bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing Foundation Models for Predicting Viral Animal Host Range in Intelligent Surveillance
Authors: Guo Jinyuan , Guo Qian , Yin Hengchuang , Han Yilun , Geng Peter X. , Hou Jiaheng , Zhang Haoyu , Tan Jie , Li Mo , Zhang Yan , Jiang Xiaoqing , Zhu Huaiqiu 
Published: February 2025

AbstractEmerging human infectious viruses originating from animals continue to pose a persistent threat to global public health. Understanding the host range of animal viruses is crucial for identifying potential spillover pathways and mitigating the risk of future pandemics. Here, we present VirHRanger, a prediction method that integrates foundation models trained on viral genome and protein sequences, alongside genomic and protein compositional traits, viral phylogeny, and protein-protein interactions. To systematically predict the animal host range, VirHRanger incorporates host taxonomy-aware neural networks trained on a comprehensive collection of animal-virus associations spanning mammals, birds, and arthropods. Within a dataset of 4,006 virus species spanning 99 viral families, our model achieved robust performance with a micro-averaged AUROC of 0.938 across all host categories, demonstrating its effectiveness in capturing generalizable host signals from viral genetic data. On a dataset of 315 novel viruses, which are associated with key reservoir animal hosts and insect vectors, VirHRanger notably outperformed the homology-based method, exhibiting a strong generalizability to novel viruses. Furthermore, VirHRanger identified host range variations among closely related viruses within theCoronaviridaefamily and successfully predicted the ability of SARS-CoV-2 to infect humans and other animal hosts. These findings highlight the potential of VirHRanger to transform sequencing data into timely insights for disease control during the early stages of zoonotic outbreaks.
Human type-I interferon omega holds potent antiviral properties and promotes cytolytic CD8+T cell responses
Authors: Nguyen Hoang Oanh , Recordon-Pinson Patricia , Andreola Marie-Line , Papagno Laura , Appay Victor 
Published: February 2025

AbstractThe type-I interferon family is well known for its critical role in innate immunity. It comprises several members, among which IFN-α2 and IFN-β are the most extensively studied, with important antiviral and immune-modulatory functions. Recent findings linking autoantibodies against type-I interferons to severe COVID-19 suggest a potential role for IFN-ω in combating SARS-CoV-2 infection. However, little is known about human IFN-ω, as most research on this interferon has been conducted in feline models. Here, we demonstrate that human IFN-ω is secreted at levels comparable to those of IFN-α2 or IFN-β upon stimulation with inflammatory agonists and triggers a robust antiviral response, inhibiting SARS-CoV-2 infectionin vitro. Moreover, IFN-ω enhances the effector functions of antigen-specific CD8+T cells primedde novofrom healthy donor cells, highlighting its capacity to promote strong cellular immunity. Our results position IFN-ω as a key member of the type-I interferon family, with promising potential for therapeutic and vaccine applications.Author SummaryType-I interferons are pleiotropic cytokines, including IFN-α and IFN-β, which are well known for their antiviral activities. Here, we report on the functional characteristics of human IFN-ω, a neglected member of the type-I IFN family, which has primarily been studied in feline models. We show here that human IFN-ω induces intense downstream signaling in cells resulting in the upregulation of antiviral genes, and efficient restriction of SARS-CoV-2 replication. IFN-ω also promotes the acquisition of strong cytolytic functions by antigen primed CD8+T cells. Overall, our findings portray human IFN-ω as a major antiviral molecule, similar to the well-studied and highly effective IFN-α2. The secretion of IFN-ω upon infection is likely to be crucial for effective control of multiple viruses, advocating for its use in therapeutic approaches in humans.
Addressing efficacy of everyday hygiene cleansing products in context of sustainable handwashing behaviour in the post-pandemic era
Authors: Pathak Sandip B. , Arora Shafali , Sayyed Jabir , Trivedi Urmi , Sherin Lincy , Kumar Nitish , Jayasekera Harshinie W. , Majumdar Amitabha , Mukherjee Sayandip 
Published: February 2025

