@article {pmid42726808,
year = {2026},
author = {Muresu, R and Rodriguez, M and Squartini, A},
title = {GenBank mining reveals novel insights into Rhizobium phylogeny: Identical 16S rRNA sequences are mainly uncoupled from species designation, host plant, and geographic origin: How this search suggested the definition of a direct 'microbial h-index'.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357973},
doi = {10.1371/journal.pone.0357973},
pmid = {42726808},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Rhizobium/genetics/classification ; *Phylogeny ; *Plants/microbiology ; *Databases, Nucleic Acid ; DNA Barcoding, Taxonomic ; },
abstract = {16S rDNA is the historical gold standard for bacterial identification, particularly in metabarcoding approaches reliant on sequence similarity thresholds. We analyzed 6,660 Rhizobium 16S rRNA gene sequences from GenBank to examine the relationship between sequence identity and three metadata: species name, host plant, and geographic origin. Using an iterative BLAST-based pipeline, we detected 116,069 pairwise matches and assessed concordance among sequences (average length 1,328 bp) sharing 100% identity. For those in which the organism name, host plant and country of isolation were present in the record, surprisingly, 66.59% of identical sequence pairs showed full discordance across all three metadata, while only 1.40% shared the same name, host, and country. The most widespread sequence, detected 371 times, was associated with over 56 different host plants across 25 countries and bore multiple species name designations. These results highlight a striking mismatch between the 16S barcode and the taxonomic, ecological, and phenotypic variability it is assumed to reflect, likely arising from the slow evolution of rRNA genes contrasted with the mobility of ecologically relevant genes via horizontal transfer on plasmids, transposons, and phages. Our findings further challenge the limitations of relying on 16S rRNA alone for fine-scale taxonomic and metadata-based inference in capturing the true functional and ecological diversity of bacteria, endorsing the critical importance of polyphasic taxonomic approaches that integrate genomic, phenotypic, and ecological data. An interesting byproduct of the analysis was to realize the possibility of treating these data as if they were 'citations.' The more one finds the same query sequence, the more that sequence can be considered biologically 'cited', i.e., re-proposed elsewhere in the world. Thus, one can also analyze the h-index of such a ranking. In our Rhizobium dataset, we calculated an h-index = 201, meaning the sequence ranked 201st had 202 identical homologues in GenBank. Although the research effort on given species is directly connected with it, this number provides a quantitative indicator of a taxon's sequence recurrence and distribution within public databases, independent of nomenclatural inconsistencies, offering a novel framework for assessing bacterial representation across global datasets.},
}

*RNA, Ribosomal, 16S/genetics
*Rhizobium/genetics/classification
*Phylogeny
*Plants/microbiology
*Databases, Nucleic Acid
DNA Barcoding, Taxonomic

@article {pmid42728906,
year = {2023},
author = {Susanna, D and Saputra, YA and Poddar, S},
title = {The effect of wind speed in increasing COVID-19 cases in Jakarta: a spatial-temporal analysis from March to September 2020.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {145},
doi = {10.12688/f1000research.128908.3},
pmid = {42728906},
issn = {2046-1402},
mesh = {*Wind ; *COVID-19/epidemiology/transmission ; Humans ; Indonesia/epidemiology ; Spatio-Temporal Analysis ; SARS-CoV-2 ; Pandemics ; Geographic Information Systems ; },
abstract = {BACKGROUND: The SARS-CoV-2 virus that causes COVID-19 is described as a highly contagious virus, and wind speed is suspected to be one of the climate elements that play a role in its spread, among others. This study aims to determine the relationship between wind speed and the increase in COVID-19 cases, as well as its potential spread, based on regional characteristics.

METHODS: The design of this study was an ecological study based on time and place to integrate geographic information systems and tested using statistical techniques. The data used were wind speed and weekly COVID-19 cases from March to September 2020. These records were obtained from the special coronavirus website of Jakarta Provincial Health Office and the Indonesian Meteorology, Climatology and Geophysics Agency. The data were analyzed by correlation, graphic/time trend, and spatial analysis.

RESULTS: The wind speed (maximum and mean) from March to September 2020 tended to fluctuate between 1.43 and 6.07 m/s. The correlation test results between the average wind speed and COVID-19 cases in Jakarta showed a strong positive correlation (r = 0.542; p value = 0.002).

CONCLUSIONS: Areas with high wind speeds tended to show an increase in the number of COVID-19 cases, especially in the coastal areas of Jakarta. Wind speed plays a role in increasing the spread of SARS-CoV-2, in people who did not implement health protocols properly. This mechanism can be worsened with support of environmental factors such as air pollution.},
}

*Wind
*COVID-19/epidemiology/transmission
Humans
Indonesia/epidemiology
Spatio-Temporal Analysis
SARS-CoV-2
Pandemics
Geographic Information Systems

@article {pmid42728944,
year = {2026},
author = {Falk, S and Crowley, LM and Grzywacz, A and , and , and , and , and , and , and , },
title = {The genome sequence of the muscid fly, Hydrotaea similis Meade, 1887 (Diptera: Muscidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {399},
doi = {10.12688/wellcomeopenres.26885.2},
pmid = {42728944},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Hydrotaea similis (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The assembly contains two haplotypes with total lengths of 884.66 megabases and 852.78 megabases. Most of haplotype 1 (90.83%) is scaffolded into 5 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 20.27 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid42728953,
year = {2026},
author = {Boyes, D and Hutchinson, F and Crowley, LM and Williams, CD and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Holly Tortrix, Rhopobota naevana (Hubner, 1817) (Lepidoptera: Tortricidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {400},
doi = {10.12688/wellcomeopenres.26882.1},
pmid = {42728953},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Rhopobota naevana (Holly Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 581.80 megabases. Most of the assembly (99.48%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.5 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid42729027,
year = {2026},
author = {Avelino, C and Karp, R and Baker, A and Metz, S and Sweet, M and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the lesser starlet coral, Siderastrea radians (Pallas, 1766) (Scleractinia: Rhizangiidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {493},
doi = {10.12688/wellcomeopenres.27286.1},
pmid = {42729027},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Siderastrea radians (lesser starlet coral; Cnidaria; Anthozoa; Scleractinia; Rhizangiidae). The genome sequence has a total length of 807.19 megabases. Most of the assembly (94.17%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.38 kilobases. Gene annotation of this assembly by Ensembl identified 47 051 protein-coding genes. From the metagenome data, we recovered two binned metagenomes assigned to the bacterial phylum Bacteroidota and class Bacteroidia.},
}

@article {pmid42729039,
year = {2026},
author = {Stewart, JM and Medina, M and Bruckner, A and May, L and Moffitt, ZJ and Lopez, JV and Woodley, CM and Metz, S and Sweet, M and Pruzinsky, N and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the maze coral, Meandrina meandrites (Linnaeus, 1758) (Scleractinia: Meandrinidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {469},
doi = {10.12688/wellcomeopenres.27184.1},
pmid = {42729039},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Meandrina meandrites (maze coral; Cnidaria; Anthozoa; Scleractinia; Meandrinidae). The genome sequence has a total length of 551.16 megabases. Most of the assembly (99.25%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.2 kilobases. Gene annotation of this assembly by Ensembl identified 30 464 protein-coding genes. We recovered two bins from the metagenome data.},
}

@article {pmid42721478,
year = {2026},
author = {Warner, S and Stucky, CH and Haegerich, T and Yauger, YJ},
title = {The Cognitive Transaction: Toward a Human Factors Research Agenda for AI in Anesthesia and Perioperative Care.},
journal = {JMIR human factors},
volume = {13},
number = {},
pages = {e102683},
doi = {10.2196/102683},
pmid = {42721478},
issn = {2292-9495},
mesh = {Humans ; *Artificial Intelligence ; *Perioperative Care/methods ; *Anesthesia/methods ; *Ergonomics ; },
abstract = {AI is now embedded in the infrastructure of perioperative care. Risk stratification algorithms, hemodynamic prediction tools, and clinical decision support systems are active in operating rooms at major health systems, and their adoption is accelerating. However, the field has studied model performance and organizational implementation while largely bypassing the moment between them: the real-time encounter in which an anesthesia provider must decide, under active case conditions, what to do with an AI-generated output. We term this the cognitive transaction and argue that it is the fundamental unit of perioperative AI implementation. The perioperative environment presents a specific constellation of conditions that existing human-AI interaction research was not designed to address. Continuous real-time decision demands, extreme time compression, high cognitive load, and consequences that unfold in seconds distinguish the operating room from the clinical contexts where most provider-AI interaction research has been conducted. What we know about AI adoption in radiology, oncology, or ambulatory care does not readily translate to this setting. The cognitive moment in anesthesia has its own structure, its own failure modes, and its own research requirements. This paper examines what those requirements are. We analyze how the operating room functions as a pre-existing human-machine cognitive system into which AI is now being inserted, and why the conditions of that system generate predictable vulnerabilities: miscalibrated trust, automation bias, and cognitive friction produced by interfaces optimized for technical accuracy rather than clinical usability. We argue that these failure modes are not incidental but structural and that they will persist regardless of model performance until the provider-AI interaction is itself treated as a research object. We identify 4 priority research domains. The first concerns the structure of provider-AI disagreement and the methods needed to distinguish automation bias from legitimate clinical insight. The second concerns the longitudinal dynamics of trust calibration across repeated clinical encounters rather than single-session experimental designs. The third concerns interface design for high-acuity workflows, specifically what constitutes a usable AI output for a provider managing a patient in real time. The fourth concerns the need for ecologically valid study designs capable of capturing provider reasoning under actual perioperative conditions rather than retrospective or survey-based proxies. The anesthesia and perioperative research community is positioned to lead this work. The clinical specificity, domain knowledge, and professional stake required to design meaningful studies are all present within the field. Evaluating the cognitive transaction under perioperative conditions, not the computational model in isolation, is both a methodological imperative and a patient safety priority.},
}

Humans
*Artificial Intelligence
*Perioperative Care/methods
*Anesthesia/methods
*Ergonomics

@article {pmid42723656,
year = {2026},
author = {Crowley, LM and Falk, S and Hutchinson, F and Grzywacz, A and , and , and , and , and , and , and , },
title = {The genome sequence of a muscid fly, Lispocephala verna (Fabricius, 1794) (Diptera: Muscidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {394},
pmid = {42723656},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Lispocephala verna (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The assembly contains two haplotypes with total lengths of 987.71 megabases and 934.62 megabases. Most of haplotype 1 (95.8%) is scaffolded into 5 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.34 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid42562267,
year = {2026},
author = {Detroja, R and Chandra, M},
title = {Integrated molecular, epidemiological, and bioinformatics perspectives on the Mpox virus: Implications for surveillance and Global Health preparedness.},
journal = {Journal of microbiological methods},
volume = {249},
number = {},
pages = {107656},
doi = {10.1016/j.mimet.2026.107656},
pmid = {42562267},
issn = {1872-8359},
mesh = {Humans ; Global Health ; Animals ; *Computational Biology/methods ; *Orthopoxvirus/genetics/immunology/classification ; Molecular Epidemiology ; Genome, Viral ; Disease Outbreaks ; Zoonoses/virology/epidemiology ; },
abstract = {Mpox has re-emerged as a significant global zoonotic threat, driven mainly by two large waves the 2022 worldwide Clade IIb outbreak and the 2024 Clade Ib epidemic in Central Africa. This review examines the challenges of interpreting this evolving virus from molecular, epidemiological, and bioinformatics perspectives, with a focus on global health workforce preparedness. Clade IIb largely moved through sexual transmission across countries, but Clade Ib has appeared in a wider population-women, children, and individuals infected through household spread without any sexual contact. Early case series suggest that Clade Ib may cause a more severe disease burden, but more research is needed to directly compare severity and fatality rates with Clade IIb due to the limited number of current studies. The review examines the virus's strategies for evading the host's immune defenses throughout its ∼197 kbp genome, including how it disrupts interferon signaling and creates decoy receptors. This review summarizes the clinical findings of PALM007 and STOMP, noting that neither trial achieved its main efficacy endpoint making routine tecovirimat use less compelling-while leaving open whether it helps particular high-risk groups. A further point is that immunity from the MVA-BN vaccine wanes with time, leading to the growing adoption of booster vaccinations. In conclusion, the review calls for a One Health approach pairing genomic tracking with ecological intelligence and including wastewater surveillance to fill existing gaps in knowledge and enhance the global handling of new orthopoxvirus threats.},
}

Humans
Global Health
Animals
*Computational Biology/methods
*Orthopoxvirus/genetics/immunology/classification
Molecular Epidemiology
Genome, Viral
Disease Outbreaks
Zoonoses/virology/epidemiology

@article {pmid42685092,
year = {2026},
author = {Vetter, D and Ahsan, M and Delicado, D and Neubauer, TA and Wilke, T and Roig, G},
title = {Speeding up taxonomy in the digital age: A deep learning approach for identifying cryptic freshwater snails.},
journal = {PLoS computational biology},
volume = {22},
number = {9},
pages = {e1014733},
pmid = {42685092},
issn = {1553-7358},
mesh = {Animals ; *Deep Learning ; *Snails/classification/anatomy & histology ; Phylogeny ; Fresh Water ; Computational Biology/methods ; Classification Algorithms ; Image Processing, Computer-Assisted/methods ; Species Specificity ; },
abstract = {Cryptic species complexes pose fundamental challenges to biologists, as species exhibit minimal morphological differences that require integrating morphology, genetics, and biogeography for identification. Here, we present a deep learning approach to support species identification in the freshwater snail genus Radomaniola (Hydrobiidae), a morphologically cryptic group from the Balkans. Our approach mirrors the integrative workflow of expert taxonomists by combining shell images, morphometric measurements, and collection‑site metadata, with optional phylogenetic information. Despite being trained on fewer than 700 specimens across 20 visually similar species with strongly imbalanced class sizes, the system achieved high identification performance. Careful control of spurious correlations, such as those arising from site‑specific imaging conditions or overly precise geographic metadata, was essential to ensure that the network learned biologically meaningful features. Across all experiments, integrating multiple data types and jointly optimizing meaningful embeddings and classification consistently improved performance over image‑only and classification‑only baselines. On specimens from collection sites seen during training we achieved a macro-averaged F1 score of 0.93. Even though this dropped as low as 0.14 when evaluating on specimens from previously unsampled localities, it could be rapidly recovered by retraining with 2-3 newly labeled specimens. Additionally, model top-3 accuracy stayed consistently above 80% in all settings. These results show that relatively lightweight deep learning models can provide practical decision support in real taxonomic workflows.},
}

Animals
*Deep Learning
*Snails/classification/anatomy & histology
Phylogeny
Fresh Water
Computational Biology/methods
Classification Algorithms
Image Processing, Computer-Assisted/methods
Species Specificity

@article {pmid42711003,
year = {2026},
author = {Ribeiro, IM and Almeida-Santos, AC and Peixe, L and Novais, C and Freitas, AR},
title = {A One Health approach to Antimicrobial Resistance: Concepts, challenges, and advances in omics.},
journal = {Advances in applied microbiology},
volume = {134},
number = {},
pages = {1-101},
doi = {10.1016/bs.aambs.2026.07.001},
pmid = {42711003},
issn = {0065-2164},
mesh = {Humans ; *One Health ; Animals ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics ; *Bacterial Infections/microbiology/drug therapy ; Multiomics ; Genomics ; },
abstract = {Antimicrobial resistance (AMR) is a global threat driven by the interplay between microbial evolution and human activity. Antimicrobial use in human and veterinary medicine, as well as in agriculture, accelerates the selection and dissemination of resistant bacteria and genes across interconnected human, animal, and environmental reservoirs. These dynamic exchanges render single-sector interventions ineffective. A One Health approach integrating human, animal, and environmental health is therefore essential to understand and mitigate the emergence and spread of AMR. This chapter focuses on bacterial antimicrobial resistance, addressing key concepts, major challenges, and emerging technologies within a One Health framework. Advances in next-generation sequencing and omics technologies have transformed our capacity to resolve AMR at unprecedented scale and resolution. These tools enable the tracking of resistance genes and high-risk clones across ecosystems, uncover transmission pathways, and identify key drivers of dissemination. Such insights support real-time epidemiological surveillance, outbreak detection, and targeted interventions. However, translating these advances into routine practice remains a major challenge, requiring harmonized methodologies, data integration, and cross-sector coordination. Addressing AMR demands sustained collaboration across disciplines and stakeholders, including clinicians, veterinarians, farmers, researchers, policymakers, industry, and the public. And framing AMR as a shared ecological and societal responsibility underscores the urgency of coordinated global action. We call for the urgent integration of One Health principles into surveillance, policy, and innovation to preserve antimicrobial effectiveness and safeguard future health.},
}

Humans
*One Health
Animals
*Drug Resistance, Bacterial
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/genetics
*Bacterial Infections/microbiology/drug therapy
Multiomics
Genomics

@article {pmid42717056,
year = {2026},
author = {Caravagna, G and Graham, TA and Sottoriva, A},
title = {A guide to understanding tumour evolution through the lens of population genetics.},
journal = {Nature reviews. Cancer},
volume = {},
number = {},
pages = {},
pmid = {42717056},
issn = {1474-1768},
abstract = {Every cancer carries the history of its own evolution, hidden in its genome. Modern DNA sequencing can catalogue millions of mutations and profile tumours across space and time, but sequencing alone struggles to answer the questions that matter most: when did key adaptations emerge, how strongly were they selected, why do some tumours relapse whereas others do not, and how will the cancer evolve next? The reason is fundamental: sequencing is a snapshot, whereas evolution is a dynamic process. Bridging this gap requires moving beyond descriptive cancer genomics towards quantitative evolutionary inference. In this Review, we argue that population genetics provides the mathematical framework needed to extract evolutionary dynamics from cancer genomes. We show how models of mutation, selection and drift transform allele frequencies from descriptive measurements into quantitative estimates of clonal fitness and evolutionary timings. We discuss how these principles extend to epigenetic inheritance, plasticity and ecological interactions within the tumour ecosystem, and examine the assumptions and limitations for their application to modern sequencing data. By reframing cancer genomes as quantitative records of evolutionary processes rather than catalogues of mutations, researchers have used population genetics to provide a foundation for understanding - and ultimately predicting - the trajectories of cancer evolution.},
}

@article {pmid42718801,
year = {2026},
author = {Tenennbaum, B and Yakubovich, E and Wang, YW and Meng, G and Moonjely, S and Trail, F and Ben Ari, J and Wang, Z and Dong, C and Townsend, JP and Yarden, O},
title = {Conserved storage-carbohydrate metabolic modules are rewired during germination of Trichoderma asperelloides and other Sordariomycetes.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1930613},
pmid = {42718801},
issn = {2673-6128},
abstract = {Conidial germination requires rapid mobilization and reorganization of storage carbohydrates, yet the network architecture underlying this process remains poorly defined in filamentous fungi. Using quantitative GC-MS/MS profiling, we provide the first quantitative identification of major soluble sugar species across four germination stages of Trichoderma asperelloides T203 and compared them with four representative models in the Sordariomycetes (Metarhizium anisopliae, Cordyceps militaris, Fusarium graminearum, and Neurospora crassa). In T. asperelloides, mannitol was the most prevalent measured sugar in dormant conidia, declined sharply at polarity establishment, and partially recovered at later stages, while trehalose displayed a reciprocal increase and other sugars remained comparatively stable. Comparative analyses revealed distinct species-specific carbon storage strategies: Dormant conidia of T. asperelloides, M. anisopliae, and C. militaris were mannitol-enriched, whereas in N. crassa and F. graminearum glucose was the most abundant; after germination onset, most species shifted toward glucose accumulation, but T. asperelloides uniquely transitioned from mannitol to trehalose dominance before partial re-accumulation of mannitol. Integration of sugar profiles with time-resolved RNA-seq and Bayesian network inference revealed conserved core interactions but also lineage-specific divergences in mannitol/trehalose-associated central-carbon modules that correspond to distinct nutrient and lifestyle strategies during early colonization. A focused analysis in T. asperelloides uncovered extensive stage-dependent transcriptional remodeling of metabolic-process genes and a mannitol-centered module involving mpd1 and mtd1 (encoding mannitol-1-phosphate 5-dehydrogenase and mannitol dehydrogenase, respectively). Antisense-based knockdown of mpd1 strongly reduced its transcript levels and led to stage-dependent upregulation of mtd1. However, these changes left mannitol content, soluble-sugar profiles, germination dynamics, and growth on mannitol essentially unchanged. Together, our comparative metabolic-network analysis shows that conidial mannitol and trehalose metabolism in T. asperelloides is embedded in a flexible, partially redundant central-carbon framework, and establishes this species as a tractable model for systems-level dissection of sugar metabolic regulation during early fungal development and colonization.},
}

@article {pmid42720568,
year = {2026},
author = {Ramirez, MR and Gomez, NJS and Ryan, A and Chipara, O and Heimer, K and Peek-Asa, C and Campo, S and Snirivasan, P and Xiong, BN and Trotter, AG and Paik, A},
title = {Multi-mode design for studying cyber aggression in texts, Facebook and Twitter messages among middle school youth.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwag222},
pmid = {42720568},
issn = {1476-6256},
abstract = {With the explosion of the internet, cyber aggression has become one of the fastest growing forms of interpersonal violence. Methods used to understand aggressive communications content have been limited primarily to surveys. Here, we present multiple methods - panel surveys, electronic capture of social media, and Ecological Momentary Assessments - to characterize both behavioral and perceptual components of cyber aggression in a study of youth from two Iowa middle schools during the 2014-2015 school year. Youth completed a survey, and a sub-sample of smartphone owners installed an electronic application that collected over 150,000 text messages, Twitter posts, and Facebook posts. The sub-sample also participated in ecological momentary assessments to collect self-reported experiences of cyber aggression. To code for aggressive content in this large sample of messages, a case-control sampling strategy was used to identify a series of "case" messages from youth who reported aggression and "control" messages from youth who reported no aggression. We further present recruitment protocols, data management and qualitative coding methods as well as descriptive characteristics of the student cohort and nested sample of messages. These methods have potential use in future studies of "big data" captured from social media.},
}

