@article {pmid41507362,
year = {2026},
author = {Elettrico, L and Piacenti, G and Levra Levron, C and Ansai, O and Croce, A and Duval, C and Proserpio, V and Donati, G},
title = {Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.},
journal = {Cell death and differentiation},
volume = {33},
number = {7},
pages = {1312-1332},
pmid = {41507362},
issn = {1476-5403},
support = {IG2023 - Id.21640//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; MFAG 2023 - Id.29203//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Fondazione Umberto Veronesi (Umberto Veronesi Foundation)/ ; },
mesh = {Humans ; Animals ; *Skin/metabolism/microbiology ; Skin Microbiome ; Multiomics ; Microbiota ; Epithelial Cells/metabolism ; },
abstract = {Skin homeostasis depends on interactions between epithelial cells and the microbiome mediated by molecular and biochemical factors. Perturbations of this interplay are linked to inflammatory disorders, including wound healing and cancer. While research has mainly illuminated shifts in microbial community composition, novel computational approaches are starting to reveal the host-microbe functional interactome in the cutaneous ecosystem. In this review, we specifically focus on known molecular and metabolic mechanisms linking skin epithelial cells and microorganisms in health and disease. Additionally, we summarise computational tools available to investigate these interactions integrating omics data. Furthermore, we present potential applications of this functional crosstalk to advance therapies targeting skin pathologies. Finally, we propose a comparative interactomics approach to envision the existence of ecological memories in the skin ecosystem, in parallel with the one described in the gut, hypothesising a link between epithelial and microbial memories in barrier tissues.},
}

Humans
Animals
*Skin/metabolism/microbiology
Skin Microbiome
Multiomics
Microbiota
Epithelial Cells/metabolism

@article {pmid42010402,
year = {2026},
author = {Gabella, JL and Gualda, IAP and Beltrame, MHA and Costa, WF and Hachmann, TF and Massago, M and de Paulo, LG and Grizzo, FMF and Gurgel, SJT and de Andrade, L},
title = {Spatiotemporal patterns of femoral fractures in older adults: healthcare access and regional inequalities in southern Brazil.},
journal = {BMC geriatrics},
volume = {26},
number = {1},
pages = {},
pmid = {42010402},
issn = {1471-2318},
mesh = {Retrospective Studies ; Secondary Data Analysis ; Humans ; Male ; Female ; Middle Aged ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Spatio-Temporal Analysis ; *Femoral Fractures/mortality/therapy ; *Health Services Accessibility/statistics & numerical data/trends ; Incidence ; *Healthcare Disparities/trends ; Hospitalization/statistics & numerical data ; Resource-Limited Settings/statistics & numerical data ; },
abstract = {BACKGROUND: Femoral fractures in older adults are associated with lethality rates of up to 30% within the first year and significantly compromised quality of life, leading to high levels of disability, institutionalization, and burden on health systems. By 2050, the global population of older adults is projected to exceed 2 billion, leading to an exponential increase in these events. In Brazil, the incidence of fractures is high and often linked to inequalities in access to diagnosis and prevention, particularly in regions with limited infrastructure. This study aimed to analyze the spatiotemporal distribution of femoral fractures in older adults and identify contextual factors associated with their occurrence. METHODS: This is an ecological and retrospective study using secondary data from 2010 to 2021 on hospitalizations for femoral fractures in older adults (≥ 60 years) in the 399 municipalities of Paraná State, Brazil. Descriptive analyses and nonparametric tests were performed to compare mortality rates according to population size. Spatiotemporal distribution was examined using space–time cubes. Spatial autocorrelation was assessed using global Moran’s I and local indicators of spatial autocorrelation (LISA). Geographically weighted regression (GWR) was applied to explore local associations with contextual variables. RESULTS: A total of 39,226 femoral fractures were recorded during the study period, with a predominance among women (66.8%). Overall lethality was 6%, being significantly higher in men. Space–time cube analysis indicated a persistent increasing trend in fractures (Z = 2.8115, p = 0.0049). Spatial analysis revealed significant positive spatial autocorrelation (I = 0.705, p < 0.001) and identified significant clusters and groupings (p < 0.05). GWR demonstrated a negative association between fracture incidence and access to specialists and osteoporosis medication, and a positive association with falls and densitometry availability in some regions. CONCLUSION: The findings indicate that the distribution of fractures is not random but rather influenced by factors such as access to diagnosis, medication, and specialized care. This evidence underscores the value of geospatial tools in the planning of health actions, enabling more targeted and equitable interventions in response to population aging.},
}

Retrospective Studies
Secondary Data Analysis
Humans
Male
Female
Middle Aged
Aged
Aged, 80 and over
Brazil/epidemiology
Spatio-Temporal Analysis
*Femoral Fractures/mortality/therapy
*Health Services Accessibility/statistics & numerical data/trends
Incidence
*Healthcare Disparities/trends
Hospitalization/statistics & numerical data
Resource-Limited Settings/statistics & numerical data

@article {pmid42103911,
year = {2026},
author = {Sun, H and Hua, Y},
title = {Study on GIS-based suitability evaluation of the landscape environment of celebrity former residences in Huanggang.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42103911},
issn = {2045-2322},
mesh = {*Geographic Information Systems ; Humans ; China ; *Conservation of Natural Resources ; *Environment ; Geography ; Ecosystem ; },
abstract = {Celebrity former residences, as cultural carriers shaped by historical evolution, embody profound cultural significance and hold immeasurable historical, social, political, and economic value. Grounded in the theories of human settlement science, settlement geography, and landscape ecology, this study takes the preserved celebrity former residences in Huanggang City as its research objects. Using the Analytic Hierarchy Process (AHP) and adopting a geographical perspective, eight geographical evaluation factors were selected in ArcGIS to represent topography, hydrology, ecology, and geomorphological stability as assessment indicators. By analyzing the relationship between these geographical factors and the spatial distribution of the residences, a suitability evaluation system for the landscape environment of celebrity former residences in Huanggang was established. The results indicate that, among the 136 officially protected celebrity residences in the city, 66 are located in highly suitable areas, accounting for 48.53%; 49 are located in suitable areas, accounting for 36.03%; 18 are located in less suitable areas, accounting for 13.24%; and 3 are located in unsuitable areas, accounting for 2.20%. In addition, a case study of the former residence of Li Siguang in Tuanfeng County demonstrates that its siting highly corresponds to the established evaluation framework. These findings suggest that geographical environmental factors are not only closely linked to the site selection of celebrity residences in Huanggang but also provide valuable references and guidance for future architectural siting and landscape environmental planning.},
}

*Geographic Information Systems
Humans
China
*Conservation of Natural Resources
*Environment
Geography
Ecosystem

@article {pmid42108422,
year = {2026},
author = {Shetty, P and Vuong, T and Li, C and Wagner, V and Myrzakhmetova, D and Peng, CC and Li, W and Ching, J and Zander, A and Weiser, S and Rosenbaum, MA and Allen, RJ and Lakemeyer, M and Mittag, M},
title = {Multiomics studies reveal how ambient temperature changes govern cellular responses of Chlamydomonas.},
journal = {The Plant cell},
volume = {38},
number = {7},
pages = {},
doi = {10.1093/plcell/koag136},
pmid = {42108422},
issn = {1532-298X},
support = {//Deutsche Forschungsgemeinschaft/ ; //DFG under Collaborative Research Centre/ ; //China Scholarship Council/ ; //Bio Pilot Plant of the Leibniz-HKI/ ; },
mesh = {*Temperature ; Multiomics ; *Chlamydomonas reinhardtii/genetics/physiology/metabolism ; *Chlamydomonas/genetics/physiology/metabolism ; Proteomics/methods ; Carbon Dioxide/metabolism ; Cilia/metabolism ; Gene Expression Profiling ; Photosynthesis ; Proteome ; Transcriptome ; },
abstract = {Photosynthetic protists, known as microalgae, face increasing temperatures due to climate change. The green biflagellate alga Chlamydomonas reinhardtii (Chlamydomonas) serves as a model for thermoregulation. While responses to thermal stress are well characterized, much less is known about the impact of ambient temperature shifts. Understanding microalgal responses to environmental temperature changes is critical, as these primary producers drive ecosystem productivity and food web dynamics. Here, Chlamydomonas grew mixotrophically at ambient temperatures from 18 °C to 33 °C. Transcriptomic profiling revealed extensive reorganization, with over 5,000 transcripts significantly affected, including those involved in algal-bacterial interactions, photoreception, lipid metabolism, photosynthesis, cilia formation, and the secretome. CO2 transfer rates and acetate levels measured at 18 °C and 28 °C suggest decreased photoautotrophic algal growth at 28 °C at first. Antagonistic bacterial activity was sustained longer at lower temperatures. Proteomic analyses of isolated cilia and secreted proteins corroborate major abundance changes within these sub-proteomes, particularly in ciliary intraflagellar transport complexes and mating-related proteins in the secretome. Together, these molecular alterations resulted in pronounced changes in growth, the lengths of cells and cilia swimming behavior, mating ability, and bacterial antagonism. These data reveal major cellular responses caused by ambient, even short-term temperature shifts.},
}

*Temperature
Multiomics
*Chlamydomonas reinhardtii/genetics/physiology/metabolism
*Chlamydomonas/genetics/physiology/metabolism
Proteomics/methods
Carbon Dioxide/metabolism
Cilia/metabolism
Gene Expression Profiling
Photosynthesis
Proteome
Transcriptome

@article {pmid42148581,
year = {2026},
author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S},
title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0377525},
pmid = {42148581},
issn = {2165-0497},
support = {//Guizhou Province 2020 Science and Technology Support Plan Project/ ; },
mesh = {Fermentation ; Multiomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism/analysis ; Metagenomics ; China ; Microbiota ; Metagenome ; Metabolomics ; *Archaea/genetics/classification/metabolism/isolation & purification ; },
abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.},
}

Fermentation
Multiomics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Alcoholic Beverages/microbiology/analysis
*Flavoring Agents/metabolism/analysis
Metagenomics
China
Microbiota
Metagenome
Metabolomics
*Archaea/genetics/classification/metabolism/isolation & purification

@article {pmid42262077,
year = {2026},
author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y},
title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0113225},
pmid = {42262077},
issn = {2165-0497},
mesh = {Animals ; Female ; Swine/blood/microbiology ; Pregnancy ; Multiomics ; *Reproduction/physiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; Litter Size ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Serum/chemistry ; },
abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.

IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.},
}

Animals
Female
Swine/blood/microbiology
Pregnancy
Multiomics
*Reproduction/physiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
Litter Size
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Metabolomics
Metagenomics
*Serum/chemistry

@article {pmid42294705,
year = {2026},
author = {Wang, J and Jiang, P and Yan, J and Shen, H and Wu, L and Wei, F and Lin, X and Xu, L},
title = {Spatial ecology meets quality control: a GIS-integrated strategy for visualizing and managing microbial contamination in sterile pharmaceutical cleanrooms.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0026826},
pmid = {42294705},
issn = {2165-0497},
support = {202423110050060//Anhui Provincial Department of Science and Technology/ ; },
mesh = {*Geographic Information Systems ; *Drug Contamination/prevention & control ; *Bacteria/classification/isolation & purification/genetics ; Quality Control ; *Environmental Monitoring/methods ; *Environmental Microbiology ; RNA, Ribosomal, 16S/genetics ; Drug Industry/standards ; Environment, Controlled ; },
abstract = {To enhance contamination source identification in sterile drug manufacturing, this study innovatively developed an integrated strategy combining geographic information system (GIS) spatial visualization with microbial contamination control. Between 2022 and 2025, researchers collected 1,117 environmental microbial isolates from sterile preparation workshops, analyzing their population structure, distribution patterns, and potential risks through 16S rRNA/ITS sequencing. GIS technology was employed to associate strain data with workshop spatial information, thereby providing a visual representation of microbial quantity, species composition, and distribution patterns. Results showed that Staphylococcus and Micrococcus dominated in clean areas, with microbial diversity highest in Controlled Not Classified (CNC) environments and lowest in A-grade areas. The microbial community structure in A-grade areas significantly differed from that in CNC/C/B-grade areas, while CNC/C/B-grade areas exhibited relative similarity. In the case study, the environmental microbial distribution maps clearly demonstrated regional variations and aggregation patterns. By identifying critical control areas and transmission pathways through contamination risk analysis, targeted interventions were designed and implemented, reducing the microbial contamination rate in target C-grade areas from 4.3% to 2.2%, thereby validating the strategy's effectiveness. This study targets the deficiency of "spatial visualization analysis" in clean area environmental monitoring. The proposed comprehensive strategy effectively fills the methodology gap in spatial analysis and contamination control for current clean area microbial monitoring. It provides a feasible framework for transforming environmental monitoring in the pharmaceutical industry from a passive surveillance system to an active early-warning system, assisting in enhancing the sterility assurance level of pharmaceutical production.IMPORTANCEAnalyzing the spatial distribution characteristics of microorganisms is crucial for developing effective pollution control strategies. However, existing environmental monitoring methods have limitations in revealing these spatial distribution patterns. This paper proposes an innovative strategy that integrates geographic information system (GIS) spatial analysis with microbial ecology research to enhance the accuracy and scientific rigor of pollution source identification and risk control. This approach enables the visualization of environmental microbial quantities, types, and spatial distribution, providing a quantitative tool for analyzing microbial contamination patterns and tracing transmission pathways. The developed "GIS-integrated strategy" methodology promotes a paradigm shift from merely confirming "microbial presence" to systematically analyzing the multidimensional relationships among "microorganism-environment-control." This study not only provides a scientific basis for formulating pollution control protocols in the pharmaceutical industry, contributing to improved sterility assurance, but also serves as a practical example of interdisciplinary integration between microbial ecology and spatial information science, demonstrating significant theoretical value and industry application prospects.},
}

*Geographic Information Systems
*Drug Contamination/prevention & control
*Bacteria/classification/isolation & purification/genetics
Quality Control
*Environmental Monitoring/methods
*Environmental Microbiology
RNA, Ribosomal, 16S/genetics
Drug Industry/standards
Environment, Controlled

@article {pmid42360987,
year = {2026},
author = {Abuzaid, AS and Abbas, HH and El Ghonamy, YK and Mostafa, MA and Rebouh, NY and Shokr, MS},
title = {A GIS-based multi-criteria framework for mapping potential irrigated agricultural zones in newly reclaimed arid agroecosystem.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351546},
pmid = {42360987},
issn = {1932-6203},
mesh = {*Geographic Information Systems ; *Agricultural Irrigation/methods ; Soil/chemistry ; Groundwater ; *Agriculture/methods ; Fuzzy Logic ; Egypt ; *Agroecology ; Ecosystem ; Conservation of Natural Resources ; },
abstract = {Geographic assessment of natural resources is a pillar for sustainable agriculture in newly developed agroecosystems. The current work provides a new framework to discriminate agricultural potential zones by integrating the analytical hierarchy process (AHP) with fuzzy logic under the geographic information system (GIS) platform. The study was conducted on 303.54 km2 (30354 ha) in the western Nile Delta fringes, Egypt. Topographic maps, field surveys, and laboratory analyses were employed to specify parameters characterizing terrain, soil, and groundwater qualities. The main criteria and their respective sub-criteria were ranked and weighted using the AHP. The GIS tools were employed to generate raster layers using ordinary kriging geostatistical models, normalize the thematic layers using fuzzy membership functions, and integrate the fuzzified layers with their AHP-derived weights using the weighted sum algorithm. Results revealed that the consistency ratio of all the developed pairwise comparison models did not exceed 10%, indicating the efficacy of AHP in allocating the specific contribution of each criterion. Salinity, sodicity, and depth were key parameters controlling soil performance; meanwhile, potential salinity and infiltration problems primarily determined the feasibility of groundwater irrigation. Among four major criteria, the greatest impact was due to groundwater quality (50%), followed by chemical soil quality (24%) and physical soil quality (21%), while slope had the least contribution (5%). The potentiality analysis indicated that the studied soils are promising since good-quality soils occupied more than 60% of the studied area. Groundwaters with good, marginal, and poor quality occupied 40, 23, and 37% of the total area, respectively. The overall potentiality map showed that 36, 26, and 38% of the studied area displayed high, moderate, and low potential for agricultural expansion, respectively. The integration of AHP with GIS tools (geostatistical analysis and fuzzy set) can enhance insight into sustainable land-use planning and suggest also timely cropping practices. Further investigations are advocated to quantify the suitable cropping patterns in the studied region.},
}

*Geographic Information Systems
*Agricultural Irrigation/methods
Soil/chemistry
Groundwater
*Agriculture/methods
Fuzzy Logic
Egypt
*Agroecology
Ecosystem
Conservation of Natural Resources

@article {pmid42361963,
year = {2026},
author = {Loc, DH and Sulesco, T and Tóth, GE and Lühken, R and Schmidt-Chanasit, J and Velavan, TP},
title = {First Mosquito-Based Molecular Evidence of Tembusu Virus in Vietnam.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108927},
doi = {10.1016/j.ijid.2026.108927},
pmid = {42361963},
issn = {1878-3511},
abstract = {BACKGROUND: Mosquito borne flavivirus diversity in Vietnam remains incompletely characterized. Tembusu virus (TMUV), an emerging flavivirus associated with ducks and other avian hosts, has been reported in poultry in Vietnam, but molecular evidence from field-caught mosquitoes has been lacking.

METHODS: We screened 10,658 mosquitoes representing four major arbovirus vector species including Aedes aegypti, Ae. albopictus, Culex quinquefaciatus, Cx. tritarniorhynchus, collected across multiple ecological settings in Vietnam. Mosquitoes were grouped into 586 pools and tested using broad range RT-PCR assays targeting flaviviruses and alphaviruses. Positive flavivirus amplicons were subjected to sequencing, and one TMUV positive pool underwent deeper sequencing and phylogenetic analysis.

RESULTS: The Cx. tritaeniorhynchus pool (25 specimens) collected in rural southern Vietnam yielded a TMUV draft genome. In the complete genome phylogeny, the Vietnamese mosquito derived sequence clustered within a distinct monophyletic clade comprising strains from China, Thailand, Taiwan, and Vietnam.

CONCLUSIONS: These findings provide the first mosquito-based molecular evidence of a TMUV related virus in Vietnam and suggest that mosquito surveillance can reveal previously unrecognized viral diversity and transmission patterns.},
}

@article {pmid42364147,
year = {2026},
author = {Villhauer, H and Hellwig, T and Labarosa, SJ and Metzger, S and Moore, J and Wysocki, A and Straube, H and Blume, DVM and Straube, J and Durka, W and Brankov, M and Konowalik, K and Lexa, M and Kheloufi, A and Mansouri, LM and Blanco Moreno, JM and Neira, P and Torra, J and Royo-Esnal, A and da Silva, LP and Santi, F and Zarantonello, AE and Rodríguez-García, E and Romeralo, C and Hampe, A and Manzanares-Vázquez, V and Myśliwy, M and Bomanowska, A and Kaczmarek, K and Kolanowska, M and Rewicz, A and Nikolić, N and Mudrák, O and Nobis, M and Nobis, A and Radak, B and Ilić, M and Baranow, P and Nowak, S and Nosalewicz, A and Krzemińska, I and Backhaus, AE and Szitár, K and Einspanier, S and Pincebourde, S and Leclerc, M and Wagner, M and Mitschunas, N and Bignon, A and Sahri, A and Saatkamp, A and Drouzas, AD and Kopriva, S and von Korff, M and Bucharova, A},
title = {Climate-driven in-situ trait variation in an annual ruderal grass across Europe.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag164},
pmid = {42364147},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Plant functional traits link environmental conditions to plant performance and adaptation. Growing evidence suggests that intraspecific trait variation can be as important as differences between species, yet large intraspecific studies of in-situ variation remain rare. While most studies have focused on plant morphological traits, the concentrations of elemental nutrients in seeds have received much less attention so far.

METHODS: We conducted a large-scale in-situ study of the widespread annual ruderal grass Hordeum murinum. We sampled 2070 individuals from 207 populations across a large part of its native range in Europe and North Africa. We measured seed ripening phenology and growth-related traits in-situ and analyzed concentrations of elemental nutrients in the seeds.

KEY RESULTS: We found that Hordeum murinum grew larger, produced seeds later, and had heavier seeds in colder and wetter regions. Plants growing in denser vegetation were taller and produced heavier seeds but formed fewer spikes. Concentrations of elemental nutrients in the seed generally declined with seed weight and were primarily driven by climatic variables, whereas soil conditions had only minor effects on plant traits and seed nutrients. Population identity explained a substantial proportion of trait variation, indicating a possible genetic component.

CONCLUSIONS: Our findings provide a comprehensive view of how Hordeum murinum responds to environmental gradients across its European distribution. Climatic variables, particularly temperature, are key drivers of reproductive timing and concentrations of elemental nutrients in the seed, whereas local environmental conditions, such as biotic pressures, are more critical for growth-related traits. Together, these patterns indicate that Hordeum murinum modulates its growth and reproductive investment along environmental gradients, balancing phenology, stress tolerance, and limited competitive capacity.},
}

@article {pmid41914406,
year = {2026},
author = {Lu, ZN and Ren, S and Hao, Y and Yuan, C},
title = {Digital Determinants of Health: Evaluating the Impact of Information and Communication Technology on Chinese Health Outcomes.},
journal = {The International journal of health planning and management},
volume = {41},
number = {4},
pages = {593-606},
doi = {10.1002/hpm.70074},
pmid = {41914406},
issn = {1099-1751},
support = {72321002//National Natural Science Foundation of China/ ; 2022WCXTD022//Guangdong Provincial Ordinary University Innovation Team Project/ ; 2022CX01013//Technology Innovation Program of Beijing Institute of Technology/ ; 2023CX13028//Technology Innovation Program of Beijing Institute of Technology/ ; },
mesh = {China ; Humans ; Female ; Male ; Digital Health ; Adult ; Middle Aged ; Surveys and Questionnaires ; *Health Status ; *Information Technology ; },
abstract = {BACKGROUND: The new generation of network information technology has become a significant tool to promote public health. The application of information and communication technology (ICT) in the traditional medical industry has changed the medical service model, improved the public medical service system, and provided diversified medical services to the public.

OBJECTIVE: This paper discusses the impact of ICT on residents' health, and analyzes the possible heterogeneity impact in different groups and its impact mechanism using the China Family Panel Studies (CFPS) data and a fixed-effects model.

METHODS: The ordinary least squares estimation method was adopted to quantitatively identify the impact mechanism of ICT applications on residents' health. Multisource big data were collected, including the CFPS questionnaire (gender, age, marriage status, work status, income level, smoking, sports, and insurance participation), regional economic development, as well as service industry development. The quantitative phase involved conducting in-depth investigation across 25 Chinese provinces. Then, a quantitative analyse-based study empirically tested the effects of internet applications on residents' health by matching macro data and micro survey data. After controlling for these identified factors, the data were tested using ordinary least squares and fixed effect models, with the assistance of STATA version 14 to measure and validate the proposed model.

RESULTS: The regression results support the conclusion that ICT can significantly improve residents' health (p < 0.001). After a series of robustness tests through replacing explanatory variables and choosing appropriate exogenous policy shocks, the results still hold. We analyse the possible heterogeneous effects and conclude that the health-promoting effect of ICT is stronger among middle-aged individuals, high-income groups, women, urban residents, unmarried individual, those who engage in sports and non-smokers.

CONCLUSIONS: Our study confirms a significant association between ICT applications and residents' health and reveals substantial heterogeneity in this effect. It also provides insights into how to apply internet information to better realise disease surveillance and prevention goals.},
}

China
Humans
Female
Male
Digital Health
Adult
Middle Aged
Surveys and Questionnaires
*Health Status
*Information Technology

@article {pmid41944781,
year = {2026},
author = {Cedden, D},
title = {Emerging experimental and bioinformatic approaches in RNA interference-based pest control research.},
journal = {Insect molecular biology},
volume = {35},
number = {4},
pages = {364-375},
doi = {10.1111/imb.70040},
pmid = {41944781},
issn = {1365-2583},
mesh = {*RNA Interference ; Animals ; *Computational Biology/methods ; *Insect Control/methods ; *Insecta/genetics ; RNA, Double-Stranded ; RNA, Small Interfering ; },
abstract = {RNA interference (RNAi) has emerged as a promising strategy for species-specific and environmentally friendly pest control, offering an alternative to conventional chemical insecticides that are increasingly constrained by resistance development and ecological concerns. RNAi-based approaches involve oral delivery of double-stranded RNA (dsRNA), which is processed into RNA-induced silencing complex (RISC)-bound small interfering RNA (siRNA) to silence essential genes of pests. This review synthesizes recent advances in experimental and bioinformatic methodologies that are facilitating and enhancing RNAi research in insect pest management. Particular emphasis is placed on molecular validation techniques that move beyond phenotype-based bioassays, including RISC-bound small RNA sequencing to resolve dsRNA processing and guide strand selection, RNA degradomics to map siRNA-mediated transcript cleavage events and transcriptomic and proteomic profiling to characterize genome-wide responses and compensatory effects. In parallel, dsRNA visualization methods provide mechanistic insight into uptake, intracellular trafficking and degradation dynamics, clarifying barriers that distinguish responsive from recalcitrant species. Complementing these experimental developments, emerging computational platforms enable insect-optimized target selection, dsRNA design and environmentally informed off-target prediction. Together, these innovations support a transition toward more predictive and mechanistically grounded RNAi-based pest control applications. The integration of high-resolution molecular tools with specialized bioinformatic pipelines is expected to enhance efficacy, safety and reproducibility, advancing RNAi-based pest control toward practical and scalable agricultural deployment.},
}

*RNA Interference
Animals
*Computational Biology/methods
*Insect Control/methods
*Insecta/genetics
RNA, Double-Stranded
RNA, Small Interfering

@article {pmid42360102,
year = {2026},
author = {Chen, J and Li, Z and Wu, J and Xing, Y and He, S and Sheng, Y and Zhu, L},
title = {Elucidating the Adverse Outcome Pathway for Grain-Quality Deterioration Induced by Brominated Flame Retardants in Rice: A Multiomics and Lifecycle Analysis.},
journal = {Environmental science & technology},
volume = {60},
number = {26},
pages = {18519-18533},
doi = {10.1021/acs.est.6c04723},
pmid = {42360102},
issn = {1520-5851},
mesh = {*Flame Retardants ; *Oryza ; Multiomics ; Halogenated Diphenyl Ethers ; Edible Grain ; },
abstract = {Brominated flame retardants (BFRs) pose a growing threat to agricultural safety, yet their dynamic transfer mechanisms and interference with crop metabolism remain poorly understood. This study systematically unravels the lifecycle translocation of BFRs in rice and deciphers the signaling-mediated cascade leading to grain-quality deterioration. BFR accumulation did not follow a simple xylem-mediated transport pattern; instead, secondary enrichment occurred during grain filling, inversely correlated with their logKow and molecular weight. In particular, the concentration of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in the panicles increased sharply from ∼1 ng/g at the heading stage to 16.5 ng/g at the filling stage, reaching 42.0 ng/g at maturity, representing an order-of-magnitude increase. This accumulation critically coincided with a marked depletion of nutritional components: amylopectin and total protein decreased by 10.3-17.7%, accompanied by a 12.5% reduction in 1000-grain weight. Through integrated transcriptomic, proteomic, and metabolomic analyses, along with a novel motif-based unbiased screening method, we deciphered the core adverse outcome pathway (AOP). BFRs advanced the abscisic acid (ABA) peak by 5 days and increasing its concentration ∼20% compared to the control. This intensified ABA signaling pathway upregulated tricarboxylic acid cycle enzymes by 2-5-fold, and redirected carbon flux from starch synthesis toward energy production. This metabolic shift accelerates the cotransport of selected BFRs (e.g., BDE-47) into the developing grain, driving premature maturation and nutritional loss. By establishing a complete "signal activation → metabolic reprogramming → pollutant co-transport → quality deterioration" AOP framework, this study provides a mechanistic foundation for understanding the potential dietary implications of BFRs in rice, offering crucial insights for safeguarding food safety and controlling agricultural contamination.},
}

