@article {pmid40689909,
year = {2025},
author = {Culbreth, AJ and Barch, DM and Nepal, S and Ben-Zeev, D and Campbell, A and Moran, EK},
title = {Passive sensing of anhedonia and amotivation in a transdiagnostic sample.},
journal = {Journal of psychopathology and clinical science},
volume = {134},
number = {8},
pages = {893-901},
pmid = {40689909},
issn = {2769-755X},
support = {R37 MH066031/MH/NIMH NIH HHS/United States ; /MH/NIMH NIH HHS/United States ; },
mesh = {*Anhedonia/physiology ; Humans ; Male ; *Ecological Momentary Assessment ; Adult ; Female ; Middle Aged ; *Major Depressive Disorder/physiopathology/diagnosis ; *Bipolar Disorder/physiopathology/diagnosis ; *Schizophrenia/physiopathology/diagnosis ; *Motivation/physiology ; Actigraphy ; Geographic Information Systems ; },
abstract = {Anhedonia and avolition are core clinical features of schizophrenia, bipolar disorder, and major depressive disorder, which have been traditionally assessed using clinical rating scales. However, recent developments in mobile technology allow for measurement of anhedonia and amotivation using passive sensors (e.g., global positioning system and actigraphy) and surveys completed in daily life (i.e., ecological momentary assessment [EMA]). The current study examined associations between clinical rating scales assessing anhedonia and amotivation and passive sensing measures. We aimed to determine the added value of passive sensing measures in explaining variability in clinical interviews, compared to models using EMA alone. We recruited a transdiagnostic sample (schizophrenia = 41, bipolar disorder = 47, and major depressive disorder = 48) to complete an in-person assessment session, as well as a 2-week EMA and passive sensing protocol. Passive sensing measures included physical distance traveled, number of phone calls sent/received, and number of texts sent/received. EMA included the assessment of interest and enjoyment in daily activities. We found that reports of interest/enjoyment in daily activities significantly predicted gold standard, clinical rating scales of anhedonia and avolition across diagnostic groups (standardized β = -0.208, p = .015, model R2 = .04). Including participant distance traveled into this model aided our ability to explain variance (standardized β = -0.280, p < .001, model R[2] = .12). Finally, adding call (standardized β = -0.170, p = .039) and text (standardized β = -0.198, p = .022) data further improved variance explained (model R[2] = .18). These data suggest that passive sensor streams strengthen the associations between assessments in daily life and gold standard ratings of anhedonia and avolition, suggesting "added value" in using these approaches to understand motivational experience in people with psychotic and mood pathology. (PsycInfo Database Record (c) 2025 APA, all rights reserved).},
}

*Anhedonia/physiology
Humans
Male
*Ecological Momentary Assessment
Adult
Female
Middle Aged
*Major Depressive Disorder/physiopathology/diagnosis
*Bipolar Disorder/physiopathology/diagnosis
*Schizophrenia/physiopathology/diagnosis
*Motivation/physiology
Actigraphy
Geographic Information Systems

@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 {pmid40692109,
year = {2025},
author = {Chiolerio, A and Konkoli, Z and Adamatzky, A},
title = {Ecosystem-based reservoir computing. Hypothesis paper.},
journal = {Bio Systems},
volume = {255},
number = {},
pages = {105525},
doi = {10.1016/j.biosystems.2025.105525},
pmid = {40692109},
issn = {1872-8324},
mesh = {*Ecosystem ; Computer Simulation ; *Ecology/methods ; Humans ; *Computational Biology/methods ; },
abstract = {Reservoir computing (RC) has emerged as a powerful computational paradigm, leveraging the intrinsic dynamics of complex systems to process temporal data efficiently. Here we propose to extend RC into ecological domains, where the ecosystems themselves can function as computational reservoirs, exploiting their complexity and extreme degree of interconnectedness. This position paper explores the concept of ecosystem-based reservoir computing (ERC), examining its theoretical foundations, empirical evidence, and potential applications. We argue that ERC not only offers a novel approach to computation, but also provides insights into the computational capabilities inherent in ecological systems and offers a new paradigm for remote sensing applications.},
}