@article {pmid42623872,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {A synthetic microbiome drives a multi-omics response to remediate 1,4-dithiane-contaminated soil and simultaneously suppresses antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143337},
doi = {10.1016/j.jhazmat.2026.143337},
pmid = {42623872},
issn = {1873-3336},
mesh = {*Soil Pollutants/metabolism ; *Microbiota ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; Multiomics ; Genes, Bacterial ; },
abstract = {1,4-Dithiane, a degradation product of abandoned Japanese chemical weapons, is a persistent organic pollutant with ecological risks. A synthetic microbiome (SM) was constructed through pollution stress screening and ratio optimization, consisting of Shinella sp., Alcaligenes faecalis, Sphingomonas sp., and Stenotrophomonas sp. at an optimal ratio of 1: 1: 2: 2. The SM achieved a 1,4-dithiane degradation rate of 95.2% and reduced intermediate accumulation. Soil remediation experiments showed complete pollutant removal within 60 days, along with improved soil health: reduced bioavailability of heavy metals (Cu, Zn, Cd), increased pH (6.47-6.95), elevated organic matter and enzyme activities, and decreased salinity and redox potential. Integration of ionomics, 16S sequencing, metagenomics, metabolomics, and HT-qPCR revealed that SM colonization reshaped microbial community structure, suppressed ARG-harboring bacteria (e.g., Pseudomonas), and activated core pathways (oxidative phosphorylation and glutathione metabolism), enhancing metabolic activity and oxidative stress tolerance. Consequently, the diversity, abundance, and diffusion potential of soil ARGs and mobile genetic elements were significantly reduced. These findings provide microbial solutions and a theoretical basis for concurrent organic pollution control and soil ecological risk management.},
}

*Soil Pollutants/metabolism
*Microbiota
*Soil Microbiology
*Drug Resistance, Microbial/genetics
Biodegradation, Environmental
Multiomics
Genes, Bacterial

@article {pmid42468162,
year = {2026},
author = {Vasileiadis, S and Valmas, MI and Pitsikoglou, DS and Rodosthenous, J and Omirou, M and Kotsopoulos, TA and Yan, Y and Fu, D and Fotidis, IA},
title = {Up-to-date, and taxonomy-curated mcrA reference databases for methanogen community profiling.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {5},
pages = {126752},
doi = {10.1016/j.syapm.2026.126752},
pmid = {42468162},
issn = {1618-0984},
mesh = {*Archaea/classification/genetics/enzymology ; *Methane/metabolism ; *Oxidoreductases/genetics ; Phylogeny ; *Databases, Genetic ; Biocuration ; },
abstract = {The methyl-coenzyme M reductase subunit alpha gene (mcrA) is an important phylogenetic marker for high throughput ecological profiling of methanogenic archaea, central to industrial biological methane production and greenhouse gas emissions. Yet, dedicated reference databases predate current relevant NCBI sequence accumulation and archaeal taxonomic revision. We present three updated mcrA reference databases: (i) one derived from NCBI-catalogued methanogen genomes (1572 sequences); (ii) a database built by expansion of a previously published reference dataset, leveraging the NCBI nucleotide collection (27,942 sequences); (iii) a curated-taxonomy version of the latter. The updated amplicon databases provide a ∼ 3.5-fold sequence richness expansion, extend genus-level richness from 31 to 83 taxa, more than 4-fold species-level richness, and incorporate novel lineages compared with the previous reference dataset (e.g. Thermoplasmatota-encompassed). All databases were formatted to support analysis with relevant contemporary software pipelines and packages. Overall, the generated databases facilitate a highly improved characterization of methanogen diversity and ecology.},
}

*Archaea/classification/genetics/enzymology
*Methane/metabolism
*Oxidoreductases/genetics
Phylogeny
*Databases, Genetic
Biocuration

@article {pmid42664271,
year = {2026},
author = {Lilja, E and Allen, RJ and Waclaw, B},
title = {Simple birth-death-mutation models predict some-but not all-aspects of the experimental evolution of antibiotic resistance.},
journal = {PLoS computational biology},
volume = {22},
number = {8},
pages = {e1014666},
doi = {10.1371/journal.pcbi.1014666},
pmid = {42664271},
issn = {1553-7358},
mesh = {*Mutation/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Models, Genetic ; Evolution, Molecular ; *Drug Resistance, Microbial/genetics ; Escherichia coli/genetics/drug effects ; Bioreactors/microbiology ; Computational Biology ; },
abstract = {Mathematical modelling of antibiotic resistance plays an important role in understanding the mechanisms of resistance emergence and spreading, testing the feasibility of new treatment protocols, and antimicrobial stewardship. However, many assumptions underlying some of the most commonly used mathematical models have not been rigorously tested experimentally. We verify whether one of these models - a birth-death-mutation process - is able to quantitatively predict the outcome of laboratory experiments. We grow bacteria in a bioreactor in conditions that closely resemble the assumptions of the model, and compare the model predictions with experimental observables such as the probability and time to resistance evolution, mutant number distribution, and the genetic composition of the evolved populations. We show that the model fails to reproduce some aspects of the experiments (failing differently for different antibiotics) but that simple modifications of the model significantly improve its predictive power. These modifications give insight into the population dynamics of resistant mutants for each antibiotic tested, and highlight the importance of quantitative modelling for accurate prediction of antibiotic resistance evolution.},
}

*Mutation/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Models, Genetic
Evolution, Molecular
*Drug Resistance, Microbial/genetics
Escherichia coli/genetics/drug effects
Bioreactors/microbiology
Computational Biology

@article {pmid42705761,
year = {2026},
author = {Shi, H and Shen, Y and Ye, Q and Yu, H and Tian, M and Wang, H and Wei, Y and Yan, S and Chen, Y and Zhang, J and Li, S and Yang, Y and Zhao, J},
title = {Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120404},
doi = {10.1016/j.foodres.2026.120404},
pmid = {42705761},
issn = {1873-7145},
mesh = {*Bacillus/metabolism/genetics ; Multiomics ; *Hot Temperature ; *Food, Fortified/microbiology ; Metabolomics ; Metagenomics ; *Food Microbiology ; },
abstract = {Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P = 0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3 °C; +4.5 °C relative to CK_M), and its group-mean temperature remained ≥ 60 °C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.},
}

*Bacillus/metabolism/genetics
Multiomics
*Hot Temperature
*Food, Fortified/microbiology
Metabolomics
Metagenomics
*Food Microbiology

@article {pmid42706571,
year = {2026},
author = {Pieroni, A and Hazarika, A and Alrhmoun, M and Yebouk, C and Dina, E and Manduzai, AK and Gillani, SW and Rexhepi, B and Ullah, I and Ali, S and Khadka, D and Khan, SM and Abbasi, AM and Suriano, E and Mendoza, JN and Soukand, R and Kalle, R},
title = {From the margins to the core: village and community scientists should increasingly shape the future of ethnobiology and ethnoecology.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {22},
number = {1},
pages = {},
pmid = {42706571},
issn = {1746-4269},
mesh = {Humans ; *Ecology/trends ; *Ethnology/trends ; Rural Population ; Knowledge ; },
abstract = {Ethnobiology was not only created as a field to understand the relationship between humans and their environments; it emerged from direct engagement with rural and Indigenous communities. Yet the great paradox is that, despite its field-based origins, the discipline continues to be reproduced within urban academic spaces that often exclude those who are assumed to be at the very heart of knowledge production. In this editorial, we do not simply propose the "inclusion" of rural or Indigenous communities. Instead, we call for a radical repositioning of the knowledge itself: Who can be considered a "scientist"? And who holds the authority to define scientific knowledge? We reject the assumption that urban academic affiliation or formal credentials are the sole basis for scientific credibility, and instead propose a different standard: knowledge should be assessed by its depth, explanatory power, and integrity when co-produced in genuine partnership with living communities. Drawing on our own experiences as researchers raised in rural villages, peripheral regions, and migrant/refugees' communities, we argue that local and Indigenous ecological knowledge is not a "raw material" for scientific research, but a form of scientific thinking in its own right with its own logic, observations, and rigour, and its own way of assessing, adapting and enacting this knowledge. We therefore call for a further step ahead in the classical structure of ethnobiology: not merely the inclusion of communities in research stages, but the recognition of some of their scholars as the core producers of scientific knowledge, from the formulation of research questions to the interpretation, dissemination and enactment of results. This transformation of the locus aims not only to improve ethnobiology as a field but also to redefine it. Without this redefinition, science will remain detached from the realities it claims to understand. With it, ethnobiology can become a more honest, more courageous discipline, better equipped to confront biodiversity loss, climate change, and the reconfiguration of more-than-human-nature relationships.},
}

Humans
*Ecology/trends
*Ethnology/trends
Rural Population
Knowledge

@article {pmid42708036,
year = {2026},
author = {Manikowska-Ślepowrońska, B and Cieślińska, K and Ślepowroński, K and Poślińska, E and Siekiera, J and Goc, M and Iliszko, LM and Jakubas, D},
title = {Individual year-round movement patterns of the GPS-tracked Grey Herons (Ardea cinerea) in Central Europe: a multi-year case study.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21659},
pmid = {42708036},
issn = {2167-8359},
mesh = {*Animal Migration/physiology ; Animals ; *Geographic Information Systems ; Seasons ; *Birds/physiology ; Germany ; Poland ; Europe ; },
abstract = {BACKGROUND: The year-round migratory behaviour of Grey Herons (Ardea cinerea) breeding in Central Europe is recognized; however, individual consistency in their movement patterns remains poorly known. In this study, we present movements of three adult Grey Herons breeding in Northern Poland and Eastern German global positioning system (GPS)-tracked between 2012 and 2020.

METHODS: We analyzed annual movement trajectories, focusing on migration distances, fidelity to breeding and wintering grounds, and the use of stop-over sites. We performed an Analysis of Variance from Summary Data (ANOVA) on summary data to compare migratory parameters across different Eurasian populations and age groups.

RESULTS: We identified four main phases in the annual cycle of all studied individuals: breeding, wintering, spring and autumn migration. Our data reveal high inter-individual variation in migratory strategies. Although two individuals changed their wintering sites from year to year, all studied ones exhibited strict fidelity to the same breeding grounds across consecutive seasons. Migration distances ranged from 175 to 1,758 km; notably, the individual breeding in Eastern Germany covered the shortest distance (mean ± SD: 221 ± 51.8 km). We observed substantial inter-individual variation in winter site fidelity, migration distances, and stop-over numbers within this Central European Grey Heron population. The herons selected the shortest migration paths during spring, but not during autumn. While the broad migratory characteristics-specifically the number of stop-overs (3.0 ± 2.8), migration distance (1,220 ± 580.4 km), and migration duration (9 ± 9 days)-closely match findings from other populations, the tracked herons in our study made fewer stop-overs during autumn migration compared to the values reported in the literature.

CONCLUSIONS: We observed inter-individual variations in the annual movement patterns of the Grey Heron, encompassing the timing of the four annual cycle phases, the range of distances covered annually and the birds' fidelity to areas used as breeding or wintering grounds. Our report provides the first long-term, high-resolution insights into the year-round movements of GPS-tracked Grey Herons from Central Europe, emphasizing that specific individuals employ diverse and flexible migratory strategies, even within the same breeding region.},
}

*Animal Migration/physiology
Animals
*Geographic Information Systems
Seasons
*Birds/physiology
Germany
Poland
Europe

@article {pmid42709282,
year = {2026},
author = {Kharmawphlang, IM and Gómez-Brandón, M and Hussain, N},
title = {Decoding next-generation heavy metal bioremediation via species-specific Earthworm and its gut microbiome interactions: insights from molecular responses, multi-omics, synthetic biology, and artificial intelligence.},
journal = {Biodegradation},
volume = {37},
number = {5},
pages = {},
pmid = {42709282},
issn = {1572-9729},
mesh = {Animals ; *Oligochaeta/metabolism/microbiology ; Biodegradation, Environmental ; Multiomics ; *Metals, Heavy/metabolism ; *Gastrointestinal Microbiome ; Synthetic Biology ; Artificial Intelligence ; *Soil Pollutants/metabolism ; },
abstract = {Heavy metal (HM) contamination represents a persistent global threat, demanding bioremediation strategies that are both mechanistically robust and ecologically sustainable. This review provides a next-generation perspective on vermiremediation by integrating species-level physiology, gut microbiome functionality, molecular detoxification pathways, synthetic biology innovations, multi-omics insights, and artificial intelligence (AI)-driven modeling into a unified framework. A central novelty of this work lies in the detailed elucidation of earthworm-microbe consortia and their synergistic contributions to metal sequestration, transformation, and detoxification-moving beyond traditional organism-centric views toward eco-engineered host-symbiont systems. We synthesize species-specific bioaccumulation patterns, toxicological responses, and detoxification mechanisms, supported by enrichment kinetic models. At the molecular scale, we highlight antioxidant defense pathways involving catalase, glutathione-S-transferase, and superoxide dismutase, alongside oxidative stress signaling, macromolecular damage, and thresholds that differentiate adaptive resilience from system failure. Advancements in synthetic biology includes gene editing, pathway reconstruction, and designer symbiotic microbes which are examined as emerging tools to enhance gut microbial functionality and engineer targeted metal-binding pathways. Multi-omics approaches provide a systems-level view of detoxification networks, revealing previously uncharacterized genes, enzymes, and metabolic signatures associated with HM tolerance and early biomarkers of sub-lethal stress. The incorporation of AI-based models introduces a data-driven dimension, enabling accurate prediction of remediation outcomes and optimization of vermiremediation strategies. Overall, this review advances vermiremediation from an empirical practice to a programmable, systems-biotechnology platform for sustainable HM bioremediation.},
}

Animals
*Oligochaeta/metabolism/microbiology
Biodegradation, Environmental
Multiomics
*Metals, Heavy/metabolism
*Gastrointestinal Microbiome
Synthetic Biology
Artificial Intelligence
*Soil Pollutants/metabolism

@article {pmid42709709,
year = {2026},
author = {Yao, T and Liu, Q and Zeng, H and Tang, J},
title = {Ecological sensitivity and sustainable spatial planning in a highly urbanized plain: An AHP-GIS and geodetector approach in the Yangtze River Delta Plain.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357598},
doi = {10.1371/journal.pone.0357598},
pmid = {42709709},
issn = {1932-6203},
mesh = {*Rivers ; *Urbanization ; *Geographic Information Systems ; China ; *Conservation of Natural Resources/methods ; *Ecosystem ; Humans ; Environmental Monitoring/methods ; },
abstract = {Rapid urbanization in plains exacerbates ecological pressures, while most ecological sensitivity (ES) research focuses on mountains, offering limited guidance for highly urbanized plains. This study assesses ES in the Yangtze River Delta Ecological Green Integrated Development Demonstration Zone (YRD EGI-DDZ) and its planning implications. Ten indicators, covering four criteria, geography, hydrology, natural resource, and human interference were integrated using Analytic Hierarchy Process (AHP) with Geographic Information System (GIS). Geodetector quantified drivers of ES spatial variation, and 2018-2020 land use data revealed recent development and fragmentation. Results show over 70% of the area under medium to extremely highly sensitivity, with high or extreme high zones clustered along Dianshan Lake, Yuandang, East Taihu, and contiguous ecological land. Low sensitivity mainly corresponds to urban land. Key drivers include land use, nighttime lights, population density, and water proximity, while elevation and slope contribute marginally. New construction land expands mainly along urban fringes and transport corridors, inserting low sensitivity strips into medium sensitivity belts and fragmenting high sensitivity cores. These findings inform a sensitivity-based zoning and corridor control framework, refining existing plans and supporting sustainable spatial development in similar plains.},
}

*Rivers
*Urbanization
*Geographic Information Systems
China
*Conservation of Natural Resources/methods
*Ecosystem
Humans
Environmental Monitoring/methods

@article {pmid42710055,
year = {2026},
author = {Roussel, T and Benhaim, E and Perrard, L and Merat, B and Vally, S and Girerd, R and Deharo, P and Desroche, LM and , },
title = {Mobile-First Web Access and Captioned Video in Francophone Cardiology Education: Multicountry Ecological Learning Analytics Study.},
journal = {JMIR mHealth and uHealth},
volume = {14},
number = {},
pages = {e90345},
doi = {10.2196/90345},
pmid = {42710055},
issn = {2291-5222},
mesh = {*Cardiology/education ; Humans ; Digital Health ; Digital Media ; Telemedicine ; Internet ; },
abstract = {BACKGROUND: Mobile health (mHealth) and online video are increasingly central to cardiology education and point-of-care decision support. However, little is known about how simple design choices, such as mobile-first web layouts and captioned videos, translate into real-world practice across countries with different income levels.

OBJECTIVE: This exploratory ecological study used routinely collected, cross-platform learning analytics from a francophone cardiology mHealth initiative to (1) describe how mobile web access and caption-enabled YouTube viewing varied across World Bank income groups and (2) examine whether greater reliance on mobile access was associated with poorer engagement on the website or on YouTube.

METHODS: We analyzed country-level analytics from the École Numérique de Cardiologie (ENC; Saint-Denis) mobile-optimized website and its companion YouTube channel (YouTube, LLC [Google LLC]) over a two-year window (September 2023 to September 2025). Countries were grouped as high-, middle-, or low-income (World Bank, three-level classification). Country-level metrics included mobile device session share; website bounce rate; time on page; and YouTube average view duration, audience retention, and intentional views. Caption-related and demographic YouTube metrics were available only as income-group aggregates and were therefore reported descriptively as between-group contrasts; country-level inferential analyses were restricted to country-level variables. Reporting followed the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) checklist.

RESULTS: Thirty-four countries contributed data: 13/34 (38%) high-income, 14/34 (41%) middle-income, and 7/34 (21%) low-income. Caption-enabled watch time was 18.8% in high-income countries (HICs), compared with 38.7% in middle-income countries (MICs) and 60.9% in low-income countries (LICs), representing a caption equity gap (CEG) of 42.1% between low- and high-income settings. Median website mobile share rose with decreasing income (36.5%, 63.3%, and 81.4%, respectively; Jonckheere-Terpstra P=.01). Across income groups, higher caption-enabled watch time coincided with a higher share of intentional views. At the country level, greater reliance on mobile access was not associated with higher bounce rate or shorter time on page, and Spearman correlations between mobile share and YouTube engagement metrics were small and nonsignificant (all |ρ|≤0.28; all P≥.18).

CONCLUSIONS: In this multicountry, francophone, mHealth learning analytics case study, mobile web access and captioned video were used most intensively in lower-income settings, and greater reliance on mobile access was not associated with measurable penalties in basic engagement metrics. These findings support treating mobile-optimized design and systematic captioning as core, low-cost, access-supporting features for equitable digital cardiology education. They also suggest that routinely collected platform indicators can serve as practical equity-monitoring signals for global mHealth initiatives, while underscoring that engagement metrics are not direct measures of learning or behavior change.},
}

*Cardiology/education
Humans
Digital Health
Digital Media
Telemedicine
Internet

@article {pmid40965469,
year = {2026},
author = {León-Domínguez, U},
title = {Towards an artificial intelligence clinical decision-support system based on immersive virtual reality for neurocognitive assessment.},
journal = {Ergonomics},
volume = {69},
number = {10},
pages = {1999-2016},
doi = {10.1080/00140139.2025.2560581},
pmid = {40965469},
issn = {1366-5847},
mesh = {Humans ; *Artificial Intelligence ; *Virtual Reality ; *Decision Support Systems, Clinical ; Algorithms ; Brain Injuries/rehabilitation ; Neuropsychological Tests ; },
abstract = {Recent cost reductions and technological advances have enabled the use of Immersive Virtual Reality (IVR) to assess performance tasks in high-fidelity 3D environments. This review outlines the current state of its application in neurocognitive assessment and examines the integration of Artificial Intelligence algorithms and biomedical sensors to standardise laboratory testing. An AI-driven clinical decision-support system (aiCDSS-IVR) is introduced as a modular framework in which immersive virtual reality, artificial intelligence, and biometric sensors are integrated to construct a digital twin that combines behavioural and physiological data for clinical decision support. This technological ecosystem could facilitate a more personalised approach to the assessment and rehabilitation of brain injuries.},
}

Humans
*Artificial Intelligence
*Virtual Reality
*Decision Support Systems, Clinical
Algorithms
Brain Injuries/rehabilitation
Neuropsychological Tests

@article {pmid42380415,
year = {2026},
author = {Atsumi, T and Hokazono, S and Kikuchi, K and Fujii, T and Takejima, K and Wada, M and Miyake, K and Yahagi, T and Nakamura, K and Takano, A and Minami, M},
title = {Supporting exploration and sustainable utilization of the medicinal plant Uncaria rhynchophylla in Kyushu, Japan through potential distribution modeling using MaxEnt and GIS.},
journal = {Journal of natural medicines},
volume = {80},
number = {5},
pages = {1417-1432},
pmid = {42380415},
issn = {1861-0293},
support = {JP24ak0101159//Japan Agency for Medical Research and Development/ ; IDEAS202541//Collaboration Research Program of IDEAS, Chubu University/ ; },
mesh = {*Uncaria ; Japan ; *Plants, Medicinal ; Geographic Information Systems ; Seasons ; Temperature ; Conservation of Natural Resources ; Medicine, Kampo ; },
abstract = {Sustainable utilization of wild medicinal plant resources requires reproducible approaches for locating and managing natural populations. In Japan, exploration and resource planning for wild medicinal plants rely heavily on expert knowledge, and reproducible approaches remain scarce. We developed a species distribution model (SDM) for Uncaria rhynchophylla (Rubiaceae), a botanical source of the crude drug Uncaria Hook used in Kampo medicine, to estimate its potential distribution and identify major environmental correlates in the Kyushu region, southern Japan. Using 122 occurrence records collected from 2021 to 2023 and nine environmental predictors, MaxEnt models were trained with background points and bootstrap replicates. Because mean minimum winter temperature in January and mean maximum summer temperature in August were highly correlated, three candidate models were compared using the small-sample corrected Akaike information criterion (AICc), test omission rates, and test area under the receiver operating characteristic curve (AUC). The model including winter minimum temperature was best supported (test AUC = 0.82; test omission rate = 24%), whereas adding summer maximum temperature provided limited improvement (ΔAICc = + 75.75). Variable importance and jackknife tests ranked winter minimum temperature as the most influential predictor, followed by slope angle and distance to the nearest rivers. The suitable area, defined using the maximum training sensitivity plus specificity (MTSS) threshold, covered 10,595 km[2] (25.9% of the terrestrial area) and formed continuous zones across hilly and low-montane regions. Targeted surveys in high-suitability areas confirmed three additional sites in the Kirishima Mountains. Overall, integrating SDM and geographic information systems provides a reproducible, data-driven, decision-support framework for the exploration, planning of sustainable harvesting, and resource management of wild medicinal plants.},
}

*Uncaria
Japan
*Plants, Medicinal
Geographic Information Systems
Seasons
Temperature
Conservation of Natural Resources
Medicine, Kampo

@article {pmid42702138,
year = {2026},
author = {Zheng, H and Huang, J and Chen, H and Xiao, Z and Chen, N and Ding, X},
title = {Long-short-term decoupled residual learning for high-resolution spatio-temporal air quality inference.},
journal = {Neural networks : the official journal of the International Neural Network Society},
volume = {205},
number = {Pt C},
pages = {109575},
doi = {10.1016/j.neunet.2026.109575},
pmid = {42702138},
issn = {1879-2782},
abstract = {Accurate high-resolution spatio-temporal air quality inference based on sparse monitoring stations is essential for environmental governance and public health. However, prevailing deep learning approaches often treat inference as direct regression on observed air quality concentrations, neglecting the distinct effects of a long-term static baseline and short-term dynamic perturbations on the inference. This limits the model's generalization ability and may cause spatial bias in the inference. In this paper, we propose a novel Spatio-Temporal Air Quality Inference Network (SAQIN) model, which provides an explicit decomposition of the static and dynamic effects in the inference. The static branch integrates high-resolution semantic segmentation, global context from remote sensing, population density, and elevation to construct a high-fidelity environmental prior. The dynamic branch employs multi-head self-attention mechanism to jointly encode geographic relationships and inter-pollutant chemical coupling effects. We further develop a residual learning module to model the inference process as a residual correction anchored to multiple reference stations and aggregates predictions through stepwise multi-station fusion with distance-weighted averaging, which successfully eliminates the Voronoi-partition-induced discontinuities and yielding a globally smooth physically plausible air quality inference field. SAQIN has been shown to demonstrate superior accuracy and strong zero-shot cross-domain generalisation when evaluated on large-scale real-world datasets, thus outperforming state-of-the-art methods across a range of criteria pollutants.},
}

@article {pmid42704537,
year = {2026},
author = {de Freitas Germano, J and Leite, G and Pimentel, M},
title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42704537},
issn = {1534-312X},
mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; },
abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.

RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.},
}

Humans
Multiomics
*Intestine, Small/microbiology
Proteomics/methods
*Blind Loop Syndrome/diagnosis/microbiology
Breath Tests/methods
Gastrointestinal Microbiome
Metagenomics/methods
Syndrome

@article {pmid42705247,
year = {2026},
author = {, },
title = {Global, regional, and national prevalence of second-hand smoke and attributable disease burden in 204 countries and territories, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.},
journal = {The Lancet. Public health},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2468-2667(26)00168-4},
pmid = {42705247},
issn = {2468-2667},
abstract = {BACKGROUND: Second-hand smoke (SHS) exposure remains a major source of morbidity and mortality among non-smokers. This study presents the first dedicated Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) publication to systematically quantify SHS prevalence and evaluate its effect as a global risk factor across a broader range of outcomes.

METHODS: Using the GBD 2023 comparative risk assessment framework, we estimated SHS exposure prevalence and attributable disease burden across 204 countries and territories from 1990 to 2023, stratified by age and sex. Exposure estimates were derived by synthesising population-based surveys and household composition data through spatiotemporal Gaussian process regression. Relative risks for nine health outcomes, now including asthma, were estimated using the Burden of Proof methodology, and applied to calculate attributable deaths and disability-adjusted life-years (DALYs).

FINDINGS: In 2023, an estimated 2·71 billion (95% UI 2·44-3·02) people worldwide were exposed to SHS, including 767 million (687-858) children aged 0-14 years. Age-standardised prevalence was highest in southeast Asia, east Asia, and Oceania (48·4% [44·0-53·4]), with female individuals in some countries experiencing nearly 1·8 times the exposure prevalence of male individuals. Despite a 22·2% (10·6-32·4) decline in global age-standardised prevalence since 1990, this progress has not been sufficient to reduce the absolute number of exposed individuals, which has remained stable globally and has risen sharply in sub-Saharan Africa (98·5% [62·0-144·4] increase) and North Africa and the Middle East (72·1% [47·8-101·8] increase). In 2023, SHS exposure accounted for 1·66 million (1·33-2·07) deaths and 44·8 million (35·8-54·3) DALYs globally. Ischaemic heart disease was the leading contributor to SHS-attributable DALYs (12·0 million [9·31-15·2]) overall, while lower respiratory infections predominated among children (5·16 million [3·48-7·12]).

INTERPRETATION: We estimated that SHS remains a substantial driver of global health loss, particularly through cardiovascular and paediatric respiratory diseases. Persistent geographical disparities and growing absolute numbers of exposed individuals in several regions underscore the urgent need for accelerated implementation and enforcement of comprehensive tobacco control measures, particularly to protect women and children in both public and domestic environments.

FUNDING: Bloomberg Philanthropies and the Gates Foundation.},
}

@article {pmid42636663,
year = {2026},
author = {Wang, D and Huang, Z and Sun, S and Song, W and Li, Y and Sun, K and Li, Z and Feng, J},
title = {Multi-omics reveal microbial functional traits and antifungal metabolites associated with lower Pseudogymnoascus destructans loads in bat cave soils.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128696},
doi = {10.1016/j.micres.2026.128696},
pmid = {42636663},
issn = {1618-0623},
mesh = {Animals ; Multiomics ; *Soil Microbiology ; *Ascomycota/drug effects/isolation & purification ; *Caves/microbiology ; *Chiroptera/microbiology ; Metabolomics ; *Antifungal Agents/pharmacology/metabolism ; China ; Microbiota/genetics ; Metagenomics ; Soil/chemistry ; },
abstract = {White-nose syndrome, caused by Pseudogymnoascus destructans (Pd), is a major fungal disease threatening hibernating bats. Cave soils can serve as environmental reservoirs for Pd, yet the microbial and biochemical mechanisms underlying naturally low Pd burdens in some cave environments remain poorly understood. Here, we integrated soil microbiome profiling, metagenomics, metabolomics, multi-omics network analysis, and in vitro validation to investigate the ecological and functional basis of differential Pd loads in hibernating bat caves in Northeast China. The three caves shared cold, humid, and weakly acidic microenvironments, but differed significantly in electrical conductivity, soil water content, nutrient availability, and extracellular enzyme activities. Soil microbial communities showed significant inter-cave variation in composition, diversity, and niche breadth, with stochastic processes contributing substantially to community assembly. Environmental variables, particularly pH and Pd load, were important predictors of microbial community structure. Functional analyses revealed that the low-Pd Gezi Cave was enriched in genes associated with organic carbon degradation, nitrogen input and retention, and secondary metabolism. Metabolomic profiling further identified cave-specific metabolite signatures, among which Biochanin A, 4-Hydroxybenzaldehyde, Vanillin, and Arachidonic acid were negatively correlated with Pd loads. Integrated pathway and network analyses showed that differential genes and metabolites jointly mapped to secondary metabolite biosynthesis, aminobenzoate degradation, and flavonoid degradation pathways, forming a microbe-metabolite-functional gene coupling network involving key taxa such as Rhodococcus, Pseudorhodoplanes, and Rhodoplanes. In vitro assays confirmed that 4-Hydroxybenzaldehyde, Coumarin, and Vanillin inhibited Pd growth. Structural equation modelling further indicated that environmental heterogeneity was associated with variation in Pd loads through microbial functional attributes and metabolite profiles. These findings suggest that naturally low-Pd cave soils are associated with coordinated environmental filtering, microbial functional specialization, and antifungal metabolite production, providing mechanistic insight into microbial and biochemical constraints on Pd persistence in cave reservoirs.},
}

Animals
Multiomics
*Soil Microbiology
*Ascomycota/drug effects/isolation & purification
*Caves/microbiology
*Chiroptera/microbiology
Metabolomics
*Antifungal Agents/pharmacology/metabolism
China
Microbiota/genetics
Metagenomics
Soil/chemistry

@article {pmid42699236,
year = {2026},
author = {Zhang, S and Si, Z and Yang, N and Chen, X},
title = {Exposure-aware multi-omics and artificial intelligence for biomarker discovery and precision prevention in diffuse glioma.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1874861},
pmid = {42699236},
issn = {1664-3224},
mesh = {Humans ; *Glioma/etiology/prevention & control/diagnosis/genetics/metabolism ; Multiomics ; *Biomarkers, Tumor ; *Brain Neoplasms/prevention & control/etiology/diagnosis/genetics ; *Artificial Intelligence ; Precision Medicine/methods ; *Environmental Exposure/adverse effects ; Animals ; Metabolomics ; },
abstract = {Diffuse gliomas are now diagnosed and studied through integrated molecular classification, radiomics, single-cell biology, spatial profiling, proteogenomics, metabolomics, and artificial intelligence. Yet many precision-medicine models still begin at diagnosis and emphasize tumor-intrinsic molecular features, leaving environmental, occupational, lifestyle, microbiome, metabolic, immune, and treatment-related exposures at the margins. This review develops an exposome-informed view of diffuse glioma biomarker discovery. Biomarker discovery is separated from clinical prevention: current evidence does not justify population-level glioma screening based on environmental exposures, but it does support systematic integration of external exposures and internal exposure-related molecular states with tumor and host biology. The synthesis focuses on five linked dimensions: the limits of current artificial intelligence and multi-omics models when exposure biology is excluded; glioma-relevant exposure domains stratified by evidence strength and measurability; genotoxic, epigenetic, vascular, neuroimmune, and immunometabolic conduits through which exposures may shape tumor ecology; computational strategies for temporally anchored integration of geospatial, occupational, clinical, liquid-biopsy, imaging, tumor-omic, single-cell, spatial, microbiome, and metabolomic data; and clinically realistic applications in high-risk surveillance, recurrence-aware monitoring, treatment-toxicity reduction, and biomarker-guided trial stratification. By aligning exposome science with systems neuro-oncology, the review outlines a translational agenda for exposure-aware glioma biomarkers while maintaining a conservative boundary between established evidence, mechanistic hypotheses, and future clinical implementation.},
}

Humans
*Glioma/etiology/prevention & control/diagnosis/genetics/metabolism
Multiomics
*Biomarkers, Tumor
*Brain Neoplasms/prevention & control/etiology/diagnosis/genetics
*Artificial Intelligence
Precision Medicine/methods
*Environmental Exposure/adverse effects
Animals
Metabolomics

@article {pmid42575387,
year = {2027},
author = {El Alaoui, O and El Khiat, A and Hakem, A and Ouzyou, B and El Omari, H and Mohammed, B and Radi, FZ and Rhazi, O and En-Niari, I and Mahfoud, S and Taam, A and Talbi, FZ},
title = {Spatiotemporal dynamics and ecological determinants of cutaneous Leishmaniasis in Errachidia Province, southeastern Morocco: A 16-year municipality-level analysis with SARIMA forecasting.},
journal = {Parasitology international},
volume = {116},
number = {},
pages = {103363},
doi = {10.1016/j.parint.2026.103363},
pmid = {42575387},
issn = {1873-0329},
mesh = {Morocco/epidemiology ; *Leishmaniasis, Cutaneous/epidemiology ; Incidence ; Animals ; Humans ; Spatio-Temporal Analysis ; Geographic Information Systems ; Female ; Seasons ; Socioeconomic Factors ; *Phlebotomus/parasitology ; Male ; Insect Vectors/parasitology ; Forecasting ; Cities/epidemiology ; },
abstract = {Leishmaniasis is a vector-borne parasitic disease transmitted by female sandflies of the genus Phlebotomus and affects approximately 1.2 million people annually in more than 90 countries worldwide. Morocco remains one of the most affected countries in North Africa, where the disease continues to represent a major public health concern. This study aimed to analyze the spatial and temporal trends of leishmaniasis incidence across all municipalities of Errachidia Province between 2010 and 2025 and to assess the influence of ecological, demographic, and socio-economic factors on its distribution. Also, the study aimed to predict the monthly CL cases using the Seasonal Autoregressive Integrated Moving Average (SARIMA) model. Epidemiological data on parasitologically confirmed cases obtained from the Errachidia Provincial Health Delegation were processed using geographic information system (GIS) tools and statistical methods to explore spatial patterns and correlations with environmental and socio-demographic variables. The models are trained and evaluated using monthly CL cases collected from 2010 to 2025, with the optimal model selected based on Akaike Information Criterion (AIC). During 16-years study period, 7034 cases were recorded in Errachidia Province, with the highest incidence reported in 2010 (860 cases per 100,000 inhabitants). Overall, the incidence showed marked temporal fluctuations but demonstrated a general decreasing trend over the study period. A pronounced spatial heterogeneity was observed between rural municipalities (Sid Ali, Melaab, and Ferkla) and urban municipalities (Errachidia, Arfoud, and Goulmima) (p < 0.01). The disease was slightly more frequent in females (54.41%) than in males (45.59%), and a significant difference was observed among age groups (p = 0.019), with the 0-9 and 10-19-year groups being the most affected. Seasonal analysis revealed a peak incidence during winter. In addition, higher incidence was associated with low- to medium-altitude municipalities, while no significant association was observed with poverty or vulnerability indices. The SARIMA (0,0,1)12 model demonstrated the best predictive performance. These findings highlight the heterogeneity and ecological determinants of leishmaniasis in southeastern Morocco and may support targeted surveillance and control strategies in high-risk areas.},
}

Morocco/epidemiology
*Leishmaniasis, Cutaneous/epidemiology
Incidence
Animals
Humans
Spatio-Temporal Analysis
Geographic Information Systems
Female
Seasons
Socioeconomic Factors
*Phlebotomus/parasitology
Male
Insect Vectors/parasitology
Forecasting
Cities/epidemiology

@article {pmid42518220,
year = {2026},
author = {Di, D and Wang, S and Qiu, W and Gai, X and Xiao, J and Wang, S and Zhuo, R and Chen, G},
title = {Multi-omics analysis reveals the mechanisms of biochar-mediated cadmium transport in Salix: insights into rhizosphere phosphorus-iron coupling and transporter expression.},
journal = {Tree physiology},
volume = {46},
number = {9},
pages = {},
doi = {10.1093/treephys/tpag104},
pmid = {42518220},
issn = {1758-4469},
mesh = {*Cadmium/metabolism ; *Salix/metabolism/genetics ; Rhizosphere ; *Iron/metabolism ; *Phosphorus/metabolism ; *Charcoal ; Biological Transport ; Multiomics ; Biodegradation, Environmental ; Plant Roots/metabolism ; },
abstract = {Biochar addition promotes cadmium (Cd) phytoremediation of woody plants, especially phosphorus (P)-modified biochar. However, the underlying mechanism of the uptake and transport of Cd transport mediated by biochar remains unclear. Here, we integrated physiological, metagenomics, transcriptomics and in situ laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging analysis to investigate how bamboo biochar (BBC) and phytic acid-modified biochar (PABC) impact Cd accumulation and transport in Salix J1010 through root-soil interface. Our results showed that PABC significantly increased Cd translocation from roots to aboveground by 77.9% and total Cd accumulation in plants by 203%, respectively. Iron plaque emerged as a key factor, with PABC-mediated inhibition of iron plaque (-44.6%) accelerating Cd uptake. This iron plaque decrease is closely accompanied by the decreased soil redox potential (Eh), enriched resin-P and inorganic P fractions, and potential coupling of P mineralization and Fe(III)-reducing processes in the rhizosphere soil. Transcriptomics analysis further revealed that PABC influenced root metal transporters expression, downregulating vacuolar sequestration-related ABC, CAX, metal tolerance protein gene families, while upregulating most ZIP, HMA and YSL genes families involved in xylem loading. LA-ICP-MS imaging corroborated the enhanced Cd transport in xylem tissue. PABC enhanced leaf cell-wall Cd binding and antioxidant defenses, thereby promoting Cd detoxification and accumulation. Collectively, the enhanced phytoremediation capacity of willow was driven by coordinating trade-offs across multiple levels, including the rhizosphere, subcellular scales and whole plant. These results provide a mechanistic basis for biochar-assisted phytoremediation strategies in Cd-contaminated soils.},
}

*Cadmium/metabolism
*Salix/metabolism/genetics
Rhizosphere
*Iron/metabolism
*Phosphorus/metabolism
*Charcoal
Biological Transport
Multiomics
Biodegradation, Environmental
Plant Roots/metabolism

@article {pmid42689779,
year = {2026},
author = {Short, S and Green Etxabe, A and Swart, E and Rivetti, C and Campos, B and Krishnan, R and Kille, P and Spurgeon, DJ},
title = {Exploiting Omic Data to Advance Predictive Ecotoxicology.},
journal = {Environmental science & technology},
volume = {60},
number = {34},
pages = {23642-23660},
doi = {10.1021/acs.est.6c01198},
pmid = {42689779},
issn = {1520-5851},
support = {101057014//European Partnership for the Assessment of Risks from Chemicals (PARC) under the EU Horizon Europe Research and Innovation Programme/ ; BB/X511468/1//Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation (UKRI)/ ; NE/S00224/2//Natural Environment Research Council (NERC)/ ; },
mesh = {*Ecotoxicology ; Genomics ; Animals ; Risk Assessment ; Computational Biology ; },
abstract = {Predicting species-specific chemical sensitivity using in silico approaches has the potential to transform environmental risk assessment, conservation, and biomonitoring, while reducing, and ultimately replacing, animal testing. Genomic and transcriptomic data capture extensive sensitivity-relevant variation, including differences in molecular targets, xenobiotic metabolism, and damage mitigation pathways. Large-scale sequencing initiatives therefore offer an unprecedented opportunity to address ecotoxicology's "too many species" problem. Although existing omic-based predictive tools provide proof of concept, they have so far been applied to a narrow set of relatively straightforward prediction scenarios. To achieve broader applicability, current and future tools must be firmly grounded in the diverse molecular mechanisms underlying differential chemical responses. Here, we critically evaluate the emerging field of predicting species sensitivity using molecular variation inferred from omic data. We analyze the strengths and limitations of current omic-based approaches and identify major sequence and ecotoxicological data gaps, as well as critical bioinformatic challenges. We then review the current knowledge of how molecular biology underlies differential chemical sensitivity, outlining research paths to allow the next generation of sensitivity prediction tools to exploit ever expanding omic data.},
}

*Ecotoxicology
Genomics
Animals
Risk Assessment
Computational Biology

@article {pmid42690503,
year = {2026},
author = {Indurthi, S and Kaur, G and Dutta, R and Madhu, S and Chodasani, B and Yadav, A and Singh, M and Meena, TK and Singh, G},
title = {Integrating genomics, multi-omics, CRISPR and speed breeding for stress-resilient vegetable legume improvement.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42690503},
issn = {1438-7948},
mesh = {*Fabaceae/genetics/metabolism ; *Plant Breeding ; Multiomics ; *Stress, Physiological/genetics ; Genomics ; Quantitative Trait Loci ; Genome, Plant ; CRISPR-Cas Systems ; Gene Editing ; },
abstract = {Vegetable legumes are nutritionally and ecologically important crops. However, their genetic improvement has not kept pace with the increasing challenges posed by climate change due to the polygenic nature of stress tolerance, narrow genetic diversity, and the persistent gap between molecular discoveries and field-level cultivar development. Although recent reviews have examined individual genomic tools or specific stress responses, a comprehensive synthesis integrating genomics-assisted breeding, multi-omics technologies, genome editing, and speed breeding within a unified crop improvement framework has been lacking. This review addresses that gap by critically evaluating how these complementary approaches can accelerate the development of stress-resilient vegetable legumes, including pea, common bean, cowpea, faba bean, cluster bean, yard-long bean, and hyacinth bean. This review synthesizes advances in QTL mapping, genome-wide association studies, transcriptomics, metabolomics, and CRISPR-based functional genomics that have identified key regulators and pathways underlying resistance to major biotic and abiotic stresses. Rather than considering these technologies independently, the review emphasizes their convergence into a systems-level breeding framework integrating genomic discovery, functional validation, predictive breeding, and accelerated generation advancement to improve breeding efficiency. Speed breeding, enabling up to seven to eight generations annually under optimized controlled-environment experimental conditions in cowpea, is discussed as a complementary strategy with genomic selection and genome editing. The review further identifies major translational bottlenecks, including transformation recalcitrance, limited genomic resources for underutilized vegetable legumes, inadequate multi-environment validation, and fragmented omics integration, and presents an integrated systems-breeding framework to bridge the gap between gene discovery and cultivar development.},
}

*Fabaceae/genetics/metabolism
*Plant Breeding
Multiomics
*Stress, Physiological/genetics
Genomics
Quantitative Trait Loci
Genome, Plant
CRISPR-Cas Systems
Gene Editing

@article {pmid42276166,
year = {2026},
author = {Wei, C and Zeng, B and Zhou, X and Qing, B and Deng, L and Wu, Y and Huang, W and Zhang, Z and Jin, Y and Peng, S and Zhang, C and Qiu, S},
title = {Proteomics in environmental pollution research: Advances, challenges, and future directions.},
journal = {Journal of proteomics},
volume = {331},
number = {},
pages = {105693},
doi = {10.1016/j.jprot.2026.105693},
pmid = {42276166},
issn = {1876-7737},
mesh = {*Proteomics/methods/trends ; *Environmental Pollution/analysis/adverse effects ; *Environmental Monitoring/methods ; Humans ; Multiomics ; Artificial Intelligence ; Animals ; },
abstract = {Environmental proteomics has emerged as a powerful approach for elucidating the molecular mechanisms underlying pollutant-induced biological effects. Although this field has developed rapidly, the systematic review of recent proteomics applications in environmental pollution research remains limited. This review explored the emerging roles of toxicoproteomics in biomarker discovery and mechanistic elucidation, as well as ecotoxicoproteomics in ecological risk assessment and bioremediation strategies. Here, we review the field, highlighting recent trends such as the integration of proteomics with genomics, transcriptomics, and metabolomics to provide a comprehensive view of biological responses to environmental stressors. We further discuss the growing application of artificial intelligence in improving proteomics data interpretation and accelerating biomarker discovery. In addition, recent technological advances in environmental proteomics are highlighted, including next-generation tissue microarray proteomics, nanoscale proteomics, single-cell proteomics, and spatial proteomics. Despite its potential, proteomics faces challenges, such as high operational costs, computational complexity in analysis, and technical limitations in low-abundance protein detection. We propose that the convergence of proteomics with artificial intelligence and multi-omics approaches offers promising solutions to these challenges, enhancing the practical application of proteomics in environmental monitoring and risk assessment.},
}

*Proteomics/methods/trends
*Environmental Pollution/analysis/adverse effects
*Environmental Monitoring/methods
Humans
Multiomics
Artificial Intelligence
Animals

@article {pmid42497665,
year = {2026},
author = {Zhang, F and Shang, J and Jiang, S and Zhang, X and Yan, S and Sun, Y and Liu, JX},
title = {AGSI: Adaptive group-enhanced strategy for iterative integration of single-cell multi-omics.},
journal = {Computer methods and programs in biomedicine},
volume = {286},
number = {},
pages = {109556},
doi = {10.1016/j.cmpb.2026.109556},
pmid = {42497665},
issn = {1872-7565},
mesh = {*Multiomics ; Animals ; Humans ; Mice ; Algorithms ; Reproducibility of Results ; *Single-Cell Analysis ; Computational Biology/methods ; Software ; Myocardial Infarction/genetics ; Leukocytes, Mononuclear/metabolism ; Brain ; },
abstract = {BACKGROUND AND OBJECTIVE: Single-cell multi-omics data integration is critical for understanding cellular heterogeneity and disease mechanisms. However, current methods face two key limitations: (1) uniform evaluation of cross-modal correspondence across all genes, neglecting the modular organization of biological systems, and (2) static integration strategies that fail to accommodate varying degrees of cell-level heterogeneity. To address these challenges, this study proposes AGSI, an adaptive framework for robust multi-omics integration through co-regulated gene modules and iterative reliability assessment.

