@article {pmid42423304,
year = {2026},
author = {Rehman, M and Sajjad, W and Kang, S and Rafiq, M and Zhao, Y},
title = {Mobilization of the ancient resistome from thawing permafrost.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1040841X.2026.2698958},
pmid = {42423304},
issn = {1549-7828},
abstract = {Permafrost, ground frozen for at least two consecutive years, covers nearly one-quarter of the Northern Hemisphere and hosts diverse microbial communities. Climate-driven thaw is releasing preserved microorganisms and genetic material into contemporary ecosystems, where ancient genetic elements may be reintroduced into modern microbes and participate in gene exchange processes. Among these, antibiotic resistance genes (ARGs), which confer resistance to antibiotics, represent a critical yet underrecognized threat. Many originate from ancient microbial ecosystems shaped by natural antibiotic production and resistance, encode mechanisms not yet observed in clinical settings, and are associated with mobile genetic elements (MGEs) that facilitate horizontal gene transfer across microbial domains. Here, we synthesize evolutionary, molecular, and ecological perspectives on the preservation, release, and mobilization of permafrost-derived ARGs. We highlight mineral-DNA interactions that enhance the long-term stability of extracellular DNA containing ARGs and review the roles of MGEs in redistributing resistance determinants following thaw. We discuss conceptual models of rare cross-domain gene transfer and consider ecological and evolutionary implications under thawing conditions. ARG release from permafrost represents a neglected environmental factor that may contribute to antimicrobial resistance (AMR) dynamics and warrants investigation. Finally, identify key knowledge gaps and propose interdisciplinary frameworks for surveillance, risk assessment, and mitigation.},
}

@article {pmid42424242,
year = {2026},
author = {Alraihan, NM and French, M and Moore, DC and Sedda, L},
title = {Public health informatics tools for dengue risk management: A systematic review.},
journal = {PLOS digital health},
volume = {5},
number = {7},
pages = {e0001495},
pmid = {42424242},
issn = {2767-3170},
abstract = {Public health informatics (PHI) tools, including Geographic Information Systems (GIS), Electronic Health Records (EHRs), and Health Information Exchange systems, are increasingly applied to dengue fever surveillance, prevention, and control. Despite their growing adoption, a synthesis of empirical evidence examining their real-world application across endemic settings has not previously been conducted. This systematic review aimed to examine how PHI tools have been applied to dengue risk management, and to evaluate the certainty of evidence supporting their use. A structured literature search was conducted across PubMed, EBSCO/MEDLINE, and Web of Science. Nineteen peer-reviewed empirical studies published between 2010 and 2024 were included following eligibility screening against pre-defined inclusion and exclusion criteria. Study quality was assessed using the Newcastle-Ottawa Scale adapted for cross-sectional studies. Certainty of evidence was evaluated using the GRADE framework across five domains: risk of bias, inconsistency, indirectness, imprecision, and publication bias. Findings were synthesised narratively and organised into three functional categories: mapping and visualisation (n = 12), epidemiological insights (n = 5), and enhanced surveillance (n = 2). GIS was the most frequently used tool, consistently identifying dengue hotspots and supporting spatial dengue risk mapping across diverse geographic settings. EHR-linked health information systems supported epidemiological profiling and, in a limited number of studies, improved outbreak detection. Certainty of evidence was rated as very low across all three categories, reflecting the low evidence associated to observational study designs, methodological heterogeneity, and the uniform reporting of positive findings across all included studies. PHI tools show consistent descriptive utility in dengue surveillance across diverse settings. However, given the very low certainty of evidence, conclusions should be interpreted with caution. Gaps remain in high-burden regions including Sub-Saharan Africa and the Middle East. Standardised evaluation frameworks, broader geographic representation, and integration with emerging digital health technologies are needed to strengthen the evidence base. Systematic review registration: PROSPERO; registration number CRD42024572021.},
}

@article {pmid42426003,
year = {2026},
author = {Lei, Z and Liu, H and Zhang, Y and Li, X and Xiao, C and Xing, G and Guo, R and Zhang, Y and Xu, J and Yang, W and Chen, H and Li, M and Lu, T and Li, S and Lu, Y and Yan, Q},
title = {The Cat Gut Microbial Genome Collection reveals global structure of the feline gut microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01088-3},
pmid = {42426003},
issn = {2055-5008},
support = {32202857//National Natural Science Foundation of China/ ; 2024BBB073//Hubei Key Research and Development Project/ ; YXYX2506//Open Research Project of Sichuan Provincial Clinical Research Center for Imaging Medicine/ ; XN202402//Open Project of Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education/ ; 2022CXRC9555//Ganzhou Science and Technology Innovation Talent Project - Youth Talent Project/ ; },
abstract = {The gut microbiome is a critical determinant of mammalian health, yet our understanding is largely derived from humans and laboratory models. The ecological principles governing the microbiome of globally important companion animals, such as cats, remain poorly defined. We generated the Cat Gut Microbial Genome Collection (CGMGC), a comprehensive resource encompassing over 40,000 microbial genomes. This collection spans 874 prokaryotic species, 6 fungal species, and 5543 viral operational taxonomic units, derived from feline gut samples across diverse geographical regions. Our analysis reveals that the cat gut microbiome is a highly host-specific ecosystem whose structure is primarily driven by geography rather than host genetics or diet. Over 50% of the identified prokaryotic species are unique to felines and contain novel taxonomic lineages. Functionally, the virome encodes a vast repertoire of auxiliary metabolic genes, indicating pervasive inter-kingdom control over bacterial hosts. Surprisingly, the feline gut shares significantly more microbial species with humans than with laboratory mice, suggesting convergent evolution in cohabiting species. The core ecological principles of the feline gut are profound host-specificity, geographic structuring, and pervasive viral modulation of bacterial function. This work redefines the feline microbiome as a unique model for host-microbe co-evolution and establishes a genomic foundation for a new era of evidence-based veterinary medicine.},
}

@article {pmid41861125,
year = {2026},
author = {Hopkins, B and Davies, P and Noble, PJ and Bunford-Davies, A and Lawson, A and Pinchbeck, G and Lloyd, I and Smith, R and Radford, AD},
title = {Reusing health records from farm animal practices at scale: A potential complementary method of surveillance.},
journal = {The Veterinary record},
volume = {199},
number = {2},
pages = {e73-e81},
doi = {10.1002/vetr.70501},
pmid = {41861125},
issn = {2042-7670},
support = {//Welsh Government/ ; //Llywodraeth Cymru/ ; //Arwain DGC/ ; },
mesh = {Animals ; Cattle ; Sheep ; *Electronic Health Records/statistics & numerical data ; *Sheep Diseases/drug therapy/epidemiology ; *Cattle Diseases/drug therapy/epidemiology ; Wales/epidemiology ; Pilot Projects ; Data Mining ; Anti-Bacterial Agents/therapeutic use ; *Population Surveillance/methods ; Animals, Domestic ; Farms ; },
abstract = {BACKGROUND: Disease in primary care frequently represents a surveillance blind spot, particularly for diseases affecting farm animals.

METHODS: Electronic health records (EHRs) were collected from four farm animal veterinary practices in Wales (February 2024‒January 2025) as part of a pilot study. Information collected included species treated, date, owner postcode, products sold and clinical free text. Text mining and topic modelling were used to describe treatments and classify syndromes.

RESULTS: In total, 32,799 records were collected. Antimicrobials were prescribed in 32.6% and 63.8% of cattle and sheep records, respectively. The most frequent antibiotic classes in both species were tetracyclines, macrolides, penicillins and penicillin‒aminoglycoside combinations. There were no recorded category A antimicrobials, and category B antimicrobials were prescribed in only 0.12% and 0.04% of cattle and sheep EHRs, respectively. Text mining and topic modelling seemed efficient methods to identify key syndromes, including mastitis, joint ill, lameness and pneumonia, and how these were treated.

LIMITATIONS: Some EHRs described more than one animal with different diagnoses, obfuscating the attribution of treatment to syndrome.

CONCLUSION: The increasing availability of EHRs at scale and in real-time represents a complementary opportunity to survey disease and treatment on farms. Text mining methods, including artificial intelligence, could efficiently identify important syndromes and provide novel insight into use of antibacterials.},
}

Animals
Cattle
Sheep
*Electronic Health Records/statistics & numerical data
*Sheep Diseases/drug therapy/epidemiology
*Cattle Diseases/drug therapy/epidemiology
Wales/epidemiology
Pilot Projects
Data Mining
Anti-Bacterial Agents/therapeutic use
*Population Surveillance/methods
Animals, Domestic
Farms

@article {pmid42049773,
year = {2026},
author = {Wei, X and Tang, D and Peng, Y and Huang, B and Zhu, Y and Liang, Z and Hu, Y},
title = {A telomere-to-telomere reference genome for Stemona tuberosa.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42049773},
issn = {2052-4463},
mesh = {*Genome, Plant ; Haplotypes ; *Stemonaceae/genetics ; *Telomere/genetics ; Datasets as Topic ; },
abstract = {Stemona tuberosa is a medicinally important species, however, a complete telomere-to-telomere (T2T) genome assembly has remained unavailable. Here, we present the first T2T genome assembly for S. tuberosa, generated by integrating PacBio HiFi, ultra-long Oxford Nanopore, Illumina, and Hi-C sequencing technologies. The assembly produced two highly contiguous haplotype-resolved genomes, with total sizes of 803.04 Mb and 795.04 Mb, and contig N50 values of 113.29 Mb and 111.11 Mb, respectively. The proportion of fully assembled chromosomes reached 100% in both haplotypes. In addition, 14 putative centromeric regions were successfully identified across 7 pseudochromosomes, along with the annotation of 25,561 and 25,854 genes in the two haplotypes, respectively. This T2T genome assembly of S. tuberosa provides a valuable reference for elucidating the genetic architecture of the species. It significantly advances our capacity to investigate structural variations, gene function, and evolutionary processes within Stemona and related medicinal plant lineages.},
}

*Genome, Plant
Haplotypes
*Stemonaceae/genetics
*Telomere/genetics
Datasets as Topic

@article {pmid42056141,
year = {2026},
author = {Li, W and Yu, D and Que, Y and Tian, H and Dong, W and Wang, E and Xu, N and Shao, K and Zhu, B and Hu, X},
title = {The first chromosomal level genome assembly and annotation of Pareuchiloglanis anteanalis.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42056141},
issn = {2052-4463},
support = {31572593//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Catfishes/genetics ; *Chromosomes ; *Genome ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Pareuchiloglanis anteanalis belonging to the genus Pareuchiloglanis, within the family Sisoridae (order Siluriformes), is a group of small benthic-dwelling freshwater fishes adapted to alpine canyon environments characterized by steep slopes, rapid currents, and marked seasonal fluctuations in water discharge between dry and flood periods. This species is primarily distributed in the Jinsha River, Dadu River, and Bailong River, all located within the upper reaches of the Yangtze River drainage. In this research, through the integration of PacBio HiFi long read sequencing and Hi-C (high-throughput chromatin capture) technology, we generated a high-quality chromosome-level genome of the P. anteanalis. The assembly yielded a genome of 873.97 Mb, with a scaffold N50 length of 50.12 Mb, covering 98.59% of the contig-level genome, were accurately mapped onto 18 chromosomes by using Hi-C data. The BUSCO analysis indicated that the completeness of the genome assembly and the annotation both reached 93.3% and 93.4%, respectively. This high-quality genomic resource provides a solid foundation for deciphering genome architecture and functional elements, thereby enabling deeper investigations into the genetic mechanisms underlying adaptation in P. anteanalis. Moreover, it offers valuable support for resource conservation, artificial propagation, and selective breeding of this native species.},
}

Animals
*Catfishes/genetics
*Chromosomes
*Genome
Molecular Sequence Annotation
Datasets as Topic

@article {pmid42106342,
year = {2026},
author = {Mateo, M and Briand, C and Korta, M and Beaulaton, L and Drouineau, H and Pella, H and Amilhat, E and Bardonnet, A and Antunes, C and De Miguel Rubio, R and Domingos, I and Fernández-Delgado, C and Labedan, M and Herrera, M and Sagnes, P and Zamora, L and Díaz, E},
title = {A database of eels and their freshwater habitats in southwestern Europe.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42106342},
issn = {2052-4463},
mesh = {Animals ; *Ecosystem ; Rivers ; *Anguilla ; Fresh Water ; Spain ; Portugal ; Animal Migration ; France ; Databases, Factual ; },
abstract = {The European eel stock (Anguilla anguilla) is outside safe biological limits. A range-wide stock assessment requires the creation and standardisation of databases that include information on eels and their habitats in different countries throughout their distribution range. The SUDOANG 1.0.4 database compiles standardised data on river courses in France and the Iberian Peninsula (Spain and Portugal). Using GIS tools, information on water surface and on other potential aquatic habitats surrounding each river segment has been collected. This common river network provides tools to quickly accumulate information along the river or along the natural path of migration from/to the sea. The database also compiles information on the surface of other habitats, human pressures (including 106400 obstacles), and provides eel abundance and biometric estimations derived from the Eel Density Analysis (EDA) model at the river reach scale for the reference year 2015. The river network supports ecological assessment of the eel habitats, and should also be useful for studies on other migratory species.},
}

Animals
*Ecosystem
Rivers
*Anguilla
Fresh Water
Spain
Portugal
Animal Migration
France
Databases, Factual

@article {pmid42174524,
year = {2026},
author = {Yuan, M and Bi, S and Chen, Z and Fan, X and Chen, X and Shen, K},
title = {Development of an interpretable machine learning model-based online tool for risk prediction of falls and fall-related injuries in Chinese middle-aged and older adults with depressive symptoms-a longitudinal study based on the CHARLS database.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {42174524},
issn = {1471-2458},
mesh = {Humans ; *Accidental Falls/statistics & numerical data ; China/epidemiology ; Longitudinal Studies ; Middle Aged ; Predictive Learning Models ; *Wounds and Injuries/epidemiology ; *Depression/epidemiology ; Risk Assessment/methods ; Aged ; Female ; Male ; *Machine Learning ; Boosting Machine Learning Algorithms ; Databases, Factual ; Prediction Algorithms ; East Asian People ; },
abstract = {BACKGROUND: This study aimed to establish and validate interpretable Machine Learning (ML) models for predicting falls and fall-related injuries in middle-aged and older adults with depressive symptoms (DS) and to develop relevant online computational tools.

