bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating Regional Diversity in Scientific Communication: A Comparative Analysis of COVID-19 Preprints and Peer-Reviewed Publications
Authors: Kim Dong Hyun , Jeon Kyu Lee , You Seng Chan 
Published: January 2025

AbstractBackgroundThe unprecedented COVID-19 pandemic has triggered extensive global research, leading to an overwhelming surge in publications with surge of preprints. Despite the proliferation of preprints during the pandemic, the specific details of their implications for global diversity, along with their utility, remain underexplored. In this study, we assess the contribution of COVID-19 preprints in diverse aspects.MethodsWe collected COVID-19-related peer-reviewed papers and preprints from SCOPUS and MedRxiv, respectively, between December 2019 to November 2022. We analyzed four key aspects of scientific communication: 1) international co-authorship patterns using network analysis and eigenvector centrality, 2) publication patterns through relative ratio analysis comparing preprint to peer-reviewed paper counts, 3) social media dissemination through analysis of X (formerly Twitter) post quotations, and 4) citation impact by comparing citation counts between peer-reviewed papers with and without preprint history. All analyses were stratified by country income levels and geographical regions.ResultsNetwork analysis revealed higher co-authorship diversity in preprints, with Sub-Saharan Africa, Latin America, and the Caribbean showing 3.9 to 4.5 times higher eigenvector centrality compared to peer-reviewed papers. Countries with lower GDP showed significantly higher preprint publication ratios (correlation coefficient: −0.38, p-value < 0.001). Social media analysis demonstrated higher engagement with preprints, as evidenced by higher median numbers of social media quotations for preprints across all income groups. Peer-reviewed papers with preprint history received significantly higher citations (median: 10, IQR: 3-30) compared to those without (median: 5, IQR: 1-15, p-value < 0.001), particularly pronounced in low- and middle-income countries.ConclusionThis study demonstrates the significant role of preprints in advancing regional diversity in scientific communication during the COVID-19 pandemic. Our findings show enhanced international collaboration through preprints, particularly benefiting researchers from lower-income regions, higher social media engagement across income groups, and increased citation impact for papers with preprint history. These results highlight preprints as an important tool for promoting more equitable global scientific discourse.
A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques
Authors: Peres Ayelet , Upadhyay Amit A. , Klein Vered , Saha Swati , Rodriguez Oscar L. , Vanwinkle Zachary M. , Karunakaran Kirti , Metz Amanda , Lauer William , Lin Mark C. , Melton Timothy , Granholm Lukas , Polak Pazit , Peterson Samuel M , Peterson Eric J , Raju Nagarajan , Shields Kaitlyn , Schultze Steven , Ton Thang , Ericsen Adam , Lapp Stacey A. , Villinger Francois , Ohlin Mats , Cottrell Christopher A. , Amara Rama R. , Derdeyn Cynthia A. , Crotty Shane , Schief William R. , Karlsson Hedestam Gunilla B. , Smith Melissa L. , Lees William , Watson Corey T. , Yaari Gur , Bosinger Steven E. 
Published: January 2025

AbstractRhesus macaques (RMs) are a vital model for studying human disease and invaluable to pre-clinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for antibody-encoding genes within the immunoglobulin (IG) loci. The complexity of the IG loci has historically made them challenging to characterize accurately. To address this, we developed novel experimental and computational methodologies to generate the largest collection to date of integrated antibody repertoire and long-read genomic sequencing data in 106 Indian origin RMs. We created a comprehensive resource of IG heavy and light chain variable (V), diversity (D), and joining (J) alleles, as well as leader, intronic, and recombination signal sequences (RSSs), including the curation of 1474 novel alleles, unveiling tremendous diversity, and expanding existing IG allele sets by 60%. This publicly available, continually updated resource (https://vdjbase.org/reference_book/Rhesus_Macaque) provides the foundation for advancing RM immunogenomics, vaccine discovery, and translational research.
PSI Atlas: a comprehensive knowledgebase of plant self-incompatibility
Authors: Wang Chen , Zhao Hong , Zhang Hongkui , Sun Sijie , Xue YongBiao 
Published: January 2025

