctica. What makes bats unique are their biological traits: a tolerance to zoonotic infections without getting clinical symptoms, long lifespans, a low incidence of tumors, and a high metabolism. As a result, they are receiving increasing attention in the field of life sciences, particularly in medical research. The rapid advancements in sequencing technology have made it feasible to comprehensively analyze the diverse biological characteristics of bats. This review comprehensively discusses the following: (1) The assembly and annotation overview of 77 assemblies from 54 species across 11 families and the transcriptome sequencing overview of 42 species from 7 families, focused on a comparative analysis of genomic architecture, sensory adaptations (auditory, visual, and olfactory), and immune functions. Key findings encompass marked interspecies divergence in genome size, lineage-specific expansions/contractions of immune-related gene families (APOBEC, IFN, and PYHIN), and sensory gene adaptations linked to ecological niches. Notably, echolocating bats exhibited convergent evolution in auditory genes (SLC26A5 and FOXP2), while fruit-eating bats displayed a degeneration of vision-associated genes (RHO), reflecting trade-offs between sensory specialization and ecological demands. (2) The annotation of the V (variable), D (diversity), J (joining), and C (constant) gene families in the TR and IG loci of 12 species from five families, with a focus on a comparative analysis of the differences in TR and IG genes and CDR3 repertoires between different bats and between bats and other mammals, provides us with a deeper understanding of the development and function of the immune system in organisms. Integrated genomic, transcriptomic, and immune repertoire analyses reveal that bats employ distinct antiviral strategies, primarily mediated by enhanced immune tolerance and suppressed inflammatory responses. This review provides foundational information, collaboration directions, and new perspectives for various laboratories conducting basic and applied research on the vast array of bat biology.},
}

@article {pmid40698863,
year = {2025},
author = {Woo, H and Eyun, SI},
title = {Applications and techniques of single-cell RNA sequencing across diverse species.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40698863},
issn = {1477-4054},
support = {RS-2022-KS221676//Korea Institute of Marine Science & Technology Promotion/ ; RS-2025-02215227//Korea Institute of Marine Science & Technology Promotion/ ; 2022R1A2C4002058//National Research Foundation of Korea/ ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Sequence Analysis, RNA/methods ; Animals ; Gene Expression Profiling/methods ; Transcriptome ; Computational Biology/methods ; },
abstract = {Single-cell ribonucleic acid sequencing (scRNA-seq) is an important tool in molecular biology, allowing transcriptomic profiling at the single-cell level. This transformative technology has provided unprecedented insights into cellular heterogeneity, lineage differentiation, and cell-type-specific gene expression patterns, significantly advancing our understanding of complex biological systems. scRNA-seq is broadly applied across various fields, including oncology, where it sheds light on intratumoral heterogeneity and precision medicine strategies, and developmental biology, where it uncovers cellular trajectories in both model and non-model organisms. Additionally, scRNA-seq has been instrumental in ecological genomics, which can help elucidate cellular responses to environmental perturbations and species interactions. Despite these advancements, several challenges remain, particularly technical and financial barriers, limiting its application to non-model organisms and tissues with complex cellular compositions. Addressing these issues will require continued innovation in single-cell isolation methods, cost-effective sequencing technologies, and sophisticated bioinformatics tools. As scRNA-seq advances, it can deepen our understanding of biological systems, with broad implications for personalized medicine, evolutionary biology, and ecological research.},
}

*Single-Cell Analysis/methods
Humans
*Sequence Analysis, RNA/methods
Animals
Gene Expression Profiling/methods
Transcriptome
Computational Biology/methods

@article {pmid40697421,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Dark Umber moth, Philereme transversata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {300},
pmid = {40697421},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Philereme transversata (Dark Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 591.75 megabases. Most of the assembly (99.1%) is scaffolded into 20 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.07 kilobases. Gene annotation of this assembly on Ensembl identified 12,207 protein-coding genes.},
}

@article {pmid40694591,
year = {2025},
author = {Gong, R and Feng, Z and Zhang, Y},
title = {Using homologous network to identify reassortment risk in H5Nx avian influenza viruses.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013301},
pmid = {40694591},
issn = {1553-7358},
mesh = {Animals ; *Influenza in Birds/virology/epidemiology ; *Reassortant Viruses/genetics ; *Influenza A virus/genetics ; Birds/virology ; Computational Biology ; Poultry/virology ; Phylogeny ; },
abstract = {The resurgence of H5Nx reassortment has caused multiple epidemics resulting in severe disease even death in wild birds and poultry. Assessing H5Nx reassortment risk is crucial for designing targeted interventions and enhancing preparedness efforts to manage H5Nx outbreaks effectively. However, the complexity in H5Nx reassortment, driven by the diversity of influenza A viruses (IAVs) and wide range of hosts, has hindered the effective quantification of reassortment risk. In this study, we utilized a network approach to explore the reassortment history using a large-scale dataset. By inferring genomic homogeneity among IAVs, we constructed an IAVs homologous network with reassortment history embedded within it. We estimated the communities within the IAVs homologous network to represent the reassortment risk of various viruses, revealing diverse reassortment risks across different H5Nx viruses. Our analysis also identified the primary hosts contributing to reassortment: domestic poultry in China, and wild birds in North America and Europe. These primary hosts are critical targets for future H5Nx reassortment interventions. Our study provides a framework for quantifying and ranking H5Nx reassortment risk, contributing to enhanced preparedness and prevention efforts.},
}

Animals
*Influenza in Birds/virology/epidemiology
*Reassortant Viruses/genetics
*Influenza A virus/genetics
Birds/virology
Computational Biology
Poultry/virology
Phylogeny

@article {pmid40691457,
year = {2025},
author = {Steckler, MR and Kumar, J and Breen, AL and Zhang, T and Hoffman, FM and Hargrove, WW and Walker, DA and Wells, AF and Droghini, A and Nawrocki, TW and Wullschleger, SD and Macander, MJ and Frost, GV and Salmon, VG and Barnett, DT and Iversen, CM},
title = {PAVC: The foundation for a Pan-Arctic Vegetation Cover database.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1271},
pmid = {40691457},
issn = {2052-4463},
mesh = {Arctic Regions ; *Plants/classification ; *Databases, Factual ; Remote Sensing Technology ; Ecosystem ; Trees ; },
abstract = {Field-measured Arctic vegetation cover data is essential for creating accurate, high-quality vegetation structure and composition maps. Extrapolating field data into high-resolution cover maps provides detailed, function-specific information for use in Earth System Models, vegetation classifications, and monitoring vegetation change over time and space. However, field campaigns that collect plant cover vary substantially in scope, method, and purpose, which makes them difficult to unify across data stores, and they are often not designed to meet remote sensing needs. In this work, we synthesized and harmonized field-based fractional cover data from various data stores to create a high-quality, consistent repository schema for remote sensing-based vegetation cover mapping applications. We developed a reproducible workflow for synthesizing visual estimate and point-intercept fractional cover data. The resultant Pan-Arctic Vegetation Cover (PAVC) database contains synthesized fractional cover at both the species and plant functional type levels. The latter includes absolute foliar cover for deciduous shrubs and trees, evergreen shrubs and trees, forbs, graminoids, lichen, bryophytes, and "other" vegetation, as well as absolute cover for litter and top cover for water and bare ground.},
}

Arctic Regions
*Plants/classification
*Databases, Factual
Remote Sensing Technology
Ecosystem
Trees

@article {pmid40688383,
year = {2025},
author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S},
title = {Analysis of metagenomic data.},
journal = {Nature reviews. Methods primers},
volume = {5},
number = {},
pages = {},
pmid = {40688383},
issn = {2662-8449},
support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; R35 GM146980/GM/NIGMS NIH HHS/United States ; R01 GM146462/GM/NIGMS NIH HHS/United States ; R01 AI173172/AI/NIAID NIH HHS/United States ; R01 AI100947/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.},
}

@article {pmid40664368,
year = {2025},
author = {Li, P and Zhu, B and Fu, J and Liu, X and Huang, K and Pan, W and Xue, Q and Zhang, H and Zhang, A and Fu, J and Jiang, G},
title = {Nontarget Screening Analysis Combined with Computational Toxicology: A Promising Solution for Identification and Risk Assessment of Environmental Pollutants in the Big Data Era.},
journal = {Environmental science & technology},
volume = {59},
number = {29},
pages = {14842-14852},
doi = {10.1021/acs.est.4c13225},
pmid = {40664368},
issn = {1520-5851},
mesh = {Risk Assessment ; *Environmental Pollutants ; *Big Data ; *Toxicology ; },
abstract = {Synthetic chemicals are intensively utilized in modern societies, and their mixtures pose significant health and ecological threats. Nontarget screening (NTS) analysis allows for the simultaneous chemical identification and quantitative reporting of tens of thousands of chemicals in complex environmental matrices, whereas the computational toxicology (CT) serves as another high-throughput means of rapidly and comprehensively screening chemicals for toxicity. To date, there has been a lack of guidance on how to combine NTS experiments and CT for the risk assessment of chemical mixtures and the prioritization of pollutants. In this perspective, the combination of two "big data" approaches in field studies is systematically proposed. The basic principles of performing NTS and CT in environmental studies are briefly outlined. The "top-down" and "bottom-up" strategies are proposed to summarize the two technologies during the experimental design stage, in accordance with research objectives and available information and tools. Following this, a universal framework combining NTS and CT is thoroughly explored. Six recommendations for future research are highlighted to enhance the utilization of this paradigm, involving multistep combination, multidisciplinary database, application platform, multilayered functionality, effect validation, and standardization.},
}

Risk Assessment
*Environmental Pollutants
*Big Data
*Toxicology

@article {pmid40583524,
year = {2025},
author = {Kanamori, S and Imamura, K and Inagawa, Y and Yamauchi, T and Ikeda, H and Okuyama, T and Muto, G and Kato, R and Iida, M and Asaoka, H and Inoue, A and Watanabe, K and Tsuno, K and Sasaki, N and Kobayashi, Y and Sakuraya, A and Komase, Y and Otsuka, Y and Iwanaga, M and Inoue, R and Kuribayashi, K and Hino, A and Shimazu, A and Tsutsumi, A and Kawakami, N and Tani, N and Eguchi, H and Kojimahara, N and Ebara, T},
title = {Physical activity interventions delivered through digital health technology for improving workers' mental health symptoms: a systematic review and meta-analysis.},
journal = {Journal of occupational health},
volume = {67},
number = {1},
pages = {},
doi = {10.1093/joccuh/uiaf035},
pmid = {40583524},
issn = {1348-9585},
support = {//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Exercise ; Randomized Controlled Trials as Topic ; *Occupational Health ; *Mental Health ; *Digital Technology ; Depression/prevention & control ; *Health Promotion/methods ; Digital Health ; },
abstract = {OBJECTIVES: This study aimed to clarify the primary preventive effects of physical activity interventions delivered through digital health technology (DHT) on workers' mental health symptoms, and to examine the conditions of attrition and adherence in these interventions.

METHODS: We examined randomized controlled trials (RCTs) that analyzed the effects of physical activity interventions delivered through DHT on workers' health outcomes. We included RCTs published in English or Japanese since 2010 and excluded studies that targeted specific diseases or secondary and tertiary prevention. We conducted the search on July 25, 2023, using Cochrane CENTRAL, Embase, PsycINFO, PubMed, and Ichushi-Web, and citation searches. We assessed risk of bias using the Cochrane Risk of Bias Tool version 2, and data were integrated using a random-effects model. Attrition rates were averaged, and adherence was qualitatively reviewed.

RESULTS: Eight studies were included in the systematic review, and 5 in the meta-analysis. Pooled effect sizes immediately after intervention were as follows: Cohen d = -0.51 (95% CI, -0.75 to -0.27) for depression and negative affect, and -0.36 (95% CI, -0.60 to -0.05) for perceived stress. The attrition rate was 16.8% and 12.4% for the control and intervention groups, with only 2 studies providing details on adherence.

CONCLUSIONS: Physical activity interventions delivered through DHT may moderately improve depression and negative affect, and slightly reduce perceived stress among workers. However, these findings should be interpreted with caution due to the limited number of studies and low evidence certainty. Future studies should explore long-term effects, additional mental health outcomes, and factors affecting adherence.},
}

Humans
*Exercise
Randomized Controlled Trials as Topic
*Occupational Health
*Mental Health
*Digital Technology
Depression/prevention & control
*Health Promotion/methods
Digital Health

@article {pmid40687154,
year = {2025},
author = {Filippova, NV and Zvyagina, EA and Bolshakov, SY and Arefyev, SP and Bulyonkova, TM and Filippov, IV and Rebriev, YA and Shiryaev, AG and Stavishenko, IV and Svetasheva, TY},
title = {Occurrence dataset of protected fungal species for the Red Data Book in Yugra Region, Western Siberia.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e155657},
pmid = {40687154},
issn = {1314-2828},
abstract = {BACKGROUND: The data paper describes a dataset of occurrences of fungal species listed in the Red Data Book of Yugra Region (Western Siberia, Russia). The dataset is based on all digitised records of fungal occurrences in the region. The authors conducted an assessment of the conservation status of fungal species for the revised third edition of the Red Data Book of Yugra. The third edition of the Red Data Book of Yugra includes a total of 61 fungal species (excluding lichens). Of these, nine species are listed on the IUCN Red List and six are included in the Red Data Book of Russia. At the time of publication, the dataset comprises 1180 records of protected species, including human observations, preserved specimens and material citations from literature.

