bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anin vitroinvestigation into the survival ofTropilaelaps mercedesaeon a range of matrices
Authors: Gill Maggie C , Chuttong Bajaree , Davies Paul , Earl Avril , Tonge George , Etheridge Dan 
Published: December 2024

ABSTRACTTropilaelapsspp. are a parasitic mite that feed and reproduce within honey bee brood (Apisspp.) and cause significant damage and mortality toApis melliferacolonies.T. mercedesaeis found outside the range of its natural hostA. dorsataand was recently detected in Europe for the first time in 2024. It is widely believed thatTropilaelapsspp. are unable to survive without brood. However, studies have demonstrated thatT. mercedesaecan survive during broodless periods while parasitisingA. dorsataand without brood in overwintering colonies ofA. melliferain temperate climates. This study sought to examine the survival ofT. mercedesaeon a range of matrices and found that mites could survive for more than 96 hours on live adultA. melliferaand more than 144 hours and 168 hours on decomposingA. melliferapupae and adults respectively. These findings could indicate one possible mechanism which allowsT. mercedesaeto survive without brood. These findings also have implications towards better understanding possible transmission routes forTropilaelaps. Previously bee sales in the form of queens and packages and used beekeeping equipment were considered a relatively low risk for transmittingTropilaelapsspp. due to the absence of live brood. This study demonstratesTropilaelaps’ability to survive in these scenarios and the increased potential for it to spread globally.
Tissue-specific apparent mtDNA heteroplasmy and its relationship with ageing and mtDNA gene expression
Authors: Wengert Simon , Giannoulis Xenofon , Kreitmaier Peter , Kautz Pauline , Ludwig Leif S. , Prokisch Holger , Casale Francesco Paolo , Heinig Matthias , Cai Na 
Published: December 2024

AbstractHeteroplasmy in the mitochondrial DNA (mtDNA) accumulates with age, but how much it occurs in tissues and how it affects function and physiology is not well-studied. Here we present a comprehensive tissue-specific map of mtDNA heteroplasmy and mtRNA modifications, and their relationships with age and mitochondrial gene expression. We propose a robust variant calling pipeline for mtDNA heteroplasmy and mtRNA modifications using bulk RNAseq data from 49 tissues in GTEx, and a calibrated phenotype association framework for both types of variants. We identify 109 associations between them and donor age, and 784 associations with tissue-specific mtDNA gene expression. Of these, 7 and 18 show cell-type specificity within tissue. In addition, we find 9 instances where these variations mediate donor age effects on mtDNA gene expression. Finally, we confirm previously identified relationships between mt-tRNA modifications and gene expression on their 5’, but read- and gene-level investigations reveal previously unmodeled complexities.
Updating Beliefs using New Evidence from a Diagnostic Decision-Support Aid in a Nurse-Led First-Seizure Clinic
Authors: Tittensor Phil , Batterham Alan M , Rowe Jacqui-Dawn , Russell Daniel , Steward Danielle , Schnabel Elizabeth , Meiklejohn Kay , Mainstone Milaana , Wellburn Shaun , Terry John R , Woldman Wessel 
Published: December 2024

SummaryRecent studies using computational and mathematical interrogation of background EEG have revealed eight biomarkers that inform a diagnostic decision-support tool called BioEP. To assess the utility of BioEP for aiding clinical decision making, we conducted a prospective single-site diagnostic belief updating study (NCT05764252). Eighty-six adults with suspected seizures attended a nurse-led, first-seizure clinic. Using a 7-point scale ranging from ‘virtually certain’ to ‘exceptionally unlikely’, two clinicians independently rated the probability of having another epileptic seizure before and after reviewing BioEP scores. Recruitment took place over 1 year. The probability ratings changed (beliefs updated) by at least one category in 35/86 participants for Reviewer 1 (41%; 95% confidence interval: 30-51%) and in 58/86 people for Reviewer 2 (67%; 58 to 77%). The impact of the presentation of new evidence from the BioEP score on reviewer beliefs was substantial and bidirectional. For Reviewer 1 n=20 lower and n=15 higher probability, with n=37 lower and n=21 higher probability for Reviewer 2. Future research will explore the impact of these biomarkers on long-term diagnostic decision making and examine robustness and generalisability in multi-site settings.
NOTE ON A SMALL FRUIT-EATING BAT FROM THE MIDDLE HOLOCENE OF LAGOA SANTA, EASTERN BRAZIL
Authors: Chahud Artur 
Published: December 2024