AbstractSelf-incompatibility (SI) is an important genetic mechanism in angiosperms that prevents inbreeding and promotes outcrossing. Although significant progress has been made in understanding SI, its molecular underpinnings and evolutionary origins remain elusive in many plant families. In eudicots, SI is typically regulated by a singleS-locus with diverseS-haplotypes, while in grasses, it is controlled by two separateSandZloci. Genome assemblies of SI plants have greatly facilitated the identification and evolutionary analysis ofS-loci. However, a comprehensive database that integrates information on the diverseS-loci has been lacking. To fill this gap, we create the Plant Self-Incompatibility Atlas (PSIA,http://www.plantsi.cn), a knowledgebase that offers an extensive compilation of plant SI, including genomic resources for assembled SI species, the origins and evolution ofSgenes, and the molecular mechanisms of the eight known SI types. In our most recent release, we have obtained more than 500 genome assemblies across 469 SI species. We have also collected 1275 nucleotide and 1130 protein sequence accessions ofSgenes from public databases, with a total of 3095Sgenes manually identified and curated. PSIA not only thoroughly explores theS-locus information of the assembled SI species but also enables users to efficiently browse, perform BLAST searches, analyze, and downloadSgenes. Additionally, PSIA acts as a comprehensive platform for comparative genomic studies ofS-loci, aiding in the exploration of the dynamic processes involved in the origin, loss, and regain of SI. Consequently, PSIA is poised to significantly enhance our understanding of angiosperm SI and offer new perspectives on plant mating systems.
Investigating The Potential of Division of Labour in Synthetic Bacterial Communities for the Production of Violacein
Authors: Mehta Harman , Jimenez Jose , Ledesma-Amaro Rodrigo , Stan Guy-Bart 
Published: January 2025

AbstractWith advancements in synthetic biology and metabolic engineering, microorganisms can now be engineered to perform increasingly complex functions, which may be limited by the resources available in individual cells. Division of labour in synthetic microbial communities offers a promising approach to enhance metabolic efficiency and resilience in bioproduction. By distributing complex metabolic pathways across multiple subpopulations, the resource competition and metabolic burden imposed on an individual cell is reduced, potentially enabling more efficient production of target compounds. Violacein is a high-value pigment with anti-tumour properties that exemplifies such a challenge due to its complex bioproduction pathway, imposing a significant metabolic burden on host cells. In this study we investigated the benefits of division of labour for violacein production by splitting the violacein bioproduction pathway between two subpopulations ofEscherichia colibased synthetic communities. We tested several pathway splitting strategies and reported that splitting the pathway into two subpopulations expressing VioABE and VioDC at a final composition of 60:40 yields a 2.5 fold increase in violacein production as compared to a monoculture. We demonstrated that the coculture outperforms the monoculture when both subpopulations exhibit similar metabolic burden levels, resulting in comparable growth rates, and when both subpopulations are present in sufficiently high proportions.
Micromorphology and ammonium transmembrane transport characteristics in roots of rice seedlings
Authors: Zhang Xiaoguo , Xu Yanan , Chen Song , Chu Guang , Xu Chunmei , Yang Yongjie , Wang Danying 
Published: January 2025

AbstractDuring the seedling stage, rice root exhibit rapid growth and absorb significant quantities of nutrients. This study involved cultivating rice seedlings in two different seedling-raising mediums characterized by high ammonium concentration (HN, NH4+1.2 mg g−1) and low ammonium concentration (LN, NH4+0.006 mg g−1). The morphology of distinct root zones (root cap, meristematic zone, elongation zone, and maturation zone) was observed under a microscope throughout root development, and variations in transmembrane flux rates of NH4+in different root zones were assessed using Non-invasive micro-test technology (NMT). Results showed that the root caps of both seminal and adventitious roots became separated from the root tip between 9 and 12 days after root emergence. During this time, the root tip transformed from a sharp to a round shape, and the distance from the maturation zone to the root tip progressively decreased from over 900 μm on 6 days after sowing (DAS) to under 500 μm on DAS12. The meristematic zone was the primary site for NH4+absorption in new root and proved to be particularly sensitive to environmental NH4+concentration. At DAS 6, the net NH4+flux rate was highest in the meristematic zone under both HN and LN treatments. Additionally, the external NH4+concentration influenced the direction of NH4+flux in the meristematic zone at DAS9, with HN being a net NH4+influx and LN being an NH4+efflux, and the net NH4+influx in the meristematic zone persisted for 3 days longer in the HN treatment compared to the LN treatment. In mature roots, the root hair zone emerged as the primary site of NH4+uptake, exhibiting an infNH4+influx rate of 40−140 pmol cm−1s−1, and this low rate of uptake could be sustained for up to 12 days after root emergence. By DAS15, a net NH4+efflux was observed in the entire seminal root, signaling the loss of NH4+absorption function 15 days post-emergence. A similar trend was noted in adventitious roots, where NH4+uptake remained functional for 12-15 days after root emergence. As rice seedlings continued to grow, new adventitious roots replaced old ones, facilitating ongoing NH4+uptake.
Contrasting dynamics and biotic association networks in estuarine microbenthic communities along an environmental disturbance gradient
Authors: Garate Leire , Chariton Anthony A. , Abad-Recio Ion L. , Bissett Andrew , Lanzén Anders 
Published: January 2025