NEW INFORMATION: The paper provides the first overview of the history of fungal conservation in Yugra (Khanty-Mansi Autonomous Okrug-Yugra, KhMAO-Yugra). For the first time, open-source data are used for the assessment of the occurrence of rare species and evaluation of their conservation status for the revised third edition of the Red Data Book of Yugra. An integrated occurrence dataset for the species included in the new edition of the Red Data Book is presented.},
}

@article {pmid40683291,
year = {2025},
author = {Winkler, AS and Brux, CM and Carabin, H and das Neves, CG and Häsler, B and Zinsstag, J and Fèvre, EM and Okello, A and Laing, G and Harrison, WE and Pöntinen, AK and Huber, A and Ruckert, A and Natterson-Horowitz, B and Abela, B and Aenishaenslin, C and Heymann, DL and Rødland, EK and Berthe, FCJ and Capua, I and Sejvar, J and Lubroth, J and Corander, J and May, J and Roth, LF and Thomas, LF and Blumberg, L and Lapinski, MK and Stone, M and Agbogbatey, MK and Xiao, N and Hassan, OA and Dar, O and Daszak, P and Guinto, RR and Senturk, S and Sahay, S and Samuels, TA and Wasteson, Y and Amuasi, JH},
title = {The Lancet One Health Commission: harnessing our interconnectedness for equitable, sustainable, and healthy socioecological systems.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(25)00627-0},
pmid = {40683291},
issn = {1474-547X},
}

@article {pmid40607556,
year = {2025},
author = {Wu, HW and Gong, CA and Gong, ZN and Zhao, YX and Qiu, HC and Chen, AK},
title = {Monitoring of salt marsh vegetation community succession process in Yellow River Delta supported by multidimensional long time-series feature dataset.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {6},
pages = {1759-1769},
doi = {10.13287/j.1001-9332.202506.029},
pmid = {40607556},
issn = {1001-9332},
mesh = {Chenopodiaceae/growth & development ; China ; Conservation of Natural Resources ; *Environmental Monitoring/methods ; *Poaceae/growth & development ; Population Dynamics ; Rivers ; *Wetlands ; Datasets as Topic ; },
abstract = {The spatial distribution of salt marsh vegetation in Yellow River Delta are highly heterogeneous. Accurate information on the historical distribution of salt marsh is of great significance for regional ecological stability and sustainable development. We constructed a long-series temporal-spatial-spectral multidimensional elicitation based on multi-source data, and accurately extracted information on the spatial distribution of typical salt marsh in the Yellow River Delta from 1996 to 2022 using a random forest (RF) model with recursive feature elimination, and further analyzed the succession of the native/invasive salt marsh communities since the diversion of the Yellow River in 1996. Compared to the single temporal spectral feature, the use of a temporal-spatial-spectral multidimensional feature set for extraction improved the overall accuracy of salt marsh vegetation classification by 8.4%. The classification effect of the sparse Suaeda salsa and the mixed area of Phragmites australis and Spartina alterniflora was optimized based on the temporal and spatial features of optical and SAR images. The distribution of salt marsh on the tidal flats after the Yellow River was diverted was obvious. The cover area of S. salsa communities decreased from 91.67 km[2] in 1996 to 38.11 km[2] in 2022, with the successional trend being influenced by the invasion of S. alterniflora. S. alterniflora was rapidly expanded and then distributed in large areas on the tidal flats on both sides of the current river channel since 2008. The area of the community reached the maximum (51.25 km[2]) in 2020. The invasion and expansion of S. alterniflora had a certain impact on the habitat pattern of the tidal flats.},
}

Chenopodiaceae/growth & development
China
Conservation of Natural Resources
*Environmental Monitoring/methods
*Poaceae/growth & development
Population Dynamics
Rivers
*Wetlands
Datasets as Topic

@article {pmid40367572,
year = {2025},
author = {Wang, H and Li, L and Wu, J and Yuan, X and Hong, L and Pu, L and Qin, S and Li, L and Yang, H and Zhang, J},
title = {Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105275},
pmid = {40367572},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Ducks/microbiology/blood/physiology/growth & development ; *Body Weight ; RNA, Ribosomal, 16S/analysis ; Metabolomics ; *Metabolome ; Male ; Bacteria/classification/isolation & purification ; Multiomics ; },
abstract = {Fledgling broiler ducks vary in body weight and growth rate. The aim of this study was to investigate the relationship between serum metabolites and the intestinal microbiota in Cherry Valley broiler ducks with different finishing weights and to reveal differences in their metabolic regulation and microbial composition. Serum and cecum content samples were collected from Cherry Valley broiler ducks of different finishing weights. Metabolites were identified and compared using untargeted metabolomics, 16S rRNA gene sequencing, multivariate statistics and bioinformatics. Six key findings emerged. First, serum biochemical parameters showed that AST and ALT levels were significantly lower in the high weight group (Group H) than in the low weight group (Group L), and serum immunoglobulin IgG levels were significantly higher in group H. Second, the chorionic height to crypt depth ratio of the duodenum was significantly higher in group H than in group L. Third, the gut microbial community diversity or abundance was lower in broiler ducks in group L. Fourth, LEfSe analysis showed that the biomarker for group L was Streptococcus, whereas for group H it was Faecalibacterium. Fifth, a total of 127 differential metabolites were identified (49 up-regulated and 78 down-regulated). Finally, Spearman's correlation analysis showed that Spearman's correlation analyses showed that the Lipid-related serum metabolites were higher in low-body recombinant broiler ducks, mainly Lathosterol, Cholesterol, Cynaratriol and Leukotriene B4. In addition to lipid-associated serum metabolites in high-body recombination, The water-soluble vitamin-like metabolite Pantothenate and the antibiotic-like metabolite Tylosin were high. The cecum microbiota is strongly associated with metabolites, especially Faecalibacterium, unclassified Tannerellaceae, Subdoligranulum, Alistipes, and [Ruminococcus] torques_group, with which it exhibits strong Correlation. Broiler ducks with higher body weights have a better intestinal villous structure, enhanced digestion and absorption, higher levels of immunoglobulin secretion and superior growth performance. Broiler ducks with different body weights differed in plasma metabolites and cecum flora. Spearman's correlation analyses showed that the Correlation between differential metabolites and differential gut microbial genera.},
}

Animals
*Gastrointestinal Microbiome
*Ducks/microbiology/blood/physiology/growth & development
*Body Weight
RNA, Ribosomal, 16S/analysis
Metabolomics
*Metabolome
Male
Bacteria/classification/isolation & purification
Multiomics

@article {pmid40091737,
year = {2025},
author = {Slipetz, LR and Falk, A and Henry, TR},
title = {Missing Data in Discrete Time State-Space Modeling of Ecological Momentary Assessment Data: A Monte-Carlo Study of Imputation Methods.},
journal = {Multivariate behavioral research},
volume = {60},
number = {4},
pages = {695-710},
doi = {10.1080/00273171.2025.2469055},
pmid = {40091737},
issn = {1532-7906},
mesh = {*Ecological Momentary Assessment ; Humans ; *Monte Carlo Method ; *Models, Statistical ; Data Interpretation, Statistical ; Bias ; Computer Simulation ; Time Factors ; },
abstract = {When using ecological momentary assessment data (EMA), missing data is pervasive as participant attrition is a common issue. Thus, any EMA study must have a missing data plan. In this paper, we discuss missingness in time series analysis and the appropriate way to handle missing data when the data is modeled as an idiographic discrete time continuous measure state-space model. We found that Missing Completely at Random, Missing At Random, and Time-dependent Missing At Random data have less bias and variability than Autoregressive Time-dependent Missing At Random and Missing Not At Random. The Kalman filter excelled at handling missing data under most conditions. Contrary to the literature, we found that using a variety of methods, multiple imputations struggled to recover the parameters.},
}

*Ecological Momentary Assessment
Humans
*Monte Carlo Method
*Models, Statistical
Data Interpretation, Statistical
Bias
Computer Simulation
Time Factors

@article {pmid40680476,
year = {2025},
author = {Roel Lesur, M and Longo, MR and Tajadura-Jiménez, A},
title = {Linking spatial metaphors to body size perception: Different roles of top-down associations and multisensory contributions when mapping auditory cues to finger length.},
journal = {Cortex; a journal devoted to the study of the nervous system and behavior},
volume = {190},
number = {},
pages = {178-191},
doi = {10.1016/j.cortex.2025.06.014},
pmid = {40680476},
issn = {1973-8102},
abstract = {Temporospatial and semantic multisensory aspects contribute to bodily and spatial perception. An informative paradigm to study this is the Auditory Pinocchio Illusion, in which participants perceive an elongation of their finger upon vertically pulling their finger and hearing a concurrent upward pitch glissando. This arguably relies on anchoring (i.e., associating) the ecologically unrelated upward pitch glissando to the finger and allows to separately assess the role of semantic and multisensory contributions. However, what is needed for this anchoring to occur is unknown. In a first Experiment, we manipulated top-down attention to the finger upon which either an ascending or descending sound would be produced. In a second experiment, we compared how different bottom-up multisensory cues (arising from actions performed on the finger) concurrent to the ascending or descending pitch affected finger length perception. Participants either pulled, touched or stretched their finger. Through a perceptual judgment task of finger landmark localization and questionnaire ratings, we measured participants' perceived finger length in both studies and separately assessed their sensory imagery skills. Our results show that attention alters finger length perception according to questionnaire ratings but not perceptual judgements, while concurrent multisensory signals similarly affect both measures. No relationship between these effects and participants' sensory imagery was found. We suggest that while top-down associations between pitch and verticality are necessary and affect questionnaire ratings, they are not sufficient to affect perceptual judgements. Bottom-up somatosensory cues seem to be additionally needed to impact such judgements in this illusion.},
}

@article {pmid40680084,
year = {2025},
author = {Laplane, L and Lamoureux, A and Richker, HI and Marquez Alcaraz, G and Fortunato, A and Shaffer, Z and Aktipis, A and Mischel, PS and Plutynski, A and Townsend, JP and Maley, CC},
title = {Applying multilevel selection to understand cancer evolution and progression.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003290},
doi = {10.1371/journal.pbio.3003290},
pmid = {40680084},
issn = {1545-7885},
abstract = {Natural selection occurs at multiple levels of organization in cancer. At an organismal level, natural selection has led to the evolution of diverse tumor suppression mechanisms, while at a cellular level, it favors traits that promote cellular proliferation, survival and cancer. Natural selection also occurs at a subcellular level, among collections of cells and even among collections of organisms; selection at these levels could influence the evolution of cancer and cancer suppression mechanisms, affecting cancer risk and treatment strategies. There may also be cancer-like processes happening at different levels of organization, in which uncontrolled proliferation at lower levels may disrupt a higher level of organization. This Essay examines how selection operates across levels, highlighting how we might leverage this understanding to improve cancer research, prevention and treatment.},
}

@article {pmid40678991,
year = {2025},
author = {Miller-Ter Kuile, A and Bui, A and Apigo, A and Lamm, S and Swan, M and Sanderlin, JS and Ogle, K},
title = {If You're Rare, Should I Care? How Imperfect Detection Changes Relationships Between Biodiversity and Global Change Drivers.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70362},
doi = {10.1111/gcb.70362},
pmid = {40678991},
issn = {1365-2486},
support = {Challenge Cost Share 21-CS-11221635-194//Rocky Mountain Research Station/ ; },
mesh = {*Biodiversity ; Animals ; Birds ; Plants ; Insecta ; *Climate Change ; Uncertainty ; Conservation of Natural Resources ; },
abstract = {Across ecosystems and biomes, most species in biological communities are rare. Many studies discount rare species when examining biodiversity patterns, assuming that common species are most influential for ecosystem functioning. There is growing evidence, however, that rare species contribute unique functions in many ecosystems; thus, discounting them produces misleading conclusions about how biodiversity is changing in the face of natural and anthropogenic forces. Rare species are more likely to be missed by multi-species sampling designs and are thus particularly vulnerable to detection error. Best practice in biodiversity assessments should include rare species and account for error in the detection process. We outline a general approach that accounts for detection error in sampling designs using multi-species occupancy and abundance models (MSOM/MSAM). We then show how uncertainty in detection can be propagated from MSOM/MSAM results to derive more accurate estimates of alpha and beta diversity metrics. Finally, we show how uncertainty in these diversity metrics can be accounted for in follow-up regression models to evaluate relationships between biodiversity and global change covariates. Using three case studies across diverse taxa (birds, insects, and plants), we demonstrate how accounting for the detection process alters the relationships between biodiversity and global change drivers in ways that are important for understanding and predicting ongoing change in these communities. Our generalizable analysis approach can aid in accounting for rare species in studies of global biodiversity.},
}

