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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Multiomics
Biodegradation, Environmental
*Arsenicals
Soil Pollutants

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Humans
*Exposome
Digital Health
*Digital Technology
Digital Media

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

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

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

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

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

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

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

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

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

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

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

@article {pmid41990036,
year = {2026},
author = {Conejero, I and de Granda-Beltrán, AM and Albarracín-García, L and Porras-Segovia, A and Barrigón, ML and Lopez-Castroman, J and Courtet, P and Artés-Rodriguez, A and Baca-Garcia, E and , },
title = {Impact of age and clinical factors on the feasibility of mobile digital monitoring in people at risk of suicide.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346772},
pmid = {41990036},
issn = {1932-6203},
mesh = {Humans ; Female ; *Suicide/psychology/statistics & numerical data ; Aged ; *Mobile Applications ; Male ; Middle Aged ; Feasibility Studies ; Age Factors ; *Suicide Prevention ; *Ecological Momentary Assessment ; Smartphone ; Adult ; Risk Factors ; Digital Health ; },
abstract = {OBJECTIVE: Assessing the risk of suicidal outcomes is challenging, particularly in older people. Smartphone-based digital phenotyping may help to monitor suicide risk through ecological momentary assessment (EMA) applications. In this real-world study, we investigated if age and other clinical factors were associated with participation in EMA at baseline, and with retention in EMA monitoring among patients at risk of suicide.

METHODS: Participation in EMA was determined by quantifying the installation of the MEmind mobile application in individuals involved in the SmartCrisis 1.0 and 2.0 studies. The patients were followed-up over a 6-month period.

RESULTS: N = 512 patients met inclusion criteria, of which 387 installed the MEmind application on their smartphone. While age as a continuous variable was not associated with using EMA at baseline, being aged older than 50 and being engaged in an intimate relationship were independently associated with longer participation in EMA (OR 2.070, 95%CI [1.054-4.066], and OR 2.103, 95%CI [1.076-4.110], respectively). In an exploratory survival analysis, we found that EMA retention increased with age (p < 0.001).

CONCLUSION: Feasibility of EMA seems warranted in older people at risk of suicide. Clinicians should be encouraged to offer EMA monitoring to older adults, as they commonly face limitations in their access to healthcare facilities.},
}

Humans
Female
*Suicide/psychology/statistics & numerical data
Aged
*Mobile Applications
Male
Middle Aged
Feasibility Studies
Age Factors
*Suicide Prevention
*Ecological Momentary Assessment
Smartphone
Adult
Risk Factors
Digital Health

@article {pmid41991939,
year = {2026},
author = {Tang, W and Yin, C and Gao, H and Lu, Z and Lu, Y and Xu, H},
title = {Chromosome level genome assembly of the American sloughgrass (Beckmannia syzigachne).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41991939},
issn = {2052-4463},
support = {31300873//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Chromosomes, Plant ; *Genome, Plant ; *Poaceae/genetics ; Datasets as Topic ; },
abstract = {American sloughgrass [Beckmannia syzigachne (Steud.) Fernald] is a problematic annual grass weed in winter wheat fields of China, which causes great loss of wheat yield. A lack of high-quality genome resources has hindered understanding of the Herbicide resistance characteristics and ecological adaptations. Here, we combined Illumina short read, PacBio long-read, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to generate a high-quality, chromosome-scale genome assembly of B. syzigachne. The genome assembly was 3.19 Gb in size, consisting of seven pseudo-chromosomes. The contig and scaffold N50 values were 62.2 Mb and 431.7 Mb, respectively. The genome assembly completeness was estimated at 97.1% by BUSCO assessment. Annotation revealed 36,944 protein-coding genes and 88.83% repeat sequences. This high-quality genome assembly is a valuable resource for future fundamental research and agricultural management of B. syzigachne, and provides significant new insights into the herbicide resistance as well as the adaptive evolution of B. syzigachne.},
}

*Chromosomes, Plant
*Genome, Plant
*Poaceae/genetics
Datasets as Topic

@article {pmid42008585,
year = {2026},
author = {Kaveladze, BT and Schueller, SM and Mohr, DC},
title = {Popular Online Content as a Treatment-as-Usual Control in Digital Mental Health Intervention Trials: Secondary Analysis of Two Online Randomized Controlled Trials With Repeated Measures.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e83707},
pmid = {42008585},
issn = {2368-7959},
mesh = {Humans ; Digital Media ; Adult ; Secondary Data Analysis ; Female ; Internet ; Randomized Controlled Trials as Topic ; *Depression/therapy ; *Anxiety/therapy ; Mental Health Teletherapy ; Digital Health ; Feasibility Studies ; },
abstract = {BACKGROUND: Treatment-as-usual (TAU) conditions are intended to reflect the support typically received in routine treatment settings. For digital mental health interventions (DMHIs) delivered online, TAU conditions should reflect the usual patterns of online help-seeking. The lack of ecologically valid TAU control conditions has been a gap in effectiveness trials of online DMHIs. In this study, mental health-related popular online content (eg, advice TikToks, lived experience vlogs, and self-care infographics) was examined as a valuable TAU control condition.

OBJECTIVE: This study examined the feasibility of popular online content as a TAU control condition in DMHI trials.

METHODS: This study was a secondary analysis of two randomized controlled trials. Both trials recruited participants online, primarily via an online study recruitment platform. In study 1 (N=916), US adults with elevated depression or anxiety were randomized to either (1) complete a single-session DHMI for depression and anxiety (n=291), (2) search the web for popular online content relevant to their struggles (n=312), or (3) search a curated library of mental health-related popular online content (n=313). In study 2 (N=431), US adults with elevated loneliness were randomized to (1) complete a single-session DHMI for loneliness (n=136), (2) search a curated library of popular online content related to loneliness (n=145), or (3) complete an attention-matched control condition (n=150). All 6 programs took approximately 10 to 20 minutes to complete and were entirely self-guided. Participants rated each program's credibility and expected benefit, as well as their feelings of distress (study 1) and loneliness (study 2). The studies did not involve interaction between participants and the research team.

RESULTS: In study 1, dropout during the treatment was 4.8% (14/291) for the single-session intervention, 25.9% (81/312) for online help-seeking, and 9.6% (30/313) for the curated library. The curated library's credibility and expected benefit score did not differ from that of the single-session intervention (Cohen d=0.08; P=.88) and was higher than that of unguided help-seeking (Cohen d=0.23; P=.01). In study 2, dropout was higher in the curated library condition (7/145, 4.8%) than in the single-session intervention and the attention-matched control condition (0/136, 0.0% and 0/150, 0.0%). The mean credibility and expected benefit score for the curated library was comparable to that of the attention-matched control condition (Cohen d=0.00; P>.99) but lower than that of the single-session intervention (Cohen d=0.32; P=.02). Changes in distress and loneliness from baseline to 8-week follow-up did not differ across the conditions in study 1. All effect sizes were small in study 1 (Cohen d<0.15), and no comparisons were statistically significant (P>.06). Similarly, in study 2, all effect sizes were small (Cohen d<0.12), and no comparisons were statistically significant (P>.25).

CONCLUSIONS: Curated libraries of popular online content are a feasible, ecologically valid TAU benchmark for effectiveness trials of online DMHIs. Future research on TAU conditions in online help-seeking contexts should better align with observed DMHI attrition rates and account for the increasingly central role of conversational artificial intelligence in online mental health support.},
}

Humans
Digital Media
Adult
Secondary Data Analysis
Female
Internet
Randomized Controlled Trials as Topic
*Depression/therapy
*Anxiety/therapy
Mental Health Teletherapy
Digital Health
Feasibility Studies

@article {pmid42015346,
year = {2026},
author = {Li, Z and Samui, S and Liu, J and Yang, Y and Liu, X and Chen, Q and Li, J and Gopinath, D and Luo, P and Shan, D},
title = {Gut microbiome and metabolic health: mechanisms and precision interventions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644677},
pmid = {42015346},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Fecal Microbiota Transplantation ; *Metabolic Diseases/microbiology/therapy/metabolism ; Precision Medicine ; Obesity/microbiology/metabolism ; Probiotics/administration & dosage ; Fatty Acids, Volatile/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Multiomics ; Prebiotics ; Metabolic Syndrome/microbiology/metabolism ; },
abstract = {The gut microbiome is increasingly recognized as a fundamental regulator of metabolic health, shaping energy balance, insulin sensitivity, inflammatory tone, and inter-organ communication through a broad spectrum of microbial metabolites that engage host signaling pathways. In this review, we synthesize current mechanistic insights into how gut microbial communities shape metabolic function, with particular emphasis on short-chain fatty acids, secondary bile acid signaling, gut barrier integrity, immune modulation, and the microbiota-gut-brain-pancreas axis. We further summarize disease-associated alterations in microbial composition and function across obesity, type 2 diabetes, metabolic dysfunction-associated steatotic liver disease, and metabolic syndrome, highlighting key microbial and metabolic features that contribute to metabolic dysfunction. Evidence from germ-free models, fecal microbiota transplantation studies, and strain-level interventions suggests that shifts in microbial ecology may causally shape metabolic outcomes. We also critically evaluate emerging microbiome-centered therapeutic strategies, including targeted probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation, while addressing factors that underlie inter-individual variability in treatment responses. In addition, we discuss the growing influence of multi-omics technologies, microbial metabolic modeling, and machine learning approaches in advancing precision microbiome medicine. To integrate these advances within a coherent framework, we outline a precision microbiome intervention pipeline linking multidimensional profiling to functional stratification and targeted therapeutic design. We also introduce a conceptual Precision Microbiome Intervention Triangle to mechanistically explain heterogeneity in responses to microbiome-targeted therapies. Collectively, these insights establish and position the gut microbiome as both a mechanistic driver and a modifiable therapeutic target in metabolic disease, and highlight key challenges and future directions for the development of personalized microbiome-based metabolic interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
Fecal Microbiota Transplantation
*Metabolic Diseases/microbiology/therapy/metabolism
Precision Medicine
Obesity/microbiology/metabolism
Probiotics/administration & dosage
Fatty Acids, Volatile/metabolism
Diabetes Mellitus, Type 2/microbiology/metabolism
Multiomics
Prebiotics
Metabolic Syndrome/microbiology/metabolism

@article {pmid42025075,
year = {2026},
author = {Liang, Y and Shi, J and Cheng, X and Feng, M and Jiao, D and Du, X and Ji, K and Hu, S and Dong, Q and Yang, G},
title = {Integrative transcriptomics and metabolomics analyses reveal changes in meat quality and muscle lipid metabolism in sheep supplemented with rumen-protected glucose.},
journal = {Meat science},
volume = {238},
number = {},
pages = {110110},
doi = {10.1016/j.meatsci.2026.110110},
pmid = {42025075},
issn = {1873-4138},
mesh = {Animals ; *Lipid Metabolism/drug effects ; *Glucose/administration & dosage ; Muscle, Skeletal/metabolism ; Dietary Supplements ; Sheep, Domestic/growth & development/metabolism ; Diet/veterinary ; Animal Feed/analysis ; Metabolomics ; Transcriptome ; Rumen ; *Red Meat/analysis ; Gene Expression Profiling ; Multiomics ; Sheep ; Male ; Oxidative Stress ; Malondialdehyde/blood ; },
abstract = {The effects of dietary rumen-protected glucose (RPG) supplementation on Dumengsa sheep growth performance, meat quality, and transcriptomic and metabolomic profiling are reported. Twelve sheep were randomly assigned to a control (basal diet, n = 6) or RPG (basal diet +1.0% RPG, n = 6) group for 100 d. RPG increased serum malondialdehyde (P = 0.015) and cholesterol (P = 0.046) concentrations, enhanced intramuscular fat content (P = 0.016), and tended to produce lower meat lightness (P = 0.072), redness (P = 0.053), and hue angle (P = 0.072) values. In total, 319 differentially expressed genes and 30 differentially abundant metabolites were identified. Transcriptomic analysis revealed RPG to alter the expression of genes related to oxidative phosphorylation, β-oxidation, and fat deposition. Metabolomic analysis revealed that RPG supplementation primarily increases the abundance of short-chain fatty acids. Integrated analysis using a Data Integration Analysis for Biomarker discovery using Latent Components (DIABLO) model revealed a strong and significant correlation (r = 0.93) between omics profiles. We report dietary supplementation with 1% RPG to modulate muscle lipid metabolism and potentially stimulate intramuscular fat deposition, but also to possibly induce a state of potential oxidative stress.},
}

Animals
*Lipid Metabolism/drug effects
*Glucose/administration & dosage
Muscle, Skeletal/metabolism
Dietary Supplements
Sheep, Domestic/growth & development/metabolism
Diet/veterinary
Animal Feed/analysis
Metabolomics
Transcriptome
Rumen
*Red Meat/analysis
Gene Expression Profiling
Multiomics
Sheep
Male
Oxidative Stress
Malondialdehyde/blood

@article {pmid42034665,
year = {2026},
author = {Sato, Y},
title = {RuSpacer: a CRISPR spacer database derived from ruminant-associated prokaryotes for virome analysis.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42034665},
issn = {2045-2322},
support = {25K18347//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Ruminants/virology/microbiology ; Rumen/microbiology/virology ; *Virome/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Prokaryotic Cells/virology ; *Databases, Genetic ; },
abstract = {Microorganisms in the ruminant gastrointestinal tract play key roles in lignocellulose degradation and energy conversion. Prokaryote-infecting viruses play a pivotal role in shaping host abundance and metabolism. Despite their importance, host-virus prediction in this environment remains limited, partly due to the lack of specialized clustered regularly interspaced short palindromic repeat spacer datasets. Here, RuSpacer, a database of 181,023 clustered regularly interspaced short palindromic repeat spacers extracted primarily from publicly available rumen-associated prokaryotic genomes, was established. Each spacer is annotated with the taxonomic identity of the genome from which it was derived. RuSpacer enables host-virus prediction via spacer-protospacer matching, particularly in the rumen ecosystem. It can also be integrated with existing publicly available spacer datasets and used for host-virus prediction in environments other than the rumen. Overall, this resource supports research on host-virus interactions, microbial ecology, and virus-based biocontrol strategies in livestock and other complex microbiomes.},
}

Animals
*Ruminants/virology/microbiology
Rumen/microbiology/virology
*Virome/genetics
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
*Prokaryotic Cells/virology
*Databases, Genetic

@article {pmid42036564,
year = {2026},
author = {Shin, D and Kim, YK},
title = {Ecological Momentary Assessment and Voice-Informed Forecast and Detection for the Diagnosis of Major Depression.},
journal = {Advances in experimental medicine and biology},
volume = {1502},
number = {},
pages = {95-109},
pmid = {42036564},
issn = {0065-2598},
mesh = {Humans ; *Major Depressive Disorder/diagnosis/psychology/physiopathology ; *Ecological Momentary Assessment ; Digital Health ; *Voice/physiology ; Predictive Value of Tests ; },
abstract = {Major depressive disorder (MDD) is a prevalent and disabling mental health condition traditionally diagnosed through subjective clinical interviews and retrospective self-reports, methods that are limited by recall biases and diagnostic heterogeneity. To address these limitations, ecological momentary assessment (EMA) and voice-based analysis have emerged as innovative diagnostic and monitoring tools. EMA captures real-time, context-rich data in naturalistic settings, providing nuanced insights into the dynamics of depressive symptoms, daily stressors, and coping strategies. Voice analysis leverages quantitative acoustic and linguistic biomarkers, reflecting underlying neurophysiological and psychomotor changes characteristic of depressive episodes. Integrating these technologies offers objective, scalable, and real-time approaches to enhance diagnostic accuracy, personalize interventions, and facilitate continuous patient monitoring. Nevertheless, practical challenges, including technological accessibility, participant adherence, data interpretation complexities, ethical concerns, and the necessity for robust validation, remain critical barriers. Future research directions highlight the need for digital phenotyping strategies using big data analytics to redefine depressive disorders beyond conventional DSM frameworks, ultimately paving the way for precision psychiatry.},
}

Humans
*Major Depressive Disorder/diagnosis/psychology/physiopathology
*Ecological Momentary Assessment
Digital Health
*Voice/physiology
Predictive Value of Tests

@article {pmid42041254,
year = {2026},
author = {Wang, M and Yang, J and Hu, T and Lin, Z and Wang, T and Liu, Z and Chen, X and Fan, X},
title = {Probing the genomic and proteomic basis of encystment in Oxytricha granulifera.},
journal = {mSystems},
volume = {11},
number = {5},
pages = {e0175725},
pmid = {42041254},
issn = {2379-5077},
support = {32570525, 32170446, 32270512//National Natural Science Foundation of China/ ; },
mesh = {*Proteomics/methods ; Multiomics ; *Protozoan Proteins/genetics/metabolism ; *Genomics/methods ; Transcriptome ; *Proteome ; *Genome, Protozoan ; },
abstract = {Protozoan encystment constitutes a pivotal survival strategy against environmental stressors; however, the molecular architecture governing this transition remains enigmatic, owing to limited genomic resources and a scarcity of integrated multi-omics investigations. Here, we elucidate the mechanisms underlying encystment in Oxytricha granulifera by reporting the first macronuclear genome assembly and conducting a comprehensive integration of transcriptomic, proteomic, and morphological analyses across vegetative and cyst stages. Morphological restructuring, typified by ciliary dedifferentiation and cyst wall formation, is molecularly supported by the downregulation of microtubule dynamics-associated genes and the concurrent upregulation of vesicle transport machinery. Furthermore, expanded gene families linked to carbohydrate metabolism and cellular acidification coincide with observed autophagic clearance and mucocyst activity, highlighting a coordinated metabolic shift essential for cyst formation. Elevated expression of the ubiquitin-proteasome system and autophagy pathways, which mediate protein turnover, along with upregulation of antioxidant enzyme genes, contributes to alleviating oxidative damage. Notably, we identified rewired post-transcriptional regulation that increases spliceosome activity and alternative splicing frequency, with each trend validated at the protein level. Concurrently, we observed a distinct epigenetic signature characterized by the significant downregulation of DNA N[6]-adenine methylation (6mA) methyltransferases (homologs of AMT1 and AMT6/7), suggesting a potential repressive role of methylation during the cyst stage. Collectively, these findings provide a multidimensional atlas of the encystment process, revealing that O. granulifera accomplishes cellular structural remodeling through a multilayered regulatory network spanning morphological, genetic, transcriptomic, and proteomic levels.IMPORTANCEOxytricha species are widely distributed in freshwater and terrestrial ecosystems, playing significant ecological roles in microbial communities. Their ability to undergo encystment provides a powerful model for studying cellular differentiation and stress adaptation in microbial eukaryotes. This study presents the first multi-omics analysis of encystment in Oxytricha granulifera, revealing microbial survival strategies through enhanced protein turnover, autophagy, alternative splicing, and DNA methylation reprogramming. These findings offer fundamental insights into dormancy mechanisms and environmental adaptation in protists, advancing our understanding of microbial resilience, evolutionary innovation, and ecological success in fluctuating environments.},
}

*Proteomics/methods
Multiomics
*Protozoan Proteins/genetics/metabolism
*Genomics/methods
Transcriptome
*Proteome
*Genome, Protozoan

@article {pmid42044372,
year = {2026},
author = {Lin, YP and Lu, SH and Lee, KC and Ma, WF and Ho, YF and Liao, WC and Yang, HT and Hong, O},
title = {Short-Term Effects of an mHealth Intervention on Healthy Behaviors and Cardiometabolic Health in Sedentary Employees: Quasi-Experimental Study.},
journal = {JMIR mHealth and uHealth},
volume = {14},
number = {},
pages = {e70074},
pmid = {42044372},
issn = {2291-5222},
mesh = {Humans ; Female ; Male ; Middle Aged ; *Sedentary Behavior ; Taiwan ; Adult ; *Health Behavior ; Digital Health ; Telemedicine/standards/statistics & numerical data ; Health Promotion/methods/standards/statistics & numerical data ; Surveys and Questionnaires ; Exercise/psychology ; },
abstract = {BACKGROUND: Sedentary employees face increased chronic health risks due to physical inactivity, immobility, and unhealthy eating behavior. Although mobile health (mHealth) interventions show promise in improving lifestyle behaviors, their effectiveness in occupational settings remains underexplored. Building on previous workplace interventions, this study developed and evaluated a mobile-enabled web app, SIMPLE HEALTH, developed with Din-J Design Co, Ltd, integrating activity tracking, healthy eating, and behavioral support for sedentary employees.

OBJECTIVE: This study evaluated the short-term effects of a 12-week mHealth intervention on physical activity, sedentary behavior, dietary habits, and cardiometabolic health indicators among sedentary employees in Taiwan.

