bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic characterisation ofListeria monocytogenesisolated from normally sterile human body fluids in Lithuania from 2016 to 2021
Authors: Slavinska Anželika , Jauneikaite Elita , Meškytė Ugnė , Kirkliauskienė Agnė , Misevič Adam , Petrutienė Aurelija , Kuisiene Nomeda 
Published: January 2025

AbstractListeria monocytogenesis a saprophytic gram positive bacterium and opportunistic foodborne pathogen that can cause listeriosis in humans. The incidence of listeriosis has been rising globally and, despite antimicrobial treatment, the mortality rates associated with the most severe forms of listeriosis such as sepsis, meningitis, and meningoencephalitis remain high. The notification of listeriosis in humans is mandatory in Lithuania and up to 10 cases are reported annually. However, no studies have described the detailed virulence and antimicrobial susceptibility profiles of any clinicalL. monocytogenesstrains in Lithuania. Accordingly, this study aimed to describe the antibiotic susceptibility of invasiveL. monocytogenesand perform in-depth characterisation of strains isolated from patients with neuroinfections through whole-genome sequencing.A total of 70 isolates were collected, mostly from infected patients aged 65 or older, between 2016 and 2021: 41 (58.6%) from blood, 19 (27.1%) from cerebrospinal fluid, five (7.1%) from wounds, one (1.4%) from pleural fluid, and one (1.4%) from a brain abscess. Two phylogenetic lineages were identified—I (n = 16/70, 22.9%) and II (n = 54/70, 77.1%)—along with three serogroups—IIa (n = 53/70, 75.7%), IVb (n = 16/70, 22.9%), and IIc (n = 1/70, 1.4%). Genomic analysis of 20 isolates showed a high level of diversity with seven genotypes: ST6 (n = 6), ST155 (n = 5), ST8 (n = 4), ST504 (n = 2), and singletons for ST37, ST451, and ST2. Phylogenetic analysis clustered these isolates into two clades defined by serogroups IVb and IIa. Notably, five isolates were clustered tightly together (difference of 6–48 core SNPs from reference and 0, 4, or 44 SNPs from each other) with ST155, previously reported in a European outbreak. Comparison with publicly availableL. monocytogenesgenomes did not identify unique clusters or genotypes. No acquired antimicrobial resistance genes were identified.Our study highlights the complementary value of whole-genome sequencing in routine PCR-based surveillance in Lithuania. This is the first study to characterise and compare genomes forL. monocytogenesassociated with neuroinfections in Lithuania using whole-genome sequencing. The retrospective detection of the ST155 clone underscores the need for a review and strengthening of epidemiological surveillance strategies in clinical and non-clinical settings in Lithuania.Data summaryThe raw sequencing reads from theL. monocytogenesisolates generated in this study are available from the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser/home) under project accession numberPRJEB80562; accession numbers for individual isolates are provided inSuppl. Table S1. Draft genomes of theL. monocytogenesstrains were submitted to the BIGSdb-Lmdatabase (https://bigsdb.pasteur.fr/listeria/) under accession numbers 110263–110281 and 108726.
Complementary assessment of fish biodiversity across the upper/lower mesophotic interface in a subtropical coral reef using eDNA metabarcoding and baited cameras
Authors: Noyes Timothy J. , Blanco-Bercial Leocadio , Mariani Stefano , Goodbody-Gringley Gretchen , McDevitt Allan D. 
Published: January 2025