*Ecosystem
Computer Simulation
*Ecology/methods
Humans
*Computational Biology/methods

@article {pmid40693914,
year = {2026},
author = {Burger, J and Gochfeld, M and Brown, KG and Cortes, M and Ng, K and Kosson, DS},
title = {Using National Land Cover Database as an indicator of successful remediation: the Department of Energy's Rocky Flats (Colorado) as a case study.},
journal = {Journal of toxicology and environmental health. Part A},
volume = {89},
number = {1},
pages = {1-17},
doi = {10.1080/15287394.2025.2534616},
pmid = {40693914},
issn = {2381-3504},
mesh = {*Environmental Restoration and Remediation ; Colorado ; Ecosystem ; *Conservation of Natural Resources ; Databases, Factual ; United States ; Environmental Monitoring/methods ; },
abstract = {Missions for federal facilities, such as the Department of Defense (DOD) and the Department of Energy (DOE), include protecting human health and the environment. The public is interested in whether ecological resources are protected on such lands, especially following remediation of legacy wastes remaining from World War II, Cold War, and industrial activities. Many DOE sites are remediated for future uses depending upon potential for exposure to residual contamination. This study: (1) examined the % ecological resources remaining on Rocky Flats following completion of cleanup, (2) compared the ecological resources (i.e. plant cover) of Rocky Flats (RF) with the surrounding 10-km and 30-km bands of land, and (3) measured % natural vegetation on RF with comparable % on three other large DOE facilities that are still undergoing remediation. Rocky Flats contains significantly more grassland than the surrounding region, with less development, and is mostly a National Wildlife Refuge open to the public. Agriculture and grazing do not occur on RF. The three sites undergoing remediation have significantly more natural habitat (climax vegetation) than their surrounding buffer areas. The aim of this study was to examine the implications of ecological protection of climax vegetation upon these sites and the importance of consistently examining regional ecologies.},
}

*Environmental Restoration and Remediation
Colorado
Ecosystem
*Conservation of Natural Resources
Databases, Factual
United States
Environmental Monitoring/methods

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

@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 {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 {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 {pmid40706521,
year = {2025},
author = {Liu, X and Zhai, WH and Liu, R and Liu, BL and Gao, RJ and Li, YW and Xiang, L and Cai, QY and Zhao, HM and Mo, CH},
title = {Integrated multi-omics analyses of molecular pathways underlying microcystin-LR toxicity in the earthworm Eisenia fetida.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118724},
doi = {10.1016/j.ecoenv.2025.118724},
pmid = {40706521},
issn = {1090-2414},
mesh = {Animals ; *Microcystins/toxicity ; *Oligochaeta/drug effects/metabolism ; Marine Toxins ; *Soil Pollutants/toxicity ; Proteomics ; Metabolomics ; Multiomics ; },
abstract = {Contamination of soil with microcystin-LR (MC-LR) has emerged as a significant environmental concern, but its toxicological impacts and underlying mechanisms on soil-dwelling invertebrates are not yet fully elucidated. Here we employed a comprehensive strategy integrating histopathological, ultrastructural, biochemical, and multi-omics (metabolomics and proteomics) analyses to investigate the effects of MC-LR on Eisenia fetida, a model soil organism. MC-LR exposure induced dose-dependent structural damage to the epidermal and intestinal tissues, disrupting antioxidant systems while elevating detoxification enzyme activity. Metabolomic profiling identified 93 significantly altered metabolites in the earthworms following exposure to MC-LR at a concentration of 0.6 mg/kg, implicating pathways such as amino acid biosynthesis, protein digestion and absorption, ATP-binding cassette transporters, and aminoacyl-tRNA biosynthesis. Proteomic analysis showed that MC-LR affected distinct pathways, particularly those associated with nucleotide binding, calcium ion binding, ATP binding, cytoskeleton, and actin filament binding. Correlations between differentially expressed metabolites and differentially expressed proteins highlighted critical roles of amino acid biosynthesis, thiamine metabolism, glutathione metabolism, and longevity regulating in earthworms' defense against MC-LR toxicity. This study advances the understanding of molecular pathways underlying MC-LR-induced toxicity in soil invertebrates, providing valuable insights into its ecological impact and potential risks.},
}

