bluuebunny/crossref_metadata_2025 huggingface dataset:
Activity-Dependent Changes in Ion Channel Voltage-Dependence Influence the Activity Patterns Targeted by Neurons
Authors: Mondal Yugarshi , Calabrese Ronald L. , Marder Eve
Published: February 2025

Neurons can maintain stable activity profiles over their lifetimes despite ion channel turnover over minutes to days. Neurons also exhibit flexibility in electrical activity by regulating the voltage-dependence of ion channels. This flexibility, combined with channel turnover can, in principle, work together to maintain a stable activity profile. We augment a classical model of activity-dependent ion channel density regulation with a mechanism that adjusts channel voltage-dependence based on activity. Our findings reveal that the timescale of these adjustments shapes the range of electrical patterns that meet an activity target. This work highlights a potentially distinct role for activity-dependent regulation of channel voltage-dependence in maintaining stable neuronal activity profiles.
Soil and water microbial communities: A source of novel antibiotics for sustainable plant disease control
Authors: Iqbal Navid , Asim Noreen , Malik Shahana , Khan Sartaj , Akbar Sadia , Yoo Youngchul , Ullah Irfan , liu Luo , Khan Shahin Shah , Lee Sang Won
Published: February 2025

Pathogenic microorganisms pose a significant threat to plant health and agricultural productivity worldwide. Herein, this study explores the potential of natural microbial communities as sources of biopesticides. We analyzed 20 soil and water samples from remote areas, isolating 121 colonies using nutrient agar. Antibacterial activity was assessed through agar diffusion, revealing that 12 colonies exhibited significant inhibitory effects against various pathogenic bacteria. Measurement of inhibition zones indicated that these colonies could produce antibiotics. Subsequently, molecular characterization with 16S rRNA and BLAST searches of 12 unidentified sequences highlighted substantial microbial diversity within the samples. This research underscores the promise of these natural microbial communities in developing biocontrol agents for managing plant diseases in greenhouse and field environments. Extraction and purification techniques could further refine these antibiotics, advancing sustainable agricultural practices.
PennPRS: a centralized cloud computing platform for efficient polygenic risk score training in precision medicine
Authors: Jin Jin , Li Bingxuan , Wang Xiyao , Yang Xiaochen , Li Yujue , Wang Ruofan , Ye Chenglong , Shu Juan , Fan Zirui , Xue Fei , Ge Tian , Ritchie Marylyn D. , Pasaniuc Bogdan , Wojcik Genevieve , Zhao Bingxin
Published: February 2025

Polygenic risk scores (PRS) are becoming increasingly vital for risk prediction and stratification in precision medicine. However, PRS model training presents significant challenges for broader adoption of PRS, including limited access to computational resources, difficulties in implementing advanced PRS methods, and availability and privacy concerns over individual-level genetic data. Cloud computing provides a promising solution with centralized computing and data resources. Here we introduce PennPRS (https://pennprs.org), a scalable cloud computing platform for online PRS model training in precision medicine. We developed novel pseudo-training algorithms for multiple PRS methods and ensemble approaches, enabling model training without requiring individual-level data. These methods were rigorously validated through extensive simulations and large-scale real data analyses involving over 6,000 phenotypes across various data sources. PennPRS supports online single– and multi-ancestry PRS training with seven methods, allowing users to upload their own data or query from more than 27,000 datasets in the GWAS Catalog, submit jobs, and download trained PRS models. Additionally, we applied our pseudo-training pipeline to train PRS models for over 8,000 phenotypes and made their PRS weights publicly accessible. In summary, PennPRS provides a novel cloud computing solution to improve the accessibility of PRS applications and reduce disparities in computational resources for the global PRS research community.
SARS-CoV-2 Aggregated Activity Level Across Ontario Canada, Measured with the US CDC Wastewater Viral Activity Level (WVAL) Metric
Authors: Delatolla Robert , DeGroot Christopher T. , McKay Robert Michael , Servos Mark R. , McAvoy Steven , Krishnakumar Sanjena , Jo Orchid , Fung Michael , Hegazy Sherif , Fletcher Tim , Simhon Albert , Pileggi Vince
Published: February 2025

The wastewater viral activity level (WVAL) was developed by the United States Centers for Disease Control and Prevention (US CDC) as a standardized metric to aggregate SARS-CoV-2 wastewater data, enabling the assessment of infection levels and trends at state/territorial, regional and national scales. This approach also facilitates comparative analysis of SARS-CoV-2 prevalence across regions. In this study, we developed and evaluated graphical methods to integrate the WVAL metric into interpretable visualizations for public health decision-making. Preliminary analysis demonstrated that WVAL values correlated strongly with clinical case counts, supporting its role as a confirmatory epidemiological measure. The WVAL framework provided a linear quantification method, allowing for the comparison of regional variations in infection patterns. This study leveraged data from the Ontario Wastewater Surveillance Initiative (Ontario WSI), which included over 100 sampling sites across seven geographical regions. Weekly mean WVAL values were computed for each site and aggregated at regional and provincial levels. In total, 59 sites contributed to the provincial WVAL calculation. The computational aggregation method followed the US CDC’s WVAL approach and was generally comparable to the Public Health Ontario (PHO) aggregation method, with the notable improvement of incorporating a linear level scale. Overall, this study demonstrated that WVAL effectively quantified SARS-CoV-2 differences at a public health regional scale. The WVAL metric proved to be a robust epidemiological tool, complementing other surveillance measures to support public health decision-making.
Sexuality and respiratory outcomes in the UK: disparities, development and mediators in multiple longitudinal studies
Authors: Tabor Evangeline , Kneale Dylan , Patalay Praveetha
Published: February 2025

Background

Limited international research suggests sexual minority individuals, in particular sexual minority women, may experience worse asthma outcomes than their heterosexual peers. However, little research has explored if a similar disparity is present in the UK.