AbstractBats represent the second most diverse order of mammals; however, their fossil and subfossil remains are still relatively understudied. In Brazil, numerous living species have been identified in cave deposits, although few fossils have been dated, with none originating from the Holocene. This study presents a specimen from the Middle Holocene, collected from Cuvieri Cave. The fossil consists of an incomplete, U-shaped mandible that includes the first molars. The specimen was identified asArtibeussp., a genus of fruit-eating bats that is currently widespread across Brazilian territory. This specimen dates to a poorly understood period in the Lagoa Santa region, when human populations had abandoned the area (referred to as the Archaic Gap)and during which the faunal population of Cervidae experienced a notable decline in the number of fossil records. The genusArtibeusis widely distributed in tropical regions and is commonly found in environments ranging from semi-arid regions to savannas and dense forests. It is not considered a paleoenvironmental indicator.
PERK Signaling Maintains Hematopoietic Stem Cell Pool Integrity under Endoplasmic Reticulum Stress by Promoting Proliferation
Authors: Zheng Manxi , Peng Qinlu , Kropp Erin M , Shen Zhejuan , Liu Suxuan , Yin Zhengyou , Matono Sho , Iwawaki Takao , Wang Xiang , Inoki Ken , Mei Yang , Li Qing , Liu Lu 
Published: December 2024

AbstractThe integrity of the hematopoietic stem cell (HSC) pool relies on efficient long-term self-renewal and the timely removal of damaged or differentiation-prone HSCs. Previous studies have demonstrated the PERK branch of the unfolded protein response (UPR) drives specific programmed cell death programs to maintain HSC pool integrity in response to ER stress. However, the role of PERK in regulating HSC fatein vivoremains unclear. Here, we demonstrate that PERK is dispensable for normal hematopoiesis and HSC self-renewal under steady-state conditions. In contrast, PERK is activated to promote HSC proliferation and depletion in response to ER stress induced by the inactivation of ER-associated degradation (ERAD), via the knockout of key components of ERAD Sel1L or Hrd1. Inhibition of PERK, either through genetic knockout or knock-in of a point mutation that eliminates PERK kinase activity, significantly restores the HSC defects induced by Sel1L or Hrd1 knockout. Mechanistic studies reveal that ERAD deficiency does not lead to HSC death or ROS accumulation. Instead, PERK promotes the activation of mTOR signaling and drives abnormal proliferation of HSCs, impairing their self-renewal potential. This process removes stressed HSCs, thereby maintaining HSC pool integrity. Our study uncovers a PERK-centered strategy employed by HSCs to preserve their pool integrity independently of apoptosis.Key pointsPERK is not required for steady-state hematopoiesis but preserves hematopoietic stem cell pool integrity in response to increased ER stress.Under ER stress induced by ERAD deficiency, PERK is activated to promote mTOR signaling and HSC hyper-proliferation, depleting damaged HSCs.
Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C.elegans
Authors: Wang Xuebin , Liu Hanzhang , Yang Wenjing , Yang Jingxuan , Sun Xuehong , Liu Qiuhan , Zhu Ying , Sun Yinghao , Liu Chunxiuzi , Shi Guiyuan , Liu Qiang , Zhang Ke , Di Zengru , Yang Wenxing , Liu He 
Published: December 2024

AbstractNeural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on the neural network architectures of male and hermaphrodite C. elegans and the association with sexually dimorphic behaviors. We applied graph theory and computational neuroscience methods to systematically discern the features of these two neural networks. Our findings revealed that a small percentage of sexual-specific neurons exerted dominance throughout the entire male neural net-work, suggesting male’s prioritized sexual-related behavior outputs. Based on the structural and dynamical characteristics of two complete neural networks, sub-networks containing sex-specific neurons and their immediate neighbors, or sub-networks exclusively comprising sex-shared neurons, we predicted dimorphic behavioral outcomes for males and hermaphrodites. To verify the prediction, we performed behavioral and calcium imaging experiments and dissected a circuit that is specific for the increased spontaneous local search in males for mate-searching. Our research sheds light on the neural circuits that underlie sexually dimorphic behaviors in C. elegans, and provides significant insights into the inter-connected relationship between network architecture and functional outcomes at the whole-brain level.
Dairy DigiD ∼ A Deep Learning-Based, Non-Invasive Biometric Identification System for Dairy Cattle Using Detectron2
Authors: Mahato Shubhangi , Bi Hanqing , Neethirajan Suresh 
Published: December 2024