*Flame Retardants
*Oryza
Multiomics
Halogenated Diphenyl Ethers
Edible Grain

@article {pmid41540071,
year = {2026},
author = {Sun, T and Hughes, AC and He, K and Yu, L},
title = {Ecological Integrity Index, timely annual tracking of biodiversity change.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {174},
pmid = {41540071},
issn = {2052-4463},
mesh = {Humans ; *Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; Datasets as Topic ; },
abstract = {Despite numerous global initiatives and policy framework to mitigate ongoing biodiversity decline, progress remains limited due to lack of biodiversity indicators that are timely, scientifically rigorous, and representative. Furthermore, databases underlying previous indicators are spatially, temporally, geographically and taxonomically biased, making it difficult to track biodiversity change dynamics and set proper biodiversity targets. Here, we constructed a new version of the global human footprint, and used it to infer temporally explicit annual shifting patterns of biodiversity across all scales by incorporating remote sensing and mapping out human pressures. This indicator (the Ecological Integrity Index- EII) successfully differentiates high- and low- biodiversity biomes, especially for deserts and tundra. Moreover, shifting annual patterns can identify global hotspots (e.g., major rainforests and regional hotspots), and shows biodiversity change dynamics at regional level based on estimating biodiversity change over time. Changes of evolving human footprint were further analyzed with relationships to biodiversity patterns. At more a local level, the patterns perfectly reflect biodiversity and intactness. Compared to other indicators (e.g., BII, BHI) in the Kunming-Montreal Global Biodiversity Framework (GBF) and biodiversity models (e.g., GLOBIO), the EII can better reflect biodiversity. EII shows a good performance, with the potential to inform biodiversity conservation efforts, and support the implementation of the post-2020 global biodiversity framework.},
}

Humans
*Biodiversity
*Conservation of Natural Resources
Ecosystem
Datasets as Topic

@article {pmid42360682,
year = {2026},
author = {Rg, C and Ott-Conn, CN and Euclide, PT and Blanchong, JA and Schmoldt, A and DeYoung, RW and Walsh, DP and Larson, WA and Latch, EK},
title = {A Practical Framework for GT-Seq Panel Optimization.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70169},
pmid = {42360682},
issn = {1755-0998},
support = {F22AP00694-00//Multistate Conservation Grant Program/ ; 107048 MSU//the Michigan Department of Natural Resources/Michigan State University Joint Wildlife Disease Initiative/ ; //UW-Milwaukee Graduate School/ ; },
mesh = {Animals ; Polymorphism, Single Nucleotide ; *Genotyping Techniques/methods ; *Deer/genetics/classification ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; DNA Primers/genetics ; },
abstract = {Genotyping-in-thousands by sequencing (GT-seq) panels are powerful tools in ecological, evolutionary and conservation genomics, yet the optimization process critical for robust and reproducible genotyping remains poorly formalized. Here, we present an iterative workflow for GT-seq panel optimization that emphasizes systematic refinement, quality control and structured decision-making to improve panel performance across diverse populations and study contexts. We illustrate this framework through the development and optimization of a GT-seq panel for white-tailed deer, a widely distributed and ecologically important North American species. From an initial set of 1200 candidate SNPs selected from a commercial microarray (OVSNP60, containing 72,728 SNPs) and prioritized for high heterozygosity, primers were designed for 646 loci. The final optimized panel contains 508 high-performing markers retained after iterative removal of overamplifying primer pairs, adjustment of primer concentrations, PCR conditions and bioinformatic filtering. The overall proportion of SNPs with more than 70% genotype rate increased from 25.5% in the first optimization round to 87.8% in the final round. Consequently, the overall genotype rate increased from 39.4% to 84%. We also identify key quality-control checkpoints and practical criteria to guide panel refinement and ensure consistent performance. By prioritizing optimization as an integral component of GT-seq panel development, this work provides a reproducible framework for generating robust, high-throughput genotyping tools in non-model species and underscores the importance of iterative refinement to maximize data quality and utility.},
}

Animals
Polymorphism, Single Nucleotide
*Genotyping Techniques/methods
*Deer/genetics/classification
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
DNA Primers/genetics

@article {pmid42359335,
year = {2026},
author = {Fraser, B and Gasparini, C and Santi, F and Böhne, A and Monteiro, R and Marcussen, T and Oomen, RA and Struck, TH and , and , and , and Denton, A and Howard, C and Howe, K and Blaxter, M and McCarthy, S and Wood, JMD and Martin, F and Sinha, S and Haggerty, L and Bortoluzzi, C},
title = {ERGA-BGE reference genome of Gambusia holbrooki, a globally invasive freshwater fish.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {48},
doi = {10.12688/openreseurope.22693.2},
pmid = {42359335},
issn = {2732-5121},
abstract = {The Gambusia holbrooki (eastern mosquitofish) reference genome will offer a crucial resource for understanding the evolution and adaptation of invasive freshwater fish species. The genome of G. holbrooki was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the genome sequence was assembled into 24 contiguous chromosomal pseudomolecules and 1 mitochondrial genome. This chromosome-level assembly encompasses 0.67 Gb, composed of 421 contigs and 318 scaffolds, with contig and scaffold N50 values of 15.9 Mb and 29.6 Mb, respectively.},
}

@article {pmid42049755,
year = {2026},
author = {Zhou, K and Kosmopoulos, JC and Colón, ED and Badciong, PJ and Anantharaman, K},
title = {V- and VL-scores unveil viral signatures and origins of protein families.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42049755},
issn = {2041-1723},
support = {DBI2047598//National Science Foundation (NSF)/ ; 42576129//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Viral Proteins/genetics/metabolism ; *Genome, Viral/genetics ; *Viruses/genetics ; Databases, Protein ; *Computational Biology/methods ; },
abstract = {Viruses are key drivers of microbial ecology and evolution, yet their study is hindered due to challenges in culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much of the viral genome, leaving key viral proteins and functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score and VL-score, designed to quantify the "virus-likeness" of protein families and genomes and create an open-access searchable database, 'V-Score-Search'. By applying V- and VL-scores to public protein databases, we link 19 - 59% of protein families with viruses representing a 5 - 8x increase over current estimates. These metrics outperform existing approaches, enabling high efficiency in detection of viral genomes, prophages, and host-derived auxiliary viral genes (AVGs) from fragmented sequences. Remarkably, we identify up to 17 times more AVGs dominated by non-metabolic proteins of unknown function. This innovation unlocks new insights into virus signatures and host interactions, with wide-ranging implications from genomics to biotechnology.},
}

*Viral Proteins/genetics/metabolism
*Genome, Viral/genetics
*Viruses/genetics
Databases, Protein
*Computational Biology/methods

@article {pmid42069816,
year = {2026},
author = {Anitha, M and Prasad, CR and Awotunde, JB and Adeniyi, AE and Aroba, OJ},
title = {Breast ultrasound images for segmentation and classification using multi-task U-Net.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42069816},
issn = {2045-2322},
mesh = {Humans ; Female ; *Breast Neoplasms/diagnostic imaging/classification ; *Ultrasonography, Mammary/methods ; Deep Learning ; Classification Algorithms ; *Image Interpretation, Computer-Assisted/methods ; *Image Processing, Computer-Assisted/methods ; Algorithms ; *Breast/diagnostic imaging ; },
abstract = {Breast ultrasound imaging is widely used for the early detection of breast cancer due to its accessibility and effectiveness, particularly in dense breast tissues. However, its diagnostic performance is often affected by operator dependency, speckle noise, low contrast, and variability in data quality. Although deep learning methods have shown promise in automated tumor segmentation and classification, their clinical applicability remains limited due to challenges such as small and imbalanced datasets, inconsistent annotations, and the lack of integrated learning strategies. In this work, we propose a Multi-Task U-Net framework that jointly performs lesion segmentation and tumor classification by leveraging shared feature representations. The proposed method incorporates a deterministic oversampling strategy for handling class imbalance, a prediction-refinement module to ensure consistency between segmentation and classification outputs, and an attention-guided feature learning mechanism to enhance lesion localization. Additionally, a curated version of the BUSI dataset is constructed by removing duplicate and inconsistent samples to ensure reliable evaluation. The proposed model achieves a Dice score of up to 0.81 in comparative evaluation, along with classification accuracy of up to 0.96-0.98, demonstrating improved performance over baseline methods. The consistent performance across both segmentation and classification tasks indicates good generalization capability despite dataset limitations. Finally, the proposed multi-task framework provides an effective and reliable solution for automated breast cancer detection in ultrasound images and shows strong potential for clinical application.},
}

Humans
Female
*Breast Neoplasms/diagnostic imaging/classification
*Ultrasonography, Mammary/methods
Deep Learning
Classification Algorithms
*Image Interpretation, Computer-Assisted/methods
*Image Processing, Computer-Assisted/methods
Algorithms
*Breast/diagnostic imaging

@article {pmid42097135,
year = {2026},
author = {Ausman, LM and Namirembe, G and Mezzano, J and Lauer, JM and Shrestha, R and Agaba, E and Bashaasha, B and Griffiths, JK and Marino-Costello, E and Wang, JS and Erhardt, JG and Gewirtz, AT and Duggan, CP and Webb, P and Ghosh, S},
title = {Maternal Aflatoxin Exposure, Birth Outcomes, and Infant Growth in Uganda.},
journal = {The American journal of tropical medicine and hygiene},
volume = {115},
number = {1},
pages = {167-175},
pmid = {42097135},
issn = {1476-1645},
mesh = {Humans ; Female ; Uganda/epidemiology ; Pregnancy ; Infant ; *Maternal Exposure/adverse effects ; *Aflatoxin B1/blood ; Adult ; Infant, Newborn ; Birth Weight ; *Child Development ; Male ; *Aflatoxins/blood ; Young Adult ; },
abstract = {The association between maternal aflatoxin exposure and infant anthropometric birth and growth outcomes was investigated in the present study, controlling for possible confounders. Pregnant women (N = 1,210) from 16 Ugandan subcounties were enrolled in a birth cohort study to track birth outcomes and subsequent growth of infants. Serum concentrations of aflatoxin B1 (AFB1)-lysine adduct, environmental enteric dysfunction markers of anti-lipopolysaccharide and anti-flagellin IgG and IgA, and markers of systemic inflammation, alpha-1 acid glycoprotein, and C-reactive protein were measured in mothers at birth and infants at 6 months of age. A generalized estimating equations model with an exchangeable correlation matrix was used to assess associations between maternal AFB1 blood concentration and weight, length, weight-for-age (WAZ), length-for-age (LAZ), and weight-for-length (WLZ) Z scores. Multivariable linear and logistic regressions were used to assess the association between infant aflatoxin concentrations and growth outcomes at 3 to 6 months of age. Serum aflatoxin concentrations in women at parturition were associated with reduced birth weight (P = 0.037) and WAZ (P = 0.034), but not with other birth outcomes. Aflatoxin concentrations in infants 6 months of age were not associated with changes in weight, height, WAZ, LAZ, or WLZ between 3 and 6 months of age. The present study confirmed an association between maternal aflatoxin and specific birth outcomes, but not between infant serum aflatoxin and infant early growth, which may be due to low exposure to aflatoxin-contaminated foods in early life. This finding highlights the importance of promoting national policy actions that minimize aflatoxin contamination of local food supplies, both on farms and in markets.},
}

Humans
Female
Uganda/epidemiology
Pregnancy
Infant
*Maternal Exposure/adverse effects
*Aflatoxin B1/blood
Adult
Infant, Newborn
Birth Weight
*Child Development
Male
*Aflatoxins/blood
Young Adult

@article {pmid42136370,
year = {2026},
author = {Wu, C and Liu, H and Carvalhais, LC and Guo, J and Cai, P and Zhong, J and Zhang, H and Jin, B and Li, G and Yang, J and Chen, J and Ge, T},
title = {Root exudate-associated microbiome assembly contributes to viral disease resistance in wheat.},
journal = {The New phytologist},
volume = {251},
number = {3},
pages = {1397-1414},
doi = {10.1111/nph.71254},
pmid = {42136370},
issn = {1469-8137},
support = {CARS-08-G09//China Agriculture Research System from the Ministry of Agriculture of P.R. China/ ; U24A20404//National Science Foundation of China/ ; 42477341//National Science Foundation of China/ ; 2022YFD1400700//National Key Research and Development Program of China/ ; 2022YFA1304401//National Key Research and Development Program of China/ ; 2024YFC3406003//National Key Research and Development Program of China/ ; //K.C. Wong Magna Fund of Ningbo University/ ; YLS-2025-ZY01012//Yuelushan Laboratory Breeding Program/ ; },
mesh = {*Triticum/microbiology/virology/immunology ; *Disease Resistance ; *Microbiota/genetics ; *Plant Diseases/virology/microbiology/immunology ; *Plant Roots/microbiology/virology ; Rhizosphere ; *Plant Exudates/metabolism ; Multiomics ; },
abstract = {Early mutualistic interactions between host plants and their rhizosphere microbes have the potential to provide soil-borne disease resistance. However, it remains unclear how the early rhizosphere microbiome protects against viral diseases such as wheat yellow mosaic virus, which is a major threat to global wheat production. We combined field trials with microbiome transplantation experiments to investigate the role of early rhizosphere microbiomes in suppressing wheat yellow mosaic disease. To uncover the underlying mechanisms, we further performed integrated multi-omics analyses of microbial communities, functional genes, and metabolic profiles. Disease-resistant wheat cultivars were consistently associated with distinct seedling rhizosphere microbiome assembly, including a lower Polymyxa graminis abundance, lower community compositional variation, and enrichment of beneficial taxa such as Bacillus, Pseudomonas, and Trichoderma. Resistant cultivars also exhibited distinct rhizosphere metabolite profiles, including higher levels of glyceraldehyde and N-acetyltryptophan, which were positively associated with keystone microbial taxa and stimulated representative isolates in vitro. Isolate-based and synthetic community validation further supported the functional relevance of these taxa, while microbial inoculation was associated with reduced vector abundance, lower virus accumulation, and activation of host defense-related pathways. Our findings showed that early cultivar-dependent rhizosphere microbiome assembly was closely linked to resistance against soil-borne viral disease in wheat.},
}

*Triticum/microbiology/virology/immunology
*Disease Resistance
*Microbiota/genetics
*Plant Diseases/virology/microbiology/immunology
*Plant Roots/microbiology/virology
Rhizosphere
*Plant Exudates/metabolism
Multiomics

@article {pmid42144817,
year = {2026},
author = {Oliveira, DN and Ordóñez-Parra, CA and Chen, SC and Arnold, AE and Davis, AS and González, AMT and Morales-Pérez, AL and Díaz-Castellanos, AR and Pérez-Enriquez, A and Fidelis, A and Carvalho, ASR and Santos, AS and Sandoval, AC and Crestani, ACV and Mairinck, ALA and Neto, ADA and Coetzee, A and Traveset, A and Andrade, ACS and Datta, A and Teles, AM and Nerlekar, AN and Sengupta, A and Munje, A and Negret, BS and Basu, B and Rocha, CS and De Melo E Silva-Neto, C and Santos, CHB and Sarmiento, C and da Cruz Vasconcelos, C and Offord, CA and López, CL and Mayta, C and Ordoñez-Salanueva, CA and Seal, CE and Cruz, CRP and Seymour, CL and Almeida, DS and Pifano, DS and Vieira, DLM and Dias, DP and Ramos-Chuquimia, D and Vieira, DCM and Sánchez, DA and Cruz-Tejada, DM and Cunha, DDS and Escobar, DFE and Santos, DL and Silva, DA and Gonçalves, EP and Damasceno, ES and Duarte, EF and Mendes, ETB and Peña-Miranda, ET and do Carmo, EM and Tarazona-Tubens, FL and Silva, FFS and Piña-Rodrigues, FCM and Souza, FC and Faria, FS and Nascimento, FA and Torres-Romero, FJ and Motta, GST and Oda, GA and Liyanage, GS and Calvi, GP and Costa, GFL and Errington, G and Joseph, GS and Da Costa, GM and Canassa, GG and Gama, G and Liang, H and Wang, HY and Yadav, H and Consolaro, HN and Ferreira, HD and Miranda, HS and Zirondi, HL and Botey, HM and Fontenele, HGV and Pritchard, HW and Pinto, ÍM and Araujo-Santos, I and Ferraz, IDK and Da Gama, IG and Zambrano, IAN and Dalling, JW and Santos, JAD and Viana, JS and Castellanos-Barliza, JJ and Rodríguez, JVD and Hoyos, JLL and Powers, JS and Corredor-Prado, JP and Vázquez-Ramírez, J and Sansevero, JBB and Vargas-Figueroa, JA and Magalhães, JGS and Borges, JPGDS and Flores, J and Ribeiro, JWF and Barlow, J and Rojas, JM and Fonseca-Altahon, JD and Morante-Filho, JC and Santos, JHSD and Silva, JN and Hurtado, JS and Ley-López, JM and Villalba-Malaver, JC and Lage, JMM and Benítez-Malvido, J and Lim, JY and Jayasuriya, KMGG and Sommerville, KD and Pradhan, K and Chong, KGJ and Mcconkey, KR and Garcia, LA and Brito, LÉ and Marín, LER and Morellato, LPC and Aona, LYS and de Oliveira, LS and Macias-Sposito, L and Martinez-Martinez, LA and Navarro, L and Daibes, LF and Coelho, LFM and Pinheiro, LFS and Melgarejo, LM and Benchimol, M and Wijayasinghe, MM and Meiado, MV and Amador-Cubides, MC and Braz, MIG and Dairel, M and Villegas, M and Guedes, MR and Conde, MMS and Magalhães, MLL and Shibata, M and Côrtes, MC and Ooi, MKJ and Prates, MB and Chua, MSE and Figueiredo, MA and Galetti, M and Ferreira, MC and Arthur, M and Soto-Avendaño, MV and Cházaro-Basañez, M and Koutouan-Kontchoi, MN and Da Silva, MAD and Alves, M and Bullón, NR and Borawake, N and Santos, NSCD and Razafindratsima, OH and Dávila-Aranda, P and Zalamea, PC and Laumann, PD and León-Lobos, P and Poschlod, P and Souza-Perera, R and Cavalcante, RAS and Gasparini, R and Rodrigues, RG and Frigeri, RBC and Alvarez-Espino, RX and Portela, RCQ and Timmers, R and Naniwadekar, R and Staneke, R and Kolb, RM and Contreras, RD and Heleno, RH and Swart, RC and Tangney, R and Madriñán, S and McInnes, SJ and Amoêdo, SC and Kim, S and Phartyal, SS and Escalante-Rebolledo, SE and Gallegos, SC and Le Stradic, S and Hernandez-Ortiz, SM and Sidhu, S and Zupo, TM and Vilas-Boas, T and Ulian, T and Shukla, U and Pivello, VR and Klein, VLG and Da Silva, VMF and De Lima, VF and Londoño-Lemos, V and Simioni, WB and Barranco-Pérez, WA and Varela, YCDS and Athugala, YS and Newby, ZJ and Silveira, FAO},
title = {Tropical Seed Trait Database: advancing seed functional ecology in the world's most biodiverse region.},
journal = {The New phytologist},
volume = {251},
number = {3},
pages = {945-958},
doi = {10.1111/nph.71268},
pmid = {42144817},
issn = {1469-8137},
support = {//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Seeds/physiology ; *Tropical Climate ; *Databases, Factual ; *Ecology ; *Quantitative Trait, Heritable ; Biodiversity ; Ecosystem ; Phenotype ; Biocuration ; },
abstract = {Plant functional traits connect biodiversity to ecosystem processes, serving as key metrics for assessing how biota responds to environmental conditions. Functional seed traits are critical because they underpin recruitment and colonization, shaping biodiversity patterns and influencing ecosystem resilience. Yet, seed traits remain underrepresented in major data repositories, with severe gaps in the tropics. Climatic, geological, and historical differences between tropical and temperate regions drive distinct regeneration dynamics, suggesting that the paucity of tropical seed trait data limits our ability to predict regeneration niches and weakens global models largely based on temperate ecosystems. To address this gap, we introduce the Tropical Seed Trait Database (TSTD), an open-access repository spanning the full ecological spectrum of tropical seeds. The TSTD is conceived as a community-driven repository of primary data contributed directly by data owners, rather than as a secondary aggregation of global databases. It was built through contributions from ecologists working across all tropical regions, reached through direct contact, and its first version compiles 78 datasets, totaling 137 583 records across 44 functional traits. Covering 5115 species in 33 countries, with the Neotropics overrepresented, the TSTD marks a crucial step toward more inclusive, globally representative trait databases that can open multiple research avenues.},
}

*Seeds/physiology
*Tropical Climate
*Databases, Factual
*Ecology
*Quantitative Trait, Heritable
Biodiversity
Ecosystem
Phenotype
Biocuration

@article {pmid42341031,
year = {2026},
author = {Volpatto, D and Contaldo, SG and Pernice, S and Beccuti, M and Cordero, F and Sirovich, R},
title = {A new cancer progression model: From synthetic tumors to real data and back.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1013991},
pmid = {42341031},
issn = {1553-7358},
mesh = {*Neoplasms/genetics/pathology ; Humans ; Disease Progression ; *Models, Biological ; Stochastic Processes ; Computer Simulation ; Computational Biology ; Mutation ; Algorithms ; Phenotype ; },
abstract = {Intratumor heterogeneity (ITH) arises from the combined effects of genetic alterations, clonal interactions, and environmental constraints, and plays a central role in therapeutic resistance and disease progression. While ITH has been extensively documented in empirical tumor data, the scientific debate regarding the biological mechanisms underlying this heterogeneity remains complex, highlighting the need for cancer evolution models that are sufficiently flexible and sophisticated to reproduce the observed behaviors and to give insights on the unobserved ones. Here, we present a stochastic modelling framework for tumor evolution that integrates genotypic inheritance with phenotype driven functional traits and resource mediated competition. Mutational events are associated with functional capabilities such as altered proliferation, increased mutation rates, limit evasion potential or enhanced control over shared resources, allowing multiple genotypes to converge on similar phenotypes. The model explicitly tracks subclonal lineages while incorporating environmental constraints that modulate growth and competition. The framework is defined through a mathematically rigorous construction and is accompanied by an efficient simulation algorithm. To facilitate exploration and reproducibility, we provide an open-source graphical user interface that allows users to configure model parameters, run simulations, and inspect clonal genealogies and population dynamics without requiring direct interaction with the underlying code. Using this model, we illustrate how ecological feedbacks can shape clonal dynamics over time, supporting an interpretation in which early tumor growth is dominated by stochastic expansion, while later evolution increasingly reflects selection for traits that alleviate environmental constraints. Rather than constituting a new evolutionary paradigm, this behaviour demonstrates how well-documented biological patterns can emerge naturally from a unified stochastic and ecological description. Overall, our approach offers a flexible and extensible platform for investigating how chance, functional traits, and environmental interactions jointly govern tumor heterogeneity.},
}

*Neoplasms/genetics/pathology
Humans
Disease Progression
*Models, Biological
Stochastic Processes
Computer Simulation
Computational Biology
Mutation
Algorithms
Phenotype

@article {pmid42341845,
year = {2026},
author = {Mancuso, M and Suranse, V and Seneci, L and Senoner, T and Koludarov, I and Sunagar, K and Fry, BG},
title = {CAPtivating toxins: Molecular evolution of CAP proteins (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1) in the chemical arsenals of diverse venomous animals.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {109199},
doi = {10.1016/j.toxicon.2026.109199},
pmid = {42341845},
issn = {1879-3150},
abstract = {The cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 (CAP) superfamily represents one of the most widely recruited molecular scaffolds in animal venoms. Despite their ubiquity, the evolutionary forces shaping their diversification are still mostly unknown. Here, we integrate Bayesian and maximum-likelihood phylogenetics with site- and branch-level selection analyses (FUBAR, MEME, CodeML, and BUSTED) to investigate CAP evolution across 12 venomous metazoan lineages, spanning insects, arachnids, centipedes, lizards, and snakes. Our results reveal a spectrum of evolutionary regimes, with purifying selection dominating across arthropods, whereas episodic and pervasive positive selection strongly shape CAP diversification in toxicoferan reptiles. Exceptional diversification was also detected in triatomine bugs and Ixodes ticks, suggesting host-driven lineage-specific adaptive pressures. Three-dimensional representations show that diversification frequently targets exposed and functionally relevant residues, supporting coevolutionary arms race scenarios. Altogether, our findings demonstrate that CAP proteins have undergone multiple recurrent trajectories of molecular innovation, reflecting the convergent interplay between ecology, structure, and lineage-specific pressures. This study establishes a comprehensive framework for understanding how a single ancestral protein scaffold has been repeatedly co-opted and diversified across the animal kingdom's chemical arsenals. Additionally, we describe a hybrid loop-β-sheet extension of the CAP1 motif based on sequence and structural conservation evidence across CAP proteins.},
}

@article {pmid42342705,
year = {2026},
author = {Liu, G and Su, D and Liu, Y and Shi, Z and Gao, S and He, X and Zhang, S and Deng, H and Xiao, J and Yao, Y and Shu, P},
title = {A chromosome-level genome assembly of SAGS Anisodus tanguticus (Maxim.) Pascher (Solanaceae) from the Tibetan region of Sichuan, China.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07697-z},
pmid = {42342705},
issn = {2052-4463},
support = {CARS-34//China Forage and Grass Research System/ ; },
abstract = {Anisodus tanguticus (Maxim.) Pascher (A. tanguticus), a cold-tolerant perennial herb in the Solanaceae family, is distributed across China's Qinghai-Tibet Plateau and extends to Nepal, Bhutan, Sikkim, and India. As a Tibetan medicinal plant, it is used to treat pain, ulcers, etc.; its roots yield antispasmodic and anesthetic compounds, and other parts are used as a feed additive for yaks to enhance cold resistance in northwest Sichuan. In this study, samples were collected from Seda County (northwestern Sichuan, China) for sequencing. Using PacBio HiFi sequencing and Hi-C scaffolding, a high-quality chromosome-scale genome assembly was generated, with a genome size of 1599.64 Mb, a scaffold N50 of 62.01 Mb, and a contig N50 of 38.51 Mb. A total of 24 superscaffolds (93.65% of the genome) were anchored to 24 chromosomes. Compared with previously reported assemblies of A. tanguticus and A. acutangulus, this assembly shows improved scaffold length and completeness. Genome annotation identified 64.95% repetitive elements and 45,930 protein-coding genes, and comparative analysis of four Anisodus genomes revealed conserved patterns of gene density, GC content, LTR, and LINE elements. This study provides the first high-quality chromosome-scale genome resource of A. tanguticus from the Qinghai-Tibet Plateau, supporting studies on phylogeny, genetic diversity, and breeding, as well as further exploration of its genomic basis of high-altitude adaptation.},
}

@article {pmid42347528,
year = {2026},
author = {Tedjou, AN and Keumeni, CR and Yougang, AP and Njiokou, F and Lines, J and Clarke, SE and Wondji, CS and Kamgang, B},
title = {Anthropophagy and Ecological Bridges: Blood-Meal Patterns of Invasive Aedes albopictus (Skuse, 1894) and Native Aedes aegypti Linnaeus, 1762 and Their Implications for Arbovirus Emergence in Central Africa.},
journal = {Tropical medicine and infectious disease},
volume = {11},
number = {6},
pages = {},
pmid = {42347528},
issn = {2414-6366},
support = {204862/WT_/Wellcome Trust/United Kingdom ; 204862/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Aedes (Ae.) aegypti and Ae. albopictus are important vectors of arboviruses. Yet their blood-feeding pattern remains poorly characterised in Africa, including Cameroon. In this study, we characterised the blood-meal sources in both species collected from vegetation, household surroundings, and animal cages across four urban sites, one rural site, and a zoo-botanical garden where humans and animals in captivity are the main hosts. Overall, Aedes mosquitoes represented about half of 10,054 female mosquitoes collected, with Ae. albopictus strongly dominating Ae. aegypti among 5001 Aedes females, and only 5.95% of females visibly blood-fed. Sequencing a 748 base pairs (bp) fragment of the cytochrome oxidase I gene from 156 blood-fed abdomens yielded 126 high-confidence host assignments, of which 98.25% were humans, indicating a strong anthropophagic pattern in both species. Unpredictably, two Ae. albopictus individuals had fed on a baboon (Papio anubis) and a frugivorous bat (Pteropodidae), as confirmed by bio informatic analyses, highlighting the species' opportunistic blood-feeding nature and providing preliminary molecular evidence consistent with a potential bridge-vector role in this setting. Despite the extreme anthropophagy of both species observed, results indicate that Ae. albopictus could also serve as a bridge vector enabling spillover of enzootic viruses to humans, including urbanised settings where wild animals are present. These findings emphasise the urgent need for enhanced arbovirus surveillance in Central Africa using a One Health approach.},
}

@article {pmid42348219,
year = {2026},
author = {Mederer, M and Gautam, A and Kohlbacher, O and Lupas, A and Elhabashy, H},
title = {Interacting Species Database (ISDB): Comprehensive Resource for Interspecies Interactions at the Molecular Level.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag419},
pmid = {42348219},
issn = {1367-4811},
abstract = {MOTIVATION: Organisms within ecological systems often engage in molecular interactions that mediate key biological processes, such as protein-protein interactions involved in host-pathogen recognition and symbiosis. Characterization of these interactions at a molecular level is essential for understanding the mechanistic, evolutionary, and functional basis of interspecies interactions, as well as for informing potential therapeutic interventions. However, progress in this field is significantly impeded by the lack of a comprehensive database of interacting species at molecular resolution and the limited availability of experimental data.