METHODS: A 2-arm quasi-experimental study was conducted at 2 aerospace industrial workplaces. A total of 101 sedentary employees (mean age 46.9, SD 12.2 years; 52/101, 51.5% female) were enrolled from 2 worksites that were assigned by coin toss to either the intervention condition (n=50) or the control condition (n=51). The intervention group participated in the SIMPLE HEALTH program, an mHealth intervention grounded in Social Cognitive Theory and the Ecological Model, consisting of 8 components: activity tracking, goal setting, behavior logging, reminders, personalized advice, educational and motivational electronic booklets, and individual and team challenges. The control group received 6 print educational booklets. Cardiometabolic biomarkers, objectively measured physical activity (Fitbit Charge 3; Fitbit Inc), occupational sitting (occupational sitting and physical activity questionnaire), and dietary behavior (3-day photographic food records and the healthy eating behavior inventory) were assessed at baseline and 12 weeks. Data were analyzed using generalized estimating equations following the intention-to-treat principle.

RESULTS: At 12 weeks, the intervention group showed a significant increase in step counts (adjusted mean difference, MD 1227.13, 95% CI 2.90-2451.36; P=.049), a more favorable between-group change in moderate physical activity (adjusted MD 0.17, 95% CI 0.01-0.33; P=.04), and favorable dietary behaviors, including reduced intake of calories (adjusted MD -144.59, 95% CI -276.57 to -12.60; P=.03), carbohydrates (adjusted MD -19.88, 95% CI -37.99 to -1.78; P=.03), fats (adjusted MD -6.99, 95% CI -13.69 to -0.29; P=.04), and grains (adjusted MD -1.46, 95% CI -2.43 to -0.50; P=.003), and increased vegetable intake (adjusted MD 0.47, 95% CI 0.06-0.88; P=.02), compared to the control group. Favorable trends were noted in diastolic blood pressure (adjusted MD -2.38, 95% CI -4.99 to 0.22; P=.07) and soft lean mass (adjusted MD 0.34, 95% CI -0.06 to 0.75; P=.10). Both groups showed significant within-group improvements in low-density lipoprotein cholesterol (intervention: P=.01; control: P=.03), body fat percentage (intervention: P<.001; control: P=.01), waist circumference (intervention: P=.001; control: P=.002), and occupational sitting (intervention: P<.001; control: P=.03), and occupational walking (intervention: P=.01; control: P=.046), but between-group differences were nonsignificant.

CONCLUSIONS: The 12-week mHealth intervention improved physical activity and dietary behaviors and showed favorable trends in cardiometabolic indicators among sedentary employees. These findings support integrating mHealth programs into employee wellness initiatives to promote healthy behaviors, mitigate productivity loss, and reduce chronic disease burden. Further research should assess long-term sustainability, scalability, and cost-effectiveness in diverse occupational settings.},
}

Humans
Female
Male
Middle Aged
*Sedentary Behavior
Taiwan
Adult
*Health Behavior
Digital Health
Telemedicine/standards/statistics & numerical data
Health Promotion/methods/standards/statistics & numerical data
Surveys and Questionnaires
Exercise/psychology

@article {pmid42047208,
year = {2026},
author = {Xu, L and Zhu, H and Jiang, S and Zheng, Q and Yu, C},
title = {Effects of IT-enabled entrepreneurship on gender equality in a digital economy: Evidence from Qualitative Studies.},
journal = {African journal of reproductive health},
volume = {30},
number = {8},
pages = {85-101},
doi = {10.29063/ajrh2026/v30i8.9},
pmid = {42047208},
issn = {1118-4841},
mesh = {Humans ; *Entrepreneurship ; Female ; *Gender Equity ; Qualitative Research ; China ; *Women's Health ; Empowerment ; Grounded Theory ; Interviews as Topic ; Digital Health ; },
abstract = {Persistent digital divides and gendered health inequalities constrain women's participation in the digital economy, even in highly connected contexts like China. This study develops an explanatory framework for how information-technology-enabled entrepreneurship (ITEE) affects women's economic security, health, and capabilities. Using a constructivist grounded theory approach based on 80 interviews in China, the analysis reveals four themes. Capability formation shows how increased income and flexibility allow women to invest in health. Algorithmic exposure highlights the dual nature of platform visibility, boosting sales but also enabling harassment and anxiety. Care negotiation examines how unpaid care duties and infrastructure impact sustainability, showcasing adaptive strategies. Trajectory configuration integrates these into differentiated pathways, from vulnerable to healthenhancing, depending on aligned support. The findings position health centrally in digital capability and link platform governance and care ecologies to sustainable empowerment, suggesting safe platforms, caring support, and integrated policies are essential for women's wellbeing.},
}

Humans
*Entrepreneurship
Female
*Gender Equity
Qualitative Research
China
*Women's Health
Empowerment
Grounded Theory
Interviews as Topic
Digital Health

@article {pmid42048645,
year = {2026},
author = {Hou, J and Zhang, Z and Cheng, X and Wang, W},
title = {Patient Concerns Regarding Artificial Intelligence Applications in Health Care: Systematic Review and Meta-Synthesis Based on Social Ecological Theory.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e85663},
pmid = {42048645},
issn = {1438-8871},
mesh = {Humans ; *Artificial Intelligence ; *Delivery of Health Care ; Digital Health ; },
abstract = {BACKGROUND: The use of artificial intelligence (AI) in health care is growing quickly, but there is not enough research that looks at patient concerns from a multilevel perspective. Existing reviews predominantly summarize patient attitudes descriptively, lacking theoretical frameworks to explain the underlying mechanisms of these concerns.

OBJECTIVE: This systematic review and meta-synthesis aimed to identify and analyze patient concerns regarding health care AI applications, using social ecological theory to reveal the multilevel interactive mechanisms of concern at the individual, interpersonal, organizational, and societal levels.

METHODS: Following the PRISMA-S (Preferred Reporting Items for Systematic Reviews and Meta-Analyses literature search extension) guidelines, databases including PubMed, Embase, Web of Science, CINAHL, and Scopus were searched on March 1, 2026. Qualitative studies exploring patient perceptions of clinical AI applications were included, excluding those involving only healthy populations, technical performance, or nonclinical settings. Two researchers independently screened the literature and assessed methodological quality using the JBI-QARI (Joanna Briggs Institute Qualitative Assessment and Review Instrument) checklist. Confidence in synthesized findings was assessed using the GRADE-CERQual (Confidence in the Evidence from Reviews of Qualitative Research) approach.

RESULTS: A total of 25 qualitative studies involving 528 participants from diverse patient groups across multiple countries were included. Six themes emerged: (1) microlevel worries about privacy and data security, including data breaches and loss of control over personal health information; (2) worries about the limits and reliability of technology, especially AI diagnostic accuracy and "black box" decision-making; (3) mesolevel effects on physician-patient relationships, including reduced face-to-face interaction and empathy; (4) trust and accountability issues, including unclear responsibility attribution and institutional oversight problems; (5) macrolevel ethical and equity issues, including algorithmic bias and health care access inequalities; and (6) worries about technology diffusion and possible replacement of health care workers.

CONCLUSIONS: This review represents the first meta-synthesis applying social ecological theory to construct patient concerns regarding medical AI. Unlike previous descriptive reviews, it reveals the interconnected "ecological imbalance" mechanisms at micro-, meso-, and macrolevels when AI is embedded in health care systems. The findings suggest that many patient concerns are based on facts rather than just misunderstandings, indicating that systemic rather than isolated interventions are needed. Practical implications include explainable algorithm design at the microlevel, improved physician-patient communication, and institutional accountability at the mesolevel, and coordinated global ethical norms and equity-promoting policies at the macrolevel. Limitations include the inclusion of studies primarily from developed regions, significant heterogeneity in AI application scenarios, and constraints inherent to secondary research. Nevertheless, addressing these multilevel concerns remains crucial for balancing technological advancement with patient-centered care and enabling sustainable AI integration.},
}

Humans
*Artificial Intelligence
*Delivery of Health Care
Digital Health

@article {pmid42143584,
year = {2026},
author = {Lv, Y and Li, A and Gu, X and Hu, J and Wen, S and Xu, S and Deng, Y and Chen, D and He, X},
title = {Integrative omics analyses of ectomycorrhizal fungi modulate root growth and defense for mitigating aluminum toxicity in Pinus massoniana.},
journal = {Tree physiology},
volume = {46},
number = {6},
pages = {},
doi = {10.1093/treephys/tpag065},
pmid = {42143584},
issn = {1758-4469},
support = {NSFC 32171753//National Natural Science Foundation of China/ ; },
mesh = {*Mycorrhizae/physiology ; *Aluminum/toxicity ; *Pinus/microbiology/growth & development/drug effects/metabolism/physiology ; *Plant Roots/growth & development/microbiology/drug effects ; Stress, Physiological ; Multiomics ; *Basidiomycota/physiology ; Transcriptome ; },
abstract = {Aluminum (Al) toxicity is a critical environmental factor limiting plant productivity in acidic soils. Some ectomycorrhizal fungi (ECMF) can mitigate Al-induced stress and promote root growth in Pinus massoniana Lamb., however the underlying molecular and metabolic mechanisms have not yet been fully elucidated. In this study, P. massoniana seedlings inoculated with Lactarius deliciosus (L.) Gray (Ld) were subjected to acidic Al stress (pH 3.8) at Al3+ concentrations of 0.0 and 1.0 mM. Root growth, transcriptomic, metabolic and hormonal characteristics of the mycorrhizal symbionts were determined and analyzed. The study aimed to identify the key metabolites and metabolic pathways involved in ECMF-enhanced Al stress tolerance of P. massoniana, and to further elucidate on the underlying mechanism of ECMF in improving the Al resistance of P. massoniana from molecular and metabolic-physiological perspectives. Results showed that Ld inoculation significantly enhanced Al tolerance and promoted root growth and branching in P. massoniana. Specifically, it activated the phenylpropanoid-lignin biosynthesis pathway in mycorrhizal symbionts, downregulated carbon metabolism pathways and reduced intracellular accumulation of citric acid and specific amino acids (L-proline, L-threonine, serine). Furthermore, Ld elevated salicylic acid and gibberellin levels, decreased jasmonic acid content, upregulated growth-promoting genes (MYC2, GH3, TCH4) and downregulated inhibitory genes (ARF9/19, DELLA). This study further refines and clarifies the mechanism underlying ECMF-enhanced Al resistance in P. massoniana, and provides a theoretical basis for the application of ECMF in the ecological restoration of P. massoniana forest areas affected by Al toxicity.},
}

*Mycorrhizae/physiology
*Aluminum/toxicity
*Pinus/microbiology/growth & development/drug effects/metabolism/physiology
*Plant Roots/growth & development/microbiology/drug effects
Stress, Physiological
Multiomics
*Basidiomycota/physiology
Transcriptome

@article {pmid42284363,
year = {2026},
author = {Utkarsh, K and Shah, NR and Banerjee, T and Abrams, DM},
title = {A new method for augmenting short time series, with application to pain events in sickle cell disease.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014389},
doi = {10.1371/journal.pcbi.1014389},
pmid = {42284363},
issn = {1553-7358},
mesh = {*Anemia, Sickle Cell/physiopathology/complications ; Humans ; *Pain/physiopathology/etiology ; Computational Biology/methods ; Reproducibility of Results ; Algorithms ; Pain Measurement/methods ; },
abstract = {Researchers across different fields, including but not limited to ecology, biology, and healthcare, often face the challenge of sparse data. Such sparsity can lead to uncertainties, estimation difficulties, and potential biases in modeling. Here we introduce a novel data augmentation method that combines multiple sparse time series datasets when they share similar statistical properties, thereby improving parameter estimation and model selection reliability. We demonstrate the effectiveness of this approach through validation studies comparing Hawkes and Poisson processes, followed by application to subjective pain dynamics in patients with sickle cell disease (SCD), a condition affecting millions worldwide, particularly those of African, Mediterranean, Middle Eastern, and Indian descent.},
}

*Anemia, Sickle Cell/physiopathology/complications
Humans
*Pain/physiopathology/etiology
Computational Biology/methods
Reproducibility of Results
Algorithms
Pain Measurement/methods

@article {pmid42302574,
year = {2026},
author = {Castro Avila, A and Cookson, R and Kontopantelis, E and Doran, T},
title = {Socioeconomic inequalities in causes of death related to behavioural risk-taking in England and Wales: A longitudinal small-area ecological study.},
journal = {Public health},
volume = {257},
number = {},
pages = {106382},
doi = {10.1016/j.puhe.2026.106382},
pmid = {42302574},
issn = {1476-5616},
abstract = {OBJECTIVES: We examined socioeconomic trends in behavioural risk-taking deaths (BRDs) before and after the 2008-09 recession at the small area level.

STUDY DESIGN: Longitudinal ecological study METHODS: We analysed death registration data for behavioural risk-taking causes (suicide, drug-related, alcohol-related, accidental, and tobacco-related) in England and Wales from 2001 to 2021 at the small areas (population 5,000-8,000) level, aggregated into area deprivation quintiles. Age and sex standardised mortality rates were calculated using annual population estimates. We used a multilevel random-slopes negative binomial segmented regression with interruptions in 2009 and 2011 to estimate the association between mortality rates and the recession.

RESULTS: There were over 6.5 million BRDs between 2001 and 2021 (92.4% tobacco-related). Mortality rates were higher among men, in more deprived areas, and in northern regions. The pre-recession declines in tobacco-related mortality slowed after 2011, especially outside London and in more deprived areas. For non-tobacco-related BRDs, mortality rates increased in the post-recession period, but patterns varied by cause and place, with the greatest increases for accidental and drug-related deaths and in deprived areas outside London. Had pre-recession trends continued, there would have been 247,093 (95% CI: 239,942-254,243) fewer tobacco-related deaths and 12,585 (95% CI: 10,510-14,661) fewer non-tobacco-related BRDs between 2011 and 2021.

CONCLUSIONS: Socioeconomic inequalities in behavioural risk-taking deaths in England and Wales were stable prior to the 2008-09 recession but widened after 2011 for specific causes, especially outside London.},
}

@article {pmid41874421,
year = {2026},
author = {Wang, J and Lu, L and Sun, Y and Messer, LF and Wu, M and Duan, Z and Shi, J and Yang, Y and Li, C and Mao, Y and Zhu, D and Rillig, MC and Wang, X},
title = {AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41874421},
issn = {1751-7370},
support = {2024YFD1700702//National Key Research and Development Program of China/ ; U24A20634//National Natural Science Foundation of China/ ; 42377381//National Natural Science Foundation of China/ ; U21A2038//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; //Alexander von Humboldt Foundation/ ; },
mesh = {*Quorum Sensing/genetics ; *Acyl-Butyrolactones/metabolism/pharmacology ; *Biofilms/growth & development ; Gene Expression Regulation, Bacterial ; *Plastics ; Multiomics ; Virulence ; },
abstract = {The biofilm colonizing plastic debris, termed "the plastisphere," is of growing global concern due to escalating plastic pollution. However, the biological mechanisms underpinning plastisphere formation remain poorly understood. Here, we analyzed public global metagenomes, revealing a significant enrichment of genes associated with quorum sensing (QS) and biofilm formation, with a pronounced signal for acyl-homoserine lactone (AHL) QS. Using controlled microfluidic and tubular column experiments, we further demonstrate that exogenous AHL actively promotes plastisphere formation, biomass accumulation, and extracellular polymeric substance production on microplastics, whereas a quorum-quenching agent (AHL acylase) effectively inhibits these processes. Multi-omics analyses revealed that AHLs can transcriptionally activate genes involved in adhesion, motility, chemotaxis, and matrix production, fundamentally reshaping community structure, restructuring inferred microbial interaction networks, and driving community assembly toward stronger deterministic selection. AHL stimulation also increased the relative abundance and expression of pathogen-associated and virulence-related functions, suggesting an elevated virulence potential within the plastisphere under QS-promoting conditions. Together, our findings establish AHL-mediated QS as a central driver of plastisphere assembly and a key determinant of risk profile, highlighting its critical role in understanding and potentially mitigating the growing environmental and health hazards associated with microplastic pollution.},
}

*Quorum Sensing/genetics
*Acyl-Butyrolactones/metabolism/pharmacology
*Biofilms/growth & development
Gene Expression Regulation, Bacterial
*Plastics
Multiomics
Virulence

@article {pmid41877492,
year = {2026},
author = {Dumas, A and Hokayem, J and Goodman, G and Venkatasubramanian, K and Chai, P},
title = {Smartphone-Based Digital Phenotyping Across Health Conditions: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e84146},
pmid = {41877492},
issn = {1438-8871},
mesh = {*Smartphone ; Humans ; Digital Health ; *Phenotype ; Mental Health ; },
abstract = {BACKGROUND: Smartphone-based digital phenotyping uses built-in sensors and usage patterns to passively capture behavioral and environmental data relevant to health and has been applied extensively in mental health and chronic disease contexts.

OBJECTIVE: This review synthesizes studies that use smartphone-based digital phenotyping, defined as approaches that rely exclusively on onboard smartphone sensors to characterize specific health conditions. To our knowledge, this work provides the most comprehensive cross-condition synthesis of smartphone-based digital phenotyping to date, spanning mental health, physical health, and substance use disorders (SUDs), and highlighting common practices, gaps, and opportunities for future research.

METHODS: We conducted a scoping review of English-language, peer-reviewed papers published between 2012 and 2025 in Google Scholar, IEEE Xplore, ACM Digital Library, and PubMed using terms such as "mobile sensing" and "digital phenotyping." Eligible papers used onboard smartphone sensors to assess health and went beyond self-report. Studies that did not rely on smartphone auxiliary sensing modalities or digital phenotyping were excluded.

RESULTS: We performed a descriptive synthesis of study characteristics, sensors, and health domains. Of 111 papers identified, 65 met inclusion criteria. Most studies were observational and relied on passive sensing. Sample sizes ranged from fewer than 10 to over 18,000 participants, with a median of 52 (IQR=26-126). Mental health conditions were most frequently examined, including depression (n=16), bipolar disorder (n=11), stress or anxiety (n=10), and schizophrenia (n=8). Less commonly studied conditions included SUDs (n=7), Parkinson disease (n=4), and sleep apnea (n=2). Sensor streams varied widely and included diverse passive smartphone data sources capturing mobility, communication, device usage, environmental context, and user interaction patterns. Ground-truth measurements most commonly relied on validated clinical scales (eg, Patient Health Questionnaire-9, Young Mania Rating Scale [YMRS], and Pittsburgh Sleep Quality Index; n=41), followed by ecological momentary assessments (n=18), clinician-confirmed diagnoses (n=9), and physiological measures such as polysomnography (n=3). Across studies, recurring methodological limitations included incomplete or inconsistent sensor descriptions, limited reporting of data quality (eg, sampling rates and missingness), and heterogeneous validation practices. These issues limit comparability and reproducibility and underscore the need for clearer reporting standards and greater data availability.

CONCLUSIONS: This scoping review provides the first comprehensive synthesis of smartphone-only digital phenotyping studies spanning mental health, physical health, and SUDs. Unlike prior reviews, this work maps behavioral associations derived exclusively from smartphone sensors across a broad range of health domains. The primary contribution of this review lies in its consolidation of behavioral associations observed across studies, enabling researchers to correlate new findings to the existing evidence base and identify opportunities for replication, extension, or clinical translation. Collectively, these findings highlight both the promise of smartphone-based digital phenotyping in real-world settings and the need for improved standardization to support translation into clinical and public health applications.},
}

*Smartphone
Humans
Digital Health
*Phenotype
Mental Health

@article {pmid41904758,
year = {2026},
author = {Gopakumar, L and Parambil, JN and Joseph, A},
title = {Biomonitoring and GIS-based spatial modelling for soil ecosystem health in rural home garden agroecosystems in Chengamanad, Kerala, India.},
journal = {Environmental science and pollution research international},
volume = {33},
number = {13},
pages = {6068-6083},
pmid = {41904758},
issn = {1614-7499},
support = {Grant No. F.15-6(DEC 2013)/2014(NET)//University Grants Commission, India/ ; },
mesh = {*Soil/chemistry ; *Ecosystem ; India ; Geographic Information Systems ; *Environmental Monitoring ; Animals ; Gardens ; Agroecology ; *Biological Monitoring ; Seasons ; Arthropods ; },
abstract = {This study addresses the microarthropod-based estimation of biological soil quality in rural home gardens using the Qualitative Biological Soil-arthropods (QBS-ar) index. Soil microarthropods, soil properties, soil nutrients, and trace elements were systematically estimated from soil samples collected from 25 home gardens during summer and northeast monsoon seasons over 5 years (2014-2018). The relationships among QBS-ar, microarthropod abundance, soil properties, and soil nutrients were assessed. The microarthropods reported from the study area included Protura, Collembola, Coleoptera, Hymenoptera, Diplopoda, Araneae, Acari, Diptera, and Hemiptera showing statistically significant variations in Summer and monsoon abundance from 2014 to 2018. The QBS-ar index values ranging from 25.28 ± 9.77 to 48 ± 13.12 in summer and from 29.48 ± 18.63 to 56.12 ± 12.55 in monsoon indicated that the home gardens were ranked medium to good in soil quality, with index values ranging from 2 to 4 throughout the study period. Discriminant analysis of soil nutrients with soil properties and microarthropod abundance showed that the 2018 dataset was distinctly separated from the other years. A notable finding was the absence of trace elements (Pb, Cd, Cr) above permissible limits. Hazard estimation through Geographic Information System (GIS), integrating soil properties, nutrients and QBS-ar, indicated that the home gardens functioned as ecosystems with reduced biological soil quality post-flood. This study is among the first to utilize combined QBS-ar scores, soil properties, soil nutrients, and trace elements for long-term soil quality estimation in rural home garden agroecosystems. The study provides a simple, scalable methodological approach for soil ecosystem monitoring and management.},
}

*Soil/chemistry
*Ecosystem
India
Geographic Information Systems
*Environmental Monitoring
Animals
Gardens
Agroecology
*Biological Monitoring
Seasons
Arthropods

@article {pmid41910342,
year = {2026},
author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D},
title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.},
journal = {mSphere},
volume = {11},
number = {4},
pages = {e0085625},
pmid = {41910342},
issn = {2379-5042},
mesh = {Humans ; Multiomics ; Metagenomics ; *Glutens/metabolism/adverse effects ; Irritable Bowel Syndrome/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metabolomics ; Metabolome ; Archaea/classification/genetics ; Bacteria/classification/genetics ; },
abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.

IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.},
}

Humans
Multiomics
Metagenomics
*Glutens/metabolism/adverse effects
Irritable Bowel Syndrome/microbiology/metabolism
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Metabolomics
Metabolome
Archaea/classification/genetics
Bacteria/classification/genetics

@article {pmid41911042,
year = {2026},
author = {Zhang, Y and Wang, S and Wu, Q and Shi, Z and Ouyang, D and Li, S and Qian, Z and Shen, X and Yang, Y and Wang, L and Su, J and Wang, H and Tian, J and Tan, Q and Zhu, Y and Zhao, B},
title = {City-Level Decision Model and Technology Pathways for Benefit-Oriented Synergistic Control of Air Pollutants and Carbon Dioxide.},
journal = {Environmental science & technology},
volume = {60},
number = {14},
pages = {10717-10727},
doi = {10.1021/acs.est.5c13715},
pmid = {41911042},
issn = {1520-5851},
mesh = {*Carbon Dioxide ; *Air Pollutants ; Air Pollution ; Cities ; China ; Decision Support Techniques ; Models, Theoretical ; },
abstract = {Climate change and air pollution control are two urgent global challenges that demand effective solutions. Cities are the fundamental units for implementing control policies of air pollutants and carbon dioxide emissions. However, research on optimized city-level pathways that maximize integrated benefits and synergies of air pollution and carbon reduction remains limited. Here, we develop a decision-making model for coordinated control of air pollutants and carbon dioxide at the city level. The model systematically evaluates the air quality-related benefits, carbon reduction benefits, and their synergies across various emission reduction measures, and uses these evaluations to construct optimized emission reduction scenario under joint air quality and carbon targets. The model is applied to Beijing, Shanghai, and Chengdu: three megacities with populations above 10 million but distinct differences in city functions, industrial structure, and resource endowments. Results show that under enhanced policy regulation, all three cities can achieve national strategy-compliant air quality improvement and carbon reduction. Structural adjustments in energy, industry, and transportation are central to all cities, but priorities vary. Beijing relies on electric vehicles and imported green power; Shanghai focuses on local green power and transportation electrification; Chengdu emphasizes dust control and promoting clean power. Across all cases, monetized benefits exceed costs, though the benefit-to-cost ratio decreases with tightened environmental targets. This research provides methodological tools for improving environmental quality and promoting low-carbon development at the city level, and offers practical references for formulating region-specific policies tailored to local conditions.},
}

*Carbon Dioxide
*Air Pollutants
Air Pollution
Cities
China
Decision Support Techniques
Models, Theoretical

@article {pmid41923171,
year = {2026},
author = {Delgadillo-Ordoñez, N and Schwarzenberg, A and Zhang, H and Beenham, L and Bensaddek, D and Raimundo, I and Terraneo, T and Benzoni, F and Peixoto, RS},
title = {Coral color morphs exhibit distinct microbial and proteomic profiles linked to stress and immune mechanisms in a changing ocean.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41923171},
issn = {2049-2618},
mesh = {*Anthozoa/microbiology/immunology/metabolism/physiology ; Animals ; Proteomics/methods ; Multiomics ; *Bacteria/classification/isolation & purification/genetics ; *Microbiota ; Oceans and Seas ; Pigmentation ; Stress, Physiological ; Metabolome ; *Proteome ; Metabolomics ; Lipidomics ; },
abstract = {BACKGROUND: Coral phenotypic plasticity facilitates acclimation and adaptation to environmental variability. Coral species often display a variety of color morphs, yet key biological and ecological implications of such phenotypic variation remain underexplored. Here, we present the first proteomic and untargeted lipidomic and metabolomic survey to explore the biological characteristics and potential ecological significance of different color morphs (pink and brown) of healthy Pocillopora verrucosa sampled along a latitudinal gradient.

RESULTS: Our multi-omic approach elucidated distinct mechanisms associated with these dominant color morphs. We discovered bacterial indicators specific to each morph: putative pathogens such as Salmonella, Escherichia-Shigella, and carotenoid-producing Gemmatimonas were notably associated with the pink morph, whereas the brown morph was associated with potentially beneficial bacteria, such as Lysobacter, Acinetobacter, and Endozoicomonas. Despite these microbiome differences, the lipidome and metabolome of P. verrucosa were surprisingly homogeneous across colors and locations, suggesting similar metabolic performances during summer conditions. Key polar and apolar lipid classes, such as fatty acids, glycerophosphocholines, and retinoids, were prevalent. Notably, our proteomic analysis revealed morph-specific expressions, with pink morphs exhibiting enhanced levels of GFP-like proteins, Ankyrin, and the enzyme pullulanase, suggesting novel putative protective roles. In contrast, the brown morphs showed a higher abundance of heat shock proteins, indicating putative differential stress response capabilities.

CONCLUSION: This comprehensive study provides the first proteomic survey of P. verrucosa and identifies key physiological pathways and trade-offs linked to color morphs, which can further contribute to enhancing our understanding of coral resilience in the face of climate change.

SIGNIFICANCE STATEMENT: Understanding the phenotypic plasticity of corals is crucial for uncovering mechanisms of resilience in warming oceans, yet the biological significance of coral color morphs still needs to be explored. Using an innovative multi-omic approach (proteomics, lipidomics, and metabolomics), we provide the first comprehensive analysis of differences between pink and brown morphs of Pocillopora verrucosa. Our data reveal key taxa, potentially pathogenic or beneficial, associated with each morph, and suggest different strategies for each color morph to cope with heat stress, either expressing proteins involved in UV protection and heterotrophic activity or enhanced levels of heat stress resilience and DNA repair. These findings offer insights into the phenotypic plasticity of coral color morphs and their differential responses to climate change. Video Abstract.},
}

*Anthozoa/microbiology/immunology/metabolism/physiology
Animals
Proteomics/methods
Multiomics
*Bacteria/classification/isolation & purification/genetics
*Microbiota
Oceans and Seas
Pigmentation
Stress, Physiological
Metabolome
*Proteome
Metabolomics
Lipidomics

@article {pmid41823308,
year = {2026},
author = {Gramaje, D and Eichmeier, A},
title = {Beyond Koch's postulates: the pathobiome paradigm in grapevine esca disease.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {4},
pages = {},
pmid = {41823308},
issn = {1574-6941},
support = {//European Regional Development Fund/ ; PID2023-147360OR-C32//Ministry of Science, Innovation and Universities/ ; },
mesh = {*Vitis/microbiology ; *Plant Diseases/microbiology ; *Ascomycota/physiology/genetics ; Host-Pathogen Interactions ; Multiomics ; Stress, Physiological ; },
abstract = {Esca is one of the most damaging fungal diseases of grapevine and continues to defy Koch's postulates. Although Phaeomoniella chlamydospora, Phaeoacremonium minimum, and Fomitiporia mediterranea are consistently associated with wood necrosis in esca-symptomatic vines, they also occur in asymptomatic vines and even in apparently healthy wood tissues without visible necrosis, and single-species but also mixed-species inoculations rarely reproduce the characteristic foliar symptoms. We hypothesize that esca is best understood as a stress-mediated pathobiome disorder of the grapevine holobiont rather than a predictable outcome of specific fungal combinations, shifting focus from pathogen identity to holobiont functional state and environmental context. In this Review, we integrate evidence from community ecology, vascular biology, and multi-omics studies to link microbial community structure and activity with host hydraulics, defence, and environmental drivers. Metabarcoding and metatranscriptomics indicate that symptom expression correlates with functional reprogramming of trunk-inhabiting fungi more than their mere presence, while metabolomics and epigenomics reveal localized physiological disruption combined with systemic regulatory responses. Climatic and edaphic stresses, particularly drought, are strongly associated with holobiont destabilization and dysbiosis, altering symptom expression without necessarily modifying pathogen occurrence. We propose a temporal, multi-phase model integrating colonization history, microbiome restructuring, and host stress physiology through long-term feedbacks. This framework emerges through convergent multi-omics evidence and generates testable predictions for early detection, microbiome-informed biocontrol, and resilience-oriented vineyard management strategies.},
}

*Vitis/microbiology
*Plant Diseases/microbiology
*Ascomycota/physiology/genetics
Host-Pathogen Interactions
Multiomics
Stress, Physiological

@article {pmid41827056,
year = {2026},
author = {Chen, X and Xu, X and Lin, Y and Shi, X and Wang, D and Zhang, T},
title = {Pilea: profiling bacterial growth dynamics from metagenomes with sketching.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41827056},
issn = {2049-2618},
support = {T21-705/20-N//University Grants Committee/ ; },
mesh = {*Bacteria/growth & development/genetics/classification ; *Metagenome ; Software ; *Metagenomics/methods ; *Computational Biology/methods ; Microbiota ; },
abstract = {BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.

RESULTS: We introduce Pilea (https://github.com/xinehc/pilea), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.

CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.},
}

*Bacteria/growth & development/genetics/classification
*Metagenome
Software
*Metagenomics/methods
*Computational Biology/methods
Microbiota

@article {pmid41840746,
year = {2026},
author = {Zoch-Lesniak, B and Steiger, E and Kroll, LE and von Stillfried, DG},
title = {Evaluating the impact of a medical telephone helpline and the use of a structured initial assessment on demand for acute and emergency care in Germany: an ecological study using secondary data.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e107343},
pmid = {41840746},
issn = {2044-6055},
mesh = {Humans ; Germany/epidemiology ; *Triage/methods ; *Hotlines/statistics & numerical data ; *Emergency Service, Hospital/statistics & numerical data ; Emergency Room Visits ; *COVID-19/epidemiology ; *Emergency Medical Services/statistics & numerical data ; SARS-CoV-2 ; After-Hours Care/statistics & numerical data ; Secondary Data Analysis ; Telephone ; },
abstract = {OBJECTIVES: To assess whether a medical telephone helpline and the use of a computer-assisted structured triage tool led to a reduction in demand for acute and emergency care in hospital emergency departments (EDs) or other ambulatory out-of-hour (OOH) services.

DESIGN: We conducted an ecological study using secondary data on outpatient care.

SETTING: The study was conducted in 10 out of 16 federal states of Germany.

PARTICIPANTS: The analysis was based on ambulatory claims data for the years 2016-2020 by 11 Associations of Statutory Health Insurance Physicians (ASHIPs) covering more than 64% of the total German population.

INTERVENTIONS: The evaluated intervention comprised two components. The first was the introduction of a 24/7 medical helpline (116117), established to assist individuals with medical concerns in accessing appropriate care. The second component was the introduction of the computer-assisted triage tool SmED (Strukturierte medizinische Ersteinschätzung in Deutschland, Structured medical initial assessment in Germany) to support call-takers by suggesting medically relevant questions to identify red flags and determine the urgency of treatment and a possible treatment facility. For the analysis, approximately 3 years before and 1 ½ years during the intervention were considered.

OUTCOME MEASURES: Main outcome was the effect on acute and emergency care which was measured as the number of personal doctor-patient contacts (1) in EDs (ED cases, data of 10 ASHIPs could be considered) and (2) in EDs or other OOH services (ED and OOH cases, data of 11 ASHIPs could be considered).

RESULTS: The analysis was limited by legal changes mandating intervention components across all study sites-leading to a loss of control groups and delayed implementation-and the onset of the COVID-19 pandemic. Across all ASHIPs and counties, the number of calls to 116117 and the number of SmED assessments showed a negative association with the number of ED cases (total change: 295.0 cases to 224.5 cases per 100 000 inhabitants, 116117 calls: r=-0.04; 95% CI -0.04 to -0.035; p≤0.001, SmED: r=-0.15; 95% CI -0.35 to 0.05; p=0.138) as well as with the combined number of ED and OOH cases (total change: 516.4 cases to 400.3 cases per 100 000 inhabitants, 116117 calls: r=-0.02; 95% CI -0.03 to -0.001; p≤0.01, SmED: r=-0.58; 95% CI -0.98 to -0.19; p≤0.01). However, the association between the number of SmED assessments and ED cases was not statistically significant. Moreover, the magnitude and direction of effects varied across ASHIPs. Sensitivity analyses restricted to time periods preceding the onset of the COVID-19 pandemic showed a non-significant negative association for 116117 calls and a significant positive association for SmED assessments with both ED cases and combined ED and OOH cases (ED cases: 116117 calls: r=-0.001; 95% CI -0.019 to -0.018; p=0.928; SmED: r=0.37; 95% CI 0.29 to 0.45; p≤0.001; ED and OOH services cases: 116117 calls: r=-0.03; 95% CI -0.06 to 0.003; p=0.077; SmED: r=0.34; 95% CI 0.20 to 0.48; p≤0.001).

CONCLUSIONS: Our findings indicate a trend suggesting that implementation of a 24/7 medical helpline may reduce the demand for acute and emergency care at EDs and OOH services, although clear evidence is lacking. The impact of SmED use remains inconclusive. Further research should ideally incorporate data linkage and controls and assess the effectiveness and efficiency of the triage process, as well as the quality of subsequent care at the individual level.},
}

Humans
Germany/epidemiology
*Triage/methods
*Hotlines/statistics & numerical data
*Emergency Service, Hospital/statistics & numerical data
Emergency Room Visits
*COVID-19/epidemiology
*Emergency Medical Services/statistics & numerical data
SARS-CoV-2
After-Hours Care/statistics & numerical data
Secondary Data Analysis
Telephone

@article {pmid41805265,
year = {2026},
author = {Kim, KW and Byun, AJS and Castillo, J and Youn, YC and Torous, J},
title = {Metadata in Smartphone-Based Cognitive Assessments: Current State and Emerging Evidence in Psychiatric Disorders.},
journal = {Harvard review of psychiatry},
volume = {34},
number = {2},
pages = {85-94},
doi = {10.1097/HRP.0000000000000453},
pmid = {41805265},
issn = {1465-7309},
mesh = {Humans ; *Smartphone ; *Mental Disorders/diagnosis ; *Ecological Momentary Assessment ; *Metadata ; Digital Health ; *Cognitive Dysfunction/diagnosis ; },
abstract = {Smartphone-based cognitive assessments have emerged as promising tools for frequent and ecologically valid monitoring of cognitive function in real-world settings. These tools enable continuous capture of cognitive and behavioral patterns, including intra-individual variability, practice-related improvement, and contextual influences. Repeated assessments offer a unique opportunity to detect subtle cognitive changes over time. The interpretability and clinical utility of the metadata generated by such assessments, however, remain underexplored. In this review, we consider the current landscape of smartphone-derived cognitive metadata in the context of cognitive and affective disorders. We focus on emerging evidence linking metadata features to functional outcomes and symptom fluctuations across conditions such as schizophrenia, bipolar disorder, and depression. Additionally, we discuss methodological considerations for optimizing metadata analysis, including test design, sampling frequency, and analytical strategies. We propose that cognitive metadata may serve as sensitive indicators of early cognitive change and support personalized mental health monitoring and targeted intervention.},
}

Humans
*Smartphone
*Mental Disorders/diagnosis
*Ecological Momentary Assessment
*Metadata
Digital Health
*Cognitive Dysfunction/diagnosis

@article {pmid41813102,
year = {2026},
author = {Shi, Y and Kim, J and Mizushima, R and Mizuno, S and Yanagisawa, T and Nakata, Y},
title = {Understanding User Perspectives to Inform Personalized Physical Activity Promotion in a Health Care App: Qualitative Focus Group Interview Study.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e85390},
pmid = {41813102},
issn = {2561-326X},
mesh = {Humans ; Female ; Focus Groups/methods ; *Exercise/psychology ; Male ; Adult ; Qualitative Research ; Middle Aged ; *Health Promotion/methods/standards ; *Mobile Applications/standards/statistics & numerical data ; Motivation ; *Perception ; Aged ; Digital Health ; },
abstract = {BACKGROUND: Health care apps are widely used to support weight loss and lifestyle modification. Many of these apps offer tailored feedback on dietary intake and nutritional behavior. However, most lack personalized features that promote physical activity (PA), which is important for weight management, metabolic health, and chronic disease prevention. To develop future personalized PA promotion functions, it is essential to understand users' perceptions of PA.

OBJECTIVE: This study aimed to explore health care app users' perception of PA, including perceived motivators and barriers.

METHODS: A qualitative study was conducted using focus group interviews with health care app users. Participants were recruited regardless of age, sex, or body mass index. A thematic analysis was conducted using a combination of inductive and deductive approaches. Question 1 ("How do you perceive the importance of physical activity?") was analyzed inductively, whereas questions 2 ("What are the motivating factors for engaging in physical activity?") and 3 ("What are the barriers to engaging in physical activity?") were analyzed deductively based on the social ecological model.

RESULTS: Eleven participants were interviewed and were unfamiliar with the term "physical activity" but recognized the importance of movement and reducing sedentary behavior. The identified motivators included improvements in mood; changes in physical appearance; support from family; alignment with personal routines and conditions (eg, goal setting, feedback, reminders, and praise); and tailoring to physical condition, daily schedules, and weather. The reported barriers included time restrictions due to work, fatigue, weather, remote work, and social pressure in workplace settings.

CONCLUSIONS: This study provides user-informed insights that can inform the design of personalized approaches better aligned with daily routines, competing demands, and situational barriers. Future work should evaluate how incorporating such user perspectives into personalized support strategies affects engagement and PA.},
}

Humans
Female
Focus Groups/methods
*Exercise/psychology
Male
Adult
Qualitative Research
Middle Aged
*Health Promotion/methods/standards
*Mobile Applications/standards/statistics & numerical data
Motivation
*Perception
Aged
Digital Health

@article {pmid41813445,
year = {2026},
author = {Hayes, G and Buck, C and Cardon, G and Cimler, R and Elavsky, S and Fezeu K, L and Harrington, JM and Kühnová, J and Oppert, JM and Sigcha, L and Van de Ven, P and Vetrovsky, T and Woods, CB and Hebestreit, A and Donnelly, AE},
title = {Standardized Methods for Evaluating Physical and Eating Behaviors: The WEALTH Cross-Sectional Study Protocol.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e70186},
pmid = {41813445},
issn = {1929-0748},
mesh = {Humans ; Cross-Sectional Studies ; *Feeding Behavior/physiology ; Female ; Adult ; *Wearable Electronic Devices/standards ; Male ; *Exercise/physiology ; Surveys and Questionnaires ; Germany ; Czech Republic ; Anthropometry/methods ; Ireland ; Digital Health ; Middle Aged ; },
abstract = {BACKGROUND: The accurate measurement of physical behaviors (PBs) and eating behaviors (EBs) is critical for designing, monitoring, and implementing public health guidelines and intervention strategies. The objective of the Wearable Sensor Assessment of Physical and Eating Behaviours (WEALTH) project was to develop standardized methods to identify daily PBs and EBs from wearable research- and consumer-grade sensors and evaluate the interaction and contexts of these behaviors.

OBJECTIVE: The aim of this paper is to describe the study design and methods and report on the descriptive characteristics of the participants.

METHODS: Within the framework of the WEALTH project, a cross-sectional study (spring 2023 to spring 2024) was completed in 5 European research centers in the Czech Republic, France, Germany, and Ireland. In each center, participants attended a research lab, completed an online questionnaire, and provided measures of anthropometry and handgrip strength. The participants were then fitted with 2 research-grade and 2 consumer-grade devices and participated in a standardized semistructured lab-based activity protocol. The latter was specifically designed to collect labeled data that simulated common PBs and EBs typical for a daily routine. Participants were then followed during a 9-day free-living data collection period, which combined the assessment of PB and EB via wearable devices and time-based, event-based, and self-initiated ecological momentary assessments (EMAs). The EMA surveys were complemented by three 24-hour dietary recalls, using validated web-based programs. Upon the completion of the survey protocol, participants completed a questionnaire that assessed the feasibility of the procedures.