AbstractPrecision livestock farming demands accurate and reliable individual animal identification for optimizing health monitoring, resource allocation, and overall herd productivity. Conventional identification methods—such as ear tagging and wearable sensors—are often invasive, potentially causing animal discomfort and affecting natural behaviors. To address these challenges, we introduce Dairy DigiD, a non-invasive biometric classification system for dairy cattle using facial image analysis. Leveraging deep learning and the Detectron2 framework, Dairy DigiD classifies cattle into four categories—young (<2 years), mature milking, pregnant, and old—using over 2,500 high-resolution facial images. A DenseNet121 model achieved a classification accuracy of 97%, showcasing its strong discriminative capability. Further, Detectron2 attained an average recall of 87% in category identification, an average precision of 96% in cattle detection, and an overall detection accuracy of 93%, demonstrating its robustness and adaptability to varied environmental conditions. Unlike traditional approaches that rely on fixed facial landmarks and can be sensitive to environmental variability, Dairy DigiD’s flexible deep learning architecture enables stable and scalable facial feature extraction. This non-invasive method minimizes animal stress, enhances data integrity, and facilitates improved herd management and welfare monitoring. In comparison to existing convolutional neural network (CNN)-based strategies, Dairy DigiD exhibits superior adaptability to real-world farm conditions, including variable lighting and complex poses. This work highlights the potential of integrating advanced computer vision and deep learning methodologies into precision dairy farming, offering an ethically aligned, efficient, and scalable approach to modern livestock management.
Emergence and Dynamics of Usutu and West Nile Viruses in the Netherlands, 2016-2022
Authors: Münger Emmanuelle , Atama Nnomzie , van Irsel Jurrian , Blom Rody , Krol Louie , van den Berg Tijs J , Braks Marieta , de Vries Ankje , van der Linden Anne , Chestakova Irina , Boter Marjan , Chandler Felicity D , Kohl Robert , Nieuwenhuijse David F , Uiterwijk Mathilde , Fouchier Ron A M , Sprong Hein , Gröne Andrea , Koenraadt Constantianus J M , Schrama Maarten , Reusken Chantal B E M , Stroo Arjan , van den Brand Judith M A , van der Jeugd Henk P , Oude Munnink Bas B , Sikkema Reina S , Koopmans Marion P G 
Published: December 2024

SummaryBackgroundMosquito-borne arboviruses, including Usutu virus (USUV) and West Nile virus (WNV), are emerging threats in Europe, with changes in climate, land use, and increased travel and trade influencing their dynamics. Understanding the emergence and establishment of these viruses in new regions is critical for informing targeted mitigation of drivers of emergence and enhancing public and wildlife health preparedness.MethodsSeven years (2016-2022) of interconnected studies were conducted in the Netherlands. Live birds were sampled by volunteer bird ringers, dead birds were referred for sampling by citizen-scientists and zoological institutions, and mosquitoes were trapped. Samples were tested for USUV and WNV using RT-PCR and screened forOrthoflavivirusantibodies using protein microarray and neutralization assays. Sequencing and phylogenetic analyses were performed.FindingsUSUV was first detected in the Netherlands in 2016, caused large outbreaks in birds until 2018, and resurged in 2022. One dominant, enzootic lineage, co-circulated alongside several limited introductions of a second lineage. A localized WNV lineage 2 outbreak occurred in live birds and mosquitoes in 2020, with another positive bird in 2022 and serological evidence of continued circulation.InterpretationWe provide the first comprehensive, multi-year documentation of two emerging arboviruses in the Netherlands. USUV was enzootically maintained over seven years and was associated with substantial bird mortality. WNV is in an early stage of establishment with no bird mortality observed. Our integrated wildlife sampling was crucial in detecting a human WNV outbreak, bringing this emerging threat to public health attention.FundingZonMw, Dutch Research Council (NWO), European Union, Government of the Netherlands
A protein cage system for producing bioactive peptides inEscherichia coli
Authors: Harding Maxim D. , Jackson Mark A. , Gilding Edward K. , Yap Kuok , Craik David J. , Sainsbury Frank , Lawrence Nicole 
Published: December 2024