RESULTS: We introduce the Interacting Species Database (ISDB), a comprehensive resource that catalogs interspecies interactions, annotated with NCBI taxonomic identifiers, interaction types and known molecular interactions. The ISDB encompasses 858,229 interacting species pairs and 171,713 interspecies protein-protein interactions within 261,287 organisms. ISDB is designed to support researchers in searching for, downloading, and depositing interspecies interaction data, which facilitates the study of ecological dynamics across diverse research domains.

AVAILABILITY: The ISDB is available via a web interface (https://www.elhabashylab.org/isdb), open-source code on GitHub (https://github.com/ElhabashyLab/ISDB) under the MIT license and is archived on Zenodo (Version v1.0.1, DOI: 10.5281/zenodo.20162385).},
}

@article {pmid42350135,
year = {2026},
author = {Liu, YT and Liu, MH and Chen, NN and Mi, N and Yu, WY and Wu, JW and Feng, R},
title = {Variation characteristics of high-temperature and drought compound disasters in Liaoning Province based on Copula function and random forest.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {37},
number = {5},
pages = {1595-1604},
doi = {10.13287/j.1001-9332.202605.028},
pmid = {42350135},
issn = {1001-9332},
mesh = {*Droughts ; *Disasters ; China ; *Hot Temperature ; Random Forest ; *Climate Change ; Geographic Information Systems ; Models, Theoretical ; Ecosystem ; },
abstract = {Under the backdrop of global climate change, the frequent occurrence of combined disasters of high temperature and drought poses severe challenges to food security, ecological environment, and sustainable socio-economic development. Based on the meteorological observation data from 1971 to 2024, we constructed an intensity index by combining the nested Copula model with the random forest algorithm, and analyzed the spatiotemporal variations, recurrence interval characteristics and intensity evolution law of compound high-temperature and drought disasters in Liaoning Province by coupling GIS technology. The results showed that the occurrence frequency of compound high-temperature and drought disasters presented a pattern of being high in the west and low in the east. The western region was a continuously expanding and intensifying high-frequency agglomeration area, while the eastern and coastal areas remained a stable low-frequency area for a long time. Compound high-temperature and drought disasters in Liaoning Province were dominated by short recurrence interval (0-2 years) events, which featured with high occurrence frequency and strong spatial agglomeration. The western region as the core high-incidence area. With the extension of the return period, the occurrence scope of disasters shrank sharply and the frequency decreased, and long recurrence interval events were only sporadically distributed in the western region. The intensity of single events experienced a phased evolution of weak occurrence-initial increase-rapid increase-maintenance-attenuation, peaking in the 1990s. The cumulative intensity gradually evolved from a pattern of single low-value agglomeration in the western region in the 1970s to a dual high-intensity agglomeration pattern in the western and central regions in the 2010s. The intensity of the core western region reached its peak at the end of the study period. In summary, the western region of Liaoning Province was the core affected area of compound high-temperature and drought disasters, and the disaster intensity showed an increasing trend. This study could provide a scientific basis for the formulation of disaster prevention and mitigation strategies and risk management in Liaoning Province.},
}

*Droughts
*Disasters
China
*Hot Temperature
Random Forest
*Climate Change
Geographic Information Systems
Models, Theoretical
Ecosystem

@article {pmid42352964,
year = {2026},
author = {Ding, Y and Liu, T and Guo, S and Zhu, J and Zhu, J and Tang, Q and Jia, Q and Li, J and Zhang, Z and Liu, X},
title = {Integrative Multi-Omics Reveals Microbiome and Genome Streamlining Underlie Ecological Divergence in Chinese and Xinjiang Cordyceps: A Preliminary Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
pmid = {42352964},
issn = {1422-0067},
support = {xjnkywdzc-2026002-7//Xinjiang academy of agricultural sciences/ ; xjnkywdzc-2026003-9//Xinjiang Academy of Agricultural sciences/ ; },
mesh = {*Cordyceps/genetics/classification/metabolism ; Multiomics ; *Microbiota/genetics ; Metabolomics/methods ; Genomics/methods ; *Genome, Fungal ; Phylogeny ; },
abstract = {Chinese Cordyceps (Ophiocordyceps sinensis) and Xinjiang Cordyceps (Paraisaria gracilis) are related entomopathogenic fungi that occupy different elevations and habitats. Whether their holobiont architectures have diverged accordingly is unknown. In this hypothesis-generating study based on samples from single locations (Altai Mountains for Xinjiang Cordyceps and Nagqu, Tibet for Chinese Cordyceps), we compared the two species using amplicon sequencing, untargeted metabolomics, and comparative genomics. Chinese Cordyceps from the sampled site comprises a specialized parasitic fungus and host-adapted bacteria for nutrient acquisition. Xinjiang Cordyceps from the Altai site contains diverse saprotrophic fungi and a rhizosphere-like bacterial consortium enriched in oxidative defense and biofilm genes, a finding that may explain why its sclerotia remain intact for 3-5 years in this population. Metabolomic profiles distinguish the two species at these sites. Xinjiang Cordyceps shows upregulation of tyrosine and porphyrin pathways, and its bacterial community shows functional enrichment in the same pathways, suggesting cross-kingdom coordination. P. gracilis has lost many gene families, and the retained species-specific genes are linked to cell adhesion and acyltransferase activity. Xinjiang Cordyceps is not a simple substitute for Chinese Cordyceps but appears to represent a different ecological strategy shaped by genome streamlining and host-microbe coadaptation. Our findings generate testable hypotheses for future large-scale, multi-population investigations.},
}

*Cordyceps/genetics/classification/metabolism
Multiomics
*Microbiota/genetics
Metabolomics/methods
Genomics/methods
*Genome, Fungal
Phylogeny

@article {pmid42353171,
year = {2026},
author = {Miao, J and Han, S and Dang, X and Chen, Q and Diao, J and Zhu, W},
title = {Benzovindiflupyr Is Associated with Metabolic Homeostasis Disturbance and Gut-Liver Axis Alterations in Zebrafish: Insights from a Multi-Omics Approach.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
pmid = {42353171},
issn = {1422-0067},
support = {2016YFD0200202//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Zebrafish/metabolism ; *Liver/metabolism/drug effects/pathology ; *Homeostasis/drug effects ; Gastrointestinal Microbiome/drug effects ; Multiomics ; Metabolomics/methods ; Oxidative Stress/drug effects ; Metabolome/drug effects ; Intestines/drug effects ; *Fungicides, Industrial/toxicity ; },
abstract = {Benzovindiflupyr (BZF) is a newly developed succinate dehydrogenase inhibitor (SDHI) fungicide that is widely used in crop protection, but its potential effects on non-target aquatic organisms remain a concern. In this study, we exposed adult zebrafish (Danio rerio) to 5.0 and 50 μg/L BZF for 28 days. We investigated its impact on the gut-liver axis using a combination of microbiome, biochemical, histological, and metabolomic analyses. BZF exposure damaged intestinal structure, downregulated barrier-related genes, and altered the composition of the gut microbiota. At the same time, serum lipopolysaccharide (LPS) levels increased, which indicates impaired intestinal barrier integrity and microbial dysbiosis. In the liver, BZF caused histopathological alterations, increased serum ALT, AST, and ALP activities, enhanced oxidative stress, and upregulated inflammation-related genes. Liver metabolomic profiling further showed marked disturbances in redox balance and metabolic homeostasis. Correlation analysis also revealed significant associations between altered microbial taxa and differential liver metabolites. Taken together, these results suggest that BZF exposure disrupted intestinal homeostasis and was associated with hepatic metabolic disturbance in zebrafish, potentially through gut-liver axis perturbation. This study expands current understanding of the toxic effects of SDHI fungicides and provides useful evidence for the ecological risk assessment of BZF in aquatic environments.},
}

Animals
*Zebrafish/metabolism
*Liver/metabolism/drug effects/pathology
*Homeostasis/drug effects
Gastrointestinal Microbiome/drug effects
Multiomics
Metabolomics/methods
Oxidative Stress/drug effects
Metabolome/drug effects
Intestines/drug effects
*Fungicides, Industrial/toxicity

@article {pmid42353853,
year = {2026},
author = {Zhang, Y and Jiang, Y and Qian, S and Jing, S and Liu, Z and Zhao, Z},
title = {Co-Analysis of Transcriptome and Metabolome Reveals Anthocyanin Accumulation in the Female Flower Tissues of Fig Cultivar 'Silu Hongyu'.},
journal = {Genes},
volume = {17},
number = {6},
pages = {},
pmid = {42353853},
issn = {2073-4425},
support = {2023-JC-QN-0194//Shaanxi Science and Technology Department/ ; ZK22-57//Shaanxi A&F Technology University/ ; LZJB2024KY008//the Modern Forestry Vocational Education Group in Northern China/ ; },
mesh = {*Anthocyanins/genetics/metabolism/biosynthesis ; *Flowers/genetics/metabolism ; *Metabolome/genetics ; *Transcriptome/genetics ; *Ficus/genetics/metabolism ; Gene Expression Regulation, Plant/genetics ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Multiomics ; Metabolomics ; },
abstract = {BACKGROUND/OBJECTIVES: Fig (Ficus carica L.) is considered a valuable fruit owing to its rich health-promoting ingredients, including anthocyanins. However, little information is available on the regulatory networks that reveal anthocyanin biosynthesis in figs, especially the new fig cultivar "Silu Hongyu" (HY).

METHODS: In this study, multi-omics analysis was performed to dissect the regulatory networks responsible for anthocyanin accumulation in the female flower tissues of HY.

RESULTS: we found that the anthocyanin content in the female flower tissues of HY is higher than that of "Chinese Ziguo" (ZG). Metabolomic profiling identified 350 differentially accumulated metabolites (DAMs), among which 108 were flavonoids. The contents of multiple metabolites responsible for anthocyanin accumulation, such as naringenin chalcones, cyanidin 3-glucoside, and pelargonidin 3,5-diglucoside, were significantly increased in the HY female flower tissues. Transcriptomic analysis revealed that 3696 differentially expressed genes (DEGs) were screened from the female flower tissues of ZG and HY, with 1730 upregulated DEGs and 1966 downregulated DEGs in HY compared to ZG. The key structural genes involved in anthocyanin biosynthesis, including FcPAL, Fc4CL, FcCHS, FcF3'H, and FcBZ1, were significantly upregulated in the female flower tissues of HY compared with ZG. KEGG analysis also demonstrated that five flavonoid biosynthesis pathways were co-enriched by DAMs and DEGs.

CONCLUSION: These findings provide a multi-omics framework that governs anthocyanin biosynthesis in the female flower tissues of HY, which will facilitate the genetic breeding and improvement of high-anthocyanin fig cultivars.},
}

*Anthocyanins/genetics/metabolism/biosynthesis
*Flowers/genetics/metabolism
*Metabolome/genetics
*Transcriptome/genetics
*Ficus/genetics/metabolism
Gene Expression Regulation, Plant/genetics
Gene Expression Profiling
Plant Proteins/genetics/metabolism
Multiomics
Metabolomics

@article {pmid42357690,
year = {2026},
author = {Deng, T and Liu, D and Zhu, X and Zhang, H and Zhang, Z},
title = {VIP-DB: A Comprehensive Database of Virus-Insect-Plant Relationships.},
journal = {Viruses},
volume = {18},
number = {6},
pages = {},
pmid = {42357690},
issn = {1999-4915},
support = {YLS-2025-ZY03018//Yuelushan Laboratory Special Program for Seed Industry/ ; },
mesh = {Animals ; *Plant Viruses/physiology/classification ; *Plant Diseases/virology ; *Insect Vectors/virology ; *Plants/virology ; *Insecta/virology ; *Databases, Factual ; Biocuration ; Host-Pathogen Interactions ; },
abstract = {Insect-mediated transmission is central to the epidemiology of plant viruses and has major implications for global food security and agricultural production. Although several resources have compiled information on plant virus transmission, evidence-traceable integration of virus-insect vector-host plant relationships remains limited. Here, we developed the Virus-Insect-Plant Database (VIP-DB), an evidence-guided database that links literature-derived virus-insect transmission records, host plant information, transmission mode annotations, taxonomic information, and traceable literature evidence. VIP-DB compiles 583 virus-insect transmission relationships, 855 virus-plant relationships with non-missing host plant information, and 1375 integrated virus-insect-plant records. Among these records, 120 lack host plant information and 51 lack transmission mode annotation. VIP-DB provides a curated and searchable resource for querying documented plant virus, insect vector, host plant, and transmission mode information. This database offers an evidence-traceable framework for comparative analyses of plant virus transmission relationships and supports future studies in plant virology, vector ecology, and disease management.},
}

Animals
*Plant Viruses/physiology/classification
*Plant Diseases/virology
*Insect Vectors/virology
*Plants/virology
*Insecta/virology
*Databases, Factual
Biocuration
Host-Pathogen Interactions

@article {pmid42331683,
year = {2026},
author = {Visser, ME and Hengeveld, GM and de Kraker, J and Athanasiadis, IN and Bakker, ES and Kissling, WD and Nmor, S and Philippart, CJM and Soetaert, K and Vriend, SJG and Woutersen, A and Zhao, Z and Zhan, Q and Hof, AF},
title = {Digital twins as a tool for ecosystem research.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2026.04.016},
pmid = {42331683},
issn = {1872-8383},
abstract = {To understand the functioning of ecosystems and to carry out scenario studies to forecast functional change, we need to integrate different fields of research. An emerging approach to do so is digital twins: innovative tools for integrated ecosystem analysis, capturing species interactions, biodiversity dynamics, and ecosystem carrying capacity. Digital twins can be characterised as (i) being tailored to and behave like a specific ecosystem, and as such accepted by empiricists as representing a description of a real ecosystem, (ii) having a dynamic interaction between the digital twin and the physical ecosystem, (iii) integrating diverse information and data sources, (iv) combining complementary models, and (v) enabling scenario studies. Development of digital twins of ecosystems is instrumental to bend the curve of biodiversity loss and enhance climate resilience, and is timely because of breakthroughs in digital technologies.},
}

@article {pmid42331863,
year = {2026},
author = {Litavský, J and Majzlan, O and Langraf, V and Iracký, S and Šerá, B},
title = {Effects of roadside habitat management on epigeic arthropod diversity: a case study from the Nitra-Selenec expressway junction.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54425-z},
pmid = {42331863},
issn = {2045-2322},
support = {VV-MVP-24-0207//Agentúra na Podporu Výskumu a Vývoja/ ; 1/0211/25//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; 1/0255/23//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; },
abstract = {Linear transport infrastructure fragments habitats, but its edges can serve as significant refuges for invertebrates. Management of these verges is crucial to realise this conservation potential, but the impact of specific habitat measures on epigeic arthropods remains poorly understood. This study assessed the impact of roadside habitat management on the diversity and composition of epigeic arthropods, using ground beetles (Carabidae) and harvestmen (Opiliones) as bioindicators at the Nitra-Selenec expressway junction, Slovakia. Over two years, we used pitfall traps to sample epigeic arthropods at ten sites managed under three different regimes: passive management (no intervention), active management with renewal/seeding (commercial grass-herb mixture), and active management with mulching only. We analysed the influence of management, vegetation structure, and landscape variables on species assemblages using redundancy analysis and predicted population trends using machine learning. We recorded 1,416 carabids (50 species) and 1,409 harvestmen (6 species). The renewal/seeding intervention had a significant negative effect on the community composition. The structure of the vegetation, specifically the cover of the herb layer and species richness of the shrub layer, were the most significant positive drivers of community assembly. Furthermore, distance from the road significantly influenced species distribution. Analysis of population trends revealed a gradual increase in carabid abundance over time, but an alarming decline in harvestmen. Active revegetation with commercial seed mixtures creates a homogeneous habitat that is less suitable for diverse epigeic communities than passive management. The structural complexity provided by various native vegetation is a key factor in supporting invertebrates. Implications for insect conservation: We recommend that roadside managers prioritise passive management or regionally appropriate native seed mixtures over commercial revegetation, maintain structural complexity of vegetation through a reduced frequency of mowing (1-2 times annually at ≥ 10 cm height), and adopt mosaic approaches that combine intensive mowing only in safety-critical zones with extensive management elsewhere.},
}

@article {pmid42333934,
year = {2026},
author = {Simčič, G and Skrbinšek, T},
title = {Wild Pedigree exploreR (wpeR): Streamlined Analysis and Visualization of Wild Pedigrees in Time and Space.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70171},
pmid = {42333934},
issn = {1755-0998},
support = {//European Commission/ ; P1-0184//Slovenian Research and Innovation Agency/ ; },
mesh = {*Pedigree ; Animals ; *Software ; *Genetics, Population/methods ; *Computational Biology/methods ; *Animals, Wild/genetics/classification ; Genotype ; },
abstract = {Advances in non-invasive genetic sampling and long-term genetic monitoring programmes have enabled collection of large individual genotype datasets for many wildlife populations, often accompanied by rich field metadata that place the genotyped individuals in time and space. These datasets allow reconstruction of multigenerational pedigrees and have the potential to provide valuable insights into population demography, reproduction, dispersal, social structure and genetic processes. But while the tools for construction of pedigrees keep improving, their interpretation remains challenging. Integrating multigenerational pedigree data with field metadata creates significant complexity, yet specialized tools to facilitate the interpretation of such datasets remain scarce. Here we introduce wild pedigree exploreR (wpeR), an R package designed to simplify exploration, organization and interpretation of complex pedigrees. The package enables users to link reconstructed pedigrees with genetic sample metadata, enabling evaluation of biological plausibility of inferred relationships, but also allowing exploration of other characteristics of individuals and populations in spatial and temporal contexts. wpeR implements a linear workflow through which the pedigree data is imported, formatted, organized into families and integrated with field metadata. The resulting dataset can be visualized through temporal plots that track individuals and families over time, as well as with spatial outputs representing parent-offspring relationships and individual movement patterns as geographic features that can be either directly visualized on maps within R, or exported to be further explored with common GIS tools. wpeR allows exploration of lineage relationships within their ecological context, bridging the gap between statistically reconstructed pedigrees and their biological interpretation. It provides a scalable and flexible framework for analyzing these complex data, providing a practical tool for researchers and managers working with genetic monitoring datasets.},
}

*Pedigree
Animals
*Software
*Genetics, Population/methods
*Computational Biology/methods
*Animals, Wild/genetics/classification
Genotype

@article {pmid42336424,
year = {2026},
author = {Yu, XY and Gao, YX and Wei, GP and Zhou, T},
title = {[Characterization and Prediction of Spatial and Temporal Evolution of Vegetation Coverage and Vegetation Resilience: A Case Study of the Ecological Restoration Project in Inner Mongolia].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {6},
pages = {3795-3803},
doi = {10.13227/j.hjkx.202504012},
pmid = {42336424},
issn = {0250-3301},
mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Environmental Monitoring ; *Environmental Restoration and Remediation ; Spatio-Temporal Analysis ; *Plant Development ; },
abstract = {The aim of this study was to analyze the spatial and temporal characteristics of vegetation coverage and resilience in Inner Mongolia， to explore the correlation between the two time series， and to predict the evolutionary trend of vegetation resilience from 2024 to 2026. Based on the kernel normalized vegetation index （kNDVI） dataset constructed by satellite （MOD13Q1V6.1） and early warning indicators， the spatial and temporal changes of vegetation coverage and vegetation resilience are assessed from 2004 to 2023 in Inner Mongolia. The correlation between the spatial changes of the vegetation coverage and vegetation resilience is analyzed using Pearson's correlation analysis， and the evolutionary trend of vegetation resilience in the next three years is predicted by the BP neural network. The results show that： ① From 2004 to 2023， approximately 85.63% of the vegetation coverage in Inner Mongolia showed an increasing trend， and the changes in vegetation resilience showed a spatial distribution pattern of increasing in the east and central part of Inner Mongolia and decreasing in the western part. ② The trends of vegetation coverage and vegetation resilience in spatial and temporal changes were not completely consistent. In the ecological restoration project， only pursuing the increase of cover may not be able to enhance the stability of the system， and more attention should be paid to the dynamic response mechanism of vegetation resilience. ③ In the next three years， the overall trend of vegetation resilience in Inner Mongolia will be upward， mainly focusing on the ecological restoration projects in the Yinshan Mountains， Horqin Sands， and Daxing'anling Mountains， but the problem of declining vegetation resilience in the ecological restoration projects in the western parts of the country and other local areas still requires further attention.},
}

China
*Ecosystem
*Conservation of Natural Resources
Environmental Monitoring
*Environmental Restoration and Remediation
Spatio-Temporal Analysis
*Plant Development

@article {pmid42337211,
year = {2026},
author = {Fenta, AA and Tsunekawa, A and Haregeweyn, N and Zegarek, M and Kabała, C and Stavi, I and Sulwiński, M and Mętrak, M and Orazov, A and Suska-Malawska, M},
title = {Unveiling fine-scale distribution of endemic shrub Prunus ledebouriana through integrating multi-source remote sensing with deep learning.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {7},
pages = {},
pmid = {42337211},
issn = {1573-2959},
support = {BOB-661-846/2023 and WNE II.2.1/03/2024//Excellence Initiative - Research University at the University of Warsaw/ ; },
mesh = {*Remote Sensing Technology ; *Prunus/growth & development ; *Deep Learning ; *Environmental Monitoring/methods ; Kazakhstan ; Convolutional Neural Networks ; Geographic Information Systems ; },
abstract = {This study aims to unveil a fine-scale spatial distribution of endemic shrub Prunus ledebouriana (Schltdl.) Y.Y.Yao in Kazakhstan's Tarbagatay National Park by integrating multi-source remote sensing with deep learning. Accurate characterization of plant species distribution requires spatially precise ground-truth data; however, conventional GPS-based methods often introduce positional uncertainties that compromise alignment with very high-resolution imagery. To overcome this limitation, we employed a hybrid ground-truthing strategy that combines very high-resolution (5 × 5 cm) drone imagery with field-based onscreen digitization, enabling the generation of spatially accurate reference data. This data was used to extract training and validation data points from 18 predictor variables, encompassing spectral bands, vegetation indices, and texture features derived from Pléiades Neo imagery (30 × 30 cm), along with ancillary topographic and climatic variables. Based on these inputs, a deep one-dimensional convolutional neural network (1D CNN) model was developed to characterize the spatial distribution of P. ledebouriana. The model achieved an overall mapping accuracy of about 80%, with feature importance analysis highlighting texture metrics as the most influential predictors. Results revealed that P. ledebouriana covers about 7.5% of the study area; with distribution strongly linked to specific topographic settings. Nearly 70% of occurrences were found between 700 and 1200 m elevation, peaking at 900-1000 m.a.s.l., and about 75% were located on moderately slopped terrains (5-30%). Aspect also influenced distribution, with 83% of occurrences on southeast- to west-facing hillslopes. The limited occurrence of P. ledebouriana in lowland agricultural areas and on steep slope terrains suggests a combined influence of anthropogenic land-use pressures and ecological preferences. This study demonstrates the potential of integrating spatially precise ground-truthing, multi-source remote sensing, and deep learning for accurately mapping plant species distribution in mountainous drylands, supporting biodiversity monitoring and conservation planning in these fragile ecosystems.},
}

*Remote Sensing Technology
*Prunus/growth & development
*Deep Learning
*Environmental Monitoring/methods
Kazakhstan
Convolutional Neural Networks
Geographic Information Systems

@article {pmid41513706,
year = {2026},
author = {Cui, J and Xu, Y and Liu, J and Zhang, X and Chen, Z and Yang, W and Ge, J and Sun, C and Zhai, Y and Chang, Z and Tian, L and Duan, Y and Song, F and Cai, W and Li, H and Tian, L},
title = {Chromosome-level genome assembly and annotation of two Asian bumble bees.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {248},
pmid = {41513706},
issn = {2052-4463},
support = {32370487//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2115 Talent Development Program//China Agricultural University (CAU)/ ; },
mesh = {Animals ; *Bees/genetics ; *Chromosomes, Insect ; *Genome, Insect ; Molecular Sequence Annotation ; Male ; Datasets as Topic ; },
abstract = {The bumblebee Bombus patagiatus Nylander, 1848 and Bombus lantschouensis Vogt, 1908 (Hymenoptera: Apidae) are ecologically important bumble bee species native to East Asia, with considerable value for agricultural pollination and domestication. Despite their ecological and economic relevance, the lack of high-quality genomic resources has hindered in-depth investigations into their genetic architecture and evolutionary adaptations. Here, we present chromosome-level genome assemblies for both species, generated using a combination of PacBio HiFi long-read sequencing, Illumina short-read resequencing, and Hi-C scaffolding. The assembled genomes span 240.28 Mb (B. patagiatus) and 241.30 Mb (B. lantschouensis), with 94.38% and 94.00% of sequences anchored to 18 chromosomes, respectively. Genome annotation identified 17,351 and 16,023 protein-coding genes in B. patagiatus and B. lantschouensis, along with comprehensive repetitive element characterization. Both assemblies exhibit exceptional completeness, with BUSCO scores exceeding 99%, confirming their high quality and reliability. These genomic resources provide a critical foundation for future research on bumble bee evolution, population genetics, and the molecular basis of domestication traits.},
}

Animals
*Bees/genetics
*Chromosomes, Insect
*Genome, Insect
Molecular Sequence Annotation
Male
Datasets as Topic

@article {pmid41974979,
year = {2026},
author = {Martín-Vélez, V and Navarro, J and Afán, I and Montalvo, T and Green, AJ},
title = {Conflicts hinder research into animal movements.},
journal = {Ambio},
volume = {55},
number = {8},
pages = {2018-2021},
pmid = {41974979},
issn = {1654-7209},
support = {10.13039/501100011033//Agencia Estatal de Investigación/ ; },
mesh = {Animals ; *Geographic Information Systems ; *Animal Migration ; *Charadriiformes/physiology ; Europe, Eastern ; *Warfare ; Influenza in Birds/transmission ; Influenza A Virus, H5N1 Subtype ; },
abstract = {Satellite tracking has revolutionized our understanding of animal migration, yet its reliability increasingly depends on the geopolitical stability of the regions frequented by wildlife. Here, we show that military-induced interference with global navigation satellite systems (GNSS) during ongoing conflicts in Eastern Europe has severely compromised the accuracy of global positioning systems (GPS)-based tracking data for black-headed gulls (Chroicocephalus ridibundus). In 2024-2025, GPS trajectories revealed erratic, low-quality, and geographically implausible positions coinciding with known zones of electronic warfare. These inaccuracies hinder efforts to locate breeding colonies, identify key stopover habitats, and assess disease transmission risks posed by migratory birds, particularly for zoonoses such as highly pathogenic avian influenza (HPAI) H5N1. Our findings illustrate how modern conflicts now extend their impact into ecological research infrastructures, calling for systematic correction methods and international coordination to safeguard the robustness of movement ecology studies and One Health models in a geopolitically unstable world.},
}

