bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intentionally vs. Spontaneously Prolonged Gaze: A MEG Study of Active Gaze-Based Interaction
Authors: Vasilyev Anatoly N. , Svirin Evgeniy P. , Dubynin Ignat A. , Butorina Anna V. , Nuzhdin Yuri O. , Ossadtchi Alexei E. , Stroganova Tatiana A. , Shishkin Sergei L. 
Published: December 2024

AbstractEye fixations are increasingly employed to control computers through gaze-sensitive interfaces, yet the brain mechanisms supporting this non-visual use of gaze remain poorly understood. In this study, we employed 306-channel magnetoencephalography (MEG) to find out what is specific to brain activity when gaze is used voluntarily for control.MEG was recorded while participants played a video game controlled by their eye movements. Each move required object selection by fixating it for at least 500 ms. Gaze dwells were classified as intentional if followed by a confirmation gaze on a designated location and as spontaneous otherwise.We identified both induced oscillatory and sustained phase-locked MEG activity differentiating intentional and spontaneous gaze dwells. Induced power analysis revealed prominent alpha-beta band synchronization (8–30 Hz) localized in the frontal cortex, with location broadly consistent with the frontal eye fields. This synchronization began 500–750 ms before intentional fixation onset and peaked shortly after it, suggesting proactive inhibition of saccadic activity. Sustained evoked responses further distinguished the two conditions, showing gradually rising cortical activation with a maximum at 200 ms post-onset in the inferior temporal cortex during intentional fixations, likely indicative of focused attentional engagement on spatial targets. These findings illuminate the neural dynamics underlying intentional gaze control, shedding light on the roles of proactive inhibitory mechanisms and attentional processes in voluntary behavior.By leveraging a naturalistic gaze-based interaction paradigm, this study offers a novel framework for investigating voluntary control under free behavior conditions and holds potential applications for enhancing hybrid eye-brain-computer interfaces.
DNA barcoding of passerine birds at an ornithological crossroad reveals significant East-West genetic lineage divergence
Authors: Tehrani Sahar Javaheri , Rezazadeh Elham , Kakhki Niloofar Alaei , Nourani Leila , Ebadi Vali , Karimi Sahar , Karami Mojtaba , Ashouri Fatemeh , Sarshar Asaad , Gossmann Toni I. , Aliabadian Mansour 
Published: December 2024

AbstractExploring genetic diversity is essential for precise species delimitation, especially within taxonomically complex groups like passerine birds. Traditional morphological methods often fail to resolve species boundaries; however, DNA barcoding, particularly through the mitochondrial cytochrome c oxidase subunit I (COI) gene, provides a powerful alternative method for accurate species identification. This study establishes a comprehensive DNA barcode library for Iranian passerine birds, analyzing 537COIsequences from 94 species across 23 families and 53 genera. We observed a pronounced barcode gap, with average intraspecific divergence at 0.4% and interspecific divergence at 18.6%. Notable intraspecific variation emerged in the Persian nuthatch (Sitta tephronota) and the Lesser whitethroat (Curruca curruca), while the goldfinch (Carduelis carduelis) showed limited genetic differentiation despite marked morphological distinctions. Phylogenetic analysis revealed significant east-west genetic splits inC. currucaandS. tephronota, reflecting geographic and zoogeographic boundaries of Iran. These findings demonstrate the effectiveness of DNA barcoding in elucidating biogeographic patterns, emphasizing the key role of Iran as an ornithological crossroads for avian biodiversity. Moreover, our results suggest that much of the genetic variation in theCOIgene arises from synonymous mutations, highlighting the role of purifying selection in shaping mtDNA diversity across species.
Evaluating the impact of COVID-19 on the HIV epidemic among men who have sex with men in Australia: A modelling study
Authors: Weng Rongxing , Kwon Jisoo A. , Hammoud Mo , Clifton Brent , Scott Nick , McGregor Skye , Gray Richard T. 
Published: December 2024