RESULTS: The final sample includes 627 participants, of whom 44% (n=275) were male. The mean age was 32.7 (SD 13.3) years, and the mean body mass index was 24.5 (SD 4.0) kg/m². The WEALTH study data will be used to develop machine learning (ML) models for classifying daily activities from wrist and hip-worn accelerometer data, evaluate EMA methods for studying interactions between PB and EB, and evaluate the feasibility and compliance of the methods. Data processing and ML model development are currently underway, with primary results expected to be published in 2026.

CONCLUSIONS: The output of the WEALTH project will be provided via a repository and a comprised toolbox of publicly available labeled data, ML models for behavior classification from accelerometer data, and a methodology to simultaneously capture EB and PB, thereby producing an integrated data collection system to support future research.},
}

Humans
Cross-Sectional Studies
*Feeding Behavior/physiology
Female
Adult
*Wearable Electronic Devices/standards
Male
*Exercise/physiology
Surveys and Questionnaires
Germany
Czech Republic
Anthropometry/methods
Ireland
Digital Health
Middle Aged

@article {pmid41813489,
year = {2026},
author = {Takano, A and Okuda, K and Sese, J and Ono, K and Matsumoto, T},
title = {Individual Variability in Physiological Responses and Psychological Conditions Associated With Methamphetamine Use: Pilot Ecological Momentary Assessment Study Using a Wearable Device and Self-Monitoring Mobile App.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e73790},
pmid = {41813489},
issn = {2561-326X},
mesh = {Humans ; Pilot Projects ; *Methamphetamine/adverse effects ; Female ; Male ; Ecological Momentary Assessment ; Adult ; *Mobile Applications/standards/statistics & numerical data ; *Wearable Electronic Devices/statistics & numerical data/standards ; Heart Rate/physiology ; Middle Aged ; Japan ; Digital Health ; *Amphetamine-Related Disorders/psychology/physiopathology ; Craving ; },
abstract = {BACKGROUND: Digital mental health approaches offer a novel means to monitor and reduce harms associated with substance use in daily life. However, limited evidence exists on their application for methamphetamine (MAMP) use, particularly regarding individual variability in physiological responses and psychological conditions.

OBJECTIVE: This pilot study aimed to explore inter- and intraindividual differences in craving, emotion, and heart rate associated with MAMP use, using data collected from a wearable device (Fitbit) and a mobile-based self-monitoring app.

METHODS: Participants were individuals with MAMP use disorder receiving outpatient treatment in Japan. The analysis included 7 participants who used MAMP during an 8-week observation period. Physiological data, including heart rate and sleep patterns, were collected using Fitbit devices, while daily self-reported MAMP use, craving intensity, and emotional status were recorded via a mobile app. After syncing the data, we visualized and summarized individual MAMP use patterns in detail. Correlations between physiological and psychological indicators and the frequency of MAMP use per day were analyzed. In addition, heart rate trends before and after MAMP use events were evaluated using a linear mixed effects model, and both interindividual variability and intraindividual variability were assessed.

RESULTS: Patterns of MAMP use varied widely across participants, with it most commonly occurring in the morning or at night, regardless of the day of the week. Craving and negative emotions were frequently reported on MAMP use days and were positively correlated with the number of MAMP use episodes per day. Participants who used MAMP more frequently exhibited relatively higher resting heart rates. Following MAMP use, heart rate increased significantly and remained elevated for up to 9 hours. Sleep duration and frequency were reduced or absent on MAMP use days. Approximately 64% of the variance in heart rate was attributable to interindividual differences, while 12% reflected variability across events within the same individual.

CONCLUSIONS: This pilot study demonstrates the feasibility and value of using digital tools to examine physiological responses and psychological conditions associated with MAMP use in real-world settings. Persistent cardiovascular activation and disrupted sleep highlight the potential risks of long-term MAMP use. Individual differences in heart rate responses, craving, and emotional states underscore the importance of personalized intervention strategies. Integrating real-time self-monitoring, notifications for elevated heart rate, and online cognitive behavioral therapy into digital therapeutic interventions may improve health outcomes for individuals with MAMP use disorder.},
}

Humans
Pilot Projects
*Methamphetamine/adverse effects
Female
Male
Ecological Momentary Assessment
Adult
*Mobile Applications/standards/statistics & numerical data
*Wearable Electronic Devices/statistics & numerical data/standards
Heart Rate/physiology
Middle Aged
Japan
Digital Health
*Amphetamine-Related Disorders/psychology/physiopathology
Craving

@article {pmid41813698,
year = {2026},
author = {Winter, M and Vogel, C and Schobel, J and Schlüter, M and Baumeister, H and Terhorst, Y and Schlee, W and Langguth, B and Heuschmann, P and Cohrdes, C and Pryss, R},
title = {Longitudinal mental health data collected via the Corona Health smartphone app during COVID-19.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41813698},
issn = {2052-4463},
support = {01KX2021//German Federal Ministry of Education and Research/ ; },
mesh = {Humans ; *COVID-19/psychology ; *Mental Health ; *Mobile Applications ; Adult ; Pandemics ; *Smartphone ; Longitudinal Studies ; Germany ; Quality of Life ; Ecological Momentary Assessment ; Surveys and Questionnaires ; SARS-CoV-2 ; Adaptation, Psychological ; Adolescent ; Female ; Telemedicine ; Young Adult ; Middle Aged ; Male ; Digital Health ; },
abstract = {Mental health impacts during the COVID-19 pandemic underscored the importance of real-time assessment methods to capture population-level changes (e.g., longitudinal changes in quality of life). This dataset contains questionnaire responses collected with the Corona Health app, a multilingual mHealth app available on Android and iOS platforms. The dataset includes baseline from 2,704 participants (i.e., adults aged 18 years and older, living in Germany) and 11,541 repeated ecological momentary assessment (EMA) responses, providing longitudinal mental health data throughout various phases during the pandemic period (i.e., data collected between July, 2020 and January, 2025). The questionnaires assessed domains such as quality of life, psychological well-being, coping mechanisms, and pandemic-related concerns. In addition to questionnaire responses, the dataset includes sensor data such as GPS location information and app usage statistics collected with participant consent. The described dataset enables researchers to examine mental health trajectories during and after COVID-19, analyze relationships between psychological factors and pandemic experiences, and investigate patterns in longitudinal mental health data.},
}

Humans
*COVID-19/psychology
*Mental Health
*Mobile Applications
Adult
Pandemics
*Smartphone
Longitudinal Studies
Germany
Quality of Life
Ecological Momentary Assessment
Surveys and Questionnaires
SARS-CoV-2
Adaptation, Psychological
Adolescent
Female
Telemedicine
Young Adult
Middle Aged
Male
Digital Health

@article {pmid41814663,
year = {2026},
author = {Wang, T and Hu, W and Song, W and Liao, X and Zheng, H and Zhang, X and Xin, X and Singh, PK and Chen, Y and Xu, Y},
title = {From triangle to pyramid: Understanding host-pathogen-microniome-environment interplay for sustainable, enviromics-empowered management of plant diseases.},
journal = {Plant communications},
volume = {7},
number = {5},
pages = {101815},
pmid = {41814663},
issn = {2590-3462},
mesh = {*Plant Diseases/microbiology/prevention & control ; *Host-Pathogen Interactions ; Multiomics ; *Microbiota ; *Plants/microbiology/genetics ; Environment ; },
abstract = {Understanding plant disease development requires moving beyond the classic disease triangle, which considers the host, pathogen, and environment. Recent advances in multi-omics have highlighted the importance of a disease pyramid that integrates the host, pathogen, microbiome, and environment to capture the complex interactions among these core biological/ecological components. This pyramid framework emphasizes how host genetic architecture, pathogen traits, microbiome dynamics, and environmental conditions collectively and interactively shape disease outcomes, plant phenotypes, and adaptive potential. The conceptual expansion from the disease triangle to a pyramid model reflects this shift, providing a more holistic and dynamic view of plant disease ecology. Environmental factors regulate host susceptibility and restructure both pathogenic and non-pathogenic microbial communities, thereby influencing infection severity and disease progression. Multi-omics approaches-encompassing hostomics, pathomics, microbiomics, and enviromics-hold strong promise for dissecting these interactions, enabling predictive disease modeling and the development of sustainable management strategies. Moreover, integrating enviromics data into resistance breeding enables the identification of key environmental variables and their interactions with host genotypes and pathogenic and non-pathogenic microbes, thereby supporting the deployment of durable resistance across diverse agroecosystems. Together, these perspectives advance a systems-level understanding of plant health and open new avenues for disease management through omics-driven breeding, microbiome-informed strategies, and environmentally responsive interventions.},
}

*Plant Diseases/microbiology/prevention & control
*Host-Pathogen Interactions
Multiomics
*Microbiota
*Plants/microbiology/genetics
Environment

@article {pmid42059404,
year = {2026},
author = {Wang, C and Liu, Y and Lin, G and Deng, X and Lin, S and Jiao, N},
title = {Molecular mechanisms, metabolic remodeling, and energy reallocation underlying calcification in the coccolithophore Gephyrocapsa huxleyi.},
journal = {Journal of phycology},
volume = {62},
number = {3},
pages = {943-958},
doi = {10.1111/jpy.70170},
pmid = {42059404},
issn = {1529-8817},
support = {42476128//National Natural Science Foundation of China/ ; 42188102//National Natural Science Foundation of China/ ; 2025029//Scientific Research Foundation of the Third Institute of Oceanography/ ; //Ocean Negative Carbon Emissions (ONCE) program/ ; },
mesh = {*Haptophyta/metabolism/physiology/genetics ; *Energy Metabolism ; *Calcification, Physiologic ; Photosynthesis ; Multiomics ; },
abstract = {Coccolithophores play a dual role in the marine carbon cycle, serving as CO2 sinks through photosynthesis while simultaneously emitting CO2 via calcification, resulting in uncertainty regarding their net carbon sequestration potential. In addition, their calcite coccoliths (CaCO3) can increase the carbon export efficiency by functioning as ballasts for organic matter. Although biogeochemically significant, the molecular mechanisms governing calcification and associated metabolic adaptations in coccolithophores remain poorly characterized, impeding accurate predictions of their responses to climate change. Through comparative multiomics analyses of calcified (RCC1266) and noncalcified (PML B92/11) Gephyrocapsa huxleyi strains, as well as chemically induced decalcified and recalcified states, we screened several ion transport genes, which potentially facilitate Ca[2+] and HCO3 [-] uptake/transport coupled with H[+] extrusion during calcification in the calcified strain, along with their associated proteins, including signal molecules and chaperones. Furthermore, an energy-intensive process was observed in calcifying cells, and this process was principally sustained by enhanced photosynthetic efficiency, supplemented by glucose accumulation as an energy reserve and COX6B translational upregulation, providing nocturnal energy. Notably, calcifying cells employed an energy conservation strategy characterized by transcriptional downregulation yet translational maintenance of photosynthesis and carbon metabolism genes while simultaneously upregulating protein biosynthesis and trafficking pathways to probably meet calcification demands, a process potentially facilitated by increased glutamine biosynthesis. Through multiomic technology, our findings provide insights into the molecular adaptations in the calcified coccolithophorid cells, revealing critical physiological trade-offs, carbon metabolism, and energy allocation that can inform predictions of their acclimation capacity under changing oceanic conditions.},
}

*Haptophyta/metabolism/physiology/genetics
*Energy Metabolism
*Calcification, Physiologic
Photosynthesis
Multiomics

@article {pmid42172829,
year = {2026},
author = {Yang, H and Xie, Y and Wang, H and Sun, H and Li, X and Yao, X and Ding, J and Wang, Q and Lv, H and Turner, BL and Sun, S and Wang, J},
title = {Multi-omics association analysis of the toxicity mechanism differences of typical veterinary antibiotics on tomatoes: From physiological inhibition to metabolic reprogramming.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142457},
doi = {10.1016/j.jhazmat.2026.142457},
pmid = {42172829},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/toxicity ; *Solanum lycopersicum/drug effects/metabolism/growth & development ; Chlortetracycline/toxicity ; Tylosin/toxicity ; Enrofloxacin/toxicity ; Oxidative Stress/drug effects ; Photosynthesis/drug effects ; Multiomics ; *Veterinary Drugs/toxicity ; *Soil Pollutants/toxicity ; Seedlings/drug effects/growth & development/metabolism ; },
abstract = {Widespread application of veterinary antibiotics is contaminating soil via animal feces, leading to uptake by plants and environmental damage. Currently, research on the toxicological mechanisms associated with various classes of antibiotics remains inadequate. Therefore, this study utilized tomato as the test species and selected three representative antibiotics-chlortetracycline (CTC), enrofloxacin (ENR), and tylosin (TYL)-to systematically evaluate their differential toxicity and associated metabolic mechanisms through 14 and 28 days exposure experiments. At the individual level, antibiotics significantly suppressed biomass accumulation and photosynthesis in tomato seedlings, the ENR exhibited maximum inhibition rates of 37.4% for fresh weight and 26.7% for plant height. In contrast, the CTC recorded peak values of 28% for leaf area and 25.1% for SPAD measurements. Furthermore, exposure to antibiotics induced oxidative stress in tomato seedlings, with SOD demonstrating its highest activation rate of 18.3% in the TYL. Within the rhizosphere microenvironment, there was a notable decrease in the abundance of the dominant phylum Bryobacter, which was accompanied by alterations in bacterial community structure, an increase in network complexity, and a reduction in modularity. Under antibiotic stress, microbial communities demonstrated distinct metabolic responses: enhanced lipid metabolism in CTC, elevated carbohydrate metabolism with ENR, and activated nucleotide metabolism associated with TYL. In summary, antibiotics present global ecological risks by inhibiting plant growth and disrupting the rhizosphere microbiome. The class-specific toxicity of these substances necessitates the implementation of targeted risk management strategies.},
}

*Anti-Bacterial Agents/toxicity
*Solanum lycopersicum/drug effects/metabolism/growth & development
Chlortetracycline/toxicity
Tylosin/toxicity
Enrofloxacin/toxicity
Oxidative Stress/drug effects
Photosynthesis/drug effects
Multiomics
*Veterinary Drugs/toxicity
*Soil Pollutants/toxicity
Seedlings/drug effects/growth & development/metabolism

@article {pmid42298119,
year = {2026},
author = {Sorboni, SG and Pourebrahim, S and Chen, JE and Hadipour, M},
title = {Anthropogenic accessibility and observer inequality dictate spatial biodiversity patterns in Malaysia.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-58296-2},
pmid = {42298119},
issn = {2045-2322},
support = {SUR-JSC-SSERV-2024-13//Sunway University/ ; },
abstract = {Global biodiversity monitoring increasingly relies on open-access community science data, but these opportunistic records harbor complex biases that can severely distort macroecological inference. Here, we disentangle how human behavior, infrastructure, and taxonomy interact to shape perceived biodiversity patterns across the two distinct biogeographic regions of Malaysia. Analyzing 336,042 research-grade iNaturalist records, we quantified observer inequality and taxonomic disproportionality. We estimated true species richness (Chao2) to map spatial inventory completeness (median = 33.3%) and employed Zero-Inflated Negative Binomial GLMMs and effort-corrected Generalized Additive Models (GAMs) to test the effects of topography, accessibility, and observer classification. We demonstrate extreme observer inequality (Gini = 0.854), with data collection heavily anchored to urban centers. Crucially, a significant three-way interaction revealed that dedicated "Power Users" successfully penetrate roadless interiors in Peninsular Malaysia, whereas casual observers remain strictly road-bound. Taxonomically, the data exhibits a severe charismatic skew, massively over-representing Aves and Reptilia while under-sampling foundational hyper-diverse clades like Insecta and Fungi. Furthermore, explicitly modeling non-linear sampling effort (user-days) rendered the effects of elevation and terrain ruggedness statistically non-significant. This demonstrates that perceived biodiversity deficits in rugged, high-elevation terrains are anthropogenic artifacts of human inaccessibility rather than true ecological absences. To meet global conservation targets, state funding and structured monitoring should complement opportunistic data by actively targeting these remote, under-sampled geographic and taxonomic shortfalls.},
}

@article {pmid41789991,
year = {2026},
author = {Shi, J and Fantke, P and Jolliet, O},
title = {A harmonized ecotoxicity dataset for honeybee based on the ECOTOX database.},
journal = {Environmental toxicology and chemistry},
volume = {45},
number = {6},
pages = {1470-1482},
doi = {10.1093/etojnl/vgag054},
pmid = {41789991},
issn = {1552-8618},
support = {//Bayer AG Crop Science Division/ ; },
mesh = {Animals ; Bees/drug effects ; *Pesticides/toxicity ; Ecotoxicology ; Databases, Factual ; *Environmental Pollutants/toxicity ; },
abstract = {Among the most crucial pollinators, managed honeybee (Apis mellifera) colonies frequently experience colony losses, which impose significant economic burdens on beekeeping and threaten the reliability of pollination services. Pesticide exposure is recognized as one stressor among others contributing to these losses. However, the curated harmonized dataset to characterize the impacts of multiple pesticides on different stages of honeybees is missing. To address this data gap, we generated an extensive and consistent honeybee ecotoxicity dataset of top (dermal)-acute 10% effective dose (ED10) and oral-chronic ED10 from the U. S. Environmental Protection Agency Ecotoxicology Knowledgebase (ECOTOX databases) for life cycle impact assessment (LCIA) and other comparative assessments. Primary harmonization and standardization were conducted to resolve inherent inconsistencies in life stages, exposure types, effect types, units, endpoints, and test types. Subsequently, weighted linear regressions were applied to extrapolate various endpoints to a harmonized ED10-equivalent (ED10eq), with R2 ranging from 0.38-0.99. The resulting integrated datasets comprise 540 chemicals across oral-chronic, oral-acute, and acute-topical exposure scenarios, consistently spanning approximately eight orders of magnitude for the adult groups and six orders of magnitude for the larval groups. Additionally, the relationship between adult and larva ecotoxicity data was analyzed, along with an uncertainty assessment for the oral-chronic and top-acute datasets, further enhancing the reliability and applicability of the harmonized data. These harmonized ecotoxicity datasets significantly enhance the LCIA framework by replacing the median effective dose (ED50) acute data with oral-chronic top-acute ED10 data, thus facilitating a more environmentally realistic assessment of pesticide impacts on honeybees.},
}

Animals
Bees/drug effects
*Pesticides/toxicity
Ecotoxicology
Databases, Factual
*Environmental Pollutants/toxicity

@article {pmid41896705,
year = {2026},
author = {Jan, S and Jan, F and Rathore, M and Singh, Y and Kapoor, P and Chaturvedi, P and Ghatak, A and Ramesh, P and Kumar, U and Prasad, M and Kumar, S and Rustgi, S and Weckwerth, W and Kalia, S and Varshney, RK and Mir, RR},
title = {Deciphering Cold Stress Resilience: Multiomics Insights in Contrasting Wheat Genotypes From the Western Himalayas.},
journal = {Plant biotechnology journal},
volume = {24},
number = {7},
pages = {4577-4598},
doi = {10.1111/pbi.70594},
pmid = {41896705},
issn = {1467-7652},
support = {BT/Ag/Network/Wheat/2019-20//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Triticum/genetics/metabolism/physiology ; Multiomics ; Genotype ; *Cold-Shock Response/genetics/physiology ; Proteomics ; Metabolomics ; Cold Temperature ; Transcriptome ; Gene Expression Regulation, Plant ; Lipidomics ; Gene Expression Profiling ; Plant Proteins/metabolism/genetics ; Metabolome ; },
abstract = {Cold stress threatens wheat productivity, particularly in regions with extreme climatic conditions. To elucidate the molecular mechanisms underlying wheat's response to cold stress, we performed a multiomics analysis integrating lipidomics, transcriptomics, proteomics and metabolomics. Our study focused on two wheat genotypes with contrasting cold tolerance levels, SKAU_52 (tolerant) and SKAU_4301 (susceptible) to capture genotype-specific responses under cold stress. Lipidomic analysis revealed significant changes in lipid composition, with unsaturated lipids such as digalactosyldiacyl glycerols (DGDGs) and monogalactosyldiacylglycerols (MGDGs) upregulated in response to cold stress. These lipids are associated with maintaining membrane fluidity, whereas saturated lipids were downregulated in the cold-tolerant genotype. Transcriptomics analysis provides a strong evidence that cold tolerance in wheat is governed by coordinated activation of the ICE-CBF-COR regulatory cascade, with the cold-tolerant genotype 'SKAU_52' showing stronger and more sustained induction across pathway tiers than the cold susceptible wheat genotype 'SKAU_4301'. Similarly, proteomic data highlighted differential abundance of proteins involved in antioxidative defence, osmotic adjustment and signal transduction, including late embryogenesis abundant (LEA) proteins. Metabolome assessment revealed substantial alterations in carbohydrate and amino acid metabolism, with sucrose and amino acids such as hydroxyproline identified as key contributors to cold tolerance. Additionally, defence hormones such as salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) exhibited genotype-specific regulation with higher accumulation in cold-tolerant genotype. Overall, this integrated multi-omics approach provides novel insights into the complex molecular mechanisms underlying cold stress adaptation in wheat, supporting the development of resilient wheat varieties capable of thriving in challenging cold environments.},
}