AbstractNew therapeutics are urgently needed to curb the spread of drug-resistant diseases. Bioactive peptides (BAPs), including antimicrobial peptides, are emerging as an exciting new class of compounds with advantages over current drug modalities, especially small molecule drugs that are prone to resistance development. However, production of BAPs currently relies heavily on chemical synthesis, which is environmentally and economically costly. To address this limitation, we developed a platform that enables the biosynthetic production of BAPs via encapsulation within self-assembling protein cages in the cytoplasm ofEscherichia coli. Using bacteriophage P22 virus-like particles (VLPs), we assessed the encapsulation of three structurally distinct classes of BAPs with activities against bacteria, cancer, and malaria. We demonstrated that encapsulation within P22 VLPs enables successful production of BAPs that are otherwise recalcitrant to recombinant expression. This approach is especially attractive for positively charged BAPs and we observed an increase in packaging efficiency within P22 VLPs that corresponded to an increase in overall positive charge. Both cyclic and linear BAPs were recovered following a simple downstream processing pipeline that involved VLP disassembly, then extraction of BAPs via enzymatic processing. This work demonstrates that encapsulation of BAPs within P22 VLPs is an effective method for biosynthetic production of BAPs inE. coli. By providing an alternative to chemical synthesis, this approach has the potential to increase accessibility and reduce the cost and burden of chemical waste for producing therapeutically valuable BAPs.
CD24-Fc resolves inflammation and rescues CD8 T cells with polyfunctionality in humanized mice infected with HIV-1 under cART
Authors: Li Guangming , Ma Jianping , Yu Haisheng , Tsahouridis Ourania , Lou Yaoxian , He Xiuting , Funaki Masaya , Mathur Poonam , Kottilil Shyamasundaran , Zheng Pan , Liu Yang , Su Lishan 
Published: December 2024

AbstractThe persistence of HIV-1 reservoirs during combination anti-retroviral therapy (cART) leads to chronic immune activation and systemic inflammation in people with HIV (PWH), associating with a suboptimal immune reconstitution as well as an increased risk of non-AIDS events. This highlights the needs to develop novel therapy for HIV-1 related diseases in PWH. In this study, we assessed the therapeutic effect of CD24-Fc, a fusion protein with anti-inflammatory properties that interacts with danger-associated molecular patterns (DAMPs) and siglec-10, in chronic HIV-1 infection model using humanized mice undergoing suppressive cART. Our findings show that CD24-Fc treatment significantly reduced inflammation and immune hyperactivation in vivo when combined with cART. CD24-Fc mediated resolution of inflammation was associated with improved recovery of CD4 T cells, reduced immune activation, restored central memory T cells and reversal of immune cell exhaustion phenotype. Notably, CD24-Fc treatment rescued CXCR5+ CD8 central memory T cell (TCM) which correlated with increased polyfunctionality in HIV-specific T cells in humanized mice and in cultured peripheral blood mononuclear cells (PBMCs) from PWH. This restoration of CXCR5+ memory CD8 T cells was associated with HIV replication inhibition, delayed viral rebound and reduced HIV-1 pathogenesis upon cART cessation. This study suggests that CD24-Fc treatment could represent a promising new therapeutic strategy for managing chronic systemic inflammation and associated diseases in PWH.Author summaryCombination antiretroviral therapy (cART) cannot block viral gene expression from activated HIV proviral DNA in reservoir cells, contributing to chronic immune activation and inflammation associated diseases in people with HIV (PWH). The therapeutic treatment of anti-inflammatory fusion protein CD24-Fc in humanized mice during suppressive cART (i) resolves inflammation and chronic HIV-1 immune pathogenesis during suppressive cART, (ii) rescues CXCR5-expressing CD8 memory T cells and enhances antiviral response in humanized mice and PWH PBMCs, (iii) delays virus rebound and reduces viral pathogenesis after cART cessation. Thus, CD24-Fc could provide a novel therapeutic strategy for treating chronic systemic inflammation and associated diseases in PWH.
CCGM: a Compound Coarse Grain Model representation for enhanced chemotype exploration, annotation and screening
Authors: Sahni Navriti , Patek Marcel , Rahman Rayees , Ravikumar Balaguru 
Published: December 2024