METHODS: Using data from the China Health and Retirement Longitudinal Study (CHARLS) survey from 2015 to 2018, 32 predictor variables related to the risk of falls and fall-related injuries in middle-aged and older adults with DS were included based on five dimensions of the health ecology model, and the important predictor variables were screened using Principal Component Analysis and LASSO regression at the same time. We further developed eight ML algorithms-Logistic Regression(LR), Support Vector Machine(SVM), Gradient Boosting Machine (GBM), Neural Network (NN), eXtreme Gradient Boosting (XGBoost), Adaptive Boosting (AdaBoost), Light Gradient Boosting Machine (LightGBM) and Categorical Boosting (CatBoost)-to construct the risk prediction model, and selected the best predictive variables based on grid search and 10-fold cross-validation. SHapley Additive exPlanations (SHAP) was used for personalised interpretation of the models. In addition, we further performed stratified analyses by dividing participants into two age groups: 45-59 years and 60 years and older.

RESULTS: Among 3,664 middle-aged and older adults with DS, the incidence rate of falls and fall-related injuries after three years of follow-up was 20.36% and 8.92%, respectively. Among all models, LightGBM had the best performance. LightGBM performed the best, with an area under the curve (AUC) of 0.821 (95% CI: 0.802-0.841) for the fall risk test set and an AUC of 0.905 (95% CI: 0.892-0.919) for the fall injury risk test set. We identified important risk factors for falls and fall-related injuries in middle-aged and older adults with DS. The optimal predictive model and risk predictors differed from those identified before stratification by age. SHAP visualises the specific contributions of these risk factors, thereby enhancing the model's value for application. Online tools to implement the model are available at https://riskpredictiontool.shinyapps.io/falls_prediction_tool/ and https://riskpredictiontool.shinyapps.io/fall_related_injuries_prediction_tool/.

DISCUSSION AND CONCLUSIONS: The results can help predict risk of falls and fall-related injuries among middle-aged and older adults with DS. These findings provide an important guide for the development of public health strategies.},
}

Humans
*Accidental Falls/statistics & numerical data
China/epidemiology
Longitudinal Studies
Middle Aged
Predictive Learning Models
*Wounds and Injuries/epidemiology
*Depression/epidemiology
Risk Assessment/methods
Aged
Female
Male
*Machine Learning
Boosting Machine Learning Algorithms
Databases, Factual
Prediction Algorithms
East Asian People

@article {pmid42418234,
year = {2026},
author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC},
title = {Evolving strategies for virus discovery.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
pmid = {42418234},
issn = {2057-5858},
mesh = {*Viruses/genetics/isolation & purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; },
abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.},
}

*Viruses/genetics/isolation & purification/classification
Genome, Viral
*Metagenomics/methods
*Virome/genetics
Artificial Intelligence
Computational Biology/methods

@article {pmid42419831,
year = {2026},
author = {Li, JW and Wang, Y and Chaurasia, A},
title = {Microbial biomarkers for OPMD progression.},
journal = {Advances in immunology},
volume = {169},
number = {},
pages = {193-212},
doi = {10.1016/bs.ai.2026.03.001},
pmid = {42419831},
issn = {1557-8445},
mesh = {Humans ; *Microbiota ; Disease Progression ; *Mouth Neoplasms/microbiology/diagnosis ; *Dysbiosis/microbiology ; Biomarkers ; *Carcinoma, Squamous Cell/microbiology/diagnosis ; *Biomarkers, Tumor ; *Precancerous Conditions/microbiology ; Metabolomics ; Multiomics ; },
abstract = {Oral potentially malignant disorders (OPMDs) present a heterogeneous risk of progression to oral squamous cell carcinoma (OSCC), underscoring the need for reliable, non-invasive biomarkers to aid in clinical stratification. This chapter evaluates the utility of the oral microbiome as a source of predictive biomarkers for OPMD progression. Current evidence indicates that OPMDs and OSCC are frequently associated with microbial dysbiosis, characterized by a shift toward anaerobic, periodontal-associated taxa, such as Fusobacterium and Porphyromonas, and a concomitant depletion of health-associated Streptococcus. However, translating these taxonomic signatures into clinical practice is hindered by overlapping community structures across healthy, premalignant, and malignant mucosal states, alongside significant confounding from periodontal inflammation and lifestyle exposures. Furthermore, the field remains divided on whether this dysbiosis acts as an upstream driver of carcinogenesis or a downstream consequence of tumor-associated microenvironmental selection. To overcome these methodological and biological limitations, this chapter advocates for an ecology-driven, multi-omics approach. By integrating taxonomic profiling with functional readouts like metabolomics and metaproteomics, and contextualizing these signals within host microenvironmental strata (e.g., hypoxia and inflammation), researchers can achieve greater mechanistic interpretability and robustness. Ultimately, microbiome-informed tools are best positioned not as standalone diagnostic tests, but as adjunctive instruments for clinical triage and risk enrichment, provided they are rigorously validated in prospective, longitudinal converter/non-converter cohorts.},
}

Humans
*Microbiota
Disease Progression
*Mouth Neoplasms/microbiology/diagnosis
*Dysbiosis/microbiology
Biomarkers
*Carcinoma, Squamous Cell/microbiology/diagnosis
*Biomarkers, Tumor
*Precancerous Conditions/microbiology
Metabolomics
Multiomics

@article {pmid42422686,
year = {2026},
author = {Lyu, Y and Luo, C},
title = {Digital access, digital health information engagement, and self-reported preventive behavior among rural adults in Guizhou, China: media-use ecologies and cross-sectional associations.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1794204},
pmid = {42422686},
issn = {2296-2565},
mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; China ; Adult ; *Rural Population/statistics & numerical data ; Middle Aged ; Digital Health ; Digital Media ; Self Report ; *Health Behavior ; Media Exposure ; Adolescent ; Young Adult ; Aged ; },
abstract = {BACKGROUND: Digital health education may help reduce health-information inequality in underdeveloped rural areas, but evidence remains limited on how rural residents encounter health information across different media environments and how digital access, usability, engagement, and self-reported preventive behavior are interrelated. This study examined media-use ecologies and cross-sectional associations among digital access and skills, digital health information engagement, and self-reported preventive behavior among rural adults in Guizhou, China.

METHODS: A cross-sectional survey was conducted among 1,265 adult rural residents recruited from five selected counties/districts in Guizhou Province using a multistage non-probability sampling design. Latent class analysis was used to characterize health-information media-use ecologies based on nine indicators of information channels and social media platforms. Regression-based cross-sectional association models examined associations among digital access and skills, perceived ease of understanding digital health content, lower operational difficulty, digital health information engagement, attitudes and willingness toward health education, and self-reported preventive behavior, adjusting for sex, age, education, income, and media-use ecology.

RESULTS: Five media-use ecologies were identified, reflecting different combinations of offline interpersonal/professional channels, traditional media, and digital platforms. Residents in omnichannel and short-video/social-platform-centered ecologies reported higher digital health information engagement, whereas those in the offline village doctor/traditional channels ecology reported the lowest engagement. Higher digital access and skills were associated with stronger engagement, and this association was attenuated after accounting for perceived ease of understanding and lower operational difficulty. Greater engagement was associated with more frequent self-reported preventive behavior, and this association was attenuated after accounting for attitudes toward health education and willingness to adopt new forms of health education.

CONCLUSION: In this non-probability adult sample from selected rural sites in Guizhou, digital health inequality was reflected not only in unequal access to devices and networks, but also in differences in understanding, usability, engagement, and self-reported preventive behavior. The findings should be interpreted as cross-sectional associations among field-feasible indicators rather than evidence of causal mechanisms.},
}

Humans
Cross-Sectional Studies
Female
Male
China
Adult
*Rural Population/statistics & numerical data
Middle Aged
Digital Health
Digital Media
Self Report
*Health Behavior
Media Exposure
Adolescent
Young Adult
Aged

@article {pmid41543584,
year = {2026},
author = {Gupta, S and Patil, AB and Soman, AS and Vijay, N},
title = {Master of none: GPRC6A gene loss is more widespread than previously known.},
journal = {Genetica},
volume = {154},
number = {1},
pages = {5},
pmid = {41543584},
issn = {1573-6857},
support = {B.T./11/IYBA/2018/03//Department of Biotechnology, Ministry of Science and Technology, India/ ; E.C.R./2017/001430//Science and Engineering Research Board/ ; },
mesh = {*Receptors, G-Protein-Coupled/genetics ; *Mammals/genetics ; Humans ; Animals ; *Synteny ; *Evolution, Molecular ; Genome ; Datasets as Topic ; },
abstract = {GPRC6A encodes a class C GPCR that can be activated by multiple ligands and potentially acts as a central regulator of diverse metabolic processes by modulating endocrine pathways. Experimental studies have reported numerous distinct functions for GPRC6A, suggesting it may be a key drug target for several metabolic disorders. Yet, the actual function of GPRC6A has been the focus of considerable debate due to contradictory results and the prevalence of loss-of-function mutations in human populations, leading to the perception of GPRC6A as a "Master of none". Interestingly, a genome-wide screen for gene loss events in vertebrate species identified the disruption of the GPRC6A gene in toothed whales, in contrast to widespread conservation in the closely related Bovidae family. We employ a synteny-informed comparative genomic approach to demonstrate that the loss of the GPRC6A gene among mammalian species is more widespread than previously reported, encompassing the entire Bovidae group within Artiodactyla and other fully aquatic mammals, including those belonging to Sirenia. An in-depth search of the genomes and short and long-read sequencing datasets of monotremes, hystricomorphs, rhinolophoid bats, pika, koala, and two shrews (white-toothed pygmy shrew and Asian house shrew) reveals at least nine independent GPRC6A gene loss events in vertebrates, highlighting its lineage-specific dispensability and raising questions regarding its ubiquitous functionality. The evolutionary loss of GPRC6A likely represents a lineage-specific response to specialised diets and ecological niches, reshaping metabolic regulation and taste perception and illuminating how niche specialisation influences gene retention or loss within the GPCR landscape across species.},
}

*Receptors, G-Protein-Coupled/genetics
*Mammals/genetics
Humans
Animals
*Synteny
*Evolution, Molecular
Genome
Datasets as Topic

@article {pmid41921848,
year = {2026},
author = {Xu, H and Sun, J and Lu, F and Luo, Y and Bie, L and Xia, Q and Wang, Y and Lin, P and Shen, G},
title = {IMDD: A Database for Exploring Tissue-Specific Gene Expression Dynamics During Holometabolous Insects.},
journal = {Journal of molecular biology},
volume = {438},
number = {18},
pages = {169781},
doi = {10.1016/j.jmb.2026.169781},
pmid = {41921848},
issn = {1089-8638},
mesh = {Animals ; *Metamorphosis, Biological/genetics ; *Gene Expression Regulation, Developmental ; *Databases, Genetic ; Drosophila melanogaster/genetics/growth & development ; *Holometabola/genetics/growth & development ; Bombyx/genetics/growth & development ; Transcriptome/genetics ; Biocuration ; Organ Specificity/genetics ; Gene Regulatory Networks ; Bees/genetics/growth & development ; },
abstract = {The intricate process of insect metamorphosis is governed by precise tissue-specific gene expression dynamics. To facilitate the exploration of these complex regulatory programs, we have developed the Insect Metamorphic Development Database (IMDD), an interactive platform for four key holometabolous species, including Drosophila melanogaster, Bombyx mori, Aedes aegypti and Apis mellifera, which hold significant ecological, economic, and medical importance. IMDD integrates over 1200 bulk-tissue transcriptomes and more than 1.4 million single-cell profiles, providing broad coverage of developmental stages. The platform is specifically designed to empower researchers to explore dynamic gene expression changes at both tissue and single-cell resolutions, investigate cellular heterogeneity, and trace cell-type transitions. By providing a user-friendly interface for dissecting the molecular underpinnings of insect development, IMDD serves as a critical resource for exploring the spatiotemporal gene regulatory networks that drive metamorphosis. The database is freely accessible at http://www.bioimdd.com/.},
}

Animals
*Metamorphosis, Biological/genetics
*Gene Expression Regulation, Developmental
*Databases, Genetic
Drosophila melanogaster/genetics/growth & development
*Holometabola/genetics/growth & development
Bombyx/genetics/growth & development
Transcriptome/genetics
Biocuration
Organ Specificity/genetics
Gene Regulatory Networks
Bees/genetics/growth & development

@article {pmid42050343,
year = {2026},
author = {Sun, H and Wang, X and Deng, H and Xie, L and Zhou, E and Tan, N and Wu, Y},
title = {The chromosome-level genome assembly and annotation of Parabotia bimaculata (Cypriniformes: Cobitidae: Botiinae).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42050343},
issn = {2052-4463},
support = {KJZD-M202401301//Major Science and Technology Research Project of Chongqing Municipal Education Commission/ ; R2022YS08//Tower Foundation Program of Chongqing University of Arts and Sciences in China/ ; },
mesh = {Animals ; *Chromosomes ; *Cypriniformes/genetics ; *Genome ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Parabotia bimaculata is a rare loach species endemic to southwestern China. A high-quality reference genome is essential for advancing research across various biological fields concerning this species. Here, we report the first chromosome-level genome assembly and annotation of P. bimaculata. The assembled genome spans 610.59 Mb with a contig N50 of 21.19 Mb. Hi-C scaffolding anchored 96.92% of the sequences into 25 pseudo-chromosomes. By integrating homology-based prediction with RNA-sequencing data, we identified 26,312 protein-coding genes, of which 23,833 (90.58%) were functionally annotated. The assembly achieved a 98.54% BUSCO completeness score. This work provides a valuable genomic resource for P. bimaculata, establishing a foundation for future studies in genomics, evolutionary biology, and conservation.},
}

