bluuebunny/crossref_metadata_2025 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

Listeria 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 summary

The 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

Mesophotic 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.
Pre-COVID-19 ex vivo cross-reactive IFN-γ cellular response to SARS-CoV-2 spike overlapping peptides is more robust among Kenyan compared to Swedish adults
Authors: Wanjiku perpetual , Orindi Benedict , Mwacharo Jedidah , Chemweno James , Karanja Henry , Kronsteiner-Dobramysl Barbara , Kai Oscar , Wright Daniel , Ochola-Oyier Lynette Isabella , Sundling Christopher , Dunachie Susanna , Warimwe George M , Farnert Anna , Bejon Philip , Ndungu Francis M , Nduati Eunice
Published: January 2025

Introduction Global WHO data indicate that Sub-Saharan African (SSA) countries, such as Kenya, experienced reduced coronavirus disease 2019 (COVID-19) severe-morbidity and mortality burdens relative to their more affluent counterparts in Europe, Asia, and North America. Methods We analysed peripheral blood mononuclear cells (PBMC) samples collected from Kenya and Sweden before and during COVID-19. Pre-COVID-19 samples were available for 80 adults and 10 infants from Kenya, and 20 adults from Sweden. COVID-19 samples were available for 39 Kenyan adults. The samples were analysed for ex vivo IFN-γ secretion using an Enzyme-Linked Immunosorbent (ELISpot) assay following in vitro stimulations with overlapping SARS-CoV-2 spike-protein peptides. T-cells expressing IFN-γ, IL-2, TNF-α, CD154, and CD107a were assessed following similar stimulations, using intracellular cytokine staining (ICS) and multiparameter flow cytometry. Results 55.7% of the Kenyan pre-COVID-19 adults were classified as responders by ELISPOT responses to spike-protein peptides, compared with 28% of Swedish pre-COVID-19 adults (p = 0.04). The frequencies for SARS-CoV-2 spike-specific TNF-α CD4+, TNF-α CD8+ and IFN-γ CD8+ T-cell responses, tended to be higher in the Kenyan adults although these differences did not reach statistical significance. Conclusion Pre-COVID-19 T-cell responses could contribute to lower morbidity and mortality associated with SARS-CoV-2 infections in SSA relative to Europe, Asia, and North America.
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

Objective

To 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.

Methods

We 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.

Results

When 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.

Conclusions

Using public information to augment mortality data increased capture of death meaningfully over reliance on EHR records alone.
Oat protein nanofibril-iron hybrids as a stable, high-absorption iron delivery platform for human nutrition
Authors: Zhou Jiangtao , Gowachirapant Sueppong , Zeder Christophe , Wieczorek Alexander , Kutzli Ines , Siol Sebastian , von Meyenn Ferdinand , Zimmermann Michael , Mezzenga Raffaele
Published: January 2025

Iron deficiency and anemia are significant global health issues, affecting nearly two billion people worldwide. The World Health Organization recommends iron fortification of foods as an effective strategy to reduce anemia rates. Available iron fortificants, however, are limited by low absorption and/or poor sensory performance. Developing new iron compounds that deliver highly bioavailable ferrous iron in foods without compromising sensory quality remains a challenge. In this work we introduce oat protein nanofibrils (OatNF) carrying ultrasmall iron nanoparticles as promising iron fortificants for foods and beverages. Tailored synthesis of OatNF hybrids can produce iron nanoparticles in either the ferrous or ferric state. When sodium ascorbate (SA) is used as the reducing agent, the OatNF carry stabilized ferrous iron which is remarkably well absorbed in humans. In iron-deficient women, geometric mean absorption is found to be 46.2% (95% CI: 39.1% to 54.7%) when given with water and 13.4% (95% CI: 9.8% to 18.3%) when given with a polyphenol-rich food, representing 76% and 66% higher absorption, respectively, than the reference compound, FeSO4. When NaOH is used as the reducing agent, the OatNF carry mainly ferric iron, which is well-absorbed and shows superior sensory performance in reactive food matrices. These promising results introduce OatNF hybrids as a possible cost-effective, plant-based and organoleptic-friendly solution to the global challenge of iron deficiency anemia.
S4-Multi: enhancing polygenic score prediction in ancestrally diverse populations
Authors: Baierl John DuChateau , Tyrer Jonathan P , Lai Ping-Hung , Gayther Simon A , Hsiao Yi-Wen , Jones Michelle R , Peng Pei-Chen R , Pharoah Paul
Published: January 2025