Methods

Pooling data from five UK longitudinal studies (total N=86,024, 4,860 (5.65% sexual minority) we examined asthma and lung function by sexuality. To explore the impact of ageing on disparities we compared asthma by sexuality at two time points approximately 10 years apart. To help understand potential causal mechanisms we used respondents aged under 18 as a negative control. Finally, we conducted a mediation analysis to examine the extent to which smoking accounts for asthma disparities.

Findings

Sexual minority respondents were more likely to report asthma (RR 1.43 [95% CI 1.26 to 1.62]) and poor lung function (RR 1.50 [95% CI 1.20 to 1.87]). Sexual minority women (RR 1.51 [95% CI 1.30 to 1.76]) and bisexual respondents (RR 1.75 [95% CI 1.35 to 2.26]) were more likely to report asthma than their heterosexual counterparts. Rates of asthma did not vary by sexuality in <18s and disparities increased between time points in adults supporting the hypothesis that disparities emerge after childhood and widen over the lifecourse. Smoking only partially mediated (proportion mediated 1%) the relationship between sexual minority status and asthma.

Conclusions

This analysis adds substantially to our understanding of how and when asthma and lung function disparities by sexuality in the UK emerge, as well as evidencing the limited role of smoking.

Key Messages

Our research question was whether respiratory health, in particular asthma, varied by sexuality and how it patterned across the lifecourse.

We found that sexual minority people were at greater risk of asthma and poor lung function than heterosexual people and this disparity emerges and widens in adulthood.

Respiratory disease can impact quality of life and mortality risk and understanding patterns and mechanisms of disease in the LGBTQ+ populations can allow us to address health inequalities.
Estimating rates of SARS-CoV-2 lineage spread from graph theory analysis and data mining of genetic sequence data streams
Authors: Goldberg Emma E. , Kupperman Michael D. , Ke Ruian
Published: February 2025

The modern enormous scale of viral genomic data, as exemplified by SARS-CoV-2, presents unique opportunities for epidemic inference and real-time monitoring. Existing methods, however, cannot efficiently process the extremely large stream of sequence data and simultaneously identify small subsets of sequences that may represent rapid population growth of newly emerged lineages. To address this gap, we developed a new approach that combines techniques in traditional graph theory and modern data mining. We represent small subsets of sequences as graph Laplacians and identify from them features of rapid population growth. From early sequence data collected in the US and the UK between 2021 and mid-2022, we identified two features—genetic diversity and matrix connectivity—that allow us to reliably estimate growth rates of newly emerged lineages. To test our model, we used data collected from mid-2022 and end-2024 and accurately predicted the growth rates of lineages that appeared during this period. Furthermore, for data collected in 2023 when the sequencing efforts were relatively high (thousands of sequences per day) in the US and the UK, our model correctly identified the most rapidly expanding lineages when they were still at low frequencies (between 1-6%). Overall, our work provides a scalable and adaptable tool to estimate the growth rate of newly emerged SARS-CoV-2 lineages. More broadly, the interpretable logic of our method suggests potential for rapid outbreak identification for other rapidly evolving pathogens.

Significance Statement

The COVID-19 pandemic has underscored the importance of rapidly identifying emerging SARS-CoV-2 lineages that may cause large outbreaks. Methods are needed that can handle a large amount of incoming genomic data and at the same time identify small groups of cases that may represent rapid growth of newly emerged lineages. To address this need, we developed an approach utilizing graph theory and data mining techniques, which we show reliably estimates the growth rates of newly emerged SARS-CoV-2 lineages. Our approach can promptly identify rapidly growing lineages, often weeks or months before they became dominant. This demonstrates its potential as a scalable tool for transmission dynamics inference, real-time outbreak monitoring, and pandemic preparedness.
High-risk HPV Prevalence and Distribution in Cervical Cancer Screening: Extended Genotyping in Correlation with Cytology and p16/Ki67 Dual Stain Results
Authors: Trzeszcz Martyna , Mazurec Karolina , Mazurec Maciej , Jach Robert , Halon Agnieszka
Published: February 2025

The prevalence of high-risk human papillomavirus (HR-HPV) in cytology combined with p16/Ki67 status using limited and two types of extended HPV genotyping has not yet been described. A total of 32,724 screening tests results between 2015-2024 were included. The overall HR-HPV-positivity rate was 15.0%. The HR-HPV prevalence in limited genotyping group was 13.9%, in extended genotyping 1 (17.8%), in extended genotyping 2 (17.2%), with statistically significant difference in the proportions of positive/negative cases (p<0.0001). No statistically significant difference was noted between extended genotyping groups (p=0.706). Extended genotyping 1: the highest p16/Ki67-positivity was observed for HR-HPV 33/58 (100.0%) and 31 (58.8%), the lowest for HR-HPV 45 (18.2%), 18 (25.0%) and 59/56/66 (28.9%). Extended genotyping 2: the highest p16/Ki67-positivity was for HR-HPV 16 (66.7%) and 31/33/52/58 (58.8%). A combined approach, implementing new technologies, could help healthcare providers in more informed decisions about patient care, supporting the prevention of cervical precancer and cancer.