METHODS: AGSI employs Latent Dirichlet Allocation to identify co-regulated gene modules and evaluates cross-modal correspondence at the module level. AGSI combines Wasserstein-enhanced similarity metrics with dual reliability modeling to progressively identify and integrate cells with high cross-modal concordance. Adaptive thresholding dynamically adjusts selection criteria throughout the iterative refinement process.

RESULTS: Extensive experiments on multiple datasets including PBMC, SNARE-seq mouse brain, 10x mouse brain, and large-scale human myocardial infarction data demonstrate that AGSI significantly outperforms seven state-of-the-art methods. Notably, AGSI achieves up to 25.6% F1 improvement over its ablation baseline and 11.9% over the best competing method on complex neural datasets, and maintains over 85% accuracy even under 50% data dropout.

CONCLUSIONS: AGSI provides a robust and scalable solution for multi-omics integration that preserves biological interpretability while achieving superior technical performance. AGSI is well suited to biomedical analyses requiring accurate cell type identification. The implementation code is available at https://github.com/CDMBlab/AGSI.},
}

*Multiomics
Animals
Humans
Mice
Algorithms
Reproducibility of Results
*Single-Cell Analysis
Computational Biology/methods
Software
Myocardial Infarction/genetics
Leukocytes, Mononuclear/metabolism
Brain

@article {pmid42681281,
year = {2026},
author = {Mussano, P and Crosino, A and Lanfranco, L and Turina, M and Forgia, M},
title = {Investigating RNA Viruses Infecting Arbuscular Mycorrhizal Fungi.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3045},
number = {},
pages = {171-183},
pmid = {42681281},
issn = {1940-6029},
mesh = {*Mycorrhizae/virology ; *RNA Viruses/genetics/isolation & purification ; *Fungal Viruses/genetics ; RNA, Viral/genetics/isolation & purification ; Computational Biology/methods ; Genome, Viral ; Virome ; },
abstract = {Fungi are known to be frequently infected by mycoviruses, which could play an important yet underexplored role in the fungal holobiont. Mycoviruses can enhance fungal traits, such as salinity tolerance and resistance to fungicides, and may also benefit plant hosts in tripartite interactions. While research on arbuscular mycorrhizal fungi (AMF) has focused on their ecological and agricultural value, few studies have explored their virome, possibly due to the difficulty of culturing AMF in the lab. This study presents an updated bioinformatic approach for virome characterization, emphasizing RNA viral ORFans and providing protocols for high-quality RNA extraction from AMF.},
}

*Mycorrhizae/virology
*RNA Viruses/genetics/isolation & purification
*Fungal Viruses/genetics
RNA, Viral/genetics/isolation & purification
Computational Biology/methods
Genome, Viral
Virome

@article {pmid42681282,
year = {2026},
author = {Berruto, F and Bortolot, M and Lumini, E and Bianciotto, V},
title = {From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3045},
number = {},
pages = {185-208},
pmid = {42681282},
issn = {1940-6029},
mesh = {*Mycorrhizae/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Soil Microbiology ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {In recent years, DNA sequencing technologies have advanced considerably with the rise of Next-Generation Sequencing (NGS) platforms, which have transformed microbial ecology research. These approaches enable the characterization of entire communities by using DNA traces to identify organisms taxonomically from a single sample. Arbuscular mycorrhizal fungi (AMF) are no exception and represent one of the most extensively studied groups of soil fungi. This chapter presents protocols for high-throughput, sequence-based analysis of AMF communities, covering the complete workflow from DNA extraction in plant or soil samples to the bioinformatic processing of sequencing data. It particularly focuses on rRNA gene metabarcoding, the most common strategy to provide estimates of AMF diversity and community composition through the amplification of DNA with taxon-specific primers followed by sequencing of barcode regions. Alternative strategies are described to accommodate different research objectives, including the selection of molecular markers.},
}

*Mycorrhizae/genetics/classification/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Soil Microbiology
DNA Barcoding, Taxonomic/methods
DNA, Fungal/genetics
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid42681626,
year = {2026},
author = {Bauer, JF and Gerczuk, M and Schindler-Gmelch, L and Schuller, B and Berking, M},
title = {Absolutist word usage in spoken language as a marker of depression: an ecological momentary assessment study.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {},
pmid = {42681626},
issn = {1471-244X},
mesh = {Humans ; Female ; Ecological Momentary Assessment ; Male ; *Depression/diagnosis/psychology ; Adult ; Middle Aged ; Severity of Illness Index ; *Language ; },
abstract = {BACKGROUND: Cognitive distortions are central to the maintenance of depression, as they bias information processing and negatively impact adaptive emotion regulation. As one manifestation of cognitive distortions, usage of absolutist words (e.g., always, never, must, completely) in written texts has been found to be indicative of underlying depression. Since absolutist word usage may allow important insights into maladaptive thinking patterns, it could be a relevant target for both monitoring and treating depressive symptoms. Therefore, we tested the relationships between absolutist word usage in spoken language with depression diagnosis, depressive symptom severity and current depressed mood.

METHOD: We recruited 144 age- and gender-matched participants with clinical depression (n = 48), subclinical depression (n = 48), and no history of depression (n = 48). By conducting smartphone-based ecological momentary assessments (EMA) three times daily for two weeks, participants provided ratings of depressed mood and speech samples, which included mood descriptions and mood-regulating statements. The Hamilton Rating Scale for Depression (HRSD) was administered at the end of the 2-week period to assess depressive symptom severity retrospectively. Group differences were calculated with ANOVAs, associations between depressed mood and absolutist word usage were evaluated with multilevel models, and the relationship between depressive symptom severity and absolutist word usage was calculated with regression models.

RESULTS: Results showed more frequent absolutist word usage over the EMA phase in individuals with clinical depression compared to individuals with no history of depression. Furthermore, absolutist word usage was negatively associated with momentary depressed mood among individuals with elevated depressive symptoms. Additional analyses testing the temporal relationship showed that greater absolutist word usage was associated with higher levels of depressed mood after 12-24 h. Accordingly, absolutist word usage was positively associated with depressive symptom severity assessed after the 2-week period.

CONCLUSION: Our results have several implications: First, absolutist word usage in spoken language appears to be an indicator of depression, which may be relevant for the optimization of depression assessment and monitoring approaches. Second, the finding that absolutist word usage was associated with lower depressed mood in the short-term, but higher depressed mood in the long-term provides important insights into the mechanisms of depression, and may help identify relevant treatment targets for clinicians.

TRIAL REGISTRATION: German Clinical Trial Registration DRKS00023670 on 19/01/2021 (https://drks.de/search/en/trial/DRKS00023670).},
}

Humans
Female
Ecological Momentary Assessment
Male
*Depression/diagnosis/psychology
Adult
Middle Aged
Severity of Illness Index
*Language

@article {pmid42684487,
year = {2026},
author = {Salim, DHC and Mello, CCS and Pereira, G and Maretto, RV and Amorim, CC},
title = {Remote sensing for monitoring and managing Eichhornia crassipes: a review of methods, applications, and decision-support frameworks.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {9},
pages = {},
pmid = {42684487},
issn = {1573-2959},
mesh = {*Eichhornia/growth & development ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Decision Support Techniques ; Ecosystem ; Conservation of Natural Resources ; Introduced Species ; },
abstract = {Eichhornia crassipes (water hyacinth) is among the world's most aggressive aquatic invasive plants, with severe ecological and socioeconomic impacts on freshwater ecosystems. Over the last two decades, remote sensing has emerged as a critical tool for monitoring its spread and supporting management decisions, offering scalable, repeatable, and increasingly precise assessments. This review synthesizes 56 studies published between 2004 and 2025, examining how different platforms (satellites, UAVs, airborne, proximal), sensor types (multispectral, hyperspectral, SAR), and analytical methods (index thresholding, object-based classification, machine learning, deep learning) have been applied to detect, classify, and quantify E. crassipes. We highlight the evolution from early single-platform approaches to recent multimodal frameworks that integrate optical, radar, and UAV data, enabling both large-scale surveillance and fine-resolution diagnostics. Evidence demonstrates that species-level discrimination, phenological tracking, and biomass estimation are now feasible, with promising developments in linking spectral responses to pollutants and stress indicators. Despite these advances, key challenges remain in harmonizing data across platforms, reducing misclassification in mixed vegetation assemblages, and translating remote sensing outputs into decision-relevant information for adaptive management. We propose a decision-support framework built on five strategic pillars: multi-scale sensor fusion, ecologically interpretable classification schemes, scalable analytical ladders, early-warning indicators, and feedback loops linking monitoring to management actions. Together, these directions show how remote sensing can move beyond detection toward more responsive and decision-oriented approaches that support the sustainable management of E. crassipes invasions across diverse aquatic environments.},
}

*Eichhornia/growth & development
*Environmental Monitoring/methods
*Remote Sensing Technology
Decision Support Techniques
Ecosystem
Conservation of Natural Resources
Introduced Species

@article {pmid42685140,
year = {2026},
author = {Krishnan, N and Zachar, I and Kun, Á and Gokhale, CS and Garay, J},
title = {Host-initiated microbial association leads to stable ectosymbiosis in an ecological model.},
journal = {PLoS computational biology},
volume = {22},
number = {9},
pages = {e1014699},
doi = {10.1371/journal.pcbi.1014699},
pmid = {42685140},
issn = {1553-7358},
mesh = {*Symbiosis/physiology ; *Models, Biological ; *Host Microbial Interactions/physiology ; Computational Biology ; Ecosystem ; },
abstract = {Microbial symbiosis is widespread among metabolically coupled cells; it presumably gave rise to mitochondria. However, how such symbioses emerge, evolve, and stabilize are unknown, particularly in the prokaryotic domain where endosymbiosis is virtually nonexistent. Yet there is growing evidence suggesting that mitochondria originated from such a metabolically driven prokaryotic partnership rather than phagocytotic predation. While prokaryotes almost ubiquitously engage in metabolic syntrophy, it is unknown whether syntrophy alone can enable stable physical associations that could pave the road toward physical integration. Here, we tested the hypothesis that syntrophy can transition into stable ectosymbiosis, using an ecological mathematical model. Starting from an existing syntrophic partnership between free-living hosts and symbionts, we demonstrate that population-level obligate ectosymbiosis can emerge and stabilize, even in unilateral syntrophy where only the symbiont consumes a host-produced metabolite. A key assumption is that the hosts' by-product inhibits their growth when it accumulates. By consuming the toxic by-product, the symbiont locally reduces hosts' self-inhibition at the contact surface, manifesting as a private benefit providing selective advantage. Our results show that due to the direct and indirect benefits, the ectosymbiotic consortium is stable against free-living forms and the consortial cooperation is ecologically selected for. Furthermore, solid metabolic coupling promotes population-level obligacy, ultimately excluding free-living individuals under stricter conditions. Our results support the hypothesis that cooperative, syntrophic microbes (particularly prokaryotes) are capable of forming stable, physical, and species-specific ectosymbiosis through inhibition reduction, providing a plausible first step toward potential, gradual endosymbiotic integration. Our work bridges the gap between models of microbial cooperation between free-living species and models that assume already-concluded, fully integrated endosymbiosis under multilevel selection.},
}

*Symbiosis/physiology
*Models, Biological
*Host Microbial Interactions/physiology
Computational Biology
Ecosystem

@article {pmid42686520,
year = {2026},
author = {Aoyama, Y and Watanabe, F and Tokutsu, K and Kinjo, Y and Muramatsu, K and Okawara, M and Kurita, T and Yoshino, K and Fushimi, K and Matsuda, S},
title = {Comparison of Perioperative Complications of Early-Stage Endometrial Cancer Between Laparotomy, Laparoscopic, and Robotic-assisted Surgery using DPC Data: A Retrospective Cohort Study in Japan.},
journal = {Journal of UOEH},
volume = {48},
number = {3},
pages = {151-160},
doi = {10.7888/juoeh.48.151},
pmid = {42686520},
issn = {0387-821X},
mesh = {Humans ; Female ; *Endometrial Neoplasms/surgery/pathology ; Retrospective Studies ; *Laparoscopy/adverse effects ; *Laparotomy/adverse effects ; *Robotic Surgical Procedures/adverse effects ; Japan/epidemiology ; *Postoperative Complications/epidemiology ; Aged ; Middle Aged ; Neoplasm Staging ; },
abstract = {Early-stage endometrial cancer can be cured surgically using three techniques: laparotomy, laparoscopic surgery, and robotic-assisted surgery. In this retrospective study, we used 4 years of data from the Japanese Diagnosis Procedure Combination to analyze perioperative sequelae for each surgical procedure. Patients with early-stage endometrial cancer were classified into three groups: laparotomy, laparoscopic surgery, and robotic-assisted surgery. The number of robotic-assisted surgeries is increasing, but hospitals with low surgical volumes performed laparotomy at a rate of 57.6%, while hospitals with higher surgical volume tended to perform fewer laparotomies and more laparoscopic and robotic-assisted surgeries. Compared with the laparotomy group, the in-hospital risk ratios and 95% confidence intervals for postoperative sequelae were 0.28 (0.18-0.44) and 0.39 (0.23-0.69) in the laparoscopic and robotic-assisted surgery groups, respectively (P = 0.001 for all). Regarding blood transfusion treatment, the incidence rate ratios were lower for laparoscopic and robotic-assisted surgery than for laparotomy (P < 0.001 for all), even after multivariable analysis. In conclusion, in early-stage endometrial cancer, laparotomy had the highest incidence of perioperative sequelae compared to laparoscopic surgery and robotic-assisted surgery.},
}

Humans
Female
*Endometrial Neoplasms/surgery/pathology
Retrospective Studies
*Laparoscopy/adverse effects
*Laparotomy/adverse effects
*Robotic Surgical Procedures/adverse effects
Japan/epidemiology
*Postoperative Complications/epidemiology
Aged
Middle Aged
Neoplasm Staging

@article {pmid42297904,
year = {2026},
author = {Sjølie, HK and Tange, AC},
title = {Timber harvesting intensity and use of decision-support tools among semi-professional private forest owners: a Norwegian case study.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42297904},
issn = {2045-2322},
mesh = {Norway ; *Forests ; *Forestry/methods ; *Conservation of Natural Resources/methods ; *Ownership ; *Decision Support Techniques ; Wood ; Biodiversity ; Humans ; Trees ; },
abstract = {Non-industrial private forest owners are known to have multiple ownership values and objectives. Their management decisions have multiple impacts on the supply of ecosystem services from forests. Forest management plans, a main decision-support tool for many forest owners, tend to be timber-oriented, potentially leading to more harvesting and more frequent use among production-oriented owners. We investigated factors explaining harvest intensity, measured as the ratio of property-level actual harvest volumes to predicted harvest volumes and the use of forest management plans among 119 semi-professional, non-industrial, private forest owners in Norway. Harvest intensity decreased with forest area and with biodiversity and nextgeneration's need as ownership objectives and increased with wood prices and owner engagement but was not impacted by short-term profit or use of forest management plans. Use of forest management plans increased with forest area, having received instructions, trust in the harvest predictions, and economic ownership objectives. By using property-level harvest prediction, we could compare harvest figures to the actual timber resource, formed by each property's forest biophysical attributes. This approach may be a valuable step in developing models that provide enhanced understanding of how forest owner behavior is shaped by preferences and objectives.},
}

Norway
*Forests
*Forestry/methods
*Conservation of Natural Resources/methods
*Ownership
*Decision Support Techniques
Wood
Biodiversity
Humans
Trees

@article {pmid42675342,
year = {2026},
author = {Rodrigues, DLG and de Andrade, JBC and Silva, GS},
title = {Seasonal and Temperature-Related Variation in Subarachnoid Hemorrhage Hospital Admissions: A Nationwide Ecological Time-Series Analysis in Brazil, 2020-2024.},
journal = {Neurocritical care},
volume = {},
number = {},
pages = {},
pmid = {42675342},
issn = {1556-0961},
abstract = {BACKGROUND: Subarachnoid hemorrhage (SAH) carries high mortality worldwide. Seasonal patterns have been documented in temperate regions, but evidence from tropical and subtropical populations remains limited. We investigated associations between meteorological variables and SAH hospital admissions across diverse climate zones in Brazil.

METHODS: We conducted an ecological time-series analysis linking nationwide SAH hospitalizations [International Classification of Diseases Version 10 (ICD-10; I60.0-I60.9)] from Brazil's Unified Health System with meteorological data from the National Institute of Meteorology (January 2020-November 2024). Quasi-Poisson generalized linear models were used to estimate relative risks (RR) per 1 °C decrease in mean minimum temperature, overall and stratified by season. Sensitivity analyses excluded the first coronavirus disease 2019 (COVID-19) pandemic year.

RESULTS: Among 9903 SAH hospital admissions over 59 months, seasonal variation was observed, with the highest proportion occurring in autumn (27.2%, n = 2697) and the lowest in spring (23.4%, n = 2316; Chi-squared p < 0.001). The mean summer-winter difference in minimum temperature was 3.6 °C. Overall, the temperature-SAH association did not reach statistical significance [RR per 1 °C decrease: 1.019; 95% confidence interval (CI): 0.994-1.045; p = 0.14]. In season-stratified analyses, winter was the only season demonstrating a significant inverse association (RR = 1.133; 95% CI 1.008-1.275; p = 0.037). This finding was robust to the exclusion of the pandemic year 2020 (RR = 1.140; 95% CI 1.013-1.282; p = 0.030). In-hospital case fatality did not differ significantly across seasons (range 5.2-5.7%; p = 0.38).