AbstractSimple hygiene behaviour such as washing hands is key to improving health of individuals and reducing community transmission of communicable diseases such as respiratory and enteric infections. Consistent and relentless messaging by global and local health authorities had resulted in heightened hygiene awareness amongst the public during the COVID-19 pandemic. Unfortunately, many of the hygiene behaviours practiced during the pandemic have proven to be unsustainable in the immediate period following the pandemic. While CDC guidelines suggest washing hands with soap for a minimum of 20 seconds to prevent the spread of germs, a hygiene intervention’s effectiveness must be evaluated in context of the prevalent hygiene behaviour. Here we report our findings from an observational study conducted across India, Pakistan, Saudi Arabia, and United Arab Emirates focusing on handwashing habit of individuals in the post-pandemic period. Across all geographies, the time spent for lathering product on skin (contact time) for a significant majority of individuals recruited for the study was found to be 10 seconds and less. To ensure that marketed hygiene formulations such as liquid cleansers and sanitizers are efficacious in inactivating pathogens under conditions practiced by the majority as a part of their daily hand washing practices, we have investigated the in-vitro antimicrobial efficacy of several hygiene cleansing formulations at 10 seconds of contact time. Our results show that well-formulated cleansing solutions can reduce the input titre of both bacterial and viral pathogens by 99.9% or more, even with brief contact. With the global resurgence of both existing and emerging pathogens in the post-pandemic world, promoting sustainable handwashing practices for infection prevention remains a challenge as it is deeply rooted in the socio-economic fabric of many countries. Therefore, it is crucial to conduct regular studies like this to reassure end-users and combat complacency regarding the composition of everyday hygiene products.HighlightsStudies of handwashing behavior in 4 countries reveals significantly short lathering durationAntimicrobial efficacy testing of marketed products was conducted against a range of pathogensSuitably formulated hygiene products can inactivate pathogens at short durations of contact
Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing
Authors: Chen Danping , Isakova Alina , Zhou Wan Joe , Wu Yunming , Zhao Boxuan Simen 
Published: February 2025

AbstractUnderstanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods particularly limited in mapping long-distance circuits and preserving cell type information. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding, and parallel single-nucleus and single-synaptosome sequencing to map neuronal connectivity at single-synapse resolution. This AAV-based approach enables simultaneous capture of both synaptic connections and molecular identities of connected neurons. We validated this approach in the mouse pontocerebellar circuit, identifying both established projections and potentially novel synaptic partnerships. Through integrated analysis of connectivity and gene expression, we identified molecular markers enriched in connected neurons, suggesting potential determinants of circuit organization. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision and gene expression information, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states. This advance in connectivity mapping methodology opens new possibilities for understanding circuit organization in complex mammalian brains.
Deep Sound Synthesis Reveals Novel Category-Defining Sound Features in the Human Auditory Cortex
Authors: Xing Lidongsheng , Formisano Elia , Riecke Lars 
Published: February 2025

AbstractThe human auditory system extracts meaning from the environment by transforming acoustic input signals into semantic categories. Specific acoustic features give rise to distinct categorical percepts, such as speech or music, and to spatially distinct preferential responses in the auditory cortex. These responses contain category-relevant information, yet their representational level and role within the acoustic-to-semantic transformation process remain unclear. We combined neuroimaging, a deep neural network, a brain-based sound synthesis, and psychophysics to identify the sound features that are internally represented in the speech- and music-selective human auditory cortex and test their functional role in sound categorization. We found that the synthetized sounds exhibit unnatural features distinct from those normally associated with speech and music, yet they elicit categorical cortical and behavioral responses resembling those of natural speech and music. Our findings provide new insights into the fundamental sound features underlying speech and music categorization in the human auditory cortex.
CHD3 regulates BMP signalling response during cranial neural crest cell specification
Authors: Mitchell Zoe H. , den Hoed Joery , Claassen Willemijn , Demurtas Martina , Deelen Laura , Campeau Philippe M. , Liu Karen , Fisher Simon E. , Trizzino Marco 
Published: February 2025

SummaryCHD3 is a component of the NuRD chromatin remodeling complex. PathogenicCHD3variants cause Snijders Blok-Campeau Syndrome, a neurodevelopmental disorder with variable features including developmental delays, intellectual disability, speech/language difficulties, and craniofacial anomalies. To unveil the role of CHD3 in craniofacial development, we differentiatedCHD3-KO induced pluripotent stem cells into cranial neural crest cells (CNCCs). CHD3 expression is low in wild-type iPSCs and neuroectoderm, but upregulated during CNCC specification, where it opens the chromatin at BMP-responsive enhancers, to allow binding of DLX5 and other factors. CHD3 loss leads to repression of BMP target genes and an imbalance between BMP and Wnt signalling, ultimately resulting in aberrant mesodermal fate. Consequently, CNCC specification fails, replaced by early-mesoderm identity, which can be partially rescued by titrating Wnt levels. Our findings highlight a novel role for CHD3 as a pivotal regulator of BMP signalling, essential for proper neural crest specification and craniofacial development.
The give and take in photosymbiosis unraveled by metabolomics of Radiolaria
Authors: Nikitashina Vera , Bartels Benjamin , Mansour Joost Samir , LeKieffre Charlotte , Decelle Johan , Hertweck Christian , Not Fabrice , Pohnert Georg 
Published: February 2025