Animals
*Geographic Information Systems
*Animal Migration
*Charadriiformes/physiology
Europe, Eastern
*Warfare
Influenza in Birds/transmission
Influenza A Virus, H5N1 Subtype

@article {pmid42329868,
year = {2026},
author = {Grimm, V and Berger, U and Mammola, S},
title = {Ten simple rules for making the supplement increase your paper's impact.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014419},
pmid = {42329868},
issn = {1553-7358},
mesh = {Humans ; *Periodicals as Topic/standards ; *Publishing/standards ; Computational Biology ; },
abstract = {Have you ever lost hours navigating supplementary materials-clicking between the main text and dozens of auxiliary files only to encounter broken links, illegible figures, and undefined variables and acronyms? If so, you're not alone. What should support scientific communication has instead become an obstacle: supplementary information (SI) increasingly suffers from inconsistent formatting, poor accessibility, and fragmented organization that impedes rather than advances understanding. This is disheartening since the SI, if used effectively, has the power to enhance transparency, credibility, and reproducibility of research. Therefore, we propose 10 simple rules to help authors design SI that genuinely increase the impact of their research. The rules emphasize treating SI with the same care as the main text, using it strategically to support the scientific narrative while preserving clarity and focus. Key recommendations include creating a single, well-structured, self-contained SI master document; ensuring explicit cross-referencing between the main text and SI; making SI machine-readable; and avoiding the misuse of SI as a substitute for proper data repositories. We also highlight the importance of creativity in choosing appropriate formats and strict adherence to journal-specific guidelines. Finally, when available, we advocate the use of standardized templates to improve consistency, readability, and reuse across studies. By following these rules, authors can substantially increase the scientific impact of their work while at the same time contributing to more sustainable research practices.},
}

Humans
*Periodicals as Topic/standards
*Publishing/standards
Computational Biology

@article {pmid42312893,
year = {2026},
author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Ji, Y and Cao, K and Fan, C and Li, D and Chen, J},
title = {Crowded Public Spaces as Hotspots of Airborne Microbial Risk: A Population-Weighted Risk Assessment in Urban Environments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04000},
pmid = {42312893},
issn = {1520-5851},
abstract = {Airborne pathogens and antimicrobial resistance (AMR) pose growing health risks in cities, where enclosed spaces, inadequate ventilation, and high population density enhance their persistence and dissemination. However, the microbial burden and risk associated with high-occupancy public spaces remain poorly quantified. Here, we compared bioaerosol characteristics across university cafeterias and a subway station, dry- and mixed-waste collection facilities (WCFs), and an urban air monitoring site by using culture-based, molecular, source-tracking, and risk-assessment approaches. The results showed that Crowded Public Spaces (CPSs) harbored culturable bacterial and AMR burdens comparable to those in WCFs, both far exceeding levels at the urban air monitoring site. Human-associated sources contributed to ∼50% of airborne bacteria, and multidrug-resistant isolates (∼60%), high-risk β-lactam ARGs, and clinically relevant pathogens were further enriched in CPSs. We further applied a population-weighted infection burden (PWIB) metric that integrates infection risk with pedestrian volume and dwell time. Although contamination levels in CPSs were similar to those in conventional microbial hotspots, CPSs contributed more to the city-scale infection burden once population exposure was taken into account. These findings reveal that urban airborne microbial risk is shaped not only by contamination intensity but also by human occupancy and exposure patterns. This study highlights the value of incorporating human activity into microbial risk assessment in high-density urban environments.},
}

@article {pmid42315803,
year = {2026},
author = {Guo, J and Frederick, J and Cunningham, L and Jacobson, NC and Fisher, AJ and Pettit, JW and McMakin, DL and Ng, MY},
title = {Feasibility and Acceptability of a Smartphone and Wearable Assessment Protocol for Adolescents with Depression.},
journal = {Research on child and adolescent psychopathology},
volume = {54},
number = {4},
pages = {},
pmid = {42315803},
issn = {2730-7174},
support = {R21MH126394/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; Female ; Adolescent ; *Smartphone ; Feasibility Studies ; *Actigraphy/instrumentation ; Child ; *Wearable Electronic Devices ; *Depression/diagnosis ; Male ; *Mobile Applications ; *Ecological Momentary Assessment ; Sleep ; Digital Health ; *Patient Acceptance of Health Care ; },
abstract = {Smartphones and wearables are low-burden tools for assessing real-time mood and behavior. Although these methods have been used with adolescents for behavioral tracking (e.g., activity, sleep), less is known about longer-term use (beyond one week) with adolescents with depression and about mobile sensing for monitoring mood for any adolescent population. This study examined acceptability and feasibility of a one-month EMA, actigraphy, and mobile sensing protocol for adolescents with elevated depressive symptoms. Adolescents aged 12 to 18 (N = 69; Mage = 15.46; 67% assigned female at birth; 42% White; 71% Hispanic or Latine; 38% sexual minority) completed EMA surveys on depressive symptoms, processes, and affect multiple times daily via a smartphone app that also collected passive sensor data (e.g., motion, geolocation). An actigraph measured physical activity and sleep. A feedback interview assessed protocol acceptability. Most participants (91%) completed all components, were willing to participate again (91%), and would recommend participation to peers (93%). EMA response rates improved (mean completion 57% to 66%) after shifting to a semi-personalized schedule with extended response windows. Actigraph wear time was high (> 70%) despite device-related issues. Sensor data availability varied by operating system, and privacy concerns influenced participation. Adherence was correlated within and between modalities, suggesting that individual compliance played a central role in consistent engagement. Findings support the feasibility and acceptability of smartphone and wearable methods for capturing real-world mood and behavior in adolescents, however careful attention to design, engagement, and ethical considerations remains essential.},
}

Humans
Female
Adolescent
*Smartphone
Feasibility Studies
*Actigraphy/instrumentation
Child
*Wearable Electronic Devices
*Depression/diagnosis
Male
*Mobile Applications
*Ecological Momentary Assessment
Sleep
Digital Health
*Patient Acceptance of Health Care

@article {pmid42318582,
year = {2026},
author = {Dodampegama, H and Sridharan, M},
title = {Collaborate and explain on-the-fly: knowledge-based reasoning and learning in ad hoc teamwork.},
journal = {Frontiers in artificial intelligence},
volume = {9},
number = {},
pages = {1765191},
pmid = {42318582},
issn = {2624-8212},
abstract = {This paper focuses on ad hoc teamwork, the problem of enabling an AI agent to collaborate with other agents without prior coordination. Methods considered state of the art for ad hoc teamwork formulate it primarily as a learning problem, using a large labeled dataset of different situations to model the action choices of other agents (or agent types) and determine the actions of the ad hoc agent. Such datasets are not readily available in practical domains, and these methods lack transparency and make it difficult to rapidly revise existing knowledge (or models) in response to changes in the domain, team composition, or agents' capabilities. Our architecture for ad hoc teamwork embeds the principles of refinement, ecological rationality, interactive learning, and explainable agency, leveraging the complementary strengths of knowledge-based and data-driven methods for reasoning and learning. Specifically, for any given goal, our architecture enables an ad hoc AI agent to determine its actions through non-monotonic logical reasoning with: (a) prior domain-specific commonsense knowledge; (b) models learned and revised rapidly to predict the behavior of other agents; and (c) anticipated abstract future goals based on generic knowledge of similar situations in a pretrained Large Language Model. In addition, the ad hoc agent processes natural language descriptions and observations of other agents' behavior, using a combination of a pretrained Large Language Model and decision-tree induction to incrementally acquire and revise knowledge in the form of objects, actions, and axioms that govern domain dynamics. Furthermore, the ad hoc agent generates relational descriptions as on-demand explanations of its decisions and beliefs, and those of other agents, in response to various types of questions. We ground and experimentally evaluate the capabilities of our architecture in VirtualHome, a realistic, physics-based 3D simulation environment. We demonstrate reliable, efficient, transparent, and scalable performance, providing a substantial improvement in performance compared with a purely knowledge-based baseline, and comparable or better performance than a purely data-driven baseline while using orders of magnitude fewer resources.},
}

@article {pmid42328538,
year = {2026},
author = {Lu, Q and Luo, J and Wang, J and Zhao, B and Wang, X and You, L},
title = {QeITH: Quantifies Tumor Ecosystem Heterogeneity to Predict Cancer Progression and Treatment Benefit.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0061},
pmid = {42328538},
issn = {2001-0370},
abstract = {Intratumor heterogeneity (ITH) is a fundamental driver of therapeutic failure and disease progression. However, the complexity of the tumor ecosystem is a critical yet underexplored aspect, making its precise quantification essential for fully deciphering ITH and its clinical implications. To address this, we developed Quantifying Ecosystem Intratumor Heterogeneity (QeITH), a computational framework that applies Shannon entropy to quantify ecosystem heterogeneity by measuring the diversity and distributional entropy of cellular compositions and functional states across single-cell, bulk, and spatial transcriptomics. At the single-cell resolution, QeITH identifies elevated ITH as intrinsic markers of malignant transformation, yet enhanced sensitivity to therapy. Pan-cancer bulk analyses further link elevated QeITH scores to increased neoantigen burden, PD-L1 expression, and unfavorable prognosis. Notably, spatial transcriptomics reveals that ecological complexity is nonuniformly distributed, peaking at invasive fronts and within tertiary lymphoid structures (TLS), where enhanced diversity within TLS modulates therapeutic vulnerability. Thus, QeITH reveals a dual role for ITH: While high scores associated with tumor aggressiveness, they also predict favorable treatment responses by capturing an immunologically active tumor ecosystem state. By integrating single-cell precision with spatial context, this framework elucidates the biological drivers of cancer progression and serves as a robust tool for optimizing personalized therapeutic strategies in precision oncology.},
}

@article {pmid41765879,
year = {2026},
author = {Yu, X and Ramli, SHB and Hamid, HA and Norowi, NM and Surip, SS and Yu, G and Zhang, C and Liu, Z},
title = {Defining "critical" maternal health information for healthy lifestyle self-management in pregnancy: perspectives of pregnant women and obstetricians in China and Malaysia.},
journal = {BMC pregnancy and childbirth},
volume = {26},
number = {1},
pages = {},
pmid = {41765879},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; Obstetricians/psychology ; Malaysia ; China ; *Healthy Lifestyle ; Adult ; Qualitative Research ; *Self-Management/psychology ; *Pregnant People/psychology ; *Maternal Health ; Social Support ; *Prenatal Care/methods ; Digital Health ; Attitude of Health Personnel ; },
abstract = {BACKGROUND: Pregnancy is a critical window for adopting and sustaining healthy lifestyle behaviors. This study explored perspectives of pregnant women and obstetricians on key lifestyle domains, barriers, and support needs during pregnancy in China and Malaysia. METHODS: A qualitative in-depth interview study was conducted from October 2023 to February 2024. Pregnant women were recruited from two antenatal clinics in China and one general hospital in Malaysia. Obstetricians involved in routine antenatal care were also interviewed. Interviews were audio-recorded, transcribed verbatim, and analyzed thematically. RESULTS: Twenty pregnant/postpartum women and six obstetricians participated. Four integrated themes from pregnant women described “critical” maternal health information as: (1) bonding-oriented interpretability that motivates health behaviors, (2) lifestyle self-management under uncertainty requiring safety boundaries and red-flag clarity, (3) social support as psychosocial coping infrastructure, and (4) digital information appraisal in partnership with clinicians. Three complementary themes from obstetricians emphasized time-pressured clinical encounters shaping communication and trust, ethically/institutionally mediated disclosure practices, and a contested digital information ecology in which digital tools may support continuity while raising credibility concerns. CONCLUSIONS: Pregnant women and obstetricians highlighted multi-domain lifestyle support needs that extend beyond clinical check-ups. Strengthening credible information access and tailored professional guidance may facilitate healthier lifestyle practices during pregnancy across contexts.},
}

Humans
Female
Pregnancy
Obstetricians/psychology
Malaysia
China
*Healthy Lifestyle
Adult
Qualitative Research
*Self-Management/psychology
*Pregnant People/psychology
*Maternal Health
Social Support
*Prenatal Care/methods
Digital Health
Attitude of Health Personnel

@article {pmid41832485,
year = {2026},
author = {Anjana, RM and Nitika, S and Kuriakose, S and Gibson, AA and Kamotho, C and Heine, M and Brant, LC and Tromp, J and Jose, AP and Ranjani, H},
title = {Digital divide in diabetes care: qualitative insights from the DIG-EQUITY study, India.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {41832485},
issn = {1471-2458},
mesh = {Humans ; India ; Female ; Qualitative Research ; Male ; Focus Groups ; Adult ; *Telemedicine/statistics & numerical data ; Digital Health ; *Digital Divide ; Middle Aged ; Interviews as Topic ; *Diabetes Mellitus/therapy ; *Healthcare Disparities ; Diabetes Mellitus, Type 2/therapy ; Pregnancy ; },
abstract = {BACKGROUND: Digital health technologies have the potential to improve health outcomes in underserved settings. However, in low and middle-income countries with weak public health systems, unequal access to digital tools can worsen existing healthcare disparities. The DIG-EQUITY study explored the facilitators and barriers to equitable use of mobile and telehealth solutions for diabetes care in India, incorporating perspectives from people with diabetes, their family members (caregivers), healthcare providers, policymakers, and community organisations. METHODS: A qualitative design was employed across urban (Chennai) and rural (Chunampet) settings in Tamil Nadu, following the 32-item COREQ checklist. A total of 54 participants (including type 1 diabetes (T1DM), type 2 diabetes (T2DM), and gestational diabetes mellitus (GDM)) were included in four focus group discussions (FGDs) and 12 key informant interviews (KIIs). Participants were purposively sampled to ensure diversity in demographics and healthcare exposure. The analysis was guided by the Social Ecological Model (SEM), which informed the structuring and interpretation of themes across domains. RESULTS: The different domains of the SEM influenced the utilisation of digital health. Individual factors such as age, digital literacy, and diabetes type shaped preferences. Interpersonal support from caregivers enabled access, particularly for older adults and children. Organisational and community influences included urban–rural infrastructure gaps, socioeconomic constraints, and shared device ownership. Policy-level concerns regarding data privacy, security, and app reliability affected trust and continued engagement. CONCLUSION: Socioeconomic status, sex, and geographic location influenced access and adoption of digital solutions. Bridging the divide through targeted digital literacy initiatives and inclusive strategies is essential to ensure equitable and effective use of digital health solutions for diabetes care in India. TRIAL REGISTRATION: The trial was registered with Central Trials Registry of India (CTRI/2022/04/041941).},
}

Humans
India
Female
Qualitative Research
Male
Focus Groups
Adult
*Telemedicine/statistics & numerical data
Digital Health
*Digital Divide
Middle Aged
Interviews as Topic
*Diabetes Mellitus/therapy
*Healthcare Disparities
Diabetes Mellitus, Type 2/therapy
Pregnancy

@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
mesh = {*Endophytes/genetics/physiology/classification ; *Symbiosis ; *Agroecology ; Genomics ; *Plants/microbiology ; Multiomics ; Agriculture ; Ecosystem ; Microbiota ; Metagenomics ; Bacteria/genetics/classification ; },
abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.},
}

*Endophytes/genetics/physiology/classification
*Symbiosis
*Agroecology
Genomics
*Plants/microbiology
Multiomics
Agriculture
Ecosystem
Microbiota
Metagenomics
Bacteria/genetics/classification

@article {pmid42171373,
year = {2026},
author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0030526},
pmid = {42171373},
issn = {2379-5077},
support = {K08AI159619//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/genetics/immunology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; *Bacterial Toxins/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Machine Learning ; Computational Biology/methods ; },
abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.},
}

Humans
*Dysbiosis/microbiology/genetics/immunology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Female
*Bacterial Toxins/genetics
*Metagenome
*Bacteria/genetics/classification
*Microbiota/genetics
Machine Learning
Computational Biology/methods

@article {pmid42275032,
year = {2026},
author = {Yuan, S and Tan, D and Zhu, D and Balcazar, JL and Wang, H and Friman, VP and Sun, M and Hu, F},
title = {Global transmission and distribution of phage-encoded cholera toxin genes constrained by toxin-repression genes and anti-phage defense systems.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42275032},
issn = {1751-7370},
mesh = {*Cholera Toxin/genetics ; *Bacteriophages/genetics ; *Vibrio cholerae/genetics/virology ; *Gene Transfer, Horizontal ; Cholera/microbiology ; Humans ; Animals ; CRISPR-Cas Systems ; Computational Biology ; },
abstract = {Cholera is a severe diarrheal disease caused by toxigenic Vibrio cholerae, whose virulence depends on lysogenic infection by CTXφ bacteriophages encoding the cholera toxin genes (ctxA and ctxB) and associated accessory genes (ace and zot). However, the global distribution and transmission dynamics of phage-encoded cholera toxin genes across environments remain poorly understood. To address this, we performed a large-scale bioinformatic analysis of publicly available whole genomes. We show that both phages and bacteria carrying toxin genes are globally distributed across human-associated, freshwater, fish, and mammalian habitats, with Vibrio and Aeromonas being the dominant bacterial taxa and Inoviridae is the most prevalent phage family. Phage-mediated horizontal gene transfer (HGT) of toxin genes occurred in both Vibrio and non-Vibrio species, with the highest transfer between Inoviridae and V. cholerae occuring predominantly among bacteria from the same habitat. Temporal analysis revealed an increase in candidate HGT events after 2000, peaking at 377845 events during 2010-2019. HGT events negatively correlated with the presence of CRISPR-Cas system and toxin-repression genes (hns, hapR, and tsrA) in host bacteria. Experimental validation indicated that H-NS and HapR inhibit phage infection by repressing phage release. Together, our results suggest that CRISPR-Cas phage defense system and toxin-repression mechanisms could constrain the spread of toxin-carrying phages, with potential implications for the occurrence and severity of cholera outbreaks worldwide.},
}

*Cholera Toxin/genetics
*Bacteriophages/genetics
*Vibrio cholerae/genetics/virology
*Gene Transfer, Horizontal
Cholera/microbiology
Humans
Animals
CRISPR-Cas Systems
Computational Biology

@article {pmid41345617,
year = {2025},
author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN},
title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1915},
pmid = {41345617},
issn = {1472-6831},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; *Mouth/microbiology ; Secondary Data Analysis ; *Microbiota ; },
abstract = {With an astounding global prevalence, both diabetes mellitus and gum disease pose significant health concerns. Gum disease has been identified as a risk factor for diabetes mellitus, and its treatment has shown improvements in markers of glucose management. We hypothesised that bacteria commonly associated with the oral microbiome could be disproportionately present in the gut of individuals with type 2 diabetes mellitus (T2DM) compared to healthy controls, suggesting a possible association between oral-associated bacteria and metabolic dysregulation. This hypothesis is supported by known interactions between the oral microbiome and systemic health, particularly the role of inflammation in both conditions. Therefore, we aimed to conduct a secondary analysis of whole-genomic sequencing data of studies published over the last twenty years (2004–2024) related to the gut microbiome of patients with T2DM to identify oral-associated bacteria in their gut compared to healthy individuals. We searched for studies related to the gut microbiome, whole metagenomics, and T2DM in Ovid Medline, EMBASE, and Web of Science databases. Studies that included whole metagenomic data from adult populations of all genders with T2DM were selected, resulting in the reanalysis of metagenomic sequencing data from a total of 9 studies (n = 1,224 metagenomes) for bacterial species data. From the 41,689 gut microbial species identified across the selected studies, 497 were classified as of oral-associated bacteria, corresponding with entries in the Human Oral Microbiome Database (HOMD). These oral bacteria comprised 1.19% of the gut microbiome. Notably, twenty oral-associated bacterial species were statistically significant in their presence among patients with diabetes compared to healthy individuals, irrespective of their abundance. Key oral pathogens included Corynebacterium striatum, Staphylococcus capitis, Kingella kingae, Corynebacterium propinquum, Prevotella sp. oral taxon 820, Prevotella scopos, Selenomonas artemidis, Bordetella pertussis, Selenomonas sp. oral taxon 137, and Staphylococcus hominis. Specifically, periodontal pathogens such as, Porphyromonas gingivalis, Tannerella forsythia, and Capnocytophaga sp. oral taxon 332 were found to be significantly higher in patients with T2DM. These bacteria are associated with conditions like endocarditis, bacteremia, and inflammatory responses, which are prevalent in both diabetes and periodontitis. Although causal relationships cannot be directly established, our findings suggest that bacteria typically originating from the oral cavity may be more prevalent in the gut microbiome of patients with T2DM, supporting the potential role of oral-gut microbial interactions in metabolic dysregulation.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology
*Gastrointestinal Microbiome
Metagenomics
*Mouth/microbiology
Secondary Data Analysis
*Microbiota

@article {pmid41582220,
year = {2026},
author = {Cai, J and Chen, X and Li, X and Zhang, M and Lin, X and Hu, Y and Feng, H and Li, X and Hu, J and Yang, S and Wang, L and Niu, X and Wang, G and Tang, B and Wang, S and Qin, Y and Cheng, Y},
title = {IGD: a multi-omics database for Ipomoea pes-caprae genomic and biological research.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {342},
pmid = {41582220},
issn = {1471-2229},
support = {2023J01442//Natural Science Foundation of Fujian Province/ ; 32170380//National Natural Science Foundation of China/ ; },
mesh = {*Ipomoea/genetics ; *Genome, Plant ; Genomics ; *Databases, Genetic ; Multiomics ; Salt-Tolerant Plants/genetics ; },
abstract = {Ipomoea pes-caprae (IPC) is a perennial halophytic vine with remarkable salt and drought tolerance, playing a critical ecological and medicinal role in tropical and subtropical coastal ecosystems. Despite the availability of a high-quality chromosome-level reference genome and abundant transcriptome data, the absence of an integrated data platform has hindered in-depth functional gene discovery and genomic research in IPC. To address this gap, we developed the IPC Genome Database (IGD), the first comprehensive multi-omics database dedicated to IPC. IGD provides high-quality genomic sequences, gene structure annotations, and functional annotations, along with transcriptomic expression profiles under salt stress across different tissues. It also includes time-course expression data of roots and leaves under salt stress treatment, as well as leaf expression profiles under cold and heat stress conditions. The platform also integrates a suite of user-friendly, interactive bioinformatics analysis and visualization tools to facilitate efficient data exploration and functional mining. In particular, we established a specialized subset of stress-responsive genes to support rapid candidate gene screening and evolutionary analysis related to IPC’s salt and stress tolerance traits. By implementing automated data integration and quality control pipelines tailored for non-model species, IGD overcomes technical challenges such as fragmented data and delayed updates. As a centralized and scalable resource, IGD significantly lowers the barrier to functional genomics research in IPC and other halophytes, promoting their application in genetic improvement and ecological sustainability. In the future, IGD will continue to incorporate more omics data from halophytic species, further enhancing its value in salt tolerance research and molecular breeding efforts.},
}

*Ipomoea/genetics
*Genome, Plant
Genomics
*Databases, Genetic
Multiomics
Salt-Tolerant Plants/genetics

@article {pmid41619051,
year = {2026},
author = {Paulino, A and Fernandes, I and Pires, RC and Usié, A and Faustino, A and Santos, J and Brás, T and Rosa, D and Paulo, OS and Duarte, MF and Marum, L},
title = {Unravelling the molecular mechanisms of vegetative-to-reproductive transition in Cynara cardunculus by RNA-Seq analysis.},
journal = {Plant molecular biology},
volume = {116},
number = {1},
pages = {15},
pmid = {41619051},
issn = {1573-5028},
mesh = {*Cynara/genetics/growth & development/metabolism/physiology ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Flowers/genetics/growth & development ; RNA-Seq ; Reproduction/genetics ; Transcriptome ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Flavonoids ; Transcription Factors/metabolism/genetics ; },
abstract = {Cynara cardunculus inflorescence plays a significant role in cheese manufacturing and human consumption due to the milk-clotting capacity and the production of edible immature capitula. Consequently, it is crucial to understand the complex cellular and molecular processes involved in the development of cardoon flowers. The current study used western wild cardoon in two developmental stages, vegetative and reproductive, to understand the molecular mechanisms mediating cardoon`s vegetative-to-reproductive transition. Transcriptome profiling identified 552 differentially expressed genes (DEGs) between vegetative and reproductive stages, with 321 upregulated in stage 4 (vegetative state) and 231 in stages 5/6 (reproductive state). Gene Ontology (GO) analysis revealed DEGs involved in biological processes such as oxidation-reduction, lipid metabolism, and defense responses. Metabolic pathways, including phenylpropanoid biosynthesis and anther/pollen development, were significantly enriched. Genes associated with lignin formation, flavonoid synthesis, and acetyltransferase activity were upregulated in the vegetative stage. At the same time, those related to flower development and sesquiterpene lactone biosynthesis were prominent in the reproductive stage. Transcription factors, including MADS-box and ethylene-responsive families, were critical in regulating developmental transitions. This study provides comprehensive insights into the morphological, chemical, and molecular dynamics of C. cardunculus across its phenological stages, underscoring the plant’s adaptability and potential for pharmaceutical and industrial applications. The findings highlight the importance of seasonal and developmental timing in optimizing the production of valuable secondary metabolites, such as cynaropicrin.},
}

*Cynara/genetics/growth & development/metabolism/physiology
Gene Expression Regulation, Plant
Gene Expression Profiling
Flowers/genetics/growth & development
RNA-Seq
Reproduction/genetics
Transcriptome
Plant Proteins/genetics/metabolism
Gene Ontology
Flavonoids
Transcription Factors/metabolism/genetics

@article {pmid41629809,
year = {2026},
author = {Wang, R and Liu, C and Ma, ZC and Qin, T and Zhang, W and Guo, H},
title = {Integrated physiology and multi-omics elucidate photosynthetic adaptation and osmolyte accumulation mechanisms in buffalograss under osmotic stress.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41629809},
issn = {1471-2229},
mesh = {*Photosynthesis/physiology ; *Osmotic Pressure ; *Poaceae/physiology/genetics/metabolism ; Drought Resistance ; Multiomics ; Adaptation, Physiological ; Plant Leaves/metabolism/physiology ; Chlorophyll/metabolism ; },
abstract = {Water deficit threatens global agriculture and ecological construction. Buffalograss (Buchloe dactyloides (Nutt.) Engelm.), a C4 perennial grass native to arid regions, is an ideal model for dissecting drought tolerance mechanisms. In this study, we investigated the physiological responses of buffalograss to PEG-induced osmotic stresses through integrated transcriptomic and metabolomic analyses. The results showed that buffalograss could maintain plant dry weight, chlorophyll content and leaf water use efficiency, simultaneously increase leaf K+ and NO3− accumulation under osmotic stress. After 20% PEG treatment, key metabolites, including amino acids (e.g., aspartate, glutamate and leucine) and other organic acids (e.g., salicylic acid and citrate) were enriched. At the transcriptional level, genes related to chlorophyll biosynthesis (e.g., GluTR, MgCH, POR and DVR) and carbon fixation (e.g., rbcL and PPDK) were coordinately upregulated, implying a proactive reinforcement of photosynthetic capacity to sustain energy supply under water deficit. Several transcripts related to uptake and transport of K+ (e.g., HAK4, KUP6, HAK16 and NHX1) and NO3− (e.g., NPF6;3, NPF2;9, NRT2;1 and NPF8;5) were significantly altered, implying accumulation of K+ and NO3− in leaves may be a strategy for buffalograss to resist drought. In the root, organic acids appear to be the main osmotic regulators. The genes involved in biosynthetic pathways of aspartate (e.g., GOT), glutamate (e.g., ALT), leucine (e.g., BCAT), salicylic acid (e.g., PTAL), citrate (e.g., CS) were significantly induced. This study provides new insights into the drought adaptation mechanisms of buffalograss, emphasizing the roles of sustained photosynthesis, inorganic ion homeostasis and organic acid accumulation.},
}