Animals
*Chromosomes
*Cypriniformes/genetics
*Genome
Molecular Sequence Annotation
Datasets as Topic

@article {pmid42143165,
year = {2026},
author = {Yang, J and Liang, BY and Fang, CY and Li, JJ and Zhang, P and Xiang, P and Zhang, LW and Liu, H},
title = {Exploring dysregulation of cuproptosis-related genes molecular clusters and candidate biomarkers in pterygium.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42143165},
issn = {2045-2322},
support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 82560205//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202208535051//China Scholarship Council/ ; 24JCQNJC02050//Tianjin Natural Science Foundation/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; 2024YNLCYXZX0343//Key Project of the Provincial Clinical Center of Yunnan Province/ ; },
mesh = {Humans ; *Pterygium/genetics/pathology/immunology/metabolism ; *Cuproptosis/genetics ; Biomarkers/metabolism ; Gene Expression Profiling ; Transcriptome ; Female ; Gene Expression Regulation ; Male ; Computational Biology/methods ; Machine Learning ; },
abstract = {Pterygium is a common ocular surface disorder, with its prevalence strongly correlated to ultraviolet (UV) exposure in geographic regions. Epidemiological investigations reveal significant demographic variations, with higher incidences observed in areas with intense UV radiation and within specific populations, notably rural individuals. Despite surgical interventions being the standard treatment, recurrent cases underline the necessity for understanding the underlying biological mechanisms contributing to pterygium pathogenesis. Recent advancements in cellular death mechanisms point to cuproptosis, a copper-dependent programmed cell death pathway, as a potential regulatory factor in ocular diseases, including pterygium. This study aims to systematically investigate the immunological significance of cuproptosis-related genes (CuRGs) in pterygium's pathogenesis using an integrative bioinformatics framework. We performed transcriptomic profiling on pterygium tissues and employed machine learning algorithms to identify pivotal biomarkers for pterygium risk stratification. Comprehensive immune profiling and functional enrichment analyses were conducted to elucidate the interplay between identified CuRGs and the immune microenvironment in pterygium. Our analysis highlighted 19 CuRGs, with eight genes displaying significant dysregulation in pterygium tissues (p < 0.05). We established robust associations between CuRG expression and prominent immune cell infiltrates, notably regulatory T cells and macrophages. Furthermore, three core biomarkers (SERTAD1, JMJD1C, CSRNP1) were identified through machine learning and validated by QPCR, with the support vector machine model demonstrating exceptional predictive performance (AUC = 0.84). Empirical validation corroborated significant downregulation of selected biomarkers in pterygium tissue samples compared to normal conjunctiva. Our findings underscore the vital role of CuRGs in modulating pterygium development through immune and metabolic interactions, establishing their potential as novel therapeutic targets. Nevertheless, our study has limitations, as these findings are hypothesis-generating and require validation in larger patient cohorts.},
}

Humans
*Pterygium/genetics/pathology/immunology/metabolism
*Cuproptosis/genetics
Biomarkers/metabolism
Gene Expression Profiling
Transcriptome
Female
Gene Expression Regulation
Male
Computational Biology/methods
Machine Learning

@article {pmid42263834,
year = {2026},
author = {Veli-Quispe, D and Urquizo-Prado, S and Cesare-Ariza, E and Ybaseta-Medina, J and Panay-Centeno, J and Tasayco-Márquez, LM and Ubillus, M and Montoya, Y and Torres-Roman, JS},
title = {Trends and regional inequalities in cerebrovascular disease mortality in Peru: An ecological time-series analysis, 2017-2025.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {35},
number = {8},
pages = {108675},
doi = {10.1016/j.jstrokecerebrovasdis.2026.108675},
pmid = {42263834},
issn = {1532-8511},
mesh = {Humans ; Peru/epidemiology ; *Cerebrovascular Disorders/mortality/diagnosis ; Female ; Male ; Time Factors ; Risk Factors ; *Health Status Disparities ; Aged ; Databases, Factual ; Middle Aged ; Risk Assessment ; Sex Distribution ; *Rural Health ; Cause of Death/trends ; Adult ; Age Distribution ; Socioeconomic Disparities in Health ; Urban Health ; Sex Factors ; Aged, 80 and over ; },
abstract = {BACKGROUND: Cerebrovascular disease remains a leading cause of mortality worldwide. In Peru, evidence on recent mortality trends and regional disparities is limited.

OBJECTIVE: To evaluate temporal trends and regional disparities in cerebrovascular disease mortality in Peru between 2017 and 2025.

METHODS: An ecological time-series study was conducted using national mortality data from the National Death Information System (SINADEF). Deaths with cerebrovascular disease as the underlying cause (ICD-10: I60-I69) were included. Age-standardised mortality rates (ASMRs) per 100,000 person-years were calculated using the SEGI world standard population. Temporal trends were analyzed using Joinpoint regression models to estimate annual percent change (APC) and average annual percent change (AAPC) with 95% confidence intervals (95% CI).

RESULTS: National cerebrovascular disease mortality rates remained relatively stable between 2017 and 2025 in both men and women. However, marked regional disparities were identified. The highest mortality rates were concentrated in Huancavelica, San Martín, and Apurímac. Among men, a significant increase was identified in Huanuco (APC: 7.6%; 95% CI: 2.6 to 12.9), whereas significant decreasing trends were observed in Lambayeque (APC: -8.0%; 95% CI: -14.0 to -1.6), Madre de Dios (APC: -5.9%; 95% CI: -11.3 to -0.2), Tacna (APC: -5.8%; 95% CI: -9.7 to -1.7), and Tumbes (APC: -5.9%; 95% CI: -10.7 to -0.9). Among women, Huanuco also showed a significant increase (APC: 7.0%; 95% CI: 4.0 to 10.1), while significant decreasing trends were identified in Callao (APC: -5.3%; 95% CI: -8.2 to -2.3), La Libertad (APC: -5.7%; 95% CI: -11.0 to -0.02), Moquegua (APC: -8.6%; 95% CI: -14.0 to -2.9), and Tacna (APC: -6.5%; 95% CI: -11.2 to -1.5).

CONCLUSION: Cerebrovascular disease mortality in Peru remained relatively stable at the national level but showed important regional heterogeneity. These findings highlight geographic disparities in mortality patterns and underscore the need for further research and region-specific public health strategies to improve cerebrovascular disease prevention and care.},
}

Humans
Peru/epidemiology
*Cerebrovascular Disorders/mortality/diagnosis
Female
Male
Time Factors
Risk Factors
*Health Status Disparities
Aged
Databases, Factual
Middle Aged
Risk Assessment
Sex Distribution
*Rural Health
Cause of Death/trends
Adult
Age Distribution
Socioeconomic Disparities in Health
Urban Health
Sex Factors
Aged, 80 and over

@article {pmid42395566,
year = {2026},
author = {Formenti, G and Absolon, DE and Abueg, LAL and Ackerman, F and Al-Ajli, FO and Aleixo, A and Antunes, A and Arcila, D and Audet, JN and Balacco, JR and Beavan, AJS and Belov, K and Betancur-R, R and Bidwell, SL and Biegler, MT and Bista, I and Blaxter, M and Boyer, K and Braasch, I and Bradbury, IR and Brajuka, N and Bronikowski, AM and Brown, T and Butler, G and Cao, S and Charvel, E and Chen, Y and Ciofi, C and Clawson, HM and Collins, JC and Correard, S and Corrigan, S and Couture, M and Crawford, AJ and D'Alessandre, ND and da Conceicao, HB and da Fonseca, RR and Daigavane, M and Dalapicolla, J and de Bruyn, M and de Jong, E and De Panis, DN and Detrich, HW and Scott, CD and Diekhans, M and Duarte, E and Durbin, R and Escalona, M and Eschenbrenner, M and Fedrigo, O and Fenn, J and Flannery, P and Forde, N and Gable, SM and Galante, PA and Ganesan, R and Gardiner, A and Garrison, E and Gemmell, NJ and Gilbert, MTP and Giudicelli, F and Gonçalves, TM and Guardia, GDA and Guarracino, A and Gupta, A and Haase, B and Hays, D and Hickey, G and Hiller, M and Hime, PM and Hogg, CJ and Horan, KM and Howe, K and Jackson, D and Jain, N and Kang, L and Kliver, S and Ko, BJ and Koepfli, KP and Komissarov, A and Komoroske, LM and Koo, B and Koren, S and Korlach, J and Kovacic, I and Krasheninnikova, K and Kuderna, LF and Langlois, RA and Lariviere, D and Larkin, DM and Lee, C and Lee, YH and Lewin, HA and Lim, D and Lou, RN and Mak, SS and Makova, KD and Marín-Gual, L and Marques-Bonet, T and Martin, FJ and Mathers, TC and Mazzoni, CJ and McCaffrey, K and McCarthy, SA and Medico, JA and Mercuri, RLV and Meyer, A and Michalak, P and Mirarab, S and Morin, PA and Mountcastle, J and Murphy, RW and Murphy, TD and Myers, EW and Naylor, GJ and Near, T and Nekrutenko, A and Ning, Z and Novak, BJ and O'Brien, MF and O'Connell, MJ and O'Toole, BP and Paez, S and Paten, B and Paulini, M and Pelan, SE and Pennell, M and Pfenning, AR and Phillippy, AM and Pinto, B and Pippel, M and Popova, M and Prylutskyi, M and Rhie, A and Crollius, HR and Ruiz-Herrera, A and Ryder, O and Safonova, Y and Santos, CA and Schatz, MC and Secomandi, S and Shaffer, HB and Shalmiyev, L and Shapiro, B and Smith, JJ and Sollitto, M and Sotero-Caio, CG and Steiner, CC and Sudmant, PH and Sweeney, DJ and Talbot, SC and Taylor, CH and Teeling, EC and Thibaud-Nissen, F and Tilley, T and Timoshevskaya, N and Traore, P and Turakhia, Y and Uliano-Silva, M and Venditti, C and Venkatesh, B and Vernes, SC and Warren, WC and Whelan, CV and Wilson, MA and Winkler, S and Wood, JM and Zhang, G and Zhao, G and Jarvis, ED and , },
title = {The Vertebrate Genomes Project Phase I: A global reference genome resource.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42395566},
issn = {2692-8205},
abstract = {The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ~70,000 extant vertebrate species[1]. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ~95% of vertebrate orders, along with additional lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods[2-4], alongside the growth of associated consortium initiatives and international collaborations[5-9]. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.},
}

@article {pmid42400857,
year = {2026},
author = {Meng, Q and Ma, M and Li, S and Han, X and Jin, T and Jiao, Y and Wang, L},
title = {Structural Variability in Bulk Soil and Rhizosphere Microbial Communities at Different Restoration Modes of Open-pit Coal Mine.},
journal = {Environmental management},
volume = {76},
number = {7},
pages = {},
pmid = {42400857},
issn = {1432-1009},
support = {HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; },
mesh = {*Soil Microbiology ; *Rhizosphere ; *Soil/chemistry ; *Coal Mining ; Nitrogen/analysis ; *Microbiota ; Bacteria ; *Environmental Restoration and Remediation/methods ; Carbon/analysis ; },
abstract = {Microbial communities serve as vital indicators of ecosystem health and play a crucial role in facilitating the restoration of degraded soil ecosystems, acting as key participants in soil nutrient cycling. However, the interaction mechanisms between microbial communities and plants in different soil zones under varying restoration approaches remain unclear. This study focused on a restoration area of a decommissioned open-pit coal mine in an alpine region, comparing the microbial community structure and nutrient characteristics of rhizosphere and bulk soils under two restoration methods: herbaceous vegetation restoration and sea-buckthorn shrub restoration. The aim is to reveal the impact of different restoration measures on the soil-microorganism interactions. The results demonstrated that soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), total potassium (TK), and available potassium (AK) contents were significantly higher in the herbaceous restoration area (O) than in the seabuckthorn area (S), by 51.7%, 88.6%, 38.2%, 13.1%, and 4.7%, respectively. Compared to bulk soil, rhizosphere soil exhibited higher microbial community diversity and richness. Furthermore, seabuckthorn rhizosphere microbial diversity surpassed that of herbaceous rhizosphere. Different restoration areas (DRE) significantly (p < 0.05) influenced the relative abundances of Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The seabuckthorn area showed higher proportions of Proteobacteria (26.48 - 42.86%) and Actinobacteria (28.26 - 45.19%) compared to the herbaceous area. Functional gene prediction revealed that the seabuckthorn area expressed significantly higher abundances of core metabolic functional genes related to energy production and conversion (C), amino acid transport and metabolism (E), carbohydrate metabolism (G), and lipid metabolism (I) than the herbaceous area. Additionally, a symbiotic functional guild comprising animal pathogens, endophytes, lichen parasites, plant pathogens, and wood saprotrophs was formed in the seabuckthorn area. Redundancy analysis (RDA) indicated significant positive correlations (p < 0.05) between Acidobacteria, Chloroflexi, Actinobacteria, and Ascomycota and the contents of SOC, TN, and total phosphorus (TP). Bacterial networks formed with Actinobacteria as the core hub, comprising 300 edges connecting 50 nodes, while fungal networks were dominated by Ascomycota. Based on these findings, this study proposes a synergistic restoration strategy characterized by "herbaceous-induced short-term priming" coupled with "seabuckthorn-driven long-term stability." This strategy provides a theoretical foundation for the targeted microbial regulation of ecological restoration in mining areas.},
}

*Soil Microbiology
*Rhizosphere
*Soil/chemistry
*Coal Mining
Nitrogen/analysis
*Microbiota
Bacteria
*Environmental Restoration and Remediation/methods
Carbon/analysis

@article {pmid42404501,
year = {2026},
author = {Hossain, MJ and Mim, NA and Akter, N and Sony, SA and Saikat, EH and Hossain, MA and Parvin, N and Evan, MR and Juma, JJ and Roy, PP and Maruf, MFI and Islam, R and Labib, A and Shatabde, ZA and Das, M and Amanulla, M},
title = {Epidemiological Trends, Public Health Challenges, and Strategic Control Priorities of Dengue in Bangladesh (2000-2024): A Narrative Review.},
journal = {Health science reports},
volume = {9},
number = {7},
pages = {e72747},
pmid = {42404501},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Dengue has evolved into a major public health crisis in Bangladesh, transitioning from sporadic outbreaks to endemic transmission with increasing frequency and severity. The unprecedented 2023 epidemic recorded more deaths than the cumulative total of the previous two decades, highlighting the urgent need for a comprehensive synthesis of epidemiological trends and control challenges.