While polygenic scores (PGSs) have shown promise in advancing precision medicine by capturing the additive effects of common germline variants on inherited disease risk, they are presently limited by reduced performance outside of European-origin populations. We extend our previously developed Bayesian polygenic model (PGM) method, select and shrink with summary statistics (S4), to improve prediction accuracy in ancestrally diverse populations. We benchmark this multi-ancestry extension (S4-Multi) against alternative methods on both simulated and biobank data predicting type 2 diabetes, breast cancer, colorectal cancer, asthma, and stroke. In simulation tests, we find that S4-Multi achieves 169% improvement on average over its single ancestry S4 counterpart at prediction in non-European target populations. S4-Multi matches or exceeds top performing methods across the ancestry continuum. In biobank tests, we find that the top-performing PGM method varies considerably by target ancestry and phenotype, with S4-Multi achieving comparable performance to top multi-ancestry methods overall. However, S4-Multi does so while including between 9% and 77% fewer genetic variants relative to competing models, suggesting potential for robust performance in clinical settings with limited available genomic data.
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

The 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

In 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.

Significance

Anticipatory 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.
ERGA-BGE genome of Cheirolophus tagananensis: an IUCN endangered shrub endemic to the Canary Islands
Authors: Pellicer Jaume , Garnatje Teresa , Vitales Daniel , Hidalgo Oriane , Valles Joan , Garcia-Fernandez Alfredo , Santos-Guerra Arnoldo , Bohne Astrid , Monteiro Rita , Fernandez Rosa , Escudero Nuria ,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics Team, Thomas Abitha , Jackson Benjamin , Wood Jonathan MD , Howe Kerstin , Blaxter Mark , McCarthy Shane , Bortoluzzi Chiara
Published: January 2025

The reference genome of Cheirolophus tagananensis, locally known as the Cabezon de Taganana, will provide an exceptional opportunity to establish a new framework to develop comparative genomic tools. These tools will help uncover the genetic basis of rapid plant radiations and microevolutionary adaptation processes of insular species on oceanic islands. This genomic resource will also serve as a resource to facilitate the establishment of better informed in situ and ex-situ conservation strategies for this narrow endemic in the face of potential habitat degradation and support taxonomic studies to better understand genetic diversity at the population, species, and genus levels. A total of 16 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 0.62 Gb, composed of 421 contigs and 235 scaffolds, with contig and scaffold N50 values of 4.0 Mb and 36.5 Mb, respectively.
Bacterial amino acid auxotrophies enable energetically costlier proteomes
Authors: Kasalo Niko , Domazet-Loso Tomislav , Domazet-Loso Mirjana
Published: January 2025

The outsourcing of amino acid (AA) production to the environment is relatively common across the tree of life. We recently showed that the massive loss of AA synthesis capabilities in animals is governed by selective pressure linked to the energy costs of AA production. Paradoxically, these AA auxotrophies facilitated the evolution of costlier proteomes in animals by enabling the increased use of energetically expensive AAs. Experiments in bacteria have shown that AA auxotrophies can provide a fitness advantage in competition with prototrophic strains. However, it remains unclear whether energy-related selection also drives the evolution of bacterial AA auxotrophies and whether this affects the usage of expensive AAs in bacterial proteomes. To investigate these questions, we computationally determined AA auxotrophy odds across 980 bacterial genomes representing diverse taxa and calculated the energy costs of all their proteins. Here, we show that auxotrophic AAs are generally more expensive to synthesize than prototrophic AAs in bacteria. Moreover, we found that the cost of auxotrophic AAs significantly correlates with the cost of their respective proteomes. Interestingly, out of all considered taxa, Mollicutes and Borreliaceae—chronic pathogens highly successful in immune evasion—have the most AA auxotrophies and code for the most expensive proteomes. These findings indicate that AA auxotrophies in bacteria, similar to those in animals, are shaped by selective pressures related to energy management. Our study reveals that bacterial AA auxotrophies act as costly outsourced functions, enabling bacteria to explore protein sequence space more freely. It remains to be investigated whether this relaxed use of expensive AAs also enabled auxotrophic bacteria to evolve proteins with improved or novel functionality.
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

Due 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 statement

Tissue-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

Information 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

Crohn’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

Extracting 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

The 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

INTRODUCTION

Despite 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.

METHODS

We 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.

RESULTS

We 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.