*Photosynthesis/physiology
*Osmotic Pressure
*Poaceae/physiology/genetics/metabolism
Drought Resistance
Multiomics
Adaptation, Physiological
Plant Leaves/metabolism/physiology
Chlorophyll/metabolism

@article {pmid41639730,
year = {2026},
author = {Hirsch, S and Ip, YCA and Brandão-Dias, PFP and Allan, EA and Kelly, R},
title = {Understanding practical barriers to the global adoption of environmental DNA (eDNA) methods, tools, and standards.},
journal = {BMC research notes},
volume = {19},
number = {1},
pages = {},
pmid = {41639730},
issn = {1756-0500},
mesh = {*DNA, Environmental/analysis/genetics ; *Environmental Monitoring/methods/standards ; Biodiversity ; Computational Biology/methods ; Conservation of Natural Resources/methods ; },
abstract = {OBJECTIVE: Environmental DNA (eDNA) is a rapidly emerging data source with the potential to support environmental monitoring and biodiversity conservation around the world. Current efforts to standardize eDNA methods and reporting are aimed at strengthening credibility and supporting adoption. In doing this, however, researchers must be mindful of diverse capacities and ecological contexts both regionally and around the world. The objective of our research is to understand how international standards for eDNA may support or hinder the uptake of eDNA methods and tools for conservation and biodiversity work. This was accomplished through two interactive workshops that brought together eDNA researchers and practitioners from around the world to surface broad and specific barriers to uptake of eDNA methods and tools. RESULTS: The most prevalent concern across all stages of the workflow was affordability. Workshop participants found the sampling and bioinformatics workflow stages to be the largest barriers. Participants also identified substantial hurdles: (1) the need for more clarity around eDNA methods and appropriate applications and protocols, (2) lack of access to suitable laboratories, (3) the need for different standards for diverse systems, species, and locations, and (4) the lack of trained experts in bioinformatics.},
}

*DNA, Environmental/analysis/genetics
*Environmental Monitoring/methods/standards
Biodiversity
Computational Biology/methods
Conservation of Natural Resources/methods

@article {pmid41656241,
year = {2026},
author = {Liu, X and Qiao, Y and He, W and Chen, X and Zhou, Q and Xu, Y and Yang, Y and Li, C and Yu, J and Luo, P},
title = {Integrated multi-omics profiling reveals effects of exogenous plant growth regulators on tobacco rhizosphere under Vulpia myuros rotation.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41656241},
issn = {1471-2229},
support = {110202101009 (XJ-01)//Key Science and Technology Project of China National Tobacco Corporation/ ; 110202201040 (XJ-11)//Key Science and Technology Project of China National Tobacco Corporation/ ; },
mesh = {*Rhizosphere ; *Nicotiana/microbiology/metabolism/drug effects ; Multiomics ; Soil Microbiology ; *Plant Growth Regulators/pharmacology/metabolism ; Microbiota/drug effects ; },
abstract = {BACKGROUND: Soil degradation poses a significant threat to agricultural sustainability. The integration of plant growth regulators (PGRs) with cover cropping systems represents a promising strategy for enhancing soil health and plant resilience. However, the synergistic effects of PGRs and cover crops on soil microbial communities and plant metabolism remain poorly understood. RESULTS: Exogenous PGRs under Vulpia myuros rotation were linked to distinct restructuring of tobacco rhizosphere microbiomes and metabolic networks. High-throughput sequencing of 16 S rRNA and ITS regions revealed that NaHS was associated with enhanced fungal diversity, promotion of beneficial saprotrophic taxa, and activation of phenylpropanoid and lignin metabolism. VB1-based treatments modulated bacterial communities, enriched cooperative Firmicutes–Proteobacteria clusters, and drove sphingolipid, coenzyme, and amino acid pathways, while multivitamins promoted synergistic microbial clusters and stimulated phenolic antioxidant and secondary metabolite production. Glutamate maintained overall microbial diversity but induced rare taxa, reshaping lipid and ceramide metabolism and activating neurotransmitter and amino acid pathways. Integrated metabolomics–microbiome analysis revealed treatment-specific microbial–metabolite interactions, including lipid remodeling, pollutant degradation, and phenolic activation, linking microbial shifts with metabolic reprogramming. Network analyses demonstrated that PGRs differentially modulate microbial co-occurrence, enhancing cooperation, centrality, or competitive partitioning, collectively optimizing rhizosphere ecological functions and plant stress adaptation. CONCLUSIONS: Our findings demonstrate that exogenous PGRs differentially reshape rhizosphere microbial communities and metabolic networks, enhancing plant stress adaptation in a cover crop system. These results provide a mechanistic basis for optimizing PGR-cover crop synergies to improve soil health and crop resilience.},
}

*Rhizosphere
*Nicotiana/microbiology/metabolism/drug effects
Multiomics
Soil Microbiology
*Plant Growth Regulators/pharmacology/metabolism
Microbiota/drug effects

@article {pmid41721912,
year = {2026},
author = {Mertens, ECA and Asscher, JJ and Sergiou, CS and van Gelder, JL},
title = {Bringing Technology to Justice-Involved Youth.},
journal = {Research on child and adolescent psychopathology},
volume = {54},
number = {2},
pages = {},
pmid = {41721912},
issn = {2730-7174},
mesh = {Humans ; Adolescent ; *Juvenile Delinquency/rehabilitation ; Digital Health ; *Virtual Reality ; },
abstract = {Conventional assessment and treatment approaches targeting justice-involved youth have typically yielded low engagement and modest long-term impact on recidivism and psychosocial functioning. Technologies such as virtual reality, smartphone applications, and wearable devices, offer promising opportunities to address such limitations by providing scalable, engaging and ecologically valid approaches that align well with the often complex needs of this population. The contributions in the special issue aim to showcase some of the potential of these technologies. The special issue originated from a 5-day international Lorentz workshop that brought together researchers and professionals working in clinical practice to explore opportunities, needs, and barriers related to technology implementation in this context. The included contributions comprise empirical case studies illustrating efficiency gains through technological support of existing practices; papers detailing innovative methods that leverage unique capabilities of specific technologies, such as enhanced accessibility and immersive experiences; state-of-the-art reviews; and a viewpoint paper addressing ethical considerations. Collectively, the contributions highlight the promise of technology as well as the need for methodologically robust research to ensure effective and ethical implementation.},
}

Humans
Adolescent
*Juvenile Delinquency/rehabilitation
Digital Health
*Virtual Reality

@article {pmid41742154,
year = {2026},
author = {Ullah, H and Selvarajan, R and Lau Vetter, MCY},
title = {Genome-mining revealed biosurfactant production capacity and gene co-occurrence patterns in diverse ecosystems.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {41742154},
issn = {1475-2859},
support = {Scholarship//Alliance of International Science Organizations/ ; IDSSE-SJBS-202501//Institute of Deep-sea Science and Engineering/ ; Y970011001//Knowledge Innovation Program of Chinese Academy of Sciences/ ; E2500001//Hainan Provincial Talent Development Bureau/ ; },
mesh = {*Biosurfactants/metabolism ; *Ecosystem ; Data Mining ; *Genome, Bacterial ; *Bacteria/genetics/metabolism/classification ; Glycolipids/biosynthesis ; Fungi/genetics/metabolism ; Genomics ; *Surface-Active Agents/metabolism ; },
abstract = {Biosurfactants produced by microorganisms play essential roles in ecosystem function and hold significance promise for biotechnological applications. However, their diversity and distribution remain poorly depicted due to the limitations of culture-based approaches. In this study, we conducted a large-scale genomic data mining of 142,135 microbial genomes of putative biosurfactant-producing taxa, spanning 21 distinct ecosystems, to systematically profile gene association with 10 major biosurfactant classes. Using a list of 18 key functional genes, we mapped their taxonomic and ecological distribution and analyzed patterns of gene co-occurrence. We found that rhamnolipid biosynthesis genes are nearly ubiquitous across microbial lineages, reflecting their fundamental role in microbial adaptation. In contrast, emulsan and serrawettin pathways are more restricted to plant-associated and fungal ecosystems. The highest diversity of biosurfactant-related genes was found in genomes recovered from nutrient-rich habitats, including plant-associated, algal, and wastewater ecosystems. Co-occurrence network analysis revealed two distinct organizational strategies: a rare, conserved core cluster of genes associated with fengycin, surfactin, iturin lichenysin and plipastatin production, and a widespread, modular periphery linked to rhamnolipid, emulsan, and serrawettin W1 pathways, that are likely driven by the need to adapt to environmental complexity. Notably, we identified previously unreported genomes with biosurfactant production potential, significantly expanding the known biodiversity and ecological range of potential producers. Our findings establish biosurfactant production as a key microbial trait shaped by habitat, with broad implications for microbial ecology, ecosystem monitoring and sustainable biotechnology. This work provides comprehensive genomic resource for biosurfactant research, laying the foundation for targeted bioprospecting and integrative functional studies.},
}

*Biosurfactants/metabolism
*Ecosystem
Data Mining
*Genome, Bacterial
*Bacteria/genetics/metabolism/classification
Glycolipids/biosynthesis
Fungi/genetics/metabolism
Genomics
*Surface-Active Agents/metabolism

@article {pmid41866514,
year = {2026},
author = {Mieres-Castro, D and Maldonado, C and Mora-Poblete, F},
title = {Multi-omics prediction of terpene constituents and phenolic traits in Eucalyptus globulus using Bayesian models and tree-based machine learning.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41866514},
issn = {1471-2229},
support = {3220576//ANID FONDECYT postdoctoral/ ; 11240273//ANID FONDECYT/ ; 1231681//ANID FONDECYT/ ; },
mesh = {*Eucalyptus/genetics/chemistry/metabolism ; Bayes Theorem ; *Terpenes/metabolism/chemistry ; *Machine Learning ; *Phenols/metabolism/chemistry ; Multiomics ; Polymorphism, Single Nucleotide ; Oils, Volatile ; },
abstract = {BACKGROUND: Terpenes and phenolic compounds are multifunctional plant metabolites that contribute to defense, signaling, and ecological interactions, while supporting industrial applications. Here, we implemented an integrative multi-omics framework to dissect the genetic and metabolic architecture of biobased compound production in a Eucalyptus globulus breeding population, a tree species of global economic importance. The dataset comprised 14,442 high-confidence SNPs genotyped using the EUChip60K array and 3,279 haplotype blocks, complemented by phenomic datasets derived from near-infrared (NIR) spectral absorbance (~ 900–2,500 nm) and pigment-related indices (chlorophyll, anthocyanins, flavonols, and nitrogen balance index). RESULTS: Gas chromatography-mass spectrometry (GC–MS) and ultra-high-performance liquid chromatography-quadrupole-time-of-flight tandem MS (UHPLC–QqTOF–MS2) revealed substantial inter-individual variation: essential oils were dominated by 1,8-cineole (42.70% ± 7.19%) and α-pinene (38.02% ± 5.20%), while phenolic extracts were enriched in phloroglucinol derivatives (92.67% ± 1.59%), notably the macrocarpal C isomer (12.98% ± 1.48%). Total additive heritability integrating SNP- and pedigree-based effects was high for MeOH extract yield (h2 = 0.721), total phenolics (h2 = 0.646), α-terpineol (h2 = 0.718), and 1,8-cineole (h2 = 0.658), indicating strong genetic control. Predictive modeling revealed that haplotype-based Bayesian approaches outperformed SNP- and phenomic-based models, with the highest accuracies for α-terpineol (prediction accuracy = 0.717), α-pinene (prediction accuracy = 0.554), and methanolic extract yield (prediction accuracy = 0.624). Feature selection identified pleiotropic markers (e.g., SNP12778, HAP205, HAP272, NIR2429) co-localized with genes involved in photosynthesis, signaling, and metabolic regulation. CONCLUSION: These findings lay the foundation for omics-assisted E. globulus breeding aimed at generating elite genotypes for large-scale production of high-value bioactive compounds with practical applications in health, agriculture, and bioenergy.},
}

*Eucalyptus/genetics/chemistry/metabolism
Bayes Theorem
*Terpenes/metabolism/chemistry
*Machine Learning
*Phenols/metabolism/chemistry
Multiomics
Polymorphism, Single Nucleotide
Oils, Volatile

@article {pmid41896359,
year = {2026},
author = {Placide, A and Kelly, M and Tartarotti, B},
title = {The de novo transcriptome of the freshwater copepod Cyclops abyssorum tatricus reveals high-elevation adaptation.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41896359},
issn = {2045-2322},
support = {10.55776/P35886//Austrian Science Fund/ ; },
mesh = {Animals ; *Copepoda/genetics/physiology ; *Transcriptome ; Gene Expression Profiling ; *Adaptation, Physiological/genetics ; Fresh Water ; Molecular Sequence Annotation ; Lakes ; Gene Ontology ; *Acclimatization/genetics ; Ecosystem ; },
abstract = {Copepods, small aquatic crustaceans, are one of the most abundant zooplankton in the world. These animals play a critical ecological role in aquatic ecosystems such as oceans, streams, or, as in this study, alpine lakes. In these ecosystems, copepods have adapted to stressful and dynamic environments, a process which can be investigated via comparative transcriptomics. An assembled transcriptome is a pre-requisite to applying transcriptomic tools in physiological research, but there are few transcriptome assemblies available for copepods. To address this gap, we assembled a de novo transcriptome of Cyclops abyssorum tatricus by merging Pacific Bioscience long reads from copepods collected in two lakes at two different time points. The final assembly consisted of 52,521 contigs with a BUSCO score of 80.7%. We annotated a total of 26,255 (49.99%) protein sequences using the eggNOG database. Gene ontology analyses revealed that most gene annotations were involved in cellular processes and signaling (34.61%). Comparisons with two other copepod species showed that the transcriptome assembly of C. abyssorum tatricus is enriched for cold acclimation genes, consistent with its long-term adaptation to cold water environments. This de novo transcriptome will enable comparative transcriptomic studies in this species, allowing us to investigate physiological adaptations to alpine environments.},
}

Animals
*Copepoda/genetics/physiology
*Transcriptome
Gene Expression Profiling
*Adaptation, Physiological/genetics
Fresh Water
Molecular Sequence Annotation
Lakes
Gene Ontology
*Acclimatization/genetics
Ecosystem

@article {pmid41913152,
year = {2026},
author = {Lysaker, DT and Struckhoff, ED and Chakravarti, I and Bognanni, OJ and Machtinger, ET},
title = {Development of the vector education, communication, and training online resource (VECTOR) library: a vector-borne disease education database.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {41913152},
issn = {1471-2458},
support = {NU50CK000637/CC/CDC HHS/United States ; },
mesh = {Humans ; United States ; Animals ; *Vector Borne Diseases/prevention & control ; *Internet ; *Databases, Factual ; *Health Education ; Information Dissemination ; *Disease Vectors ; },
abstract = {BACKGROUND: The emergence of invasive arthropod vectors and the rising prevalence of vector-borne diseases (VBDs) affecting humans and domestic animals have spurred a rapid increase in educational materials. In the United States, the Cooperative Extension System (Extension) can play a role in developing and sharing these resources. MAIN TEXT: Extension has historically served rural and agricultural audiences but has expanded to provide information to a variety of other communities throughout the states it serves. One topic that Extension has begun to expand its focus on in certain areas of the U.S. is VBDs. Due to the way each Extension service may focus on and address its own set of issues and topics, regional gaps in material and a lack of information sharing between institutions may arise. We created the Vector Education, Communication, and Training Online Resource (VECTOR) Library as a repository of educational materials related to vectors and VBDs, developed by Extension offices from across the United States, to address issues of knowledge sharing and access. We hope to continue curating VBD content from Extension offices, as well as to add educational materials created by other non-Extension university departments and each state’s state public health department. CONCLUSION: This database offers a single platform for accessing educational VBD materials from Extension offices nationwide.},
}

Humans
United States
Animals
*Vector Borne Diseases/prevention & control
*Internet
*Databases, Factual
*Health Education
Information Dissemination
*Disease Vectors

@article {pmid41922959,
year = {2026},
author = {Sun, Y and Zhang, F and Yan, S and Kong, X and Wang, H and Shang, J and Liu, JX},
title = {DHGCMDA: a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41922959},
issn = {1471-2105},
support = {62472250//National Natural Science Foundation of China/ ; },
mesh = {*MicroRNAs/genetics ; Humans ; *Computational Biology/methods ; Graph Neural Networks ; Algorithms ; },
abstract = {BACKGROUND: Accumulating evidence demonstrates that microRNA (miRNA) dysregulation drives the pathogenesis of diverse human diseases via intricate, context-dependent molecular mechanisms. Hence, prediction of miRNA-disease association types is a critical prerequisite for dissecting functional roles of miRNAs in disease initiation and progression. Although computational methods offer cost-effective, time-efficient alternatives to wet-lab experiments for miRNA-disease association type prediction, most of them are hampered by three key limitations: excessive reliance on association-derived similarity metrics gives rise to quantification bias, traditional pairwise graph architectures inadequately capture high-order biological interactions, and existing representation learning strategies fail to generate consistent embeddings across heterogeneous views and modalities. RESULTS: To address these issues, this study presents DHGCMDA, a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction. Specifically, dual-view hypergraphs are first constructed based on heterogeneous similarity data to avoid excessive reliance on association-derived similarity metrics. A hypergraph convolutional network is then employed to capture high-order topological relationships between miRNAs and diseases, with its convolution cooperatively integrated with contrastive learning, intra-modality for cross-view consistency and cross-modality for embedding space alignment, to enhance feature representation quality. Finally, an attention-guided adaptive view fusion strategy dynamically weights and integrates distinct view representations, and type-aware message passing via heterogeneous graph Transformer simultaneously enables prediction of association presence and functional types. 5-fold cross-validation on HMDD v2.0 and v3.2 datasets demonstrates that DHGCMDA outperforms several state-of-the-art methods. Furthermore, case studies on breast neoplasms and hepatocellular carcinoma reveal that most predicted association types are corroborated by published literature, thereby validating the efficacy of DHGCMDA in miRNA-disease association type prediction. CONCLUSIONS: DHGCMDA exhibits robust discriminative power and generalization capability, providing a reliable computational alternative for miRNA-disease association type prediction. The source code is publicly available at https://github.com/CDMBlab/DHGCMDA .},
}

*MicroRNAs/genetics
Humans
*Computational Biology/methods
Graph Neural Networks
Algorithms

@article {pmid41942920,
year = {2026},
author = {Barjij, I and Lamsyah, O and Kdadri, S and Lkhoyaali, S and Najem, S and Naciri, S and Inrhaouen, H and Elghissassi, I and Boutayeb, S and Mrabti, H and Errihani, H},
title = {Spatial and temporal intratumoral heterogeneity in breast cancer: a systematic and conceptual review of single-cell and spatial omics studies.},
journal = {BMC cancer},
volume = {26},
number = {1},
pages = {},
pmid = {41942920},
issn = {1471-2407},
mesh = {Humans ; Female ; *Breast Neoplasms/genetics/pathology ; *Single-Cell Analysis/methods ; Multiomics ; Tumor Microenvironment/genetics ; Spatial Transcriptomics ; Single-Cell Gene Expression Analysis ; Genetic Heterogeneity ; },
abstract = {BACKGROUND: Spatial and temporal intratumoral heterogeneity (ITH) remains a major challenge in the diagnosis, prognosis, and treatment of breast cancer. Recent advances in single-cell and spatial omics technologies have enabled unprecedented resolution of subclonal architectures, evolutionary trajectories, and microenvironmental interactions. This systematic and conceptual review aimed to synthesize and integrate current evidence on spatiotemporal ITH in human breast cancer, bridging empirical data with mechanistic interpretation through high-resolution profiling platforms. METHODS: We conducted a systematic review following PRISMA 2020 guidelines, searching three databases (PubMed, Scopus, and Web of Science) and screening 1037 records published between January 2018 and May 2025. 19 original studies were included based on predefined eligibility criteria targeting single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, or multi-omics approaches applied to human breast tumor samples. Data extraction focused on study design, technologies used, subclonal dynamics, spatial/temporal resolution, tumor–immune interactions, and risk of bias. RESULTS: The included studies analyzed over 400,000 single cells from diverse breast cancer subtypes, with a predominance of triple-negative breast cancer. Subclonal plasticity was a recurrent feature, often characterized by EMT (epithelial-to-mesenchymal transition) signatures, cell-cycle heterogeneity, and immune evasion. Spatial analyses revealed discrete ecological niches shaped by immune exclusion and stromal patterning, while temporal assessments uncovered therapy-driven clonal selection, metabolic reprogramming, and enhancer remodeling. Interclonal and tumor–immune communication were consistently associated with poor prognosis or therapeutic resistance. Most studies were judged to have low or moderate risk of bias, with transparent reporting and accessible data pipelines. CONCLUSIONS: Single-cell and spatial omics studies provide critical insights into the evolutionary ecology of breast cancer. By conceptually integrating spatial, temporal, and microenvironmental dimensions, this review highlights convergent evolutionary programs underlying tumor aggressiveness and resistance. Spatiotemporal ITH is a key driver of disease progression, and its systematic characterization could inform biomarker development, personalized therapies, and future multi-modal diagnostics. Continued integration of spatial, temporal, and functional data is essential to move from descriptive maps to clinically actionable frameworks.},
}

Humans
Female
*Breast Neoplasms/genetics/pathology
*Single-Cell Analysis/methods
Multiomics
Tumor Microenvironment/genetics
Spatial Transcriptomics
Single-Cell Gene Expression Analysis
Genetic Heterogeneity

@article {pmid41945111,
year = {2026},
author = {Lai, Z and Zhang, B and Fu, Z and Li, R and Qian, Y and Zhang, Y and Xu, P and Du, Y},
title = {Research advances on Cordyceps sinensis and its components in relation to omics biomarkers for the neurological disorders.},
journal = {Die Naturwissenschaften},
volume = {113},
number = {3},
pages = {},
pmid = {41945111},
issn = {1432-1904},
support = {2026ZL0010//Zhejiang Traditional Chinese Medicine Science and Technology Program of China/ ; 82202605//National Natural Science Foundation of China/ ; 2023, DU YAOQIANG//Zhejiang Provincial Special Support Program for Cultivation of High-Level Innovative Health Talents of China/ ; },
mesh = {*Cordyceps/chemistry ; Animals ; *Nervous System Diseases/drug therapy ; Humans ; Biomarkers/analysis ; Multiomics ; Neuroprotective Agents/pharmacology ; },
abstract = {Cordyceps is a traditional medicinal fungus belonging to the species Ophiocordyceps sinensis. It grows in the alpine ecological zone of the Tibetan Plateau and exhibits dual characteristics of both insects and fungi. The primary species include Cordyceps sinensis and Cordyceps militaris. Rich in bioactive components such as cordycepin, polysaccharides, adenosine, and peptides, cordyceps demonstrates broad applications in immune regulation, anti-tumor activity, anti-inflammatory, and neuroprotection. Cordyceps sinensis and its components show great therapeutic potential in neurological diseases such as epilepsy, Alzheimer’s disease and Parkinson’s disease through multi-level and multi-target actions However, current research faces challenges including unclear mechanisms of action and insufficient clinical translation. In this review, we analyze the molecular mechanisms underlying cordyceps’ neuroprotective effects, including the regulating of apoptosis, improvement of mitochondrial function, and promoting of nerve repair. Utilizing network pharmacology, we explore the multi-targeted actions of cordyceps and predict the key pathways. Further we summarize the research progress in the integrated multi-omics analyses (genomics, transcriptomics, proteomics and metabolomics), to reveal the synergistic roles of cordyceps components in treating neurological disorders and identify potential molecular biomarkers. Additionally, we highlight the findings from preclinical experiments and animal models on cordyceps-based drugs, discussing their advantages and challenges for clinical application. Future studies should prioritize systematic exploration of standardized drug development, advanced multi-omics integration, and rigorous clinical trials. This will provide a more robust scientific foundation and practical guidance for the treatment of neurological diseases with cordyceps.},
}

*Cordyceps/chemistry
Animals
*Nervous System Diseases/drug therapy
Humans
Biomarkers/analysis
Multiomics
Neuroprotective Agents/pharmacology

@article {pmid41951704,
year = {2026},
author = {Rocchi, L and Mattioli, S and Collin, A and Bonnefous, C and Warin, L and Tuyttens, F and Thobe, P and Re, M and Castellini, C},
title = {First evaluation framework based on the one welfare concept in extensive broiler rearing systems.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41951704},
issn = {2045-2322},
support = {N˚816172//European Commission/ ; },
mesh = {Animals ; *Animal Welfare ; *Chickens/growth & development ; *Animal Husbandry/methods ; Humans ; Decision Support Techniques ; Environment ; },
abstract = {The One Welfare concept has emerged to counter the traditional separation of human well-being, environmental sustainability, and animal welfare, emphasizing their interdependence within specific ecological and socio-technical contexts. Despite its promise, the practical operationalization of One Welfare as an evaluation framework remains limited. This study proposes and tests an operational One Welfare approach (OWA) for extensive broiler rearing systems (ERS), explicitly promoting direct and indirect links between animal and human welfare and situating them within the environmental performance. Although ERS constitute a minor share of EU broiler output (≈ 5%), interest in and adoption of ERS have grown markedly over the past two decades, underscoring the need for assessment tools that capture their broader contributions. Conventional evaluation methodologies, designed around intensive systems, tend to prioritize yield, short-term efficiency, and market indicators, and may therefore underrepresent the ecological, social, and welfare advantages achievable in diversified, outdoor systems. We implemented a multicriteria decision analysis (MCDA) using the One Welfare Approach to synthesize indicators across the animal welfare, environmental, economic, and social pillars in a broiler case study. The framework proved feasible despite data constraints (limited availability and some invariant parameters typical of ERS, and its outputs aligned with published evidence on slow-growing genotypes in outdoor systems, supporting construct validity. The Key results showed that: (1) Environmental enrichment with olive trees improved OWA performance: all enriched options outperformed their non-enriched counterparts, showing that tree/shrub cover increases outdoor use, reduces predation and fear, and improves integument condition in free-range birds. (2) Under enrichment, RJ_E ranked first overall. Flow decomposition indicated that CB_E exhibited higher positive flow (Phi+), but RJ_E had a lower negative flow (Phi[-]); given the non-compensatory OWA stance, suppressing negatives proved more decisive than marginal gains in positives. A weight-sensitivity check showed ranking stability across pillars, with limited shifts confined to the Economic pillar, where criterion values were tightly clustered. Taken together, these findings indicate that One Welfare assessment can capture trade-offs and synergies that conventional metrics overlook, offering actionable guidance for extensive organic broiler systems. The approach is compatible with prevailing outcome-based welfare assessment practice. It can be simplified into a transparent index for on-farm self-assessment and external communication, provided that its governance and evidence base meet current best practice expectations.},
}

Animals
*Animal Welfare
*Chickens/growth & development
*Animal Husbandry/methods
Humans
Decision Support Techniques
Environment