Statement of Significance

The transition to HPV-based cervical cancer screening is progressively advancing. By investigating of HR-HPV prevalence and distribution in limited or extended genotyping, cytology and p16/Ki67 dual-stain, our study aimed to support evidence-based decision-making processes and help guide of medical interventions of public health policies targeted to incorporation of new technologies.
Global, regional, and national burden of chronic kidney disease-related heart failure from 1990 to 2021: an analysis of data from the Global Burden of Disease Study 2021
Authors: Ji Jinzhong , Chu Feifan , Guan Qing , Chen Lumin , Ma Yuning , Chen Zujie , Ji Qiwei , Sun Mingxin , Ren Gaozhan , Huang Tingyang , Song Haihan , Lin Weiqiang , Lin Xiuquan , Zhou Hao
Published: February 2025

Background

The global burden of chronic kidney diseases related heart failure (CKD-related HF) has yet to be reported. The study aims to analyze the global burden of CKD-related HF.

Methods

Utilizing the data from the Global Burden of Disease Study 2021, we delineated the prevalence and years lived with disability (YLDs) of CKD-related HF at global, regional, and national levels, alongside its age and sex distributions, as well as temporal trends. Furthermore, we conducted transnational inequality analysis and frontier analysis. Additionally, we analyzed the burden of CKD-related HF with diverse etiological factors.

Results

Over the past three decades, the global burden of CKD-related HF has escalated, reaching 1,936,886 cases in 2021, with an age-standardized prevalence of 24.21 per 100,000 and an age-standardized YLDs rate of 3.07 per 100,000. This burden is projected to continue rising over the next decade. The burden of CKD-related HF is notably concentrated among the elderly and children. Notably, there is health inequity in its distribution, disproportionately affecting low sociodemographic index (SDI) groups, although alleviation opportunities exist across all SDI levels. Globally, the primary contributors to CKD-related HF are type 2 Diabetes Mellitus (T2DM) and hypertension, apart from CKD of other and unspecified causes.

Conclusions

The global burden of CKD-related HF has witnessed increase and is projected to persist over the next decade. Certain populations, including children, the elderly, and regions with low SDI levels, experienced a heavier burden. Effective management of primary diseases contributes to mitigating the burden of CKD-related HF.
Sex and gender differences in OCD: A scoping review
Authors: Van Zandt Meghan , Olfson Emily , Stahnke Brittany , Taylor Samantha , Bloch Michael H. , Pittenger Christopher , Pushkarskaya Helen
Published: February 2025

This scoping review explores sex and gender differences in obsessive-compulsive disorder (OCD) as reported in the literature between 2009 and 2021. A comprehensive PubMed search was conducted without restrictions, using terms related to sex, gender, and OCD. 5,973 articles were screened by two reviewers, with 909 assessed at the full-text level. Of these, 541 were included: 37 meta-analyses, 8 systematic reviews, 25 narrative reviews, and 471 original reports. Original reports were categorized by focus — symptomology and burden (66), comorbidities (121), epidemiology (134), human genetics (68), altered neurocognitive and neurobiological functioning (36), treatment (42), and animal models (29) — and assessed for quality using CASP checklists. There was abundant research on sex and gender effects in OCD, but limited synthesis. Identified methodological concerns included inconsistent assessments of sex and gender, variability in OCD symptom measurement, failure to account for menstrual cycle effects, and a lack of genome-wide and full-brain imaging studies. Biases in results may arise from not accounting for gender differences in insight, help-seeking behaviors, and comorbidity. We identify critical knowledge gaps and develop hypotheses for future research, incorporating recommendations for precision medicine approaches. Investigating sex and gender differences in OCD can advance equitable mental health care by addressing the specific needs of diverse populations. Appreciating these effects offers a pathway to better understanding the complexity of OCD, fostering targeted interventions and a more nuanced approach to treatment and prevention.
Senolytics restore hematopoietic stem cell function in sickle cell disease
Authors: Barve Aditya , Cornwell Adam , Sriram Pramika , Kopyov Alex , Dabas Preeti , Kooienga Emilia , Kelley Zakiya , Johnson James , Myers Jacquelyn A. , Obeng Esther A. , Kang Guolian , Olufadi Yunus , Cain Terri , Talbot Lindsay , Spence David , Cortes Mauricio , Miller Sam , Loeffler Dirk , Sharma Akshay , McKinney-Freeman Shannon
Published: February 2025