*Biodiversity
Animals
Birds
Plants
Insecta
*Climate Change
Uncertainty
Conservation of Natural Resources

@article {pmid40677746,
year = {2025},
author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D},
title = {Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19674},
pmid = {40677746},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; Pacific Ocean ; Animals ; *Aquatic Organisms/genetics/classification ; Biodiversity ; Electron Transport Complex IV/genetics ; *Databases, Nucleic Acid/standards ; *Databases, Genetic ; },
abstract = {DNA barcoding is a widely used tool for species identification, with its reliability heavily dependent on reference databases. While the quality of these databases has long been debated, a critical knowledge gap remains in their comprehensive evaluation and comparison at regional scales. Marine metazoan species in the western and central Pacific Ocean (WCPO), a region characterized by high biodiversity and limited sequencing efforts, are an example of this gap. This study developed a systematic workflow to assess mitochondrial cytochrome c oxidase subunit I (COI) barcode coverage and sequence quality in two commonly used reference databases for DNA barcoding: the nucleotide reference database from the National Center for Biotechnology Information (NCBI); and from the Barcode of Life Data System (BOLD). Comparative analyses across marine phyla and WCPO regions identified significant barcode gaps and quality problems, providing insights to guide future barcoding efforts. NCBI exhibited higher barcode coverage, but lower sequence quality compared to BOLD. Quality issues, including over- or under-represented species, short sequences, ambiguous nucleotides, incomplete taxonomic information, conflict records, high intraspecific distances, and low inter-specific distances were identified in both databases, likely resulting from contamination, cryptic species, sequencing errors, or inconsistent taxonomic assignment. The barcode identification number (BIN) system in BOLD demonstrated potential for identifying and addressing problematic records, highlighting the benefits of curated databases. Significant barcode deficiencies and quality issues were observed in the south temperate region of WCPO and phyla such as Porifera, Bryozoa, and Platyhelminthes. Additionally, the COI barcode showed limited species-level resolution for certain taxa, including Scombridae and Lutjanidae. Addressing barcode coverage gaps, improving taxonomic representation, and enhancing sequence quality will be essential for strengthening future barcoding initiatives and advancing biodiversity monitoring and conservation in the WCPO and beyond. This study highlights the need for standardized database curation and sequencing practices to improve the global reliability and applicability of DNA barcoding.},
}

*DNA Barcoding, Taxonomic/methods/standards
Pacific Ocean
Animals
*Aquatic Organisms/genetics/classification
Biodiversity
Electron Transport Complex IV/genetics
*Databases, Nucleic Acid/standards
*Databases, Genetic

@article {pmid40674907,
year = {2025},
author = {Fan, Q and Hu, Y and Huang, S and Guo, Y and Guo, J and Liu, F and Qi, W and Liu, H and Qu, J},
title = {Anti-epidemic pharmaceuticals predominantly contributed to PPCPs flux in the Yangtze River during 2020.},
journal = {Water research},
volume = {286},
number = {},
pages = {124228},
doi = {10.1016/j.watres.2025.124228},
pmid = {40674907},
issn = {1879-2448},
abstract = {The COVID-19 pandemic triggered a surge in pharmaceutical consumption, yet its impact on large-scale riverine systems remains poorly quantified. This study investigated the spatiotemporal distribution, sources and transport flux of 58 pharmaceuticals and personal care products (PPCPs) across the Yangtze River Basin (3400 km mainstream and 8 tributaries) during 2020. The mean concentration of PPCPs was 200.2 ± 205.7 ng/L in 2020, with caffeine (28.2 %), carbamazepine (13.2 %), and metronidazole (9.2 %) as dominant compounds. It was estimated that 449.8 tons of PPCPs were discharged into the sea via the Yangtze River in 2020, of which 48 % (216.0 tons) originated from COVID-19-related pharmaceuticals (e.g., metronidazole, diclofenac). Compared to pre-pandemic levels (2018), the river experienced additional pollution pressure from 209.6 tons of COVID-19 related pharmaceutical emissions. Source apportionment identified post-consumer anthropogenic activities (domestic discharges, clinical effluent outflows, and veterinary applications) as primary contributors (p < 0.05), while industrial sources associated with pharmaceutical production contributed little. Low ecological risks were observed in the study area, likely attributable to high wastewater treatment rates (>90 % in most cities) and the high efficacy of centralized wastewater management. This study provided the first basin-scale quantitative evidence of pandemic-driven PPCP pollution, offering critical insights for balancing public health emergencies with sustainable water resource governance.},
}

@article {pmid40670386,
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 = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1195},
pmid = {40670386},
issn = {2052-4463},
support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; OT2OD034190//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01HG011274//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; OT2 OD034190/OD/NIH HHS/United States ; 60NANB20D166//United States Department of Commerce | National Institute of Standards and Technology (NIST)/ ; P01 CA272295/CA/NCI NIH HHS/United States ; S10 OD028587/OD/NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R35GM133747//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1936791//National Science Foundation (NSF)/ ; U01CA253405//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54 AG089334/AG/NIA NIH HHS/United States ; R01 CA266279/CA/NCI NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; 1919691//National Science Foundation (NSF)/ ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24HG011853//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
mesh = {Humans ; Whole Genome Sequencing ; *Genome, Human ; *Pancreatic Neoplasms/genetics ; *Carcinoma, Pancreatic Ductal/genetics ; Cell Line, Tumor ; },
abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic variants. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.},
}

Humans
Whole Genome Sequencing
*Genome, Human
*Pancreatic Neoplasms/genetics
*Carcinoma, Pancreatic Ductal/genetics
Cell Line, Tumor

@article {pmid40669920,
year = {2025},
author = {Piedboeuf-Potyka, K and Hering, R and Schulz, M and Mackowiak, M and Brinks, R and Kuß, O and Hoyer, A and Tönnies, T},
title = {Incidence of type 2 diabetes by socioeconomic deprivation in Germany between 2014 and 2019: an ecological study.},
journal = {BMJ open},
volume = {15},
number = {7},
pages = {e094824},
pmid = {40669920},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; Adult ; *Social Deprivation ; Socioeconomic Factors ; },
abstract = {OBJECTIVE: To estimate type 2 diabetes incidence trends by sex and socioeconomic position (SEP) and evaluate trends in SEP-related inequalities in incidence.

DESIGN: Ecological study using ambulatory claims data and regression-based modelling.

SETTING: All 401 counties in Germany, covering the entire country.

PARTICIPANTS: All individuals with statutory health insurance (~85% of the population). Incident cases of type 2 diabetes were identified annually from 2014 to 2019 using the International Statistical Classification of Diseases and Related Health Problems, 10th revision codes.

Incident type 2 diabetes at the county level, adjusted for age and modelled using a mixed negative binomial regression. SEP was measured using the German Index of Socioeconomic Deprivation, and a random intercept accounted for county-level heterogeneity.

RESULTS: The incidence of type 2 diabetes decreased between 2014 and 2017 and plateaued thereafter. Trends were similar between sexes and deprivation levels. The greatest difference was observed between high and low deprivation, with an incidence rate ratio of 1.20 (95% CI: 1.14 to 1.27) among men and 1.21 (95% CI: 1.14 to 1.27) among women in 2014.

CONCLUSIONS: There was a positive trend in the decline in age-adjusted type 2 diabetes incidence between 2014 and 2019. However, social inequality persisted with deprived groups at higher risk of type 2 diabetes. The level of inequality was comparable between men and women. Continued monitoring is essential to assess whether these short-term trends persist over time.},
}

Humans
*Diabetes Mellitus, Type 2/epidemiology
Germany/epidemiology
Female
Male
Incidence
Middle Aged
Aged
Adult
*Social Deprivation
Socioeconomic Factors

@article {pmid40661153,
year = {2025},
author = {Castoe, TA and Daly, M and Jungo, F and Kirchhoff, KN and Koludarov, I and Mackessy, S and Macrander, J and Mehr, S and Modica, MV and Sanchez, EE and Zancolli, G and Holford, M},
title = {A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications.},
journal = {Integrative organismal biology (Oxford, England)},
volume = {7},
number = {1},
pages = {obaf026},
pmid = {40661153},
issn = {2517-4843},
abstract = {Venoms are complex bioactive mixtures that have independently evolved across diverse animal lineages, including snails, insects, sea anemones, spiders, scorpions, and snakes. Despite the growing interest in venom research, data is fragmented across disparate databases which lack standardization and interoperability. A vision for the proposed VenomsBase platform presented here seeks to address these challenges by using the best practices approach in creating a centralized, open-access platform adhering to FAIR principles (Findable, Accessible, Interoperable, and Reproducible). VenomsBase will unify venom datasets, standardize terminology, and enable comparative analyses across species, facilitating novel toxin discovery and functional annotation. Key features of VenomsBase include user-friendly data submission modules with built-in validation, advanced cross-species analysis tools, and integration of multidisciplinary datasets spanning genomics, transcriptomics, proteomics, functional assays, and ecological metadata. A modular, cloud-based design will ensure scalability, while heuristic scoring systems will guide users toward high-confidence data entries. To promote accessibility, the envisioned VenomsBase will provide tutorials, regular training sessions, case studies, and feedback loops, supporting researchers at all levels. By harmonizing venom research and addressing the limitations of outdated or nonstandardized methods, VenomsBase aims to revolutionize the field, while being continuously improved and refined by venom experts. This initiative will unlock venoms' potential to make groundbreaking discoveries, address global health challenges, and foster collaboration and innovation across the scientific community.},
}

@article {pmid40660705,
year = {2025},
author = {Fernando Devasahayam, BR and Uthe, H and Poeschl, Y and Deising, HB},
title = {Confrontations of the Pathogenic Fungus Colletotrichum graminicola With a Biocontrol Bacterium or a Ubiquitous Fungus Trigger Synthesis of Secondary Metabolites With Lead Structures of Synthetic Fungicides.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70145},
pmid = {40660705},
issn = {1462-2920},
support = {//Deutsches Zentrum für integrative Biodiversitätsforschung Halle-Jena-Leipzig/ ; },
mesh = {*Colletotrichum/metabolism/genetics/physiology ; *Fungicides, Industrial/metabolism/chemistry ; Secondary Metabolism ; *Aspergillus nidulans/metabolism/genetics/physiology ; *Bacillus amyloliquefaciens/metabolism/physiology/genetics ; Zea mays/microbiology ; Plant Diseases/microbiology ; Biological Control Agents ; Multigene Family ; },
abstract = {Microbial biological control agents are increasingly used as an alternative to synthetic pesticides. The application of these microorganisms massively affects all members of plant-colonising microbial communities, including pathogenic fungi. In the majority of cases, the resulting competition for ecological niches is decided by the toxicity of microbial secondary metabolites (SMs) formed. In this study, we devised confrontation experiments employing the fungal maize pathogen Colletotrichum graminicola and antagonistic partners, that is the biocontrol bacterium Bacillus amyloliquefaciens and the ubiquitous ascomycete Aspergillus nidulans. Transcriptome studies uncovered strong de-regulation of the vast majority of the C. graminicola secondary metabolite biosynthetic gene clusters (SMBGCs), with 69% and 86% of these clusters de-regulated at confrontation sites with B. amyloliquefaciens or A. nidulans, respectively. In the biocontrol bacterium and in A. nidulans confronting the maize pathogen, 100% and 74% of the SMBGCs were transcriptionally de-regulated, respectively. Correspondingly, non-targeted high-resolution LC-MS/MS revealed a large repertoire of 1738 and 1466 novel features formed in the fungus-bacterium and fungus-fungus confrontation, respectively. Surprisingly, several of these belong to chemical classes with lead structures of synthetic fungicides.},
}

*Colletotrichum/metabolism/genetics/physiology
*Fungicides, Industrial/metabolism/chemistry
Secondary Metabolism
*Aspergillus nidulans/metabolism/genetics/physiology
*Bacillus amyloliquefaciens/metabolism/physiology/genetics
Zea mays/microbiology
Plant Diseases/microbiology
Biological Control Agents
Multigene Family

@article {pmid40659674,
year = {2025},
author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J},
title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1222},
pmid = {40659674},
issn = {2052-4463},
support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; },
abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.},
}

*Rivers/microbiology
China
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Microbiota
Metagenomics
*Genome, Archaeal
Databases, Genetic
*Genome, Bacterial

@article {pmid40659395,
year = {2025},
author = {Ka, MM and Gaye, ND and Tukakira, J and Kyem, D and Gary-Webb, T and Sattler, L and Jobe, M and Gaye, B},
title = {Trends over time in age-standardised prevalence of cardiometabolic risk factors in Senegal between 1975 and 2021 by sex: an ecological study from the WHO Inequality Data Repository.},
journal = {BMJ open},
volume = {15},
number = {7},
pages = {e101323},
pmid = {40659395},
issn = {2044-6055},
mesh = {Humans ; Senegal/epidemiology ; Male ; Female ; Prevalence ; Middle Aged ; *Diabetes Mellitus/epidemiology ; Adult ; *Hypertension/epidemiology ; *Obesity/epidemiology ; *Cardiometabolic Risk Factors ; Sex Factors ; World Health Organization ; Aged ; *Cardiovascular Diseases/epidemiology ; *Tobacco Use/epidemiology/trends ; Young Adult ; Overweight/epidemiology ; Risk Factors ; Adolescent ; Sex Distribution ; },
abstract = {OBJECTIVE: We aimed to analyse the time trends of cardiometabolic risk factors in Senegal from 1975 to 2021.