METHODS: This narrative review synthesizes published literature, surveillance reports, and national health data from 2000 to 2024 to examine the evolving epidemiology, clinical characteristics, transmission dynamics, and public health responses related to dengue in Bangladesh.

RESULTS: Epidemiological analysis reveals a dramatic rise in incidence and mortality, with widespread geographic expansion beyond Dhaka into southern and rural districts and a shift toward earlier seasonal peaks. Serotype transitions, particularly the dominance of DENV-3 followed by DENV-2-likely intensified disease severity through secondary infections. High case fatality rates were observed among females and older adults, with a substantial proportion of deaths occurring within 24 h of hospitalization, suggesting critical gaps in care-seeking and clinical management. Transmission dynamics are shaped by interactions between Aedes vector ecology, climate change, rapid urbanization, human mobility, and extensive insecticide resistance to pyrethroids. Public health responses remain constrained by passive surveillance, limited vector control efficacy, healthcare system strain, and insufficient community engagement.

CONCLUSIONS: The dengue burden of Bangladesh underscores the need for integrated and adaptive control strategies. Strengthening multi-domain surveillance (epidemiological, entomological, genomic), implementing resistance-aware Integrated Vector Management incorporating novel approaches such as Wolbachia, enhancing healthcare readiness, promoting community-driven behavioral interventions, integrating climate adaptation measures, and advancing vaccine and therapeutic research within a One Health framework are critical for sustainable dengue prevention and control.},
}

@article {pmid42406780,
year = {2026},
author = {Colombo, EH and Tarnita, CE and Bonachela, JA},
title = {Zooplankton feeding behavioral signatures in the morphology of macroscale prey spatial distribution.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014411},
pmid = {42406780},
issn = {1553-7358},
mesh = {Animals ; *Zooplankton/physiology ; *Feeding Behavior/physiology ; *Models, Biological ; *Predatory Behavior/physiology ; Ecosystem ; Food Chain ; Computational Biology ; Phytoplankton/physiology ; },
abstract = {The problem of pattern and scale remains central in ecology, bridging fundamental and applied questions. Marine microbial communities are a case in point. For instance, to understand the role of zooplankton in oceanic biogeochemistry, their response to changes in environmental conditions, and the implications for ecosystem services (e.g., fisheries), it is critical to understand zooplankton trophic interactions and how they change in a rapidly changing climate. This understanding, however, remains elusive because, unlike for phytoplankton, for which remote sensing of macroscale patterns can provide insight into their microscale dynamics and community composition, obtaining this information for zooplankton largely rests on quantifying the difficult-to-monitor microscale interactions among millions of individuals with different behaviors, and between individuals and their environment. Here, we investigate whether it is possible to obtain indirect information on zooplankton from the macroscale spatial distribution of their prey. To tackle this "problem of scale," we develop a rigorous coarse-graining methodology that connects individual-level properties with macroscale spatial patterns. We demonstrate that the shape of the prey spatial distribution can encode information about zooplankton feeding behavior and community dynamics. Specifically, we predict a change in dominant feeding behavior-from non-motile to motile feeding-as one moves from areas of high to areas of low prey density. These computational results are validated by our analysis of satellite images of oceanic blooms around the globe, which suggests novel opportunities for remote sensing approaches: the potential tracking of consumer behavioral signatures in the large-scale patterns of the resource. Importantly, the scaling-up methodology developed here to check for those signatures is general, and can be used to link scales rigorously and systematically in any system in which the complexity of individual dynamics makes connecting scales intractable.},
}

Animals
*Zooplankton/physiology
*Feeding Behavior/physiology
*Models, Biological
*Predatory Behavior/physiology
Ecosystem
Food Chain
Computational Biology
Phytoplankton/physiology

@article {pmid42407401,
year = {2026},
author = {Ibrahim, NA and Mehta, H and Sulieman, AME and Mir, RH and Fatima, SB and Adnan, M and Surti, M},
title = {Trichoderma-mediated biogenic synthesis of metal nanoparticles: Implications for soil health, plant resilience, and sustainable agroecosystems.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128614},
doi = {10.1016/j.micres.2026.128614},
pmid = {42407401},
issn = {1618-0623},
mesh = {*Trichoderma/metabolism ; *Metal Nanoparticles/chemistry ; Plant Development ; Soil Microbiology ; Agriculture/methods ; Agroecology ; Green Chemistry Technology ; Antifungal Agents/pharmacology ; Soil/chemistry ; Plants/microbiology ; Agrochemicals ; },
abstract = {The growing demand for sustainable agricultural practices has accelerated interest in eco-friendly alternatives to conventional agrochemicals. Among these, metal nanoparticles synthesized through biological routes have emerged as promising tools for crop protection and productivity enhancement. Trichoderma species, widely recognized for their biocontrol and plant growth-promoting properties, have gained considerable attention as efficient biofactories for the green synthesis of metal nanoparticles. The diverse metabolites produced by these fungi facilitate the reduction and stabilization of metal ions, resulting in nanoparticles with desirable physicochemical and biological properties. This review provides a comprehensive overview of the biosynthesis of metal nanoparticles by Trichoderma species, highlighting the underlying mechanisms, adaptation strategies to metal stress, and key physicochemical and biological factors influencing nanoparticle formation. Furthermore, the major types of Trichoderma-derived metal nanoparticles and their roles in antibacterial and antifungal activities, as well as plant growth promotion, are discussed. The potential of these nanoparticles to enhance plant health and support sustainable agricultural practices while minimizing the use of synthetic agrochemicals is also examined. Current limitations, challenges associated with field-level applications, and future research directions required for the successful translation of laboratory findings into practical agricultural systems are also discussed. Overall, Trichoderma-mediated nanoparticles represent a promising and sustainable approach for advancing next-generation agricultural technologies.},
}

*Trichoderma/metabolism
*Metal Nanoparticles/chemistry
Plant Development
Soil Microbiology
Agriculture/methods
Agroecology
Green Chemistry Technology
Antifungal Agents/pharmacology
Soil/chemistry
Plants/microbiology
Agrochemicals

@article {pmid42417989,
year = {2026},
author = {Castner, MD and Kitchen, C and Xiong, C and Bittle, MJ and Nestadt, PS and Wilcox, HC and Kharrazi, H},
title = {Assessing the utility of health access data and social determinants of health in ecological suicide prediction models.},
journal = {Social psychiatry and psychiatric epidemiology},
volume = {},
number = {},
pages = {},
pmid = {42417989},
issn = {1433-9285},
support = {R01 MH124724/MH/NIMH NIH HHS/United States ; R56 MH117560/MH/NIMH NIH HHS/United States ; R01 MH124724/MH/NIMH NIH HHS/United States ; },
abstract = {PURPOSE: Assess the utility of access to healthcare, clinical conditions, and social determinants of health (SDoH) variables in population-level suicide prediction models.

METHODS: Negative binomial regression models were constructed using data from population-level surveys, state death certificates, federal records of behavioral health services, and U.S. Census data. Outcomes of interest were suicidal ideation and suicide attempt (SISA), inpatient psychiatric hospitalization (IPH), and suicide death. The relative changes in pseudo R[2] were used to assess the impact of variable categories (i.e., clinical conditions, access to healthcare, and geo-derived SDoH) when added to a demographic-only baseline suicide prediction model.

RESULTS: Clinical data showed a significant impact, with the largest percent increase in pseudo R[2] compared to the demographic-only baseline model (321.9% for SISA; 736.9% for IPH; 18.9% for suicide death). Access to healthcare and geo-derived SDoH also improved model performances for all outcomes, but considerably lower than clinical variables. Models with all variable categories had the highest pseudo R[2], with .68, .58, and .46 for SISA, IPH, and suicide, respectively. Availability of emergency mental health services was found to be protective against IPH (IRR .90; 95% CI .84-.96) and suicide death (IRR .91; 95% CI .84-.97).

CONCLUSIONS: Clinical data proved to have the most effective variables in predicting a continuum of suicidal behaviors. While the impacts of access to healthcare and SDoH factors were comparatively limited, these variables also contributed to additional model improvements. These findings show the utility of population-level healthcare services and SDoH for ecological suicide behavior risk prediction.},
}

@article {pmid42390742,
year = {2026},
author = {Wu, S and Tatsis, EC},
title = {In Silico Identification and Comparative Synteny of Biosynthetic Gene Clusters in Plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3054},
number = {},
pages = {15-27},
pmid = {42390742},
issn = {1940-6029},
mesh = {*Multigene Family ; *Synteny ; *Computational Biology/methods ; *Plants/genetics/metabolism ; Software ; *Biosynthetic Pathways/genetics ; Genomics/methods ; Genome, Plant ; Computer Simulation ; Molecular Sequence Annotation ; },
abstract = {Biosynthetic gene clusters (BGCs) are often encoding specialized metabolic pathways in plants, yet effective methods for the comparison across multiple species are still evolving. In this protocol, we present a bioinformatics approach combining plantiSMASH and MCScan for the identification, annotation, and comparative analysis of BGCs in plant genomes. The methodology involves using plantiSMASH to predict and annotate potential BGCs, followed by the use of MCScan to perform syntenic analysis, enabling the exploration of the conservation and evolutionary dynamics of BGCs across different plant species. Here, we provide a step-by-step guide for installing and configuring the necessary software, preparing genomic data, and executing the analysis. This methodology, integrated with transcriptomic and metabolomic data, can be used to verify the functional relevance of the identified BGCs in specific biosynthetic pathways. It is applicable to a broad range of plant species and serves as a framework for the discovery and characterization of BGCs. The described methodology can significantly enhance research in plant genomics and metabolic engineering by offering new insights into the organization and function of BGCs.},
}

*Multigene Family
*Synteny
*Computational Biology/methods
*Plants/genetics/metabolism
Software
*Biosynthetic Pathways/genetics
Genomics/methods
Genome, Plant
Computer Simulation
Molecular Sequence Annotation

@article {pmid42391637,
year = {2026},
author = {Cui, B and van Beijnum, BJ and Tabak, M and Wang, Y},
title = {Sensor-Based Monitoring of Knee Osteoarthritis Symptoms in Free-Living Settings: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e84262},
pmid = {42391637},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; Monitoring, Physiologic/instrumentation ; *Osteoarthritis, Knee/physiopathology/diagnosis ; Quality of Life ; *Wearable Electronic Devices ; },
abstract = {BACKGROUND: Knee osteoarthritis is a heterogeneous condition characterized by chronic pain, stiffness, and fatigue that fluctuate rapidly over time. Traditional clinical assessments provide only static diagnoses of disease severity, failing to capture the dynamic, day-to-day symptom variability that impacts patient quality of life. While wearable technologies offer the potential for continuous, high-frequency monitoring, previous reviews have examined general technological interventions for knee osteoarthritis management, yet they lack a specific synthesis of technologies for symptom monitoring.

OBJECTIVE: This study aims to synthesize current research on sensor technologies used for the continuous monitoring of knee osteoarthritis symptoms in free-living or simulated daily environments. Specifically, the review seeks to (1) map sensor modalities to specific symptom domains (biomechanical, physiological, and behavioral); (2) evaluate the alignment between objective sensor metrics and patient-reported outcome measures; and (3) identify gaps in current monitoring paradigms.

METHODS: A systematic literature search was conducted across PubMed, Embase, Web of Science, and IEEE Xplore. The review followed the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines. Eligibility criteria included studies involving participants with knee osteoarthritis using wearable or portable sensors capable of continuous monitoring (eg, inertial measurement units and electrocardiography) and assessing clinical symptoms (eg, pain, fatigue, and stiffness). Studies relying solely on stationary laboratory equipment (eg, force plates) without a portable component were excluded to ensure relevance to real-world applicability. Data regarding sensor types, sampling frequencies, monitored symptoms, and the statistical association between objective features and subjective symptom severity (key findings) were extracted.

RESULTS: A total of 16 studies met the inclusion criteria. The summary constructed from the results revealed a distinct technological saturation: the majority of studies (n=6) used inertial measurement units to quantify biomechanical deficits (eg, gait asymmetry and range of motion), which showed robust correlations with functional limitations. In contrast, there was a notable scarcity of research using physiological sensors (eg, electrocardiography and bioimpedance) to monitor systemic symptoms. Crucially, findings highlighted a significant discrepancy between subjective and objective data, particularly in sleep monitoring, where poor self-reported sleep quality predicted pain exacerbations despite stable objective actigraphy metrics. Furthermore, most systems operated as passive data loggers, with a lack of integration into active feedback loops.