DISCUSSION

Our 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.
Metabolic network divergence: polyamine and ethylene dynamics in Arabidopsis thaliana and Solanum lycopersicum
Authors: Cermanova Katerina , Bublava Petra , Darbandsari Mersa , Fellner Martin , Novak Ondrej , Karady Michal
Published: January 2025

Polyamines are ubiquitously present in all living organisms. In plants, together with phytohormone ethylene, their metabolism plays a crucial role in plant stress and ontogenesis. We have evaluated differences in the responses of model plants Arabidopsis thaliana and Solanum lycopersicum to abiotic stresses and metabolic modulators based on key metabolite levels. Previous approaches have often focused separately on either polyamines, amino acids, or ethylene precursors. As these pathways are directly interconnected, their simultaneous evaluation can significantly impact our understanding of their core mechanisms. We have therefore developed a novel and validated liquid chromatography - tandem mass spectrometry based method, enabling quantification of fourteen compounds: the amino acids L-arginine, L-citrulline, L-ornithine; biogenic amines Nα-acetyl-L-ornithine and agmatine; the polyamines putrescine, spermidine, spermine, thermospermine, N-acetylputrescine, cadaverine, homospermidine; together with methionine and 1-aminocyclopropane-1-carboxylic acid, serving as key non-volatile precursors of ethylene. Our analysis revealed distinct metabolic responses between Arabidopsis and tomato, highlighted by species-specific differences in polyamine metabolism and ethylene precursors dynamics. Drought and salinity stresses triggered fundamentally different metabolic adjustments, with drought consistently inducing higher metabolite levels and spermine showing stress-specific responses. Metabolic inhibitor treatments with aminoguanidine and L-norvaline revealed further divergencies, mainly demonstrated as significant variations in ethylene precursor levels. For all approaches, Arabidopsis displayed more pronounced metabolic fluctuations compared to tomato. These results provide direct insights into contrasting metabolic plasticity and the interconnected roles of polyamines, amino acids, and ethylene precursors in plant responses and adaptations.
Discovery of Chirally-dependent Protein O-2-Hydroxyglutarylation by D2HG and L2HG
Authors: Zhang Zheng , Liu Yi-Kai , Luo Zhuojun , Wu Meng-Ju , Evans Claudia N. , Qu Zihan , Xue Fanglei , Zhang Zhong-Yin , Parkinson Elizabeth I. , Bardeesy Nabeel , Tao W. Andy
Published: January 2025

Mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 are common in multiple types of human cancer, leading to the accumulation of D-2-hydroxyglutarate (D2HG) and the promotion of tumorigenesis1. Here we discovered a novelO-2- hydroxyglutarylation by D2HG using chemical proteomics and further revealed distinct chiral preferences for D/L2HG modifications. Notably, we identified two kinases, MRCKA and SLK, modified by D2HG and L2HG respectively, and detected reduced phosphorylation of their substrates, suggesting an inhibitory effect of D/L 2HG modifications on the kinases’ activity.
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

Background and Aims

Assessing 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.

Methods

We 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 Results

Seedlings 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.

Conclusions

Dry-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.
Increased RAMP3 expression enhances GLP-1 mediated Glucose Stimulated Insulin Secretion in a Manner Dependent on Ca2+ Mobilisation
Authors: Pearce Abigail , Sisk Claudia , Harris Matthew , Yeung Ho Yan , Carvalho Sabrina , Ladds Graham
Published: January 2025

The targeting of the Glucagon-like peptide-1 receptor (GLP-1R) for diabetes and obesity is not a novel strategy, with recent therapeutics showing efficacy in weight loss and glycaemic control. However, they are also associated with side effects, including gastrointestinal disruptions and pancreatitis. Developing agonists with different signalling profiles, or that exert some tissue selectivity can circumvent these on-target, unwanted effects. Receptor activity-modifying proteins (RAMPs) offer the potential to do both, through modulation of agonist binding and signalling, as well as surface expression. The GLP-1R was found to interact with RAMP3, with the heterodimer able to bind agonist at the cell surface. RAMP3 expression biased the receptor towards Ca2+ mobilisation, away from the canonical cAMP-driven signalling. When examining G protein coupling, the interaction with RAMP3 reduced activation of the cognate Gαs, but increased secondary couplings to Gαq and Gαi. These increased couplings led to an elevation in glucose-stimulated insulin secretion when cells overexpressing RAMP3 were stimulated with GLP-1. The effects of this interaction can then inform selection of models and peptide design when targeting this receptor for therapeutic intervention.