DESIGN: Ecological study of publicly available data from the WHO Health Inequality Data Repository.

SETTING: Disaggregated datasets from publicly available sources.

PRIMARY OUTCOME: Trends of age-standardised prevalence rates, stratified by sex for tobacco use, obesity, diabetes and hypertension, were analysed for significance.

PARTICIPANTS: Only data from Senegal were included in this study.

RESULTS: Tobacco use decreased in both sexes between 2000 and 2021, from 1.7% to 0.7% (p value 0.04) in females and from 28.1% to 12.8% (p value 0.04) in males. Obesity and overweight increased in both sexes between 1975 and 2016, from 14.2% to 35.9% (p value <0.001) in females and from 7.2% to 19.5% (p value<0.001) in males. Diabetes increased in both sexes between 1980 and 2014, from 4% to 7.3% (p value <0.001) in females and from 3.6% to 7.5% (p value <0.001) in males. Between 1990 and 2019, hypertension increased in females from 39.1% to 42.9% (p value <0.001). The prevalence of hypertension in males first rose from 37.5% to 40.0% (p value <0.001), then decreased to 37.3% (p value 0.013).

CONCLUSION: Our findings highlight changes in cardiometabolic risk factors in Senegal between 1975 and 2020 by sex. While tobacco use declined, rates of obesity, diabetes and hypertension increased. These findings underscore the need for strategies to mitigate this increase in cardiometabolic risk factors and a consequential rise in non-communicable diseases.},
}

Humans
Senegal/epidemiology
Male
Female
Prevalence
Middle Aged
*Diabetes Mellitus/epidemiology
Adult
*Hypertension/epidemiology
*Obesity/epidemiology
*Cardiometabolic Risk Factors
Sex Factors
World Health Organization
Aged
*Cardiovascular Diseases/epidemiology
*Tobacco Use/epidemiology/trends
Young Adult
Overweight/epidemiology
Risk Factors
Adolescent
Sex Distribution

@article {pmid40658737,
year = {2025},
author = {Lundberg, DS and Kersten, S and Mehmetoğlu Boz, E and Pramoj Na Ayutthaya, P and Zhu, W and Poersch, K and Yuan, W and Swartz, S and Müller, D and Bezrukov, I and , and Weigel, D},
title = {A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003237},
pmid = {40658737},
issn = {1545-7885},
mesh = {*Arabidopsis/growth & development/genetics/microbiology/immunology/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; Plant Diseases/microbiology/genetics/immunology ; Plant Leaves/microbiology/growth & development/genetics/metabolism ; Salicylic Acid/metabolism ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; Alleles ; Microbiota ; },
abstract = {When wild plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild Arabidopsis thaliana populations maintain significant functional variation at the ACD6 locus, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet they are of smaller stature, their leaves senesce earlier, and they set fewer seeds compared to plants with the standard allele. We hypothesized that ACD6 hyperactivity would not only affect the growth of microbial pathogens but also more generally change leaf microbiome assembly. To test this in an ecologically meaningful context, we compared plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both outdoors and in naturally lit and climate-controlled indoor conditions, taking advantage of near-isogenic lines as well as a natural accession and a CRISPR-edited derivative. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. The genetic precision of CRISPR-edited plants allowed us to conclude that ACD6 genotype had no effect on mature field plants in our setting, despite reproducibly dramatic effects on greenhouse plants. We conclude that additional abiotic and/or microbial signals present outdoors-but not in the greenhouse-greatly modulate ACD6 activity. This raises the possibility that the fitness costs of other commonly studied immune system genes may be grossly misjudged without field studies.},
}

*Arabidopsis/growth & development/genetics/microbiology/immunology/metabolism
*Arabidopsis Proteins/genetics/metabolism
Plant Diseases/microbiology/genetics/immunology
Plant Leaves/microbiology/growth & development/genetics/metabolism
Salicylic Acid/metabolism
Gene Expression Regulation, Plant
Disease Resistance/genetics
Alleles
Microbiota

@article {pmid40656455,
year = {2025},
author = {Komosar, M and Tamburro, G and Graichen, U and Comani, S and Haueisen, J},
title = {Combination of spatial and temporal de-noising and artifact reduction techniques in multi-channel dry EEG.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1576954},
pmid = {40656455},
issn = {1662-4548},
abstract = {INTRODUCTION: Dry electroencephalography (EEG) allows for recording cortical activity in ecological scenarios with a high channel count, but it is often more prone to artifacts as compared to gel-based EEG. Spatial harmonic analysis (SPHARA) and ICA-based methods (Fingerprint and ARCI) have been separately used in previous studies for dry EEG de-noising and physiological artifact reduction. Here, we investigate if the combination of these techniques further improves EEG signal quality. For this purpose, we also introduced an improved version of SPHARA.

METHODS: Dry 64-channel EEG was recorded from 11 healthy volunteers during a motor performance paradigm (left and right hand, feet, and tongue movements). EEG signals were denoised separately using Fingerprint + ARCI, SPHARA, a combination of these two methods, and a combination of these two methods including an improved SPHARA version. The improved version of SPHARA includes an additional zeroing of artifactual jumps in single channels before application of SPHARA. The EEG signal quality after application of each denoising method was calculated by means of standard deviation (SD), signal to noise ratio (SNR), and root mean square deviation (RMSD), and a generalized linear mixed effects (GLME) model was used to identify significant changes of these parameters and quantify the changes in the EEG signal quality.

RESULTS: The grand average values of SD improved from 9.76 (reference preprocessed EEG) to 8.28, 7.91, 6.72, and 6.15 μV for Fingerprint + ARCI, SPHARA, Fingerprint + ARCI + SPHARA, and Fingerprint + ARCI + improved SPHARA, respectively. Similarly, the RMSD values improved from 4.65 to 4.82, 6.32, and 6.90 μV, and the SNR values changed from 2.31 to 1.55, 4.08, and 5.56 dB.

DISCUSSION: Our results demonstrate the different performance aspects of Fingerprint + ARCI and SPHARA, artifact reduction and de-noising techniques that complement each other. We also demonstrated that a combination of these techniques yields superior performance in the reduction of artifacts and noise in dry EEG recordings, which can be extended to infant EEG and adult MEG applications.},
}

@article {pmid40651964,
year = {2025},
author = {Onofri, S and Moeller, R and Billi, D and Balsamo, M and Becker, A and Benvenuto, E and Cassaro, A and Catanzaro, I and Cockell, CS and Desiderio, A and Ellis, T and Gonzáles-Pastor, JE and Hahn, C and Leys, N and Leo, P and Maurel, MC and Pacelli, C and Pavletic, B and Ripa, C and Rothschild, LJ and Surdo, L},
title = {Synthetic biology for space exploration.},
journal = {NPJ microgravity},
volume = {11},
number = {1},
pages = {41},
pmid = {40651964},
issn = {2373-8065},
support = {4000132667/20/NL/CLR/pt//European Space Agency (ESA)/ ; },
abstract = {Human space exploration faces different challenges. Topics like Bioregenerative Life Support Systems, In Situ Resource Utilization, and radiation protection, still require for more suitable solutions to be applied in long-term space exploration. Synthetic biology could be a powerful tool for enabling human exploration of space and planets. This paper explores key topics including resource utilization, life support systems, radiation protection, and human health, providing recommendations for short-, mid-, and long-term advancements in space exploration.},
}

@article {pmid40650501,
year = {2025},
author = {Davies, H and Smyth, S and Pinchbeck, G and Pirmohamed, M and Savory, R and Noble, PJ and Killick, D},
title = {An e-Reporting Tool for Facilitating Submission of Veterinary Adverse Drug Reaction Reports.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {4},
pages = {e70173},
pmid = {40650501},
issn = {1939-1676},
support = {204822/z/16/z/WT_/Wellcome Trust/United Kingdom ; VM0541//Veterinary Medicines Directorate/ ; },
mesh = {Animals ; *Adverse Drug Reaction Reporting Systems ; Electronic Health Records ; United Kingdom ; *Veterinary Drugs/adverse effects ; *Veterinary Medicine ; },
abstract = {BACKGROUND: Adverse events (AEs) are under-reported in veterinary medicine. The ability to report AEs directly from the practice management system (PMS) has been suggested to facilitate reporting. The Small Animal Veterinary Surveillance Network (SAVSNET) informatics system provides an opportunity to integrate reporting into the workflow such that reports can be submitted directly to the National Competent Authority, the Veterinary Medicines Directorate (VMD).

OBJECTIVES: Develop an AE reporting form linked to the PMS allowing for pre-population of some fields from the electronic health record (EHR). Analyze the quality of submitted reports.

ANIMALS: Animals attending United Kingdom (UK) first-opinion veterinary practices participating in SAVSNET.

METHODS: An AE "reporting button" was developed and available in the normal clinical workflow for SAVSNET enrolled practices using the Robovet PMS. The button facilitated capture of pertinent information relating to AEs, including the ability to append clinical notes from the associated EHR. After submission, reports were automatically submitted daily to the VMD. Report quality was assessed using an adapted version of the vigiGrade scoring system, which was used to compare the quality of reports submitted to the VMD via standard routes to those submitted via SAVSNET. Assessment of reports submitted via SAVSNET, was conducted twice. First, considering only information contained in the report and second, considering information contained in both the report and associated clinical notes.

RESULTS: Sixty reports were submitted during the first 18 months by 42 different veterinary practices. The quality of SAVSNET reports was significantly improved by information contained within the clinical notes. These reports were more likely to be well-documented than those submitted via standard routes.

Adverse event reports populated using EHR data are well documented and can support efficient reporting of AEs in veterinary medicine.},
}

Animals
*Adverse Drug Reaction Reporting Systems
Electronic Health Records
United Kingdom
*Veterinary Drugs/adverse effects
*Veterinary Medicine

@article {pmid40648098,
year = {2025},
author = {Quisbert-Trujillo, E and Vuillerme, N},
title = {Towards the Operationalization of Health Technology Sustainability Assessment and the Early Eco Design of the Internet of Medical Things.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {13},
pages = {},
pmid = {40648098},
issn = {1424-8220},
support = {ANR-23-IACL-0006//National Research Agency (ANR), France/ ; ANR-10-AIRT-05//Investissements d'avenir, French program/ ; ANR-15-IDEX-02//Investissements d'avenir, French program/ ; },
mesh = {*Digital Health/economics/ethics ; *Sustainable Development/economics ; Humans ; *Internet of Things/economics/ethics ; },
abstract = {An increasing number of scholars are raising concerns about the sustainability of digital health, calling for action to prevent its harmful effects on the environment. At this point, however, the comprehensive appraisal of emerging technology in the health sector remains theoretically challenging, and highly difficult to implement in practice and in ecological design. Indeed, background factors such as the rapid evolution of technology or effectiveness-efficiency tradeoffs complicate the task of distinguishing the benefits of digital health from its drawbacks, rendering early Health Technology Sustainability Assessment (HTSA) extremely complex. Within this context, the aim of this article is to draw attention to the pragmatism that should be adopted when anticipating the sustainability of technological innovation in the medical field, while simultaneously proposing an assessment framework grounded in a structural and conceptual dissection of the fundamental purpose of smart technologies and the Internet of Medical Things (IoMT). Building on this, we demonstrate how our framework can be strategically applied through a rapid back-of-the-envelope assessment of the economic and ecological balance when introducing IoMT prototypes for treating a specific condition, based on a preliminary simulation of a defined clinical outcome. In this manner, the article presents evidence that challenges two primary hypotheses, and also encourages reflection on the central role of information and its interpretation when addressing key barriers in the HTSA of digital health. Thereby, it contributes to advancing cost-benefit and cost-effectiveness evaluation tools that support eco design strategies and guide informed decision-making regarding the integration of sustainable IoMT systems into healthcare.},
}

*Digital Health/economics/ethics
*Sustainable Development/economics
Humans
*Internet of Things/economics/ethics