CONCLUSIONS: Unlike previous reviews focused solely on biomechanics, this study innovatively maps the use of sensors across a multidimensional symptom spectrum, revealing a critical gap in the monitoring of fatigue and physiological stress. The findings suggest that current sensor applications are limited by a lack of integration with subjective patient experiences. Real-world implementation requires a hybrid monitoring paradigm that combines the ecological validity of wearable sensors with the clinical relevance of patient-reported outcomes. This approach paves the way for digital phenotyping and active feedback systems, offering a personalized strategy for managing the complex symptom burden of knee osteoarthritis.},
}

Humans
Digital Health
Monitoring, Physiologic/instrumentation
*Osteoarthritis, Knee/physiopathology/diagnosis
Quality of Life
*Wearable Electronic Devices

@article {pmid42391685,
year = {2026},
author = {Hirose, K and Inomata, Y and Povinec, PP and Tsumune, D and Yamada, M and Zheng, J},
title = {Temporal trends and tracing capabilities of plutonium in the western North Pacific Ocean.},
journal = {Journal of environmental radioactivity},
volume = {298},
number = {},
pages = {108086},
doi = {10.1016/j.jenvrad.2026.108086},
pmid = {42391685},
issn = {1879-1700},
abstract = {Plutonium is a valuable temporal and spatial tracer in biogeochemical research due to its strong chemical reactivity, serving as a significant resource for tracking water mass movement. Because two major sources of plutonium exist in the North Pacific Ocean - global fallout (GF-Pu) from nuclear weapons tests and close-in fallout from the US Pacific Proving Ground (PPG-Pu), investigating its distribution and cycling is highly viable. Here, we examine temporal and spatial changes in [239,240]Pu activity concentrations and [240]Pu/[239]Pu atom ratios in surface and deep waters by analyzing Pu data from 1960 to 2020. Surface [239,240]Pu in the subarctic North Pacific has showed a declining trend after 2000, with a rate of decrease comparable to that in the subtropical region (apparent half-life of 6.4 y). Deep [239,240]Pu levels in the North Pacific also declined on a decadal timescale, likely reflecting the northward flow of deep water with low [239,240]Pu concentrations near 20°N. The [240]Pu/[239]Pu atom ratio in surface waters of the subtropical North Pacific indicates that GF-derived Pu ([240]Pu/[239]Pu atom ratio of 0.18) dominated surface Pu levels until 1980, after which PPG-derived Pu ([240]Pu/[239]Pu atom ratio of 0.33) became the dominant component. In the deep waters of the North Pacific, PPG-Pu signals were detected in the subarctic region during 1981 and 1988. Consequently, the [240]Pu/[239]Pu atom ratio serves as a powerful tool for unraveling the complexities of Pu cycling. These observations are important for better understanding of surface and deep-water flows, vertical motion, and biogeochemical processes in the western North Pacific Ocean.},
}

@article {pmid42392792,
year = {2026},
author = {Abbà, S and Vallino, M and Cicerone, A and Cirrincione, S and Aiuto, B and Galetto, L and Rossi, M},
title = {Multi-Omics Profiling of the Scaphoideus titanus Yeast-Like Symbiont Guides the Bioinformatic Discovery of Related Fungal Symbioses in Insects.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70361},
pmid = {42392792},
issn = {1462-2920},
support = {CUP B17G23000320005//Ministero dell'Agricoltura, della Sovranità Alimentare e delle Foreste; Project MICOTI/ ; },
mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology ; Phylogeny ; Computational Biology ; Multiomics ; Proteomics ; *Hypocreales/genetics/classification ; Genomics ; },
abstract = {Symbiotic partnerships have opened new ecological niches and contributed to the remarkable diversification of insects. The leafhopper Scaphoideus titanus, a phloem-feeding insect known to be the primary vector of Flavescence dorée phytoplasma, harbours two primary endosymbionts: the bacterium 'Candidatus Karelsulcia muelleri' and a yeast-like symbiont (YLS). While most studies on insect-associated microorganisms have focused on obligate bacterial symbionts, fungal endosymbionts, although documented for almost a century, are only now gaining renewed attention for their evolutionary and ecological significance. In this study, we integrated genomic and proteomic data with phylogenetic analyses to elucidate the functional and evolutionary features of the YLS associated with S. titanus. Using a data-independent proteomic approach supported by a newly sequenced symbiont genome, we defined the proteins expressed by the YLS that may contribute to host physiology. Comparative analyses across the five currently available YLS genomes enabled a proteome-wide phylogenetic reconstruction within the genus Ophiocordyceps, refining the evolutionary placement of these symbioses. Finally, large-scale mining of NCBI transcriptomic Sequence Read Archive datasets using a novel computational workflow, combined with an extensive literature survey, identified several new candidate insect hosts and provided a comprehensive inventory of species harbouring these fungal partners.},
}

Animals
*Symbiosis
*Hemiptera/microbiology
Phylogeny
Computational Biology
Multiomics
Proteomics
*Hypocreales/genetics/classification
Genomics

@article {pmid41604136,
year = {2026},
author = {Qian, Z and Tian, J and Chen, Q and Zhang, Y and Zhang, C and Yin, S and Zhang, K},
title = {Multi-Omics Analysis Uncovers Acute Hypoxia-Induced Gut Damage and the Underlying Protective Mechanisms of Probiotic Clostridium butyricum B3 in Yellow Catfish (Pelteobagrus fulvidraco).},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {5},
pages = {6945-6964},
pmid = {41604136},
issn = {1867-1314},
support = {JBGS[2021]034//The "JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; 32102760//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Catfishes/microbiology/metabolism ; *Probiotics/administration & dosage/pharmacology ; *Clostridium butyricum/physiology ; Multiomics ; *Hypoxia/metabolism ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Acute hypoxia stress poses a significant challenge in aquaculture, not only compromising gut health but also resulting in substantial economic losses. Using an integrated multi-omics approach, this study demonstrates that hypoxia severely disrupts the intestinal function of yellow catfish (Pelteobagrus fulvidraco), specifically manifesting as phospholipid metabolism disorders, inhibited fatty acid β-oxidation, reduced short-chain fatty acid (SCFA) synthesis, imbalanced gut microbiota (e.g., decreased levels of beneficial lactic acid bacteria Lactococcus and Clostridium sensu stricto 1), and downregulation of detoxification pathways mediated by cytochrome P450. Building upon the previously isolated and identified high-yield SCFA-producing probiotic Clostridium butyricum B3 from yellow catfish in early work, this research further investigated the efficacy and mechanisms of B3 supplementation in mitigating hypoxia-induced intestinal barrier damage in yellow catfish. The results indicated that the supplementation of C. butyricum B3, particularly at a dose of 3.0 × 10[7] CFU/g, significantly reduced histological damage, enhanced the expression of key tight junction proteins (such as ZO-1 and Claudin), and modulated hypoxia-inducible factor signaling pathways (including HIF-1α, FIH, and PHD). Furthermore, the application of C. butyricum B3 restored microbial ecological balance by promoting the growth of beneficial bacteria like Cetobacterium and inhibiting potential pathogens such as Acinetobacter. In conclusion, these findings underscore the potential of C. butyricum B3 as a novel probiotic strategy for enhancing fish hypoxia tolerance and maintaining intestinal integrity, offering valuable insights for sustainable aquaculture practices.},
}

Animals
*Catfishes/microbiology/metabolism
*Probiotics/administration & dosage/pharmacology
*Clostridium butyricum/physiology
Multiomics
*Hypoxia/metabolism
Gastrointestinal Microbiome/drug effects

@article {pmid42283564,
year = {2026},
author = {Ardizzone, CM and Lammons, JW and Lan, RS and Elnaggar, JH and Lillis, RA and Toh, E and Pack, LM and Mott, PD and Jacobs, CD and Yeruva, L and Taylor, CM and Quayle, AJ},
title = {Integrated multi-omics analysis uncovers cervicovaginal ecological networks and their association with Chlamydia trachomatis load.},
journal = {Infection and immunity},
volume = {94},
number = {7},
pages = {e0068125},
doi = {10.1128/iai.00681-25},
pmid = {42283564},
issn = {1098-5522},
support = {T32 AI060519/NH/NIH HHS/United States ; R01 AI118860/NH/NIH HHS/United States ; },
mesh = {Female ; Humans ; Multiomics ; *Chlamydia trachomatis/physiology ; *Vagina/microbiology ; *Chlamydia Infections/microbiology ; Cytokines/metabolism ; Microbiota ; Vaginosis, Bacterial/microbiology ; Tryptophan/metabolism ; *Cervix Uteri/microbiology ; Metabolome ; RNA, Ribosomal, 16S/genetics ; *Bacterial Load ; Tandem Mass Spectrometry ; },
abstract = {Chlamydia trachomatis (Ct) is a causal agent of upper reproductive tract pathology. There is a broad spectrum of cervical Ct load in infected women, and upper tract infection is associated with higher cervical Ct load. Recent studies indicate that bacterial vaginosis (BV) can modulate host-Ct outcomes. To identify features associated with BV status and Ct load, we performed an integrated multi-omics analysis of the cervicovaginal microbiome, tryptophan metabolome, and cytokines. Samples were analyzed using 16S rRNA gene sequencing, targeted UPLC-MS/MS quantification of tryptophan metabolites, and multiplex cytokine profiling. Ordination analyses showed that BV status was separated by the microbiome, metabolome, and cytokines, whereas Ct load was separated only by cytokines. K-means clustering of tryptophan metabolites defined three metabolome state types (MSTs). MST I, associated primarily with Lactobacillus crispatus-dominated community state type (CST) I, exhibited high tryptophan availability, indole-3-lactic acid, and complete kynurenine-pathway activity. Both MST II and MST III were associated with BV-associated CST IV and showed marked tryptophan depletion. MST II was broadly depleted of most tryptophan metabolites, while MST III was enriched in downstream microbially derived indole pathway metabolites and kynurenic acid. Hierarchical all-against-all association testing revealed coordinated relationships linking clusters of bacterial taxa, metabolites, and cytokines. Importantly, multi-omics network analyses identified integrated microbial-metabolic-immune modules that predicted high versus low Ct load, highlighting CXCL9, CXCL10, IL-17, BV-associated taxa, and indole pathway metabolites as key discriminative features. Results demonstrate that cervical Ct load reflects coordinated microbial-metabolic-immune ecological states rather than microbiome composition alone and refine current models of Ct-BV interactions.},
}

Female
Humans
Multiomics
*Chlamydia trachomatis/physiology
*Vagina/microbiology
*Chlamydia Infections/microbiology
Cytokines/metabolism
Microbiota
Vaginosis, Bacterial/microbiology
Tryptophan/metabolism
*Cervix Uteri/microbiology
Metabolome
RNA, Ribosomal, 16S/genetics
*Bacterial Load
Tandem Mass Spectrometry

@article {pmid42374709,
year = {2026},
author = {Yuan, R and Shu, P and Salam, M and Wu, S and Liu, Y and Li, H and Li, W},
title = {Cadmium(II) Loading Exacerbates the Negative Effects of Nanobiochar on Daphnia magna: Evidence from Toxicity Test and Multiomics Analysis.},
journal = {Environmental science & technology},
volume = {60},
number = {27},
pages = {19090-19105},
doi = {10.1021/acs.est.6c01162},
pmid = {42374709},
issn = {1520-5851},
mesh = {Animals ; *Daphnia magna/drug effects ; *Cadmium ; Multiomics ; Water Pollutants, Chemical ; Toxicity Tests ; Daphnia ; Charcoal ; },
abstract = {Micro- (M-BC) and nanobiochar (N-BC) particles exhibit strong environmental mobility and superior adsorption capacity for heavy metals. This raises concerns regarding their ecological risks to aquatic ecosystems. However, systematic studies on the toxicity of contaminant-laden M-BC and N-BC to aquatic biota remain scarce. Here, we prepared the cadmium (Cd(II))-loaded complexes (M-BC-Cd and N-BC-Cd), identified the acute toxicity of M-BC-Cd and N-BC-Cd on zooplankton Daphnia magna, and emphasized the response in D. magna induced by N-BC and N-BC-Cd. The results indicated that N-BC alone induced minimal adverse effects on D. magna. N-BC demonstrated a higher Cd(II) adsorption capacity than M-BC, leading to a lower LC50 level for N-BC-Cd. In chronic toxicity tests, exposure to N-BC-Cd resulted in a 30% reduction in the survival of D. magna compared to that of N-BC. The particles of N-BC-Cd caused more severe impairment in growth, reproduction, and oxidative stress responses. While N-BC primarily affected predation efficiency and disrupted metabolic pathways, the amplified toxicity of N-BC-Cd was attributed to a synergistic effect of prey limitation, metabolic dysregulation, oxidative stress, inhibition of signal transduction, and down-regulation of lysosomal proteins. This finding provides novel insights into assessing the environmental risks of biochar particles in aquatic ecosystems.},
}

Animals
*Daphnia magna/drug effects
*Cadmium
Multiomics
Water Pollutants, Chemical
Toxicity Tests
Daphnia
Charcoal

@article {pmid42390619,
year = {2026},
author = {Ahlendorf, A and Aharoni, A and Vahabi, K and Fischer, TG and Allard, PM and Augustin, M and Bathe, U and Broadhurst, DI and Broeckling, C and Buescher, J and Covaci, A and da Silva, KM and de Vos, RCH and Devi, MG and Döll, S and Frey, M and Frolov, A and Gaquerel, E and Gautam, V and Charria-Girón, E and Goossens, A and Grosjean, J and Halabalaki, M and Iturrospe, E and Kultima, K and Herman, S and Kutchan, TM and Larbat, R and Meier, R and Mikropoulou, EV and Mouille, G and Nicolotti, L and Shahaf, N and Perreau, F and Pétriacq, P and Reichelt, M and Reinke, SN and Robeyns, R and Soboleva, A and Spring, O and Sreenivasan, AP and Tissier, A and Totozafy, JC and Tsugawa, H and Valls-Fonayet, J and van de Lavoir, M and van der Hooft, JJJ and Vergara, F and Wishart, D and Wessjohann, LA and Wolfender, JL and Ziegler, J and Balcke, GU and Neumann, S},
title = {The MassBank contributions of the mFam collaboration.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {4},
pages = {},
pmid = {42390619},
issn = {1573-3890},
mesh = {*Metabolomics/methods ; *Tandem Mass Spectrometry/methods ; Animals ; *Metabolome ; Databases, Factual ; Mass Spectrometry/methods ; },
abstract = {INTRODUCTION: The analysis of metabolic profiles using high resolution mass spectrometry (MS) data provides deep insights into biological processes. In metabolomics, MS analysis generates a large number of features that represent metabolites. However, identifying specific metabolites from these features can be challenging. One of the major bottlenecks in the metabolomics field is the identification of MS features, which is a prerequisite for any biochemical interpretation. By identifying similarities and differences within a metabolite family (mFam), evaluating MS features at the metabolite family level can help assigning functional roles to individual MS features. These data can help interpreting metabolic pathways and processes within a biological system. For the assignment of metabolite families to MS features, it is important to have good quality, reliable, and comprehensive spectral libraries.