Sickle Cell Disease (SCD) is a blood disorder affecting millions worldwide. Emerging evidence reveals that SCD pathophysiology increases risk of myeloid malignancies and hematopoietic stem cell (HSC) dysfunction, possibly due to pathological stress on bone marrow. To investigate this further, we interrogated mice and individuals with SCD and observed extended cell cycle times, oxidative stress, DNA damage, senescence, and dysregulation of molecular programs associated with these processes in bone marrow hematopoietic stem and progenitor cells (HSPCs). Human SCD HSPCs displayed poor hematopoietic potentialex vivo. SCD mice displayed a dramatic loss of transplantable bone marrow HSPCs, which was reversed upon treatment of SCD mice with the senolytic agent, ABT-263 (navitoclax). Thus, senolytics restore bone marrow function during SCD in mice and represent a novel strategy to improve bone marrow health in individuals with SCD and improve the safety of potentially curative gene therapies that utilize autologous HSPCs from individuals with SCD.
Mismatch repair and homologous recombination are yin-yang partners in hybrid zygote meiosis
Authors: Chuang Chi-Ning , Hung Ya-Ling , Kim Hong-Xiang , Yao Jhong-Syuan , Liu Hou-Cheng , Chen Sheng-Yuan , Jovanska Lavernchy , Hsueh Yi-Ping , Chen Ruey-Shyang , Wang Ting-Fang
Published: February 2025

Mismatch repair (MMR) is believed to prevent homologous recombination (HR) between homologous chromosomes, causing infertility in hybrids between closely related species. We report that HR and MMR are yin-yang partners in the response to genetic polymorphisms and that several budding yeast HR genes (i.e.,RAD51,RAD54,ZMM) exhibit anti-MMR activities. This yin-yang relationship biases MMR in wild-type interspecies (Saccharomyces cerevisiae/Saccharomyces paradoxus) hybrid zygotes and intraspeciesS. cerevisiaehybrid zygotes with anti-MMR mutations, resulting in excessive (rather than insufficient) interhomolog HR, including negative crossover interference, allelic conversion or even disruption. The anti-MMR function ofS. cerevisiaeRad54 prevails over its accessory role in promoting Rad51-mediated strand exchange during hybrid meiosis. Srs2 (the yeast ortholog ofEsherichia coliUvrD helicase) facilitates the MMR system by dissembling Rad51-ssDNA presynaptic filaments. Sgs1 (the yeast ortholog ofE. coliRecQ helicase) acts after MMR-dependent recognition of heteroduplex mismatches to promote crossover clustering and allelic switching.

In brief

Excessive interhomolog recombination leads to hybrid infertility

Highlights

Homologous recombination (HR) antagonizes mismatch repair (MMR) in hybrid meiosis.

Anti-MMR mutations of HR genes (RAD51,RAD54,orZMM) cause hybrid sterility.

Hybrid sterility is due to excessive (rather than insufficient) interhomolog HR.

Hybrid sterility-inducing anti-MMR mutations can be rescued by repressing MMR genes.
In vivoImaging and Tracking of VRE-microbiota Interactions via Anaerobic Fluorescent Reporters in Extremely Drug-resistant Bacteria
Authors: Treat Benjamin R. , Hobeika Joseph , Duggar Marygrace , Fields Trinity , Guy Cliff , Black Mollie , Kohler Christina M. , Margolis Elisa B.
Published: February 2025

Vancomycin-resistantEnterococcus faecium(VREfm) has emerged as a major nosocomial pathogen, but studying its host and microbiome interactions remains challenging due to limited genetic tools. Current obstacles include extensive intrinsic and acquired resistance that precludes use of conventional selection markers, poor plasmid maintenance, and oxygen-dependent reporters unsuitable for gut environments. Here we present an integrated toolkit that enables robust genetic manipulation andin vivotracking of VREfm. We developed a universal puromycin selection system effective across diverse clinical isolates and an enhancedpheS**counterselection marker for stable genomic integration. We identified two neutral genomic loci that support reporter genes insertion without fitness cost. Using this system, we demonstrate long-term tracking of VREfm colonization, strain competition and host-microbiome interactions in mouse models via chromosomally-integrated anaerobic fluorescent proteins (eUnaG2 and smURFP). This toolkit advances the study of VREfm pathogenesis by enabling stable genetic manipulation of even the most resistant clinical isolates and direct visualization of host-microbe interactions in ecologically and immunologically relevantin vivoenvironments.
Multi-Omics Analysis of Wound Microbiome andStaphylococcus aureusin Pressure Ulcer
Authors: Guo Changyuan , Jiang Guilai , Li Yuanyuan , Zhao Jun , Li Jilin , Li Shengkai , Zhou Zhemin , Xie Erfan , Li Heng
Published: February 2025