AbstractMesophotic Coral Ecosystems (MCEs) occur in the middle to lower photic zone (∼30–150 m) of tropical and subtropical regions, are often extensions of shallow reef communities, and generally hold great importance for local commercial fisheries. Compared to their shallower counterpart, MCEs have been traditionally understudied, primarily due to their inaccessibility with traditional monitoring methodologies. In this study, we aim to provide an interdisciplinary assessment of the biodiversity of Bermudan reef fish communities from the upper/lower mesophotic interface (60 m) by utilising a combination of environmental DNA (eDNA) metabarcoding and baited remote underwater videos (BRUVs). In total, 155 species from 137 genera were detected by eDNA metabarcoding whilst a total of 85 species from 53 genera were detected by BRUVs. The combined species detections totalled 182 species with approximately half of those detections unique to this study when compared to previous studies. Both methodologies found differences in α-diversity between study locations, with each method independently detecting the highest species richness at the same location. The species assemblage at each location was dominated (∼80%) by species known to occur throughout the shallow reef system and the upper mesophotic, whilst species only known to inhabit mesophotic ecosystems accounted for ∼6% at each location. These findings suggest a high level of species continuity with the adjacent shallower reef systems. The complementary nature of eDNA metabarcoding and BRUVs allows for a more accurate characterisation of fish biodiversity at the upper/lower mesophotic interface, which can lead to a more comprehensive understanding of ecosystem structure and more informed management decisions.
Augmenting Fact and Date of Death in Electronic Health Records using Internet Media Sources: A Validation Study from Two Large Healthcare Systems
Authors: LeNoue-Newton Michele , al-Garadi Mohammed , Ngan Kerry , Pillai Haritha , Reeves Ruth M. , Park Daniel , Westerman Dax M. , Hernández-Muñoz José J. , Wang Xi , Kuzucan Aida , Wang Shirley V. , Lin Kueiyu Joshua , Fuller Candace , McPheeters Melissa , Matheny Michael E. , Desai Rishi J. 
Published: January 2025

AbstractObjectiveTo evaluate the validity of death ascertainment from publicly available internet media (IM) sources by benchmarking against state and Federal vital statics data for patients in two large healthcare systems from the US.MethodsWe extracted names and dates of birth and death from publicly available data—including obituaries and memorial websites—using previously developed natural language processing models. These data were probabilistically matched to electronic health records (EHRs) from Mass General Brigham (MGB) and Vanderbilt University Medical Center (VUMC) on first name, last name, and date of birth. Using reference standards from state vital statistics databases from MA, CT, and VT for MGB and the National Death Index (NDI) for VUMC patients, we reported positive predicted values (PPV) considering cases where dates of death from IM sources were within 7 days of the reference standard to be true positives. We also reported sensitivity of deaths ascertained from IM sources.ResultsWhen probabilistically matching 8.1 million deaths extracted from public data to 78,848 deaths observed in the reference standards across two sites, 30,607 (38.8%) matched exactly. A PPV of 98.2% for MGB and 98.9% for VUMC was observed for exact matches, while <6% for non-exact matches. Considering only the exact matches, IM sources led to an improvement in sensitivity of death capture by 24% in MGB and 18% in VUMC, compared to using EHRs alone for death ascertainment.ConclusionsUsing public information to augment mortality data increased capture of death meaningfully over reliance on EHR records alone.
From Toxicogenomics Data to Cumulative Assessment Groups: A Mechanistic Framework for Chemical Grouping
Authors: Canzler Sebastian , Lehmann Julienne , Schor Jana , Busch Wibke , Hackermüller Jörg 
Published: January 2025

AbstractThe grouping of chemicals based on shared properties or molecular mechanisms of action is pivotal for advancing regulatory toxicology, reducing data gaps, and enabling cumulative risk assessments. This study introduces a novel framework usingChemical-Gene-Phenotype-Disease (CGPD) tetramers derived from the Comparative Toxicogenomics Database (CTDbase). Our approach integrates toxicogenomics data to identify and cluster chemicals with similar molecular and phenotypic effects across diverse categories, including pesticides, pharmaceuticals, and industrial chemicals such as bisphenols and per- and poly-fluoroalkyl substances (PFAS). We validated our method by comparing CGPD Tetramer-based clusters with cumulative assessment groups (CAGs) for pesticides, demonstrating strong overlap with established groupings while identifying additional compounds relevant for risk assessment. Key examples include clusters associated with endocrine disruption and metabolic disorders.By bridging omics-derived molecular data with phenotypic and disease endpoints, this framework provides a comprehensive tool for chemical grouping and supports evidence-based regulatory decision-making, facilitating the transition to next-generation risk assessment methodologies.
High-beta bursts in SMA mediate anticipatory muscle inhibition in a bimanual motor task
Authors: Manyukhina V. , Bonnefond M. , Abdoun O. , Rienzo F. Di , Barlaam F. , Daligault S. , Delpuech C. , Schmitz C. 
Published: January 2025