Animals
*Microcystins/toxicity
*Oligochaeta/drug effects/metabolism
Marine Toxins
*Soil Pollutants/toxicity
Proteomics
Metabolomics
Multiomics

@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 = {25},
number = {17-18},
pages = {6-18},
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/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Proteomics/methods ; Coculture Techniques ; Feces/microbiology ; *Proteome/analysis ; },
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.},
}

Humans
*Gastrointestinal Microbiome
*Proteomics/methods
Coculture Techniques
Feces/microbiology
*Proteome/analysis

@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 {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 {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 {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 {pmid40726282,
year = {2025},
author = {de Mol, F and Fritzsche, R and Gerowitt, B},
title = {Weed biodiversity and herbicide intensity as linked via a decision support system.},
journal = {Pest management science},
volume = {81},
number = {10},
pages = {6667-6677},
pmid = {40726282},
issn = {1526-4998},
support = {//South Baltic Cross-border cooperation EU programme/ ; //German Federal Agency/ ; FKZ 351984070//Federal Ministry/ ; },
mesh = {*Herbicides ; *Biodiversity ; *Plant Weeds/drug effects ; *Weed Control/methods ; Germany ; *Decision Support Techniques ; Triticum/growth & development ; },
abstract = {BACKGROUND: Extensive herbicide use is one reason for the declining biodiversity of arable weeds. This study aimed to investigate (i) whether herbicide decisions recommended by a decision support system increase the weed species diversity compared to standard recommendations, and (ii) whether high weed species diversity reduces herbicide intensity, which in turn contributes to higher diversity. Data on weeds and herbicide applications in winter wheat fields in north-eastern Germany were collected in 15 field trials over 2 years. Five treatments differed in the way of decision-making for herbicide application, including two treatments according to recommendations of decision support systems.

RESULTS: Along the Hill's series biodiversity metrics, the untreated control had the highest species richness (13.5 m[-2]) per field but showed increasingly stronger dominance structures than the treated plots (equivalent species richness: 1.7-2.0 m[-2]). The treatment frequency index as a metric for herbicide intensity was significantly lowest in the decision support system with low reliability (1.07). Path models, including weed diversity and density in autumn, weed diversity in summer, and herbicide intensity as a mediating variable showed a significant decreasing effect of Shannon diversity on herbicide intensity in all treatments. Only the decision support systems reacted to low weed densities with a significant reduction of the herbicide intensity.

CONCLUSION: Higher weed species diversity contributes to lower herbicide intensity, which is ecologically and economically valuable. Decision support systems for herbicide application should have other target functions than cost reduction for contributing to biodiversity. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

*Herbicides
*Biodiversity
*Plant Weeds/drug effects
*Weed Control/methods
Germany
*Decision Support Techniques
Triticum/growth & 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 = {44},
number = {11},
pages = {3118-3130},
doi = {10.1093/etojnl/vgaf190},
pmid = {40728939},
issn = {1552-8618},
support = {MCIN/AEI/10.13039/501100011033/FEDER//Ministry of Science, Innovation and Universities of Spain/ ; PID2022-137402OB-I00//BeingHavior/ ; 2020-02293//Swedish Research Council Formas/ ; 2020-01052//Swedish Research Council Formas/ ; SMK-1954 and SMK21-0069//Kempe Foundations/ ; 23-07274S//Czech Science Foundation/ ; #334739//Research Council of Norway/ ; },
mesh = {*Ecotoxicology ; Animals ; *Environmental Pollutants/toxicity ; Humans ; },
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.},
}

*Ecotoxicology
Animals
*Environmental Pollutants/toxicity
Humans

@article {pmid40729790,
year = {2025},
author = {Michel, A and Prade, M and De Bandt, D},
title = {Pregabalin and gabapentin use in France from 2012 to 2023, impact of prescription restrictions, a time series analysis.},
journal = {The International journal on drug policy},
volume = {145},
number = {},
pages = {104929},
doi = {10.1016/j.drugpo.2025.104929},
pmid = {40729790},
issn = {1873-4758},
mesh = {*Pregabalin/administration & dosage/economics ; *Gabapentin/administration & dosage/economics ; France ; Humans ; *Practice Patterns, Physicians'/statistics & numerical data/trends ; Prescription Drug Misuse ; Databases, Factual ; Drug Prescriptions/statistics & numerical data ; },
abstract = {INTRODUCTION: Gabapentinoids use is accompanied by increased misuse, particularly for pregabalin. In May 2021, France introduced secure prescription requirements for pregabalin. This paper aims to analyse variations in gabapentinoid dispensing, with a focus on changes in prescription rules.