@article {pmid40646719,
year = {2025},
author = {Tong, X and Kobayashi, Y and Ikeda, M and Wen, H and Akimoto, S-i and Shigenobu, S},
title = {Draft genome sequences of Buchnera aphidicola from three aphid species (Hemiptera: Aphididae: Eriosomatinae) associated with gall formation on elm trees.},
journal = {Microbiology resource announcements},
volume = {14},
number = {7},
pages = {e0033625},
pmid = {40646719},
issn = {2576-098X},
support = {Special Postdoctoral Researcher Fellowship//RIKEN/ ; 22K20588//Japan Society for the Promotion of Science/ ; 24-IMS-C279//National Institute for Basic Biology/ ; },
abstract = {The Buchnera aphidicola genomes from eriosomatine gall-forming aphids Tetraneura sorini, Tetraneura akinire, and Eriosoma harunire were sequenced, with genome sizes of 533,871, 530,863, and 627,315 bp, respectively. These genomes shed light on Buchnera's role in aphid symbiosis and adaptation.},
}

@article {pmid40646401,
year = {2025},
author = {Cobos, ME and Dunnum, JL and Armién, B and González, P and Juárez, E and Salazar, JR and Cook, JA and Colella, JP},
title = {Selecting Sites for Strategic Surveillance of Zoonotic Pathogens: A Case Study in Panamá.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {40646401},
issn = {1612-9210},
support = {ftd06-089//PICANTE (Pathogen Informatics Center for Analysis, Networking, Translation, and Education, US National Science Foundation)/ ; 347998861//Climate Change Capacity Building Program: Research and Public Health Action Award from the Centers for Infectious Diseases/ ; 111130150.501.274//Ministry of Economy and Finance of Panama/ ; FPI-MEF-056//Ministry of Economy and Finance of Panama/ ; PHoEZyTV I-II//Ministry of Economy and Finance of Panama/ ; ftd06-089//Gorgas Memorial Institute of Studies of Health, Secretaria Nacional de Ciencia y Tecnología/ ; },
abstract = {Surveillance and monitoring of zoonotic pathogens is key to identifying and mitigating emerging public health threats. Surveillance is often designed to be taxonomically targeted or systematically dispersed across geography; however, those approaches may not represent the breadth of environments inhabited by a host, vector, or pathogen, leaving significant gaps in our understanding of pathogen dynamics in their natural reservoirs and environments. As a case study on the design of pathogen surveillance programs, we assess how well 20 years of small mammal surveys in Panamá sampled available environments and propose a multistep approach to selecting survey localities in the future. We use > 8000 georeferenced mammal specimen records, collected as part of a long-term hantavirus surveillance program, to test the completeness of country-wide environmental sampling. Despite 20 years of surveillance, our analyses identify a few key environmental sampling gaps. To refine surveillance strategies, we select a series of "core" historically sampled localities for continued surveillance, supplemented with additional environmentally distinct sites to more completely represent available environments in Panamá. Based on lessons learned through decades of surveillance, we propose a series of recommendations to improve strategic sampling of wildlife for zoonotic pathogen surveillance.},
}

@article {pmid40642517,
year = {2025},
author = {Zapata-Bedoya, S and Velandia-González, M and Contreras, M and Ortiz, C and Neira, Y and La Torre, L and García, S and Salas, D and Carrizales, CJ and Echazú Torres, CD and Ojeda Ocampo, JR and Cox, A and Villalta Coro, MG and Hernándes Rocha, TA},
title = {[Validation of satellite estimates for health interventions: use of microcensus data in Bolivia, 2024Validação de estimativas por satélite para intervenções de saúde: o uso de microcensos na Bolívia, 2024].},
journal = {Revista panamericana de salud publica = Pan American journal of public health},
volume = {49},
number = {},
pages = {e71},
pmid = {40642517},
issn = {1680-5348},
abstract = {OBJECTIVE: To provide more accurate population estimates to support the operation of Bolivia's immunization program.

METHODS: This cross-sectional ecological study calculated population estimates using geospatial covariates extracted from Meta Data for Good and WorldPop satellite imagery, and validated them with the results of a microcensus conducted in five Bolivian municipalities.

RESULTS: Of the 6077 buildings identified in satellite images, 4505 residential buildings were found to be occupied. Of these, 3087 (68.52%) agreed to participate in the survey. A total of 17 617 people were expected and 13 397 were enumerated. Field enumeration identified fewer people under 30 years of age and more people over 60 years of age than expected. The Meta images provided excellent matches when analyzing population estimates by sex. Meta matched best with enumeration in rural areas, and WorldPop matched best with enumeration in urban areas.

CONCLUSIONS: This study demonstrates that combining geospatial analysis with microcensus validation can significantly improve health planning, enabling equitable resource distribution and more effective immunization coverage.},
}

@article {pmid40642052,
year = {2025},
author = {Temmerman, M and Peeters, E and Delacroix, C and Arunda, M and Khalid, S and Hanson, C and Ojong, SA},
title = {The impact of implementing the women's reproductive rights agenda on climate change.},
journal = {Frontiers in global women's health},
volume = {6},
number = {},
pages = {1594066},
pmid = {40642052},
issn = {2673-5059},
abstract = {The 1994 International Conference on Population and Development (ICPD) established sexual and reproductive health and rights (SRHR) as foundational to sustainable development. Thirty years later, advancing women's reproductive rights (WRR), encompassing agency, decision-making autonomy, and universal access to family planning-remains critical not only for health and gender equity but also for mitigating environmental degradation. By reducing unintended pregnancies and empowering women to align childbearing with personal and ecological capacity, WRR alleviates ecological stressors such as deforestation while enhancing health resilience in climate-vulnerable communities. Yet, despite well-documented linkages between population dynamics and environmental change, contemporary climate policies and funding mechanisms persistently exclude WRR. This oversight undermines the potential of reproductive justice to enhance climate resilience. Additionally, claims that integrating WRR into climate agendas covertly promotes population control or represses women in low- and middle-income countries are fundamentally misleading. Crucially, research is needed to quantify the specific environmental impacts of WRR, underscoring the urgent need for robust global models to predict and validate these co-benefits. Strengthening this evidence base is imperative to inform policies that integrate WRR indicators into climate financing frameworks, ensuring gender-responsive programming. Bridging this gap requires interdisciplinary collaboration to develop metrics that capture WRR's role in reducing resource consumption and enhancing adaptive capacity. Embedding WRR within climate agendas would harmonize reproductive justice with environmental action, unlocking synergies between gender equity, health resilience, and sustainability. Fulfilling the ICPD's vision demands centering WRR in global climate strategies, thereby advancing a just and livable future for all.},
}

@article {pmid40641609,
year = {2025},
author = {O'Connor, L and Behar, S and Tarrant, S and Stamegna, P and Pretz, C and Wang, B and Savage, B and Scornavacca, T and Shirshac, J and Wilkie, T and Hyder, M and Zai, A and Toomey, S and Mullen, M and Fisher, K and Tigas, E and Wong, S and McManus, DD and Alper, E and Lindenauer, PK and Dickson, E and Broach, JP and Kheterpal, V and Soni, A},
title = {Healthy at Home for COPD: An Integrated Digital Monitoring, Treatment, and Pulmonary Rehabilitation Intervention.},
journal = {BMC digital health},
volume = {3},
number = {},
pages = {},
pmid = {40641609},
issn = {2731-684X},
support = {KL2 TR001455/TR/NCATS NIH HHS/United States ; TL1 TR000145/TR/NCATS NIH HHS/United States ; U54 HL143541/HL/NHLBI NIH HHS/United States ; UL1 TR001453/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of morbidity and mortality in the United States. Frequent exacerbations result in higher use of emergency services and hospitalizations, leading to poor patient outcomes and high costs. The objective of this study is to demonstrate the feasibility of a multimodal, community-based intervention in treating acute COPD exacerbations.

RESULTS: Over 18 months, 1,333 patients were approached and 100 (7.5%) were enrolled (mean age 66, 52% female). Ninety-six participants (96%) remained in the study for the full enrollment period. Fifty-five (55%) participated in tele-pulmonary-rehabilitation. Participants wore the smartwatch for a median of 114 days (IQR 30-210) and 18.9 hours/day (IQR16-20) resulting in a median of 1034 minutes/day (IQR 939-1133). The rate at which participants completed scheduled survey instruments ranged from 78-93%. Nearly all participants (85%) performed COPD ecological momentary assessment at least once with a median of 4.85 recordings during study participation. On average, a 2.48-point improvement (p=0.03) in COPD Assessment Test Score was observed from baseline to study completion. The adherence and symptom improvement metrics were not associated with baseline patient activation measures.

CONCLUSIONS: A multimodal intervention combining preventative care, symptom and biometric monitoring, and MIH services was feasible in adults living with COPD. Participants demonstrated high protocol fidelity and engagement and reported improved quality of life.},
}

@article {pmid40488574,
year = {2025},
author = {Débarre, F and Hensel, Z},
title = {A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data.},
journal = {Molecular biology and evolution},
volume = {42},
number = {6},
pages = {},
pmid = {40488574},
issn = {1537-1719},
support = {UIDB/04612/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04612/2020//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {*SARS-CoV-2/genetics ; Humans ; Animals ; Chiroptera/virology ; *Genome, Viral ; Genotype ; China ; Sequence Analysis, RNA ; RNA, Viral/genetics ; Datasets as Topic ; },
abstract = {In 2021, Jesse Bloom published a study addressing why the earliest SARS-CoV-2 sequences in Wuhan from late December 2019 were not those most similar to viruses sampled in bats. The study concluded that recovered partial sequences from Wuhan and annotation of Wuhan links for other sequences increased support for one genotype as the progenitor of the SARS-CoV-2 pandemic. However, we show that the collection date for the recovered sequences was January 30, 2020, later than that of hundreds of other SARS-CoV-2 sequences. Mutations in these sequences also exhibit diversity consistent with SARS-CoV-2 sequences collected in late January 2020. Furthermore, we found that Wuhan exposure history was common for early samples, so Bloom's annotation for a single familial cluster does not support that an early genotype was undersampled in Wuhan. Both the recovered partial sequences and additional annotation align with contemporaneous data rather than increase support for a progenitor. Our findings clarify the significance of the recovered sequences and are supported by additional data and analysis published since mid-2021.},
}

*SARS-CoV-2/genetics
Humans
Animals
Chiroptera/virology
*Genome, Viral
Genotype
China
Sequence Analysis, RNA
RNA, Viral/genetics
Datasets as Topic

@article {pmid39631859,
year = {2025},
author = {Suzuki, T and Nagasu, H and Ebara, T and Kagiyama, N and Kishi, T and Yano, Y and Kario, K and Nishiyama, A and Arima, H and Kawai, F and Shibata, S and Node, K and Mizuno, A},
title = {Unraveling the Implications of Digit Bias in Digital Health - A Literature Review.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {64},
number = {14},
pages = {2090-2099},
doi = {10.2169/internalmedicine.4666-24},
pmid = {39631859},
issn = {1349-7235},
mesh = {Humans ; Bias ; *Digital Technology ; Digital Health ; },
abstract = {Digital health, which encompasses digital medicine and therapy, integrates advanced technologies across healthcare. Central to this transformation is 'digitization,' which converts continuous analog data into a discrete digital form. However, this process is challenging. First, digitization inherently has the potential to introduce information loss, thereby diminishing the richness and complexity of data. Second, "digit bias," a cognitive distortion, emerges in the interpretation phase, where individuals' perceptions of and reactions to digital data are intrinsically skewed. There exist two major cognitive biases during digitization process: "digit preferences," where healthcare providers prioritize specific numbers, and "left digit bias" where continuous variables are disproportionately estimated by focusing on the leftmost digit. Although information loss and cognitive biases can cause significant distortions in healthcare, the effects of this "digitization" process have not been adequately quantified, and the accumulation of further evidence in this field is anticipated.},
}

Humans
Bias
*Digital Technology
Digital Health

@article {pmid40623094,
year = {2025},
author = {Morison, C and Stark, D and Huang, W},
title = {Single-cell mutational burden distributions in birth-death processes.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013241},
pmid = {40623094},
issn = {1553-7358},
mesh = {*Single-Cell Analysis/methods ; Humans ; *Neoplasms/genetics ; *Mutation/genetics ; Computational Biology ; *Models, Genetic ; Cell Division/genetics ; },
abstract = {Genetic mutations are footprints of cancer evolution and reveal critical dynamic parameters of tumour growth, which otherwise are hard to measure in vivo. The mutation accumulation in tumour cell populations has been described by various statistics, such as site frequency spectra (SFS), single-cell division distributions (DD) and mutational burden distributions (MBD). While DD and SFS have been intensively studied in phylogenetics especially after the development of whole genome sequencing technology of bulk samples, MBD has drawn attention more recently with the single-cell sequencing data. Although those statistics all arise from the same somatic evolutionary process, an integrated understanding of these distributions is missing and requires novel mathematical tools to better inform the ecological and evolutionary dynamics of tumours. Here we introduce dynamical matrices to analyse and unite the SFS, DD and MBD and derive recurrence relations for the expectations of these three distributions. While we successfully recover classic exact results in pure-birth cases for the SFS and the DD through our new framework, we derive a new expression for the MBD and approximate all three distributions when death is introduced. We demonstrate a natural link between the SFS and the single-cell MBD, and show that the MBD can be regenerated through the DD. Counter-intuitively, the single-cell MBD is mainly driven by the stochasticity arising in the DD, rather than the extra stochasticity in the number of mutations at each cell division.},
}