AbstractIn motor networks, motor inhibition can be driven by sensorimotor mu rhythm (8-12Hz) or beta bursts (13-30Hz). In this study, we aimed to investigate whether mu or beta activity supports efficient anticipatory inhibition, as reflected by a decrease in electromyographic (EMG) activity. To test this, we recorded magnetoencephalography (MEG) in 16 adults performing a Bimanual Load Lifting Task (BLLT), where participants lifted a load with one hand supported by the other. In anticipation of unloading, elbow flexors in the supporting arm are inhibited to prevent elbow deflection. We observed that optimal postural stabilization occurs when flexor inhibition happens approximately 30 ms before unloading begins. Stronger EMG inhibition in this time interval correlated negatively with high-gamma power (90-130Hz), reflecting reduced neural excitability, and positively with high-beta power in the medial supplementary motor area (SMA). In contrast, no significant correlation was observed in the mu-range (8-12 Hz). Meanwhile, high-beta and high-gamma power were negatively correlated. Mediation analysis confirmed that gamma power significantly mediates the relationship between beta power and EMG inhibition. Beta burst probability and directed connectivity analysis using the Phase Slope Index indicated that high-beta bursts are transmitted from the middle prefrontal cortex (mPFC) and elbow-related primary motor cortex (M1) to the SMA. Our findings suggest that, in the voluntary unloading task, anticipatory muscle inhibition at the optimal time is driven by a reduction in excitability within the SMA, likely facilitated by high-beta bursts originating from the mPFC-M1-SMA network.SignificanceAnticipatory motor processes represent a form of higher-order motor control evolved in humans to enable precise hand manipulation. In this study, we used a bimanual coordination task where precise force control is achieved by sending an inhibitory motor command to the elbow flexors before an anticipated forearm disturbance, which requires accurate timing and pattern selection. We demonstrate that timely anticipatory inhibition is associated with the transmission of high-beta bursts (22-28Hz) to the supplementary motor area, suppression of which enables precise inhibitory control over the flexor muscle. These findings suggest the neural mechanisms underlying anticipatory postural control and provide the first direct evidence linking beta activity to muscle inhibition.
High-resolution spatial transcriptomics of stem and storage root vascular cambia highlights key regulatory processes for xylem parenchyma differentiation in cassava
Authors: Rüscher David , Sonnewald Uwe , Zierer Wolfgang 
Published: January 2025

SummaryDue to their high carbohydrate content, the storage roots of cassava are an important food source for hundreds of millions of people worldwide. In contrast to the woody stems of the plant, the xylem of the storage roots produces mainly starch-rich storage parenchyma cells and only few tracheary elements and almost no fibers. Despite these obvious differences, both stems and storage roots are formed by a vascular cambium. To find more insights into the differences in the regulation of cell division and differentiation in stems and storage roots, a cryo-sectioning approach was utilized, to generate high-resolution transcriptome profiles spanning the entire vascular cambium of both tissues. We observed that storage parenchyma formation is connected to the repression of secondary cell wall formation through a decrease in expression levels of key players in the NAC/MYB regulatory network, as well as decreases in the downstream pathways for lignin and hemicellulose biosynthesis. Additionally, the expression ofMeWOX14, a transcription factor associated with GA signaling and xylem fiber differentiation, is strongly reduced in storage roots compared to stem xylem. By contrast, the expression ofMeKNOX1, a well-known meristem regulator, as well as most cassavaLSHgenes and several ABA-related transcription factors were associated with parenchyma cells. Our data suggest that the repression of secondary cell wall formation and GA signaling, together with an active auxin and ABA signaling, as well as extendedMeKNOX1activity could control storage parenchyma formation in cassava storage roots.Significance statementTissue-specific expression data is still scarce for cassava and the regulatory mechanisms controlling the formation and differentation of secondary vasculature cells are largely unknown in this species. By performing a cryosectioning approach on cassava stems and storage roots, we generated highly-resolved, tissue-specific transcriptomic data, identified key factors for parenchyma cell formation in storage roots and propose a working model for further research.
Fisher Information and the Dynamics of Multicellular Aging
Authors: Hale Zachary F. , Cánez Gonzalo A. , Michaels Thomas C.T. 
Published: January 2025