MATERIEL AND METHOD: We performed an ecological study using the French national health insurance database from January 2012 to December 2023. We analysed pregabalin and gabapentin doses sold by city pharmacies expressed in monthly defined daily dose per thousand inhabitant a day (DDD/TID) between January 2012 and December 2023. Dose sales trends before and after May 2021 were compared using segmented analysis of Autoregressive Integrated Moving Average models. Descriptive analysis was performed to analyse associated expenses expressed in euros.

RESULTS: Between 2012 and 2020, pregabalin doses sold rose from 3.228 DDD/TID to 4.908 DDD/TID. After the reform, they declined to 3.923 DDD/TID in 2023. Gabapentin doses sold increased from 1.042 DDD/TID to 1.257 DDD/TID between 2012 and 2020, then rose further post-reform, reaching 1.705 DDD/TID. Costs related to the pregabalin doses sold decreased from €132.47 to €51.36 million from 2012 to 2023. Costs related to gabapentin decrease from €32.31 to €26.84 million between 2012 and 2021, then increase to €37.70 million in 2023.

DISCUSSION: These data suggest that the May 2021 reform has reduced pregabalin consumption and induced an increase of gabapentin use. Cost implications remain of difficult interpretation due to multiple confounding factors. Further research could clarify these trends and be used to optimize prescription practices.},
}

*Pregabalin/administration & dosage/economics
*Gabapentin/administration & dosage/economics
France
Humans
*Practice Patterns, Physicians'/statistics & numerical data/trends
Prescription Drug Misuse
Databases, Factual
Drug Prescriptions/statistics & numerical data

@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},
mesh = {China ; *Environmental Pollution ; *Environmental Policy ; Industry ; *Conservation of Natural Resources ; },
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.},
}

China
*Environmental Pollution
*Environmental Policy
Industry
*Conservation of Natural Resources

@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 {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 {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 {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 {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 {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 {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},
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 {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 {pmid40755083,
year = {2025},
author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H},
title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70023},
pmid = {40755083},
issn = {1755-0998},
support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; },
mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; },
abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).},
}

*DNA, Environmental/genetics
*DNA Barcoding, Taxonomic/methods
*Computational Biology/methods
*Genetic Variation
*Metagenomics/methods
*Software
Sequence Analysis, DNA/methods

@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 {pmid40762139,
year = {2025},
author = {Kwong, SLT and Budd, AM and Hung, JY and Villacorta-Rath, C and Uthicke, S},
title = {Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology (ONT).},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70026},
pmid = {40762139},
issn = {1755-0998},
support = {//Australian Institute of Marine Science/ ; },
mesh = {Animals ; *DNA Methylation ; *Epigenome ; Computational Biology/methods ; },
abstract = {DNA methylation is crucial for genome regulation and provides key insights into the interaction between genetics and environmental factors, offering valuable perspectives for ecological research. However, knowledge of DNA methylation patterns in nonmodel invertebrates remains limited. The present study addresses this knowledge gap by conducting the first methylome profiling of the Pacific crown-of-thorns seastar (CoTS; Acanthaster cf. solaris), a coral-eating species that aggravates the decline of Indo-Pacific coral reefs. Using Oxford Nanopore Technology (ONT) we generated long-read sequences, covering over 90% of CpG dinucleotides in the CoTS genome. Our analysis revealed a mosaic methylation landscape with moderate genome-wide methylation levels of 37.7%. Comparative analysis highlights the intermediate methylation state observed in other deuterostome invertebrates, positioning them between the hypomethylated genomes of protostomes and the hypermethylated genomes of vertebrates. Methylation in CoTS was predominantly localised within gene bodies, especially in intronic regions, enabling modulation of gene expression and potentially supporting fitness in dynamic marine environments. Additionally, elevated methylation in repetitive elements suggests a role in genome defence. This study demonstrates the effectiveness of ONT for comprehensive methylome analysis in ecologically important nonmodel species and deepens our understanding of the epigenetic landscape in deuterostome invertebrates. We also present a detailed laboratory and bioinformatics workflow, including modified phenol-chloroform protocols that address the challenge of extracting high molecular weight DNA from marine invertebrates. Together with the methylome profiles, these resources serve as a foundation for future research, enabling investigations into DNA methylation functions, applications for CoTS outbreak management and comparative studies across diverse lineages.},
}