CONCLUSIONS: SAH hospital admissions in Brazil exhibit modest seasonal variation, with a significant association with temperature observed only during the winter months. These findings extend evidence on environmental determinants of SAH to a tropical and subtropical setting, though the small effect size and ecological design warrant cautious interpretation.},
}

@article {pmid42676645,
year = {2026},
author = {Olafusi, CO and Afolabi, IS and Ogunlana, OO},
title = {Salivary gland microbiome of Anopheles gambiae: a mini-review of acquisition, composition, and functional significance.},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1911294},
pmid = {42676645},
issn = {2673-8600},
abstract = {The salivary gland (SG) is the final barrier for Plasmodium transmission to humans but remains comparatively understudied relative to the midgut microbiome. This review synthesizes current knowledge on SG microbiome acquisition routes, composition, and functional significance. Acquisition may occur via larval filter feeding, vertical (egg smearing), transstadial, or horizontal transmission during blood feeding, though their relative contributions are unknown. Compositional studies show Gram-negative genera Serratia, Elizabethkingia, Acinetobacter, Pseudomonas, and Asaia predominate; Plasmodium infection correlates with increased Serratia and decreased Elizabethkingia abundance. While immune-related genes (e.g., cecropins, defensin, GNBP, SRPN6) expressed in the SG may be modulated by resident bacteria, direct evidence of their effect on sporozoite invasion remains lacking. Gram-negative bacteria trigger Toll, Imd, and JAK-STAT pathways, but emerging evidence suggests the SG may mount a distinct, locally independent immune response compared to the systemic pathway. Paratransgenesis using Asaia shows promise, yet SG-targeted effector delivery remains untested. Ecological pressures common in West Africa, including agricultural pesticides, insecticide resistance, and larval water contamination, may influence mosquito-associated bacteria, but no studies explicitly link these to the SG microbiome. Significant knowledge gaps persist, notably the absence of field studies in high-burden regions like Nigeria and the lack of experimental manipulation to establish causality. Addressing these priorities is critical to determine whether the SG microbiome can be exploited as a transmission-blocking target.},
}

@article {pmid42678384,
year = {2026},
author = {Devecchi, S and Reppas-Chrysovitsinos, E and Tromer Dragsdahl, ALS and Pizzol, L and Semenzin, E and Zabeo, A and Hristozov, D and Rydberg, T},
title = {Planetary Boundaries and Absolute Sustainability in Life Cycle Assessment - past, present, and future.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag150},
pmid = {42678384},
issn = {1551-3793},
abstract = {Efforts to steer the social metabolism (i.e., how human societies interact with nature) towards sustainability are pulling assessment practice in two directions: "relative" product-to-product comparisons and "absolute" product-to-limit benchmarking, where the limit works as benchmark for the assessment. Within approaches such as Safe and Sustainable by Design, inherently threshold-based "absolute" chemical Risk Assessment is coupled to Life Cycle Assessment, which has traditionally been used as a tool for comparing alternatives. This coupling is driving the development of methodologies for comparative assessment of (eco)toxicological impact potentials (e.g., chemical footprinting). In parallel, the emergence of the Planetary Boundaries framework has renewed the interest in shifting from comparative assessments towards absolute benchmarking against global environmental limits, leading to Absolute Environmental Sustainability Assessment. This paper reviews how environmental limits are incorporated into Life Cycle Assessment through early distance to target methods (such as Ecological Scarcity, Environmental Themes, Eco-Indicator 95) to support business-driven eco-efficiency decisions and how impacts were anchored in national or regional targets and critical loads. We then discuss how the Planetary Boundaries framework reorganizes limits around Earth-system processes and how Planetary Boundaries based Life Cycle Assessment translates global boundaries into Life Cycle Assessment indicators and Planetary Boundaries based "budgets" for products and sectors. Across these developments, we show that setting and allocating thresholds reflects conflicting notions of "weak" and "strong" sustainability and is unavoidably value-laden and argue that making this "valuesphere" explicit is crucial if Planetary Boundaries based Life Cycle Assessment is to inform credible, product-level Safe and Sustainable by Design decisions on absolute sustainability.},
}

@article {pmid42678936,
year = {2026},
author = {Mock, T and Bilcke, G and Flaum, E and Fu, S and Hoch, L and Moog, K and Rijsdijk, N and Ruck, EC and Bishop, IW and Duchene, C and Gilbertson, R and Hopes, A and Johns, C and Manfellotto, F and Roberts, WR and Belshaw, N and Chandola, U and Chaerle, P and Chepurnova, O and Deleu, D and D'hondt, S and Di Costanzo, F and Dudin, O and Flori, S and Gaikwad, T and Groisillier, A and Hall, A and Ji, P and Lavier-Aydat, LJ and Lewis, WH and Menicot, S and Pinseel, E and Pottier, E and Sarkozi, K and Smerilli, A and Strauss, J and Thierens, S and Toseland, A and Touhami, Y and Utting, R and Van Bel, M and van Oosterhout, C and Wu, Y and Yang, F and Allhusen, E and Bolton, JJ and Bowler, C and Brinkhoff, T and Poehlein, A and Brovarone, T and Chen, N and Clark, G and Clark, MD and Copetti, D and Cui, Z and Deng, B and Jian, J and John, U and Jungblut, AD and Kang, J and Kristoffersen, JB and Lee, J and Liu, S and Mann, DG and Medlin, L and Moulton, V and Radojicic, J and Sato, S and Trobajo, R and Wolf, K and Yamada, N and Ye, N and Zhang, L and Zhuang, Y and Dey, G and Di Dato, V and Helliwell, K and Jaubert, M and Kroth, PG and Montresor, M and Romano, G and Rynearson, TA and Talag, J and Valentin, KU and Vincent, F and Waller, RF and Wheeler, G and Alverson, AJ and Barry, K and Boston, L and Falciatore, A and Ferrante, MI and Guo, J and Grimwood, J and Hayes, R and Herdean, A and Jenkins, J and Kim, M and Kooistra, WH and Kuo, A and Lipzen, A and Poulsen, N and Schmutz, J and Tirichine, L and Vandepoele, K and Verret, F and Vyverman, W and Grigoriev, IV},
title = {The 100 Diatom Genomes Project.},
journal = {PLoS biology},
volume = {24},
number = {9},
pages = {e3003947},
doi = {10.1371/journal.pbio.3003947},
pmid = {42678936},
issn = {1545-7885},
mesh = {*Diatoms/genetics/classification ; *Genome ; Biodiversity ; Transcriptome ; Genomics ; Phylogeny ; },
abstract = {One hundred diatom species have been selected for genome and transcriptome sequencing. The 100 Diatom Genomes Project aims to provide a scalable framework for understanding diatom biodiversity, ecology and evolution, and for investigating their use in biotechnology.},
}

*Diatoms/genetics/classification
*Genome
Biodiversity
Transcriptome
Genomics
Phylogeny

@article {pmid42678946,
year = {2026},
author = {Hardy, MJ and Williams, CK and Ladman, BS and Pitesky, ME and Overton, CT and Casazza, ML and Matchett, EL and Prosser, DJ and Legagneux, P and Lefebvre, J and Buler, JJ},
title = {Using high frequency GPS data to assess wintering goose proximity to commercial poultry facilities on the Delmarva peninsula for avian influenza risk management and surveillance.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0355415},
doi = {10.1371/journal.pone.0355415},
pmid = {42678946},
issn = {1932-6203},
mesh = {Animals ; *Influenza in Birds/epidemiology/prevention & control/virology ; *Geese/virology ; Seasons ; Influenza A Virus, H5N1 Subtype/isolation & purification ; Geographic Information Systems ; Disease Outbreaks/prevention & control ; Risk Management ; *Poultry/virology ; *Poultry Diseases/epidemiology/virology ; },
abstract = {The ongoing global outbreak of Highly Pathogenic Avian Influenza Virus (HPAIv) Clade 2.3.4.4 H5N1 in poultry, which was first detected in the United States (USA) in February 2022, underscores the importance of improving food biosecurity and wild bird surveillance. The Delmarva Peninsula is vital to wintering waterfowl and to poultry production, thereby increasing the risk of HPAIv outbreaks. By using fine-scale GPS tracking of Greater Snow Geese (GSGO, N = 59) and Canada Geese (CANG, N = 9) over four winters (2019-2023), we 1) demonstrate a risk ranking system for poultry facilities based on exposure to wintering waterfowl, and 2) model this exposure in relation to temporal, geographic, and land cover factors. We showed that an ordinal-percentile ranking system, based on goose points per hour (gp/h) at poultry facilities, effectively predicted HPAIv H5N1 outbreak risks in the Delmarva Peninsula. Seven facilities with outbreaks were in the 78-99th risk percentile, including one ranked among the top 25 of 6,021 facilities. Such ranking criteria could be used to guide biosecurity efforts when response teams' resources are limited. Notably, one-third of Delmarva poultry facilities had GPS-marked waterfowl present during winters, indicating a significant presence despite our limited sample sizes. We analyzed the variability in goose exposure rates near poultry facilities over four winters. Time (week) during winter was the key predictor of exposure, with greater GSGO presence in mid-late winter (Dec 15 to Feb 28) and CANG exposure peaking in early winter (Nov 28 to Dec 11), then stabilizing until late winter (Feb to Mar 13), whereupon exposure increased again. Colder temperatures (below 0°C) significantly increased GSGO exposure as they sought waste grain for energy. Goose exposure for both species was high throughout the winter, necessitating 24-hour surveillance. Proximity to sewage treatment plants (≤2 km), National Wildlife Refuges (≤5 km), water bodies (≤5 km), and the coast (≤20 km) increased exposure levels. Additionally, inland areas with features such as reservoirs and lakes supported large numbers of geese near facilities.},
}

Animals
*Influenza in Birds/epidemiology/prevention & control/virology
*Geese/virology
Seasons
Influenza A Virus, H5N1 Subtype/isolation & purification
Geographic Information Systems
Disease Outbreaks/prevention & control
Risk Management
*Poultry/virology
*Poultry Diseases/epidemiology/virology

@article {pmid42680193,
year = {2026},
author = {Biondi, L and Silva, F and Gomes, N and Maior, RS and Silva, S and Soares, SC},
title = {From fascination to fear and disgust: cross-cultural assessment of emotional and aesthetic responses to snake imagery.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2078},
pages = {},
doi = {10.1098/rspb.2026.1328},
pmid = {42680193},
issn = {1471-2954},
support = {UID/04810/2020//Fundação para a Ciência e a Tecnologia/ ; 2022.06494.CEECIND//Fundação para a Ciência e a Tecnologia/ ; 2021.05287.BD//Fundação para a Ciência e a Tecnologia/ ; 308291/2020-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Fear ; *Snakes/anatomy & histology ; Humans ; Portugal ; Female ; Cross-Cultural Comparison ; Brazil ; *Disgust ; *Emotions ; Male ; Esthetics ; Adult ; },
abstract = {The primate visual system is thought to have evolved under selective pressures favouring rapid detection of snakes, ancestral predators that shaped perceptual and attentional mechanisms. Yet, the transition from visual detection to subjective fear remains poorly understood and may depend on specific morphological cues. Here, we examined how snake morphology modulates human emotional and aesthetic responses across ecological and cultural contexts. A total of 377 participants from Portugal (low snake biodiversity) and Brazil (high snake biodiversity) rated images of 92 snake species on fear, disgust, beauty, valence, arousal and perceived size. Cluster analyses revealed three consistent emotional profiles across populations: a High-Fear cluster (mainly viperids, boids and mimics with threatening traits), a High-Valence cluster (mostly harmless colubrids and dipsadids), and a smaller High-Disgust cluster (fossorial or limbless reptiles). Cluster membership was unaffected by country, indicating cross-cultural consistency in emotional evaluations of snake morphology. Species in the High-Fear cluster exhibited higher edge density. By contrast, greater exposure to snakes, particularly in natural environments, was associated with lower Snake Fear Questionnaire scores. These results support the view that humans rely on evolutionarily conserved morphological heuristics (e.g. triangular heads, keeled scales and disruptive patterns) to assess potential threats, while individual predispositions and experience modulate response intensity.},
}

Animals
*Fear
*Snakes/anatomy & histology
Humans
Portugal
Female
Cross-Cultural Comparison
Brazil
*Disgust
*Emotions
Male
Esthetics
Adult

@article {pmid42230654,
year = {2026},
author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F},
title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42230654},
issn = {2055-5008},
mesh = {Animals ; *Rumen/microbiology ; *Methane/metabolism ; Cattle ; *Metabolome ; *Pichia/physiology/metabolism ; Female ; *Microbiota ; Lactation ; Animal Feed/analysis ; Bacteria/classification/genetics/metabolism ; Multiomics ; },
abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.},
}

Animals
*Rumen/microbiology
*Methane/metabolism
Cattle
*Metabolome
*Pichia/physiology/metabolism
Female
*Microbiota
Lactation
Animal Feed/analysis
Bacteria/classification/genetics/metabolism
Multiomics

@article {pmid42669713,
year = {2026},
author = {Jiao, X and Yang, Y and Li, F and Zheng, JS and Lai, Y and Li, B and Wang, T and Dong, Y and Wang, Y and Li, Y and Li, R and Wu, Z and Wu, G and Yuan, J and Zhang, S and Li, S and Liu, G and Shi, J and Xiong, F and Pan, A and Liang, G and Huang, Y and Pan, XF},
title = {Longitudinal dynamics of the maternal gut virome associate with metabolic features of preterm birth.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42669713},
issn = {2041-1723},
support = {82473646//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/metabolism/virology ; *Virome/genetics ; *Gastrointestinal Microbiome ; Feces/virology/microbiology ; Adult ; Longitudinal Studies ; Metabolome ; Infant, Newborn ; Multiomics ; },
abstract = {Preterm birth (PTB) remains a major pregnancy complication, yet the role of the maternal gut virome in its etiology is largely unknown. Here we show that the maternal gut virome undergoes ecological destabilization prior to PTB, coupled with distinct host metabolic remodeling. Nested within the Tongji-Huaxi-Shuangliu Birth Cohort, we integrate longitudinal gut virome and bacteriome profiles from 300 stool samples, alongside matched serum metabolomes and clinical profiles, from 100 pregnant women (50 with PTB and 50 with term birth) across early, middle, and late pregnancy. We reveal that although the maternal gut virome is highly personalized and longitudinally stable within individuals, PTB is characterized by reduced virome convergence and specific alterations in viral populations emerging during mid-to-late pregnancy. Host-phage analyses identify remodeling of Klebsiella- and Prevotella-associated viral communities linked to PTB risk. PTB-associated virome alterations are further associated with amino acid metabolic remodeling, particularly glutamate- and aspartate-related pathways, supported by reproducible virus-metabolite associations and enriched viral auxiliary metabolic genes. In addition, L-aspartate partly mediates associations between monocyte-related inflammatory indices and PTB. Multi-omics modeling demonstrates that virome-metabolome signatures achieve strong predictive performance for both PTB and imminent delivery, with viral features contributing substantially to prediction accuracy and retaining predictive value in external validation. Collectively, these findings highlight the maternal virome and its metabolic signatures as key determinants of PTB susceptibility.},
}

Humans
Female
Pregnancy
*Premature Birth/metabolism/virology
*Virome/genetics
*Gastrointestinal Microbiome
Feces/virology/microbiology
Adult
Longitudinal Studies
Metabolome
Infant, Newborn
Multiomics

@article {pmid42670999,
year = {2026},
author = {Rahman, MS and Jalil, A and Ahmed, S},
title = {Integrated risk assessment of industrial wastewater in a Bangladeshi export processing zone.},
journal = {Journal of water and health},
volume = {24},
number = {8},
pages = {1187-1204},
pmid = {42670999},
issn = {1477-8920},
mesh = {Bangladesh ; *Water Pollutants, Chemical/toxicity/analysis ; Risk Assessment ; *Wastewater/analysis/chemistry ; Animals ; *Environmental Monitoring ; *Industrial Waste/analysis ; Daphnia magna/drug effects ; Metals, Heavy/analysis ; Geographic Information Systems ; },
abstract = {Industrial wastewater from export processing zones may comply with regulatory standards while concealing ecological risks not captured by routine monitoring. This study aimed to (1) evaluate effluent quality and regulatory compliance in the Chattogram Export Processing Zone (CEPZ), Bangladesh; (2) develop an integrated risk assessment framework integrating the Effluent Quality Index (EQI), ecotoxicity, metal speciation, and geographic information system (GIS) analysis; and (3) identify high-risk discharge corridors. Treated effluents (n = 6) and drinking water were analyzed for physicochemical parameters, Pb and Cr, acute ecotoxicity using Daphnia magna (EC50), metal speciation (Visual MINTEQ), and spatial distribution against ECR 2023 and WHO guidelines. Although pH and metal concentrations complied with regulatory limits, 5-day biochemical oxygen demand (95-180 mg L[-1]) exceeded the ECR limit (30 mg L[-1]) by up to 600%, while chemical oxygen demand (240-326 mg L[-1]) exceeded the 200 mg L[-1] limit by 63%. The washing-finishing sector exhibited the highest pollution burden (EQI = 3.10) and toxicity (EC50 = 18.5%). Metal speciation showed that 45-88% of regulated heavy metals occurred as bioavailable organic complexes. EQI correlated with EC50 (R[2] = 0.84, p < 0.01); GIS identified a 2-km high-risk corridor, potentially exposing 50,000-75,000 residents.},
}

Bangladesh
*Water Pollutants, Chemical/toxicity/analysis
Risk Assessment
*Wastewater/analysis/chemistry
Animals
*Environmental Monitoring
*Industrial Waste/analysis
Daphnia magna/drug effects
Metals, Heavy/analysis
Geographic Information Systems

@article {pmid42673461,
year = {2026},
author = {Trindade-Santos, I and Webb, TJ and Heim, NA and Knope, ML and Monarrez, PM and Payne, JL and Finnegan, S and McClain, CR},
title = {Nonuniform resizing of marine life under climate change.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {36},
pages = {e2606099123},
doi = {10.1073/pnas.2606099123},
pmid = {42673461},
issn = {1091-6490},
mesh = {Animals ; *Climate Change ; Oceans and Seas ; *Mollusca/physiology ; *Aquatic Organisms/physiology ; Body Size ; Ecosystem ; Global Warming ; Biomass ; },
abstract = {Global warming is often predicted to drive universal declines in animal body size, but empirical evidence remains equivocal. This is particularly true in marine systems, where body size distributions are influenced not only by temperature but also by oxygen and productivity, all of which are expected to be greatly altered in future oceans. Differences in regional climate trajectories and the physiology of marine taxa also suggest that body size responses will not be spatially or ecologically uniform. We address these complexities by projecting future changes in mean body size across species within ocean basins using a database of 23,329 marine mollusc species. We quantify how body size distributions change across energetic gradients and forecast assemblage level shifts of the five major classes of molluscs across all 10 oceanic basins. Under high greenhouse gas emission scenarios, we project a significant decline in body size in 68% of class-basin combinations (34 of 50), with some clades expected to shrink by ~16% in mean length by 2100. However, these responses are not universal but are governed by clade-level differences in dominant ecological and physiological strategies and the geography of climate change. Because biomass scales allometrically with length, these trends can correspond to substantial changes in the mass of the average species, from a 46% decline to a 15% increase depending on clade and region. Such widespread functional disruptions may threaten critical ecosystem services (carbon sequestration, nutrient cycling, and human food provisioning), with implications for global marine ecosystem functioning and services.},
}

Animals
*Climate Change
Oceans and Seas
*Mollusca/physiology
*Aquatic Organisms/physiology
Body Size
Ecosystem
Global Warming
Biomass

@article {pmid42668906,
year = {2026},
author = {Durante, F and Prendini, L and Pizzolotto, R and Wérenne, G and Baert, L and Musschoot, T and Dekoninck, W},
title = {A Darwin Core dataset of scorpions (Arachnida, Scorpiones) from the Royal Belgian Institute of Natural Sciences (RBINS) Collections.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e188187},
pmid = {42668906},
issn = {1314-2828},
abstract = {BACKGROUND: This data paper details the publication of a dataset derived from the scorpion (Order Scorpiones C.L. Koch, 1850) collections preserved at the Royal Belgian Institute of Natural Sciences (RBINS), Brussels. The dataset includes all 3,652 specimens mostly identified to genus or species level during a recent re-evaluation. To maximise accessibility and interoperability, the entire dataset was fully standardised using the Darwin Core (DwC) standard and published as open data. The published dataset comprises a significant collection of records, encompassing eleven families, 56 genera and 117 species of scorpions. Geographically, the specimens originate from a wide range of locations, in 59 countries. The records within this dataset span a substantial chronological period, with collection dates ranging from 1872 to 2023. Most of the specimens were collected during expeditions led by researchers of RBINS.

NEW INFORMATION: The mobilisation and standardisation of this rich historical collection provide a valuable resource for global biodiversity informatics, supporting crucial research in taxonomy, ecology and biogeography of the order Scorpiones.},
}

@article {pmid41212304,
year = {2026},
author = {Luther, L and Raugh, IM and Webber, LBG and Grant, PM and Beck, AT and Mittal, VA and Walker, E and Strauss, GP},
title = {Elevated defeatist performance beliefs predict state increases in negative symptoms in daily life in clinical high-risk for psychosis youth: implications for mobile health treatments.},
journal = {European archives of psychiatry and clinical neuroscience},
volume = {276},
number = {6},
pages = {2811-2820},
pmid = {41212304},
issn = {1433-8491},
support = {R21-MH119438/MH/NIMH NIH HHS/United States ; R01-MH116039/MH/NIMH NIH HHS/United States ; R21-MH119438/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Psychotic Disorders/physiopathology/therapy/psychology ; Adolescent ; Female ; Male ; Ecological Momentary Assessment ; *Depression/physiopathology/etiology ; Risk ; Digital Health ; },
abstract = {BACKGROUND: Negative symptoms are a strong predictor of conversion to a formal psychotic disorder in youth at clinical high-risk for developing psychosis (CHR). Identification of temporally precise mechanisms underlying increases in negative symptoms could enhance early intervention and specifically support the utility of mobile health treatments. Guided by Cognitive Behavioral models of psychopathology, we examine whether a core type of biased thinking-defeatist performance beliefs (DPB)-is a real-world mechanism of negative symptoms as well as a secondary symptom that is common in CHR youth: depressed mood.

METHODS: CHR youth (n = 119) and healthy control (CN; 59) subjects completed ecological momentary assessment surveys assessing DPB, negative symptoms, and depressed mood for six days.

RESULTS: CHR youth reported elevated DPB in daily life compared to CN. Greater DPB were associated with greater concurrent negative symptoms and depressed mood in daily life. Time-lagged analyses demonstrated that increased DPB at time t led to elevations in negative symptoms and depressed mood at t + 1 above and beyond the effects of the respective symptom at time t; DPB also varied across time of day, study day, day of the week, activity context, and social partners.