AbstractIntroductionThe initial phase of the coronavirus disease 2019 (COVID-19) pandemic caused significant interruptions to human immunodeficiency virus (HIV) prevention and healthcare services. In Australia, these interruptions coincided with a large reduction in HIV diagnoses but it is unknown if this reflects a reduction in incidence or barriers to testing. We aimed to understand the changes in HIV transmission among men who have sex with men in Australia and the impact of disruptions to HIV prevention, testing and treatment services due to the COVID-19 pandemic and the public health response by incorporating time-sensitive factors in real-world situations.MethodsWe developed a mathematical model to estimate monthly HIV incidence between January 2020 and August 2022. We obtained aggregated monthly data for sexual partners, condom use, HIV testing, pre-exposure prophylaxis (PrEP) use, and migration. Three scenarios were simulated: 1) a COVID scenario with all changes in place; 2) a no COVID-19 scenario where input parameters remained at pre-COVID-19 values, and 3) a no COVID-19 scenario with continued PrEP scale-up.ResultsIn the absence of the COVID-19 pandemic, the estimated number of cumulative infections from January 2020 to August 2022 would have been 1,266 [95% Percentile Interval (PI): 1,100–1,466] compared to 915 [95% PI: 729–1,181] for the COVID-19 scenario (a 27.7% reduction). The largest reduction in infections (44.3%) occurred in 2020 with 273 (95% PI: 221– 344) infections versus 490 (95% PI: 435–552) in the no-COVID scenario. There was a rebound with 387 infections (95% PI: 307–502) in 2021, followed by a reduction to a stable level by August 2022. Our model identified reductions in sexual partners as the leading factor contributing to the change in HIV infections and diagnoses (−24.8% and −10.5%, respectively).ConclusionsA substantial reduction in new HIV infections and diagnoses in Australia occurred during the early stages of the COVID-19 pandemic, which was largely due to reduced HIV transmission. A rebound in infections as sexual partnerships increased between 2021-2022, highlights the imperative to maintain vigorous response efforts and take advantage of the gains made to virtually eliminate HIV transmission in Australia.
Hair salons as a promising space to provide HIV and sexual and reproductive health services for young women in Lesotho: A citizen scientist mixed-methods study
Authors: Chiaborelli Malena , Kopeka Mamaswatsi , Sekhesa Pontšo , Sehrt Madeleine , Mohloanyane Tsepang , Ballouz Tala , Menges Dominik , Brown Jennifer A. , Belus Jennifer M. , Gerber Felix , Raeber Fabian , Williams Andréa , Jackson-Perry David , Hyöky Meri , Conserve Donaldson F. , Hampanda Karen , Amstutz Alain ,   the Hair SALON Citizen Scientist Working Group
Published: December 2024

AbstractIntroductionAdolescent girls and young women in southern Africa are disproportionately affected by HIV and sexual and reproductive health (SRH) challenges. There is a need for more accessible and de-medicalized community spaces to offer HIV/SRH services for this key population. We aimed to assess the acceptability and feasibility of offering HIV/SRH services at hair salons in Lesotho.MethodsWe used an innovative citizen scientist mixed-methods approach, whereby hair stylists were recruited through social media, completed questionnaires, and recruited women clients aged 15-35 years as respondents. A stepwise verification process including GPS, pictures, and a local mobile payment system ensured data quality. Subsequently, we conducted individual in-depth interviews among 14 stylists and clients, following the rapid thematic analysis framework, supported by natural language processing. Clients and stylists were involved at the design, implementation, and results interpretation stage.ResultsWe recruited 157 hair stylists (median age 29; [interquartile range 25-33]; across all ten districts of Lesotho) and 308 women clients (median age 26 [22–30]). Among stylists, 93.6% were comfortable offering oral HIV self-testing (HIVST), 92.4% pre-exposure prophylaxis (PrEP), and 91.7% post-exposure prophylaxis (PEP). Among clients, 93.5%, 88.3%, and 86.4% felt comfortable receiving the above-mentioned services at a hair salon, respectively. Immediate demand was 30.8% for HIVST, 22.1% for PrEP, and 14.9% for PEP. Acceptability and demand were higher for family planning methods and menstrual health products. 90.4% of stylists thought that offering HIV/SRH services would positively impact their business. The majority of clients visit their salon once or twice a month. Salons were more accessible than the nearest health facility in terms of cost and time, but only 21.0% have an additional confidential space. Qualitative analysis confirmed high acceptability of hair salons as an accessible, less judgemental space than clinics, but raised concerns regarding confidentiality and stylists’ roles.ConclusionsThis study suggests that offering HIV/SRH services in hair salons in Lesotho is largely acceptable and feasible with some addressable barriers. A pilot intervention, based on recommendations from this study, is warranted to translate these findings into practice.
Intermittent fasting alters tumor burden, autophagy, and metabolites in chronic lymphocytic leukemia
Authors: Stringer Eleah , Wei Zhengxiao , Punch Samantha , Costie Nathalie , Han Jun , Goodlett David , Nathoo Farouk S. , Lum Julian J. , Macpherson Nicol 
Published: December 2024