AbstractStructurally similar compounds often exhibit similar bioactivity, making similarity estimation an essential step in many cheminformatics workflows. Traditionally, compound similarity has been evaluated using diverse molecular representations, such as molecular fingerprints, compound 3D structural features, and physicochemical properties. These methods have proven effective, particularly during the early stages of drug discovery, where the primary goal is to identify initial hits from large compound libraries. However, these representation and methods often fall short during the hit-to-lead development phase, where modifications to the core scaffold or chemotype are performed and evaluated. To address this limitation, we developed the Compound-Coarse-Grain-Model (CCGM), a framework that represents structural features of a compound as nodes and edges within a simplified graph. This approach augments the pharmacophore and chemotype features of the compound within the graph, enabling the identification of compounds with similar chemotype and pharmacophore features more effectively than conventional methods. CCGM is particularly useful for when screening large libraries to identify compounds with similar chemotypes and for filtering generative designs to retain designs with similar pharmacophore features.
Illuminating the Potential: Light Harvesting and Semiconducting Properties of Bacterial Microcompartment Shell Proteins
Authors: Bedi Silky , Rose S M , Sinha Sharmistha 
Published: December 2024

AbstractBiomaterials with self-assembly, genetic tunability, self-healing, and biocompatibility hold promise for next-generation electronics. This study explores disc-like shell proteins from bacterial microcompartments as photovoltaic materials. These self-assembling proteins exhibit semiconducting properties, including a low work function and non-linear I-V behavior. Notably, under UV light, they generate significant photocurrent without external voltage, demonstrating efficient electron transfer. Electron conduction occurs via tunneling, enabled by distinct electron-rich surface regions. High responsivity and quantum efficiency outperform prior protein-based systems, emphasizing their potential in photocurrent and light-harvesting applications. Genetic mutations revealed a proton-coupled electron transfer (PCET) mechanism, where tyrosine residues strategically positioned near proton abstraction sites enhance photocurrent generation. This study highlights the innovative capabilities of shell proteins for energy-efficient devices and demonstrates how genetic engineering can further optimize biomaterial performance, paving the way for sustainable electronic applications.
A Conditional Degron Tag for RNA Sensing in Bacteria
Authors: Simons Tyler J. , Hammond Ming C. 
Published: December 2024

ABSTRACTHere we report the development of a conditional degron system for use in bacteria in which a tagged fluorescent protein (FP) reporter, mVenus-S1, is stabilized only in the presence of TAR RNA. The functional design takes advantage of the bipartite nature of the ssrA degron sequence, so that TAR RNA binding to the inserted Tat peptide sequence blocks degron recognition to rescue protein activity. Several fluorescent proteins and a chemiluminescent enzyme can be tagged and activated using this system, and our results reveal that chromophore maturation time correlates with fold change, with up to ∼60-fold turn-on. Finally, we designed a functional biosensor foroxySsRNA and integrated it into a single transcript in which the FP and RNA-based biosensor are encoded on the same mRNA. To our knowledge, this is the first proof-of-concept for a novel biosensor design that expresses both protein and RNA components from a single transcript. The streamlined system is fully genetically encoded, does not require an exogenous fluorophore, and permits both components to be coordinated by expression from the same promoter.
Deep learning-based stride segmentation with wearable sensors: effects of data quantity, sensor location, and task
Authors: Anderson Anthony J. , Gonzalez Michael , Eguren David , Khan Naima , Zuccaroli Isabella , Hirczy Siegfried , Kelly Valerie E. , Muir Brittney C. , Kontson Kimberly 
Published: December 2024

AbstractAccurate stride segmentation from wearable sensors is foundational for digital gait assessment tools, yet systematic evaluations of deep learning approaches across varied real-world mobility tasks remain limited. We developed and assessed Temporal Convolutional Network (TCN) models for stride segmentation using data from 121 older adults with and without Parkinson’s disease, specifically evaluating how performance varies with model development data quantity, sensor location, and movement complexity. Using a fixed-size test set of 40 participants, we found that lower limb sensors achieved F1 scores above 95% during walking with just 5–10 training participants, but performance declined substantially during more complex movements such as 180° turns. Foot-mounted sensors maintained robust performance across tasks (F1: 99.3% walking, 96.7% turning, 88.4% stationary and transitional movements), while wrist sensors showed marked degradation (F1: 88.4% walking, 72.3% turning, 50.0% stationary and transitional movements). Our findings demonstrate that it is important to tailor performance testing for digital gait assessment tools to both sensor location and use case, as performance achieved during controlled walking may not generalize to complex movements in daily life.