CONCLUSIONS: DPB may be a promising shared mechanism contributing to negative symptoms and depressed mood in CHR youth in their daily life. Findings also provide proof-of-concept support for the utility of mobile health treatments targeting DPB by identifying key moments where DPB fluctuate in CHR youths' everyday environments.},
}

Humans
*Psychotic Disorders/physiopathology/therapy/psychology
Adolescent
Female
Male
Ecological Momentary Assessment
*Depression/physiopathology/etiology
Risk
Digital Health

@article {pmid42398615,
year = {2026},
author = {Majeed, A and Javaid, MH and Mahreen, N and Hussain, M and Kang, Y and Hussain, K and Su, J},
title = {Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems.},
journal = {International journal of biological macromolecules},
volume = {375},
number = {},
pages = {153356},
doi = {10.1016/j.ijbiomac.2026.153356},
pmid = {42398615},
issn = {1879-0003},
mesh = {Multiomics ; *Grassland ; *Plants/microbiology/genetics/metabolism ; *Microbiota/genetics ; Metagenomics/methods ; *Nucleic Acids/genetics ; Ecosystem ; },
abstract = {Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.},
}

Multiomics
*Grassland
*Plants/microbiology/genetics/metabolism
*Microbiota/genetics
Metagenomics/methods
*Nucleic Acids/genetics
Ecosystem

@article {pmid40055331,
year = {2025},
author = {Guerrero, PC and Contador, T and Díaz, A and Escobar, C and Orlando, J and Marín, C and Medina, P},
title = {Southern Islands Vascular Flora (SIVFLORA) dataset: A global plant database from Southern Ocean islands.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {397},
pmid = {40055331},
issn = {2052-4463},
mesh = {Islands ; *Biodiversity ; *Plants/classification ; Climate Change ; Ecosystem ; Oceans and Seas ; Databases, Factual ; },
abstract = {The Southern Islands Vascular Flora (SIVFLORA) dataset is a globally significant, open-access resource that compiles essential biodiversity data on vascular plants from islands across the Southern Ocean. The SIVFLORA dataset was generated through five steps: study area delimitation, compiling the dataset, validating and harmonizing taxonomy, structuring dataset attributes, and establishing file format and open access. Covering major taxonomic divisions, SIVFLORA offers a comprehensive overview of plant occurrences, comprising 14,589 records representing 886 species, 95 families, and 42 orders. This dataset documents that 58.62% of the taxa are native, 9.61% are endemic, and 31.77% are alien species. The Falkland/Malvinas Archipelago, the most species-rich, contrast sharply with less diverse islands like the South Orkney Archipelago. SIVFLORA serves as a taxonomically harmonized, interoperable resource for investigating plant diversity patterns, ecosystem responses to climate change in extreme environments, island biogeography, endemism, and the effects of anthropogenic pressures on Southern Ocean flora.},
}

Islands
*Biodiversity
*Plants/classification
Climate Change
Ecosystem
Oceans and Seas
Databases, Factual

@article {pmid40061226,
year = {2025},
author = {Ab Kadir, MA and Abdul Manaf, R and Mokhtar, SA and Ismail, LI},
title = {Identifying leptospirosis hotspots in Selangor: uncovering climatic connections using remote sensing and developing a predictive model.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18851},
pmid = {40061226},
issn = {2167-8359},
mesh = {*Leptospirosis/epidemiology ; Humans ; Malaysia/epidemiology ; Cross-Sectional Studies ; Geographic Information Systems ; *Remote Sensing Technology ; Incidence ; Climate Change ; Climate ; },
abstract = {BACKGROUND: Leptospirosis is an endemic disease in countries with tropical climates such as South America, Southern Asia, and Southeast Asia. There has been an increase in leptospirosis incidence in Malaysia from 1.45 to 25.94 cases per 100,000 population between 2005 and 2014. With increasing incidence in Selangor, Malaysia, and frequent climate change dynamics, a study on the disease hotspot areas and their association with the hydroclimatic factors could enhance disease surveillance and public health interventions.

METHODS: This ecological cross-sectional study utilised a geographic information system (GIS) and remote sensing techniques to analyse the spatiotemporal distribution of leptospirosis in Selangor from 2011 to 2019. Laboratory-confirmed leptospirosis cases (n = 1,045) were obtained from the Selangor State Health Department. Using ArcGIS Pro, spatial autocorrelation analysis (Moran's I) and Getis-Ord Gi* (hotspot analysis) was conducted to identify hotspots based on the monthly aggregated cases for each subdistrict. Satellite-derived rainfall and land surface temperature (LST) data were acquired from NASA's Giovanni EarthData website and processed into monthly averages. These data were integrated into ArcGIS Pro as thematic layers. Machine learning algorithms, including support vector machine (SVM), Random Forest (RF), and light gradient boosting machine (LGBM) were employed to develop predictive models for leptospirosis hotspot areas. Model performance was then evaluated using cross-validation and metrics such as accuracy, precision, sensitivity, and F1-score.

RESULTS: Moran's I analysis revealed a primarily random distribution of cases across Selangor, with only 20 out of 103 observed having a clustered distribution. Meanwhile, hotspot areas were mainly scattered in subdistricts throughout Selangor with clustering in the central region. Machine learning analysis revealed that the LGBM algorithm had the best performance scores compared to having a cross-validation score of 0.61, a precision score of 0.16, and an F1-score of 0.23. The feature importance score indicated river water level and rainfall contributes most to the model.

CONCLUSIONS: This GIS-based study identified a primarily sporadic occurrence of leptospirosis in Selangor with minimal spatial clustering. The LGBM algorithm effectively predicted leptospirosis hotspots based on the analysed hydroclimatic factors. The integration of GIS and machine learning offers a promising framework for disease surveillance, facilitating targeted public health interventions in areas at high risk for leptospirosis.},
}

*Leptospirosis/epidemiology
Humans
Malaysia/epidemiology
Cross-Sectional Studies
Geographic Information Systems
*Remote Sensing Technology
Incidence
Climate Change
Climate

@article {pmid40064777,
year = {2025},
author = {Crespo-Bellido, A and Martin, DP and Duffy, S},
title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2912},
number = {},
pages = {125-143},
pmid = {40064777},
issn = {1940-6029},
mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; *Software ; Genome, Viral ; Algorithms ; Sequence Alignment ; *Computational Biology/methods ; Evolution, Molecular ; },
abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.},
}

*Geminiviridae/genetics
*Recombination, Genetic
*Software
Genome, Viral
Algorithms
Sequence Alignment
*Computational Biology/methods
Evolution, Molecular

@article {pmid40067093,
year = {2025},
author = {Zhang, G and Ristola, P and Su, H and Kumar, B and Zhang, B and Hu, Y and Elliot, MG and Drobot, V and Zhu, J and Staal, J and Larralde, M and Wang, S and Yi, Y and Yu, H},
title = {BioArchLinux: community-driven fresh reproducible software repository for life sciences.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
pmid = {40067093},
issn = {1367-4811},
mesh = {*Software ; *Computational Biology/methods ; *Biological Science Disciplines ; Programming Languages ; Reproducibility of Results ; },
abstract = {MOTIVATION: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research.

RESULTS: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment.

The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.},
}

*Software
*Computational Biology/methods
*Biological Science Disciplines
Programming Languages
Reproducibility of Results

@article {pmid40073274,
year = {2025},
author = {Aucello, R and Pernice, S and Tortarolo, D and Calogero, RA and Herrera-Rincon, C and Ronchi, G and Geuna, S and Cordero, F and Lió, P and Beccuti, M},
title = {UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
pmid = {40073274},
issn = {1367-4811},
support = {//Ministero dell'Univerisita' e della Ricerca/ ; },
mesh = {*Models, Biological ; *Software ; *Systems Biology/methods ; Escherichia coli/metabolism/genetics ; Computer Simulation ; Clostridioides difficile ; *Computational Biology/methods ; },
abstract = {MOTIVATION: Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognizable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, e.g. to the cancer evolution study.

RESULTS: To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system's multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved, thanks to the hybridization of two analysis approaches that capture a system's different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal's effectiveness was demonstrated by mechanistically simulating the metabolic output of Escherichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.

GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E. coli  https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile  https://github.com/qBioTurin/EpiCell_CDifficile.},
}

*Models, Biological
*Software
*Systems Biology/methods
Escherichia coli/metabolism/genetics
Computer Simulation
Clostridioides difficile
*Computational Biology/methods

@article {pmid40074756,
year = {2025},
author = {Wei, P and Song, Y and Tian, R and Wang, Y and Chen, J and Yuan, Z and Zhou, W},
title = {CaecilianTraits, an individual level trait database of Caecilians worldwide.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {428},
pmid = {40074756},
issn = {2052-4463},
support = {32170445//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Amphibians/anatomy & histology/classification ; *Databases, Factual ; Biological Evolution ; Biodiversity ; },
abstract = {Functional traits differ among species, which determine the ecological niche a species occupies and its ability to adapt to environment. However, differences in traits also exist at intraspecific level. Such variations shape differences in individual survival capabilities. Investigating intraspecific differences of functional traits is important for ecology, evolutionary biology and biodiversity conservation. Individual trait-based approaches have been applied in plant ecology. But for animals, most databases only provide data at the species level. In this study, we presented a global database of morphological traits for caecilians (Amphibia, Gymnophiona) at both species and individual level. Caecilians are a unique group of amphibians characterized by their secretive habits, which have limited our understanding of this taxon. We compiled the most comprehensive database covering 218 out of 222 known species, with 215 of them have individual level data. This database will facilitate research in the ecology, evolutionary biology, conservation biology, and taxonomy of caecilians. Furthermore, this dataset can be utilized to test ecological and evolutionary hypotheses at the individual level.},
}

Animals
*Amphibians/anatomy & histology/classification
*Databases, Factual
Biological Evolution
Biodiversity

@article {pmid40074806,
year = {2025},
author = {Tang, Y and Hu, H and Chen, S and Hao, B and Xu, X and Zhu, H and Zhan, W and Zhang, T and Hu, H and Chen, G},
title = {Multi-omics analysis revealed the novel role of NQO1 in microenvironment, prognosis and immunotherapy of hepatocellular carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8591},
pmid = {40074806},
issn = {2045-2322},
support = {24B0413//the Scientific Research Project of the Hunan Provincial Department of Education/ ; 2024JJ7455//Natural Science Foundation of Hunan Province/ ; 20224310NHYCG04//University of South China Clinical Research 4310 Program/ ; 20224310NHYCG01//University of South China Clinical Research 4310 Program/ ; 82473965//National Natural Science Foundation of China/ ; 2023JJ50156//the Natural Science Foundation of Hunan Province/ ; 202250045223//Science and technology innovation Program of Hengyang City/ ; ZYYD2024CG17//Central Government Guided Local Science and Technology Development Fund Project in Xinjiang Uygur Autonomous Region/ ; 2024WK4008//Hunan Province Innovation Ecological Construction Plan Science and Technology Assistance Project in Xinjiang Uygur Autonomous Region/ ; SYTG-Y202429//Health Technology Promotion Project in Xinjiang Uygur Autonomous Region/ ; },
mesh = {Humans ; *Carcinoma, Hepatocellular/therapy/genetics/pathology/mortality/immunology/metabolism ; *NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism ; *Liver Neoplasms/therapy/genetics/pathology/mortality/immunology/metabolism ; *Tumor Microenvironment/genetics ; *Immunotherapy/methods ; Prognosis ; Male ; Gene Expression Regulation, Neoplastic ; Female ; Tumor-Associated Macrophages/immunology/metabolism ; Middle Aged ; Cell Line, Tumor ; Nomograms ; Multiomics ; },
abstract = {NAD(P)H dehydrogenase quinone 1 (NQO1) is overexpressed in various cancers and is strongly associated with an immunosuppressive microenvironment and poor prognosis. In this study, we explored the role of NQO1 in the microenvironment, prognosis and immunotherapy of Hepatocellular carcinoma (HCC) using multi-omics analysis and machine learning. The results revealed that NQO1 was significantly overexpressed in HCC cells. NQO1[+]HCC cells were correlated with poor prognosis and facilitated tumor-associated macrophages (TAMs) polarization to M2 macrophages. We identified core NQO1-related genes (NRGs) and developed the NRGs-related risk-scores in hepatocellular carcinoma (NRSHC). The comprehensive nomogram integrating NRSHC, age, and pathological tumor-node-metastasis (pTNM) Stage achieved an area under the curve (AUC) above 0.7, demonstrating its accuracy in predicting survival outcomes and immunotherapy responses of HCC patients. High-risk patients exhibited worse prognoses but greater sensitivity to immunotherapy. Additionally, a web-based prediction tool was designed to enhance clinical utility. In conclusion, NQO1 may play a critical role in M2 polarization and accelerates HCC progression. The NRSHC model and accompanying tools offer valuable insights for personalized HCC treatment.},
}

Humans
*Carcinoma, Hepatocellular/therapy/genetics/pathology/mortality/immunology/metabolism
*NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism
*Liver Neoplasms/therapy/genetics/pathology/mortality/immunology/metabolism
*Tumor Microenvironment/genetics
*Immunotherapy/methods
Prognosis
Male
Gene Expression Regulation, Neoplastic
Female
Tumor-Associated Macrophages/immunology/metabolism
Middle Aged
Cell Line, Tumor
Nomograms
Multiomics

@article {pmid40079420,
year = {2025},
author = {Jurburg, SD},
title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14102},
pmid = {40079420},
issn = {1755-0998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Metagenomics/methods
Microbiota
Animals
*DNA Barcoding, Taxonomic/methods
Biodiversity
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid40086783,
year = {2025},
author = {Yang, JZ and Li, JH and Liu, JL and Zhou, AD and Wang, H and Xie, XL and Zhang, KK and Wang, Q},
title = {Multiomics analysis revealed the effects of polystyrene nanoplastics at different environmentally relevant concentrations on intestinal homeostasis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {372},
number = {},
pages = {126050},
doi = {10.1016/j.envpol.2025.126050},
pmid = {40086783},
issn = {1873-6424},
mesh = {Animals ; Mice ; *Polystyrenes/toxicity ; Homeostasis/drug effects ; *Microplastics/toxicity ; Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects ; Male ; Metabolomics ; Multiomics ; },
abstract = {Nanoplastics pollution is a global issue, with the digestive tract being one of the first affected organs, requiring further research on its impact on intestinal health. This study involved orally exposing mice to polystyrene nanoplastics (PS-NPs) at doses of 0.1, 0.5, or 2.5 mg/d for 42 days. The effects on intestinal health were thoroughly assessed via microbiomics, metabolomics, transcriptomics, and molecular biology. Our study demonstrated that the administration of all three doses of PS-NPs resulted in increased colonic permeability, heightened colonic and peripheral inflammation, reduced levels of antimicrobial peptides, and shortened colonic length. These effects may be attributed to a reduction in the abundance of probiotic bacteria, such as Clostridia_UCG-014, Roseburia, and Akkermansia, alongside an increase in the abundance of the pathogenic bacterium Desulfovibrionaceae induced by PS-NPs. Furthermore, we underscored the crucial role of histidine metabolism in PS-NPs-induced colonic injury, characterized by a significant reduction of L-histidine, which is closely related to microbial ecological dysregulation. Corresponding to microbiota deterioration and metabolic dysregulation, transcriptome analysis revealed that PS-NPs may disrupt colonic immune homeostasis by activating the TLR4/MyD88/NF-κB/NLRP3 signaling pathway. In conclusion, this study provided novel insights into the mechanisms by which PS-NPs disrupt intestinal homeostasis through integrated multiomics analysis, revealing critical molecular pathway and providing a scientific basis for future risk assessment of nanoplastics exposure.},
}

Animals
Mice
*Polystyrenes/toxicity
Homeostasis/drug effects
*Microplastics/toxicity
Gastrointestinal Microbiome/drug effects
*Intestines/drug effects
Male
Metabolomics
Multiomics

@article {pmid40087979,
year = {2025},
author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A},
title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14099},
pmid = {40087979},
issn = {1755-0998},
support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659/WT_/Wellcome Trust/United Kingdom ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; },
mesh = {*Aquatic Organisms/parasitology ; *RNA, Ribosomal/genetics ; Microalgae/parasitology ; *Parasites/genetics/classification ; *Databases, Genetic ; },
abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.},
}

*Aquatic Organisms/parasitology
*RNA, Ribosomal/genetics
Microalgae/parasitology
*Parasites/genetics/classification
*Databases, Genetic

@article {pmid40089216,
year = {2025},
author = {Torres-Roman, JS and Quispe-Vicuña, C and Benavente-Casas, A and Julca-Marin, D and Rios-Garcia, W and Challapa-Mamani, MR and Rio-Muñiz, LD and Ybaseta-Medina, J},
title = {Trends in stroke mortality in Latin America and the Caribbean from 1997 to 2020 and predictions to 2035: An analysis of gender, and geographical disparities.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {34},
number = {6},
pages = {108286},
doi = {10.1016/j.jstrokecerebrovasdis.2025.108286},
pmid = {40089216},
issn = {1532-8511},
mesh = {Humans ; Latin America/epidemiology ; Female ; Male ; *Stroke/mortality/diagnosis ; Caribbean Region/epidemiology ; Risk Factors ; Sex Factors ; Middle Aged ; Sex Distribution ; Time Factors ; Databases, Factual ; Aged ; Adult ; *Health Status Disparities ; Age Distribution ; Forecasting ; Risk Assessment ; Age Factors ; Young Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Stroke is a leading cause of death and disability globally, with significant public health implications. In Latin America, while mortality rates have declined, the number of stroke cases has increased due to prevalent risk factors like high blood pressure and obesity. Unlike Europe, recent trends in stroke mortality in this region remain underreported.

OBJECTIVE: This study evaluates stroke mortality rates in Latin America Latin American and Caribbean (LAC) countries from 1997 to 2020 and predictions to 2035.

METHODS: This ecological observational study utilized mortality data from the World Health Organization database. Trends were analyzed using Joinpoint regression to evaluate the annual percent change (APC) by sex and country. Predicted mortality rates through 2035 were calculated using the Nordpred package in R. Changes in stroke mortality were assessed by disentangling the effects of population growth, aging, and risk factor modifications, based on age-specific rates and projections. Results were presented as absolute case numbers and relative percentages.

RESULTS: From 1997 to 2020, twelve countries presented significant reductions in stroke mortality rates for men in LAC, the main ones being Chile (-4.2 %), El Salvador (-4.2 %), and Puerto Rico (-4.0 %). Thirteen countries reported a reduction in their mortality for women, mainly in Puerto Rico (-4.3 %), Chile (-3.7 %), Argentina, El Salvador, and Uruguay (-3.5 %). By 2035, an increase in deaths among men and women is expected, mainly due to the increase in population structure and size. However, a decrease in the mortality rate will be reported, mainly due to the reduction of risk factors.