ABSTRACTEstuarine ecosystems experience a range of anthropogenic pressures. Consequently, robust monitoring tools are essential for their management and protection. Utilising environmental DNA in routine monitoring programs enables the inclusion of benthic microorganisms, which are not only good indicators of environmental condition, but also play critical roles in ecosystem functioning. In this study we collect eDNA from sediment samples across time in six estuaries, from the Basque coast (Spain), under varying degrees of disturbance. To identify potential indicators of biotic integrity (environmental health status), we used time series data to examine the prokaryotic microbial communities and consensus networks associated with different levels of pollution. In general, sediment communities were relatively temporally stable, with the moderately and heavily disturbed sites showing more variation. The consensus networks also differed significantly in their topologies, with more impacted estuaries having fewer nodes, edges and connectance, among others, and higher modularity compared to those less impacted. Moreover, the potential keystone taxa and predicted functional profiles differed between consensus networks. This illustrates how modelled association networks can reveal new insights regarding the state of estuarine ecosystems and their potential functional processes.
NERINE reveals rare variant associations in gene networks across multiple phenotypes and implicates anSNCA-PRL-LRRK2subnetwork in Parkinson’s disease
Authors: Nazeen Sumaiya , Wang Xinyuan , Morrow Autumn , Strom Ronya , Ethier Elizabeth , Ritter Dylan , Henderson Alexander , Afroz Jalwa , Stitziel Nathan O. , Gupta Rajat M. , Luk Kelvin , Studer Lorenz , Khurana Vikram , Sunyaev Shamil R. 
Published: January 2025

AbstractGene networks encapsulate biological knowledge, often linked to polygenic diseases. While model system experiments generate many plausible gene networks, validating their role in human phenotypes requires evidence from human genetics. Rare variants provide the most straightforward path for such validation. While single-gene analyses often lack power due to rare variant sparsity, expanding the unit of association to networks offers a powerful alternative, provided it integrates network connections. Here, we introduce NERINE, a hierarchical model-based association test that integrates gene interactions that integrates gene interactions while remaining robust to network inaccuracies. Applied to biobanks, NERINE uncovers compelling network associations for breast cancer, cardiovascular diseases, and type II diabetes, undetected by single-gene tests. For Parkinson’s disease (PD), NERINE newly substantiates several GWAS candidate loci with rare variant signal and synergizes human genetics with experimental screens targeting cardinal PD pathologies: dopaminergic neuron survival and alpha-synuclein pathobiology. CRISPRi-screening in human neurons and NERINE converge onPRL, revealing an intraneuronal α-synuclein/prolactin stress response that may impact resilience to PD pathologies.
The secreted Nimrod NimB1 negatively regulates early steps of apoptotic cell phagocytosis inDrosophila
Authors: Dolgikh Asya , Rommelaere Samuel , Ghanem Aseel , Petrignani Bianca , Poidevin Mickael , Kurant Estee , Lemaitre Bruno 
Published: January 2025