Significance Statement

G Protein-Coupled Receptors, such as the Glucagon-Like Peptide-1 (GLP-1) Receptor are common drug targets, although not without side effects due to on-target, unwanted signalling outputs. This study identifies an interacting protein, which alters its signalling to promote insulin secretion. This may improve the therapeutic potential of GLP-1 mimetics, by enhancing effectual signalling over that associated with unwanted effects, by directly targeting this receptor complex.
Integrative Mendelian Randomization for Detecting Exposure-by-group Interactions Using Group-Specific and Combined Summary Statistics
Authors: Xu Ke , Maydanchik Nathaniel , Kang Bowei , Chen Jianhai , Chen Qixiang , Xu Gongyao , Tasaki Shinya , Bennett David A. , Chen Lin S.
Published: January 2025

Interactions between risk factors and covariate-defined groups are commonly observed in complex diseases. Existing methods for detecting interactions typically require individual-level data. The data availability and the measurements of risk exposures and covariates often limit the power and applicability in assessing interactions. To address these limitations, we propose int2MR, an integrative Mendelian randomization (MR) method that leverages GWAS summary statistics on exposure traits and group-separated and/or combined GWAS statistics on outcome traits. int2MR can assess a broad range of risk exposure effects on diseases and traits, revealing interactions unattainable with incomplete or limited individual-level data. Simulation studies demonstrated that int2MR effectively controls type I error rates under various settings while achieving considerable power gains with the integration of additional group-combined GWAS data. We applied int2MR to two data analyses. First, we identified risk exposures with sex-interaction effects on ADHD, and our results suggested potentially elevated inflammation in males. Second, we detected age-group-specific risk factors for Alzheimer's disease pathologies in the oldest-old (age 95+), many of which were related to immune and inflammatory processes. Our findings suggest that reduced chronic inflammation may underlie the distinct pathological mechanisms observed in this age group. int2MR is a robust and flexible tool for assessing group-specific or interaction effects, providing insights into disease mechanisms.
Morphology and connectivity of retinal horizontal cells in two avian species
Authors: Günther Anja , Balaji Vaishnavi , Leberecht Bo , Forst Julia J. , Rotov Alexander Y. , Woldt Tobias , Abdulazhanova Dinora , Mouritsen Henrik , Dedek Karin
Published: January 2025

In the outer vertebrate retina, the visual signal is separated into intensity and wavelength information. In birds, seven types of photoreceptors (one rod, four single cones, and two members of the double cone) mediate signals to >20 types of second-order neurons, the bipolar cells and horizontal cells. Horizontal cells contribute to color and contrast processing by providing feedback signals to photoreceptors and feedforward signals to bipolar cells. In fish, reptiles, and amphibians they either encode intensity or show color-opponent responses. Yet, for the bird retina, the number of horizontal cell types is not fully resolved and even more importantly, the synapses between photoreceptors and horizontal cells have never been quantified for any bird species. With a combination of light microscopy and serial EM reconstructions, we found four different types of horizontal cells in two distantly related species, the domestic chicken and the European robin. In agreement with some earlier studies, we confirmed two highly abundant cell types (H1, H2) and two rare cell types (H3, H4), of which H1 is an axon-bearing cell, whereas H2-H4 are axonless. Horizontal cell contacts to photoreceptors were type-specific and similar to the turtle retina, which confirms the high degree of evolutionary conservation in the vertebrate outer retina. Our data further suggests that H1 and potentially H2 cells may encode intensity, whereas H3 and H4 may represent color opponent horizontal cells which may contribute to the birds’ superb color and/or high acuity vision.
TransBrain: A computational framework for translating brain-wide phenotypes between humans and mice
Authors: Huang Shangzheng , Zhang Tongyu , Dong Changsheng , Shi Yingchao , Peng Yingjie , Liu Xiya , Li Kaixin , Wang Qi , He Yini , Xiao Fengqian , Tian Xiaohan , Xian Junxing , Zhang Changjiang , Wu Qian , Zou Yijuan , Li Long , Liu Bing , Wang Xiaoqun , Li Ang
Published: January 2025

Despite remarkable advances in whole-brain imaging technologies, the lack of quantitative approaches to bridge rodent preclinical and human studies remains a critical challenge. Here we present TransBrain, a computational framework enabling bidirectional translation of brain-wide phenotypes between humans and mice. TransBrain improves human-mice homology mapping accuracy through: (1) a novel detached region-specific deep neural networks trained on integrated multi-modal human transcriptomics to improve cortical correspondence (89.5% improvement over the original transcriptome), which revealed two evolutionarily conserved gradients explaining >50% of cortical organizational variance, and (2) random walk-based graph representation learning to construct a unified cross-species latent space incorporating anatomical hierarchies and structural connectivity. We demonstrated TransBrain's utility through three cross-species applications: quantitative assessment of resting-state brain organizational features, inferring human cognitive functions from mouse optogenetic circuits, and translating molecular insights from mouse models to individual-level mechanisms in autism. TransBrain enables quantitative cross-species comparison and mechanistic investigation of both normal and pathological brain functions.
Investigation of charged Higgs bosons production from vectorlike
T
quark decays at
eγ
collider
Authors: Benbrik Rachid , Berrouj Mbark , Boukidi Mohammed
Published: January 2025