@article {pmid41954832,
year = {2026},
author = {Kong, X and Sun, Y and Shang, J and Zhang, X and Tang, X and Wang, H and Qiu, D and Zhang, Y and Liu, JX},
title = {MsDGCN: multi-scale diffusion graph convolutional network for the prediction of drug-disease association.},
journal = {Journal of computer-aided molecular design},
volume = {40},
number = {1},
pages = {},
pmid = {41954832},
issn = {1573-4951},
support = {62472250//National Natural Science Foundation of China/ ; },
mesh = {Graph Neural Networks ; Humans ; *Drug Repositioning/methods ; *Computational Biology/methods ; Boosting Machine Learning Algorithms ; },
abstract = {Drug-disease association prediction is crucial for accelerating drug repurposing, yet existing computational models largely focus on integrating biological attributes while neglecting topological regulatory patterns within heterogeneous biological networks. To address this, we propose MsDGCN, a novel multi-scale diffusion graph convolutional network. The model is built upon two key innovations: a multi-scale architecture that captures complex topological signals through meta-path guided diffusion and cross-path attention mechanisms, and a dedicated hard negative mining strategy that selects biologically plausible confounders to sharpen the decision boundary. To handle severe data imbalance, an XGBoost classifier with dynamic class weighting is integrated to model nonlinear feature interactions. Extensive ten-fold cross-validation demonstrates that MsDGCN significantly outperforms state-of-the-art baselines across key metrics, confirming its capability to effectively leverage network topology for improved drug-disease association prediction. MsDGCN provides a robust and generalizable framework for predicting drug-disease associations. Code and data are available at: https://github.com/CDMBlab/MsDGCN.},
}

Graph Neural Networks
Humans
*Drug Repositioning/methods
*Computational Biology/methods
Boosting Machine Learning Algorithms

@article {pmid41992084,
year = {2026},
author = {Lu, W and Dong, Y and Dong, Z and Xie, Y and Zhang, H and Han, Y and Zhang, D and Liu, Y and Weng, Q},
title = {Multi-omics analysis reveals seasonal variation in ovarian lipid metabolism associated with vitamin D3 in the muskrats.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41992084},
issn = {1471-2164},
support = {202410022032//National Undergraduate Training Programs for Innovation and Entrepreneurship/ ; NO. BLX202219//Fundamental Research Funds for the Central Universities/ ; No. BLRC 2023C02//5·5 Engineering Research & Innovation Team Project of Beijing Forestry University/ ; 7232240//Beijing Municipal Natural Science Foundation/ ; },
mesh = {Animals ; Female ; *Lipid Metabolism ; *Seasons ; *Arvicolinae/metabolism/genetics ; *Cholecalciferol/metabolism/blood ; *Ovary/metabolism ; Multiomics ; Receptors, Calcitriol/metabolism/genetics ; Metabolomics ; Gene Expression Profiling ; Transcriptome ; },
abstract = {BACKGROUND: Seasonal reproduction is critical for animals adapting to environmental changes, yet the mechanisms driving these shifts remain incompletely understood. Gut microbiota are increasingly recognized as important modulators of reproductive health, but their roles in seasonal breeding species remain unclear. RESULTS: In the muskrat (Ondatra zibethicus), a well-established seasonal breeder, morphological and histological analyses revealed enhanced follicular development during the breeding season (BS). Subsequent integrated ovarian transcriptomics and metabolomics identified that lipid metabolic processes were significantly enriched during the BS. This was validated by the increased expression of key lipid metabolic enzymes (e.g., DGAT1, CPT1A) and elevated triglyceride content in BS ovaries. Systemically, we found that serum vitamin D3 (VD3) and ovarian vitamin D receptor (VDR) expression were significantly elevated during BS. In contrast, analysis of upstream factors during the non-breeding season (NBS) showed a significant enrichment of gut Lactobacillus and a concurrent elevation of plasma lithocholic acid (LCA), a known VDR agonist. Correlation analyses confirmed that both Lactobacillus and LCA were inversely associated with serum VD3 levels. Critically, in vitro experiments demonstrated that VD3 treatment enhanced the expression of key lipid metabolism genes in muskrat granulosa cells. CONCLUSIONS: Collectively, our findings provide evidence for a gut microbiota-VD3-ovary axis that modulates seasonal ovarian lipid metabolism and function. This axis represents a new layer of host-microbiota interaction in reproductive physiology.},
}

Animals
Female
*Lipid Metabolism
*Seasons
*Arvicolinae/metabolism/genetics
*Cholecalciferol/metabolism/blood
*Ovary/metabolism
Multiomics
Receptors, Calcitriol/metabolism/genetics
Metabolomics
Gene Expression Profiling
Transcriptome

@article {pmid41997985,
year = {2026},
author = {Orozco, LR and Weaver, AE and Klee, DJ and Pauli, CS and Grassa, CJ and Vergara, D and Baptista, A and White, K and Emery, BF and Castro, NRM and Garuda, S and Guerrero, RF and Keegan, BC and Kane, NC},
title = {Network ontology transcript annotation identifies genetic signals underlying sex determination.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41997985},
issn = {2045-2322},
mesh = {*Gene Regulatory Networks ; *Sex Determination Processes/genetics ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Flowers/genetics ; Transcriptome ; Gene Ontology ; Molecular Sequence Annotation ; Signal Transduction ; },
abstract = {Cannabis sativa L. (marijuana, hemp, cannabis) is an angiosperm species currently evolving sex chromosomes. Genetic mechanisms, primarily an XY chromosome system, dictate cannabis sex expression in dioecious populations. However, sexual expression is also governed by the interplay of hormone regulatory gene networks, influenced by both genetic and environmental factors. Within the species, some populations exhibit dioecy, monoecy, or a gradient of both. Dioecious individuals produce exclusively male or female flowers, while monoecious plants bear both male and female flowers. Remarkably, through interruption of phytohormone signal transduction via abiotic stressors, genetically male or female cannabis are able to produce flowers of the opposite sex. Previous transcriptomic analysis have identified genes associated with masculinization through the application of phytohormone signal disruption using silver thiosulfate treatment. We analyzed transcriptomic data from cannabis treated with colloidal silver to similarly induce masculinization. Using Nota (Network ontology transcript annotation), a multilayer network analysis (Random-Walk-with-Restart) tool, we identified candidate genes involved in sex-determination. Nota and a companion program Jack facilitate multi-layer network analyses, enabling discovery and annotation of gene-trait associations. Our findings highlight Nota’s robust application to enrich the genetic architecture of complex traits, particularly in non-model systems like cannabis, and complex traits such as sex determination. Our analyses identified genes associated with cell wall morphogenesis and embryogenic tissue homeostasis, indicating that silver ion treatment perturbs phytohormone signal transduction through metal ion imbalance. In this reproductive strategy, cannabis is able to make use of its widely investigated sex-determining genetic architecture to navigate transient changes in co-expression and cross-cellular signaling driving embryogenic cell wall re-patterning.},
}

*Gene Regulatory Networks
*Sex Determination Processes/genetics
Gene Expression Regulation, Plant
Gene Expression Profiling
Flowers/genetics
Transcriptome
Gene Ontology
Molecular Sequence Annotation
Signal Transduction

@article {pmid41998442,
year = {2026},
author = {Paveen, P and Ryota, K and Kumar, V},
title = {Omics-informed insights into biochar-Trichoderma interactions in plant-soil systems: mechanisms of defense and context-dependent responses.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998442},
issn = {1573-0972},
mesh = {*Trichoderma/physiology/metabolism ; *Plants/microbiology/metabolism/immunology ; Multiomics ; Proteomics ; Soil Microbiology ; *Charcoal ; Metabolomics ; Signal Transduction ; Soil/chemistry ; Cyclopentanes/metabolism ; Oxylipins/metabolism ; Salicylic Acid/metabolism ; },
abstract = {The combined application of biochar and Trichoderma spp. represents a promising strategy for enhancing plant resilience and soil health; however, the molecular mechanisms underlying their synergistic interactions remain poorly understood and inadequately integrated. This review critically synthesizes evidence from transcriptomic, proteomic, metabolomic, and microbiome analyses to elucidate how biochar-Trichoderma interactions modulate plant defense signaling pathways and stress adaptation responses. Transcriptomic analyses reveal context-dependent activation of the jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signaling pathways. Correspondingly, proteomic and metabolomic datasets demonstrate variable yet recurrent upregulation of pathogenesis-related (PR) proteins, reactive oxygen species (ROS)-scavenging enzymes, and phenylpropanoid-derived metabolites. Notably, accumulating evidence suggests that these molecular responses are highly context-dependent, varying substantially with soil type, biochar physicochemical characteristics, and Trichoderma strain specificity. We critically examine major methodological limitations in existing omics investigations, including inadequate reproducibility under field conditions and insufficient integration of molecular and ecological datasets. Finally, we propose a systems biology framework for designing functionally optimized biochar–microbe formulations and identify research priorities for translating insights into agronomically robust and field-deployable technologies.},
}

*Trichoderma/physiology/metabolism
*Plants/microbiology/metabolism/immunology
Multiomics
Proteomics
Soil Microbiology
*Charcoal
Metabolomics
Signal Transduction
Soil/chemistry
Cyclopentanes/metabolism
Oxylipins/metabolism
Salicylic Acid/metabolism

@article {pmid42310879,
year = {2026},
author = {Wu, B and Pan, Y and Harefa, AMS and Zhou, H and Li, J and Wang, Y and Hansen, PJ and Lundholm, N and Altenburger, A and Li, Q},
title = {Decoding a Multigenomic Symphony: Divergent Evolutionary Tempos Across the Four Genomic Compartments of Teleaulax Cryptophytes.},
journal = {Molecular ecology},
volume = {35},
number = {12},
pages = {e70441},
doi = {10.1111/mec.70441},
pmid = {42310879},
issn = {1365-294X},
support = {SKJC-2024-01-002//Sanya Yazhou Bay Science and Technology City/ ; 32370666//National Natural Science Foundation of China/ ; 4181-00484//Danmarks Frie Forskningsfond/ ; SYSPG20241211173844007//Shenzhen Science and Technology Program/ ; },
mesh = {*Cryptophyta/genetics ; *Evolution, Molecular ; Cell Nucleus/genetics ; *Symbiosis/genetics ; Genome, Plastid/genetics ; *Genome, Plant ; Genome, Mitochondrial ; Phylogeny ; Plastids/genetics ; Biological Evolution ; },
abstract = {Secondary endosymbiosis drives eukaryotic diversification by integrating genetic compartments from disparate lineages, yet how the host and endosymbiont genomes co-evolve over deep time remains poorly understood. Cryptophytes provide a compelling model to dissect this integration, as they uniquely retain four distinct genomes within a single cell: the host nucleus and mitochondrion, alongside a red algal-derived plastid and its relict nucleus (nucleomorph). Here, we investigate the evolutionary and regulatory dynamics of these four coexisting genomes in two ecologically important cryptophytes, Teleaulax amphioxeia and Teleaulax acuta. We reveal a striking decoupling of evolutionary tempos across these genomic compartments. Plastid genomes exhibit structural and functional stasis, while mitochondrial genomes, despite also maintaining high synteny, show faster sequence evolution and mobile element invasion. Nucleomorph genomes evolves even more rapidly, but their gene expression is rigid, with regulatory flexibility limited to a small, conserved set of plastid-supporting genes. Intriguingly, Teleaulax host nuclear genomes have undergone massive expansion, likely driven by ancient whole-genome duplication that might explain their greatest divergence among the four genomic compartments. This divergence is further characterised by differential expansion of gene families (e.g., PHYB-like photoreceptors and motor-related proteins) potentially linked to ecological adaptation. Diel transcriptomic analyses highlight conserved core metabolic responses across both species, but also unveil lineage-specific adaptations, such as enhanced circadian regulation in T. acuta associated with PHYB-like gene expansion. Overall, our findings uncover a constraint gradient from plastid stasis to high evolutionary flexibility toward nucleus, highlighting how secondary plastid-bearing cells achieve a balance between long-term stability and adaptive innovation.},
}

*Cryptophyta/genetics
*Evolution, Molecular
Cell Nucleus/genetics
*Symbiosis/genetics
Genome, Plastid/genetics
*Genome, Plant
Genome, Mitochondrial
Phylogeny
Plastids/genetics
Biological Evolution

@article {pmid42311787,
year = {2026},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Regal Piercer, Pammene regiana (Zeller, 1849) (Lepidoptera: Tortricidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {232},
pmid = {42311787},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Pammene regiana (Regal Piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 863.59 megabases. Most of the assembly (99.44%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.5 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genome assemblies for eukaryotic species found in Britain and Ireland.},
}

@article {pmid40646445,
year = {2025},
author = {Duan, G and Liang, C and Su, J and Liang, Y and Li, W and Zhang, J and Zhang, Y},
title = {Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {903},
pmid = {40646445},
issn = {1471-2229},
support = {ZYYD2022C02//Central Guidance on Local Science and Technology Development Fund/ ; 32360095//National Natural Science Foundation of China/ ; },
mesh = {*Cicer/genetics/metabolism/physiology ; *Salt Stress/genetics ; *Transcriptome ; Metabolomics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Metabolome ; Salt Tolerance/genetics ; Multiomics ; Stress, Physiological ; },
abstract = {BACKGROUND: Salinity, a major abiotic stress, significantly impairs crop productivity by inducing osmotic, ionic, and secondary stresses that disrupt metabolic processes. Chickpea (Cicer arietinum L.), a diploid annual legume of the Fabaceae family, is one of the major pulse crops cultivated by farmers with limited resources. While previous studies have explored salt tolerance in chickpeas, this study provides a comprehensive multi-omics perspective. Exploring the mechanism of chickpea adaptation to the saline environment can effectively supplement the problem of single source of plant protein. RESULTS: The present study analyzed the transcriptomic and metabolomic profiles of two distinct chickpea varieties, DY3 and DY1, with contrasting salinity tolerance capacities. The salinity tolerance of DY3 was associated with greater biomass, higher antioxidant enzyme activity, and higher photosynthetic efficiency. Transcriptomic analysis revealed that the genes induced in DY3 under salinity stress were associated with ion homeostasis, antioxidant defense system, and plant hormone signaling. Metabolomics analysis revealed significant enrichment of components of diverse secondary metabolites pathways, as well as carbohydrate metabolism. Integrated multi-omics analysis highlighted the anthocyanin biosynthesis pathway, functioning within the broader flavonoid metabolic network, as a key regulator of salt tolerance in the chickpea. Subsequent, RT-qPCR confirmed the upregulation of key genes associated with anthocyanin metabolism. CONCLUSIONS: These findings reveal the key regulatory role of the flavonoid pathway in salt tolerance of chickpeas, offering insights for breeding improved varieties.},
}

*Cicer/genetics/metabolism/physiology
*Salt Stress/genetics
*Transcriptome
Metabolomics
Gene Expression Profiling
Gene Expression Regulation, Plant
*Metabolome
Salt Tolerance/genetics
Multiomics
Stress, Physiological

@article {pmid40830831,
year = {2025},
author = {Jiang, W and Liu, X and Li, W and Yang, J and Li, P and Xie, M and Zhou, G},
title = {Dual-omics analysis reveals B vitamin regulation and metabolism in Areca Catechu inflorescence.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {757},
pmid = {40830831},
issn = {1471-2164},
support = {Hnky2024-23//the Education Department of Hainan Province/ ; HSZK-KYQD-202421//the Hainan Normal University Talent Research Start-up Fund Project Funding/ ; },
mesh = {*Metabolomics ; *Vitamin B Complex/metabolism ; *Areca/metabolism/genetics ; Gene Expression Regulation, Plant ; *Inflorescence/metabolism/genetics ; Gene Expression Profiling ; Multiomics ; Transcriptome ; Metabolome ; Plant Proteins/genetics/metabolism ; },
abstract = {Areca catechu flowers are an important component of traditional Chinese medicine for the treatment of various diseases. Studies on its secondary metabolites have largely focused on pyridine alkaloids yet a high-resolution metabolic profile of another important nutrient and coenzyme, the B vitamins, remains lacking. Here, we analyzed the levels of eight B vitamins in the inflorescence of A. catechu by targeted metabolomics. Our results showed that pantothenic acid and riboflavin were the predominant B vitamins, and that different B vitamins exhibited tissue-specific expression patterns within the various parts of the inflorescence. Furthermore, panoramic expression profiles of genes related to B vitamin biosynthesis in the inflorescence were mapped. Notably, we characterized a key rate-limiting enzyme in the thiamine biosynthesis pathway, the thiazole synthase (AcTHI1), that plays a crucial role in regulating thiamine biosynthesis. Additionally, integrated transcriptomic and targeted metabolomic analyses revealed hub transcription factors, including AcNAC73, AcMYB61, and AcARF9, that are associated with the regulation of pantothenic acid and thiamine metabolism. Taken together, our results lay a foundation for understanding the regulation of B vitamin metabolism during the development of A. catechu inflorescence and provide a theoretical basis for the development of the medicinal and nutritional potential of the plant.},
}

*Metabolomics
*Vitamin B Complex/metabolism
*Areca/metabolism/genetics
Gene Expression Regulation, Plant
*Inflorescence/metabolism/genetics
Gene Expression Profiling
Multiomics
Transcriptome
Metabolome
Plant Proteins/genetics/metabolism

@article {pmid40836216,
year = {2025},
author = {Wang, T and Tang, C and De, K and Qi, J and Li, Y and Li, X},
title = {Integrated transcriptomic and metabolomic analysis reveals stage-associated molecular profiles in Ophiocordyceps sinensis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {763},
pmid = {40836216},
issn = {1471-2164},
support = {K9922050//Qinghai Province Science and Technology Department project/ ; QHCY-2023-057//Protective Harvesting and Utilization Project for Ophiocordyceps sinensis in Qinghai Province/ ; LHZX-2022-01//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 2021-SF-A4//The major science and technology projects of Qinghai Province/ ; },
mesh = {*Metabolomics/methods ; *Gene Expression Profiling ; Multiomics ; *Transcriptome ; *Hypocreales/genetics/metabolism ; *Metabolome ; Amino Acids/metabolism ; },
abstract = {Ophiocordyceps sinensis is globally recognized for its exceptional nutritional and medicinal properties. Variations in the edible qualities and tonic values of O. sinensis at different harvesting stages remain poorly understood in terms of compositional changes and regulatory mechanisms. Utilizing UPLC-MS/MS and transcriptome sequencing (RNA-seq), this study unveiled discrepancies in metabolite accumulation and gene expression of O. sinensis across various harvesting stages. Metabolomics analysis identified 596 differentially accumulated metabolites (DAMs), primarily enriched in amino acid-related metabolic pathways such as tyrosine, tryptophan, cysteine, and methionine metabolism. The up accumulation of organic acids and derivatives with delayed harvesting led to distinct abundances and compositions of amino acids, peptides, analogs, and fatty acids and conjugates, ultimately influencing the quality of O. sinensis. Transcriptomic analysis revealed 2550 differentially expressed genes (DEGs) at different harvesting stages, with KEGG-based enrichment analysis highlighting their involvement in amino acid-related activities like tyrosine metabolism and fatty acid degradation. The upregulation of these DEGs in amino acid-related pathways presents a promising target for studying O. sinensis quality. Integrative metabolomic and transcriptomic analyses indicated potential roles for DDC (G6O67_000335), TYR (G6O67_005660), AOC (G6O67_005457), and fahA (G6O67_004634) in the synthesis pathways of amino acids, peptides, and their analogs, suggesting a possible indirect association with O. sinensis quality. These findings offer novel insights into the molecular mechanisms underlying the quality formation and metabolic evolution of O. sinensis.},
}

*Metabolomics/methods
*Gene Expression Profiling
Multiomics
*Transcriptome
*Hypocreales/genetics/metabolism
*Metabolome
Amino Acids/metabolism

@article {pmid41085836,
year = {2025},
author = {Vidal-Silva, IM and Loza, A and Gutierrez-Rios, RM},
title = {Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {384},
pmid = {41085836},
issn = {1573-0972},
support = {IN202524//PAPIIT-DGAPA/ ; 319234//Ciencia Básica y/o Ciencia de Frontera. Modalidad: Paradigmas y Controversias de la Ciencia 2022/ ; },
mesh = {Biodegradation, Environmental ; *Computational Biology/methods ; *Bacteria/metabolism/genetics/classification ; *Hydrocarbons, Aromatic/metabolism ; Environmental Pollutants/metabolism ; Multiomics ; Genomics ; Metagenomics ; Polycyclic Aromatic Hydrocarbons/metabolism ; Metabolic Networks and Pathways ; Anaerobiosis ; },
abstract = {Aromatic hydrocarbons (AHs) are persistent environmental pollutants with high toxicity. Bacterial degradation of AHs provides a sustainable and cost-effective approach for the remediation of sites contaminated with both mono- and polycyclic aromatic hydrocarbons. Aerobic degradation of AHs typically involves oxygenases-mediated hydroxylation followed by aromatic ring cleavage. In contrast, anaerobic degradation relies on diverse activation mechanisms that ultimately converge on the central intermediate benzoyl-CoA. Over the past decades, research on bacterial degradation of AHs has grown steadily, supported by advances in omics and bioinformatics. In this review, we summarize the current knowledge on the pathways, enzymes, and microbial diversity involved in AH degradation, highlighting how omics and bioinformatic approaches are advancing our understanding of this process. However, to improve our knowledge of microbial AHs catabolism, it is crucial to prioritize the characterization of novel enzymes and pathways, especially those mediating anaerobic and hybrid degradation strategies. Addressing this gap requires the development of specialized resources that incorporate a broader taxonomic diversity and an expanded inventory of anaerobic genes and enzymes supported by experimental evidence. Equally important is the integration of multi-omics technologies, artificial intelligence, and ecological modeling into unified analytical pipelines. These efforts will be key to fully unlocking microbial metabolic potential and guiding more effective bioremediation and monitoring strategies for AHs.},
}

Biodegradation, Environmental
*Computational Biology/methods
*Bacteria/metabolism/genetics/classification
*Hydrocarbons, Aromatic/metabolism
Environmental Pollutants/metabolism
Multiomics
Genomics
Metagenomics
Polycyclic Aromatic Hydrocarbons/metabolism
Metabolic Networks and Pathways
Anaerobiosis

@article {pmid41372785,
year = {2025},
author = {Zhou, Y and Pan, J and Cheng, H and Xiao, L and Zhang, W and Huang, H and Liu, K and Fang, L and Ma, W and Xia, Y and Li, J and Lv, D and Hu, Y and Chang, Y and Wang, Z and Tao, H and Zhang, C and Li, C and Peng, Y and Zhao, Q and Zhang, Y and Mei, J and Wang, X and Wei, T and Zhou, M and Zhang, Y and Chen, Q and Chan, NY and Zhang, B and Wing, YK and Lei, B and Zhang, J},
title = {Digital multi-modal approaches to subtyping insomnia disorder (DIMOSI): study design, rationale, digital platform, and preliminary baseline characteristics of a national prospective cohort study.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {74},
pmid = {41372785},
issn = {1471-244X},
mesh = {Humans ; *Sleep Initiation and Maintenance Disorders/classification/diagnosis/psychology ; Prospective Studies ; Female ; Adult ; Male ; Digital Health ; Middle Aged ; Wearable Electronic Devices ; Research Design ; Surveys and Questionnaires ; Young Adult ; Sleep ; },
abstract = {BACKGROUND: Insomnia disorder exhibits complex manifestations and heterogeneous clinical trajectories. Accurate subtyping of insomnia might enhance understanding of its clinical presentations and facilitate precision management. The Digital Multi-modal approaches to Subtyping Insomnia disorder (DIMOSI) study is a national prospective cohort study utilizing multi-modal assessments to explore the subtypes of insomnia disorder, their natural trajectories, and related mental health outcomes. METHODS: A total of 4,000 adult participants meeting International Classification of Sleep Disorders, 3rd Edition (ICSD-3) criteria for insomnia disorder will be recruited from community or clinical settings. Eligible participants will be invited to complete the multi-dimensional assessments via a digital platform, including a structured interview, questionnaires, cognitive tasks, sleep-activity diary, physiological characteristics, and ecology momentary assessments, as well as 7-day physical activity and sleep tracking using wearable devices. All participants will be followed up at 6 and 12 months. The primary outcome is the identification of multi-modal subtypes of insomnia disorder and their correlates. Secondary outcomes include the longitudinal trajectories of these subtypes, associated risk factors, and mental health outcomes. RESULTS: As of June 30, 2025, a total of 2937 patients with insomnia disorder have been recruited, with a mean age of 37.3 years (SD = 12.6), 59.3% from outpatient clinics, and 66.5% female. Among the participants, 2850(97.1%) were suffering from current insomnia disorder, while the mean score of the ISI was 15.5 ± 5.8. A total of 2134 participants (72.7%) wore accelerometers, while 2429 (82.7%) wore wearable EEG monitors for continuous assessments. DISCUSSION: The DIMOSI study is a large-scale national prospective cohort investigating insomnia disorder utilizing a self-developed digital multi-modal platform. It integrates comprehensive subjective and objective assessments from 33 centers in China. The current study offers a unique opportunity to explore subtypes of insomnia disorder and their natural course and their correlates through the digital multi-modal platform that provides enriched and comprehensive assessments. It may provide the potential to inform the development of personalized prevention and intervention strategies, ultimately improving patient outcomes. TRIAL REGISTRATION: Clinical Trial Registry Name: Digital Multi-modal approaches to deep phenotyping insomnia disorder. Registration Number: ChiCTR2200056425. Date of Registration: 2022-02-05.},
}

Humans
*Sleep Initiation and Maintenance Disorders/classification/diagnosis/psychology
Prospective Studies
Female
Adult
Male
Digital Health
Middle Aged
Wearable Electronic Devices
Research Design
Surveys and Questionnaires
Young Adult
Sleep

@article {pmid41430187,
year = {2025},
author = {Lee, E and Hwang, J and Kim, DW and Choi, BY and Bae, HJ and Won, SH and Park, YH and Kim, S},
title = {Association between high carbohydrate to dietary fiber ratio and risk of dementia in older adults: analysis from the UK biobank.},
journal = {BMC neurology},
volume = {26},
number = {1},
pages = {33},
pmid = {41430187},
issn = {1471-2377},
mesh = {Humans ; *Dementia/epidemiology ; United Kingdom/epidemiology ; Female ; *Dietary Fiber/administration & dosage ; *Dietary Carbohydrates/administration & dosage ; Aged ; Male ; Middle Aged ; Biological Specimen Banks ; Prospective Studies ; UK Biobank ; Risk Factors ; Magnetic Resonance Imaging ; Cohort Studies ; },
abstract = {BACKGROUND: The dietary carbohydrate-to-fiber ratio (CFR) provides a comprehensive measure of carbohydrate quality; however, its association with cognitive outcomes remains unexplored. Given the distinct health effects of different types of carbohydrates, understanding the impact of CFR on dementia risk and brain structure is valuable. METHODS: This prospective cohort study analyzed 107,785 UK Biobank participants aged ≥ 55 years who completed at least one 24-hour dietary recall between 2011 and 2012, with follow-up until April 2024. CFR was calculated as the ratio of daily carbohydrate intake to fiber intake. Total carbohydrate and dietary fiber intake were included as secondary exposures. CFR outliers were excluded using Tukey’s method (3.0 × interquartile range). The primary outcome was all-cause dementia incidence identified through linked hospital and death registry data. Secondary outcomes were hippocampal volume, entorhinal cortical thickness and frontal cortical thickness. Cox proportional hazards models estimated dementia risk, and multiple linear regression analyzed MRI markers. Models were adjusted for age, sex, education, BMI, physical activity, smoking, alcohol intake, hypertension, diabetes, and total energy intake. Interactions between dietary factors and polygenic risk score (PRS) were examined. RESULTS: During a median follow-up of 11.8 years, 2,000 dementia cases occurred, corresponding to incidence rates of 1.44 and 1.82 per 1,000 person-years in the lowest and highest CFR quartiles, respectively. A higher CFR was significantly associated with increased dementia risk (HR per 1 SD = 1.07, 95% CI: 1.02–1.12, p = 0.003). The association was slightly attenuated in individuals with increased genetic susceptibility (p for interaction = 0.02). Total carbohydrate intake was associated with dementia risk (HR per 1 SD = 1.15, 95% CI: 1.05–1.25, p = 0.001), whereas fiber intake was not (p = 0.99). An elevated CFR was also associated with reduced entorhinal cortical thickness (FDR p = 0.03) and with thinner frontal pole, medial orbitofrontal cortex, and rostral middle frontal cortex (all FDR p = 0.01) among 14,388 participants with MRI data. CONCLUSIONS: A higher CFR was associated with increased dementia risk, reduced entorhinal thickness, and thinner frontal cortical regions, suggesting that CFR may serve as a practical indicator of carbohydrate quality with potential implications for dietary and public health approaches to cognitive aging.},
}