AbstractInformation theory has long been integrated into the study of biological aging, for example in examining the roles of genetic and epigenetic fidelity in cellular and organismal longevity. Here, we introduce a theoretical model that interprets aging in multicellular systems through the lens of Fisher information. Previous theories have suggested that the aging of multicellular organisms is an inevitable consequence of the inherent tension between individual cell reproduction and the homeostasis of the multicellular system. Utilizing concepts from information theory and statistical mechanics, we show that Fisher information parametrizes the dynamics of this tension through non-monotonic behaviour which depends on an optimal balance of competition and cooperation between cells. Moreover, Fisher information suggests that the ability to infer true biological age from a sample evolves through complex dynamics over an organism’s lifespan.
IFN-γ-Induced Intestinal Epithelial Cell-Type-Specific Programmed Cell Death: PANoptosis and Its Modulation in Crohn’s Disease
Authors: Lee Chansu , Kim Ji Eun , Cha Yeo-Eun , Moon Ji Hwan , Kim Eun Ran , Chang Dong Kyung , Kim Young-Ho , Hong Sung Noh 
Published: January 2025

AbstractCrohn’s disease (CD) is a chronic inflammatory bowel disease (IBD) and is considered a Th1-mediated disease, supported by the over-expression of interferon-gamma (IFN-γ) in the intestinal lamina propria. To evaluate the response of intestinal epithelial cells (IECs) to IFN-γ, we established small intestinal organoids (enteroids) derived from non-IBD controls and CD patients. IFN-γ stimulated programmed cell death (PCD) of IECs in both control and CD enteroids in a dose-dependent manner. Pyroptosis, apoptosis and necroptosis were activated in enteroids, suggesting that PANoptosis was the main process of IFN-γ-induced PCD in IECs. The response to IFN-γ depends on the cell type of the IECs. IFN-γ induced depletion of enterocytes with upregulation of PANoptosis-associated genes, while leading to expansion of goblet cells without significant change in PANoptosis-associated gene expression. Individual PCD inhibitors were insufficient to block IFN-γ-induced cytotoxicity, whereas the selective JAK1 inhibitor (upadacitinib) effectively blocked IFN-γ-induced cytotoxicity and PANoptosis. Furthermore, PANoptosis was significantly activated in surgically resected tissues and in publicly available single-cell RNA-sequencing datasets of intestinal tissues from patients with CD. In conclusion, IFN-γ induces PANoptosis in enterocytes, which can be treated with a selective JAK1 inhibitor in patients with CD.
Glyco-PAINT-APP: Subcellular analysis of immune cell-lectin binding enables correlation of glycan binding parameters to receptor biology
Authors: Steuten Kas , Bakker Johannes J.A. , Doelman Ward , Torres-García Diana , Riera Roger , Albertazzi Lorenzo , van Kasteren Sander I. 
Published: January 2025

AbstractExtracting single-molecule glycan binding data from primary cells has not been possible to date. Here, we presentGlyco-PAINT-APP(Automated Processing Pipeline), an automated method that enables the extraction of subcellular glycan interaction kinetics using a Points Accumulation for Imaging in Nano-Topography (PAINT)-based approach. This approach leverages an algorithm for precise, high-throughput subcellular analysis of glycan binding dynamics, facilitating the exploration of functional correlations between glycoform binding patterns and immune cell polarization. Using synthetic glycans and glycosylated antigens, we demonstrate the ability of the technique to automatically correlate high glycan binding regions in dendritic cells with increased uptake and cross-presentation efficiency of these antigens. Additionally, we show how the method can uncover subtle differences in glycan binding preferences between resting and polarized macrophages. Taken together, Glyco-PAINT-APP has the potential to enable new insights into the cell-intrinsic heterogeneity of glycan-structure-activity relationships in immune cells.
Extracting massive ecological data on state and interactions of species using large language models
Authors: Keck François , Broadbent Henry , Altermatt Florian 
Published: January 2025