*Single-Cell Analysis/methods
Humans
*Neoplasms/genetics
*Mutation/genetics
Computational Biology
*Models, Genetic
Cell Division/genetics

@article {pmid40641182,
year = {2025},
author = {Sung, HM and Kim, SH and Kwon, EJ and Jeong, SH and Lee, HM and Kim, YH and Oh, CK},
title = {Single-Cell Transcriptomic Analysis Reveals Hair Cell-Specific Molecular Responses to Polystyrene Nanoplastics in a Zebrafish Embryo Model.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70028},
pmid = {40641182},
issn = {1470-8744},
support = {RS-2023-00301938//NRF/ ; 30-2023003//Pusan National University Yangsan Hospital/ ; },
abstract = {Polystyrene nanoplastics (PSNPs) have emerged as pervasive environmental pollutants with potential toxicological effects on aquatic ecosystems. Their small size, hydrophobicity, and structural stability enable penetration into biological tissues, inducing diverse toxic responses. This study investigates the physiological and molecular impacts of PSNPs on zebrafish embryos using single-cell RNA sequencing and phenotypic analyses. While PS-NP exposure at environmentally relevant concentrations caused no significant changes in survival or overt phenotypes, it led to alterations in cell type proportions and gene expression. Differentially expressed gene (DEG) analysis revealed the upregulation of genes such as col1a1a, fgfbp2b, cytl1, and fstl1a, which were validated in vivo. These genes are associated with extracellular matrix remodeling, immune regulation, and tissue repair, suggesting that PSNPs activate defensive and reparative mechanisms in response to environmental stress. These findings highlight the molecular and cellular responses to PSNP exposure in zebrafish embryos and underscore the importance of evaluating the ecological risks posed by nanoplastics.},
}

@article {pmid40640514,
year = {2025},
author = {Jaman, T and Bhaskar, S and Saikhom, V and Gogoi, RB and Sarma, KK and Aggarwal, SP},
title = {GeoAI-based soil erosion risk assessment in the Brahmaputra River Basin: a synergistic approach using RUSLE and advanced machine learning.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {8},
pages = {901},
doi = {10.1007/s10661-025-14314-w},
pmid = {40640514},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; *Machine Learning ; Rivers ; Risk Assessment ; Geographic Information Systems ; *Soil Erosion/statistics & numerical data ; Remote Sensing Technology ; Soil/chemistry ; India ; },
abstract = {Soil erosion is a critical environmental issue in the Brahmaputra River Basin, threatening agricultural productivity, water resources, and ecological balance. This study employs the revised universal soil loss equation (RUSLE) alongside remote sensing, geographic information systems (GIS), and advanced machine learning models like random forest (RF) and gradient boosting (GB) to analyze soil erosion patterns from 2005 to 2024. The analysis revealed that average annual soil loss increased from 15.8 tons/ha/year in 2005 to 25.4 tons/ha/year in 2024, marking a 60.76% rise over two decades. Peak erosion rates were observed in 2020, with localized hotspots recording up to 32,130 tons/ha/year. Spatial analysis from 2005 to 2024 indicated substantial variability, with soil loss values ranging from - 7.024 to 9034 tons/ha in 2005. Topographic influence, quantified using the LS factor, revealed that 47.2% of the basin area has slopes steeper than 16°, significantly contributing to elevated erosion risk. The rainfall erosivity (R-factor) fluctuated throughout the period, peaking at 2305.73 MJ mm/ha h year in 2015 but declining to 799.21 MJ mm/ha h year by 2024, indicating a temporal shift in rainfall patterns. Vegetation cover improvements during this time reduced the mean C-factor from 0.52 to 0.34, though 13.8% of the basin (approximately 3.05 million ha) still falls under high to very high erosion risk zones. RF model predictions achieved an R[2] of 0.915 and RMSE of 4.82, while GB attained an R[2] of 0.952 with RMSE of 3.97, indicating superior predictive performance. These findings underscore the urgent need for targeted soil conservation measures, afforestation programs, and sustainable watershed management. The integration of AI-driven modeling with remote sensing and GIS provides a robust framework for long-term soil erosion monitoring, enabling informed decision-making for climate adaptation in the region.},
}

*Environmental Monitoring/methods
*Machine Learning
Rivers
Risk Assessment
Geographic Information Systems
*Soil Erosion/statistics & numerical data
Remote Sensing Technology
Soil/chemistry
India

@article {pmid40638618,
year = {2025},
author = {Nagel, CL and Chen, S and Allore, HG and Botoseneanu, A and Newsom, JT and Bishop, N and Dorr, DA and Kaye, J and Quiñones, AR},
title = {Longitudinal sequencing of cardiometabolic multimorbidity among older adults and association with subsequent dementia onset.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326309},
pmid = {40638618},
issn = {1932-6203},
mesh = {Humans ; Aged ; Female ; Male ; *Dementia/epidemiology/etiology ; *Multimorbidity ; Longitudinal Studies ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/complications ; Cluster Analysis ; },
abstract = {BACKGROUND: Patterns of development of cardiometabolic multimorbidity (CMM) and the impact of specific cardiometabolic disease combinations on cognitive function are not well understood. This study utilizes sequence analysis to describe the ordering and timing of cardiometabolic disease accumulation over a five-year period and to assess both sociodemographic predictors and cognitive outcomes of typical cardiometabolic disease sequences.

METHODS: We analyzed data from the National Health and Aging Trends Study (2011-2022), including respondents aged ≥65 years without CMM or cognitive impairment at baseline (N = 4956). We used sequence analysis with optimal matching and hierarchical cluster analysis to describe temporal patterns of cardiometabolic disease accumulation and to construct a typology by clustering similar sequences. Sociodemographic predictors of CMM cluster membership were assessed using multinomial logistic regression and discrete time survival analysis was used to examine the association of CMM clusters with subsequent dementia development.

RESULTS: 11.8% of respondents developed CMM within 5-years. From a total of 366 distinct cardiometabolic disease sequences, we identified eight cardiometabolic sequence clusters. The first five clusters, "No Cardiometabolic Disease" (N = 2283, 46.1%); "Diabetes Only" (N=642, 13.0%); Heart Disease Only" (N = 297, 6.0%); "MI Only" (N = 145, 2.9%); "Stroke Only" (N = 132, 2.7%), were composed of persons who did not develop CMM over the observation period. The sixth cluster, "Incident CVD with Multimorbidity" (N = 656, 13.2%), was largely composed of persons with no conditions at baseline who developed incident cardiometabolic disease and/or CMM during the observation period (N = 477, 72.7%) and the seventh cluster, "Diabetes Multimorbidity" (N = 333, 6.7%), primarily consisted of persons with diabetes who developed incident CMM. Finally, the eight cluster (N = 468, 9.4%) was characterized by mortality early in the observation period with minimal CMM development during the observation period. Black and Hispanic race/ethnicity, lower wealth, and obesity were associated with increased likelihood of membership in one or both of the clusters characterized by CMM development. We observed increased dementia risk among persons in the Incident CVD with Multimorbidity cluster (HR = 1.32, 95% CI = 1.04-1.67) and the Diabetes MM cluster (HR = 1.88, 95% CI = 1.44,2.44).

CONCLUSIONS: Development of cardiometabolic multimorbidity is more likely among minoritized and/or low-income older adults and is associated with increased risk of subsequent dementia. Targeted approaches to cardiometabolic disease prevention and risk reduction may be an effective means of slowing or preventing the onset of cognitive decline among these groups.},
}

Humans
Aged
Female
Male
*Dementia/epidemiology/etiology
*Multimorbidity
Longitudinal Studies
Aged, 80 and over
*Cardiovascular Diseases/epidemiology/complications
Cluster Analysis

@article {pmid40638150,
year = {2025},
author = {Fujioka, E and Yoshimura, K and Ujino, T and Yoda, K and Fukui, D and Hiryu, S},
title = {High-Resolution GPS Tracking of Perch-Hunting Bats, Rhinolophus nippon, during Nightly Foraging Behavior.},
journal = {Zoological science},
volume = {42},
number = {3},
pages = {249-259},
doi = {10.2108/zs240033},
pmid = {40638150},
issn = {0289-0003},
mesh = {Animals ; *Chiroptera/physiology ; *Feeding Behavior/physiology ; *Geographic Information Systems ; Echolocation ; Flight, Animal ; Male ; },
abstract = {While the echolocation behavior and specialized adaptive auditory system of the greater horseshoe bat (Rhinolophus ferrumequinum) are well documented, comprehensive insights into its wild ecology, especially its detailed nocturnal movements for foraging behavior, remain scarce. Therefore, our objective was to obtain information on the spatiotemporal features of the movements of the Japanese greater horseshoe bat (Rhinolophus nippon), a close relative of R. ferrumequinum, during foraging. Hence, we investigated the nightly flight paths of R. nippon using high-resolution GPS data loggers. Initially, hidden Markov modeling analysis classified bat flight paths into two behavioral patterns: commuting and area-restricted behavior, the latter primarily corresponding to foraging activities. Focusing on foraging behavior along their trajectory, we observed that R. nippon repeatedly foraged with brief stops lasting only a few minutes and an average distance of approximately 300 m between any two foraging sites. Notably, one individual covered a considerable distance (23.6 km) from its roost, possibly because of irregular social behavior during the mating season. Furthermore, for commuting, bats occasionally used forest roads, which were located along the middle of relatively steep slopes. In cases of echolocations with limited detection distances, echoes from the ground and adjacent tree lines offered crucial navigation cues, underscoring the significance of forest roads as nightly movement routes for echolocating bats. Overall, our findings highlight the importance and urgency of ongoing research on bat movement ecology in Japan.},
}

Animals
*Chiroptera/physiology
*Feeding Behavior/physiology
*Geographic Information Systems
Echolocation
Flight, Animal
Male

@article {pmid40270457,
year = {2025},
author = {Selim, S and San, BT and Koc-San, D and Selim, C},
title = {A two-level approach to geospatial identification of optimal pitaya cultivation sites using multi-criteria decision analysis.},
journal = {Journal of the science of food and agriculture},
volume = {105},
number = {11},
pages = {5851-5862},
doi = {10.1002/jsfa.14297},
pmid = {40270457},
issn = {1097-0010},
mesh = {*Fruit/growth & development/chemistry ; Geographic Information Systems ; Decision Support Techniques ; *Cactaceae/growth & development/chemistry ; Soil/chemistry ; Temperature ; },
abstract = {BACKGROUND: Pitaya, also known as dragon fruit, is one of the most popular and expensive fruits in the world. It has been commercially produced since the early 20th century. This plant requires a specific growing environment and ecological conditions, so it is typically cultivated under greenhouse conditions in Türkiye. However, there is a clear need for a comprehensive assessment of outdoor adaptation and/or outdoor growing areas for sustainable yield at the regional scale.

RESULTS: This study presents a multi-criteria decision-making analysis-based geographical information system (GIS) study to identify and evaluate the suitability of outdoor growing areas for pitaya. In this study, eight crucial factors were identified for outdoor pitaya cultivation: temperature, rainfall, soil pH, soil depth, land use capability, altitude, slope and aspect. An analytical hierarchy process was conducted to determine the weights for each parameter, followed by a weighted overlay analysis using GIS tools. The range of weight values was obtained between 0.2748 and 0.0319. The area of the best places for pitaya cultivation was calculated to be 9245.7 ha (11.7%). It was determined that 32.63%, 37.57% and 18.1% of the locations were moderately suitable, less appropriate and unsuitable, respectively.