This study employs a multi-omics approach to investigate the wound microbiome andStaphylococcus aureusin pressure ulcers. Metagenomic sequencing and associated technologies were utilized to examine bacterial populations, identify dominant species, and study biofilm formation inS. aureusthrough metabolomic and proteomic characteristics. The results revealed a significant reduction in microbial diversity in pressure ulcer samples compared to controls, withStaphylococcus, Corynebacterium, andKlebsiellabeing the most prevalent genera. Functional prediction analysis indicated differences in pathogenic invasiveness and biofilm formation factors among the groups. The presence of antimicrobial resistance genes was higher in the pressure ulcer group, particularly inStaphylococcusspp. strains. Whole-genome sequencing of 29S. aureusisolates identified various clonal complexes andspatypes, with the majority possessing genes conferring resistance to β-lactam antimicrobials and virulence factors. Histopathological examination and fluorescent in situ hybridization confirmed the presence ofS. aureusin biofilm structures. In vitro biofilm formation tests and metabolomic and proteomic analyses provided insights into the interactions betweenS. aureusstrains and their biofilm formation, revealing enriched pathways related to metabolic processes and membrane composition. This research offers a scientific foundation for understanding the colonization patterns ofS. aureusbiofilms in pressure ulcer wounds.
ERK plays a conserved dominant role in pancreas cancer cell EMT heterogeneity driven by diverse growth factors and chemotherapies
Authors: Barbeau Michelle C. , Brown Brooke A. , Adair Sara J. , Bauer Todd W. , Lazzara Matthew J.
Published: February 2025

Epithelial-mesenchymal transition (EMT) occurs heterogeneously among malignant carcinoma cells to promote chemoresistance. Identifying the signaling pathways involved will nominate drug combinations to promote chemoresponse, but cell population-level studies are inherently fraught, and single-cell transcriptomics are limited to indirect ontology-based inferences. To understand EMT heterogeneity at a signaling protein level, we combined iterative indirect immunofluorescence imaging of pancreas cancer cells and tumors and mutual information (MI) modeling. Focusing first on MAP kinase pathways, MI predicted that cell-to-cell variation in ERK activity surprisingly dominated control of EMT heterogeneity in response to diverse growth factors and chemotherapeutics, but that JNK compensated when MEK was inhibited. Population-level models could not capture these experimentally validated MI predictions. The dominant role of ERK was predicted by MI even when analyzing seven potential EMT-regulating signaling nodes. More generally, this work provides an approach for studying highly multivariate signaling/phenotype relationships based on protein measurements in any setting.
RadiSeq: a single- and bulk-cell whole-genome DNA sequencing simulator for radiation-damaged cell models
Authors: Mathew Felix , Galarneau Luc , Kildea John
Published: February 2025

Objective

To build and validate a simulation framework to perform single-cell and bulk-cell whole genome sequencing simulation of radiation-exposed Monte Carlo cell models to assist radiation genomics studies.

Approach

Sequencing the genomes of radiation-damaged cells can provide useful insight into radiation action for radiobiology research. However, carrying out post-irradiation sequencing experiments can often be challenging, expensive, and time-consuming. Although computational simulations have the potential to provide solutions to these experimental challenges, and aid in designing optimal experiments, the absence of tools currently limits such application. Monte Carlo toolkits exist to simulate radiation exposures of cell models but there are no tools to simulate single- and bulk-cell sequencing of cell models containing radiation-damaged DNA. Therefore, we aimed to develop a Monte Carlo simulation framework to address this gap by designing a tool capable of simulating sequencing processes for radiation-damaged cells.

Main Results

We developed RadiSeq – a multi-threaded whole-genome DNA sequencing simulator written in C++. RadiSeq can be used to simulate Illumina sequencing of radiation-damaged cell models produced by Monte Carlo simulations. RadiSeq has been validated through comparative analysis, where simulated data were matched against experimentally obtained data, demonstrating reasonable agreement between the two. Additionally, it comes with numerous features designed to closely resemble actual whole-genome sequencing. RadiSeq is also highly customizable with a single input parameter file.

Significance

RadiSeq enables the research community to perform complex simulations of radiation-exposed DNA sequencing, supporting the optimization, planning, and validation of costly and time-intensive radiation biology experiments. This framework provides a powerful tool for advancing radiation genomics research.
The extensive diversity of nairoviruses reveals the complexity and high risk of tick-borne diseases in northeastern China
Authors: Liu Ziyan , Wei Zhiwei , Liu Yu , Wang Zedong
Published: February 2025

The increasing burden of tick-borne virus infections is becoming a global public health concern. In the current study, we identified nine tick-borne nairoviral species in northeastern China through metagenomic sequencing, which are phylogenetic classified into four groups: I) Wetland virus (WELV), II;) Songling virus (SGLV), Ji’an nairovirus (JANV), Yanbian nairo tick virus 1 (YBNTV-1), Shanxi tick virus 2 (SXTV-2), III;) Yezo virus (YEZV), and IV;) Beiji nairovirus (BJNV), Yichun nairovirus (YCNV), and Hunchun nairovirus (HCNV). These nairoviruses are influenced by both the species of ticks and their geographical distribution. Apart from the previously isolated pathogenic WELV, SGLV, YEZV, and BJNV, we successfully isolated JANV and YBNTV-1, which can replicate in Vero and HEK-293T cells. Two routes of nairovirus spread into northeastern China were evaluated. Group I and II viruses, vectored byHaemaphysalissp. ticks, likely originated in Central or East China and spread via migratory birds along the Chinese coastline. Group III; and IV viruses, vectored byIxodes persulcatusticks, are believed to have originated in Europe and spread via rodents across the Eurasian continent. Our study reveals the extensive diversity and wide distribution of tick-borne nairoviruses in northeastern China, highlights the potential pathogenic risk of the newly discovered nairoviruses, and clarifies their origins and potential migration routes. The results will be of crucial significance for the tick-borne diseases control and prevention in China.
Infectome Analysis of Small Mammals in Southern China Reveals Ecological Associations and Emerging Threats from Diverse Pathogens
Authors: Xin Genyang , Wang Daxi , Zhang Xin , Cen Qingquan , Peng Minwu , Liao Yuqi , Wang Jing , Le Shijia , Cheng Jinxia , Wu Wei-chen , Hou Xin , Luo Gengyan , Gou Qinyu , Kong Jianbin , Pan Zhu , Li Dongqing , Gan Shipei , Chen An , Zhao Hailong , Shi Peibo , Ren Zirui , Zhao Weiqi , Liu Jiajun , Jia Penghui , Sun Changyun , Lin Wenqing , Wu Jun , Kuang Guopeng , Chen Jingdiao , Li Junhua , Holmes Edward C. , Deng Ziqing , Shi Mang
Published: February 2025