Animals
*DNA Methylation
*Epigenome
Computational Biology/methods

@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 = {60},
number = {14},
pages = {2287-2298},
doi = {10.1080/10826084.2025.2540938},
pmid = {40763003},
issn = {1532-2491},
support = {R21 DA056684/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Social Media/statistics & numerical data ; *Substance-Related Disorders/psychology ; *Opioid-Related Disorders/psychology ; Social Stigma ; },
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.},
}

Humans
*Social Media/statistics & numerical data
*Substance-Related Disorders/psychology
*Opioid-Related Disorders/psychology
Social Stigma

@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 {pmid40763614,
year = {2025},
author = {Wang, C and Xia, A and Feng, D and Li, L and Zhang, J and Huang, Y and Zhu, X and Zhu, X and Trably, E and Liao, Q},
title = {Impacts of intermittent electrical stimulation on continuous electro-anaerobic digestion from wastewater: performance and multi-omics insights.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124319},
doi = {10.1016/j.watres.2025.124319},
pmid = {40763614},
issn = {1879-2448},
mesh = {*Multiomics ; *Wastewater/chemistry ; Anaerobiosis ; Sewage/microbiology ; *Waste Disposal, Fluid/methods ; Electric Stimulation ; Bioreactors/microbiology ; Methane/analysis/metabolism ; Proteome/metabolism ; },
abstract = {The recently reported electro-anaerobic digestion with intermittent electrical stimulation (IEAD) offers new opportunities for renewable energy storage. However, the mechanistic insights and resilience of long-term continuous and stable IEAD are still yet to be better understood. This study lasted up to 155 days of continuous operation of IEAD in up-flow anaerobic sludge blanket bioreactors to evaluate the long-term effects of different intermittent power periods on IEAD performance. The optimal electrical stimulation period was obtained for 12 h:12 h intermittence, resulting in a 15.9 % improvement of the specific methane yield while achieving an organic removal efficiency higher than 98 %. Intermittent electrical stimulation favored biofilm growth, electroactive substance secretion, and enhanced electrochemical activity and cellular repair. Genomic analysis demonstrated that IEAD microbial community was dominated by Methanothrix, whereas continuous energization promoted Methanobacteriaceae enrichment. Proteomic analysis suggested that intermittent power supply preserved functional proteins and upregulated dominant enzymes such as acetyl-CoA carboxylase biotin carboxyl carrier protein and enoyl-CoA hydratase, while conferring flexible carbon source allocation and electron transfer capacity to the suspension zone. Life cycle assessment results showed that the IEAD system could achieve an energy conversion rate of 20.6 and low carbon emissions of 7.3 g CO2-eq/MJ.},
}

*Multiomics
*Wastewater/chemistry
Anaerobiosis
Sewage/microbiology
*Waste Disposal, Fluid/methods
Electric Stimulation
Bioreactors/microbiology
Methane/analysis/metabolism
Proteome/metabolism

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*Telemedicine
Humans

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*Deep Learning
Humans
Geographic Information Systems
*Crowding
Algorithms