*Triticum/genetics/metabolism/physiology
Multiomics
Genotype
*Cold-Shock Response/genetics/physiology
Proteomics
Metabolomics
Cold Temperature
Transcriptome
Gene Expression Regulation, Plant
Lipidomics
Gene Expression Profiling
Plant Proteins/metabolism/genetics
Metabolome

@article {pmid41949699,
year = {2026},
author = {Shen, H and Zhang, L and Ma, X and Yin, Y and Wang, J and Tan, B},
title = {Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.},
journal = {Science China. Life sciences},
volume = {69},
number = {7},
pages = {2230-2248},
pmid = {41949699},
issn = {1869-1889},
mesh = {Multiomics/methods ; *Machine Learning ; Humans ; *Microbiota/genetics ; Computational Biology/methods ; *Host Microbial Interactions ; Benchmarking ; Algorithms ; Data Analytics ; Translational Research, Biomedical ; },
abstract = {The human microbiome is a dynamic ecosystem that profoundly influences host physiology through complex molecular interactions. Advances in high-throughput profiling now enable multi-omics measurements at scale, yet integration remains difficult due to biological complexity, technical variability, sparsity, and small cohorts. This review targets bioinformatics practitioners and clinical microbiology researchers applying machine learning to host-microbiome studies. Here, we survey state-of-the-art methods for integrating heterogeneous data types and highlight algorithmic innovations for high dimensionality and small cohorts. We also examine approaches for interpretability that translate mechanistic insight into clinically actionable models. Finally, we outline a standardized benchmarking framework emphasizing open data, rigorous evaluation, and biologically informed architectures. By synthesizing multi-omics measurements with advanced analytics, we chart a pathway toward personalized, microbiome-based therapies while deepening our understanding of host-microbiome crosstalk.},
}

Multiomics/methods
*Machine Learning
Humans
*Microbiota/genetics
Computational Biology/methods
*Host Microbial Interactions
Benchmarking
Algorithms
Data Analytics
Translational Research, Biomedical

@article {pmid42030616,
year = {2026},
author = {Rosić, I and Sokić, M and Ranković, T and Medić, O and Berić, T and Stanković, S and Dillon, MM and Nikolić, I},
title = {Filling in the blanks: In silico prediction of novel type III secreted effectors in the Pseudomonas syringae species complex.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 1},
pages = {109083},
doi = {10.1016/j.compbiolchem.2026.109083},
pmid = {42030616},
issn = {1476-928X},
mesh = {*Pseudomonas syringae/genetics/metabolism ; *Computational Biology ; Genome, Bacterial ; *Computer Simulation ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Predicting novel type III secreted effectors (T3SEs) in bacteria remains challenging because of their extensive sequence diversity and our heavy reliance on features derived from previously annotated genes. The available tools for predicting T3SS effectors produce a high number of false positives, which complicates their reliable identification. To address this gap, we developed a new bioinformatics workflow and meta-analysis designed to improve confidence in novel T3SE prediction by integrating multiple complementary approaches, including Effectidor2, Bastion3, EffectiveT3, curated effector databases, all-vs-all BLAST comparisons, comparative genomics, and localization-based features. We applied this approach to 57 complete P. syringae genomes, a diverse species complex whose pathogenicity is closely tied to its type III secreted effector (T3SE) content, allowing us to reduce an initial collection of 283 candidate T3SEs to 15 high-confidence predictions. By applying our newly customized EffRank scoring pipeline, three candidates emerged as high-confidence novel T3SEs in P. syringae strains: PsaNZ45_RS26420 (P. syringae pv. actinidiae ICMP20586), ACOZ4J_RS28825 (P. syringae pv. actinidiae FX219), and RRP28_RS13015 (P. syringae pv. actinidiae Yunnan2.4). Furthermore, our scoring pipeline successfully detected and removed likely false positive T3SEs, such as YenB-like toxins, among the high-confidence candidates that persisted through earlier curation steps, highlighting the challenges and biases of current publicly available prediction tools. Finally, we also characterized the final T3SE repertoires of each strain, which were consistent with phylogroup clustering based on the core-genome. As expected, PG1 strains carried larger and more conserved T3SE repertoires and contributed the majority of the promising novel T3SE candidates, while the likely false-positive YenB-like toxin was detected in PG2.},
}

*Pseudomonas syringae/genetics/metabolism
*Computational Biology
Genome, Bacterial
*Computer Simulation
*Bacterial Proteins/genetics/metabolism

@article {pmid42293552,
year = {2026},
author = {Aldriwesh, MG and Bin Shuraym, H and Asiri, NY and Asiri, WY and Abukhalid, NF and Alasiri, A and Alghoribi, MF},
title = {Microbiome and One Health in GCC countries: current status, research gaps, and future directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821688},
pmid = {42293552},
issn = {1664-302X},
abstract = {BACKGROUND: Microbiome science has emerged as a central component of the One Health framework, linking human, animal, and environmental health. Although global microbiome research has expanded rapidly, a comprehensive evaluation of microbiome research development and integration across the Gulf Cooperation Council (GCC) countries remains lacking. This systematic review aimed to characterize microbiome research in the GCC countries, identify major research gaps, and evaluate alignment with One Health principles while proposing a strategic framework to support coordinated regional development.

METHODS: This systematic review followed PRISMA 2020 guidelines. A structured search of PubMed, ScienceDirect, Google Scholar, and EBSCO databases identified microbiome-related studies published up to January 31, 2025. Eligible studies included original research conducted in the GCC countries (Saudi Arabia, Qatar, Kuwait, United Arab Emirates, Oman, and Bahrain) investigating human, animal, or environmental microbiomes. Findings were synthesized descriptively to assess study distribution, research design, analytical methodologies, and thematic focus.

RESULTS: A total of 110 studies met the inclusion criteria. Human microbiome studies accounted for 49% of publications, followed by environmental microbiome studies (40%) and animal microbiome studies (11%). Research output increased substantially after 2020 but remained uneven among the GCC countries, with Saudi Arabia contributing 44% of publications, whereas Bahrain and Oman together accounted for fewer than 7%. Most studies were observational and primarily used 16S rRNA gene sequencing on Illumina platforms. Human studies focused mainly on gut and oral microbiomes and frequently investigated metabolic disorders such as obesity and diabetes. Animal microbiome research was limited and largely centered on camels, with minimal investigation of livestock relevant to food security. Environmental studies predominantly examined soil and desert environments. No included study simultaneously investigated human, animal, and environmental microbiomes within an integrated One Health study design.

CONCLUSION: Microbiome research in the GCC countries is growing but remains uneven and largely disconnected across human, animal, and environmental studies, with limited adoption of One Health approaches. A coordinated regional strategy integrating governance, infrastructure, funding, and workforce development is needed to advance translational microbiome research and strengthen the GCC's contribution to global health, food security, and environmental sustainability.},
}

@article {pmid42294911,
year = {2026},
author = {Duque-Jaramillo, A and Symeonidi, E and Neumann, M and Ashkenazy, H and Allen, M and Weigel, D and Karasov, TL},
title = {Biosynthetic gene clusters in Pseudomonas viridiflava have a fitness cost during Arabidopsis thaliana infection.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021226},
doi = {10.1128/msystems.00212-26},
pmid = {42294911},
issn = {2379-5077},
abstract = {UNLABELLED: Specialized or secondary metabolites mediate biotic interactions, including virulence and defense. In plant-pathogenic Pseudomonas, certain specialized metabolites can enhance colonization of plant hosts, yet their broader contribution to plant-microbe interactions and the relative importance of different metabolites remain unclear. Specialized metabolites are products of enzymes encoded in biosynthetic gene clusters (BGCs), whose prediction from genome sequences has become routine but whose functional roles are rarely tested experimentally. Here, we characterize the BGC repertoire of 225 P. viridiflava isolates from Arabidopsis thaliana and assess BGC contributions to fitness and disease severity in planta. The BGC landscape of P. viridiflava was dominated by non-ribosomal peptide synthetase (NRPS) and NRPS-like BGCs, which accounted for 50% of the predicted BGCs. One-third of the BGC families were restricted to a single isolate. Transposon mutagenesis coupled with random barcode transposon sequencing (RB-TnSeq) revealed that the majority of BGCs reduce rather than increase fitness during A. thaliana infection, with the magnitude of the fitness cost varying across host genotypes. This cost could be due to exploitation of public goods by cheater mutant strains. In single-isolate plant infections, where public goods are not available, we found 11/34 BGC families correlated with disease severity. Yet, only two of these (an N-acetylglutaminylglutamine amide [NAGGN] and an NRPS) were negatively associated with disease severity, which is positively correlated with bacterial growth in this pathosystem, further indicating that BGCs are generally not beneficial in planta. Our findings reveal extensive and largely uncharacterized biosynthetic potential in populations of P. viridiflava and indicate that candidate metabolites are likely not adaptive for direct interactions with the plant, but perhaps for microbe-microbe interactions either in planta or in other ecological niches.

IMPORTANCE: Bacteria, including plant-associated bacteria such as Pseudomonas viridiflava, produce a vast array of chemical compounds, called secondary or specialized metabolites, that can mediate their interaction with the plant host or other microorganisms. Some of these compounds are known to directly influence how bacteria interact with plants, but it has been unclear whether this is a general rule. We studied a large collection of closely related leaf-dwelling P. viridiflava-a plant pathogen-that varied in their ability to cause disease. We found that very few of the gene clusters responsible for making specialized metabolites improved the ability of the bacteria to colonize its natural host Arabidopsis thaliana. On the contrary, carrying these gene clusters often reduced bacterial growth and disease severity in plants. Specialized metabolites may instead primarily be important for interacting with other microbes, different host species, or under environmental conditions we did not test. These are questions that remain for future research.},
}

@article {pmid42296150,
year = {2026},
author = {Shirani, F and Freeman, BG},
title = {Environmental "knees" and "wiggles" as strong stabilizers of species' range limits set by interspecific competition.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014336},
doi = {10.1371/journal.pcbi.1014336},
pmid = {42296150},
issn = {1553-7358},
mesh = {Animals ; *Ecosystem ; *Models, Biological ; *Competitive Behavior/physiology ; Gene Flow ; *Biological Evolution ; Species Specificity ; Computational Biology ; },
abstract = {Whether interspecific competition is a major contributing factor to setting species' range limits has been debated for a long time. Theoretical studies have proposed that the interactions between interspecific competition and disruptive gene flow along an environmental gradient can halt range expansion of ecologically similar species where they meet. However, the stability of such range limits has not been well addressed. We use a deterministic mathematical model of adaptive range evolution over a continuous habitat to show that the range limits set by interspecific competition are unlikely to be evolutionarily stable if the environmental optima for fitness-related traits vary (almost) linearly in space. That is, in a linear environment without a dispersal barrier or a third (or more) species, the range borders formed between two competing species constantly move towards the weaker species. We demonstrate that environmental nonlinearities such as "knees" and "wiggles"-wherein an isolated sharp change or a step-like change occurs in the steepness of a trait optimum-can strongly stabilize competitively formed range limits. The stabilization mechanism relies on the contrast that such nonlinearities create in the level of disruptive gene flow to the peripheral population of each species, and succeeds when an additional process, such as Allee effects, prevents the establishment of an infinitesimal population in the presence of an abundant competitor. We show that the stability of the range limits at these nonlinearities is robust against moderate environmental disturbances. Whether strong disturbances such as rapid high-amplitude climate changes can destabilize such range limits depends on how the competitive dominance of the species changes across the nonlinearity. Therefore, our findings underscore the importance of assessing species' competitive ability when predicting responses to climate change, and identify geographic regions where established range limits are likely to persist as well as regions where shifting limits may eventually stabilize.},
}

Animals
*Ecosystem
*Models, Biological
*Competitive Behavior/physiology
Gene Flow
*Biological Evolution
Species Specificity
Computational Biology

@article {pmid42296265,
year = {2026},
author = {Chen, L and Chen, L and Jin, LN and Qiu, A and Jia, Y and Zhang, P and Ji, Y and Xu, C and Zhang, Y and Li, D and Chen, J},
title = {Nasal Instillation of Complex Metal Oxide Particles Induces Brain Metal Accumulation and Neurobehavioral Toxicity in Mice.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16262},
pmid = {42296265},
issn = {1520-5851},
abstract = {The rapid expansion of complex metal oxide particles (CMOPs) in energy technologies raises emerging health concerns, yet their neuropsychiatric impacts remain unclear. Using intranasal exposure to lithium iron phosphate (LFP) and nickel-cobalt-manganese oxide (NCM) at dose levels selected with reference to reported ambient and occupational monitoring scenarios (0.8 and 8 mg/kg/day, n = 8 per group), we show that short-term CMOP exposure induces distinct neurobehavioral alterations in mice, characterized by changes in cognitive performance, risk assessment, and stress-related coping behavior. These changes co-occurred with dose-dependent brain accumulation of Li, Ni, Mn, and Co. Unexpectedly, low-dose exposure yielded 5-17-fold higher brain bioaccumulation factors than high-dose exposure, indicating disproportionate brain retention at lower exposure levels. Neurotransmitter profiling showed alterations consistent with perturbation of catecholamine metabolism, the tryptophan-kynurenine pathway, and the glutamate-glutamine cycle. At the molecular level, brain metal burden was associated with changes in barrier-related, neuroimmune, and synaptic signaling markers prioritized in relation to behavioral outcomes. Collectively, the findings indicate that short-term CMOP exposure can co-occur with brain metal bioaccumulation and neurobehavioral dysfunction, supporting the need for future inhalation-based and chronic studies to better define toxicokinetics, exposure relevance, and long-term health implications.},
}

@article {pmid42298048,
year = {2026},
author = {Bell, AR and Rakotonarivo, S and Manzoor, T and Moreira, R and Schaafsma, M and Fiwa, L and Zhang, W},
title = {US funding cuts offer a rare chance to remodel Global North-Global South research collaboration.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
pmid = {42298048},
issn = {2397-3374},
}

@article {pmid41795303,
year = {2026},
author = {Zeng, Y and Zhang, J and Wang, Q and Han, X and Liu, L and Yang, K and Zhang, R and Luo, K and Ren, L and Liu, S},
title = {Dual-layered epigenetic regulation links water body size constraints to somatic growth in an allotetraploid fish.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101787},
doi = {10.1016/j.cbd.2026.101787},
pmid = {41795303},
issn = {1878-0407},
mesh = {*Tetraploidy ; *Goldfish/genetics/growth & development ; *Carps/genetics/growth & development ; *Epigenesis, Genetic ; Multiomics ; Hybridization, Genetic ; *Adaptation, Biological ; Muscle Development ; Eye/growth & development ; Male ; Female ; Animals ; *Body Size/genetics ; Promoter Regions, Genetic ; Enhancer Elements, Genetic ; },
abstract = {Polyploidy endows fish with genomic plasticity to colonize restricted environments, yet the molecular mechanisms linking ecological constraints to somatic growth remain elusive. Here, we investigated the adaptive response of an allotetraploid lineage (Carassius auratus × Cyprinus carpio) to contrasting water body sizes using multi-omics approaches. We found that spatial constraints triggered targeted transcriptional remodeling specifically in the eye and muscle. This response effectively links sensory perception to growth regulation. Meanwhile, we identified a dual-layered epigenetic strategy. Environmental stress forced a reduction in the active gene pool via promoter silencing, while concurrently depressing the expression levels of growth-related structural genes through enhancer inhibition. Interestingly, this plasticity exhibited striking subgenome asymmetry. The Cyprinus subgenome displayed higher epigenetic responsiveness and acted as the primary adaptive buffer, exemplified by the targeted repression of a Cyprinus-derived enhancer regulating the mTOR gene rps6kb1a. Our findings demonstrate how subgenome-biased epigenetic remodeling aligns growth phenotypes with ecological constraints, offering molecular insights into the evolutionary success of polyploids in fragmented habitats.},
}

*Tetraploidy
*Goldfish/genetics/growth & development
*Carps/genetics/growth & development
*Epigenesis, Genetic
Multiomics
Hybridization, Genetic
*Adaptation, Biological
Muscle Development
Eye/growth & development
Male
Female
Animals
*Body Size/genetics
Promoter Regions, Genetic
Enhancer Elements, Genetic

@article {pmid41795790,
year = {2026},
author = {Özkan Vardar, D and Ekmen, B and Çalı, A},
title = {Interactions between polystyrene-derived micro- and nanoplastics and the microbiota: a systematic review of multi-omics mouse studies.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {44},
number = {2},
pages = {141-159},
doi = {10.1080/26896583.2026.2636868},
pmid = {41795790},
issn = {2689-6591},
mesh = {Animals ; *Polystyrenes/toxicity ; *Microplastics/toxicity ; Mice ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; },
abstract = {Micro- and nanoplastics (MNPs), especially polystyrene-derived particles (PS-MPs/PS-NPs), have become a growing concern due to their increasing presence in the environment and their proven biological toxicity. Although PS particles have been identified in various human tissues, including feces, placenta, and blood, their impact on the gut microbiota and microbiota-driven metabolic pathways remains insufficiently synthesized. This systematic review aims to compile current in vivo evidence from mouse studies to assess how PS-MP/NP exposure influences gut microbial diversity, taxonomic composition, microbial metabolites, and subsequent physiological outcomes. A PRISMA-guided literature search identified 15 controlled mouse studies published between 2010 and 2024. Across these studies, PS exposure consistently induced gut dysbiosis, characterized by reductions or shifts in alpha-diversity, distinct beta-diversity clustering, loss of beneficial commensals such as Lactobacillus, Bifidobacterium, and members of Ruminococcaceae, and enrichment of opportunistic or pro-inflammatory taxa including Proteobacteria, Helicobacter, and Staphylococcus. Notably, MNPs particles induced more pronounced microbial disruption than micro-sized forms. Overall, current experimental evidence indicates that PS-MPs/PS-NPs induce multidimensional toxicity by simultaneously disrupting gut microbial ecology and host metabolic pathways. These findings emphasize the need for standardized methodologies in microplastic research and highlight the importance of clarifying the long-term health effects of human exposure to micro- and nanoplastics.},
}

Animals
*Polystyrenes/toxicity
*Microplastics/toxicity
Mice
Multiomics
*Gastrointestinal Microbiome/drug effects
*Nanoparticles/toxicity

@article {pmid42263638,
year = {2026},
author = {Lucas, ER and Ellis, E and Paustian, K and Dorsey, S and Toor, GS},
title = {Modeling soil organic carbon stocks and changes in agricultural cropping systems using a decision support tool and process-based model.},
journal = {Journal of environmental management},
volume = {411},
number = {},
pages = {130171},
doi = {10.1016/j.jenvman.2026.130171},
pmid = {42263638},
issn = {1095-8630},
mesh = {*Agriculture/methods ; *Soil/chemistry ; *Carbon/analysis ; *Decision Support Techniques ; Models, Theoretical ; },
abstract = {Soil organic carbon (SOC) is a key indicator of soil health, yet changes in SOC often take decades to detect. Assessment tools, accessible to non-expert users, are needed to accurately and cost-effectively quantify SOC stocks. Soil sampling and analysis are ideal for quantification but are also resource- and time-intensive. A decision-support tool, COMET-Farm, could improve the transition to low-C agricultural supply chains; however, it was designed to estimate ΔSOC rather than SOC stocks directly, and its accuracy across diverse agricultural settings remains uncertain. We investigated whether the COMET-Farm tool could accurately estimate SOC stocks on 15 working farms in Maryland with variable management practices, including tillage, cover cropping, manure application, and irrigation. Field-measured SOC stocks (0-20 cm soil depth) of 17.1 to 73.6 Mg ha[-1] were compared with model-predicted values using farmer-reported data in (i) COMET-Farm with default inputs supplied to DayCent, versus (ii) expert-applied DayCent. We found COMET-Farm predictions were lower than measured SOC stocks (R[2] = 0.101; RMSE = 18.80 Mg ha[-1]), while expert-applied DayCent predictions more closely matched field measurements (R[2] = 0.73; RMSE = 7.89 Mg ha[-1]). Poorly drained soils and long-term manure applications caused greater discrepancies between measured and predicted SOC. These findings suggest that COMET-Farm estimates could improve with better model initialization, more accurate site-specific soil data, such as measured soil texture and drainage conditions, and more regionally representative land-use histories. With these improvements and further testing, COMET-Farm could be expanded beyond its original purpose of estimating ΔSOC to directly estimate SOC stocks for non-expert users.},
}

*Agriculture/methods
*Soil/chemistry
*Carbon/analysis
*Decision Support Techniques
Models, Theoretical