Small mammals harbor a diverse array of zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viral diversity, with limited attention paid to bacteria and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome of 2,408 individual samples, representing lung, liver, and gut tissues from 858 animals collected throughout Guangdong province, China, with a study design that accounted for host species, tissue, season, and geographic location. We identified 76 pathogen species, including 29 RNA viruses, 12 DNA viruses, 5 bacteria, and 30 eukaryotic pathogens, 33 of which were newly discovered. Tissue distribution analysis revealed distinct organotropisms, suggesting varied transmission routes, while host distribution analysis showed that each animal carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Our characterization of the geographic and seasonal patterns revealed that pathogen richness was primarily influenced by region, host species, and season, while pathogen composition was largely shaped by host genetic distance. Collectively, these data provide the first comprehensive insight into the dynamics of the pathogen infectome in these key mammalian disease reservoirs, highlighting the major factors driving pathogen diversity and transmission.
Cross-membrane cooperation among bacteria can facilitate intracellular pathogenesis
Authors: Schator Daniel , Kumar Naren G , Chong Samuel Joseph U , Jung Timothy K , Jedel Eric , Smith Benjamin E , Evans David J , Fleiszig Suzanne M J
Published: February 2025

Pseudomonas aeruginosais a Gram-negative opportunistic pathogen able to cause life- and sight-threating infections. Once considered an extracellular pathogen, numerous studies have shown it can survive intracellularly. Previously, we showed thatP. aeruginosainside cells can diversify into distinct subpopulations in vacuoles and the cytoplasm. Here, we report that the transition from vacuoles to cytoplasm requires collaboration with the extracellular subpopulation, through Ca2+influx enabled by their type III secretion system (T3SS) translocon pore proteins. Moreover, we show that collaboration amongP. aeruginosasubpopulations can contribute to disseminating intracellular bacteriain vivoin a mouse infection model. This study provides the basis for future studies to investigate how cooperation of extracellular and intracellular bacteria within the host may contribute to disease progression and persistence.
Functional Specialization for Language Processing in Inferior Frontal Regions During Early Childhood: Evidence from functional near-infrared spectroscopy individual functional channels of interest approach
Authors: Luo Haolun , Yu Tao , Li Qun , Sheng Li
Published: February 2025

Early language acquisition represents a fundamental achievement in cognitive development, yet the neural mechanisms underlying this process remain debated. Using functional near-infrared spectroscopy (fNIRS) with an innovative functional Channel of Interest (fCOI) approach, we investigated the functional specialization for language processing in bilateral inferior frontal regions during early childhood. In two experiments involving adults (N=20) and toddlers (N=22, ages 2-4 years), participants completed language processing and cognitive control tasks. Results demonstrated early functional specialization in the language-selective region of left inferior frontal gyrus, which showed selective responses to linguistic content while remaining insensitive to cognitive demand manipulations in both age groups. However, language selectivity in the homologous right hemisphere region was present only in adults, suggesting continued development of language organization beyond early childhood. The MD regions showed complementary patterns, with right-hemispheric selectivity for cognitive control emerging early. These findings provide evidence for early neural specialization of language processing in the left hemisphere, while revealing ongoing development in right hemispheric organization. Our results support models of early language-specific neural circuits rather than gradual differentiation from domain-general mechanisms, while highlighting the protracted development of language organization.

RESEARCH HIGHLIGHTS

Validated language localizer task in fNIRS using individual functional Channel of Interest approach, enabling reliable investigation of early language networks.

Demonstrated a double dissociation between neural processors in inferior frontal gyrus for language and domain-general cognition (cognitive load) in children as young as 2.

Supports early neural specialization for language processing rather than gradual emergence from domain-general networks.
Nucleon form factors from generalized parton distributions
Authors: Ghasemzadeh Leila , Sartipi YarAahmadi Pegah , Arbabifar Fatemeh , Morshedian Nader , Atashbar Tehrani Shahin
Published: February 2025

In this paper, we introduce a novel for generalized parton distributions (GPDs), named GSAMA24. This aims to provide a more accurate and comprehensive description of the internal structure of hadrons by incorporating advanced parametrizations and fitting techniques. We compare the performance of the GSAMA24 with three established models: the extended Regge (ER), modified Gaussian (MG), and M-HS22 . The GSAMA24 is designed to address limitations observed in previous models by offering improved flexibility in the t dependence and skewness parameter ξ. Our analysis involves fitting the GSAMA24 to experimental form factor data and evaluating its predictive power against the ER, MG, and M-HS22 models. The comparison is based on key metrics such as the accuracy of form factor predictions, the consistency with known GPD properties, and the computational efficiency of the fitting process. Results indicate that the GSAMA24 provides a superior fit to the experimental data, particularly in the high momentum transfer region, where it outperforms the ER and MG models. Additionally, the GSAMA24 demonstrates better agreement with the theoretical expectations of GPD behavior compared to the M-HS22 model. These findings suggest that the GSAMA24 is a promising tool for future studies of hadronic structure and could significantly enhance our understanding of the spatial and momentum distributions of quarks and gluons within hadrons.