Humans
*Dementia/epidemiology
United Kingdom/epidemiology
Female
*Dietary Fiber/administration & dosage
*Dietary Carbohydrates/administration & dosage
Aged
Male
Middle Aged
Biological Specimen Banks
Prospective Studies
UK Biobank
Risk Factors
Magnetic Resonance Imaging
Cohort Studies

@article {pmid41634580,
year = {2026},
author = {Gong, X and Chen, B and Yang, L and Zhang, Y and Chang, S and Yang, T and Chen, Y and Zhu, Y and Wang, Z and He, X and Xue, L},
title = {Location and growth period influence the bioactive compounds of Angelica sinensis (Oliv.) diels: multi-omics insights.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41634580},
issn = {1471-2229},
support = {24JRRA1134; 2024YQ-04//the Natural Science Foundation of Gansu Province of China; the Outstanding Youth Fund of the Gansu Academy of Sciences/ ; 22ZSCQ037//Intellectual Property Plan Project Gansu Province of China/ ; 24JRRA1137; 2024QN-13//the Science and Technology Program of Gansu Province of China; the Young Scientists Fund Project of Gansu Academy of Sciences/ ; },
mesh = {*Angelica sinensis/growth & development/metabolism/genetics/microbiology/chemistry ; Multiomics ; Rhizosphere ; Soil Microbiology ; Bacteria/genetics ; Fungi/genetics ; Gene Expression Profiling ; Microbiota ; Plant Roots/microbiology ; Transcriptome ; },
abstract = {Angelica sinensis, a traditional medicinal herb, exhibits significant variations in efficacy quality linked to geographical origin and rhizosphere microbiome composition. However, the microbial factors driving the synthesis of its bioactive compounds in authentic (historically recognized for superior quality geoherbs, Min County) and adjacent regions remain poorly understood. This study integrated transcriptomic profiling of plant tissues with 16 S rRNA (bacteria) and ITS (fungi) sequencing of rhizosphere soils over multiple growth stages in authentic and near-authentic regions (the latter characterized by a similar climate but differing soil ecology). By combining these data with targeted metabolomics and soil property analysis, substantial regional and temporal variations in bioactive compound levels and soil properties were identified. Specifically, 2,367 differentially expressed genes (DEGs), 417 bacterial amplicon sequence variants (ASVs), and 295 fungal ASVs were detected with significant abundance shifts. Key genera, including Vicinamibacter and Bacillus (bacteria), and Bisifusarium and Longitudinalis (fungi), were linked to secondary metabolite production. Functional differences, such as those related to chitinolysis and fermentation pathways, were also observed. Co-occurrence networks revealed correlations between plant genes and microbial communities. Notably, soil parameters, including organic matter, total nitrogen, and soil alkaline phosphatase, were identified as key factors influencing microbial community structure. The rhizosphere microbiome was further associated with nutrient absorption, potentially impacting bioactive compound accumulation. This multi-omics analysis highlights the role of regional and growth-period variations in A. sinensis quality, offering valuable insights for optimizing its cultivation and efficacy across diverse regions.},
}

*Angelica sinensis/growth & development/metabolism/genetics/microbiology/chemistry
Multiomics
Rhizosphere
Soil Microbiology
Bacteria/genetics
Fungi/genetics
Gene Expression Profiling
Microbiota
Plant Roots/microbiology
Transcriptome

@article {pmid42153259,
year = {2026},
author = {Katchborian-Neto, A and de Jesus Nicácio, K and Bueno, PCP and Ferreira, MS and Fernandes Alves, M and de Oliveira Silva, D and Dos Santos, WT and de Monroe Gonçalves, M and de Paula, ACC and Dias, DF and Soares, MG and Edrada-Ebel, R and Lago, JHG and Chagas-Paula, DA},
title = {The Metabolome of the Ocotea spp.: From Biosynthetic Aspects to Bioactive Chemical Scaffolds by Integrating the Genus Chemical Database (OcoteaDB).},
journal = {Journal of natural products},
volume = {89},
number = {6},
pages = {1631-1654},
doi = {10.1021/acs.jnatprod.5c01567},
pmid = {42153259},
issn = {1520-6025},
mesh = {*Metabolome ; *Databases, Chemical ; Molecular Structure ; Alkaloids/chemistry ; Terpenes/chemistry/metabolism ; },
abstract = {The genus Ocotea is a significant source of bioactive agents within the Lauraceae, yet it remains underexplored. Despite its ethnomedicinal relevance and chemical diversity, Ocotea species remain taxonomically challenging as they belong to the multifaceted "Ocotea complex", a phylogenetically unresolved group. Moving beyond previous literature Ocotea surveys, this review provides the first curated, genus-specific data set of both volatile and nonvolatile specialized metabolites. Covering research articles from 1830 to 2025, this review provides the most comprehensive synthesis to date, documenting 984 unique chemical compounds across 115 species. This effort culminated in the construction of the Ocotea Chemical Database (OcoteaDB), a novel digital resource created to streamline the genus's chemical diversity for the global scientific community. Furthermore, it presents current knowledge of biosynthetic routes leading to key bioactive scaffolds, including aporphinoid and benzylisoquinoline alkaloids, lignoids, glycosylated flavonoids, and a diverse array of terpenoids, while addressing the stereochemical and structural intricacies unique to the genus. This review lays a robust foundation to drive future Ocotea-focused bioprospecting studies and guides research in the fields of natural products, chemophenetics, metabolomics, and medicinal chemistry regarding the Ocotea species, its chemical scaffolds, and specialized metabolites.},
}

*Metabolome
*Databases, Chemical
Molecular Structure
Alkaloids/chemistry
Terpenes/chemistry/metabolism

@article {pmid42166742,
year = {2026},
author = {Bowman, GI and Seymour, N and Reynolds, C and Evans, LM},
title = {Development and validation of an electronic health record-based frailty index in the UK Biobank.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {81},
number = {7},
pages = {},
doi = {10.1093/gerona/glag131},
pmid = {42166742},
issn = {1758-535X},
support = {//PetaLibrary and computational analysis was supported by the Blanca and Alpine high performance computing resources at the University of Colorado Boulder/ ; //University of Colorado Boulder, the University of Colorado Anschutz, and Colorado State University/ ; },
mesh = {Humans ; *Electronic Health Records ; Female ; Male ; United Kingdom/epidemiology ; *Frailty/diagnosis/mortality ; Aged ; UK Biobank ; *Geriatric Assessment/methods ; Proportional Hazards Models ; Biological Specimen Banks ; },
abstract = {BACKGROUND: Frailty, an age-related loss of the ability to withstand stressors, is commonly measured using health deficit indices, often using survey or questionnaire data. We aimed to develop an electronic frailty index (eFI) using electronic health record (EHR) data linkages in the UK Biobank and assess its association with mortality.

METHODS: We calculated an eFI using 43 deficits, each corresponding to phecodes mapped to the United Kingdom (UK) and international classification coding systems. We compared this eFI to a validated 49-item survey-based FI for the UK Biobank (UKB) and assessed associations of the eFI with risk of all-cause mortality (follow-up ≤ 10.2 years) and mortality following a stressor (heart attack or stroke) using Cox proportional hazard models.

RESULTS: Mean eFI in this cohort (N = 208,982) was 0.058 (SD = 0.06) and was higher in females than males. A 10% higher baseline frailty was associated with higher risk of all-cause mortality (HR (95% CI)=2.00 (1.93-2.07)), although the magnitude of this association decreased when adjusting for socioeconomic-related covariates (HR (95% CI)=1.44 (1.38-1.51)). Associations were stronger in men than women. Electronic frailty index predicted mortality following both heart attack and stroke (HR (95% CI) = 1.59 (1.25-2.04) and HR = 1.33 (1.13-1.57), respectively).

CONCLUSIONS: This EHR-based eFI has robust associations with mortality, suggesting that it can be used as a valid measure of frailty in the UKB and can potentially be applied to other datasets with EHR data.},
}

Humans
*Electronic Health Records
Female
Male
United Kingdom/epidemiology
*Frailty/diagnosis/mortality
Aged
UK Biobank
*Geriatric Assessment/methods
Proportional Hazards Models
Biological Specimen Banks

@article {pmid42169502,
year = {2026},
author = {Isaacs, KK and Williams, AJ and Phillips, K and Jahne, M and Thimons, S},
title = {A curated geospatial dataset of chemicals used in hydraulic fracturing and their functions.},
journal = {Journal of environmental quality},
volume = {55},
number = {3},
pages = {e70185},
doi = {10.1002/jeq2.70185},
pmid = {42169502},
issn = {1537-2537},
support = {//Oak Ridge Institute for Science and Education/ ; },
mesh = {*Hydraulic Fracking ; *Water Pollutants, Chemical/analysis ; Databases, Factual ; },
abstract = {Produced water (PW) is generated by the oil and gas industry as a byproduct of conventional extraction and hydraulic fracturing (HF) activities. Chemicals used in HF must be evaluated for risk to humans and ecological species when considering the conditions of PW reuse. FracFocus (FF) is a public database of chemicals used in HF where operators of wells report information either voluntarily or as mandated under specific state statutes. However, data reported to FF is standardized in terms of neither chemical identifier nor chemical function. Here, using cheminformatic methods, we develop a curated database of chemicals reported to FF, harmonized to chemical identifiers and function categories used by the US Environmental Protection Agency, facilitating linkage to toxicity and other data in its CompTox Chemicals Dashboard. The resulting dataset of over 5.7 million records reflects 1567 unique chemical substances and 45 unique functions. This dataset provides a resource to risk assessors and environmental programs when evaluating the potential impact of HF chemicals in PW reuse.},
}

*Hydraulic Fracking
*Water Pollutants, Chemical/analysis
Databases, Factual

@article {pmid42213775,
year = {2026},
author = {Yuan, K and Lian, Y and Huang, P and Cao, F and Yang, X and Lu, Y and Ding, X and Wang, L and Yang, H and Ye, Z and Chen, Q and Fu, J and Yuan, S and Fan, Y and Cai, S and Du, D and Ren, J and Zhang, X and Xu, H},
title = {Integrative analysis reveals intra-tumoral microbial enterotypes shape host transcriptomes in colorectal cancer.},
journal = {Cell reports},
volume = {45},
number = {6},
pages = {117413},
doi = {10.1016/j.celrep.2026.117413},
pmid = {42213775},
issn = {2211-1247},
mesh = {*Colorectal Neoplasms/microbiology/genetics/immunology/pathology ; Humans ; Animals ; *Transcriptome/genetics ; Bacteroides fragilis ; Mice ; *Microbiota/genetics ; Tumor Microenvironment/immunology/genetics ; Multiomics ; Mice, Inbred C57BL ; },
abstract = {The intratumor microbiome and host gene regulation are key contributors to colorectal cancer (CRC), yet their interactions remain unclear. To investigate the interplay between intra-tumoral microbe and host gene, we analyzed paired tumor and normal tissues from 31 patients. Integrated multi-omics analysis identified 4,197 significant bacteria-gene correlation pairs involving 30 bacterial taxa. Patient stratification based on these associations reveals two distinct molecular subgroups characterized by unique microbial signatures and immune profiles. In a mouse model, Bacteroides fragilis alters the tumor immune microenvironment, promoting myeloid-derived suppressor cell (MDSC)-mediated CXCL signaling that impaired CD8[+] T cell activation and promotes exhaustion. B. fragilis directly promotes CXCL2 expression and ROS production in MDSCs, which subsequently drives CD8[+] T cell exhaustion and immune evasion. These findings reveal that intra-tumoral microbiota influence host transcriptomes and immune modulation in CRC, supporting microbiome-based molecular stratification and offering insights into potential microbiota-targeted therapies.},
}

*Colorectal Neoplasms/microbiology/genetics/immunology/pathology
Humans
Animals
*Transcriptome/genetics
Bacteroides fragilis
Mice
*Microbiota/genetics
Tumor Microenvironment/immunology/genetics
Multiomics
Mice, Inbred C57BL

@article {pmid42227660,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Zhang, SR and Lai, JL and Zhang, Y and Luo, XG},
title = {Synergistic Remediation of Organic Arsenicals via an Integrated Plant-Microbe Remediation Platform: A Multiomics Interrogation of Degradation and Detoxification Mechanisms.},
journal = {Environmental science & technology},
volume = {60},
number = {24},
pages = {17366-17381},
doi = {10.1021/acs.est.6c02129},
pmid = {42227660},
issn = {1520-5851},
mesh = {Multiomics ; Biodegradation, Environmental ; *Arsenicals ; Soil Pollutants ; },
abstract = {The organic arsenic compounds diphenylarsonic acid (DPAA) and phenylarsonic acid (PAA) are pervasive and hazardous soil pollutants. To address this, we constructed a remediation system by first screening and combining two functional bacteria: Bacillus subtilis and Bacillus cereus. This synthetic consortium rapidly degraded DPAA and PAA within 24 h, primarily through the cleavage of arsenic-carbon bonds and aromatic rings, facilitated by specific enzymes (ArsI and ring-opening dioxygenase). Concurrently, we employed alfalfa, a plant capable of efficiently absorbing inorganic arsenic released during microbial degradation. This plant-microbe system, tested over 60 days in contaminated soil, successfully removed both organic pollutants and the derived inorganic arsenic. Multiomics analyses confirmed that the remediation process beneficially restructured the soil environment, stimulating microbial activity and key metabolic functions and reducing potential risks like antibiotic resistance genes. This integrated strategy, verified through multiomics to drive beneficial soil ecosystem restructuring, provides a novel and mechanistically informed approach for the sustainable cleanup of complex organoarsenical contamination.},
}

Multiomics
Biodegradation, Environmental
*Arsenicals
Soil Pollutants

@article {pmid42287835,
year = {2026},
author = {Yu, H and Gao, C and Xu, J and Wu, X and Zhang, J},
title = {Hepatic lipid metabolic dysregulation mediates fluxapyroxad-induced hepatotoxicity: Insights from multi-omics profiling.},
journal = {Ecotoxicology and environmental safety},
volume = {320},
number = {},
pages = {120352},
doi = {10.1016/j.ecoenv.2026.120352},
pmid = {42287835},
issn = {1090-2414},
mesh = {Animals ; Zebrafish/metabolism ; *Lipid Metabolism/drug effects/genetics ; *Liver/drug effects/metabolism/pathology ; Multiomics ; *Fungicides, Industrial/toxicity ; *Water Pollutants, Chemical/toxicity ; *Chemical and Drug Induced Liver Injury/metabolism ; Lipidomics ; Gene Expression Profiling ; },
abstract = {Fluxapyroxad (FLU), a widely used succinate dehydrogenase inhibitor (SDHI) fungicide, can enter aquatic environments and pose potential risks to aquatic organisms. This study investigated the hepatotoxic effects of long-term FLU exposure in adult zebrafish exposed to 0, 30, 60, and 90 μg/L FLU for 28 days. High-dose (90 μg/L) exposure significantly reduced body weight, increased liver weight, and induced hepatic vacuolization and reduced glycogen storage in histological analysis. Transcriptomic analysis of the high-dose group revealed significant upregulation of lipid metabolism-related genes (ldlr, lpin1, apoc2), enriched in PPAR signaling and non-alcoholic fatty liver disease pathways; lipidomic profiling showed widespread lipid alterations (especially phosphatidylcholine species), with glycerophospholipid metabolism as the most affected pathway, and 11 differential lipid species including PC(18:0/16:0) and TG(20:0/14:0/14:0) were identified as candidates. Integrated multi-omics analysis demonstrated that high-dose FLU exposure triggered hepatic lipid metabolic disorders via dysregulated expression of genes involved in lipid synthesis, transport and degradation. These findings reveal the mechanism of FLU-induced hepatotoxicity, and provide reference for identifying FLU-responsive hepatic differential lipids, as well as ecological risk assessment of FLU and related SDHI fungicides in aquatic systems.},
}

Animals
Zebrafish/metabolism
*Lipid Metabolism/drug effects/genetics
*Liver/drug effects/metabolism/pathology
Multiomics
*Fungicides, Industrial/toxicity
*Water Pollutants, Chemical/toxicity
*Chemical and Drug Induced Liver Injury/metabolism
Lipidomics
Gene Expression Profiling

@article {pmid42303245,
year = {2026},
author = {Tiao, PH and Chan, HY and Huang, YM},
title = {Navigating Diabetes Management in the Digital Era: Scoping Review of Online Health Information-Seeking Behavior.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e82081},
doi = {10.2196/82081},
pmid = {42303245},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; *Information Seeking Behavior ; *Diabetes Mellitus/therapy ; Digital Media ; *Internet ; },
abstract = {BACKGROUND: Online health information seeking (OHIS) has become a central component of chronic disease management within an increasingly interactive, algorithm-mediated digital ecosystem. For individuals with diabetes, ongoing self-management demands create sustained needs for accessible, actionable health information. Although prior reviews have described general information-seeking behaviors, few have integrated technological evolution, multilevel determinants, and equity considerations specific to diabetes.

OBJECTIVE: This scoping review maps patterns of OHIS among individuals with diabetes, identifies the types of information sought, synthesizes the multilevel determinants of OHIS, and explores temporal shifts across major phases of digital health development.

METHODS: This scoping review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) and Preferred Reporting Items for Systematic Reviews and Meta-Analyses literature search extension (PRISMA-S) reporting guidelines and was guided by the Sample, Phenomenon of Interest, Design, Evaluation, Research type framework. Five electronic databases (PubMed, Scopus, Web of Science, CINAHL, and Embase) were systematically searched for English-language empirical studies from inception to May 4, 2026. Eligible studies included empirical research investigating OHIS behaviors among individuals with type 1 diabetes, type 2 diabetes, or gestational diabetes. Data were extracted using a standardized charting form and synthesized descriptively. Determinants were organized according to the Social Ecological Model, and qualitative findings were analyzed using content analysis. Studies were stratified into 3 periods reflecting shifts in digital infrastructure: early web environments (2002-2010), expansion of social media and mobile technologies (2011-2018), and integrated digital and artificial intelligence (AI)-enabled ecosystems (2019-2025).

RESULTS: Eighty-one studies from 32 countries met the inclusion criteria. The use of digital sources diversified over time. Early studies emphasized search engines and institutional websites, whereas later studies increasingly reported engagement with social media platforms and online communities. Mobile health apps and generative AI chatbots appeared in recent publications, although evidence on AI use remained limited. The most frequently sought content included self-management and lifestyle guidance, general diabetes knowledge, and treatment-related information. Determinants of OHIS operated across multiple levels. At the individual level, younger age, greater educational attainment, higher income, and better eHealth literacy were associated with increased engagement, while psychological factors such as perceived knowledge gaps and a desire for autonomy motivated searching. Interpersonal influences included peer support and clinician communication. Organizational and environmental factors encompassed health care access, digital infrastructure, information quality, and platform characteristics. Persistent disparities were observed among older adults and socioeconomically disadvantaged groups.

CONCLUSIONS: This review synthesizes OHIS among individuals with diabetes through the lenses of technological evolution, multilevel determinants, and digital health equity. Unlike previous reviews that focused on specific platforms or general information-seeking behaviors, it maps the transition from web-based resources to social media and emerging AI-enabled ecosystems. This temporally informed synthesis advances understanding of digital engagement in diabetes self-management, identifies key evidence gaps, and informs clinical, organizational, and policy strategies to promote equitable access to trustworthy online health information.},
}

Humans
Digital Health
*Information Seeking Behavior
*Diabetes Mellitus/therapy
Digital Media
*Internet

@article {pmid42303641,
year = {2026},
author = {Yang, J and Han, S and Li, L and Peng, J and Liu, J and Liu, J and Han, Z},
title = {Study on the mechanical characteristics of the stress relaxation in the carbonate rock after high-temperature acidification.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42303641},
issn = {2045-2322},
support = {52404020//National Natural Science Foundation of China/ ; U1762216//The National Natural Science Foundations of China/ ; 2023ZZ14YJ07//Tarim Oilfield Co., LTD. Phase IV Project/ ; 2025ZD1402405//The National Key Special Project in China/ ; },
abstract = {To elucidate the mechanism by which acidification influences wellbore stability in deep reservoir formations, this study investigates the rheological and mechanical behaviors of the carbonate rock subjected to high-temperature acid etching. A novel experimental system was developed to characterize the stress relaxation behavior of the acid-etched carbonate rock, and the characteristics of the stress relaxation curves under various acid etching conditions and strain levels were systematically analyzed. Combined with Burgers model and the Levenberg-Marquardt algorithm, the evolution of rheological parameters of the carbonate rock under different acid etching regimes was quantitatively evaluated. The results indicate that the acid-etched carbonate rock exhibit significant rheological mechanical properties due to the presence of developed microcracks and complex pore structures. Under the identical acid etching duration and temperature, the initial stress, residual stress, and time required for stress relaxation stabilization all increase with increasing the strain level. Overall, the stress relaxation magnitude prior to the core fracture ranges from 15 to 25 MPa, and the stabilization time for the core stress relaxation falls between 5 and 7 h. The stress relaxation behavior of the acid-etched carbonate core is well described by the Burgers model. At fixed strain levels and temperatures, the instantaneous shear modulus [Formula: see text] decreases linearly with extended acid etching time, whereas the instantaneous shear modulus [Formula: see text] and the viscosity coefficients [Formula: see text] and [Formula: see text] exhibit exponential degradation. The final variation ranges of the key rheological parameters are determined as follows: instantaneous shear modulus [Formula: see text] ranges from 5 × 10[3] to 2 × 10[4] MPa, instantaneous shear modulus [Formula: see text] ranges from 6 × 10[5] to 2 × 10[6] MPa, viscosity coefficient [Formula: see text] ranges from 2 × 10[7] to 8 × 10[7] MPa h, and viscosity coefficient [Formula: see text] ranges from 1 × 10[5] to 1.2 × 10[6] MPa h. Furthermore, the evolutionary equations correlating the global model fitting parameters with the porosity of acid-etched samples are established, using acid etching time as an intermediate variable. The results of this study provide a theoretical basis for the analysis of wellbore stability after acidification and the selection of acid fracturing completion methods of deep reservoirs.},
}

@article {pmid42304410,
year = {2026},
author = {Schmelkin, L and Chung, S and Haldane, A and Townsend, JP and Carnevale, V and Levy, RM and Kumar, S},
title = {Epistasis plays a limited role in driving entrenchment during neutral protein evolution.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-04157-0},
pmid = {42304410},
issn = {1474-760X},
support = {GM132090-04/GM/NIGMS NIH HHS/United States ; GM139540-05/GM/NIGMS NIH HHS/United States ; AI178849//National Institute of Allergy and Infectious Diseases/ ; 1934848//National Science Foundation/ ; },
abstract = {BACKGROUND: Substitutional entrenchment arising from epistatic interactions renders previously acceptable amino-acid states unfavorable over evolutionary time and has often been attributed to novel adaptive processes. However, recent simulations based on Potts-Hamiltonian models have suggested that entrenchment may also emerge during protein evolution governed by the neutral theory of molecular evolution (NTME).

RESULTS: Here, we re-examine this conclusion by assessing whether substitutions permitted in such simulations are consistent with empirical expectations of NTME. Since Potts models are inferred from a large collection of homologous rather than orthologous sequences, they may allow substitutions that are incompatible with NTME. Our analysis revealed that Potts-based simulations permit amino-acid substitutions whose Hamiltonian energies (PHE, φ) often fall outside empirically derived NTME φ neighborhoods, thus allowing non-neutral evolution of domain sequences. To prevent such transgressions, we implement simulations that impose purifying selection whenever Potts-acceptable substitutions depart from the NTME φ neighborhood. When these substitutions are eliminated, we observed limited substitutional entrenchment, with site-specific amino-acid preferences remaining stable over biologically relevant timescales in neutral protein evolution. We further find that overdispersion of the molecular clock is modest and scales directly with the proportion of evolutionary lineages displaying epistasis-driven among-site rate heterogeneity, independent of entrenchment.