ABSTRACTEmerging preclinical data suggests dietary interventions, including intermittent fasting, may play a key role in altering cancer progression. In a feasibility trial monitoring cellular, clinical, and qualitative changes, ten patients with chronic lymphocytic leukemia followed time-restricted eating for three months, and five patients for six months. Seven of fifteen participants (47%) experienced a decrease or stabilization in malignant lymphocyte counts on time-restricted eating, while malignant lymphocyte accumulation slowed in five participants (33%) or had no effect in three participants (20%). A reduction in malignant lymphocyte counts were accompanied by an unexpected decline in cellular autophagy in malignant lymphocytes. Metabolite profiling identified microbial-derived bile acid metabolites, glycoursodeoxycholic, taurochenodeoxycholic, glycolithocholic and ursodeoxycholic acid, and short-chain fatty acids, dehydrolithocholic and apocholic acid, that changed with time-restricted eating. Participant quality of life improved during time-restricted eating. These results connect time-restricted eating with shifts in autophagy, microbial-derived metabolites, tumor progression, and quality of life.
A high-resolution meiotic crossover map from single-nucleus ATAC-seq reveals insights into the recombination landscape in mammalian sperm
Authors: Novakovic Stevan , Harris Caitlin , Liu Ruijie , McCarthy Davis J. , Crismani Wayne 
Published: December 2024

AbstractMeiotic crossovers promote correct chromosome segregation and the shuffling of genetic diversity. However, the measurement of crossovers remains challenging, impeding our ability to decipher the molecular mechanisms that are necessary for their formation and regulation. Here we demonstrate a novel repurposing of the single-nucleus Assay for Transposase Accessible Chromatin with sequencing (snATAC-seq) as a simple and high-throughput method to identify and characterise meiotic crossovers from sperm nuclei. We first validate the feasibility of obtaining genome-wide coverage from snATAC-seq by using ATAC-seq on bulk haploid mouse sperm, ensuring adequate variant detection for haplotyping. Subsequently, we adapt droplet-based snATAC-seq for crossover detection, revealing over 25,000 crossovers in F1 hybrid mice. Comparison between wildtype and a hyper-recombinogenicFancm-deficient mutant mouse model confirmed an increase in crossover rates in this genotype, however a distribution which was unchanged. We also find that regions with the highest rate of crossover formation are enriched for DMC1 and PRDM9, with a subset that is further enriched for DMC1 inFancm-deficient mice. Our findings demonstrate the utility of snATAC-seq as a robust and scalable tool for high-throughput crossover detection, offering insights into meiotic crossover dynamics and elucidating the underlying molecular mechanisms. It is possible that the research presented here with snATAC-seq of haploid sperm could be extended into fertility-related diagnostics.
Functional specialization of the subdomains of a bactofilin driving stalk morphogenesis inAsticcacaulis biprosthecum
Authors: Jacq Maxime , Caccamo Paul D. , Brun Yves V. 
Published: December 2024