CONCLUSION: Our final findings show a reduction in stroke mortality trends in LAC countries between 1997 and 2020, due to creating public awareness about vascular risk factors by authorities and the implementation of effective health policies. By 2035, an overall increase in mortality is expected, mainly due to population change in each country.},
}

Humans
Latin America/epidemiology
Female
Male
*Stroke/mortality/diagnosis
Caribbean Region/epidemiology
Risk Factors
Sex Factors
Middle Aged
Sex Distribution
Time Factors
Databases, Factual
Aged
Adult
*Health Status Disparities
Age Distribution
Forecasting
Risk Assessment
Age Factors
Young Adult
Aged, 80 and over

@article {pmid40091604,
year = {2025},
author = {Tu, M and Liu, N and He, ZS and Dong, XM and Gao, TY and Zhu, A and Yang, JB and Zhang, SB},
title = {Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum.},
journal = {Plant biotechnology journal},
volume = {23},
number = {6},
pages = {2162-2181},
pmid = {40091604},
issn = {1467-7652},
support = {202403AC100032//Key Research and Development Program of Yunnan Province/ ; YNWR-CYJS-2020-023//High-level Talent Support Plan of Yunnan Province/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32170393//National Natural Science Foundation of China/ ; 2024YFF1306703//National Key Research and Development Program of China/ ; 202201AU070123//Yunnan Fundamental Research Project/ ; 202301AT070306//Yunnan Fundamental Research Project/ ; },
mesh = {*Flowers/metabolism/genetics ; *Orchidaceae/genetics/metabolism ; *Odorants/analysis ; Terpenes/metabolism ; Gene Expression Regulation, Plant ; Transcriptome ; Volatile Organic Compounds/metabolism ; Genomics ; Plant Proteins/metabolism/genetics ; Multiomics ; },
abstract = {Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.},
}

*Flowers/metabolism/genetics
*Orchidaceae/genetics/metabolism
*Odorants/analysis
Terpenes/metabolism
Gene Expression Regulation, Plant
Transcriptome
Volatile Organic Compounds/metabolism
Genomics
Plant Proteins/metabolism/genetics
Multiomics

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

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

@article {pmid40096239,
year = {2025},
author = {Dinnage, R and Kleineberg, M},
title = {Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012887},
pmid = {40096239},
issn = {1553-7358},
mesh = {Animals ; *Birds/anatomy & histology ; *Imaging, Three-Dimensional/methods ; Computational Biology ; *Beak/anatomy & histology ; *Artificial Intelligence ; Deep Learning ; },
abstract = {Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phenotypes at unprecedented scales. However, in order to meet the potential of this revolution we need new data analysis tools to deal with the complexity and heterogeneity of large-scale phenotypic data such as 3D shapes. In this study we explore the potential of generative Artificial Intelligence to help organize and extract meaning from complex 3D data. Specifically, we train a deep representational learning method known as DeepSDF on a dataset of 3D scans of the bills of 2,020 bird species. The model is designed to learn a continuous vector representation of 3D shapes, along with a 'decoder' function, that allows the transformation from this vector space to the original 3D morphological space. We find that approach successfully learns coherent representations: particular directions in latent space are associated with discernible morphological meaning (such as elongation, flattening, etc.). More importantly, learned latent vectors have ecological meaning as shown by their ability to predict the trophic niche of the bird each bill belongs to with a high degree of accuracy. Unlike existing 3D morphometric techniques, this method has very little requirements for human supervised tasks such as landmark placement, increasing it accessibility to labs with fewer labour resources. It has fewer strong assumptions than alternative dimension reduction techniques such as PCA. Once trained, 3D morphology predictions can be made from latent vectors very computationally cheaply. The trained model has been made publicly available and can be used by the community, including for finetuning on new data, representing an early step toward developing shared, reusable AI models for analyzing organismal morphology.},
}

Animals
*Birds/anatomy & histology
*Imaging, Three-Dimensional/methods
Computational Biology
*Beak/anatomy & histology
*Artificial Intelligence
Deep Learning

@article {pmid40102641,
year = {2026},
author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J},
title = {Information storage across a microbial community using universal RNA barcoding.},
journal = {Nature biotechnology},
volume = {44},
number = {2},
pages = {269-276},
pmid = {40102641},
issn = {1546-1696},
support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; },
mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods ; Escherichia coli/genetics ; Plasmids/genetics ; *Information Storage and Retrieval/methods ; RNA, Bacterial/genetics ; RNA, Catalytic/genetics ; Wastewater/microbiology ; },
abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.},
}

*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*DNA Barcoding, Taxonomic/methods
Escherichia coli/genetics
Plasmids/genetics
*Information Storage and Retrieval/methods
RNA, Bacterial/genetics
RNA, Catalytic/genetics
Wastewater/microbiology

@article {pmid40102961,
year = {2025},
author = {Hinojosa-Alvarez, S and Mendoza-Portillo, V and Chavez-Santoscoy, RA and Hernández-Pérez, J and Felix-Ceniceros, A and Magallón-Gayón, E and Mar-Silva, AF and Ochoa-Zavala, M and Díaz-Jaimes, P},
title = {The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {5},
pages = {},
pmid = {40102961},
issn = {2160-1836},
support = {CF-2023-G-493//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {Animals ; *Genome ; Molecular Sequence Annotation ; *Genomics/methods ; *Perciformes/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; *Fishes/genetics ; Whole Genome Sequencing ; Computational Biology/methods ; },
abstract = {For the first time, the complete genome assembly of the dolphinfish (Coryphaena hippurus), a tropical cosmopolitan species with commercial fishing importance was sequenced. Using a combination of Illumina and Nanopore sequencing technologies, a draft genome of 497.8 Mb was assembled into 6,044 contigs, with an N50 of 200.9 kb and a BUSCO genome completeness score of 89%. This high-quality genome assembly provides a valuable resource to study adaptive evolutionary processes and supports conservation and management strategies for this ecologically and economically significant species.},
}

Animals
*Genome
Molecular Sequence Annotation
*Genomics/methods
*Perciformes/genetics
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing
*Fishes/genetics
Whole Genome Sequencing
Computational Biology/methods

@article {pmid40111995,
year = {2025},
author = {Eales, O and Shearer, FM and McCaw, JM},
title = {How immunity shapes the long-term dynamics of influenza H3N2.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012893},
pmid = {40111995},
issn = {1553-7358},
mesh = {Humans ; *Influenza, Human/immunology/epidemiology/transmission/virology ; *Influenza A Virus, H3N2 Subtype/immunology/genetics ; Computational Biology ; *Models, Immunological ; Adult ; Aged ; Middle Aged ; Adolescent ; },
abstract = {Since its emergence in 1968, influenza A H3N2 has caused yearly epidemics in temperate regions. While infection confers immunity against antigenically similar strains, new antigenically distinct strains that evade existing immunity regularly emerge ('antigenic drift'). Immunity at the individual level is complex, depending on an individual's lifetime infection history. An individual's first infection with influenza typically elicits the greatest response with subsequent infections eliciting progressively reduced responses ('antigenic seniority'). The combined effect of individual-level immune responses and antigenic drift on the epidemiological dynamics of influenza are not well understood. Here we develop an integrated modelling framework of influenza transmission, immunity, and antigenic drift to show how individual-level exposure, and the build-up of population level immunity, shape the long-term epidemiological dynamics of H3N2. Including antigenic seniority in the model, we observe that following an initial decline after the pandemic year, the average annual attack rate increases over the next 80 years, before reaching an equilibrium, with greater increases in older age-groups. Our analyses suggest that the average attack rate of H3N2 is still in a growth phase. Further increases, particularly in the elderly, may be expected in coming decades, driving an increase in healthcare demand due to H3N2 infections.},
}

Humans
*Influenza, Human/immunology/epidemiology/transmission/virology
*Influenza A Virus, H3N2 Subtype/immunology/genetics
Computational Biology
*Models, Immunological
Adult
Aged
Middle Aged
Adolescent

@article {pmid40112992,
year = {2025},
author = {Wei, L and Luo, Z and Wu, X and Liu, C and Shi, Y and Zhang, Q and Chen, M and Qin, W},
title = {Multi-omics analysis provided insights into the fruit softening of postharvest okra under carboxymethyl chitosan treatment.},
journal = {International journal of biological macromolecules},
volume = {307},
number = {Pt 3},
pages = {142149},
doi = {10.1016/j.ijbiomac.2025.142149},
pmid = {40112992},
issn = {1879-0003},
mesh = {*Chitosan/analogs & derivatives/pharmacology ; *Fruit/drug effects/metabolism/genetics ; *Abelmoschus/genetics/metabolism/drug effects ; Gene Expression Regulation, Plant/drug effects ; Transcriptome/drug effects ; *Metabolomics/methods ; Metabolome/drug effects ; Gene Expression Profiling ; Pectins/metabolism ; Multiomics ; },
abstract = {To understand the potential regulatory mechanism of carboxymethyl chitosan (CMCS) treatment on postharvest softening of okra, a joint analysis of physiologic index, transcriptome and metabolome was used. The results showed that CMCS could delay the deterioration of the apparent quality of okra and reduce the degradation of chlorophyll. CMCS can reduce the accumulation of WSP and CSP and the decrease of NSP, and inhibit the enzyme activities of pectin degradation (PE, PG, PL). The results of metabolic pathways related to quality and texture showed that CMCS could increase the metabolic level of pentose phosphate pathway (PPP), inhibit the expression of membrane lipid degradation-related genes, and balance the expression of antioxidant-related genes. Ethylene and abscisic acid (ABA) are two important phytohormones. CMCS down-regulates the biosynthesis of ethylene and increases the expression of ABA. The combined analysis of transcriptome and metabolome showed that CMCS could significantly up-regulate flavonoid biosynthesis metabolites and transcriptional expression levels. Cellulose and pectin are important polymers to maintain the rigidity of okra cell wall. CMCS treatment can slow down the accumulation of cellulose by regulating the expression of DEGs related to cellulose synthesis (CesA) and degradation (EGase). CMCS slowed down the degradation of pectin by down-regulating the expression of pectin degradation-related genes. These results indicate that the quality of okra is deteriorated and the fruit is softened during cold storage. CMCS treatment can improve the nutritional quality of okra and slow down its texture decline. In this study, the regulatory effect of CMCS on softening and quality deterioration of okra during cold storage was discussed at the molecular level, which provided a reference for improving the quality of postharvest okra.},
}

*Chitosan/analogs & derivatives/pharmacology
*Fruit/drug effects/metabolism/genetics
*Abelmoschus/genetics/metabolism/drug effects
Gene Expression Regulation, Plant/drug effects
Transcriptome/drug effects
*Metabolomics/methods
Metabolome/drug effects
Gene Expression Profiling
Pectins/metabolism
Multiomics

@article {pmid40117176,
year = {2025},
author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP},
title = {Healthy microbiome-moving towards functional interpretation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40117176},
issn = {2047-217X},
support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Dysbiosis/microbiology ; Phylogeny ; *Microbiota ; Principal Component Analysis ; Computational Biology/methods ; },
abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).},
}

Humans
*Gastrointestinal Microbiome/genetics
*Inflammatory Bowel Diseases/microbiology
*Metagenomics/methods
Dysbiosis/microbiology
Phylogeny
*Microbiota
Principal Component Analysis
Computational Biology/methods

@article {pmid40120189,
year = {2025},
author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y},
title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.},
journal = {Water research},
volume = {279},
number = {},
pages = {123497},
doi = {10.1016/j.watres.2025.123497},
pmid = {40120189},
issn = {1879-2448},
mesh = {*Sewage ; *Ammonia ; Anaerobiosis ; Iron/chemistry ; Methane ; *Peracetic Acid/chemistry ; Multiomics ; },
abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.},
}

*Sewage
*Ammonia
Anaerobiosis
Iron/chemistry
Methane
*Peracetic Acid/chemistry
Multiomics

@article {pmid40123484,
year = {2025},
author = {Poulin, R},
title = {To bin or not to bin: why parasite abundance data should not be lumped into categories for statistical analysis.},
journal = {Parasitology},
volume = {152},
number = {3},
pages = {338-345},
pmid = {40123484},
issn = {1469-8161},
mesh = {Animals ; *Host-Parasite Interactions ; *Parasites/physiology ; *Parasitology/methods ; Data Interpretation, Statistical ; *Parasitic Diseases/parasitology ; },
abstract = {The impact of macroparasites on their hosts is proportional to the number of parasites per host, or parasite abundance. Abundance values are count data, i.e. integers ranging from 0 to some maximum number, depending on the host-parasite system. When using parasite abundance as a predictor in statistical analysis, a common approach is to bin values, i.e. group hosts into infection categories based on abundance, and test for differences in some response variable (e.g. a host trait) among these categories. There are well-documented pitfalls associated with this approach. Here, I use a literature review to show that binning abundance values for analysis has been used in one-third of studies published in parasitological journals over the past 15 years, and half of the studies in ecological and behavioural journals, often without any justification. Binning abundance data into arbitrary categories has been much more common among studies using experimental infections than among those using naturally infected hosts. I then use simulated data to demonstrate that true and significant relationships between parasite abundance and host traits can be missed when abundance values are binned for analysis, and vice versa that when there is no underlying relationship between abundance and host traits, analysis of binned data can create a spurious one. This holds regardless of the prevalence of infection or the level of parasite aggregation in a host sample. These findings argue strongly for the practice of binning abundance data as a predictor variable to be abandoned in favour of more appropriate analytical approaches.},
}

Animals
*Host-Parasite Interactions
*Parasites/physiology
*Parasitology/methods
Data Interpretation, Statistical
*Parasitic Diseases/parasitology

@article {pmid40125978,
year = {2025},
author = {Bailey, N and Stevison, L and Samuk, K},
title = {Correcting for Bias in Estimates of θ w and Tajima's D From Missing Data in Next-Generation Sequencing.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14104},
pmid = {40125978},
issn = {1755-0998},
support = {R35 GM147501/GM/NIGMS NIH HHS/United States ; R35GM147501/GM/NIGMS NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Genetic Variation ; Software ; *Computational Biology/methods ; Bias ; },
abstract = {Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator (θ w) of genetic diversity, and Tajima's D , used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (VCFtools, PopGenome, pegas and scikit-allel). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of θ w across programs. We found a consequent bias in estimates of Tajima's D , though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular pixy software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.},
}

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

@article {pmid40132265,
year = {2025},
author = {Gu, J and Shen, Y and Guo, L and Chen, Z and Zhou, D and Ji, G and Gu, A},
title = {Investigation of the mechanisms of liver injury induced by emamectin benzoate exposure at environmental concentrations in zebrafish: A multi-omics approach to explore the role of the gut-liver axis.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {138008},
doi = {10.1016/j.jhazmat.2025.138008},
pmid = {40132265},
issn = {1873-3336},
mesh = {Animals ; Zebrafish ; *Ivermectin/analogs & derivatives/toxicity ; *Liver/drug effects/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology ; *Water Pollutants, Chemical/toxicity ; Metabolomics ; Lipid Metabolism/drug effects ; *Insecticides/toxicity ; RNA, Ribosomal, 16S/genetics ; Multiomics ; },
abstract = {Emamectin benzoate (EMB) is a lipophilic pesticide that enters aquatic systems and adversely affects non-target organisms. This study investigated the long-term effects of EMB on zebrafish, exposing them to concentrations of 0, 0.1, 1, and 10 μg/L from the 4-hour post-fertilization (hpf) embryo stage to the 120-day post-fertilisation (dpf) adult stage. We found that exposure to 1 μg/L EMB induced liver damage, manifested as impaired liver function (elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT)), histopathological damage (lipid accumulation), as well as inflammatory and oxidative damage, with a dose - dependent effect. Non-targeted metabolomic analysis revealed an increase in lipid molecules in the liver, affecting the pathways related to glycerophospholipid metabolism. In addition, EMB exposure resulted in damage to the intestinal barrier and inflammatory responses in zebrafish. 16S rRNA sequencing demonstrated that EMB exposure resulted in notable alterations in the gut microbiota composition. Notably, the abundance of Plesiomonas and Cetobacterium increased in the EMB exposure group and exhibited a positive correlation with the majority of liver lipid metabolites. In contrast, reductions in Muribaculaceae and Alloprevotella were negatively correlated. The results of this study indicate that long-term exposure to EMB disrupts the gut microbiota, leading to the dysregulation of hepatic phospholipid metabolism. These findings provide new insights into the health risks associated with EMB and highlight its potential threats to higher organisms, including mammals.},
}

Animals
Zebrafish
*Ivermectin/analogs & derivatives/toxicity
*Liver/drug effects/metabolism/pathology
Gastrointestinal Microbiome/drug effects
*Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology
*Water Pollutants, Chemical/toxicity
Metabolomics
Lipid Metabolism/drug effects
*Insecticides/toxicity
RNA, Ribosomal, 16S/genetics
Multiomics

@article {pmid40136165,
year = {2025},
author = {Aquino, ÉC and Borowicc, SL and Alves-Souza, SN and Teixeira, RA and Ishitani, LH and Malta, DC and Morais Neto, OL},
title = {Distribution of garbage codes in the Mortality Information System, Brazil, 2000 to 2020.},
journal = {Ciencia & saude coletiva},
volume = {30},
number = {3},
pages = {e09442023},
doi = {10.1590/1413-81232025303.09442023},
pmid = {40136165},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; *Information Systems/statistics & numerical data ; Cause of Death/trends ; Time Factors ; Linear Models ; *Mortality/trends ; },
abstract = {The analysis of the causes of death is essential to understand the main problems that affect the health level of the population of a region or country. The garbage codes (GC) provide little useful information about causes of death. This study aims to identify the proportion of GC among the deaths registered and to analyze their temporal distribution in Brazil from 2000 to 2020. It's an ecological time-series study of the evolution of the proportion of GC in Brazil. Time series analysis was performed using segmented linear regression models (joinpoint). Between 2000 and 2020, 39.9% of deaths that occurred in Brazil were coded with GC. Between 2000 and 2007, there was a continuous and persistent reduction in the proportion of GC (APC -2.1; P < 0.001). Between 2007 and 2015, there continued to be a reduction, albeit to a lesser extent (APC = -0.7; P = 0.013). Between 2015 and 2018, there was no significant trend of the proportion of GC (APC = -2.3; P = 0.172), which persisted from 2018 (APC 3.2; P < 0.079). Although a reduction in the proportion of GC in Brazil was observed until 2018, this trend did not persist after that year. Reducing the proportion of GC allows managers to plan health policies more adequately for the population.},
}

Brazil/epidemiology
Humans
*Information Systems/statistics & numerical data
Cause of Death/trends
Time Factors
Linear Models
*Mortality/trends

@article {pmid40143245,
year = {2025},
author = {Culot, A and Abriat, G and Furlong, KP},
title = {High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
pmid = {40143245},
issn = {1999-4915},
mesh = {*Genome, Viral ; *Bacteriophages/genetics ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; *Phage Therapy/methods ; Humans ; },
abstract = {Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.},
}

*Genome, Viral
*Bacteriophages/genetics
*Molecular Sequence Annotation/methods
*Computational Biology/methods
*Phage Therapy/methods
Humans

@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; },
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}

*Floods
Salinity
RNA, Ribosomal, 16S/genetics
Geologic Sediments/microbiology
Metabolomics
Microbiota
Multiomics

@article {pmid40156461,
year = {2025},
author = {Sharma, G and Deuis, JR and Jia, X and Crawford, T and Rahnama, S and Undheim, EAB and Vetter, I and Chin, YK and Mobli, M},
title = {Refining the NaV1.7 pharmacophore of a class of venom-derived peptide inhibitors via a combination of in silico screening and rational engineering.},
journal = {FEBS letters},
volume = {599},
number = {12},
pages = {1717-1732},
pmid = {40156461},
issn = {1873-3468},
support = {FTl10100925//Australian Research Council/ ; DE160101142//Australian Research Council/ ; APP1102267//National Health and Medical Research Council/ ; APP1080405//National Health and Medical Research Council/ ; 2017086//National Health and Medical Research Council/ ; APP1034958//National Health and Medical Research Council/ ; //University of Queensland/ ; 101039862/ERC_/European Research Council/International ; },
mesh = {*NAV1.7 Voltage-Gated Sodium Channel/chemistry/metabolism/genetics ; Humans ; *Peptides/chemistry/pharmacology ; Animals ; *Voltage-Gated Sodium Channel Blockers/chemistry/pharmacology ; Structure-Activity Relationship ; Amino Acid Sequence ; Computer Simulation ; Protein Engineering ; *Scorpion Venoms/chemistry/pharmacology ; Computational Biology ; Pharmacophore ; },
abstract = {Ion channels are among the main targets of venom peptides. Extensive functional screening has identified a number of these peptides as modulators of the voltage-gated sodium channel subtype NaV1.7, a potential target for the treatment of chronic pain. In this study, we used a bioinformatic approach that can automatically identify NaV1.7 gating modifier toxins from sequence information alone. The method further enables the incorporation of evolutionarily accessible sequence space in structure-activity relationship studies. The in silico method identified a putative NaV1.7 inhibitor, μ-theraphotoxin Cg4a, which we produced recombinantly and confirmed as a NaV1.7 inhibitor. Using structural and mutagenesis studies, we propose an improved definition of the pharmacophore of this class of NaV1.7 inhibitors, aiding future in silico screening and classification of NaV1.7 inhibitors.},
}

*NAV1.7 Voltage-Gated Sodium Channel/chemistry/metabolism/genetics
Humans
*Peptides/chemistry/pharmacology
Animals
*Voltage-Gated Sodium Channel Blockers/chemistry/pharmacology
Structure-Activity Relationship
Amino Acid Sequence
Computer Simulation
Protein Engineering
*Scorpion Venoms/chemistry/pharmacology
Computational Biology
Pharmacophore

@article {pmid40163742,
year = {2025},
author = {Ghassemi Nedjad, C and Bolteau, M and Bourneuf, L and Paulevé, L and Frioux, C},
title = {Seed2LP: seed inference in metabolic networks for reverse ecology applications.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
pmid = {40163742},
issn = {1367-4811},
support = {//French National Research Agency/ ; },
mesh = {*Metabolic Networks and Pathways ; *Software ; *Computational Biology/methods ; Models, Biological ; Algorithms ; },
abstract = {MOTIVATION: A challenging problem in microbiology is to determine nutritional requirements of microorganisms and culture them, especially for the microbial dark matter detected solely with culture-independent methods. The latter foster an increasing amount of genomic sequences that can be explored with reverse ecology approaches to raise hypotheses on the corresponding populations. Building upon genome-scale metabolic networks (GSMNs) obtained from genome annotations, metabolic models predict contextualized phenotypes using nutrient information.

RESULTS: We developed the tool Seed2LP, addressing the inverse problem of predicting source nutrients, or seeds, from a GSMN and a metabolic objective. The originality of Seed2LP is its hybrid model, combining a scalable and discrete Boolean approximation of metabolic activity, with the numerically accurate flux balance analysis (FBA). Seed inference is highly customizable, with multiple search and solving modes, exploring the search space of external and internal metabolites combinations. Application to a benchmark of 107 curated GSMNs highlights the usefulness of a logic modelling method over a graph-based approach to predict seeds, and the relevance of hybrid solving to satisfy FBA constraints. Focusing on the dependency between metabolism and environment, Seed2LP is a computational support contributing to address the multifactorial challenge of culturing possibly uncultured microorganisms.