CONCLUSIONS: These results demonstrate that significant entrenchment is not an inherent property of epistasis during protein evolution consistent with NTME. Our findings establish baseline expectations for neutral evolution with epistasis and suggest that pronounced entrenchment observed in natural protein evolution likely reflects non-neutral evolutionary histories, including adaptation.},
}

@article {pmid42306263,
year = {2026},
author = {Brook, JBH and Salo, T and Luo, AC and Bagautdinova, J and Rush, S and Alexander-Bloch, AF and Baller, EB and Calkins, ME and Cieslak, M and Cooper, EC and Detre, JA and Elliott, MA and Fair, DA and Freedman, P and Gehrman, PR and Gur, RC and Gur, RE and Klein, A and Laney, N and Laumann, TO and Mehta, K and Merikangas, K and Milham, MP and Mitchell, JA and Moore, TM and Nelson, SM and Ruparel, K and Sevchik, BL and Shanmugan, S and Shou, H and Taso, M and White, LK and Wolf, DH and Tisdall, MD and Roalf, DR and Satterthwaite, TD},
title = {An open, fully-processed data resource for studying mood and sleep variability in the developing brain.},
journal = {Aperture neuro},
volume = {6},
number = {SI 1},
pages = {},
pmid = {42306263},
issn = {2957-3963},
abstract = {Brain development during adolescence and early adulthood coincides with shifts in emotion regulation and sleep. Despite this, few existing datasets simultaneously characterize affective dynamics, sleep variation, and multimodal measures of brain development. Here, we describe the study protocol and initial release (n = 10) of an open data resource of neuroimaging paired with densely sampled behavioral measures in adolescents and young adults. All participants complete multi-echo functional MRI, compressed-sensing diffusion MRI, and advanced arterial spin-labeled MRI. Behavioral measures include ecological momentary assessment, actigraphy, extensive cognitive assessments, and detailed clinical phenotyping focused on emotion regulation. Raw and processed data are openly available without a data use agreement and will be regularly updated as accrual continues. Together, this resource will accelerate research on the links between mood, sleep, and brain development.},
}

@article {pmid42306785,
year = {2026},
author = {Broeckhoven, C and Minne, B and Hui, C},
title = {ArmourTraits: A comparative dataset on the ecological and evolutionary correlates of dermal armour in squamates.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112904},
pmid = {42306785},
issn = {2352-3409},
abstract = {The evolution of defensive traits is a central topic in evolutionary biology, yet quantitative data linking variation in defensive morphology to ecological and environmental factors remain limited. ArmourTraits is a comprehensive dataset that quantifies variation in body armour across 131 species from two distantly related squamate lineages, Cordyliformes and Anguimorpha, which convergently evolved armour in the form of osteoderms. The dataset integrates morphological measurements of osteoderm expression and hindlimb skeletal traits derived from micro-computed tomography scans, species-level ecological, life-history, and environmental data, as well as estimated predation risk and a time-calibrated phylogeny. By providing standardised, quantitative metrics of defensive morphology alongside locomotor traits and associated ecological variables, ArmourTraits enables phylogenetic comparative analyses of ecological correlates, functional trade-offs, convergent evolution, and the diversification of defensive traits across squamates.},
}

@article {pmid42118191,
year = {2026},
author = {Mansingh, A and Pradhan, A and Gopinath, JS and Rout, M and Panda, BP and Ekka, NJ},
title = {Assessing the climatic effects of landscape transformation through long-term temperature trends in an industrial region of eastern India.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {6},
pages = {},
pmid = {42118191},
issn = {1573-2959},
mesh = {India ; *Environmental Monitoring ; *Climate Change ; *Temperature ; Industry ; Forests ; Urbanization ; Geographic Information Systems ; Conservation of Natural Resources ; },
abstract = {Rapid industrial expansion in emerging urban districts is increasingly transforming land systems and modifying local thermal regimes, yet long-term assessments from secondary industrial hubs remain limited. This study evaluates three decades (1993-2023) of land use/land cover (LULC) change and associated land surface temperature (LST) dynamics in Jharsuguda district, eastern India, using multi-temporal Landsat imagery integrated with GIS-based analysis. Six LULC classes were delineated using maximum likelihood supervised classification and validated with ground control points and normalized difference vegetation index (NDVI), yielding overall classification accuracies exceeding 91% (kappa > 0.90). Substantial forest decline was observed, with very dense forest decreasing by 65.47%, moderately dense forest by 26.37%, and open forest by 64.54%. In contrast, built-up area expanded by 317.87%, while non-forest land increased by 21.01%, reflecting accelerated industrialization and urban growth. Concurrently, the pre-monsoon LST range widened from 7-37 °C in 1993 to 16-52 °C in 2023. The proportion of land exceeding 40°C in April increased dramatically from 0 to 59%, indicating intensification of the urban heat island effect. Correlation and random forest analyses demonstrate that forested landscapes exert a significant cooling influence, whereas built-up and non-forest surfaces consistently elevate LST, with seasonal variability in their relative importance. The findings highlight a strong spatial-temporal linkage between industrial expansion, forest degradation, and surface warming. This study provides critical evidence to inform climate-responsive land-use planning, emphasizing urban greening, forest conservation, and nature-based solutions to mitigate heat stress and strengthen regional climate adaptation strategies.},
}

India
*Environmental Monitoring
*Climate Change
*Temperature
Industry
Forests
Urbanization
Geographic Information Systems
Conservation of Natural Resources

@article {pmid42141314,
year = {2026},
author = {Yang, J and Liao, Z and Li, J and Liu, M and Mao, Y and Yang, G and Liu, L},
title = {Integrative metabolomic and transcriptomic analyses reveal coordinated variation in phenolic acid metabolism and redox-related traits in Ocimum basilicum accessions.},
journal = {Planta},
volume = {263},
number = {6},
pages = {},
pmid = {42141314},
issn = {1432-2048},
support = {2025ZNSFSC0184//Sichuan Provincial Natural Science Foundation General Project/ ; 2023ZYDF076//Mianyang Science and Technology Program/ ; CXTD2023LX01//Innovation Team Project of Mianyang Normal University/ ; QD2023A01//Scientific research initiation project of Mianyang Normal University/ ; },
mesh = {*Ocimum basilicum/genetics/metabolism ; Oxidation-Reduction ; *Hydroxybenzoates/metabolism ; Gene Expression Profiling ; Metabolomics/methods ; Antioxidants/metabolism ; Gene Expression Regulation, Plant ; Transcriptome ; Multiomics ; },
abstract = {This study describes the enzymatic and transcriptional correlates of phenolic acid biosynthesis in Ocimum basilicum, suggesting an association between accession-specific metabolic diversity and differences in redox homeostasis under common‑garden conditions. The metabolic diversity of phenolic acids in Ocimum basilicum contributes to its distinct chemical profiles and potential nutraceutical value, but the transcriptional correlates underlying accession-specific variation remain unclear. This study employed an integrated multi-omics approach combining LC-MS/MS metabolomics, antioxidant enzyme assays, and transcriptome sequencing to profile four O. basilicum accessions (G002, G083, G082, and G122). We identified 292 phenolic acids, with 267 showing differential accumulation based on our screening criteria (VIP > 1 and fold change ≥ 2 or ≤ 0.5, used for metabolite prioritization rather than formal statistical inference). Accessions G002 and G122 exhibited distinct antioxidant profiles, characterized by lower lipid peroxidation (MDA), distinct SOD/POD activities, and elevated levels of specific metabolites including rosmarinic acid methyl ester and 5-O-caffeoylshikimic acid. Transcriptomic analysis revealed that the differential expression of key phenylpropanoid pathway genes (e.g., HCT, C3'H, RAS) is correlated with these distinct metabolic profiles. Correlation and network analyses further suggest an association between variation in phenolic acid accumulation to variations in antioxidant enzyme activities. Additionally, computational prediction suggested that the key differential metabolites are predicted to possess multi-target interactions with proteins relevant to human health, providing a basis for hypothesis generation. Our integrative analysis provides insights into the metabolic plasticity of O. basilicum under basal conditions and highlights specific genetic and metabolic signatures associated with O. basilicum redox homeostasis and phenolic acid diversity. These findings provide a basis for further investigation of metabolic variation among accessions.},
}

*Ocimum basilicum/genetics/metabolism
Oxidation-Reduction
*Hydroxybenzoates/metabolism
Gene Expression Profiling
Metabolomics/methods
Antioxidants/metabolism
Gene Expression Regulation, Plant
Transcriptome
Multiomics

@article {pmid42150167,
year = {2026},
author = {Kunas, B and Jung, O and Schranz, C and Schmoigl-Tonis, M and Mehlis, J and Laireiter, AR},
title = {Multimodal Personalized Mobile Health Just-in-Time Adaptive Intervention for Occupational Stress Management: Pilot Study.},
journal = {JMIR mHealth and uHealth},
volume = {14},
number = {},
pages = {e79642},
pmid = {42150167},
issn = {2291-5222},
mesh = {Humans ; Pilot Projects ; *Occupational Stress/psychology/therapy ; Male ; Adult ; Female ; Surveys and Questionnaires ; Mobile Applications/standards/statistics & numerical data ; Telemedicine/standards ; Middle Aged ; Digital Health ; },
abstract = {BACKGROUND: As digital health solutions gain traction, there is an urgent need for effective, person-centered stress management tools for employees. Advances in wearable stress monitoring and machine learning now enable the collection of high-resolution, real-time data and the delivery of personalized interventions with respect to both timing and content. Despite this technological progress, there remains a notable paucity of mobile health (mHealth) interventions that capitalize on these capabilities to implement just-in-time adaptive interventions (JITAIs).

OBJECTIVE: This pilot study aimed to examine the preliminary effects of the RELAX mHealth app, which uses a JITAI framework to reduce occupational stress, with a particular focus on initial indications of stress reduction, the influence of the app's degree of personalization on these effects, and overall user experience.

METHODS: A 2-arm randomized trial was conducted with 46 employees across two phases of 3 weeks each. Participants used the RELAX mHealth app, which adapts intervention timing based on real-time stress data and tailors content according to users' preferences. Stress was assessed via multiple heart rate variability (HRV) parameters measured with wearable sensors, alongside subjective questionnaires and ecological momentary assessment (EMA) questionnaires. Usability and user satisfaction were also evaluated. In the second phase, a group randomization was implemented, with two groups of different degrees of in-app personalization.

RESULTS: The findings were mixed. While selected subjective stress indicators decreased from baseline to the end of the study, one physiological measure increased. Retrospective chronic stress (P=.048) and arousal related to the most recent stress event prior to EMA entry (P=.02) were reduced; however, the low frequency (LF)-to-high frequency (HF) ratio of HRV increased (P=.03). Other stress variables, such as work-related stress, valence of daily experiences, and momentary arousal, showed no change over the course of the study. No between-group differences were observed with respect to the assigned degree of personalization. Additionally, usability increased (P<.001), whereas satisfaction decreased at a trend level (P=.05).

CONCLUSIONS: Although the results provide selective preliminary indications of stress reduction with app use, the variability of outcomes raises concerns about its current practical utility. The effects are also discussed with regard to the specific design of the prototype and the study setup. Technical issues and user discomfort were noted despite increasing usability over the study period, indicating areas for improvement in the developed prototype. Given the absence of a control group and the use of interventional arms only, no definitive conclusions about effects can be drawn. Nevertheless, this study highlights both the potential and the challenges of a personalized mHealth approach to occupational stress management. Further refinement of the app and more comprehensive evaluations are needed to fully understand the impact and functional usability of this JITAI-based approach in real-world settings.},
}

Humans
Pilot Projects
*Occupational Stress/psychology/therapy
Male
Adult
Female
Surveys and Questionnaires
Mobile Applications/standards/statistics & numerical data
Telemedicine/standards
Middle Aged
Digital Health

@article {pmid41980997,
year = {2026},
author = {Liu, M and Huang, Q and Tang, H and Wang, Z and Zheng, W and Wang, Z and Huang, X and Zhang, Y and Wang, Y and Huang, L},
title = {A chromosome-scale nuclear genome and complete mitogenome of the bio-control fungus Cordyceps cateniannulata.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41980997},
issn = {2052-4463},
mesh = {*Cordyceps/genetics ; *Genome, Fungal ; *Genome, Mitochondrial ; Datasets as Topic ; },
abstract = {Cordyceps cateniannulata, a recently characterized entomopathogenic fungus, has been employed in biological control, plant disease management, and growth promotion. In this study, the complete genomic sequences of C. cateniannulata were generated using BGI, PacBio, and Hi-C sequencing platforms. The nuclear genome spans 32.71 Mb, comprising seven pseudochromosomes (chromosome-scale scaffolds) with an N50 length of 4,790,175 bp and a guanine-cytosine content of 53.82%. For the first time, a fully assembled mitochondrial genome of 24,712 bp and a ribosomal DNA tandem repeat sequence of 7,974 bp were obtained. Furthermore, after meticulous annotation and manual refinement of structural features, 10,744 protein-coding genes and 156 non-coding RNAs were identified. This study has produced the high-quality whole-genome map of the C. cateniannulata, offering substantial theoretical significance and application potential for the innovative exploitation of Cordyceps fungal germplasm resources. Additionally, it provides novel perspectives on the evolutionary trajectory, infection strategies, and ecological adaptability of entomopathogenic fungi.},
}

*Cordyceps/genetics
*Genome, Fungal
*Genome, Mitochondrial
Datasets as Topic

@article {pmid42037368,
year = {2026},
author = {Arango, C and Vieta, E and Fañañás, L and Courtet, P and De Picker, L and Kas, MJH and Kéri, P and Mohr, P and Myin-Germeys, I and Penninx, BWJH and Reif, A and Kuzman, MR and Leboyer, M and Fiorillo, A and Cataln, A},
title = {Precision medicine in mental health: applications, challenges, and recommendations.},
journal = {European psychiatry : the journal of the Association of European Psychiatrists},
volume = {69},
number = {1},
pages = {e53},
pmid = {42037368},
issn = {1778-3585},
mesh = {Humans ; *Precision Medicine/methods ; *Mental Disorders/therapy/diagnosis ; Europe ; Digital Health ; *Psychiatry/methods ; *Mental Health ; },
abstract = {Mental disorders represent a major and growing public health challenge in Europe and worldwide, characterised by marked clinical, biological, and functional heterogeneity, that limits the effectiveness of current diagnostic and therapeutic approaches. In recent years, advances in precision medicine have initiated a paradigm shift in psychiatry, offering new opportunities to improve prevention, prediction, diagnosis, treatment selection, and long-term management by integrating biological, psychological, social, and environmental information.This EPA Guidance Paper provides an overview of the current state of precision medicine in mental health and outlines its potential clinical, scientific, and policy implications. We review key advances in genomics, epigenetics, neuroimaging, transcriptomics, digital technologies, and artificial intelligence, highlighting their relevance across the full clinical pathway, from risk prediction and early detection to treatment personalisation and monitoring. We also examine major barriers to implementation, including limited biomarker validation, insufficient representativeness of research populations, ethical and regulatory challenges, data protection concerns, and inequalities in access across healthcare systems.Based on the available evidence, we propose strategic recommendations to support the responsible and equitable integration of precision approaches into mental health care in Europe. These include strengthening translational research, promoting multidisciplinary collaboration, updating regulatory and ethical frameworks, enhancing professional training, and prioritising mental health within national and European research and health agendas. By addressing these challenges, precision psychiatry has the potential to contribute to more effective, person-centred, and sustainable mental health care, while supporting innovation, reducing stigma, and improving outcomes for patients and society.},
}

Humans
*Precision Medicine/methods
*Mental Disorders/therapy/diagnosis
Europe
Digital Health
*Psychiatry/methods
*Mental Health

@article {pmid42060133,
year = {2026},
author = {Chow, PI and Slipetz, L and Daniel, KE and Sun, S and Henry, T},
title = {Identifying person-level factors to guide digital mental health treatments for cancer survivors: an ecological momentary assessment study.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {34},
number = {5},
pages = {},
pmid = {42060133},
issn = {1433-7339},
mesh = {Humans ; Female ; Ecological Momentary Assessment ; *Cancer Survivors/psychology ; Middle Aged ; Male ; Digital Health ; Adult ; Sleep Duration ; *Neoplasms/psychology ; Aged ; Emotional Regulation ; Interpersonal Relations ; Affect ; Mental Health ; Smartphone ; Pain/epidemiology ; },
abstract = {PURPOSE: The growing population of cancer survivors in the US highlights the need for adaptive digital mental health treatments that can help address a large gap in mental health treatment. Although just-in-time adaptive interventions (JITAIs) hold promise for improving mental health outcomes, none have been developed specifically for cancer survivors, in part due to their complexity. The purpose of this study was to identify survivor-level factors that could inform the development and optimization of adaptive treatments aimed at improving affective outcomes in this population.

METHODS: A total of 426 adults diagnosed with cancer within the past five years participated in a 5-week observational study. Participants completed smartphone-based surveys three times per day assessing momentary affect, affective forecasting, emotion regulation attempts, social interaction quality, pain, and sleep duration from the previous night. Linear mixed-effects models were conducted at the momentary level to examine associations with positive affect (PA) and negative affect (NA).

RESULTS: Higher momentary PA was associated with longer sleep duration the previous night, lower pain, fewer emotion regulation attempts, higher-quality social interactions, and forecasting one's future affect as more positive. In contrast, higher momentary NA was associated with shorter sleep duration the previous night, greater pain, more frequent emotion regulation attempts, poorer-quality social interactions, and forecasting one's future affect as more negative.

CONCLUSION: These findings identify several modifiable meta-emotion and psychosocial factors that may serve as promising targets for future JITAIs designed to improve affective well-being among cancer survivors.},
}

Humans
Female
Ecological Momentary Assessment
*Cancer Survivors/psychology
Middle Aged
Male
Digital Health
Adult
Sleep Duration
*Neoplasms/psychology
Aged
Emotional Regulation
Interpersonal Relations
Affect
Mental Health
Smartphone
Pain/epidemiology

@article {pmid42069381,
year = {2026},
author = {Kuhn, E and Hallenbeck, HW and Owen, JE},
title = {Assessment and Treatment of Posttraumatic Stress Disorder via Digital Mental Health Technology.},
journal = {The Psychiatric clinics of North America},
volume = {49},
number = {2},
pages = {359-375},
doi = {10.1016/j.psc.2025.08.025},
pmid = {42069381},
issn = {1558-3147},
mesh = {Humans ; *Stress Disorders, Post-Traumatic/therapy/diagnosis ; Digital Health ; Mobile Applications ; Telemedicine ; Digital Media ; Virtual Reality Exposure Therapy/methods ; Ecological Momentary Assessment ; },
abstract = {This article presents a review of examples of digital mental health technology (DMHT) for assessing and treating posttraumatic stress disorder (PTSD), including research supporting these innovative solutions. Tools for assessing PTSD are reviewed, including digital administration of self-report measures, ecological momentary assessment methods, personal sensing, electronic medical record and other naturalistic data sources, and emerging digital assessment tools. Next, DMHTs for PTSD treatment are reviewed, including Internet-based interventions, mobile mental health apps, virtual reality therapy, and several emerging digital interventions. DMHT applications for PTSD have demonstrated promise in research and are beginning to be used in clinical practice.},
}

Humans
*Stress Disorders, Post-Traumatic/therapy/diagnosis
Digital Health
Mobile Applications
Telemedicine
Digital Media
Virtual Reality Exposure Therapy/methods
Ecological Momentary Assessment

@article {pmid42075636,
year = {2026},
author = {Marano, G and Acanfora, M and Mandracchia, G and Traversi, G and Mazza, O and Pallotti, A and Veneziani, G and Lai, C and Caroppo, E and Mazza, M},
title = {Digital and Immersive Technologies for Rehabilitation in Complex Psychosis: State of the Art and Future Directions.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
pmid = {42075636},
issn = {1648-9144},
mesh = {Humans ; *Psychotic Disorders/rehabilitation/psychology ; Digital Health ; Telemedicine ; Virtual Reality ; },
abstract = {Complex psychosis (CP) remains one of the most challenging conditions in mental health, characterized by persistent symptoms, cognitive impairment, functional disability, and reduced autonomy. Traditional rehabilitation approaches, although essential, are often insufficient to address the multidimensional needs of these individuals. Over the past decade, rapid advances in digital health have opened new opportunities to enhance psychosocial rehabilitation, improve engagement, and personalize treatment pathways. This narrative review synthesizes current evidence on the use of digital and immersive technologies in the rehabilitation of people with CP, including virtual reality (VR), augmented reality (AR), telerehabilitation platforms, mobile health (m-Health) applications, digital phenotyping, and AI-assisted cognitive remediation. We examine clinical trials, feasibility studies, and real-world implementations published between 2015 and 2025, highlighting the efficacy of VR-based social cognition training, remote cognitive remediation, ecological momentary interventions, and hybrid digital-in-person rehabilitation models. Mechanisms of action, transfer to real-world functioning, and predictors of engagement are described. Barriers such as digital literacy, access disparities, privacy concerns, and clinical integration are critically discussed. We also outline future directions, including adaptive algorithms, biosensor integration, and the development of multimodal digital ecosystems tailored to individual recovery trajectories. By integrating technological innovation with recovery-oriented care, digital rehabilitation tools have the potential to transform the treatment landscape for people with CP. This review offers a roadmap for clinicians, researchers, and policymakers seeking to incorporate evidence-based digital solutions into modern psychiatric rehabilitation.},
}

Humans
*Psychotic Disorders/rehabilitation/psychology
Digital Health
Telemedicine
Virtual Reality

@article {pmid42102286,
year = {2026},
author = {Petit, P and Vuillerme, N},
title = {The Digital Exposome: A Life Course Framework for Health in the Digital Age.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e90153},
pmid = {42102286},
issn = {1438-8871},
mesh = {Humans ; *Exposome ; Digital Health ; *Digital Technology ; Digital Media ; },
abstract = {Digital technologies are reshaping human behavior, health care delivery, and population health; however, their cumulative effects across the lifespan remain underexplored. This viewpoint argues that exposures arising from interactions with digital technologies should be formally integrated into exposome science as a distinct, measurable component of the human environment. Our aims are to (1) redefine the digital component of the exposome (the digital exposome) within the broader exposome framework, (2) examine its life course implications for health and equity, and (3) outline a research and policy agenda to enable its systematic measurement and integration into clinical and public health practice. Digital technology-related exposures can confer benefits such as enhanced health monitoring, personalized interventions, improved access to care, and the promotion of healthy behaviors. However, they may also introduce potential risks, including mental health challenges, cognitive and circadian disruptions, sedentary lifestyles, exposure to misinformation, and widening inequities among vulnerable populations. Despite their ubiquity, digital technology-related exposures remain poorly integrated into clinical medicine, epidemiology, or public and global health policies. Drawing on interdisciplinary evidence from exposure science, epidemiology, and digital phenotyping research, we propose a refined conceptual definition of the digital exposome grounded in the classical exposome domains. We propose redefining the digital exposome as the full spectrum of exposures resulting from interactions or proximities with digital technologies and their combined influence on health across the lifespan. This framework conceptualizes digital technology-related exposures as a dynamic set of environmental influences operating through sociotechnical, behavioral, and biological pathways over the life course. To operationalize this framework, we discuss practical approaches using validated behavioral instruments, objective device use logs, ecological momentary assessments, smartphone-based digital phenotyping, and wearable sensing technologies. Systematic measurement, large-scale longitudinal studies, and harmonized exposure metrics are needed to characterize the cumulative health impacts of digital environments more accurately. Emerging tools such as digital markers or biomarkers and digital phenotypes offer promising opportunities to link real-world technology use with physiological and biological outcomes, thereby supporting precision medicine and population health strategies. Ethical governance, privacy safeguards, and equity considerations must be embedded from the start, drawing on emerging exposomethics frameworks. Recognizing the digital exposome as a modifiable determinant of health offers a foundation for evidence-based guidance, prevention strategies, and policy interventions suited to increasingly digital societies. By integrating digital technology-related exposures into exposome science, clinical practice, and public health research, this viewpoint seeks to foster interdisciplinary dialogue, guide future empirical work, and support the development of safer and more equitable digital environments across the lifespan.},
}

Humans
*Exposome
Digital Health
*Digital Technology
Digital Media

@article {pmid42108299,
year = {2026},
author = {Wang, F and Zhang, H},
title = {Microbial Omics Analysis for Multispecies Symbioses in Staple and Traditional Fermented Foods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {217-240},
pmid = {42108299},
issn = {1940-6029},
mesh = {*Fermented Foods/microbiology ; *Symbiosis ; Fermentation ; *Food Microbiology/methods ; *Microbiota ; Multiomics ; Vegetables/microbiology ; Humans ; },
abstract = {Fermented foods represent a cornerstone of global culinary traditions, underpinned by intricate microbial communities that drive flavor development and preservation. This chapter examines the microbial ecology and functional interactions across representative staple and traditional fermented foods, including fermented vegetables (sauerkraut, kimchi), fermented condiments (soy sauce, vinegar, miso, doubanjiang), and fermented alcoholic beverages (Chinese baijiu, wine, sake, Huangjiu). Recent meta-omics advances have revealed dynamic community succession, cross-feeding networks, quorum-sensing mechanisms, and key microorganisms contributing to flavor metabolites and health-promoting compounds. Furthermore, synthetic microbial communities and starter engineering are discussed as strategies to standardize fermentation, enhance quality, and develop novel functional products.},
}

*Fermented Foods/microbiology
*Symbiosis
Fermentation
*Food Microbiology/methods
*Microbiota
Multiomics
Vegetables/microbiology
Humans

@article {pmid41956654,
year = {2026},
author = {Xian, S and Wang, X and Wang, Y and Zhang, W and Liu, X and Shen, G and Zhang, Z and Hou, X and Xu, F and Chen, A},
title = {Flavor remodeling in Paocai during round spontaneous fermentation: an integrative analysis of active microbial succession and metabolic processes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 2},
pages = {118973},
doi = {10.1016/j.foodres.2026.118973},
pmid = {41956654},
issn = {1873-7145},
mesh = {*Fermentation ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; *Food Microbiology ; *Fermented Foods/microbiology/analysis ; *Taste ; Microbiota ; Multiomics ; Lactiplantibacillus plantarum/metabolism ; },
abstract = {Traditional paocai is a representative Chinese fermented vegetable that is typically produced through successive fermentation cycles. However, the mechanisms underlying flavor differences between paocai fermented in fresh and aged brine during continuous fermentation remain unclear, particularly the dynamic coupling among environmental variation, active microbial communities, and flavor development across fermentation rounds. Here, comprehensive two-dimensional gas chromatography-mass spectrometry and metatranscriptomic analyses were integrated with nonlinear modeling, machine learning, and time-decay relationship analysis to investigate physicochemical evolution, microbial succession, and flavor formation during continuous fermentation of traditional paocai. The results showed that pH, organic acids, and microbial diversity exhibited pronounced nonlinear dynamics across 11 successive fermentation rounds. Random forest analysis identified Phenylethyl alcohol, Hexadecanoic acid, ethyl ester, and Tetradecanoic acid, ethyl ester as key volatile compounds discriminating fermentation rounds. Lactiplantibacillus plantarum and Lactobacillus japonicus were identified as core microorganisms throughout continuous fermentation, while microbial community structures progressively diverged from their initial states, consistent with a significant time-decay relationship. Multi-omics integration using O2PLS further revealed tight and complex cross-omics associations between active microbial taxa and volatile flavor compounds, enabling reconstruction of key flavor-related metabolic pathways during successive fermentation rounds of Sichuan paocai. Comparative metatranscriptomic analyses between fresh and aged paocai clarified the metabolic basis underlying flavor differentiation at later fermentation stages. Overall, this study elucidates flavor evolution in paocai under continuous round fermentation from microbial ecological and metabolic perspectives, providing a theoretical basis for flavor regulation and quality stabilization in traditional fermented foods.},
}

*Fermentation
Gas Chromatography-Mass Spectrometry
Volatile Organic Compounds/analysis
*Food Microbiology
*Fermented Foods/microbiology/analysis
*Taste
Microbiota
Multiomics
Lactiplantibacillus plantarum/metabolism

@article {pmid41960380,
year = {2026},
author = {Chen, L and Yao, W},
title = {Fall detection and pre-impact prediction technologies in older adults: a scoping review of translational maturity and public health integration.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1737644},
pmid = {41960380},
issn = {2296-2565},
mesh = {Humans ; *Accidental Falls/prevention & control ; *Wearable Electronic Devices ; *Public Health ; Aged ; Digital Health ; Prediction Algorithms ; },
abstract = {OBJECTIVE: To map the current landscape of wearable and sensor-based fall detection and pre-impact prediction technologies relevant to older adults and to evaluate their translational maturity within public health contexts.

METHODS: A scoping review was conducted following PRISMA-ScR guidelines. Four electronic databases (PubMed, Web of Science, Scopus, and IEEE Xplore) were systematically searched for studies published between January 2005 and September 2025. Eligible studies reported the development or validation of fall detection or pre-impact prediction systems incorporating wearable, vision-based, environmental, or multimodal sensing modalities. In total, 243 studies were included in the overall synthesis, with a predefined subgroup of 21 studies involving real-world or mixed real-world validation in older adult populations (≥65 years).

RESULTS: Across the 243 included studies, wearable inertial measurement unit (IMU)-based systems constituted the dominant technological stream, and post-fall detection remained the most frequently investigated functional objective. However, more than half of studies relied primarily on laboratory-based simulated fall protocols. Within the real-world validated older adult subgroup (n = 21), 71.4% focused on post-fall detection, 19.0% investigated pre-impact prediction, and 9.5% addressed fall risk modeling. While technical performance metrics such as sensitivity and specificity were frequently reported under controlled conditions, evidence regarding long-term adherence, workflow integration, and health economic impact was limited. A maturity gradient emerged across modalities, with wearable detection systems demonstrating stronger ecological grounding than predictive, multimodal, and ecosystem-level approaches.

CONCLUSION: Although technological innovation in fall-related sensing systems has expanded rapidly, translational maturity remains uneven. Bridging the gap between algorithmic performance and scalable public health implementation will require robust real-world validation, longitudinal adherence evaluation, implementation science frameworks, and economic assessment. Advancing along a continuum from reactive detection toward predictive and personalized prevention represents a critical pathway for supporting safe and independent aging.},
}

Humans
*Accidental Falls/prevention & control
*Wearable Electronic Devices
*Public Health
Aged
Digital Health
Prediction Algorithms

@article {pmid41988563,
year = {2026},
author = {Guo, RL and Sun, Y},
title = {Digital art as a novel medium for health communication: enabling interactive interventions and reconstructing health experiences in public health.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1786916},
pmid = {41988563},
issn = {2296-2565},
mesh = {Humans ; Digital Media ; *Health Communication/methods ; *Public Health ; *Art ; *Health Promotion/methods ; Digital Health ; },
abstract = {This perspective article explores digital art as an innovative medium for health communication. It argues that traditional health communication-often unidirectional and emotionally detached-frequently fails to support lasting behavioral change. In contrast, digital art introduces interactivity, immersive environments, and emotionally resonant narratives, enabling more engaging forms of health messaging and fostering deeper public involvement and awareness. Drawing on social cognitive theory, experiential learning, and media ecology, the article develops a conceptual framework and examines practical strategies such as narrative reconstruction, data visualization, and community-based co-creation. It also addresses key challenges, including issues of access, content accuracy, and ethical use of personal data in artistic health interventions. Looking forward, this perspective calls for stronger interdisciplinary collaboration, supportive policies, and evidence-based research to further integrate digital art into public health practice. By doing so, digital art could contribute meaningfully to more inclusive, participatory, and sustainable approaches to health promotion.},
}

Humans
Digital Media
*Health Communication/methods
*Public Health
*Art
*Health Promotion/methods
Digital Health