AbstractEfferocytosis, the efficient clearance of apoptotic cells (ACs) by phagocytes, is vital for maintaining tissue homeostasis. Here, we reveal the role of the secreted protein NimB1 in reducing apoptotic cell recognition and binding in the early stages of efferocytosis. NimB1 is expressed in macrophages (also called plasmatocytes) and binds to ACs in a phosphatidylserine-dependent manner. Structural analysis shows that NimB1 shares striking similarities with the bridging molecule NimB4, and possesses two phosphatidylserine-binding motifs, supporting its role in efferocytosis. Larval macrophages of NimB1 null mutants display a hyper-phagocytic phenotype characterized by increased engulfment of ACs. Confocal imaging reveals that NimB1 specifically inhibits early steps in internalization of ACs, but does not impact phagosome maturation. We find that NimB1 is a secreted factor that negatively regulates efferocytosis, antagonizing the role of NimB4. Our study and the analogous opposing roles of Draper Isoforms II and I in efferocytosis suggest that a balance of negative and positive regulators allows optimization of the rate of apoptotic cell clearance by macrophages.
Anillin directly cross-links microtubules with filamentous actin
Authors: Bareja Ilina , Kučera Ondřej , Petitjean Irene Istúriz , Sabo Jan , Braun Marcus , Lansky Zdenek , Koenderink Gijsje H. , Dogterom Marileen 
Published: January 2025

AbstractComplex morphogenetic processes such as cell division require a tight coordination of the activities of microtubules and actin filaments. There is evidence that anillin, conventionally known as an actin-binding and bundling protein, regulates microtubule-actin crosstalk during cell division. However, it is unknown whether anillin binds directly to microtubules and whether it is sufficient to establish crosslinking between microtubules and actin filaments. Here we address both questions by developing an in-vitro system to observe anillin-mediated interactions with actin filaments and dynamic microtubules using total internal reflection fluorescence microscopy. We find that anillin can interact directly with microtubules and promote microtubule bundling. We confirm that anillin binds and bundles actin filaments and find that it has a strong preference for actin bundles over individual filaments. Moreover, we show that anillin can directly crosslink microtubules and actin filaments, can cause sliding of actin filaments on the microtubule lattice, and can transport actin filaments by the growing microtubule tip. Our findings indicate that anillin can potentially serve as a direct regulator of microtubule-actin crosstalk, e.g. during cell division.
Harnessing Computational Insights to Identify Potent Inhibitors for Human Metapneumovirus (HMPV): A Synergistic Approach with Natural Compounds
Authors: Dubey Amit , Kumar Manish , Tufail Aisha , Dwivedi Vivek Dhar 
Published: January 2025

AbstractHuman metapneumovirus (HMPV), a leading cause of acute lower respiratory tract infections, has emerged as a global health challenge due to its high prevalence, particularly among children, the elderly, and immunocompromised individuals. Despite its significant impact, no targeted antivirals or vaccines are available. This study employs a comprehensive computational pipeline to identify and evaluate potential inhibitors of the HMPV matrix protein (PDB: 5WB0). Natural compounds such as epigallocatechingallate (EGCG), rutin, and quercetin, along with control drugs, were screened for their therapeutic potential.Virtual screening identified EGCG (−9.1 kcal/mol), rutin (−9.0 kcal/mol), and quercetin (−8.8 kcal/mol) as top binders, surpassing standard drugs like ribavirin (−8.9 kcal/mol). Molecular docking revealed stable binding interactions, including hydrogen bonding with residues Arg143 and Glu186. Molecular dynamics (MD) simulations over a 1000 ns trajectory confirmed the stability of these complexes, with EGCG displaying the lowest RMSD (2.1 Å) and consistent hydrogen bonding throughout the simulation. Density Functional Theory (DFT) calculations highlighted favorable electronic properties, with EGCG showing a low band gap (3.29 eV) and high dipole moment (3.12 D), indicative of strong reactivity and binding potential. ADMET profiling revealed excellent oral bioavailability for EGCG (84%) and quercetin (88%), with minimal toxicity risks. The Molecular Electrostatic Potential (MESP) mapping identified highly reactive regions on the molecular surface, correlating with nucleophilic and electrophilic binding capabilities. The findings position EGCG, rutin, and quercetin as promising candidates for HMPV therapy, providing a strong foundation for further experimental validation and preclinical development.
Genome structural variation in natural Caenorhabditis elegans populations
Authors: Lesack Kyle J. , Wasmuth James D. 
Published: January 2025