OBJECTIVE: We initiated a global effort to collect high-resolution MS/MS spectra of metabolites from labs working in different fields, including metabolomics of animals, microorganisms, and plants. The mFam-MS/MS collection delivers valuable training data to assign machine-readable classified information on the unknown metabolites.

RESULTS: The mFam collaboration used a standardized metadata template and has developed a globally curated MS/MS spectral library of 7,872 spectra with 2,126 unique metabolites. This library was compiled from 47 datasets contributed by 25 laboratories measured on 12 instrument types, including QTOF, Orbitrap, and Ion Mobility-QTOF systems. It comprises 4,646 spectra in positive mode and 3,226 in negative mode. This standardized resource significantly enhances metabolite identification capabilities, supports the development of machine learning-based annotation tools, and accelerates the discovery of novel metabolites. All spectra are available under the collective contributor label mFam in the MassBank system, including the web interface and the 2025.10 data release available at GitHub and Zenodo.},
}

*Metabolomics/methods
*Tandem Mass Spectrometry/methods
Animals
*Metabolome
Databases, Factual
Mass Spectrometry/methods

@article {pmid42390741,
year = {2026},
author = {Konkel, Z and Slot, J},
title = {Generalized Gene Cluster Detection Using CLOCI.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3054},
number = {},
pages = {1-14},
pmid = {42390741},
issn = {1940-6029},
mesh = {*Multigene Family ; Algorithms ; *Genomics/methods ; *Software ; *Computational Biology/methods ; Evolution, Molecular ; Clustering Algorithms ; Synteny ; },
abstract = {Metabolic gene clusters (MGCs) are genomic loci that contain multiple genes that are functionally and genetically linked. MGCs collectively encode a spectrum of metabolic functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Due to their diverse ecological functions, identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Gene cluster detection algorithms have historically been specialized for detecting biosynthetic gene clusters that contain canonical "core" biosynthetic functions, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization.We developed CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier) as a generalized, unbiased gene cluster detection algorithm. CLOCI generalizes gene cluster detection by identifying signatures of coordinated gene evolution that underlie all classes of MGCs. CLOCI first detects selection on gene colocalization by identifying and circumscribing shared synteny loci across a dataset of genomes into homologous locus groups. Gene clusters comprise a subset of these homologous locus groups, and CLOCI implements orthogonal proxies of coordinated gene evolution, such as quantifying loss and horizontal transfer of a locus, to enrich MGCs from homologous loci. Here, we describe the conceptual framework of the CLOCI algorithm and present a description of its implementation (see Note 1).},
}

*Multigene Family
Algorithms
*Genomics/methods
*Software
*Computational Biology/methods
Evolution, Molecular
Clustering Algorithms
Synteny

@article {pmid42330077,
year = {2026},
author = {Creus-Martí, I and Moya, A and Santonja, FJ},
title = {CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014328},
doi = {10.1371/journal.pcbi.1014328},
pmid = {42330077},
issn = {1553-7358},
mesh = {*Microbiota/genetics/physiology ; *Software ; *Computational Biology/methods ; Bacteria/genetics/classification ; Animals ; Longitudinal Studies ; Humans ; Models, Biological ; },
abstract = {In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on pairwise interactions, CoDaLoMic also captures interactions among groups of bacteria, providing a more robust methodological framework for studying microbial relationships at the community level. In addition, the package facilitates the analysis of microbiome variability in relation to host health status and allows for the identification of groups of taxa that exhibit similar temporal dynamics. Working with time series data makes it possible to understand not only the current state of a microbial community but also its dynamics over time, which is essential for identifying patterns of ecological succession, detecting events of dysbiosis or recovery, and inferring potential causal relationships between taxa. On the other hand, focusing on interactions among groups of bacteria, rather than analyzing only pairwise relationships, enables a more integrated and functionally meaningful view of the microbiome. Many key ecological functions are the result of the collective behavior of functionally related groups of taxa. Two datasets have been considered in CoDaLoMic, one real and one simulated. The real dataset contains the information of the genera present in the microbiome of the Blatella germanica cockroach at 105 time points. The simulated dataset is defined taking Lotka-Volterra structure into account. CoDaLoMic is available at CRAN.},
}

*Microbiota/genetics/physiology
*Software
*Computational Biology/methods
Bacteria/genetics/classification
Animals
Longitudinal Studies
Humans
Models, Biological

@article {pmid42387942,
year = {2026},
author = {Saudreau, C and Tarazona, V and De Bandt, D},
title = {French Consumption of Methylphenidate in Primary Care From 2016 to 2023, Impact of Prescribing Policy Changes-A Time-Series Analysis.},
journal = {Pharmacoepidemiology and drug safety},
volume = {35},
number = {7},
pages = {e70424},
pmid = {42387942},
issn = {1099-1557},
mesh = {*Methylphenidate/therapeutic use/economics/administration & dosage ; France ; Humans ; *Central Nervous System Stimulants/therapeutic use/economics/administration & dosage ; *Attention Deficit Disorder with Hyperactivity/drug therapy ; *Practice Patterns, Physicians'/trends/statistics & numerical data/economics ; *Primary Health Care/trends/statistics & numerical data/economics ; Drug Prescriptions/statistics & numerical data ; Health Policy ; Databases, Factual ; Drug Utilization/trends ; },
abstract = {PURPOSE: In France, methylphenidate, mainly used in the treatment of ADHD, has been subject to prescription restrictions that were relaxed at the end of 2021. This study analyses trends in methylphenidate consumption in France and examines changes following the modification to prescribing rules in 2021.

METHODS: This ecological study was based on data from the Medic'AM database, which records reimbursed outpatient drug dispensation in France from January 2016 to December 2023. Methylphenidate sales were expressed as defined daily dose per thousand inhabitants per day (DDD/TID) and expenditure as euros per thousand inhabitants. Time-series analyses were conducted to assess changes in methylphenidate sales and associated expenditure following modifications to prescribing arrangements in September and November 2021.

RESULTS: Methylphenidate consumption rose from 0.607 DDD/TID per month in 2016 to 1.457 DDD/TID in 2023, an increase of 84%. Associated expenditure followed a similar upward trend. A more pronounced increase in methylphenidate sales was observed after the end of 2021.

CONCLUSION: The study shows a clear increase in methylphenidate sales after 2021, coinciding with changes in prescribing regulations. Given the ecological design, this temporal association cannot be interpreted as causal. The observed trends likely reflect multiple factors, including regulatory changes, increased recognition of ADHD, and evolving clinical practices. These findings highlight how changes in prescribing policies may be associated with variation in healthcare utilization and expenditure.},
}

*Methylphenidate/therapeutic use/economics/administration & dosage
France
Humans
*Central Nervous System Stimulants/therapeutic use/economics/administration & dosage
*Attention Deficit Disorder with Hyperactivity/drug therapy
*Practice Patterns, Physicians'/trends/statistics & numerical data/economics
*Primary Health Care/trends/statistics & numerical data/economics
Drug Prescriptions/statistics & numerical data
Health Policy
Databases, Factual
Drug Utilization/trends

@article {pmid42389374,
year = {2026},
author = {Perea García, JO and Kano, F and Sibierska, M and Fiala, V and Skrok, MK and Danel, DP and Ratajczak, EK and Zywiczynski, P and Wacewicz, S},
title = {Gaze in context: non-human eyes can be more salient under ecologically relevant conditions.},
journal = {Evolutionary human sciences},
volume = {8},
number = {},
pages = {e25},
pmid = {42389374},
issn = {2513-843X},
abstract = {Primate eyes vary strikingly in pigmentation, yet the drivers of said variation are strongly debated. Recent revisions of the cooperative eye hypothesis propose that the human eye's sclera evolved to enhance gaze communication specifically under challenging conditions of visibility. We tested this idea under ecologically realistic conditions by presenting observers with a live model wearing contact lenses that simulated either a human-like or a chimpanzee-like eye. At a university lab, observers judged gaze direction at different viewing distances and lighting levels. We found no overall difference in efficacy of different eye types. Contrary to expectations, chimpanzee-like eyes outperformed human-like eyes in dim lighting and close-viewing conditions. Human-like eyes yielded the highest accuracy under bright, far-viewing conditions, consistent with a long-distance signalling advantage. Our results demonstrate that ecological visual constraints shape the potential informativeness of distinct ocular configurations. We hypothesize that species-typical eye appearances may be tuned to their species-typical visual ecology.},
}

@article {pmid42091894,
year = {2026},
author = {Solano, I and Bro-Jørgensen, J and Lazagabaster, IA and Thomas, CD and Manzano, S},
title = {NAMPHORA: a fossil and modern pollen database from Northern Africa and adjacent Mediterranean and Arabian regions.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42091894},
issn = {2052-4463},
support = {Grant: NE/S00713X/1//Adapting to the Challenges of a Changing Environment (ACCE) Doctoral Training Partnership, funded by the Natural Environment Research Council (NERC)/ ; Grant: RPG-2021-104//Biodiversity in Ancient Egypt during Societal Transitions (BEAST) project, funded by Leverhulme Trust/ ; Grant: RYC2021-034991-I//Ministerio de Ciencia e Innovación de España MCIN/AEI/10.13039/501100011033 and European Union NextGenerationEU/PRTR./ ; Grant: PID2024-161027NA-I00 DivAS-Cape//MICIU/AEI/ 10.13039/501100011033 and by the ERDF/EU/ ; },
mesh = {*Pollen ; *Fossils ; Africa, Northern ; Mediterranean Region ; Climate ; *Databases, Factual ; Plants ; },
abstract = {Northern Africa's climate and vegetation underwent significant changes throughout the Holocene, particularly in connection with the termination of the African Humid Period ca. 5500 years ago. Fossil pollen records are key to reconstructing past environments, yet current databases for this region are limited by the omission of significant unpublished data, taxonomic inconsistencies, and the lack of standardised plant trait information. To address these issues, we introduce the Northern African, Arabian, and Mediterranean Pollen Holocene Records Archive (NAMPHORA)- a comprehensive, machine-readable and taxonomically-harmonised database compiling fossil and modern pollen records alongside plant functional traits, and ecological and phytogeographical information. This database includes all of Africa to the north of 7.52° N and constitutes the most complete and comprehensive resource (836 pollen records; 853 harmonised pollen types, and 13 key standardised plant traits) to improve palaeoecological reconstructions, enhance biogeographical analyses, and refine climate models for northern Africa during the Holocene. It enables direct data retrieval via programming languages such as R, and all datasets and code are openly available via Zenodo.},
}

*Pollen
*Fossils
Africa, Northern
Mediterranean Region
Climate
*Databases, Factual
Plants

@article {pmid42387317,
year = {2026},
author = {Chen, Z and Wang, S and Sun, Z and Liao, H and Longji, Y and Zhang, Q and Wang, J},
title = {An AI-Driven Multi-Omics Framework Identifies CASP8 as a Clinically Actionable Pyroptosis Biomarker in Bladder Cancer.},
journal = {BioFactors (Oxford, England)},
volume = {52},
number = {4},
pages = {e70130},
doi = {10.1002/biof.70130},
pmid = {42387317},
issn = {1872-8081},
mesh = {*Urinary Bladder Neoplasms/genetics/pathology/metabolism ; Humans ; *Biomarkers, Tumor/genetics/metabolism ; *Caspase 8/genetics/metabolism ; *Pyroptosis/genetics ; Machine Learning ; Multiomics ; Gene Expression Regulation, Neoplastic ; Cell Line, Tumor ; Tumor Microenvironment/genetics ; Genomic Instability ; Artificial Intelligence ; },
abstract = {Despite rapid advances in multi-omics technologies, translating candidate biomarkers into clinical practice for bladder cancer remains challenging due to the difficulty of linking complex genomic instability to interpretable biological processes. To address this, we developed an AI-driven multi-omics discovery framework integrating single-cell RNA sequencing, multi-cohort transcriptomics, and machine learning-based genomic inference. By analyzing chromosomal aneuploidy and copy number variations at single-cell resolution, we identified malignant cell populations and constructed a consensus pyroptosis scoring system, followed by machine learning-assisted biomarker screening and experimental validation. Our results reveal that while global pyroptosis activity is elevated in the bladder cancer microenvironment, malignant cells with high genomic instability exhibit significant pyroptosis suppression. Through this pipeline, CASP8 was identified as a key clinically relevant biomarker; its low expression correlates strongly with increased tumor mutation burden, frequent driver gene alterations (including TP53 and RB1), and poor survival outcomes. Functional assays further confirmed that CASP8 loss promotes malignant phenotypes and alters cell death programs. Ultimately, this study establishes a next-generation framework for biomarker translation, highlighting CASP8 as a clinically actionable link between genomic instability and pyroptosis dysregulation, and demonstrating the power of AI-integrated strategies in accelerating bladder cancer research from bench to bedside.},
}

*Urinary Bladder Neoplasms/genetics/pathology/metabolism
Humans
*Biomarkers, Tumor/genetics/metabolism
*Caspase 8/genetics/metabolism
*Pyroptosis/genetics
Machine Learning
Multiomics
Gene Expression Regulation, Neoplastic
Cell Line, Tumor
Tumor Microenvironment/genetics
Genomic Instability
Artificial Intelligence