@article {pmid42263641,
year = {2026},
author = {Hendler, R and Tischew, S and Hensen, H and Metze, K and Schütz, L and Bade, K and Fischer, C},
title = {Successful restoration of heathlands and grasslands associated with long-term habitat preferences of cattle and horses: Insights from GPS tracking.},
journal = {Journal of environmental management},
volume = {411},
number = {},
pages = {130113},
doi = {10.1016/j.jenvman.2026.130113},
pmid = {42263641},
issn = {1095-8630},
mesh = {Animals ; Cattle ; *Grassland ; *Ecosystem ; Horses ; Germany ; Geographic Information Systems ; Seasons ; *Conservation of Natural Resources ; Herbivory ; },
abstract = {Long-term, year-round grazing by large herbivores is increasingly used to restore degraded temperate heathlands and grasslands, yet the behavioral mechanisms of grazers underlying restoration remain insufficiently understood. We combined over 13 years of high-resolution GPS-tracking data of free-ranging Heck cattle and Konik horses with repeated vegetation surveys across various habitat types (encroachment-derived Calamagrostis epigejos stands, dry sandy grasslands, dry heaths, and pioneer forests) in Central Germany. We quantified how habitat preference and vegetation structure co-develop under low-intensity, year-round grazing following abandonment. Habitat preference differed among habitat types and showed clear seasonal patterns. Preference values were consistently higher in summer than in winter for both grazer species, reflecting selective use of productive regrowth. Winter preferences were weak, indicating low selectivity and homogeneous space use that facilitated grazing in habitats otherwise avoided during the growing season, including dry heaths and pioneer forests. Across the study period, we detected long-term shifts in habitat preference that corresponded with vegetation changes associated with the restoration of dry heaths and sandy grasslands. As standing biomass declined, C. epigejos and grass litter decreased, open soil increased, and Calluna vulgaris advanced into the optimal phase. These structural improvements reduced forage-quality contrasts among habitats, resulting in progressively weaker preference patterns and a more even distribution of habitat use across the landscape. Our results provide rare long-term empirical evidence linking grazer behavior and vegetation dynamics in conservation grazing systems and highlight that year-round extensive grazing, rather than summer-only grazing, is required to achieve stable long-term restoration outcomes.},
}

Animals
Cattle
*Grassland
*Ecosystem
Horses
Germany
Geographic Information Systems
Seasons
*Conservation of Natural Resources
Herbivory

@article {pmid42269263,
year = {2026},
author = {Li, M and Zhou, S and Jiang, M and Geng, J and Ni, H and Li, G and Zhao, Y and Dong, Y},
title = {ABA-cytokinin crosstalk regulate drought tolerance in Ziziphus jujuba var. spinosa through the phenylpropanoid pathway: insights from physiological and multi-omics integration.},
journal = {Plant physiology and biochemistry : PPB},
volume = {236},
number = {},
pages = {111466},
doi = {10.1016/j.plaphy.2026.111466},
pmid = {42269263},
issn = {1873-2690},
mesh = {*Abscisic Acid/pharmacology/metabolism ; Drought Resistance ; *Cytokinins/metabolism/pharmacology ; *Ziziphus/metabolism/physiology/genetics/drug effects ; Gene Expression Regulation, Plant/drug effects ; Multiomics ; *Propanols/metabolism ; Droughts ; Plant Proteins/metabolism/genetics ; Seedlings/metabolism ; Plant Growth Regulators ; Stress, Physiological ; Cytochrome P-450 Enzyme System/metabolism ; },
abstract = {Drought stress is a major constraint in jujube production. Although abscisic acid (ABA) and cytokinin exert opposing effects on plant growth, recent findings revealed that their combined application enhanced drought tolerance in jujube; however, the underlying mechanism remains elusive. In this study, three exogenous treatments were applied to sour jujube seedlings under drought stress: 5 mg L[-1] ABA, a cytokinin mixture of 50 mg L[-1] 6-benzylaminopurine (6-BA) and 100 mg L[-1] kinetin (KT), and a combined ABA and cytokinins solution. Transcriptomic and metabolomic analyses were integrated to elucidate how ABA and cytokinins jointly modulate drought responses. The results showed that ABA induced stem thickening, enhanced osmotic regulation and antioxidant capacity, upregulated the expression of cytochrome P450 84A1-like (CYP84A1) involved in lignin biosynthesis, and downregulated cinnamyl alcohol dehydrogenase (CAD). In contrast, cytokinins promoted stem elongation by upregulating elongation factor 2 and L-lactate dehydrogenase B, downregulating anthocyanin synthase (ANS) and peroxidase, and altering galactose/starch metabolism, thereby prioritizing growth at the expense of stress tolerance. The combined treatment reconciled these opposing effects, enhancing stress defense without compromising cytokinin-mediated growth advantage, inducing 3018 differential genes and 285 metabolites. The phenylpropanoid biosynthesis pathway was identified as central to ABA-cytokinin crosstalk, with upregulation of two CADs contributing to drought resistance and four genes encoding CAD, peroxidase, and cinnamate 4-hydroxylase (C4H) playing a critical role in this crosstalk. Additionally, beta-glucosidase 18 (BGLU18) was identified as a candidate gene correlated with 13 phenylpropanoids. Our findings reveal the molecular link between the phenylpropanoid pathway and ABA-cytokinin crosstalk in jujube drought tolerance.},
}

*Abscisic Acid/pharmacology/metabolism
Drought Resistance
*Cytokinins/metabolism/pharmacology
*Ziziphus/metabolism/physiology/genetics/drug effects
Gene Expression Regulation, Plant/drug effects
Multiomics
*Propanols/metabolism
Droughts
Plant Proteins/metabolism/genetics
Seedlings/metabolism
Plant Growth Regulators
Stress, Physiological
Cytochrome P-450 Enzyme System/metabolism

@article {pmid42284784,
year = {2026},
author = {Luo, P and Liu, X and Mao, Y and Yang, J and Wang, X and Cai, L and Filatova, I and Liu, Y},
title = {Enhanced PFHxS degradation by DBD combined with microbubbles and sulfite: Synergistic effects and mechanisms.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142684},
doi = {10.1016/j.jhazmat.2026.142684},
pmid = {42284784},
issn = {1873-3336},
abstract = {Perfluorohexane sulfonate (PFHxS), a persistent member of the PFAS family, remains challenging to degrade, and its transformation mechanisms are not yet fully understood. Here, a dielectric barrier discharge coupled with microbubbles and sulfite (DBD/MBs/sulfite) system was developed for PFHxS degradation. Among all tested systems, the ternary process achieved the best performance, reaching 96.7% degradation and 26.3% defluorination within 60 min, with rate constant of 0.049 min[-1]. The enhancement mainly arose from the coupling of MB-enhanced gas-liquid interfacial transport and sulfite-mediated reactive-species conversion under DBD conditions. Higher discharge power and sulfite concentration enhanced PFHxS degradation, whereas higher initial PFHxS concentration reduced removal efficiency but increased energy yield. Reactive-species identification by optical emission spectroscopy (OES), electron spin resonance (ESR), and scavenging experiments showed that PFHxS degradation proceeded through a complex oxidative-reductive network involving SO4[-]•, •OH, eaq[-], [1]O2, •O2[-], and nitrogen-related oxidizing species, among which SO4[-]• and •OH were the dominant radicals. Electronic-structure analysis indicated that PFHxS reactivity was highly localized at the sulfonate end, especially around O14, O16, and S15. Combined with LC-MS identification of intermediates, the pathways involved desulfonation, H/F exchange, hydroxylation, sequential -CF2 elimination, and C-C bond cleavage, leading to shorter-chain and structurally simplified products. Acidic conditions favored PFHxS degradation, whereas coexisting anions exerted inhibition. Nevertheless, the system still achieved 77.8% degradation in the most inhibitory realistic water matrix, demonstrating good matrix tolerance. Overall, the DBD/MBs/sulfite system provided an efficient and adaptable strategy for PFHxS removal and offered mechanistic insight into plasma-assisted degradation of perfluorinated sulfonates.},
}

@article {pmid42290710,
year = {2026},
author = {Pereira, CA and Nascimento, JM and Grellert da Silva, M and Carvalho, JT and Kaster, MP},
title = {Analysis of health infrastructure and suicide rates in Brazil: a nationwide ecological spatial-temporal study, 2009-2023.},
journal = {Lancet regional health. Americas},
volume = {60},
number = {},
pages = {101519},
pmid = {42290710},
issn = {2667-193X},
abstract = {BACKGROUND: Suicide remains a major global health concern and disproportionately affects low- and middle-income countries (LMICs), where socio-economic stressors and limited healthcare resources contribute to higher burdens. This study characterizes annual patterns of suicide rates in Brazil from January 2009 until December 2023, across its five geographic regions (North, Northeast, Southeast, South, and Central-West). Additionally, we constructed a harmonized dataset integrating sociodemographic and healthcare infrastructure indicators, and identified which municipal-level infrastructure components are most informative for classifying suicide rate categories.

METHODS: We integrated nationwide data from the Mortality Information System (SIM/SUS), the National Registry of Healthcare Establishments (CNES), and demographic estimates from the Brazilian Institute of Geography and Statistics (IBGE). Primary analyses were conducted using municipality-level annual observations across all Brazilian cities covering more than 170,000 suicide deaths nationally. Suicide was expressed annually as rates per 100,000 inhabitants and categorized as low, moderate, or high. Using a data-mining workflow with XGBoost classifier models, we identified healthcare infrastructure features most relevant for distinguishing suicide rate categories. Secondary analyses focused on the sociodemographic characterization of suicide deaths and on the distribution of Psychosocial Care Centers (CAPS), as well as their correlation with suicide rates.

FINDINGS: Across the descriptive analyses, suicide rates increased in all Brazilian regions (2009: 4·5, 95% CI 4·4-4·6; 2023: 7·6, 95% CI 7·5-7·7). Machine learning models identified healthcare infrastructure components (e.g., healthcare establishments, registered professionals, primary care units, diagnostic services, and mental health facilities) as the most informative features for distinguishing municipalities by suicide rate categories (low, moderate, or high), with accuracy across regions ranging from 72% (95% CI 69-75%) to 79% (95% CI 76-81%). CAPS availability was correlated with lower suicide rates across all regions (ρ = -0·71 to -0·81, p < 0·01).

INTERPRETATION: In this exploratory analysis, general healthcare infrastructure features are associated with variations in suicide mortality, suggesting that access to basic and mental health services is an informative predictor for distinguishing suicide rate patterns across regions. Findings at the aggregate level cannot be assumed to be consistent at the individual level.

FUNDING: Santa Catarina State Research and Innovation Support Foundation (FAPESC) and the Research Program for the Unified Health System (PPSUS); Brazilian National Council for Scientific and Technological Development (CNPq); Department of Science and Technology of the Secretariat of Science, Technology, Innovation and the Health Economic-Industrial Complex of the Ministry of Health of Brazil (Decit/SECTICS); and Coordination for the Improvement of Higher Education Personnel (CAPES).},
}

@article {pmid42292476,
year = {2026},
author = {Zhou, Y and Li, Z and Chu, Y and Zhou, Z and Zhang, T and Yi, N and Sun, W and Yan, J and Yan, Z and Zhu, A},
title = {Reframing precision nutrition in irritable bowel syndrome: a mechanism-informed conceptual framework for responder prediction and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1809221},
pmid = {42292476},
issn = {1664-3224},
mesh = {Humans ; *Irritable Bowel Syndrome/diet therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; FODMAP Diet ; *Precision Medicine/methods ; Multiomics ; Translational Research, Biomedical ; },
abstract = {BACKGROUND: The low-Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is widely used for irritable bowel syndrome (IBS), but response varies markedly across patients. This heterogeneity has shifted the field from testing average efficacy toward forecasting individual benefit and translating microbiome science into practical precision-nutrition tools.

METHODS: We present a conceptual analysis grounded in evidence mapping from human IBS studies that paired dietary interventions (primarily low-FODMAP pathways) with baseline microbiome and/or multi-omics measurements. Findings are organized within a "microbiome-to-model" roadmap that specifies responder endpoints, candidate data layers (taxa, functions, metabolites and volatile signatures), modeling choices, and the validation and implementation requirements needed for clinical decision support.

RESULTS: Three recurring signals emerge across cohorts. Baseline microbial ecology can stratify response, but taxonomic features alone often fail to transport across studies. Functional readouts, including metabolites and volatile signatures, are closer to symptom mechanisms and can improve interpretability; however, clinical deployment is still limited by endpoint heterogeneity, imperfect exposure and adherence measurement, batch effects, and insufficient external validation and calibration.

CONCLUSION: IBS is well suited for microbiome-informed responder prediction, provided that models are developed with deployment in mind. Progress will depend on validation-first study designs, harmonized responder endpoints and adherence capture, robust multi-omics pipelines, and biologically interpretable decision rules that can be prospectively tested and monitored for temporal instability in real-world care.},
}

Humans
*Irritable Bowel Syndrome/diet therapy/microbiology/metabolism
*Gastrointestinal Microbiome
FODMAP Diet
*Precision Medicine/methods
Multiomics
Translational Research, Biomedical

@article {pmid42270437,
year = {2026},
author = {De Keyzer, ELR and Herder, F and Böhne, A and Jiménez, FC and Burskaia, V and Kukowka, S and Tracey, A and Denton, AL and Oatley, G and , and , and , and Mokodongan, DF and Wowor, D and Svardal, H},
title = {Ancient and Recent Riverine Gene Flow Contributed to the Adaptive Radiation of Sailfin Silversides in Wallace's Dreampond.},
journal = {Molecular ecology},
volume = {35},
number = {11},
pages = {e70414},
pmid = {42270437},
issn = {1365-294X},
support = {G0A9B24N//Fonds Wetenschappelijk Onderzoek/ ; V408023N//Fonds Wetenschappelijk Onderzoek/ ; 12A8423N//Fonds Wetenschappelijk Onderzoek/ ; 11A2P26N//Fonds Wetenschappelijk Onderzoek/ ; ID2022SIN349A102//VLIRUOS/ ; 54084//VLIRUOS/ ; ID2025SIN4SEL104//VLIRUOS/ ; 48620//Universiteit Antwerpen/ ; },
mesh = {Animals ; Indonesia ; *Gene Flow ; *Phylogeny ; *Genetic Speciation ; Hybridization, Genetic ; Lakes ; Sequence Analysis, DNA ; Rivers ; *Killifishes/genetics ; },
abstract = {While adaptive radiations significantly contribute to the world's biodiversity, much is unknown about the genetic and ecological factors underlying these rapid successions of speciation. It has been suggested that hybridisation can facilitate the speciation process by generating genetic diversity on which diversifying selection can act. Sailfin silverside fishes (Telmatherinidae) in the Malili Lakes system in Sulawesi have diversified within the last 2 million years. To establish a phylogenetic framework and investigate the presence of hybridisation in this radiation, we assembled and annotated a chromosome-scale reference genome of the riverine sailfin silverside Telmatherina bonti and generated whole genome sequences of all species of Telmatherina in Lake Matano, South Sulawesi, Indonesia, one of the world's oldest and deepest lakes. We reconstructed the phylogenetic relationships and inferred past and ongoing introgression patterns. Genome-wide tests confirmed two monophyletic clades, sharpfins and roundfins. However, within clades, we found mismatches between morphology-based taxonomic assignments and genome-wide genetic relationships. We found signs of both old and ongoing introgression between river-dwelling T. bonti and the lacustrine sharpfin group, as shown in elevated D-statistic, f4-ratio and f-branch statistic. Levels of excess allele sharing between riverine species and the three most common lacustrine species declined with increasing distance from the river-inlet, indicating ongoing introgression at the lake-river interface. This combination of past and ongoing hybridisation in a radiating species flock makes Lake Matano Telmatherina a particularly valuable system to study fundamental mechanisms driving rapid speciation under genomic exchange. The phylogenomic framework elaborated in this study provides the foundation for studies of the processes shaping this charismatic radiation.},
}

Animals
Indonesia
*Gene Flow
*Phylogeny
*Genetic Speciation
Hybridization, Genetic
Lakes
Sequence Analysis, DNA
Rivers
*Killifishes/genetics

@article {pmid42275639,
year = {2026},
author = {Rueda, A and Martin, J and Parkington, K and Perivolaris, A and Teferra, BG and Lee, GH and Tassone, VK and Lin, Q and Ivanov, M and Darnell, B and Beavers, L and Campbell, DM and Torres, A and Lou, W and Nazarov, A and Ashbaugh, A and Kapralos, B and Litz, B and Jetly, R and Dubrowski, A and Strudwick, G and Krishnan, S and Bhat, V},
title = {Digital Health Monitoring and Intervention Suite for Stress in Frontline Nurses: Prospective Cohort Trial.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e77818},
pmid = {42275639},
issn = {2561-326X},
mesh = {Humans ; Female ; Prospective Studies ; Adult ; Digital Health ; *Nurses/psychology/statistics & numerical data ; Male ; Frontline Workers/psychology ; *Stress, Psychological/psychology ; Middle Aged ; Cohort Studies ; Monitoring, Physiologic/methods/instrumentation ; },
abstract = {BACKGROUND: Stress among health care workers (HCWs) contributes to burnout, workforce attrition, and adverse patient outcomes. Although virtual reality (VR), psychoeducation, ecological momentary assessments (EMAs), and wearables have independently shown promise in stress research, no integrated digital suite has combined controlled stress induction, intervention delivery, and longitudinal real-world monitoring in HCWs.

OBJECTIVE: This study aimed to evaluate the feasibility, engagement, and preliminary effectiveness of a multimodal Digital Health Monitoring and Intervention suite for Stress framework integrating VR simulation, psychoeducation, EMAs, and wearable biometrics. We examined (1) the impact of VR simulation and psychoeducation on stress outcomes and (2) associations between physiological and self-reported mental health outcomes.

METHODS: Ninety-nine nurses (mean age 33.7, SD 8.9 yr, 87% female) were enrolled in 2023. We conducted a single-arm prospective cohort study (NCT05923398). Using convenience sampling, participants were recruited from social media advertisements, flyers, and email notices distributed through professional listservs. Participants completed ≥2-week baseline monitoring, a single VR session (2 runs separated by a brief psychoeducation intervention), and 12-week follow-up. In-VR stress was assessed using the Subjective Units of Distress Scale (SUDS) and 4-item Moral Injury Outcome Scale (MIOS-4), with synchronous heart rate variability. Longitudinal outcomes included weekly and biweekly EMAs alongside 70 wearable-derived features. Paired t tests, aligned rank transform ANOVA, and Pearson correlations informed study objectives, with P values adjusted for multiple comparisons. Qualitative content analysis classified emotional responses during and after VR.

RESULTS: VR significantly increased subjective stress across checkpoints in both runs, with attenuation in Run B relative to Run A (all P<.001). No significant heart rate variability differences were observed between runs (P=.15). During VR, 92% (91/99) of participants felt stressed, 36% (36/99) reported anxiety or nervousness, and 51% (50/99)-78% (77/99) endorsed anger, guilt, shame, and/or betrayal. Most (59/99, 60%) HCWs returned to an emotional baseline post-VR, although 12% (12/99) reported lingering distress. Immediate reliable improvements in anger, guilt, shame, and/or betrayal occurred for 50% (50/99)-75% (74/99) of participants post intervention. Anxiety (mean -0.53, SD 2.34; P=.03) and stress (mean -3.05, SD 11.35; P=.01) decreased 2 weeks post intervention, but were not sustained at 12 weeks. Increased sleep restlessness was the only wearable feature showing significant changes (mean 2.46%, SD 5.43; Padj<.001). In-VR stress correlated with 12-week real-world stress (SUDS: r=0.57-0.58; MIOS-4: r=0.58-0.61; all P<.01). Data completion exceeded 90%, with 71% achieving full compliance.