Seed2LP is available on https://github.com/bioasp/seed2lp.},
}

*Metabolic Networks and Pathways
*Software
*Computational Biology/methods
Models, Biological
Algorithms

@article {pmid40167332,
year = {2025},
author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF},
title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14105},
pmid = {40167332},
issn = {1755-0998},
support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; },
mesh = {*Metagenomics/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Metagenome ; },
abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.},
}

*Metagenomics/methods
*Biodiversity
*DNA, Environmental/genetics
*Computational Biology/methods
DNA Barcoding, Taxonomic/methods
Metagenome

@article {pmid40169791,
year = {2025},
author = {Ding, DY and Tang, Z and Zhu, B and Ren, H and Shalek, AK and Tibshirani, R and Nolan, GP},
title = {Quantitative characterization of tissue states using multiomics and ecological spatial analysis.},
journal = {Nature genetics},
volume = {57},
number = {4},
pages = {910-921},
pmid = {40169791},
issn = {1546-1718},
support = {P01 AI177687/AI/NIAID NIH HHS/United States ; U54 HG010426/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Spatial Analysis ; *Genomics/methods ; Single-Cell Analysis/methods ; Multiomics ; },
abstract = {The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease.},
}

Humans
*Spatial Analysis
*Genomics/methods
Single-Cell Analysis/methods
Multiomics

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

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

@article {pmid40173380,
year = {2025},
author = {Zagorščak, M and Abdelhakim, L and Rodriguez-Granados, NY and Široká, J and Ghatak, A and Bleker, C and Blejec, A and Zrimec, J and Novák, O and Pěnčík, A and Baebler, Š and Perez Borroto, L and Schuy, C and Županič, A and Afjehi-Sadat, L and Wurzinger, B and Weckwerth, W and Pompe Novak, M and Knight, MR and Strnad, M and Bachem, C and Chaturvedi, P and Sonnewald, S and Sasidharan, R and Panzarová, K and Gruden, K and Teige, M},
title = {Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.},
journal = {Plant physiology},
volume = {197},
number = {4},
pages = {},
pmid = {40173380},
issn = {1532-2548},
support = {//H2020-SFS-2019-2/ ; P4-0165//Slovenian Research Agency/ ; //Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_026/0008446//European Regional Development Fund-Project/ ; },
mesh = {*Solanum tuberosum/physiology/genetics/metabolism ; *Stress, Physiological/genetics ; Phenotype ; Droughts ; Proteomics ; Metabolomics ; Gene Expression Regulation, Plant ; Transcriptome ; Plant Leaves/physiology ; Plant Tubers ; Multiomics ; },
abstract = {Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.},
}

*Solanum tuberosum/physiology/genetics/metabolism
*Stress, Physiological/genetics
Phenotype
Droughts
Proteomics
Metabolomics
Gene Expression Regulation, Plant
Transcriptome
Plant Leaves/physiology
Plant Tubers
Multiomics

@article {pmid40173850,
year = {2025},
author = {Vivien, R and Martin, P},
title = {Maintaining taxonomic accuracy in genetic databases: A duty for taxonomists-Reanalysis of the DNA sequences from Mercan et al. (2024) on the genus Potamothrix (Annelida, Clitellata) in Turkish lakes.},
journal = {Zootaxa},
volume = {5575},
number = {4},
pages = {555-562},
doi = {10.11646/zootaxa.5575.4.5},
pmid = {40173850},
issn = {1175-5334},
mesh = {Turkey ; Animals ; Lakes ; Phylogeny ; *Databases, Genetic/standards ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; *Polychaeta/classification/genetics ; },
abstract = {Public DNA sequence databases such as GenBank are widely used for identification of organisms in ecological and taxonomic studies. It is important that these public databases contain as few mistakes as possible and that any errors detected in these databases are reported. Here, we reanalyzed the COI sequences of Mercan et al. (2024) and showed that they were mistakenly considered by these authors as belonging to different populations (haplotypes) within the species Potamothrix hammoniensis (Tubificinae). We found that they corresponded to four distinct Tubificinae lineages (species), Pothamothrix alatus paravanicus, Potamothrix bavaricus, Tubifex sp. and Potamothrix sp. Despite these identification errors, the data from Mercan et al. (2024) remain interesting as they provide new information on the diversity of the genus Potamothrix in Turkey. Prompt measures must be taken to correct these errors and prevent them from being detrimental to future studies.},
}

Turkey
Animals
Lakes
Phylogeny
*Databases, Genetic/standards
*Databases, Nucleic Acid/standards
Sequence Analysis, DNA
*Polychaeta/classification/genetics

@article {pmid40178345,
year = {2025},
author = {Riobueno-Naylor, A and Gomez, I and Quan, S and Hutt Vater, C and Montes, M and Hoskova, B and Lai, BS},
title = {Methods for integrating public datasets: insights from youth disaster mental health research.},
journal = {European journal of psychotraumatology},
volume = {16},
number = {1},
pages = {2481699},
pmid = {40178345},
issn = {2000-8066},
mesh = {Humans ; Adolescent ; *Disasters ; United States/epidemiology ; *Mental Health/statistics & numerical data ; Male ; Female ; *Depression/epidemiology ; *Datasets as Topic ; Databases, Factual ; },
abstract = {Introduction: Weather-related disasters pose significant risks to youth mental health. Exposure to multiple disasters is becoming more common; however, the effects of such exposure remain understudied. This study demonstrates the application of integrative data approaches and FAIR (Findable, Accessible, Interoperable, Reusable) data principles to evaluate the relationship between cumulative disaster exposure and youth depression and suicidality in the United States, taking into account contextual factors across levels of social ecology.Methods: We combined data from five public sources, including the Youth Risk Behavior Surveillance System (YRBS), Federal Emergency Management Agency (FEMA), United States Census Bureau, Center for Homeland Defense and Security School Shooting Safety Compendium, and Global Terrorism Database. The integrative dataset included 415,701 youth from 37 districts across the United States who completed the YRBS between 1999 and 2021. The YRBS served as the core dataset.Results: This data note highlights strategies for harmonizing diverse data formats, addressing geographic and temporal inconsistencies, and validating integrated datasets. Automated data cleaning and visualization techniques enhance accuracy and efficiency. Planning for sensitivity analyses before data cleaning is recommended to improve the data integration process and enhance the robustness of findings.Discussion: This integrative approach demonstrates how leveraging FAIR principles can advance trauma research by facilitating large-scale analyses of complex public health questions. The methods provide a replicable framework for examining population-level impacts of phenomena and highlight opportunities for expanding trauma research.},
}

Humans
Adolescent
*Disasters
United States/epidemiology
*Mental Health/statistics & numerical data
Male
Female
*Depression/epidemiology
*Datasets as Topic
Databases, Factual

@article {pmid40179423,
year = {2025},
author = {Dejeante, R and Valeix, M and Chamaillé-Jammes, S},
title = {Do Mixed-Species Groups Travel as One? An Investigation on Large African Herbivores Monitored Using Animal-Borne Video Collars.},
journal = {The American naturalist},
volume = {205},
number = {4},
pages = {451-458},
doi = {10.1086/734410},
pmid = {40179423},
issn = {1537-5323},
mesh = {Animals ; Video Recording ; *Herbivory ; *Giraffes/physiology ; *Equidae/physiology ; *Antelopes/physiology ; Social Behavior ; Geographic Information Systems ; Ecosystem ; },
abstract = {AbstractAlthough prey foraging in mixed-species groups benefit from a reduced risk of predation, whether heterospecific groupmates move together in the landscape, and more generally to what extent mixed-species groups remain cohesive over time and space, remains unknown. Here, we used GPS collars with video cameras to investigate the movements of plains zebras (Equus quagga) in mixed-species groups. Blue wildebeest (Connochaetes taurinus), impalas (Aepyceros melampus), and giraffes (Giraffa camelopardalis) commonly form mixed-species groups with zebras in savanna ecosystems. We found that zebras adjust their movement decisions solely on the basis of the presence of giraffes, being more likely to move in zebra-giraffe herds, and this was correlated with a higher cohesion of such groups. Additionally, zebras moving with giraffes spent more time grazing, suggesting that zebras benefit from foraging in the proximity of giraffes. Our results provide new insights into animal movements in mixed-species groups, contributing to a better consideration of mutualism in movement ecology.},
}

Animals
Video Recording
*Herbivory
*Giraffes/physiology
*Equidae/physiology
*Antelopes/physiology
Social Behavior
Geographic Information Systems
Ecosystem

@article {pmid40179878,
year = {2025},
author = {Li, Y and Liu, X and Guo, L and Han, K and Fang, S and Wan, X and Wang, D and Xu, X and Jiang, L and Fan, G and Xu, M},
title = {SpaGRN: Investigating spatially informed regulatory paths for spatially resolved transcriptomics data.},
journal = {Cell systems},
volume = {16},
number = {4},
pages = {101243},
doi = {10.1016/j.cels.2025.101243},
pmid = {40179878},
issn = {2405-4720},
mesh = {Animals ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; Humans ; *Gene Regulatory Networks/genetics ; Drosophila/genetics ; Computational Biology/methods ; },
abstract = {Cells spatially organize into distinct cell types or functional domains through localized gene regulatory networks. However, current spatially resolved transcriptomics analyses fail to integrate spatial constraints and proximal cell influences, limiting the mechanistic understanding of tissue organization. Here, we introduce SpaGRN, a statistical framework that reconstructs cell-type- or functional-domain-specific, dynamic, and spatial regulons by coupling intracellular spatial regulatory causality with extracellular signaling path information. Benchmarking across synthetic and real datasets demonstrates SpaGRN's superior precision over state-of-the-art tools in identifying context-dependent regulons. Applied to diverse spatially resolved transcriptomics platforms (Stereo-seq, STARmap, MERFISH, CosMx, Slide-seq, and 10x Visium), complex cancerous samples, and 3D datasets of developing Drosophila embryos and larvae, SpaGRN not only provides a versatile toolkit for decoding receptor-mediated spatial regulons but also reveals spatiotemporal regulatory mechanisms underlying organogenesis and inflammation.},
}

Animals
*Transcriptome/genetics
*Gene Expression Profiling/methods
Humans
*Gene Regulatory Networks/genetics
Drosophila/genetics
Computational Biology/methods

@article {pmid40180917,
year = {2025},
author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA},
title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3204},
pmid = {40180917},
issn = {2041-1723},
support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; },
abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
*Metagenomics/methods
*Bacterial Proteins/genetics/metabolism
*Bacteria/genetics/classification/metabolism
Phylogeny
Computational Biology/methods

@article {pmid40185844,
year = {2025},
author = {Amin, NU and Islam, F and Umar, M and Muhammad, W and Rahman, SU and Gaafar, AZ and Shah, TA and Dauelbait, M and Bourhia, M},
title = {Evaluation of crop phenology using remote sensing and decision support system for agrotechnology transfer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11582},
pmid = {40185844},
issn = {2045-2322},
mesh = {*Remote Sensing Technology/methods ; *Crops, Agricultural/growth & development ; Biomass ; *Agriculture/methods ; *Decision Support Techniques ; Plant Leaves/growth & development ; Seasons ; },
abstract = {The decision support system for agro-technology transfer (DSSAT) is a worldwide crop modeling platform used for crops growth, yield, leaf area index (LAI), and biomass estimation under varying climatic, soil and management conditions. This study integrates DSSAT with satellite remote sensing (RS) data to estimates canopy state variables like LAI and biomass. For LAI estimation, Moderate Resolution Imaging Spectroradiometer (MODIS) product (MCD15A3H for LAI and MOD17A2 / MOD17A3 products for biomass) are used. Field data for Sheikhupura district is provided by National Agriculture Research Council (NARC) and used for the calibration and validation of the model. The results indicate strong agreement between the DSSAT and RS derived estimates. Correlation coefficients (R[2]) for LAI varied from 0.82 to 0.90, while for biomass ranged from 0.92 to 0.99 over two farms and two growing seasons (2012-2014). The index of agreement (D-index) ranged from 0.79 to 0.96 across the two farms and two growing seasons (2012-2014) affirming the model's durability. However, the biomass estimated from RS data is underestimated due to saturation phenomenon in the optical RS. The performance metrics, comprising the coefficient of residual mass (CRM) and normalized root mean square error (nRMSE), further substantiate the approach utilized. This study will help decision and policymakers and researchers to apply geospatial techniques for the sustainable agriculture practices.},
}

*Remote Sensing Technology/methods
*Crops, Agricultural/growth & development
Biomass
*Agriculture/methods
*Decision Support Techniques
Plant Leaves/growth & development
Seasons

@article {pmid40188731,
year = {2025},
author = {Li, Y and Huang, S and Jiang, S and Yang, L and Huang, J and Yang, Q and Jiang, Z and Shi, J and Ma, Z and Li, E and Zhou, F},
title = {Multi-omics insights into antioxidant and immune responses in Penaeus monodon under ammonia-N, low salinity, and combined stress.},
journal = {Ecotoxicology and environmental safety},
volume = {295},
number = {},
pages = {118156},
doi = {10.1016/j.ecoenv.2025.118156},
pmid = {40188731},
issn = {1090-2414},
mesh = {Animals ; *Penaeidae/immunology/physiology/drug effects ; *Ammonia/toxicity ; Salinity ; *Antioxidants/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Stress, Physiological ; Transcriptome ; Nitrogen/toxicity ; Multiomics ; },
abstract = {Ammonia nitrogen and salinity are critical environmental factors that significantly impact marine organisms and present substantial threats to Penaeus monodon species within aquaculture systems. This study utilized a comprehensive multi-omics approach, encompassing transcriptomics, metabolomics, and gut microbiome analysis, to systematically examine the biological responses of shrimp subjected to low salinity, ammonia nitrogen stress, and their combined conditions. Metabolomic analysis demonstrated that exposure to ammonia nitrogen stress markedly influenced the concentrations of antioxidant-related metabolites, such as glutathione, suggesting that shrimp mitigate oxidative stress by augmenting their antioxidant capacity. The transcriptomic analysis revealed an upregulation of genes linked to energy metabolism and immune responses and antioxidant enzymes. Concurrently, gut microbiome analysis demonstrated that ammonia nitrogen stress resulted in a marked increase in Vibrio populations and a significant decrease in Photobacterium, indicating that alterations in microbial community structure are intricately associated with the shrimp stress response. A comprehensive analysis further indicated that the combined stressors of ammonia nitrogen and salinity exert a synergistic effect on the immune function and physiological homeostasis of shrimp by modulating antioxidant metabolic pathways and gut microbial communities. These findings provide critical systematic data for elucidating the mechanisms through which ammonia nitrogen and salinity influence marine ecosystems, offering substantial implications for environmental protection and ecological management.},
}

Animals
*Penaeidae/immunology/physiology/drug effects
*Ammonia/toxicity
Salinity
*Antioxidants/metabolism
*Water Pollutants, Chemical/toxicity
Oxidative Stress
Gastrointestinal Microbiome/drug effects
Metabolomics
Stress, Physiological
Transcriptome
Nitrogen/toxicity
Multiomics

@article {pmid40197051,
year = {2025},
author = {Shamash, M and Sinha, A and Maurice, CF},
title = {Improving gut virome comparisons using predicted phage host information.},
journal = {mSystems},
volume = {10},
number = {5},
pages = {e0136424},
pmid = {40197051},
issn = {2379-5077},
mesh = {*Bacteriophages/genetics/classification/physiology ; *Virome/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; Feces/virology/microbiology ; Metagenomics/methods ; Computational Biology/methods ; Bacteria/virology ; },
abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.

IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.},
}

*Bacteriophages/genetics/classification/physiology
*Virome/genetics
Humans
*Gastrointestinal Microbiome/genetics
Animals
Mice
Feces/virology/microbiology
Metagenomics/methods
Computational Biology/methods
Bacteria/virology

@article {pmid40198416,
year = {2025},
author = {Huan, F and Gao, S and Gu, Y and Ni, L and Wu, M and Li, Y and Liu, M and Yang, Y and Xiao, A and Liu, G},
title = {Molecular Allergology: Epitope Discovery and Its Application for Allergen-Specific Immunotherapy of Food Allergy.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {37},
pmid = {40198416},
issn = {1559-0267},
support = {32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; },
mesh = {Humans ; *Food Hypersensitivity/therapy/immunology ; *Allergens/immunology/chemistry/genetics ; *Desensitization, Immunologic/methods ; Animals ; *Epitopes, T-Lymphocyte/immunology ; *Epitopes, B-Lymphocyte/immunology ; *Epitopes/immunology ; Computational Biology ; Epitope Mapping ; },
abstract = {The prevalence of food allergy continues to rise, posing a significant burden on health and quality of life. Research on antigenic epitope identification and hypoallergenic agent design is advancing allergen-specific immunotherapy (AIT). This review focuses on food allergens from the perspective of molecular allergology, provides an overview of integration of bioinformatics and experimental validation for epitope identification, highlights hypoallergenic agents designed based on epitope information, and offers a valuable guidance to the application of hypoallergenic agents in AIT. With the development of molecular allergology, the characterization of the amino acid sequence and structure of the allergen at the molecular level facilitates T-/B-cell epitope identification. Alignment of the identified epitopes in food allergens revealed that the amino acid sequence of T-/B-cell epitopes barely overlapped, providing crucial data to design allergen molecules as a promising form for treating (FA) food allergy. Manipulating antigenic epitopes can reduce the allergenicity of allergens to obtain hypoallergenic agents, thereby minimizing the severe side effects associated with AIT. Currently, hypoallergenic agents are mainly developed through synthetic epitope peptides, genetic engineering, or food processing methods based on the identified epitope. New strategies such as DNA vaccines, signaling molecules coupling, and nanoparticles are emerging to improve efficiency. Although significant progress has been made in designing hypoallergenic agents for AIT, the challenge in clinical translation is to determine the appropriate dose and duration of treatment to induce long-term immune tolerance.},
}

Humans
*Food Hypersensitivity/therapy/immunology
*Allergens/immunology/chemistry/genetics
*Desensitization, Immunologic/methods
Animals
*Epitopes, T-Lymphocyte/immunology
*Epitopes, B-Lymphocyte/immunology
*Epitopes/immunology
Computational Biology
Epitope Mapping

@article {pmid40198742,
year = {2025},
author = {Choi, H and Lee, CH},
title = {The impact of climate change on ecology of tick associated with tick-borne diseases.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012903},
pmid = {40198742},
issn = {1553-7358},
mesh = {*Climate Change ; *Tick-Borne Diseases/transmission/epidemiology/prevention & control ; Animals ; *Ticks/physiology ; Humans ; *Models, Biological ; Population Dynamics ; Computational Biology ; },
abstract = {Infectious diseases have caused significant economic and human losses worldwide. Growing concerns exist regarding climate change potentially exacerbating the spread of these diseases, particularly those transmitted by vectors such as ticks and mosquitoes. Tick-borne diseases, such as Severe Fever with Thrombocytopenia Syndrome (SFTS), can be particularly detrimental to elderly and immunocompromised individuals. This study utilizes a mathematical modeling approach to predict changes in tick populations under climate change scenarios, incorporating tick ecology and climate-sensitive parameters. Sensitivity analysis is performed to investigate the factors influencing tick population dynamics. The study further explores effective tick control strategies and their cost-effectiveness in the context of climate change. The findings indicate that the efficacy of tick population reduction varies greatly depending on the timing of control measure implementation and the effectiveness of the control strategies exhibits a strong dependence on the duration of implementation. Furthermore, as climate change intensifies, tick populations are projected to increase, leading to a rise in control costs and SFTS cases. In light of these findings, identifying and implementing appropriate control measures to manage tick populations under climate change will be increasingly crucial.},
}

*Climate Change
*Tick-Borne Diseases/transmission/epidemiology/prevention & control
Animals
*Ticks/physiology
Humans
*Models, Biological
Population Dynamics
Computational Biology

@article {pmid40199921,
year = {2025},
author = {Chaudhary, VB and Nokes, LF and González, JB and Cooper, PO and Katula, AM and Mares, EC and Pehim Limbu, S and Robinson, JN and Aguilar-Trigueros, CA},
title = {TraitAM, a global spore trait database for arbuscular mycorrhizal fungi.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {588},
pmid = {40199921},
issn = {2052-4463},
support = {DEB-2205650//National Science Foundation (NSF)/ ; Feodor Lynen Fellowship//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; },
mesh = {Databases, Factual ; *Mycorrhizae/genetics ; Phylogeny ; *Spores, Fungal/genetics ; Symbiosis ; },
abstract = {Knowledge regarding organismal traits supports a better understanding of the relationship between form and function and can be used to predict the consequences of environmental stressors on ecological and evolutionary processes. Most plants on Earth form symbioses with mycorrhizal fungi, but our ability to make trait-based inferences for these fungi is limited due to a lack of publicly available trait data. Here, we present TraitAM, a comprehensive database of multiple spore traits for all described species of the most common group of mycorrhizal fungi, the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina). Trait data for 344 species were mined from original species descriptions and used to calculate newly developed fungal trait metrics that can be employed to explore both intra- and inter-specific variation in traits. TraitAM also includes an updated phylogenetic tree that can be used to conduct phylogenetically-informed multivariate analyses of AM fungal traits. TraitAM will aid our further understanding of the biology, ecology, and evolution of these globally widespread, symbiotic fungi.},
}

Databases, Factual
*Mycorrhizae/genetics
Phylogeny
*Spores, Fungal/genetics
Symbiosis

@article {pmid40200134,
year = {2025},
author = {Hu, X and Pan, L and Fu, C and Zhu, Q and Hao, J and Wang, X and Nawaz, M and Qu, J and Zhang, J and Chen, Y and Zong, J and Liao, L and Tang, M and Wang, Z},
title = {A multi-omics analysis reveals candidate genes for Cd tolerance in Paspalum vaginatum.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {441},
pmid = {40200134},
issn = {1471-2229},
support = {No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; ZDYF2023XDNY078//the Hainan Province Science and Technology Special Fund/ ; XTCX2022STC10//Collaborative Innovation Center Project of Ecological Civilization in Hainan University/ ; KJRC2023C21//Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; No.32060409//the National Natural Science Foundation of China/ ; XTCX2022NYB08//Collaborative Innovation Center Project of Nanfan and High-Efficiency Tropical Agriculture in Hainan University/ ; },
mesh = {*Cadmium/toxicity ; *Paspalum/genetics/drug effects/metabolism/physiology ; Genome-Wide Association Study ; *Genes, Plant ; Gene Expression Regulation, Plant ; Multiomics ; },
abstract = {Cadmium (Cd) pollution in the farmland has become a serious global issue threatening both human health and plant biomass production. Seashore paspalum (Paspalum vaginatum Sw.), a halophytic turfgrass, has been recognized as a Cd-tolerant species. However, the underlying genetic basis of natural variations in Cd tolerance still remains unknown. This study is possibly the first to apply genome-wide association studies (GWAS) and selective sweep analysis to identify potential Cd stress-responsive genes in P. vaginatum. We identified a total of 89 candidate genes and 656 putative selective sweeps regions. Based on the correlation analysis of differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs), we identified the 55 key genes associated with metabolic changes induced by Cd treatment as the Cd tolerance-related genes. These genes showed significantly higher expression in Cd-tolerant accessions as compared to Cd-susceptive accessions. Therefore, our multi-omics study revealed the molecular and genetic basis of Cd tolerance, which may help develop Cd tolerant crop varieties.},
}

*Cadmium/toxicity
*Paspalum/genetics/drug effects/metabolism/physiology
Genome-Wide Association Study
*Genes, Plant
Gene Expression Regulation, Plant
Multiomics