AbstractStructural variation, involving large alterations in chromosome structure, drives genetic diversification and the emergence of new phenotypes. These changes are widespread in natural populations and play an important role in adaptation and speciation. For many species, research has been limited to laboratory adapted strains and experimental evolution, which may not reflect the diversity of structural variants in the wild. Furthermore, technological limitations have proved to be a major barrier to accurate and comprehensive variant calling. In this study, we used PacBio sequencing data from 14 wildCaenorhabditis elegansstrains to characterize structural variants in a natural population. With long-reads, we overcame limitations associated with short-read approaches and leveraged population-level data to further refine the accuracy of variant calls. We found that large, rapidly evolving gene families, such as GPCR, F-Box, and C-Type lectin, were prominent among the variants predicted to have phenotypic consequences. These results shed light on the significant role of structural variants in the evolution ofCaenorhabditis elegansin its wild habitats and the limitations of treating N2 as the reference wild-type.
Exosomes derived from highly scalable and regenerative human progenitor cells promote functional improvement in a rat model of ischemic stroke
Authors: Lee Jieun , Var Susanna R. , Chen Derek , Natera-Rodriguez Dilmareth E. , Hassanipour Mohammad , West Michael D. , Low Walter C. , Grande Andrew W. , Larocca Dana 
Published: January 2025

AbstractGlobally, there are 15 million stroke patients each year who have significant neurological deficits. Today, there are no treatments that directly address these deficits. With demographics shifting to an older population, the problem is worsening. Therefore, it is crucial to develop feasible therapeutic treatments for stroke. In this study, we tested exosomes derived from embryonic endothelial progenitor cells (eEPC) to assess their therapeutic efficacy in a rat model of ischemic stroke. Importantly, we have developed purification methods aimed at producing robust and scalable exosomes suitable for manufacturing clinical grade therapeutic exosomes. We characterized exosome cargos including RNA-seq, miRNAs targets, and proteomic mass spectrometry analysis, and we found that eEPC-exosomes were enhanced with angiogenic miRNAs (i.e., miR-126), anti-inflammatory miRNA (i.e., miR-146), and anti-apoptotic miRNAs (i.e., miR-21). The angiogenic activity of diverse eEPC-exosomes sourced from a panel of eEPC production lines was assessedin vitroby live-cell vascular tube formation and scratch wound assays, showing that several eEPC-exosomes promoted the proliferation, tube formation, and migration in endothelial cells. We further applied the exosomes systemically in a rat middle cerebral artery occlusion (MCAO) model of stroke and tested for neurological recovery (mNSS) after injury in ischemic animals. The mNSS scores revealed that recovery of sensorimotor functioning in ischemic MCAO rats increased significantly after intravenous administration of eEPC-exosomes and outpaced recovery obtained through treatment with umbilical cord stem cells. Finally, we investigated the potential mechanism of eEPC-exosomes in mitigating ischemic stroke injury and inflammation by the expression of neuronal, endothelial, and inflammatory markers. Taken together, these data support the finding that eEPCs provide a valuable source of exosomes for developing scalable therapeutic products and therapies for stroke and other ischemic diseases.
Niacin protects against vascular calcification via enhanced SIRT1 and SIRT6 signaling and promoted VSMC autophagy
Authors: Kong Chao-hua , Wu Li-da , Sun Yue , Jiang Xiao-min , Shi Yi , Wang Feng , Wang Dong-chen , Gu Yue , Zhou Wen-ying , Luo Jin-que , Chao Yue-lin , Chen Shao-liang 
Published: January 2025

AbstractBackgroundVascular calcification (VC) is a common pathologic state that often accompanies calcium-phosphorus metabolism disorder and chronic kidney diseases (CKDs) in aging individuals. Vascular smooth muscle cell (VSMC) has been widely acknowledged as one of the main cell types that involved in this process. Niacin, a lipid-lowering reagent, has been demonstrated to be beneficial in atherosclerotic disease. The correlation and mechanism between niacin and vascular calcification have not been reported so far.Methods and resultsRCS analysis based on large clinical databases indicated that diet that riches in niacin can protect against abdominal artery calcification (AAC). Our data showed that niacin treatment remarkably reduced VSMC osteogenic differentiation and senescence-associated markers under osteogenic stimulation. Moreover, niacin treatment alleviated CKD and vitamin D3-induced vascular calcification in C57BL/6J mice. Mechanistically, we for the first time demonstrated that niacin supplementation inhibited vascular calcification via maintaining both Sirtuin 1 (SIRT1) and Sirtuin 6 (SIRT6) levels. Moreover, we verified that niacin activated SIRT1 and SIRT6 promoted VSMC autophagy flux.ConclusionsThese findings may help to develop novel therapeutic strategies in the treatment and prevention of vascular calcification.