AbstractMarine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments they are among the most important primary producers. Systematic studies of radiolarian biology are limited because Radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian photosymbiosis we address here the metabolic contributions of the partners to the performance of the holobiont. Therefore, we describe the metabolic inventory of two highly abundant photosymbiotic Radiolaria – colony-forming Collodaria and single-celled Acantharia and compare their metabolomes to metabolomes of respective free-living algae. Most of the metabolites detected in the symbiosis are not present in the free-living algae, suggesting a significant transformation of symbionts’ metabolites by the host. The metabolites identified in both the holobiont and the free-living algae encompass molecules of primary metabolism and a number of osmolytes, including dimethylsulfoniopropionate. Mass spectrometry imaging revealed the presence of dimethylsulfoniopropionate in both the symbionts and host cells, indicating that the algae provide osmolytic protection to the host. Furthermore, our findings suggest a possible dependence of Collodaria on symbiotic vitamin B3. Distinctive differences in phospholipid composition between free-living and symbiotic stages indicate that the algal cell membrane may undergo rearrangement in the symbiosis. Our results demonstrate a strong interdependence and rewiring of the algal metabolism underlying Radiolaria-microalgae photosymbioses.
Implicit Emotional Biases in Anxiety and Depression: A Fast Periodic Visual Stimulation Study
Authors: Vandenheever David , Davidson Haleigh , Kemp Jennifer , Murphy Zack , Kujawa Autumn , Shi Catherine , Nadorff Michael , Bates-Brantley Kayla , Sidwell MacKenzie 
Published: February 2025

AbstractAnxiety and depression are among the leading global causes of disability, yet their underlying neural mechanisms remain poorly understood. Traditional event-related potential (ERP) studies have shown attentional biases in anxiety and blunted responses to positive stimuli in depression, but limitations in sensitivity and interpretability hinder their clinical application. Fast Periodic Visual Stimulation (FPVS) offers an objective, high signal-to-noise ratio (SNR) approach to measuring neural responses to emotional stimuli. In this study, we applied FPVS with affective images to assess differences in emotional processing between individuals with anxiety and healthy controls across two experimental phases, optimizing stimulus presentation parameters. The results revealed that individuals with anxiety exhibited increased neural responses to negative stimuli compared to positive stimuli, as well as reduced responses to high-arousal stimuli, particularly in occipito-temporal and central-parietal regions. Additionally, individuals with comorbid depression showed blunted responses to high-arousal stimuli across multiple brain regions, consistent with reduced emotional reactivity. These findings support the feasibility of FPVS as a rapid and reliable tool for assessing emotional processing differences in clinical populations, with potential applications in translational research and psychiatric screening
A protocol for error prevention and quality control in camera trap datasets
Authors: Silva‐Rodríguez Eduardo A. , Cortés Esteban I. , Vasquez‐Ibarra Viviana , Gálvez Nicolás , Cusack Jeremy , Ohrens Omar , Moreira‐Arce Darío , Farías Ariel A. , Infante‐Varela José 
Published: February 2025

Abstract

Camera traps are a mainstream methodology in applied ecology, but surprisingly there are no widely accepted protocols to ensure the quality of the data obtained from these devices.

We reviewed a sample of 147 articles from the recent camera‐trapping literature and found that only 4.8% report a measure of quality control.

We propose a framework to process media files obtained from camera traps that minimises errors by adopting a series of systematic procedures. Before classification, the focus is on detecting camera malfunctions, correcting storage and programming errors and establishing clear exclusion criteria. Classification can follow different approaches, including single or double human‐eye review, which can be supported by artificial intelligence.

The protocol is followed by quality control procedures that enable users to determine whether a dataset meets quality standards and is ready to be analysed, or if further revision is needed.

Synthesis and applications: The proposed protocol introduces quality control as a key component of camera trap data processing, thus reducing error rates and making the reporting process more transparent. These principles also apply to other methods, such as autonomous sound‐recording units. We suggest that by adopting formal quality control procedures, applied ecology will be able to capitalise the many advantages brought by new technologies and data processing tools.
HPWPs, Creativity, and Innovative Performance: Moderating Role of Knowledge Sharing
Authors: Babar Sumbal , Yasmeen Aiza , Rehman Wali ur 
Published: February 2025

ABSTRACTThis paper examines the effect of high‐performance work practices (HPWP) on innovation performance in the SME context, in particular how creativity and knowledge sharing support this linkage. The study draws on social cognitive theory and the ability, motivation, and opportunity (AMO) framework to outline a moderated mediation model of creativity and knowledge sharing unpacking the critical, but underexplored, link between HPWP and employee innovation performance in SMEs. Hypotheses are tested through time‐lagged (T1 and T2), multisource (dyadic, i.e., 269 sample including employees and managers) data from SMEs in Pakistan. The findings provide support for the hypothesized moderated mediation relationships including that creativity mediates the positive association between HPWP and employee innovation performance, and that knowledge sharing acts as a key moderator. These findings provide important guidelines for SMEs seeking to innovate for the future, highlighting not just the importance of HPWP but significantly how they operate to foster creativity and leverage knowledge sharing behavior.
Enhanced Microglial Engulfment of Dopaminergic Synapses Induces Parkinson's Disease‐Related Executive Dysfunction in an Acute LPC Infusion Targeting the mPFC
Authors: Liu Yehao , Chen Rui , Mu Chunyan , Diao Junjie , Guo Yurong , Yao Xiaoyu , Shi Shijie , Wang Mengying , Zhang Zhi , Qin Xiaoling , Tang Chuanxi 
Published: February 2025