CONCLUSION: The selection of comparable production sites will be guided by the study. Such suitable site selection studies are extremely significant since the cultivation of the pitaya plant, which has a high commercial value for economically developing countries, will be crucial to the growth of agricultural employment in these nations. Future research will be guided by this study's methodology and analysis strategies. © 2025 Society of Chemical Industry.},
}

*Fruit/growth & development/chemistry
Geographic Information Systems
Decision Support Techniques
*Cactaceae/growth & development/chemistry
Soil/chemistry
Temperature

@article {pmid40634743,
year = {2025},
author = {Zheng, H and Wu, D and Wang, S and Li, X and Jin, LN and Zhao, B and Li, S and Sun, Y and Dong, Z and Wu, Q and Chen, X and Liu, Y and Chen, J and Tian, H and Liu, Q and Jiang, J and Kan, H and He, K and He, H and Chen, C and Zhao, J and Weichenthal, S and Ji, JS and Cohen, AJ and Hao, J and Li, Q},
title = {Control of toxicity of fine particulate matter emissions in China.},
journal = {Nature},
volume = {643},
number = {8071},
pages = {404-411},
pmid = {40634743},
issn = {1476-4687},
mesh = {China ; *Particulate Matter/toxicity/analysis ; Humans ; *Air Pollution/prevention & control/analysis/legislation & jurisprudence/statistics & numerical data/adverse effects ; *Air Pollutants/toxicity/analysis ; Vehicle Emissions/analysis ; Particle Size ; Environmental Exposure/analysis ; },
abstract = {Fine particulate matter (particulate matter with a diameter of 2.5 μm or less; PM2.5) causes millions of premature deaths globally[1], but not all particles are equally harmful[2-4]. Current air-pollution control strategies, prioritizing PM2.5 mass reduction, have provided considerable health benefits but further refinements based on differences in the toxicity of various emission sources may provide greater benefits[5-7]. Here we integrated field measurements with air-quality modelling to assess the unequal toxicities of PM2.5 from various anthropogenic sources. Our findings revealed that the toxicity per unit of PM2.5 mass differed substantially between major sources, differing by up to two orders of magnitude. PM2.5 from solid fuel combustion in residential stoves had the highest toxicity, followed by those from the metallurgy industry, brake wear, diesel vehicles, petrol vehicles, the cement industry and power plants. We further analysed the source contributions of toxicity-adjusted PM2.5 emissions and population exposures in China. From 2005 to 2021, both the PM2.5 mass and relative-potency-adjusted emissions substantially decreased. Although industrial sources contributed 57.5% to the reduction in PM2.5 mass emissions, the reduction in relative potency-adjusted emissions was driven by residential combustion (approximately 80%). Clean-air policies should consider the differing toxicities of PM2.5 when formulating source-specific emission control regulations. This study proposes a cellular toxicity-based framework for PM2.5 reduction that could address the specific health risks in diverse regions, but further epidemiological studies will be required to confirm their relevance to human health outcomes and their application to public policy.},
}

China
*Particulate Matter/toxicity/analysis
Humans
*Air Pollution/prevention & control/analysis/legislation & jurisprudence/statistics & numerical data/adverse effects
*Air Pollutants/toxicity/analysis
Vehicle Emissions/analysis
Particle Size
Environmental Exposure/analysis

@article {pmid40632788,
year = {2025},
author = {Wang, L and Wang, T and Zhang, XW and Lin, XF and Li, J and Liao, JB and Wang, RW},
title = {Evolution of foraging behaviour induces variable complexity-stability relationships in mutualist-exploiter-predator communities.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013245},
pmid = {40632788},
issn = {1553-7358},
mesh = {Animals ; *Predatory Behavior/physiology ; *Models, Biological ; *Biological Evolution ; Population Dynamics ; Ecosystem ; Computational Biology ; *Feeding Behavior/physiology ; *Symbiosis/physiology ; Computer Simulation ; Food Chain ; },
abstract = {Early ecological theory predicts that complex ecological networks are unstable and are unlikely to persist, despite many empirical studies of such complexity in nature. This inconsistency has fascinated ecologists for decades. To resolve the complexity-stability debate, coupling population dynamics and trait dynamics is considered to be an important way to understand the long-term stability of ecological community assemblages. However, we still do not know how eco-evolutionary feedbacks affect the relationship between complexity and stability in ecologically realistic networks with both antagonistic and mutualistic interactions. Here, we explored an adaptive network model to evaluate how the evolution of foraging preference to determine the relationship between network complexity (i.e., connectance) and stability (i.e., community persistence at steady state) in mutualist-exploiter-predator communities (MEST). Our theoretical results showed: (i) adaptive foraging of the top predator contributes to the stability of mutualism and intermediate intensity of foraging adaptations can lead to chaotic dynamics in a four-species MEST community; (ii) the complexity-stability relationship may show positive monotonic, negative monotonic, peaked and double-peaked patterns in general MEST communities, while the double-peaked pattern is only obtained when both the adaptation intensity and interspecific competition are high. Furthermore, model predictions may be consistent with both the negative monotonic pattern revealed in freshwater communities and the peaked pattern revealed in marine communities. Finally, we infer that foraging adaptations of the top predator may alter positive or/and negative feedback loops (trait-mediated indirect effects) to affect the stability of general MEST communities. Our adaptive network framework may provide an effective way to address the complexity-stability debate in real ecosystems.},
}

Animals
*Predatory Behavior/physiology
*Models, Biological
*Biological Evolution
Population Dynamics
Ecosystem
Computational Biology
*Feeding Behavior/physiology
*Symbiosis/physiology
Computer Simulation
Food Chain

@article {pmid40631490,
year = {2025},
author = {Ogle, K and Barber, JJ and Strange, BM and Boone, RD and Formanack, AM and Peltier, DMP},
title = {Identifying the Climate Conditions Associated With Extreme Growth States in Trees Across the Western United States.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70317},
doi = {10.1111/gcb.70317},
pmid = {40631490},
issn = {1365-2486},
support = {2213599//US National Science Foundation Macrosystems Biology and NEON-Enabled Science/ ; //USGS-Southwest Climate Adaptation Science Center/ ; },
mesh = {*Trees/growth & development ; *Climate Change ; United States ; Droughts ; *Cycadopsida/growth & development ; *Magnoliopsida/growth & development ; *Climate ; Seasons ; },
abstract = {Climate extremes-e.g., drought, atmospheric rivers, heat waves-are increasing in severity and frequency across the western United States of America (USA). Tree-ring widths reflect the concurrent and legacy effects of such climate extremes, yet our ability to predict extreme tree growth is often poor. Could tree-ring data themselves identify the most important climate variables driving extreme low- and high-growth states? How does the importance of these climate drivers differ across species and time? To address these questions, we explored the spatial synchrony of extreme low- and high-growth years, the symmetry of climate effects on the probability of low- and high-growth years, and how climate drivers of extreme growth vary across tree species. We compiled ring widths for seven species (four gymnosperms and three angiosperms) from 604 sites in the western USA and classified each annual ring as representing extreme low, extreme high, or nominal growth. We used classification random forest (RF) models to evaluate the importance of 30 seasonal climate variables for predicting extreme growth, including precipitation, temperature, and vapor pressure deficit (VPD) during and up to four years prior to ring formation. For four species (three gymnosperms, one angiosperm) for which climate was predictive of growth, the RF models correctly classified 89%-98% and 80%-95% of low- and high-growth years, respectively. For these species, asymmetric climate responses dominated. Current-year winter hydroclimate (precipitation and VPD) was most important for predicting low growth, but prediction of high growth required multiple years of favorable moisture conditions, and the occurrence of low-growth years was more synchronous across space than high-growth years. Summer climate and temperature (regardless of season) were only weakly predictive of growth extremes. Our results motivate ecologically relevant definitions of drought such that current winter moisture stress exerts a dominant role in governing growth reductions in multiple tree species broadly distributed across the western USA.},
}

*Trees/growth & development
*Climate Change
United States
Droughts
*Cycadopsida/growth & development
*Magnoliopsida/growth & development
*Climate
Seasons

@article {pmid40628867,
year = {2025},
author = {Lee, CT and Ng, CH and Tnah, LH and Ng, KKS and Diway, B and Khoo, E and Lee, SL},
title = {DNA profile database of Koompassia malaccensis in Malaysia and its application in forensic investigation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24504},
pmid = {40628867},
issn = {2045-2322},
support = {05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; },
mesh = {Malaysia ; Microsatellite Repeats/genetics ; *Forensic Genetics/methods ; *Databases, Nucleic Acid ; Humans ; Gene Frequency ; *DNA Fingerprinting/methods ; Databases, Genetic ; Genotype ; },
abstract = {DNA profiling has been an important tool in human forensic for almost four decades, revolutionising criminal investigations. In recent years, it has also been utilised in timber identification and geographical traceability of stolen logs, with notable increase in forensic DNA analysis related to forest crimes, driven by the growing concerns over illegal logging and forest conservation. In this study, DNA profile database for a tropical timber species, Koompassia malaccensis was established, with a total of 1465 samples from 56 locations across Malaysia genotyped using nine short tandem repeat (STR) markers. Based on the results of cluster analyses, the STR database was partitioned into WM (West Malaysia), EM (East Malaysia) and PS (Peat Swamp) Database. Thereafter, each regional/ecological database was characterised for forensic parameters and allele frequencies. Due to weak population differentiation, the percentage of individuals correctly assigned to the population of origin was low. However, the assignment tests to the region of origin were highly accurate (mean = 99.6%). The STR database is robust and has been used to assist the enforcement agencies in the investigation of forest crimes involving K. malaccensis. A case study is presented to demonstrate its application for individual identification in forensic context.},
}

Malaysia
Microsatellite Repeats/genetics
*Forensic Genetics/methods
*Databases, Nucleic Acid
Humans
Gene Frequency
*DNA Fingerprinting/methods
Databases, Genetic
Genotype

@article {pmid40626351,
year = {2025},
author = {Shirakawa, T and Ide, H and Ikehata, Y and Lu, Y and Kinouchi, R and Iwasa, T and Koga, K and Tateishi, S and Fujino, Y and Yasui, T and Horie, S},
title = {Impact of Symptoms of Late-Onset Hypogonadism as a Potential Driver of Presenteeism.},
journal = {American journal of men's health},
volume = {19},
number = {4},
pages = {15579883251343972},
pmid = {40626351},
issn = {1557-9891},
mesh = {Humans ; Male ; *Hypogonadism/epidemiology/diagnosis ; *Presenteeism/statistics & numerical data ; Middle Aged ; Aged ; Adult ; Fatigue/etiology ; Testosterone/blood ; Surveys and Questionnaires ; Erectile Dysfunction ; Age of Onset ; },
abstract = {Presenteeism, defined as attending work despite physical or mental health issues that impair full productivity, is a prevalent concern with significant implications for workplace efficiency and employee well-being. Testosterone, the primary male sex hormone, plays a vital role in sustaining physical energy, cognitive function, and emotional stability-key factors for optimal work performance. This study explores the association between late-onset hypogonadism (LOH) and presenteeism, emphasizing how LOH-related symptoms such as fatigue, reduced libido, erectile dysfunction, and mood disturbances may contribute to reduced workplace productivity. Data from 96 male patients aged 27 to 76 years, who sought treatment at a university hospital for LOH-related symptoms, were analyzed using blood tests and validated questionnaires, including the Aging Males' Symptoms (AMS) scale, Work Functioning Impairment Scale (WFun), and Sexual Health Inventory for Men. Significant correlations were observed between AMS scores and both work functioning impairment and erectile dysfunction, indicating a strong link between LOH symptoms and presenteeism. In addition, symptoms such as fatigue, diminished motivation, and poor sleep quality were identified as exacerbating factors for work-related impairments. The greatest strength of this study lies in its focus on clinically diagnosed LOH patients, a factor that significantly distinguishes it from prior research on presenteeism in general working populations. This study underscores the potential benefits of testosterone replacement therapy, lifestyle modifications, and workplace wellness programs in addressing presenteeism among employees with LOH. Further research is necessary to assess the efficacy of these interventions in mitigating presenteeism and improving employee well-being.},
}

Humans
Male
*Hypogonadism/epidemiology/diagnosis
*Presenteeism/statistics & numerical data
Middle Aged
Aged
Adult
Fatigue/etiology
Testosterone/blood
Surveys and Questionnaires
Erectile Dysfunction
Age of Onset

@article {pmid40623431,
year = {2025},
author = {Wang, L and Liu, N and Zhou, Y and Zheng, F and Jian, S and Liu, X},
title = {Multi-omics analyses provide insights into the molecular basis for salt tolerance of Phyla nodiflora.},
journal = {The Plant journal : for cell and molecular biology},
volume = {123},
number = {1},
pages = {e70325},
doi = {10.1111/tpj.70325},
pmid = {40623431},
issn = {1365-313X},
support = {2021-400//National Key R&D Program of China (Key Special Project for Marine Environmental Security and Sustainable Development of Coral Reefs)/ ; 32371326//National Natural Science Foundation of China/ ; 32070551//National Natural Science Foundation of China/ ; 2023B1212060046//Science and Technology Planning Project of Guangdong Province/ ; E3330900-01//Science and Technology Projects in Guangzhou/ ; },
mesh = {*Salt Tolerance/genetics ; Genome, Plant/genetics ; Gene Expression Regulation, Plant ; Abscisic Acid/metabolism ; Transcriptome ; Plant Proteins/genetics/metabolism ; Salt Stress ; Salt-Tolerant Plants/genetics ; Genomics ; Multiomics ; },
abstract = {The perennial herbaceous plant, Phyla nodiflora (Verbenaceae), which possesses natural resistance to multiple abiotic stresses, is widely used as a pioneer species in island ecological restoration. Due to the lack of information about its genome, the mechanism underlying its tolerance to environmental stresses, such as salinity, is almost entirely unknown. Here, we report on the high-quality genome of P. nodiflora that is 403.07 Mb in size, and which was assembled and anchored onto 18 pseudo-chromosomes. Genomic synteny revealed that P. nodiflora underwent two whole genome duplication events, which promoted the expansion of genes related to environmental adaptation and the biosynthesis of secondary metabolites. An integrated genomic and transcriptomic analysis suggested that salt stress tolerance in P. nodiflora is associated with the expansion and activated expression of genes related to abscisic acid (ABA) homeostasis and signaling. The expansion of ZEP family genes may contribute to the consistent increase in ABA levels under salt stress. Lysine acetylomic analysis revealed that exposure to salt led to widespread protein deacetylation, with these proteins primarily involved in signal transduction, carbohydrate transport and metabolism, and transcription regulation. Deacetylation of glutathione S-transferase increased enzymatic activities in response to salt-induced oxidative stress. Collectively, the genomic, transcriptomic, and lysine acetylomic analyses provide profound insight into the molecular basis of the adaptation of P. nodiflora to salt stress, and will be helpful to engineer salt-tolerant plants for ecological restoration.},
}