Within the extended framework of the two-Higgs-doublet model type II (2HDM-II), enhanced by a vectorlike quark (VLQ) doublet TB, we present a comprehensive analysis of the process e−γ→bνeT¯ at future high-energy eγ colliders, focusing on the decays T¯→H−b¯ and H−→t¯b. Using current theoretical and experimental constraints, we calculate production cross sections for both unpolarized and polarized beams at center-of-mass energies of s=2 and 3 TeV, demonstrating that polarized beams significantly enhance detection prospects by increasing production rates. By analyzing kinematic distributions, we establish optimized selection criteria to effectively separate signal events from background. At s=2  TeV with an integrated luminosity of 1500  fb−1, we find exclusion regions within sRd∈[0.085,0.16] for mT∈[1000,1260]  GeV and a discovery potential within sRd∈[0.14,0.17] for mT∈[1000,1100]  GeV, with these regions expanding to sRd∈[0.05,0.15] for mT∈[1000,1340]  GeV and sRd∈[0.11,0.17] for mT∈[1000,1160]  GeV at 3000  fb−1. At s=3  TeV and 1500  fb−1, we identify exclusion regions of sRd∈[0.055,0.135] for mT∈[1000,1640]  GeV and discovery regions of sRd∈[0.09,0.15] for mT∈[1000,1400]  GeV, which further expand to sRd∈[0.028,0.12] for mT∈[1000,1970]  GeV and sRd∈[0.04,0.122] for mT∈[1000,1760]  GeV at 3000  fb−1. Our findings emphasize the increased detection potential at higher center-of-mass energies, particularly at 3 TeV compared to 2 TeV, with notable improvements when polarized beams are utilized. We also account for the effects of initial state radiation, beamstrahlung, and systematic uncertainties, which influence both exclusion and discovery prospects.

Published by the American Physical Society
2025
Particle approximations of Wigner distributions for
n
arbitrary observables
Authors: Sabbagh Ralph , Movilla Miangolarra Olga , Hezari Hamid , Georgiou Tryphon T.
Published: January 2025

A class of signed joint probability measures for n arbitrary quantum observables is derived and studied based on quasicharacteristic functions with symmetrized operator orderings of Margenau-Hill type. It is shown that the Wigner distribution associated with these observables can be rigorously approximated by such measures. These measures are given by affine combinations of Dirac delta distributions supported over the finite spectral range of the quantum observables and give the correct probability marginals when coarse-grained along any principal axis. We specialize to bivariate quasiprobability distributions for the spin measurements of spin-1/2 particles and derive their closed-form expressions. As a side result, we point out a connection between the convergence of these particle approximations and the Mehler-Heine theorem. Finally, we interpret the supports of these quasiprobability distributions in terms of repeated thought experiments.

Published by the American Physical Society
2025
Navigating the complexities of export order processing: challenges for Indian agri exporters
Authors: Rathee Ankit , Chhikara Kuldip Singh , Solanki Poonam
Published: January 2025

Purpose

The study aims to identify the major challenges encountered by Indian exporters of agricultural products in the course of fulfilling export orders.

Design/methodology/approach

To achieve the objectives, a questionnaire and interview method are used to gather data from a randomly selected sample of 300 agri-exporters in Haryana, India. The study categorizes the various perceived constraints into problem variables or factors using factor analysis. Then, the aggregated scales are regressed against predictors, to validate the proposed hypotheses.

Findings

The results demonstrate that the broad challenges faced by agri-exporters of India are related to logistics, technological and quality assurance, financial, supply-chain bottlenecks and customs-related documentation. Furthermore, the findings confirm that the predictors have a significant effect on the identified constraints. Notably, the export experience emerged as the most influential variable contributing to overcome the challenges faced by Indian agri-exporters.

Research limitations/implications

The study’s exclusive focus on the exporter’s perspective limits a comprehensive understanding. Incorporating data from logistics providers, customs agents and financial institutions could offer a more holistic view of the challenges.

Originality/value

The study offers new insights and contributes to the existing knowledge base by presenting a comprehensive analysis of the challenges faced by exporters and modeling them.