ABSTRACTThe dysfunction of the dopaminergic projection from the ventral tegmental area (VTA) to the medial prefrontal cortex (mPFC) is believed to play a key role in the pathophysiology of Parkinson's disease (PD) accompanied by executive dysfunction (EDF). In this study, we identified an abnormal increase in lysophosphatidylcholine (LPC) levels in PD patients, which closely correlates with the severity of cognitive impairment. LPC disrupts the miR‐2885/TDP‐43 signaling pathway in microglia, driving dopaminergic presynaptic engulfment. In LPC‐exposed mice, microglial activation via miR‐2885/TDP‐43/p65 signaling led to inflammatory cytokine and complement release, marking dopaminergic synapses for phagocytosis with a “PS/C1q” signal. Following the inhibition of LPC‐induced microglial activation through chemogenetic methods, we observed a significant reduction in the phagocytosis of dopaminergic synapses, resulting in improved executive function. The miR‐2885 disrupted LPC‐induced dopaminergic phagocytosis and alleviated EDF. Furthermore, the accumulation of excessive TDP‐43 due to the loss of miR‐2885 promoted the engulfment of dopaminergic synapses by facilitating the entry of p65 into the nucleus. Inhibiting TDP‐43 levels effectively mitigated LPC‐induced EDF. Additionally, supplementing dopamine receptor agonists enhanced the excitability of regional glutamatergic neurons, leading to improved executive function. In summary, LPC exposure in the mPFC impairs microglial regulation, leading to dopaminergic synaptic loss and underactivity of glutamatergic neurons. These changes drive the development of executive dysfunction in PD.
Negative interest rates, bank capital and lending behaviours
Authors: Dai Zixuan , Xu Lei 
Published: February 2025

AbstractWe examine the impact of negative interest rate policies (NIRP) on the link between the capital adequacy ratio (CAR) and bank lending behaviours. Through a sample from 29 Organisation for Economic Cooperation and Development (OECD) countries, we find that NIRP improves the marginal effect of CAR on bank lending. Mortgage and corporate loans can both benefit from the building up of CAR after NIRP. Nevertheless, NIRP adversely affects CAR's marginal effect on the lending behaviours of global systemically important banks (G‐SIBs). Moreover, the influence of NIRP is heterogeneous depending on bank‐specific characteristics such as size and capital level.
Using Environmental DNA Sampling for Simultaneous Detection of Hosts and Their Pathogens: A Case Study With the Critically Endangered Frog Genus Atelopus
Authors: Voyles Jamie , Richards‐Zawacki Corinne L. , Byrne Allison Q. , Estrada Angie , Ibáñez Roberto , Rodriguez Keely M. , Goldberg Caren S. 
Published: February 2025

ABSTRACTStudying declining and rare species is inherently challenging, particularly when the cause of rarity is emerging infectious diseases (EIDs). Tracking changes in the distribution of pathogens that cause EIDs, and the species made scarce by them, is necessary for conservation efforts, but it is often a time and resource intensive task. Here, we demonstrate how using environmental DNA (eDNA) to detect rare species—and the pathogens that threaten them—can be a powerful tool to understand disease dynamics and develop effective conservation strategies. Amphibian populations around the world have undergone rapid declines and extinctions due to the emerging fungal pathogen, Batrachochytrium dendrobatidis (Bd). We developed and validated a qPCR assay using eDNA sampling methods for some of the most imperiled amphibian species, harlequin frogs (Atelopus varius, Atelopus zeteki, and Atelopus chiriquiensis), and applied this assay in concert with a standard qPCR assay for Bd in rainforest streams of Panamá. We confirmed the presence of Atelopus at sampling locations across three regions. In addition, we used genomic analysis of eDNA samples to show that Bd in Panamá falls within the Global Panzootic Lineage, a lineage associated with disease‐induced declines. We detected Bd DNA in most of our historic sites, and its concentration in water samples correlated with stream characteristics and the pathogen load of the local amphibian community. These results suggest that some populations of Atelopus persist in their historic localities. They also show how eDNA analysis can be effectively used for monitoring species presence, pathogen concentrations, and the distribution and spread of pathogen lineages. EIDs are a growing threat to endangered species around the world. Simultaneous detection of rare and declining host species and their pathogens with eDNA will help to provide key insights for effective conservation management.