Published by the American Physical Society
2025
Corrections from spacetime dependent electromagnetic fields to Wigner functions and spin polarization
Authors: Yang Shi-Zheng , Gao Jian-Hua , Pu Shi
Published: February 2025

We have derived the Wigner equations at global equilibrium with constant vorticity but spacetime dependent electromagnetic fields up to second order in a semiclassical expansion. We obtain the new second-order contributions to the charge currents and energy-momentum tensor from the varying electromagnetic fields. We also compute the new corrections to the spin polarization pesudovector from both constant and varying electromagnetic fields. We also find that the spacetime dependent electromagnetic field provides a tighter constraint on the solutions of Wigner functions in global equilibrium compared with a constant electromagnetic field.

Published by the American Physical Society
2025
Thermodynamic matrix exponentials and thermodynamic parallelism
Authors: Duffield Samuel , Aifer Maxwell , Crooks Gavin , Ahle Thomas , Coles Patrick J.
Published: February 2025

Thermodynamic computing exploits fluctuations and dissipation in physical systems to efficiently solve various mathematical problems. It was recently shown that certain linear algebra problems can be solved thermodynamically, leading to a speedup scaling with the matrix dimension. Here, we provide a thermodynamic algorithm for exponentiating a real matrix. We describe a simple electrical circuit involving coupled oscillators, which can implement our algorithm. We also show that this algorithm provides an asymptotic speedup that is linear in the dimension. Finally, we introduce the concept of thermodynamic parallelism to explain this speedup, stating that thermodynamic noise provides a resource leading to effective parallelization of computations.

Published by the American Physical Society
2025
“I think it made me a better person”: fostering personal-social development among immigrant youth through the SExT theatre programme
Authors: Taylor Shira B. , Calzavara Liviana , Flicker Sarah , Kontos Pia , Schwartz Robert
Published: February 2025

Purpose

Immigrant youth face both unique and disproportionate barriers to sexual health. Targeted sexual health education to redress these disparities requires creative and inclusive approaches that consider personal and community challenges and strengths. This study piloted a novel intervention: SExT: Sex Education by Theatre, a theatre-based, culturally-relevant, participatory action research programme delivered in an immigration destination neighbourhood in Toronto, Canada.

Design/methodology/approach

Nineteen youth were trained as peer educators. They participated in theatre-based workshops on sexual health topics which culminated in a performance for local peers. Mixed methods evaluation included surveys which investigated changes in personal and social development over three time-points (pre, post, 4-month follow-up). The impact of the intervention on peer educators was explored in greater depth using qualitative peer interviews and focus groups.

Findings

Quantitative study findings indicated that peer educators experienced significant improvements in personal growth, social inclusion and social engagement after participating in SExT and these improvements were maintained at follow-up. Thematic qualitative analysis further indicates that meaningful involvement in a sex education theatre intervention may protect against adverse outcomes and promote self-actualization, connection and active citizenship.

Originality/value

This research stands out for its innovative approach to addressing sexual health disparities among immigrant youth in Toronto using culturally relevant theatre-based peer education. SExT may serve as a model for sexual health interventions for newcomer youth and other priority groups in diverse contexts.
House prices drivers in Greece and Portugal: a cointegration analysis
Authors: Gkiosis Petros , Chapsa Xanthippi
Published: February 2025

Purpose

The purpose of the article is to contribute to the existing growth literature by exploring the complex dynamics between house prices and macroeconomic factors such as gross domestic product (GDP) per capita, interest rates, employment and inflation in two countries sharing common geopolitical and socioeconomic characteristics, namely Greece and Portugal.

Design/methodology/approach

The autoregressive distributed lag (ARDL) cointegration methodology is applied, as proposed by Pesaran and Shin (1995) and Pesaran et al. (2001) in the presence of structural breaks. The bounds-testing ARDL model is used due to its numerous advantages, while the unit root test with breaks was performed in order to capture events capable of causing regime changes.

Findings

The analysis reveals evidence of a strong association between housing prices and inflation in both the long run and the short run. With respect to the other housing price determinants, evidence is mixed according to the country selected.

Originality/value

This work is inspired by the determinant role of housing prices in the economic system, household wealth and the standard of living in the last decades. Using various theoretical and methodological approaches, these studies have focused on the importance attached to several factors affecting house prices, such as GDP per capita, inflation, employment, interest rates, etc.
Human vs virtual influencers and message framing: enhancing environmental awareness, activism and sustainable purchase intentions through effective messaging
Authors: Nazir Mehvish , Wani Tahir Ahmad
Published: February 2025

Purpose

With the advent of metaverse, virtual influencers (VIs) are on the rise and so is their usage in advertisement of various products and services. This study aims to explore the domain of sustainable marketing and presents whether a VI can be more effective than their human counterparts (HIs) when it comes to environmental messaging. The study uses the concept of message frames to check which message frame and influencer type leads to more effective communication and ultimately sustainable purchase decisions.