@article {pmid42275736,
year = {2026},
author = {Barcan, RA and Carradori, S and Samsing, F and Nguyen, NL and He, L and Wang, Y and Barcan, AS},
title = {Machine learning in applied microbiology, from data quality to model validation and implementation.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128588},
doi = {10.1016/j.micres.2026.128588},
pmid = {42275736},
issn = {1618-0623},
mesh = {*Machine Learning ; *Microbiology ; Reproducibility of Results ; Microbiota ; Classification Algorithms ; Predictive Learning Models ; Humans ; Databases, Factual ; },
abstract = {Machine learning (ML) is now widely applied in microbiology, but its reliability varies markedly across domains. In this review, we analysed data from 254 scientific articles that evaluates ML through three linked dimensions including data readiness, model suitability, and deployment readiness across diagnostics and pathogen identification, virology, microbiome research, industrial and environmental microbial biotechnology. This framework helps distinguish robust progress from performance inflated by methodological limitations. Our review shows that pathogen identification and antimicrobial resistance prediction consistently achieve strong performance when supported by curated datasets, reliable labels, and comprehensive reference databases. However, their practical value remains limited by internal validation, lineage confounding, and uneven transfer across strains, institutions, and regions. In virological studies, predictive stability is further challenged by incomplete reference databases, changing taxonomy, and temporal drift during outbreaks. In microbiome research, ML classifiers can detect disease and environmental signals, but their generalization across cohorts remains weak because of compositional data structure, technical bias, and incomplete metadata. Industrial bioprocessing and environmental applications show promise when process data are rich and controlled, but deployment beyond laboratory or site-specific settings remains limited. Across structured microbiological datasets, classical supervised models often remain competitive with deep learning while being easier to interpret and validate. Detailed quantitative benchmarks supporting these comparisons are synthesized in the main text and summary tables. Overall, progress will depend less on algorithmic novelty than on interoperable and well-annotated datasets, representative sampling, standardized benchmarking, reproducible workflows, and prospective multi-site validation.},
}

*Machine Learning
*Microbiology
Reproducibility of Results
Microbiota
Classification Algorithms
Predictive Learning Models
Humans
Databases, Factual

@article {pmid42321367,
year = {2026},
author = {Wang, X and Zhang, C and Wang, H and Reid, K and Merilä, J},
title = {How precise are mutation rate estimates? Comparison of different approaches to estimate de novo mutation rates.},
journal = {Heredity},
volume = {135},
number = {6},
pages = {445-452},
pmid = {42321367},
issn = {1365-2540},
support = {202111159018//University Grants Committee (UGC)/ ; },
mesh = {Animals ; *Mutation Rate ; *Computational Biology/methods ; Sequence Analysis, DNA ; Mutation ; High-Throughput Nucleotide Sequencing ; },
abstract = {Availability of de novo mutation rate (µ) estimates based on approaches that rely on bioinformatic validations has increased tremendously during the past few years, but the accuracy and precision of these estimates often remain unclear as Sanger sequencing validation of the mutations is often lacking. We used both long- and short-read sequencing data and different bioinformatic pipelines to estimate µ, as well as false positive (FPR) and negative (FNR) rates, for family trios of flat-headed loaches (Oreonectes platycephalus). By comparing estimates against PCR-verified mutations, we observed that the top-performing approach (as ranked by the F1 score of seven approaches at the same depth) still exhibited a 4% false positive rate (FPR) alongside a 12% false-negative rate (FNR). Across the remaining methods, FPR values ranged from 4-12%, and FNRs from 8-19%. Irrespective of the bioinformatic approach used, long-read data yielded consistently lower µ estimates than short-read data because of the larger callable genome sizes. In addition, a higher mapping depth resulted in a lower FNR. These results call for caution regarding de novo mutations without Sanger sequencing validation in non-model organisms and raise the possibility that many published µ-estimates, especially those based on low mapping depths, might be biased.},
}

Animals
*Mutation Rate
*Computational Biology/methods
Sequence Analysis, DNA
Mutation
High-Throughput Nucleotide Sequencing

@article {pmid42386298,
year = {2026},
author = {McGuinn, LA and Ngirwe, P and Walton, S and Wei, K and Tung, I and Tare, I and Mbayiwa, K and Keenan, KE and Burrows, K},
title = {Using mobile sensing and wearable technologies to assess the impact of ambient temperature on mental health among low-income black women in Chicago: a study protocol.},
journal = {BMJ open},
volume = {16},
number = {7},
pages = {e109062},
pmid = {42386298},
issn = {2044-6055},
mesh = {Adult ; Female ; Humans ; *Black or African American/psychology ; Chicago ; Digital Health ; Ecological Momentary Assessment ; Longitudinal Studies ; *Mental Health ; *Poverty ; Research Design ; Sleep ; Temperature ; },
abstract = {INTRODUCTION: Growing evidence suggests that higher ambient temperatures may increase the risk of mental health disorders and exacerbate existing conditions. Despite this, most studies evaluating the association between temperature and mental health rely on hospitalisation records or insurance claims data, which only capture the most severe outcomes. To effectively intervene to prevent mental health crises associated with ambient temperature, it is necessary to identify and develop novel ways to reach patients before they require care. Digital health tools offer a promising way to address these gaps, particularly in communities most affected by climate inequities.

METHODS AND ANALYSIS: This study aims to recruit 70 low-income black women from Chicago who are already enrolled in the Nutrition and Pregnancy Study for a 4-week longitudinal observational study. The primary objective is to examine how ambient temperature affects positive and negative affect (primary outcome), as well as sleep and physiologic markers. Over a 4-week summer period, participants will wear a smartwatch and complete ecological momentary assessment surveys three times daily. We will monitor indoor temperature and humidity using home-based sensors and link these data with wearable and self-reported mental health measures. Daily outdoor ambient temperature will also be linked. Statistical analyses will use mixed-effects longitudinal models with distributed lags to assess delayed and cumulative temperature effects.

ETHICS AND DISSEMINATION: This study has been reviewed and approved by the Institutional Review Board at the University of Chicago (IRB24-026). At the completion of the study, participants will have the option to receive a summary of their own data, with a plain-language summary of the study findings. Findings will be disseminated through peer-reviewed publications and presentations at national and international conferences. Dissemination efforts will also include engagement with local community stakeholders and public health partners to inform future climate and health efforts.},
}

Adult
Female
Humans
*Black or African American/psychology
Chicago
Digital Health
Ecological Momentary Assessment
Longitudinal Studies
*Mental Health
*Poverty
Research Design
Sleep
Temperature

@article {pmid42386781,
year = {2026},
author = {Wu, M and Sonnentag, O and Lara, MJ and Ran, Y and Chen, HW and Zhang, W and Ciais, P and Elberling, B and Li, X and Chen, A and Wang, S and Yi, Y and Peng, C and Chen, D},
title = {Vegetation browning patterns under compound soil and atmospheric dryness in northern permafrost ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75131-4},
pmid = {42386781},
issn = {2041-1723},
support = {42525105//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Significant changes in vegetation greenness and browning have been observed across the northern permafrost zone, with important implications for ecosystem functioning and carbon uptake. While recent research has improved our understanding of the drivers of greening, the processes behind browning - especially the low-stature shrubs and herbaceous vegetation, which is more directly exposed to soil and atmospheric moisture deficits - remain less clear. To characterize browning patterns, we integrate multiple remote sensing datasets - including normalized difference vegetation index (NDVI), solar-induced chlorophyll fluorescence (SIF), and foliar chlorophyll concentration (FCC) - with gross primary productivity (GPP) simulations from CMIP6 Earth system models (ESM). We identify significant browning trends (-0.033 to - 0.025 decade-1, from MODIS NDVI) from 2001 to 2018, affecting approximately 20 % (~600,000 km[2]) of the study region. Browning is primarily modulated by compound soil and atmospheric dryness, reflected by declining soil moisture concurrent with increasing vapor pressure deficit. We further show that regional warming and changes in precipitation, together with permafrost-related constraints on infiltration and storage, modulate the spatial heterogeneity of compound dryness. CMIP6 projections suggest that compound dryness is likely to persist or intensify in permafrost ecosystems, implying continued risk of productivity loss, especially when combined with pulse disturbances such as wildfires.},
}

@article {pmid42371860,
year = {2026},
author = {Saini, P and Iquebal, MA and Jaiswal, S and Angadi, UB},
title = {Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42371860},
issn = {1758-0463},
support = {BT/PR40161/BTIS/137/32/2021//Indian Council of Agricultural Research/ ; //Department of Biotechnology/ ; },
mesh = {Animals ; *Microsatellite Repeats/genetics ; *Cyprinidae/genetics ; *Genome/genetics ; *Chromosomes/genetics ; *Databases, Genetic ; *Databases, Nucleic Acid ; Genomics ; },
abstract = {The family Cyprinidae represents the most taxonomically diverse group of freshwater fishes, encompassing over 3 000 species of ecological and economic importance in aquaculture, conservation, and ecological monitoring. Simple sequence repeats (SSRs), also known as microsatellites, are highly informative molecular markers widely used for genetic diversity analysis, population structure assessment, and marker-assisted breeding. However, comprehensive genome-wide SSR resources for cyprinids remain limited. Existing databases, such as FishMicrosat, provide restricted taxonomic coverage and lack standardized chromosome-level datasets suitable for comparative genomic analyses. To address this gap, we developed CypriSSR, a genome-wide SSR database encompassing 11 representative cyprinid species. Chromosome-level genome assemblies were retrieved from NCBI. SSR loci were identified using MISA, and primer pairs were designed using Primer3. In total, over 7.8 million SSR loci were identified. Mononucleotide repeats were the most abundant class (39-53%), followed by dinucleotide and trinucleotide motifs. SSRs were predominantly distributed in genic regions (54%-71% across species), suggesting potential functional roles. Each database entry includes repeat type, genomic coordinates, primer sequences, melting temperatures, and predicted PCR product sizes. The CypriSSR web interface enables flexible querying of SSR markers based on species, chromosome, motif class, and genomic location, and supports sequence similarity searches through an integrated BLAST module along with data export options. CypriSSR provides a comprehensive and standardized multi-species microsatellite resource for cyprinid genomes and supports applications in population genetics, molecular breeding, and conservation genomics. Database URL: http://46.202.167.198/fishssr/.},
}

Animals
*Microsatellite Repeats/genetics
*Cyprinidae/genetics
*Genome/genetics
*Chromosomes/genetics
*Databases, Genetic
*Databases, Nucleic Acid
Genomics

@article {pmid42383019,
year = {2026},
author = {Oh, Y and Campbell, K and Shults, J and Saby, J and Marsh, ED},
title = {Minimum data requirements and automated preprocessing for reliable EEG biomarkers in Rett syndrome.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1791834},
pmid = {42383019},
issn = {1664-2295},
abstract = {BACKGROUND: Electroencephalography (EEG) is a promising biomarker for Rett syndrome (RTT), but excessive artifact and variable tolerance for longer recording sessions pose challenges for reliable biomarker development. Establishing an automated preprocessing pipeline that matches human review and defining the minimum data needed for stable quantitative EEG (qEEG) features can support more patient-friendly protocols and provide consistent multisite analysis results.

METHODS: A mean of 10 min of resting-state EEG from 117 participants (1-18 year old; 236 sessions) in the multisite R61 RTT study was processed using a fully automated, correction-based preprocessing pipeline incorporating artifact handling, adaptive channel rejection, ASR, and ICA-based cleaning. Spectral power was extracted from artifact-free 4-s epochs. The proposed pipeline is validated using an established rejection-based pipeline. Feature stability as a function of cumulative data length was then assessed using two complementary frameworks: a Statistical Convergence approach and a Model-Based Inflection approach, and potential systemic dependencies were evaluated using permutation analyses. The relationship between clinical measures was also assessed.

RESULTS: The correction-based pipeline retained substantially more data than the rejection-based workflow (mean retention = 95.0% vs. 28.4%; p < 0.001) while preserving strong feature correspondence across frequency bands. Stable power estimates were achieved after 19-34 epochs (= 76-136 s). Based on permutation analysis, there was no statistically significant difference in minimum stabilization threshold between RTT and TD. However, the RTT group exhibited higher rates of intrinsic signal instability than typically developing (TD) controls. Age-stratified analysis revealed that the minimum epochs did not significantly differ between age groups. Spectral associations with clinical severity were preserved when using only the minimum data required for stability, as well as in an ecologically valid scenario of truncating the raw EEG up to minimum epoch recommendation and reprocessing it.

CONCLUSIONS: With the proposed correction-based pipeline, approximately 3 min of raw resting-state EEG are sufficient to obtain stable and clinically meaningful spectral features in children with Rett syndrome. These findings support shorter, more feasible EEG acquisitions and provide a reproducible framework for data sufficiency in multisite neurodevelopmental studies.},
}

@article {pmid42384029,
year = {2026},
author = {Martinho, DV and Costa, R and VAN DEN Hoek, D and Clemente, FM and Gonzalo-Skok, O and Gouveia, ÉR and Campos, P and Ribeiro, AS and Field, A and Sarmento, H},
title = {A critical commentary on CrossFit Research® with coach insights on training monitoring and physical assessment.},
journal = {The Journal of sports medicine and physical fitness},
volume = {},
number = {},
pages = {},
doi = {10.23736/S0022-4707.26.17836-0},
pmid = {42384029},
issn = {1827-1928},
abstract = {BACKGROUND: CrossFit[®] has experienced rapid global growth, yet scientific research often fails to reflect the realities of training and competition in this sport. Studies frequently rely on inconsistent terminology, non-specific testing protocols, and heterogeneous samples, limiting the ecological validity and practical application of findings. This critical commentary aims to evaluate the methodological challenges in CrossFit[®] research and to highlight the importance of contextualizing scientific inquiry through the perspectives of coaches actively working within the sport.

METHODS: A targeted review of the CrossFit[®] literature was conducted, with a focus on sampling descriptions, testing protocols, and training monitoring approaches. In addition, semi-structured interviews were conducted with five national and international-level CrossFit[®] coaches. Analysis of coach responses was used to contextualize gaps in the literature.