CONCLUSIONS: This study moves beyond single-tool interventions to demonstrate the feasibility and preliminary effectiveness of an integrated, multimodal stress platform within a single coordinated framework. This trial demonstrates high engagement, short-term symptom responsiveness, ecological validity, and emotional safety. The framework provides a scalable model for proactive stress identification, skills training, and implementation in high-risk occupational settings. Randomized controlled trials are needed to establish sustained efficacy and optimize deployment for real-world implementation.},
}

Humans
Female
Prospective Studies
Adult
Digital Health
*Nurses/psychology/statistics & numerical data
Male
Frontline Workers/psychology
*Stress, Psychological/psychology
Middle Aged
Cohort Studies
Monitoring, Physiologic/methods/instrumentation

@article {pmid42281079,
year = {2026},
author = {Mapinduzi, J and Daniels, K and Kossi, O and Verbrugghe, J and Bonnechère, B},
title = {Wearable Sensors and Artificial Intelligence for Ecological Knee Osteoarthritis Assessment: Development and Feasibility of a Hybrid Digital Phenotyping Framework.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {11},
pages = {},
pmid = {42281079},
issn = {1424-8220},
mesh = {Aged ; Female ; Humans ; Middle Aged ; Digital Health ; Feasibility Studies ; *Intelligent Systems ; *Monitoring, Physiologic/instrumentation/methods ; *Osteoarthritis, Knee/diagnosis/physiopathology ; Phenotype ; *Wearable Electronic Devices ; },
abstract = {Osteoarthritis (OA) is a highly prevalent musculoskeletal disorder and a major cause of disability, posing growing challenges for healthcare systems worldwide. Conventional supervised clinical assessments provide valuable insights but are largely limited to cross-sectional snapshots and often fail to reflect the variability of real-world functioning, physical activity patterns, and symptom fluctuations experienced by individuals with OA, especially those with knee OA. This perspective introduces a multisensor digital phenotyping framework for smart knee OA assessment, integrating supervised laboratory evaluations with unsupervised continuous monitoring in daily living environments using wearable sensors, smart insoles, activity trackers, and mobile devices. Feasibility was tested in 40 participants (20 knee OA patients, 20 controls). Raw data from questionnaires, electronic goniometry, dynamometry, force plate, connected insoles, and seven-day home monitoring were harmonized via a standardized pipeline aligned with the ICF framework. The pipeline employed anomaly detection, missing data imputation, z-score normalization, and cloud-based storage. This framework is envisioned to facilitate advanced data integration and machine-learning-ready analytics, enabling longitudinal monitoring, pattern recognition, and individualized health profiling. By conceptually bridging cross-sectional and continuous sensing modalities, this approach has the potential to enhance ecological validity, support earlier identification of functional decline, and inform data-driven clinical decision-making. Key methodological, technological, and ethical challenges-including data quality, interpretability, privacy, digital literacy, and clinical adoption-are also highlighted. Overall, this paper underscores the promise of AI-enabled multisensor digital phenotyping to advance smart, personalized, and precision healthcare for individuals with knee OA.},
}

Aged
Female
Humans
Middle Aged
Digital Health
Feasibility Studies
*Intelligent Systems
*Monitoring, Physiologic/instrumentation/methods
*Osteoarthritis, Knee/diagnosis/physiopathology
Phenotype
*Wearable Electronic Devices

@article {pmid41722541,
year = {2026},
author = {Ashaolu, TJ and Suttikhana, I},
title = {Probiotic therapeutics: A critical review of mechanisms, clinical efficacy, and the frontier of precision microbiome modulation.},
journal = {International immunopharmacology},
volume = {175},
number = {},
pages = {116412},
doi = {10.1016/j.intimp.2026.116412},
pmid = {41722541},
issn = {1878-1705},
mesh = {*Probiotics/therapeutic use ; Humans ; Animals ; Precision Medicine ; *Gastrointestinal Microbiome ; Multiomics ; Irritable Bowel Syndrome/therapy/microbiology ; },
abstract = {Probiotic therapeutics are evolving from generalized wellness supplements to precision Live Biotherapeutic Products aimed at specific disease targets. This review elucidates the multi-layered mechanistic framework of probiotic action, which spans ecological niche modulation, epithelial barrier reinforcement, and systemic signaling via the gut-brain axis. While clinical efficacy is established for conditions like antibiotic-associated diarrhea, trial outcomes remain highly heterogeneous for complex disorders such as irritable bowel syndrome and metabolic syndrome. We deconstruct this variability, attributing it to critical factors often overlooked in study design: stringent strain-specificity, host-specific colonization resistance, and the lack of standardized core outcome sets. The field is now advancing toward precision microbiome modulation through next-generation biotics like Akkermansia muciniphila, synbiotics, and engineered microbial therapeutics. We conclude that integrating multi-omics technologies with artificial intelligence is essential to transition from empirical supplementation to personalized, evidence-based clinical practice.},
}

*Probiotics/therapeutic use
Humans
Animals
Precision Medicine
*Gastrointestinal Microbiome
Multiomics
Irritable Bowel Syndrome/therapy/microbiology

@article {pmid42025964,
year = {2026},
author = {Liao, Z and Chen, Y and Wang, L and Chen, A and Gu, X and Li, X and Guo, Y and Du, Z and Li, W and Zhu, B and Zhao, W and Niu, J},
title = {Gut-Liver Axis Disruption Induced by Total Fish Oil Substitution with Black Soldier Fly Oil Impairs Growth and Health in Rainbow Trout (Oncorhynchus mykiss): Insights from Multiomics Analysis.},
journal = {The Journal of nutrition},
volume = {156},
number = {6},
pages = {101545},
doi = {10.1016/j.tjnut.2026.101545},
pmid = {42025964},
issn = {1541-6100},
mesh = {Animals ; *Liver/drug effects/metabolism ; *Fish Oils/pharmacology/administration & dosage ; *Oncorhynchus mykiss/growth & development ; Multiomics ; Animal Feed/analysis ; Gastrointestinal Microbiome/drug effects ; *Gastrointestinal Tract/drug effects ; Diet/veterinary ; },
abstract = {BACKGROUND: Black soldier fly oil (BSFLO) is a sustainable alternative to fish oil (FO), but its dose-dependent effects on fish health remain unclear.

OBJECTIVES: This study evaluated the effects of dietary BSFLO on growth, liver health, fillet quality, and gut-liver metabolism in rainbow trout.

METHODS: In a feeding trial, 480 rainbow trout (initial body weight: 215.16 ± 2.30 g; 12 mo old) were allocated to 6 dietary treatments (4 replicate tanks per treatment, 20 fish per tank): FO control or BSFLO replacing FO at 20% (BSFLO20), 40% (BSFLO40), 60% (BSFLO60), 80% (BSFLO80), or 100% (BSFLO100). After 8 wk of feeding trail, growth performance, plasma biochemistry, tissue histology, gut microbiota (16S rRNA), and multiomics (transcriptomics, proteomics, and metabolomics) were analyzed.

RESULTS: The BSFLO60 and BSFLO80 groups had significantly higher growth rate compared with FO (P < 0.05). The hepatosomatic index increased in BSFLO40, BSFLO60, BSFLO80, and BSFLO100 groups (P < 0.05). The BSFLO100 group exhibited a lower aspartate aminotransferase-to-alanine transaminase ratio in plasma, and hepatic tissue showed more lipid vacuolation. In muscles, hardness, springiness, and chewiness decreased in the BSFLO100 group, while adhesiveness and cohesiveness increased (P < 0.05). Gut microbiota analysis showed higher abundance of Firmicutes and Staphylococcus species in the BSFLO100 group. Transcriptomics and qRT-PCR revealed upregulation of srebp1, pparα, pparγ, fasn, acc1, and atgl, with downregulation of cpt1. Proteomics and Western blotting indicated that BSFLO100 led to the upregulation of peroxisome proliferator-activated receptor γ expression and acetyl-CoA carboxylase phosphorylation, along with inhibited phosphorylation of AMP-activated protein kinase α and carnitine palmitoyltransferase 1. Metabolomics showed reductions in SFAs and MUFAs, increases in omega-3 PUFAs, elevated glycolytic intermediates and amino acids, and declines in tricarboxylic acid cycle- and glutamate-related metabolites.

CONCLUSIONS: A moderate BSFLO inclusion (60%) improves growth, whereas complete replacement (100%) reshapes the gut microbiota, activates the peroxisome proliferator-activated receptor γ lipogenic axis, and suppresses AMP-activated protein kinase/oxidative pathways, jointly inducing hepatic steatosis and inferior muscle texture.},
}

Animals
*Liver/drug effects/metabolism
*Fish Oils/pharmacology/administration & dosage
*Oncorhynchus mykiss/growth & development
Multiomics
Animal Feed/analysis
Gastrointestinal Microbiome/drug effects
*Gastrointestinal Tract/drug effects
Diet/veterinary

@article {pmid42098572,
year = {2026},
author = {Wang, WL and Yang, CH and Nordgren, R and Li, J and Intille, S and Dunton, GF and Hedeker, D},
title = {Modeling intraindividual means and variances from ecological momentary assessment data: comparing standard computational formulas to mixed-effects location-scale model estimates.},
journal = {Journal of behavioral medicine},
volume = {49},
number = {2},
pages = {254-274},
pmid = {42098572},
issn = {1573-3521},
support = {R01 CA240713/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Ecological Momentary Assessment/statistics & numerical data ; *Models, Statistical ; Computer Simulation ; Data Interpretation, Statistical ; },
abstract = {Traditionally, intraindividual means and variances derived from ecological momentary assessment (EMA) data have been calculated using standard computational formulas (SCF), such as subject-level means and standard deviations. However, these SCF methods assume uniform precision across subjects, disregarding variation in the number of observations, missing data issues, and the non-continuous nature of data scales. This study evaluated the predictive accuracy of the coefficients of intraindividual means and variances computed via SCF against those estimated using random effects from a Mixed-Effects Location Scale (MELS) model. A five-scenario simulation study was conducted: (1) varying numbers of observations per subject, (2) varying mean-to-variance ratios, (3) varying proportions of missing data under a missing completely at random (MCAR) assumption, (4) varying proportions of missing data under a missing at random (MAR) assumption, and (5) varying categories of ordinal scale responses. Bias and coverage of the mean levels and variability coefficients were compared across methods. In addition, a real-life dataset was used to compare the difference of means and variances between SCF and MELS approaches. Results consistently showed that the MELS model approach outperformed SCF method, yielding lower bias and higher coverage of the coefficients across all scenarios. These findings support the use of MELS for more accurate and reliable estimation of intraindividual means and variances in EMA data, highlighting its advantages for subsequent predictive modeling.},
}

Humans
*Ecological Momentary Assessment/statistics & numerical data
*Models, Statistical
Computer Simulation
Data Interpretation, Statistical

@article {pmid42172788,
year = {2026},
author = {Ge, H and Wang, J and Wu, DY and Zhou, H},
title = {Investigating the relationship between psychological stress and physical activity through individual-based geographic ecological momentary assessment.},
journal = {Social science & medicine (1982)},
volume = {403},
number = {},
pages = {119411},
doi = {10.1016/j.socscimed.2026.119411},
pmid = {42172788},
issn = {1873-5347},
mesh = {Humans ; *Stress, Psychological/psychology/epidemiology ; Female ; *Ecological Momentary Assessment ; Ontario ; Male ; Adult ; *Exercise/psychology ; Accelerometry ; Geographic Information Systems ; Young Adult ; Middle Aged ; Self Report ; },
abstract = {Physical Activity (PA) is known to buffer stress, yet evidence remains limited when examining real-time stress responses alongside objective measures of activity and environmental exposures in daily life. To address the gap, this study employs a Geographic Ecological Momentary Assessment (GEMA) framework that integrates accelerometer, GPS tracking, and survey data. The primary objective of this study is to assess the association between self-reported psychological stress and moderate-to-vigorous physical activity (MVPA) during the hours preceding GEMA prompts. Additionally, the study examines whether engaging in MVPA later in the day is associated with greater reductions in stress relative to morning baseline levels. Data were collected from 130 participants in the City of Mississauga, Ontario, over 7 days. Results revealed that higher levels of MVPA in the 5-h window preceding GEMA prompts were associated with significantly lower odds of reporting higher stress. On weekends, the stress-reduction effect was stronger after completing PA later in the day than on weekdays. Lower-income participants engaged in outdoor MVPA in environments perceived as safer, more beautiful, and greener compared to those of higher-income participants. Yet, no significant association was found between stress and environmental exposures, possibly because aggregated exposure measures were not sensitive enough to capture short-term changes in the daily context. The findings demonstrate the value of GEMA in capturing interactions among behaviour, environment, and health, and suggest that future research should apply more dynamic GEMA approaches to better assess short-term environmental exposures and stress.},
}

Humans
*Stress, Psychological/psychology/epidemiology
Female
*Ecological Momentary Assessment
Ontario
Male
Adult
*Exercise/psychology
Accelerometry
Geographic Information Systems
Young Adult
Middle Aged
Self Report

@article {pmid42256231,
year = {2026},
author = {Gomez-Ramirez, U and De La Torre-González, C and Villamor, P and Huante Guido, M and Contreras-Rodríguez, A and Velázquez-Guadarrama, N},
title = {Recolonization dynamics of the middle ear microbiota following MESNA-assisted dissection in pediatric cholesteatomatous chronic otitis media.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1830192},
pmid = {42256231},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/drug effects ; *Otitis Media/microbiology/surgery ; RNA, Ribosomal, 16S/genetics ; *Ear, Middle/microbiology/surgery ; *Mesna/therapeutic use ; Chronic Disease ; Child ; Female ; Male ; Bacteria/classification/genetics/isolation & purification ; *Cholesteatoma, Middle Ear/surgery/microbiology ; Child, Preschool ; DNA, Bacterial/genetics ; Computational Biology ; Sequence Analysis, DNA ; },
abstract = {INTRODUCTION: Cholesteatomatous chronic otitis media (CCOM) remains a clinical challenge due to its high recurrence rates despite surgical intervention. Sodium 2-mercaptoethanesulphonate (MESNA) is used to assist dissection, yet its impact on the middle ear microbiome and ecological recovery remains poorly understood. The aim of this study is to characterize the microbiota of paediatric CCOM and evaluate the ecological shifts induced by MESNA-assisted surgery.

METHODS: We analyzed 16S rRNA gene sequences (V3-V4) from middle ear tissue of paediatric patients with CCOM (CCOM Before MESNA, n = 13; CCOM After MESNA, n = 13) and healthy controls (n = 11). Bioinformatic processing was performed via QIIME2 and DADA2. We employed a Compositional Data Analysis (CoDA) framework, centering on Aitchison distances, ALDEx2 for differential abundance, and consensus co-occurrence networks (SparCC, SPIEC-EASI, and CLR-Pearson). Functional potential was inferred using PICRUSt2.

RESULTS: CCOM was associated with a marked reduction in microbial network connectivity, decreasing from 185 edges in healthy controls to only two total edges in the CCOM Before MESNA stage. Cutibacterium emerged as a candidate keystone pathobiont, exhibiting profound ecological isolation and predicted metabolic shifts toward lipid catabolism and biofilm formation in dysbiotic states. MESNA application disrupted the disease-associated community equilibrium, initiating secondary succession. However, post-treatment recovery was marked by taxonomic homogenization and the expansion of Pseudomonas in several patients.

DISCUSSION: Our findings identify network fragmentation and functional dysbiosis as the ecological signatures of pediatric CCOM. While MESNA disrupts the dysbiotic equilibrium, it does not fully restore a healthy stable climax community within the studied timeframe, as defined in ecological succession theory. These results support a paradigm shift from simple pathogen eradication toward ecological restoration as a strategy to prevent disease recurrence in CCOM patients.},
}

Humans
*Microbiota/drug effects
*Otitis Media/microbiology/surgery
RNA, Ribosomal, 16S/genetics
*Ear, Middle/microbiology/surgery
*Mesna/therapeutic use
Chronic Disease
Child
Female
Male
Bacteria/classification/genetics/isolation & purification
*Cholesteatoma, Middle Ear/surgery/microbiology
Child, Preschool
DNA, Bacterial/genetics
Computational Biology
Sequence Analysis, DNA

@article {pmid42258566,
year = {2026},
author = {Tran-Nam, H and Che-Ngoc, H},
title = {A black-winged kite improved fuzzy clustering handling imbalanced uncertain data.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0349753},
pmid = {42258566},
issn = {1932-6203},
mesh = {Clustering Algorithms ; *Fuzzy Logic ; Algorithms ; *Data Mining/methods ; Cluster Analysis ; Soft Computing ; Uncertainty ; },
abstract = {Clustering uncertain data is a fundamental problem in data mining. Imbalance among uncertain objects significantly degrades clustering performance, as minority clusters are repeatedly overshadowed by dominant ones. Consequently, existing clustering techniques often fail due to initialisation biases and inadequate similarity modelling. This paper proposes a novel algorithm, the Black-winged Kite Improved Fuzzy clustering for probability density Functions (BKIFF), which combines an optimisation-based initialisation strategy with an enhanced fuzzy clustering framework. Specifically, BKIFF incorporates the Hellinger distance into the clustering objective to more reliably capture similarities between probability density functions (pdfs), and introduces improved membership updating and prototype estimation mechanisms tailored for uncertain and imbalanced data formulated as Improved Fuzzy clustering for probability density Functions (IFF) while theoretical convergence is established. In addition, the algorithm employs Black-winged Kite Optimisation (BKO) to enhance prototype selection, improving clustering stability and convergence. As a result, comprehensive experiments with synthetic Gaussian probability distributions, skewed pdfs, and real-world image datasets demonstrate that BKIFF consistently outperforms baseline methods such as FCF, FCF-[Formula: see text], KMEANS, and Self-Updating. Across all three examples, BKIFF achieves near-perfect ARI, improving from near-zero values in highly imbalanced cases {20,50,80,100}
by approximately 30-35% in moderate settings, while increasing NMI by about 25-95%. Additionally, it reduces computational time by approximately 95-99% compared to baseline methods. In conclusion, BKIFF demonstrates superior performance and opens up new possibilities for applications in medical diagnostics, ecological analysis, and high-dimensional uncertain data mining, particularly in imbalanced environments.},
}

Clustering Algorithms
*Fuzzy Logic
Algorithms
*Data Mining/methods
Cluster Analysis
Soft Computing
Uncertainty

@article {pmid42263378,
year = {2026},
author = {Zeng, Y and Makuková, J and Báčová, J and Roušar, T and Ševčovičová, A and Roch, T and Qin, P and Jelínková, Š and Vlček, A and Wu, Y and Monfort, O and Motola, M},
title = {When TiO2 meets pharmaceuticals: Photocatalytic degradation and environmental safety unveiled.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120353},
doi = {10.1016/j.ecoenv.2026.120353},
pmid = {42263378},
issn = {1090-2414},
abstract = {Building on our previous work on electrochemically synthesized anatase TiO2 nanoparticles (NPs), this study evaluates their environmental relevance by linking pharmaceutical photocatalytic degradation with transformation product identification and toxicity-oriented assessment. The incomplete removal of pharmaceuticals in wastewater treatment plants raises concerns about both parent compounds and transformation products formed during advanced treatments. Here, the synthesized TiO2 NPs were applied to the photocatalytic degradation of ibuprofen (IBU) and paracetamol (PCT) under ultraviolet A (UVA) irradiation. The TiO2 NPs showed higher degradation efficiency than commercial P25, with Kobs of 10.82 × 10[-3] min[-1] for IBU and 10.75 × 10[-3] min[-1] for PCT, and approximately 95% removal for both pollutants after 4 h of UVA irradiation. Liquid chromatography tandem mass spectrometry (LC-MS/MS) identified 8 transformation products for IBU and 9 for PCT, suggesting degradation pathways involving hydroxylation, decarboxylation, bond cleavage, and formation of smaller oxygenated products. In-vitro assays were performed using A549 lung cells and HepG2 liver cells. In A549 cells, TiO2 NPs caused no significant decrease in dehydrogenase activity at 1-100 µg/mL after 24 and 48 h. In HepG2 cells, TiO2 NPs showed lower cytotoxicity than P25, with viability remaining at approximately 68% after 48 h at 250 µg/mL, compared with about 60% for P25. IBU and PCT solutions before and after 4 h of photocatalytic treatment maintained HepG2 viability above 90%. The toxicity-oriented assessment, supplemented by Ecological Structure Activity Relationships (ECOSAR) software predictions, suggested that further transformation could reduce predicted ecological concern.},
}

@article {pmid42269581,
year = {2026},
author = {Jimenez, MF and Khalighifar, A and Horton, KG},
title = {Within-Night Variation in Predictor Importance Highlights Dynamic Nature of Bird Migration.},
journal = {Ecology letters},
volume = {29},
number = {6},
pages = {e70422},
pmid = {42269581},
issn = {1461-0248},
support = {/NASA/NASA/United States ; },
mesh = {Animals ; *Animal Migration ; *Birds/physiology ; Seasons ; Radar ; },
abstract = {Ecological forecasting is increasingly important for conservation. Predicting nocturnal bird migration events is a promising vehicle for forecasts but isn't often explored at fine temporal scales. We use weather surveillance radar to examine dynamic drivers of migration in 2-h periods throughout a night. We assess the relative importance of terrestrial, atmospheric and sampling predictors (which relate to radar position and scan timing) across spring and fall. Atmospheric conditions were consistently strong predictors. In contrast, terrestrial predictors contributed relatively little to explaining variation in activity. Sampling variables, such as time after sunset, varied in importance, with the highest influence shortly after sunset. We highlight the temporal variability in predictors of migration, emphasising it as a dynamic process, involving continuous decisions and adjustments rather than following fixed routes. We underscore the value of radar for capturing transitions between habitats while revealing key limitations and opportunities for understanding fine-scale migratory behaviour.},
}