AbstractThe contemporary ecological crisis calls for integration and synthesis of ecological data describing the state, change and processes of ecological communities. However, such synthesis depends on the integration of vast amounts of mostly scattered and often hard-to-extract information that is published and dispersed across hundreds of thousands of scientific papers, for example describing species-specific interactions and trophic relationships. Recent advancements in natural language processing (NLP) and in particular the emergence of large language models (LLMs) offer a novel, and potentially revolutionary solution to this persistent challenge, for the first time creating the opportunity to access and extract virtually all data ever published. Here, we demonstrate the transformative potential of LLMs by extracting all types of biological interactions among species directly from a corpus of 83,910 scientific articles. Our approach successfully extracted a network of 144,402 interactions between 36,471 taxa. Performance analysis shows that the model exhibits a high sensitivity (70.0%) and excellent precision (89.5%). Our approach proves that LLMs are capable of carrying out complex extraction tasks on key ecological data on a very large scale, paving the way for a multitude of potential applications in ecology and beyond.
Neuroimaging and plasma biomarker differences and commonalities in Lewy body dementia subtypes
Authors: Hannaway Naomi , Zarkali Angeliki , Bhome Rohan , Dobreva Ivelina , Thomas George EC , Veleva Elena , Gorostiaga Belio Irene , Tucker Katie , Heslegrave Amanda , Zetterberg Henrik , Weil Rimona S 
Published: January 2025

AbstractINTRODUCTIONDespite ongoing debate about whether Parkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB) are separable diseases or a single Lewy body dementia (LBD) spectrum, there are limited neuroimaging investigations of differences between these conditions.METHODSWe used fixel-based diffusion MRI and plasma measures to examine white matter integrity and burden of amyloid pathology (using tau phosphorylated at theonine-217 (p-tau217) in 47 patients with DLB, 21 PDD, 29 PD and 23 age-matched controls.RESULTSWe show reduced fibre cross-section in LBD versus PD, and increased concentrations of plasma neurofilament light chain and p-tau217; with p-tau217 and fibre cross-section associated with cognition. Fibre density was reduced in PDD versus DLB, but neither plasma measures nor fibre cross-section differed between LBD subtypes.DISCUSSIONOur findings suggest differences in white matter integrity between DLB and PDD that are driven by distinct processes from those causing changes in white matter integrity in LBD compared with PD.
Phenotypic integration of post-germination traits inQuercus suber: morphological development is mediated by acorn mass; leaf physiology by populations’ aridity
Authors: Vicente Eduardo , Carme Marion , Costa e Silva Filipe , Stiti Boutheina , Vizcaíno-Palomar Natalia , Benito Garzón Marta 
Published: January 2025

AbstractBackground and AimsAssessing intra-specific trait covariation across populations is essential to understand species’ adaptive responses to climatic variation. However, in tree species, this is understudied for early-life stages despite they are more vulnerable to environmental changes and that climatic adaptations can differ between tree ages. In this paper, we studied the integrated phenotype ofQuercus suberduring the months following germination. For that, we studied the covariation of key traits involved in seedlings’ water and C economies along a gradient of aridity at seed origin.MethodsWe performed a provenance trial with 157Q. suberseedlings originating from 7 different populations across the species distribution. The seedlings were germinated and grown during 4 months under common conditions. Acorn mass along with 11 above- and below-ground traits involved in water and C use were measured. Their covariation in response to aridity at seed origin was analyzed using structural equation modelling (SEM). The variation of individual traits to increasing aridity and the mediation of acorn mass was also tested.Key ResultsSeedlings from arid populations displayed higher leaf evaporative demand coupled with a greater root water uptake capacity. Their leaf physiology also depicted a greater C acquisition capacity, strongly linked to traits conferring drought and heat tolerance. The development of above- and below-ground tissues responded mainly to acorn mass, whereas leaf physiology variations were associated to populations’ aridity.ConclusionsDry-origin seedlings display a more acquisitive strategy at the whole-plant level compared with seedlings from mesic provenances. This allows a greater water and carbon uptake capacities following germination, which is critical for their survival during their first summer. Leaf physiology adjustments to populations’ climate contrasts with its plasticity observed by other studies addressing juvenile trees, highlightingQ. subervarying adaptive strategies at different life stages.