RESULTS: Coaches reported relying primarily on competition results, training observations, and subjective feedback to guide programming, rather than standardized physical testing or technology-based monitoring. The remote nature of many coach-athlete relationships further complicates data collection and training analysis.

CONCLUSIONS: CrossFit[®] research must improve its methodological rigor by adopting sport-specific assessments, clearly defining participant characteristics, and embracing the realities of coaching practice. Integrating qualitative insights and prioritizing ecological validity will help bridge the gap between science and the sport's unique demands.},
}

@article {pmid42386290,
year = {2026},
author = {Sahana, KS and Madhu, B and Manjunatha, MC and Chaithra, M and Mounika Sree, M and Suraj, BM and Yashashwini, A and Snehalatha, B},
title = {Spatial autocorrelation and regression approach for delineating maternal mortality and its associated factors in Karnataka, India.},
journal = {BMJ open},
volume = {16},
number = {7},
pages = {e094191},
doi = {10.1136/bmjopen-2024-094191},
pmid = {42386290},
issn = {2044-6055},
mesh = {Humans ; Female ; *Maternal Mortality/trends ; Retrospective Studies ; India/epidemiology ; Pregnancy ; Geographic Information Systems ; Spatial Analysis ; Spatial Regression ; Risk Factors ; },
abstract = {OBJECTIVES: The main objective of this study is to assess the temporal distribution of taluk (sub-district)-level maternal mortality trends within Karnataka and identify the hotspots and medical and non-medical factors that were significantly contributing to maternal deaths.

DESIGN: Spatial patterns and determinants of maternal mortality were investigated using a retrospective ecological study design.

DATA SOURCE: Maternal mortality data were collected from the Directorate of Health and Family Welfare Services, Government of Karnataka, while political boundaries of state, districts and taluks were downloaded from the Karnataka Geographic Information System Portal.

METHODOLOGY: Taluk-wise (sub-district level) maternal mortality ratio was mapped using GeoPandas software. Global and local Moran's I along with spatial regression was performed using GeoDa software in evaluating the spatial dependence and identifying significant predictors of maternal mortality.

RESULTS: Maternal mortality varied geographically, according to thematic maps, and local indicators of spatial autocorrelation map showed high-high clustering (nine taluks (5.1%)) with positive Moran's I (0.114). Descriptive analysis of time of death revealed that the majority of maternal deaths (39.82%) occurred within 48 h postpartum, followed by 2-7 (20.95%) and 8-30 (16.23%) days. The spatial error model showed negative associations for antenatal care at the sub-centre, SDHs, deliveries conducted by doctors and private hospital (β=-0.047 to -0.184, p<0.05), and a positive association was found for below poverty line, stillbirths, parity 1 and deliveries at medical colleges (β=0.112-0.758, p<0.05) with a λ value of 0.286. Primary postpartum haemorrhage, sepsis, hypertensive disorder of pregnancy, cardiorespiratory disorders and other direct and indirect causes were identified as major contributors to maternal mortality in the spatial lag model (β=0.273 to 1.926, p<0.05, ρ=-0.077).

CONCLUSION: Spatial analysis revealed geographic hotspots, temporal risk windows and socio-economic and medical determinants of maternal mortality in Karnataka. These findings provide actionable evidence for spatially targeted, temporally focused and socio-clinically comprehensive maternal health interventions.},
}

Humans
Female
*Maternal Mortality/trends
Retrospective Studies
India/epidemiology
Pregnancy
Geographic Information Systems
Spatial Analysis
Spatial Regression
Risk Factors

@article {pmid42139758,
year = {2026},
author = {van Lill, M and Steenkamp, ET and Palmer, M and Beukes, CW and Venter, SN},
title = {Using the SeqCode to validate the names of reclassified lineages of rhizobia and agrobacteria.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126720},
doi = {10.1016/j.syapm.2026.126720},
pmid = {42139758},
issn = {1618-0984},
mesh = {*Rhizobiaceae/classification/genetics ; *Bartonellaceae/classification/genetics ; Phylogeny ; *Genome, Bacterial ; Datasets as Topic ; Sequence Analysis, DNA ; Terminology as Topic ; Conserved Sequence ; },
abstract = {Genome-based taxonomy offers a powerful means to resolve long-standing ambiguities in the classifications of agrobacteria and rhizobia, two bacterial groups with major ecological and agricultural significance. We applied a robust phylogenomic framework to genomes of the families Bartonellaceae and Rhizobiaceae to comprehensively reassess evolutionary relationships. Species trees were constructed using nucleotide sequences of 92 conserved genes and amino acid sequences of 120 ubiquitous proteins, clarifying relationships that were previously obscured by marker-limited historical classifications. These analyses demonstrated several instances of taxonomic inconsistencies across genera, most notably within Mesorhizobium, which forms a paraphyletic assemblage spanning multiple divergent lineages. These findings were further reinforced by the genome-wide similarity metric, average amino acid identity (AAI), which supported reclassifications at both genus and species levels, reflecting natural discontinuities between lineages. We propose the reclassification of eight species and five new genera and the validation of their names primarily under the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). As genome-based resources expand, and with the availability of new nomenclatural frameworks such as the SeqCode, genome-informed taxonomy offers a powerful approach to delineate taxa into biologically meaningful groups that can be formally recognised. The revised taxonomy presented here brings greater coherence to the systematics of agrobacteria and rhizobia and provides a framework for future evolutionary investigations into these agriculturally and ecologically significant bacterial groups.},
}

*Rhizobiaceae/classification/genetics
*Bartonellaceae/classification/genetics
Phylogeny
*Genome, Bacterial
Datasets as Topic
Sequence Analysis, DNA
Terminology as Topic
Conserved Sequence

@article {pmid42212967,
year = {2026},
author = {Albudoor, N and Anaya, JB},
title = {Extracting Word Frequencies From Child Language Corpora: A New Tool for Developmental Psycholinguistic Research.},
journal = {Journal of speech, language, and hearing research : JSLHR},
volume = {69},
number = {7},
pages = {3341-3350},
doi = {10.1044/2026_JSLHR-25-00280},
pmid = {42212967},
issn = {1558-9102},
mesh = {Humans ; *Child Language ; *Psycholinguistics/methods ; *Vocabulary ; Language Tests ; Child, Preschool ; *Language Development ; Databases, Factual ; Child ; },
abstract = {PURPOSE: We introduce childeswordfreq, an R-based tool for extracting frequency data from the CHILDES (Child Language Data Exchange System) database. This tool provides researchers with the ability to efficiently analyze word and phrase frequencies across multiple languages and speaker roles within the CHILDES database. The resulting frequency measures can be used for stimulus selection in experimental studies and for analyzing patterns in child language development. To illustrate the tool's utility, we conducted a case study using items from the Expressive One-Word Picture Vocabulary Test-Fourth Edition (EOWPVT-4), comparing their frequencies in CHILDES with adult-based Subtitle-based Word Frequency Database for American English estimates to assess how input frequency differs between child and adult linguistic environments.

CONCLUSIONS: The childeswordfreq package provides an accessible route for incorporating information on how frequently words are used in child-directed speech into research workflows. The results of our case study highlight why such access is critical. The CHILDES and SUBTLEX-US frequencies diverged in patterned ways tied to developmental progression, with earlier items on the EOWPVT-4 being overrepresented in child-directed speech and later items being more prominent in an adult corpus. These findings demonstrate how adult norms can diverge from frequency distributions relevant for acquisition. By grounding analyses in child-based input patterns, childeswordfreq strengthens developmental interpretations and supports more ecologically aligned research.

SUPPLEMENTAL MATERIAL: https://doi.org/10.23641/asha.32273607.},
}

Humans
*Child Language
*Psycholinguistics/methods
*Vocabulary
Language Tests
Child, Preschool
*Language Development
Databases, Factual
Child

@article {pmid42284942,
year = {2026},
author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.},
journal = {Water research},
volume = {303},
number = {},
pages = {126258},
doi = {10.1016/j.watres.2026.126258},
pmid = {42284942},
issn = {1879-2448},
mesh = {*Microbiota ; Risk Assessment ; Biodegradation, Environmental ; Multiomics ; Sulfur/metabolism ; },
abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.},
}

*Microbiota
Risk Assessment
Biodegradation, Environmental
Multiomics
Sulfur/metabolism

@article {pmid42368544,
year = {2026},
author = {Liu, J and Yu, K and Song, H and Ma, J and Bijani, M and Wu, L and Xu, L and Ahmad, MN and Xu, P and Zhao, J},
title = {ZDAM: a new deep learning model for bean leaf disease diagnosis.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1842022},
pmid = {42368544},
issn = {1664-462X},
abstract = {INTRODUCTION: Accurate disease diagnosis is crucial for enhancing agricultural productivity and reducing postharvest losses, directly impacting food quality and safety. Traditional detection methods often rely on extensive feature modeling and perform poorly in complex field environments.

METHODS: This study proposes a deep learning model called ZDAM, based on an improved ZFNet integrated with a dual attention mechanism. The classical ZFNet is first optimized to improve feature extraction efficiency. A combined channel and spatial attention mechanism is then incorporated to refine feature representation for disease identification in key crops. Finally, a residual module is added to boost accuracy.

RESULTS: Evaluated on a dataset of 11,903 bean leaf images covering healthy leaves and four disease types, including leaf mould, rust, mosaic, and white spot, the model achieves an average recognition accuracy of 99.02%, outperforming MobileMamba, Vision Transformer, and Chest- OMD.

DISCUSSION: This approach offers a scalable solution for automated disease monitoring, supporting postharvest quality preservation and sustainable crop production.},
}

@article {pmid42370032,
year = {2026},
author = {Zheng, H and Wang, S and Li, X and Li, Q and Wu, D and Klimont, Z and Zhao, D and Huang, L and Dong, Z and Wu, Q and Jiang, J and Jin, LN and He, H and He, K and Zhao, J and Liu, Q and Weichenthal, S and Cohen, AJ and Hao, J},
title = {Toxicity-informed control of global PM2.5 emissions.},
journal = {National science review},
volume = {13},
number = {11},
pages = {nwag301},
pmid = {42370032},
issn = {2053-714X},
abstract = {Fine particulate matter (PM2.5) remains a leading environmental health risk, yet air pollution control policies typically assume equal toxicity across emission sources. Unravelling the unequal toxicities in global PM2.5 emissions can support more effective air pollution control. Here, we integrate cell-based toxicological profiles with global emission inventories to develop the first global dataset of toxicity-adjusted PM2.5 emissions. We show that global toxicity-adjusted emissions are dominated by residential solid-fuel combustion, and that hotspots of PM2.5 mass and toxicity diverge substantially, with the highest toxicities occurring largely in regions reliant on traditional biomass. Low-income countries exhibit disproportionately high toxicity-adjusted emissions relative to their energy use, revealing a strong global environmental inequity. Incorporating unequal toxicities reshapes emission-control priorities, shifting many countries from mass-dominated industrial or power sectors towards residential combustion. We propose a toxicity-informed framework for air pollution control, which is adaptable to diverse socioeconomic contexts and can enhance global health and sustainability.},
}

@article {pmid42370731,
year = {2026},
author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L},
title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0040726},
doi = {10.1128/msystems.00407-26},
pmid = {42370731},
issn = {2379-5077},
abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.},
}

@article {pmid42371175,
year = {2026},
author = {Iqbal, MS and Alahmari, AK and Khan, MF and Farooqui, S and Iqbal, MZ and Khan, SU and Khan, N and Seshadri, VD and Abdelgawwad El-Sehrawy, AAM},
title = {Clonal Metamorphosis: Deconstructing MPN Evolution with Single-Cell and Spatial Multi-Omics.},
journal = {Clinical and experimental medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42371175},
issn = {1591-9528},
mesh = {Humans ; Multiomics ; *Single-Cell Analysis/methods ; *Clonal Evolution/genetics ; *Myeloproliferative Disorders/genetics/pathology ; Single-Cell Gene Expression Analysis ; Mutation ; Tumor Microenvironment ; Spatial Transcriptomics ; },
abstract = {Myeloproliferative neoplasms (MPNs) present a fundamental paradox: despite sharing a small set of canonical driver mutations in JAK2, CALR, or MPL, patients exhibit striking heterogeneity in disease latency, clinical presentation, and evolutionary trajectories to myelofibrosis or secondary acute myeloid leukemia. This review synthesizes recent advances in single-cell and spatial multi-omic technologies that are resolving this paradox by moving analysis from bulk averages to individual cells and their microenvironmental ecosystems. We examine how targeted single-cell DNA sequencing reconstructs clonal architectures and phylogenies, revealing that driver mutations arise within complex mosaics where mutation order, co-mutation context, and cellular ancestry determine phenotypic outcomes. Integrated single-cell transcriptomic and epigenomic profiling exposes within-clone heterogeneity, lineage biases, and functional states that explain variable penetrance and therapy responses. Spatial transcriptomics, especially when integrated with single-cell transcriptomics, histopathology, and multiplex proteomics, further demonstrates that malignant hematopoietic stem and progenitor cells actively remodel bone marrow niches, creating localized inflammatory and fibrotic microenvironments that select for aggressive subclones. Together, these approaches support a new ecological model of MPN pathogenesis in which early epigenetic hits create permissive stem cell reservoirs, clonal competition and cooperation shape disease progression, and non-cell-autonomous niche and immune signals drive malignant metamorphosis. We discuss how this framework refines prognostication, informs rational combination therapies targeting both malignant cells and their ecosystem, and enables real-time monitoring of clonal dynamics, ultimately charting a course from descriptive atlases to actionable clinical strategies.},
}

Humans
Multiomics
*Single-Cell Analysis/methods
*Clonal Evolution/genetics
*Myeloproliferative Disorders/genetics/pathology
Single-Cell Gene Expression Analysis
Mutation
Tumor Microenvironment
Spatial Transcriptomics

@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