Animals
*Animal Migration
*Birds/physiology
Seasons
Radar

@article {pmid42269612,
year = {2026},
author = {Balakrishnan, CN and Toda, Y and Ko, MC and Wirthlin, ME and Driver, RJ and Bolton, PE and Miller, ET and Mendez-Aranda, D and Dikow, RB and Frandsen, PB and Shogren, EH and Bennett, KFP and Anderson, HL and Bursell, MG and Cramer, JF and Sadanandan, KR and Nakagita, T and Pizo, MA and Caetano, DS and Anciães, M and Ferreira, CF and Berv, JS and Long, KM and Lim, HC and Moncrieff, AE and Kingston, SE and White Carreiro, ND and Friedrich, SR and Cuta, CA and Pease, JB and Nevue, AA and Tomlinson, C and Zimin, A and Louder, MIM and Brewer, MS and Bay, RA and Ruegg, K and Smith, TB and Ishimaru, Y and Pfenning, AR and Frankl-Vilches, C and Gahr, M and Mello, CV and Kimball, RT and Braun, EL and Blake, JG and Day, LB and Ryder, TB and Moore, IT and Horton, BM and Schlinger, BA and Fuxjager, MJ and Warren, WC and DuVal, EH and Boyle, WA and Loiselle, BA and Braun, MJ and Baldwin, MW},
title = {Genomic and physiological changes in a sexually selected and frugivorous bird radiation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.05.021},
pmid = {42269612},
issn = {1879-0445},
abstract = {Across diverse organisms, the strength and ecological drivers of sexual selection vary enormously. In birds, some of the families with the most elaborate plumage and display-such as birds of paradise, manakins, and cotingas-are also specialist frugivores, yet links between shifts in diet, changes in breeding system, and the evolution of elaborate traits are poorly understood. We focus on manakins, a radiation of frugivorous Neotropical birds well known for spectacular courtship rituals and colorful plumage, and present an integrative analysis of the transition in both diet and mating systems in this clade to examine the causes and consequences of strong sexual selection. In manakins, we find reduced genetic diversity on the Z sex chromosome relative to autosomes, a predicted signature of sexual selection. We also identify targets of positive selection across the manakin radiation, including genes related to muscle function, visual perception, and the transition to frugivory. Among these, we observe selection on sugar-sensing taste receptors, as well as on lactase-phlorizin hydrolase, implicated in the consumption of chemically defended fruits. For both, we confirm that selection signatures correspond to functional changes and infer the relative time of these changes, as well as of shifts in diet, breeding systems, and plumage coloration: elaborated traits evolved subsequent to changes in mating systems and after key physiological changes facilitating fruit-eating. Altogether, these results suggest that intensified frugivory set the stage for the radiation of one of the planet's most colorful and acrobatic avian lineages.},
}

@article {pmid41725240,
year = {2026},
author = {Anum, H and Ishfaq, S and Yu, K and Krutovsky, KV and Cheng, R and Tong, Y},
title = {Integrated Physiological and Omics Responses of Red Lettuce (Lactuca sativa) Driven by Varying Light Spectrum: Insights Into Anthocyanin Synthesis.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70791},
doi = {10.1111/ppl.70791},
pmid = {41725240},
issn = {1399-3054},
support = {2022YFDZ0086//Key Research and Development Program, Department of Science and Technology, Inner Mongolia Autonomous Region, China/ ; //Innovation Project of the Institute of Evironment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China/ ; },
mesh = {*Lactuca/radiation effects/physiology/genetics/metabolism ; *Anthocyanins/biosynthesis/metabolism ; *Light ; Gene Expression Regulation, Plant/radiation effects ; Plant Leaves/radiation effects/metabolism/physiology ; Multiomics ; Chlorophyll/metabolism ; Gene Expression Profiling ; Flavonoids/metabolism ; Transcriptome ; Plant Proteins/metabolism/genetics ; },
abstract = {The health benefits of anthocyanins for humans are well established. However, the influence of spectral light composition in plant factories on plant growth and anthocyanin biosynthesis remains poorly understood. This study selected red lettuce as a model plant due to its high anthocyanin content. Using a plant factory with artificial lighting, we applied three light treatments: control (R:B = 160:40), T1 (R:B:G = 130:20:50) and T2 (R:B:G = 75:75:50) to examine their effects on plant physiology and anthocyanin production. A multi-omics analysis further identified potential pathways and genes regulating anthocyanin synthesis under different light conditions. Plants under T2 had higher levels of anthocyanins, flavonoids, phenolics, and carotenoids. Conversely, fresh and dry biomass, total leaf area, chlorophyll content, and sugar levels were higher in red lettuce leaves grown under T1. In total, 110 anthocyanidin metabolites and 573 genes showed differential expression under different light combinations. Transcriptomic analysis revealed a substantial increase in the activity of genes related to anthocyanin precursors, such as PAL and 4-CL, as well as structural genes involved in anthocyanin synthesis, including F3H, DFR, ANS, and UDP-glucosyltransferase, specifically under T2. Furthermore, our findings identified 14 transcription factors, comprising 4 bHLH, 3 MYB, 3 bZIP, and 4 WRKY genes, which could play crucial roles in regulating anthocyanin biosynthesis. These findings lay the groundwork for investigating the molecular mechanisms underlying anthocyanin biosynthesis in lettuce leaves. Moreover, they provide valuable insights that could contribute to advancements in leaf color genetics for lettuce production in plant factories.},
}

*Lactuca/radiation effects/physiology/genetics/metabolism
*Anthocyanins/biosynthesis/metabolism
*Light
Gene Expression Regulation, Plant/radiation effects
Plant Leaves/radiation effects/metabolism/physiology
Multiomics
Chlorophyll/metabolism
Gene Expression Profiling
Flavonoids/metabolism
Transcriptome
Plant Proteins/metabolism/genetics

@article {pmid41752312,
year = {2026},
author = {Alhassan, GN and Ozturkcan, A and Cavdar, SC},
title = {Global Disparities in Teletherapy Adoption: A Cross-Income Analysis of Mental Health Access.},
journal = {International journal of environmental research and public health},
volume = {23},
number = {2},
pages = {},
pmid = {41752312},
issn = {1660-4601},
mesh = {Humans ; Mental Health Teletherapy ; *Health Services Accessibility/statistics & numerical data ; Developing Countries ; *Healthcare Disparities/statistics & numerical data ; *Mental Disorders/therapy ; Digital Health ; Socioeconomic Disparities in Health ; *Telemedicine ; },
abstract = {Mental health disorders affect nearly one billion people worldwide, yet treatment gaps exceed 75% in low- and middle-income countries. Teletherapy has emerged as a scalable solution, but its adoption differs sharply by economic context. This comparative ecological policy analysis used secondary aggregate data from WHO, World Bank, ITU, and national reports to examine teletherapy adoption in low-income (Nigeria, Kenya), middle-income (South Africa, India), and high-income countries (Norway, Canada). Descriptive statistics and simple linear regression were applied, with findings interpreted through the Consolidated Framework for Implementation Research (CFIR), Technology Acceptance Model (TAM), and Diffusion of Innovations theory. High-income countries achieved widespread adoption (>70%), enabled by universal broadband, comprehensive regulation, and strong reimbursement. Middle-income countries showed moderate uptake (15-30%), constrained by rural-urban digital divides and inconsistent policies. Low-income countries reported minimal integration (<5%), limited by unreliable internet, severe workforce shortages, high data costs, and sociocultural barriers. Digital infrastructure, regulatory maturity, and mental health workforce density explained 78% of the cross-country variance in adoption rates (R[2] = 0.78). Equitable scale-up of teletherapy directly supports SDGs 3, 9, 10, and 17. Targeted investment and cross-income collaboration are essential to prevent digital mental health solutions from exacerbating existing inequities.},
}

Humans
Mental Health Teletherapy
*Health Services Accessibility/statistics & numerical data
Developing Countries
*Healthcare Disparities/statistics & numerical data
*Mental Disorders/therapy
Digital Health
Socioeconomic Disparities in Health
*Telemedicine

@article {pmid41761014,
year = {2026},
author = {Karmakar, D and Saha, P},
title = {In silico structural and dynamic stability analysis of an endo-1,4-β-xylanase from Agrobacterium sp. strain DKPNP3, isolated from the gut of Gonocephalum sp.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {3},
pages = {},
pmid = {41761014},
issn = {1572-9699},
mesh = {*Coleoptera/microbiology ; Animals ; Molecular Dynamics Simulation ; Enzyme Stability ; *Agrobacterium/enzymology/isolation & purification/genetics/classification ; *Endo-1,4-beta Xylanases/chemistry/metabolism/genetics ; Molecular Docking Simulation ; Protein Conformation ; Phylogeny ; Amino Acid Sequence ; Computational Biology ; Computer Simulation ; Models, Molecular ; Molecular Weight ; },
abstract = {Xylanases are one of the most important hydrolytic enzymes involved in plant hemicellulose degradation with potential industrial as well as ecological significance. This study presents a comprehensive characterization of an endo-1,4-β-xylanase enzyme from Agrobacterium sp. Strain DKPNP3 isolated from the beetle gut of Gonocephalum sp. (Coleoptera: Tenebrionidae). Bioinformatics analyses were performed, including physicochemical characterization, phylogenetic assessment, conserved domain identification, secondary and tertiary structure prediction, subcellular localization prediction, homology modeling, structural validation, molecular docking and molecular dynamics simulation to assess the stability of this protein. The enzyme belongs to the glycoside hydrolase family 10 (GH10) with 339 amino acids, molecular weight of 37.8 kDa, and acidic in nature (pi 5.8). The homology model demonstrated high structural reliability, with an ERRAT score of 96.364% and a QMEAN Z-score of 0.59. Molecular dynamics simulations demonstrated that the enzyme is structurally stable in both its apo and ligand-bound forms. The apo form showed stability comparable to a well-characterized synthetic construct xylanase from Bacillus halodurans (GenBank accession number: MW311490), which was used as a positive control. Furthermore, simulations performed at multiple temperatures indicated retention of conformational integrity under different thermal conditions, suggesting potential thermostability. The intracellular nature of the enzyme, as predicted by in silico analysis, was confirmed by experimental validation using Congo Red-xylan agar assay and quantification with di nitro salicylic acid (DNSA).},
}

*Coleoptera/microbiology
Animals
Molecular Dynamics Simulation
Enzyme Stability
*Agrobacterium/enzymology/isolation & purification/genetics/classification
*Endo-1,4-beta Xylanases/chemistry/metabolism/genetics
Molecular Docking Simulation
Protein Conformation
Phylogeny
Amino Acid Sequence
Computational Biology
Computer Simulation
Models, Molecular
Molecular Weight

@article {pmid41762157,
year = {2026},
author = {Ryan, SJ and Huxley, PJ and Lippi, CA and Pawar, S and Cator, L and Rund, SSC and Johnson, LR},
title = {MIReVTD, a minimum information standard for reporting vector trait data.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {41762157},
issn = {2047-217X},
support = {2016265//NSF/ ; 2016264//NSF/ ; 2016282//NSF/ ; },
mesh = {Animals ; *Aedes/genetics ; Humans ; *Mosquito Vectors/genetics ; *Computational Biology/methods ; *Software ; Vector Borne Diseases/transmission ; },
abstract = {Vector-borne diseases pose a persistent and increasing challenge to human, animal, and agricultural systems globally. Mathematical modeling frameworks incorporating vector trait responses are powerful tools for assessing risk and predicting vector-borne disease impacts. Developing these frameworks and the reliability of their predictions hinge on the availability of experimentally derived vector trait data for model parameterization and inference of the biological mechanisms underpinning transmission. Trait experiments have generated data for many known and potential vector species, but the terminology used across studies is inconsistent, and accompanying publications may share data with insufficient detail for reuse or synthesis. The lack of data standardization can lead to information loss and prohibit analytical comprehensiveness. Here, we present MIReVTD, a Minimum Information standard for Reporting Vector Trait Data. Our reporting checklist balances completeness and labor intensity to make these important experimental data easier to find and reuse, without onerous effort for scientists generating the data. To illustrate the standard, we provide an example reproducing results from an Aedes aegypti mosquito study.},
}

Animals
*Aedes/genetics
Humans
*Mosquito Vectors/genetics
*Computational Biology/methods
*Software
Vector Borne Diseases/transmission

@article {pmid41771790,
year = {2026},
author = {Wang, S and Zhou, T and Wang, X and Zhao, J and Wang, X},
title = {Bridging the gap: Prevotella/Segatella's impact on gut barrier function and advanced cultivation strategies to realize the uses in gut health.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638001},
pmid = {41771790},
issn = {1949-0984},
mesh = {Humans ; Intestinal Barrier Function ; *Prevotella/growth & development/physiology/isolation & purification/genetics ; *Gastrointestinal Microbiome ; Probiotics ; Animals ; Multiomics ; },
abstract = {Prevotella and Segatella are important, keystone genera in the gut microbiota, renowned for their exceptional fiber-degrading capacity. These genera critically modulate gut microbial composition, influence host metabolic pathways and gut barrier function, and exhibit formidable ecological niche competitiveness, underscoring their pivotal role in gut ecosystem dynamics. While they dominate healthy gut microbiomes, their probiotic potential on epithelial barrier function has been disproportionately overlooked. This review comprehensively elucidates their microbial eco-profiling and the underlying molecular mechanisms in sustaining intestinal barrier function, considering physical, chemical, biological, and microbiological dimensions, thereby providing insights relevant to the prevention and treatment of intestinal diseases such as inflammatory bowel disease, irritable bowel syndrome, and metabolic disorders. Most importantly, we have summarized 23 current commercial and research-based isolation and cultivation approaches for Prevotella/Segatella, integrating the emerging high-throughput methodologies to expand the available strain repertoire. We also emphasize the critical need for subsequent research to characterize strain-specific functional profiles through multi-omics approaches, which will be essential for developing targeted and personalized microbial therapeutics.},
}

Humans
Intestinal Barrier Function
*Prevotella/growth & development/physiology/isolation & purification/genetics
*Gastrointestinal Microbiome
Probiotics
Animals
Multiomics

@article {pmid41772970,
year = {2026},
author = {Javal, M and Lehmann, P and Bierman, A and Koštál, V and Moos, M and Smit, C and Vogel, H and Conlong, DE and Terblanche, JS},
title = {Integrative -omics approaches reveal mechanisms of combined heat stress and extreme hypoxia tolerance in a Cerambycid beetle larva.},
journal = {The Journal of experimental biology},
volume = {229},
number = {6},
pages = {},
doi = {10.1242/jeb.251552},
pmid = {41772970},
issn = {1477-9145},
support = {//Stellenbosch University/ ; //South African Sugarcane Research Institute/ ; },
mesh = {Animals ; *Coleoptera/physiology/growth & development/genetics ; Larva/physiology/growth & development/genetics ; *Heat-Shock Response ; Transcriptome ; Metabolomics ; *Metabolome ; Multiomics ; *Oxygen/metabolism ; *Thermotolerance ; Hot Temperature ; },
abstract = {Atmospheric oxygen, which is essential for energy metabolism, can directly influence an animal's heat tolerance by affecting oxygen transport processes, especially in those living in oxygen-poor environments such as plant tissues, underground or aquatic environments. Yet, oxygen availability and heat tolerance are rarely studied together, limiting our ability to predict their combined effects on insect performance. This study examines the larval tolerance of a large xylophagous cerambycid beetle Cacosceles newmannii to combined hypoxic and thermal stress using performance assays (duration of righting response) coupled with metabolomic and transcriptomic analyses. Metabolomic profiling showed that most metabolites were downregulated in the body but upregulated in the haemolymph as stress increased. Transcriptomic profiles clustered primarily by temperature (25°C vs 35°C), independent of oxygen level. Cacosceles newmannii appeared capable of modulating its performance to reduce the energy costs and physiological damage induced by hypoxia. This suggested a high baseline hypoxia tolerance rather than a rapid plastic (induced) physiological hypoxia response, probably due to the species' endophytic lifestyle. Conversely, thermal stress led to a predictable increase in metabolic activity but did not markedly affect performance, triggering adjustments to maintain cellular functions while limiting the impact of stresses expected under conditions of high temperature, such as desiccation. In short, our study highlights the distinct metabolic pathways mobilised to cope with hypoxic versus thermal stress, emphasizing the importance of integrated approaches in understanding insect responses to environmental challenges. These findings have significant implications for understanding the ecology of the species, with applications for pest management and sustainable agriculture in the context of climate change.},
}

Animals
*Coleoptera/physiology/growth & development/genetics
Larva/physiology/growth & development/genetics
*Heat-Shock Response
Transcriptome
Metabolomics
*Metabolome
Multiomics
*Oxygen/metabolism
*Thermotolerance
Hot Temperature

@article {pmid41777690,
year = {2026},
author = {Ivanova, NV and Watson, LC and Comte, J and Bessonov, K and Abrahamyan, A and Crevecoeur, S and Watson, SB},
title = {Rapid assessment of phytoplankton assemblages using Next Generation Sequencing and Barcode of Life Data System: a widely applicable HAB-ID toolkit for detecting and monitoring biodiversity loss and harmful algal blooms.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20747},
pmid = {41777690},
issn = {2167-8359},
mesh = {*Phytoplankton/genetics/classification ; *High-Throughput Nucleotide Sequencing/methods ; *Harmful Algal Bloom ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Cyanobacteria/genetics/classification ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Harmful algal blooms have important implications for the health, functioning, and services of aquatic ecosystems. Our ability to detect and monitor these events is often challenged by the lack of rapid and cost-effective methods to identify bloom-forming organisms and their potential for toxin production. Here, we developed and applied a combination of DNA barcoding and Next Generation Sequencing (NGS) for the rapid assessment of phytoplankton community composition with a focus on two important indicators of ecosystem health: toxigenic bloom-forming cyanobacteria and impaired planktonic biodiversity. To develop this molecular toolset for identification of cyanobacterial and algal species present in HABs (harmful algal blooms), hereafter called HAB-ID, we achieved three goals: creating a validated reference database, optimizing molecular protocols, and developing original bioinformatics pipeline tailored to uncertainty of algal taxonomy. The BOLD (Barcode of Life Data System) 16S reference database from cultures of 211 cyanobacterial and algal strains representing 102 species with particular focus on bloom and toxin producing taxa was constructed with Sanger sequencing and further refined using Single Molecule Real Time Sequencing (SMRT-sequencing). Using the new reference database of 16S rDNA sequences and constructed mock communities of mixed strains for protocol validation, we developed new NGS primer sets which can recover 16S from both cyanobacteria and eukaryotic algal chloroplasts. We also developed DNA extraction protocols for cultured algal strains and environmental samples, which match commercial kit performance and offer a cost-efficient solution for large scale ecological assessments of harmful blooms while giving benefits of reproducibility and increased accessibility. Our innovative bioinformatics pipeline was designed to handle low taxonomic resolution for problematic genera of cyanobacteria such as the Anabaena-Aphanizomenon-Dolichospermum complex, two clusters of Anabaena (I and II), Planktothrix and Microcystis. This newly developed HAB-ID toolset was further validated by applying it to assess cyanobacterial and algal composition in field samples from waterbodies with recurrent HABs events.},
}

*Phytoplankton/genetics/classification
*High-Throughput Nucleotide Sequencing/methods
*Harmful Algal Bloom
*DNA Barcoding, Taxonomic/methods
*Biodiversity
*Cyanobacteria/genetics/classification
Computational Biology/methods
RNA, Ribosomal, 16S/genetics

@article {pmid41790862,
year = {2026},
author = {Acs, R and Ibrahim, A and Zhuang, H and Chérubin, LM},
title = {Contrastive learning for passive acoustic monitoring: A framework for sound source discovery and cross-site comparison in marine soundscapes.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1014005},
pmid = {41790862},
issn = {1553-7358},
mesh = {*Acoustics ; Animals ; Clustering Algorithms ; *Sound ; Computational Biology ; *Environmental Monitoring/methods ; Cluster Analysis ; Sound Spectrography/methods ; Fishes/physiology ; Autoencoder ; Marine Biology/methods ; Biodiversity ; *Machine Learning ; Reproducibility of Results ; Signal Processing, Computer-Assisted ; Aquatic Organisms/physiology ; },
abstract = {Passive acoustic monitoring (PAM) is a powerful tool for studying marine biodiversity, but large-scale analysis of underwater recordings is constrained by noise, overlapping signals, and limited labeled data. Here, we present a scalable, unsupervised contrastive learning framework for marine soundscapes. Using a large PAM dataset spanning multiple biogeographies, we show that the proposed approach organizes recordings into clusters with well-defined internal structure, as assessed using intrinsic clustering metrics and within-cluster similarity. The resulting clusters reveal recurring acoustic patterns that correspond to broad sound-source categories, including biological sounds such as fish calls and choruses, and anthropogenic sounds such as vessel noise, without explicitly enforcing these distinctions during training. Compared with established approaches, including cepstral features, variational autoencoders, and supervised pipelines, the proposed framework produces embeddings that support more compact and stable unsupervised clustering while preserving fine-scale acoustic variation beyond predefined species labels. By learning a shared representation across recordings from multiple sites and years, we examine the reproducibility of acoustic patterns across locations and identify both site-shared and site-specific sound signatures. Although the method is not designed to recover coarse species labels, it enables label-efficient analysis by reducing reliance on manual annotation and supporting exploratory characterization of complex marine soundscapes. Together, these results highlight multi-positive contrastive learning with a teacher network and acoustically informed augmentations as an effective strategy for scalable, discovery-driven analysis of passive acoustic monitoring data.},
}

*Acoustics
Animals
Clustering Algorithms
*Sound
Computational Biology
*Environmental Monitoring/methods
Cluster Analysis
Sound Spectrography/methods
Fishes/physiology
Autoencoder
Marine Biology/methods
Biodiversity
*Machine Learning
Reproducibility of Results
Signal Processing, Computer-Assisted
Aquatic Organisms/physiology