*Salt Tolerance/genetics
Genome, Plant/genetics
Gene Expression Regulation, Plant
Abscisic Acid/metabolism
Transcriptome
Plant Proteins/genetics/metabolism
Salt Stress
Salt-Tolerant Plants/genetics
Genomics
Multiomics

@article {pmid40622159,
year = {2025},
author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB},
title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021425},
doi = {10.1128/msystems.00214-25},
pmid = {40622159},
issn = {2379-5077},
abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.},
}

@article {pmid40622136,
year = {2025},
author = {Fukuta, M and Fukano, S and Maekawa, N and Kobayashi, S and Okamoto, S and Hirano, M and Nio-Kobayashi, J and Kariwa, H and Kawakami, S and Konnai, S and Yoshii, K},
title = {Development of blood-brain barrier-penetrating antibodies for neutralizing tick-borne encephalitis virus in the brain.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0018425},
doi = {10.1128/msphere.00184-25},
pmid = {40622136},
issn = {2379-5042},
abstract = {UNLABELLED: Tick-borne encephalitis virus (TBEV) belongs to the genus Flavivirus and causes tick-borne encephalitis (TBE), a disease characterized by severe neurological symptoms with a high mortality rate. Currently, no specific antiviral treatments have been developed for TBE. The blood-brain barrier (BBB) restricts drug delivery to the central nervous system, posing a major challenge in developing effective therapies targeting TBEV in the brain. In this study, we developed recombinant anti-TBEV antibodies fused with BBB-penetrating rabies virus glycoprotein (RVG) peptides to facilitate their transport across the BBB. The fusion of RVG peptides to the C-terminus of the heavy chain of whole antibodies or single-chain variable fragment had minimal impact on their neutralizing ability against TBEV. The RVG fusion enhanced antibody binding to the surface of a human brain endothelial cell line and increased permeability in an in vitro BBB model. The RVG-fused antibodies exhibited a higher transport efficiency to the brain than the non-fused antibodies following peripheral injection in mice. Notably, the peripheral administration of the RVG-fused whole antibody after viral invasion into the brain significantly neutralized TBEV in the brains of infected mice. These findings suggest that RVG-fused antibodies represent a promising therapeutic strategy for treating TBE once the virus has entered the brain.

IMPORTANCE: Tick-borne encephalitis virus is a neuroinvasive pathogen that causes severe neurologic disease, significantly affecting patients' quality of life. No specific antiviral treatment is available for tick-borne encephalitis caused by virus multiplication in the brain. The delivery of drugs to the brain via peripheral administration is often obstructed by the blood-brain barrier. To develop targeted antiviral therapies for brain infections, we engineered recombinant antibodies capable of crossing the blood-brain barrier via brain-targeted ligands. These antibodies exhibited permeability across the blood-brain barrier in both in vitro and in vivo models and notably effectively neutralized the virus within the brain following peripheral administration. This study is the first to highlight the therapeutic potential of brain-targeted recombinant antibodies after viral entry into the brain, offering a promising pathway for the development of effective antiviral treatments for tick-borne encephalitis.},
}

@article {pmid40441315,
year = {2025},
author = {Zhang, B and Yang, M and Liu, W},
title = {Integrating multi-omics analysis unveils the key mechanisms of PQS-enhanced Algicidal activity in Enterobacter hormaechei F2.},
journal = {Genomics},
volume = {117},
number = {4},
pages = {111060},
doi = {10.1016/j.ygeno.2025.111060},
pmid = {40441315},
issn = {1089-8646},
mesh = {Quorum Sensing/drug effects ; *Enterobacter/genetics/drug effects/metabolism ; *Quinolones/pharmacology/metabolism ; Proteomics ; Metabolomics ; Bacterial Proteins/metabolism/genetics ; Transcriptome ; Multiomics ; },
abstract = {Quorum sensing, as a pivotal bacterial signaling pathway, exhibits substantial potential for regulating algicidal activity. This study pioneers the integration of multi-omics analyses (transcriptomics, proteomics, metabolomics) with phenotypic profiling to systematically unravel the molecular mechanisms underlying Pseudomonas Quinolone Signal (2-heptyl-3-hydroxy-4(1H)-quinolinone, PQS)-enhanced algicidal activity in Enterobacter hormaechei F2. Co-cultivation with PQS triggered marked reductions in algal biomass and chlorophyll-a levels, outperforming traditional approaches. Fourier-transform infrared spectroscopy (FTIR) revealed PQS-induced metabolic disruption and membrane degradation in algal cells. Transcriptomic profiling identified novel regulatory hubs, including upregulated glycolysis (tktA, transketolase), fatty acid degradation (fadE, acyl-CoA dehydrogenase), and chemotaxis (malE, maltose-binding protein) pathways. Proteomics confirmed PQS-driven enrichment of terpenoid precursors, notably DXS synthase (1-deoxy-D-xylulose-5-phosphate synthase), and quorum sensing effectors. Metabolomics highlighted amino acid derivatives (e.g., L-glutamate) and heterocyclic antibiotics as dominant algicidal metabolites. Crucially, multi-omics integration delineated a core network of 46 key nodes (e.g., ribose transporter rbsB, L-glutamate) coordinating energy metabolism, motility, and algicide synthesis. Fatty acid degradation enzymes (e.g., FadE) and flagellar assembly regulators (e.g., FlgK) emerged as previously unrecognized targets, with PQS significantly enhancing bacterial swarming motility (p < 0.01) and biofilm formation. These findings establish the first mechanistic framework linking PQS signaling to algicidal process, demonstrating its role in synchronizing metabolic flux toward terpenoid synthesis while optimizing bacterial-algal interactions. Key pathways-including chemotaxis (malE) and terpenoid biosynthesis (DXS synthase)-provide actionable targets for engineering bioaugmented consortia or precision algicidal formulations. This work advances quorum sensing-driven strategies for sustainable harmful algal bloom (HAB) mitigation, offering scalable solutions for aquaculture and eutrophic water remediation with minimal ecological disruption. By bridging molecular mechanisms to field applications, the study underscores the translational potential of this approach in global water security initiatives.},
}

Quorum Sensing/drug effects
*Enterobacter/genetics/drug effects/metabolism
*Quinolones/pharmacology/metabolism
Proteomics
Metabolomics
Bacterial Proteins/metabolism/genetics
Transcriptome
Multiomics

@article {pmid40620901,
year = {2025},
author = {Schrama, N and Tilman, AR and Vasconcelos, VV},
title = {Majority illusion drives the spontaneous emergence of alternative states in common-pool resource games with network-based information.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112831},
pmid = {40620901},
issn = {2589-0042},
abstract = {Common-pool resources (CPRs), including fisheries and the atmosphere, are critical for ecological, social, and economic sustainability but are easily overused. We use an agent-based model to investigate how social networks shape resource extraction outcomes. Networks with highly visible nodes can create a "majority illusion" in which most users believe high-intensity extraction is dominant, even if it is not. This misperception can push the entire population toward one of two possible states: an abundant, high-welfare resource or a depleted, low-welfare one. Aligning users' environmental impact with their visibility can mitigate this effect and steer the system toward a single, predictable outcome. These results suggest that network-based policies, such as reshaping information flows, particularly targeting high-impact hubs, could help stabilize cooperative behaviors and encourage sustainable management of CPRs, reducing the risk of tragedy-of-the-commons scenarios.},
}

@article {pmid40619084,
year = {2025},
author = {Liu, X and Hu, Z and Gao, J},
title = {Assessment of soil and groundwater pollution risks from coal gangue backfilling: A case study in Inner Mongolia mining areas.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122303},
doi = {10.1016/j.envres.2025.122303},
pmid = {40619084},
issn = {1096-0953},
abstract = {This study evaluates the environmental risks of coal gangue (CG) filling through leaching experiments and numerical simulation methods. The results show that under acidic conditions, the leaching concentration of heavy metals in CG is relatively high, with copper concentration reaching 0.80 mg/L, exceeding Class I discharge standards. Under neutral conditions, the leachate indicators meet national standards. Although the reclaimed soil meets the agricultural land standards, its fertility level is relatively low (soil quality index 0.416), and cadmium, due to its high toxicity coefficient, becomes the primary ecological risk factor. The use of a layered compaction process can effectively control the migration of leachate. Numerical simulations indicate that the maximum migration depth of pollutants is 17 m, with concentrations stabilizing after 2500 days. The high mineralization of groundwater is primarily influenced by the geological background values, and the fluoride contamination plume has a diffusion range of less than 204 m. The study suggests that engineered CG filling reclamation presents controllable environmental risks and resource utilization potential. However, it is important to note that the study has limitations, such as a short monitoring period and uncertainties in the model predictions. It is recommended to conduct long-term field monitoring to comprehensively assess the environmental impact.},
}

@article {pmid40617847,
year = {2025},
author = {Kindt, R and Siddique, I and Dawson, I and John, I and Pedercini, F and Lillesø, JP and Graudal, L},
title = {The Agroforestry Species Switchboard, a global resource to explore information for 107,269 plant species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1150},
pmid = {40617847},
issn = {2052-4463},
mesh = {*Plants/classification ; *Databases, Factual ; Biodiversity ; Forestry ; },
abstract = {The Agroforestry Species Switchboard is a comprehensive vascular plant database that guides users to information for a particular taxon from a global but fragmented set of resources. Via standardized species names, a user can rapidly determine which among the 59 contributing databases contain information for a species of interest, and understand how this information can be accessed. By providing taxonomic identifiers to World Flora Online, it is straightforward to check for changes in taxonomy. Among the 59 databases referenced, ten covered over 10,000 species, 20 between 1,000 and 10,000 species, and 22 between 100 and 1,000 species. The top ten plant families for species richness across covered databases were the Fabaceae (9,537 species), Asteraceae (6,041), Rubiaceae (4,812), Poaceae (3,947), Myrtaceae (3,544), Euphorbiaceae (2,689), Malvaceae (2,478), Rosaceae (2,374), Lauraceae (2,334) and Lamiaceae (2,107). Information included in the Switchboard distinguishes 54,812 tree-like species, covering most known tree species globally. Among its applications, the Switchboard can assist species selection for ecological restoration projects to synergize biodiversity and human well-being objectives.},
}

*Plants/classification
*Databases, Factual
Biodiversity
Forestry

@article {pmid40617215,
year = {2025},
author = {Jiao, Y and Miao, X and Liu, X and Gao, Y and Guo, J and Liu, C and Wang, L and Qian, T and Wang, X and Hong, S},
title = {Innovative engineering of red-emissive carbon dots for profoundly sensitive and recyclable determination of malachite green in fish tissue.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {344},
number = {Pt 1},
pages = {126631},
doi = {10.1016/j.saa.2025.126631},
pmid = {40617215},
issn = {1873-3557},
abstract = {Accurate measurement of hazardous synthetic dye is highly attractive for environmental and food safety inspection. Herein, red fluorescent carbon dots (R-CDs) are meticulously engineered by employing Azure A as a fluorophore to optimize the optical characteristics, thereby promoting high-efficiency fluorescence emission at 648 nm. The constructed R-CDs demonstrate excitation-independent characteristics remarkable photostability and superior water solubility. It is encouraging that the developed R-CDs demonstrate a specific response to MG, effectively differentiating it from other substances. The engineered R-CDs demonstrate concentration-responsive fluorescence quenching towards MG, exhibiting rapid response time with a well-defined linear detection range of 0.09-8.21 μM and ultralow detection limit of 24.2 nM. Furthermore, the spike recovery analysis of MG in fish tissue demonstrated robust performance with recoveries of 97.63-106.0 % (RSD <6.37 %), highlighting the analytical reliability for MG identification in aquatic products. The aforementioned results underscore the significant potential of the developed R-CDs for MG detection in aquatic products and bolster their application in food safety inspections.},
}