Design/methodology/approach

A 2 × 2 experimental design was employed to check the effect of the type of influencer (HI vs VIs) on message effectiveness using positive and negative message frames which ultimately affect the purchase intentions of the followers. A combination of two-way ANOVA along with PLS-SEM was used to validate the hypothesized relationships.

Findings

The findings from the structural equation modelling revealed that HIs still continue to be better at communicating environmental messages than VIs. Further, in lines with the previous research this study highlighted the importance of negative message frames in enhancing the effectiveness of posts related to environmental causes. Additionally, the study revealed a positive association between message effectiveness, consequential awareness, environmental activism and sustainable purchase intentions.

Originality/value

Though there is an emergent interest in VIs, scant literature exists on how they encourage sustainable consumer behaviour. This study attempts to fill this gap by assessing the comparison between VIs and HIs in terms of promoting sustainable consumption. It is a novel effort in the crossover of sustainable marketing and influencer marketing.
Lexical density in English newspapers – a cross-analysis of the New York Times and Arab News
Authors: Alzahrani Hayat
Published: February 2025

Purpose

This study examines the lexical density of articles from The New York Times (TNYT) and Arab News (AN), analyzing its impact on the readability and accessibility of content for general audiences, particularly non-native English speakers. It also considers other features affecting readability in these newspapers.

Design/methodology/approach

The chosen method for lexical density is Ure’s content-to-total word ratio, while readability is calculated with the help of the Flesch–Kincaid Grade Level. The analysis involves the use of descriptive statistics and Pearson’s correlation coefficient to determine the relationship between lexical density and readability. A qualitative content analysis is used for in-depth analysis of contextual factors affecting text comprehensibility. The dataset comprises 100 articles: 50 articles from TNYT and 50 articles from AN, between 2022 and 2024 and covered topics related to climate change and the environment.

Findings

The findings revealed that AN has an average lexical density of 56.54% while TNYT has 57.96%. Nevertheless, the above difference is not statistically significant. In addition, lexical density has a positive correlation (0.6332) with Flesch–Kincaid Grade-Level scores. Therefore, this implies that reading comprehension decreases as lexical density increases. Qualitative findings indicate that AN emphasizes regional adaptation and increased contextual explanations, which can increase comprehensibility for non-native English speakers.

Research limitations/implications

One of the limitations of this research involves the exploration of two English-language newspapers from Western and Middle-Eastern world regions. This means that the findings cannot accurately reflect the audiences in these two regions. Additionally, this study did not involve the comparison of tolerance thresholds for lexical density among different groups, such as native and non-native English language speakers. In the future, researchers should examine the same topic by considering other Western and Middle-Eastern newspapers that were not covered in this study. In addition, interviews with experts and tests should be administered to compare the impacts of lexical density on comprehensibility between native and non-native English language speakers.

Originality/value

This research contributes to the knowledge of how lexical density affects readability in Western and non-Western English newspapers. It provides insights for media outlets aiming to enhance content accessibility for diverse, global audiences.
Investigation of the Potential Treatment Effect of Botulinum Toxin Type A in Ovarian Torsion: Findings From the Rat Model
Authors: Ateş Çağlayan , Dilbaz Berna , Ergani Seval Yılmaz , Seçken Pelin , Köse Caner
Published: February 2025

Background

The aim of this study was to investigate the effects of botulinum toxin A on histological abnormalities, loss of ovarian reserve, and angiogenesis within the ovarian torsion–detorsion paradigm.

Methods

A total of 45 female Wistar albino rats were used for the study. The rats were randomly divided into five groups (n = 9 in each group): Control, Torsion, Torsion + Detorsion, Torsion + Detorsion + Botulinum toxin, and Botulinum toxin only. Follicular cell degeneration, vascular congestion, hemorrhage, inflammation, and vascular endothelial growth factor (VEGF) expression scores were compared histopathologically between the groups. Follicle numbers were compared. Anti‐mullerian hormone levels were measured before and after torsion, detorsion, and treatments.

Results

Follicular cell degeneration, vascular congestion, hemorrhage, inflammation, and VEGF expression differed significantly between groups for each score (p < 0.001). The VEGF expression score was found to increase more in the torsion + detorsion + botulinum toxin group than in the torsion + detorsion group (2.67 ± 0.71 and 2.22 ± 0.67, respectively). There was a significant difference between the groups in secondary follicle counts (p = 0.04). The groups showed statistically significant differences in their anti‐mullerian hormone levels (p < 0.001).

Conclusion

This initial investigation of the effects of botulinum toxin on ovarian torsion (OT) has shown that botulinum toxin type A has the potential to be a useful adjunct treatment for fertility preservation. Our results proved the ovarian protective effect of botulinum toxin type A in rats with OT. Therefore, botulinum toxin type A may be a potential preventive agent against ovarian damage caused by torsion in the future.