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid40846910,
year = {2025},
author = {Lu, M and Wang, S and Zhou, Y and Wang, X and Su, H and Gong, Y and De, J},
title = {Multi-omics profiling reveals single-seed mutants of Ephedra saxatilis as dominant variants in high-altitude Xizang.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1118},
pmid = {40846910},
issn = {1471-2229},
support = {32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; },
mesh = {*Altitude ; *Ephedra/genetics/metabolism/physiology ; Germination/genetics ; *Seeds/genetics/metabolism/ultrastructure/physiology ; Tibet ; Mutation ; Metabolomics ; Transcriptome ; Multiomics ; },
abstract = {Ephedra species, important Tibetan medicinal plants, are widely distributed across the Qinghai-Tibet Plateau at altitudes of 2700-5000 m. Their adaptation to high-altitude environments, such as low temperatures, strong UV radiation and low oxygen, is still poorly understood. This study investigated the morphological, metabolic, and genetic mechanisms underlying the reproductive advantage of a unique single-seed variant observed in high-germination-rate Ephedra species. Seeds from six Ephedra species were collected for germination assays and electron microscopic analysis. Results showed that E. saxatilis, E. intermedia, and E. monosperma exhibited significantly higher germination rates (Germination rates > 65%) and predominantly produced single-seed variants, while others mainly produced double seeds. Analysis of burr and fold numbers of phenotypic traits showed a significant positive correlation with germination rates. Time-course metabolomics analysis identified 762 KEGG annotated metabolites, and revealed E. saxatilis as the dominant species due to its faster metabolic rate, particularly simulated high-altitude conditions. Absolute hormone quantification highlighted the single-seed variant of E. saxatilis as the dominant type, with ABA content peaking in the shed seed coat. ABA exhibited antagonistic interactions with 2MeScZR, SA, IAA, GA7, IPR, and t-CA, suggesting a complex hormonal regulation network. Co-expression network analysis integrating transcriptome and hormone data predicted 23 key genes regulating seed germination adaptation. This study provides novel insights into the ecological and evolutionary significance of single-seed variation in high-altitude adaptation. The findings have potential applications in high-altitude plant breeding, conservation, and sustainable utilization of Ephedra species. Future research should focus on the genetic basis of single-seed variation and its role in other high-altitude plant species.},
}

*Altitude
*Ephedra/genetics/metabolism/physiology
Germination/genetics
*Seeds/genetics/metabolism/ultrastructure/physiology
Tibet
Mutation
Metabolomics
Transcriptome
Multiomics

@article {pmid40848298,
year = {2025},
author = {Jia, Y and Chen, L and Jin, LN and Zhang, P and Chen, L and Fan, C and Liu, H and Ji, Y and Li, D and Chen, J},
title = {Environmentally Relevant Levels of Ozone Enhance Klebsiella pneumoniae Pulmonary Colonization and Cross-Organ Translocation.},
journal = {Environmental science & technology},
volume = {59},
number = {35},
pages = {18424-18439},
doi = {10.1021/acs.est.5c02782},
pmid = {40848298},
issn = {1520-5851},
mesh = {*Klebsiella pneumoniae ; *Ozone/toxicity ; Animals ; Lung/microbiology ; Mice ; Klebsiella Infections ; },
abstract = {Ozone (O3) is a major global air pollutant. Recent epidemiological studies have suggested links between O3 exposure and outbreaks of infectious diseases. However, whether environmentally relevant levels of O3 exacerbate the colonization and infection of airborne pathogens remains unclear. This study demonstrated that exposure to environmentally relevant levels of O3 (0.15 and 0.60 ppm) significantly enhanced pulmonary colonization of low-dose Klebsiella pneumoniae (1 × 10[3] CFU/mouse) in mice, which failed to colonize without O3 exposure. Unexpectedly, in vivo and in vitro coculture experiments with BEAS-2B bronchial epithelial cells demonstrated that O3 exposure also enhanced the ability of K. pneumoniae to penetrate the lung-blood barrier, thereby inducing bacteremia that spread to the liver and caused severe liver injury. O3 exposure reduced the proportions of T cells, B cells, and macrophages in the lungs and altered the expression of key pulmonary genes (Tlr4, Il-18, Traf6, and Tgf-β1) involved in resisting K. pneumoniae colonization. In addition, lipid peroxidation product MDA in plasma acted as a mediator in the signal transmission along the lung-liver axis. This study underscores the critical role of air pollutants in pathogen colonization and infection, emphasizing the urgent need to address air quality to mitigate respiratory health risks.},
}

*Klebsiella pneumoniae
*Ozone/toxicity
Animals
Lung/microbiology
Mice
Klebsiella Infections