AbstractBactofilins are a recently discovered class of cytoskeletal protein, widely implicated in subcellular organization and morphogenesis in bacteria and archaea. Several lines of evidence suggest that bactofilins polymerize into filaments using a central β-helical core domain, flanked by variable N- and C-terminal domains that may be important for scaffolding and other functions. However, a systematic exploration of the characteristics of these domains has yet to be performed. InAsticcacaulis biprosthecum, the bactofilin BacA serves as a topological organizer of stalk synthesis, localizing to the stalk base and coordinating the synthesis of these long, thin extensions of the cell envelope. The easily distinguishable phenotypes of wild-typeA. biprosthecumstalks andΔbacA“pseudostalks” make this an ideal system for investigating how mutations in BacA affect its functions in morphogenesis. Here, we redefine the core domain ofA. biprosthecumBacA using various bioinformatics and biochemical approaches to precisely delimit the N- and C-terminal domains. We then show that loss of these terminal domains leads to cells with severe morphological abnormalities, typically presenting a pseudostalk phenotype. BacA mutants lacking the N- and C-terminal domains also exhibit localization defects, implying that the terminal domains of BacA may be involved in its subcellular positioning, whether through membrane interactions through the N-terminal domain or through interactions with the stalk-specific morphological regulator SpmX through the C-terminal domain. We further show that point mutations that render BacA defective for polymerization lead to stalk synthesis defects. Overall, our study suggests that BacA’s polymerization, membrane association, and interactions with other morphological factors all play a crucial role in the protein’s function as a morphogenic regulator. The specialization and modularity of the terminal domains may underlie the remarkable functional versatility of the bactofilins in different species.Author summaryBacteria exhibit a wide variety of shapes and structures, many of which are crucial for their cellular functions. Among these structures is the stalk—a thin, tubular extension of the cell envelope formed by bacteria such asAsticcacaulis biprosthecum. Stalk synthesis inAsticcacaulis biprosthecumrelies on the bactofilin BacA, a self-polymerizing cytoskeletal protein, whose deletion results in the dysregulation of stalk synthesis, and the formation of short, stubby “pseudostalks”. We use this unique phenotype to characterize the subdomains of BacA, and find that BacA’s ability to coordinate stalk synthesis depends on its conserved polymerization domain as well as its flanking N- and C-terminal domains, which are essential for proper localization and interactions. Our findings highlight how bactofilins combine conserved and variable regions to generate complex structures that serve as a platform for evolving new functions.
Functional diversification of the MADS-box gene family in fine-tuning the dimorphic transition ofTalaromyces marneffei
Authors: Hu Xueyan , Zhang Yun , Wang Juan , Du Minghao , Yang Yang , Cai James J. , Yang Ence 
Published: December 2024

AbstractThe dynamic transition between yeast and hypha is a crucial adaptive mechanism for many human pathogenic fungi, includingTalaromyces marneffei, a thermodimorphic fungus responsible for causing fatal talaromycosis. In the current study, we elucidated the roles of the MADS-box gene family in fine-tuning the dimorphic transition inT. marneffeithrough functional diversification. Utilizing adaptive laboratory evolution, we identified an enrichment of MADS-box genes in mutants deficient in yeast-to- mycelium transition. Further phylogenetic analyses revealed a significant expansion of MADS-box gene family withinT. marneffei.Functional genetic manipulations revealed that overexpression ofmads9, as opposed to its paralogmads10, effectively impeded the hyphal-to-yeast transition. Through integrating RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), we demonstrated thatmads9and the previously characterizedmadsAmodulated the rate of hyphal-to-yeast conversion by orchestrating metabolic pathways and membrane dynamics, respectively, with mutual regulation via shared target genes. Our findings illuminated the distinct functional roles of the MADS-box family in regulating dimorphic transitions inT. marneffei, offering new insights into fungal adaptability.
Defense systems and prophage detection inStreptococcus mutansstrains
Authors: Claisse O. , Mosterd C. , Marrec C. Le , Samot J. 
Published: December 2024

AbstractAlthough the species is extensively studied, limited data are available on antiphage defense systems (APDSs) inStreptococcus mutans. The present study aimed to explore the diversity and the occurrence of APDSs and to search for prophages in the genomes of clinical isolates ofS. mutansusing bioinformatics tools.Forty-four clinical isolates ofS. mutanswere obtained from saliva samples of people with Parkinson’s disease. Genomic DNA was extracted, sequenced using Illumina MiSeq technology, and analyzed for the presence of defense systems using DefenseFinder. CRISPR- Cas systems were characterized using CRISPRCasFinder, and prophages were detected by the PhiSpy pipeline from RAST. AcrFinder and AcrHub were used to identify anti-CRISPR proteins.Each strain harbored between 6 and 12 APDS, with restriction-modification systems being the most prevalent, followed by the MazEF toxin-antitoxin system and CRISPR-Cas systems. Type II-C CRISPR-Cas systems were not identified here inS. mutans. Novel variations in type II-A signature protein Cas9 were identified, allowing their classification into four distinct groups. Variability in direct repeat sequences within the same CRISPR array was also observed, and 80% of the spacers were classified as targeting "dark matter". A unique prophage, phi_37bPJ2, was detected, showing high similarity with previously described phages. The AcrIIA5 protein encoded by phi_37bPJ2 was conserved and suggested to remain functionally active.This study reveals the diversity of APDSs inS. mutansand the limited presence of prophages. The findings provide a foundation for future research on the evolutionary dynamics of these systems and their role inS. mutansadaptation to phage pressure.
ASalmonella entericaserovar Typhimurium Genome-wide CRISPRi Screen Reveals a Role for Type 1 Fimbriae in Evasion of Antibody-Mediated Agglutination
Authors: Lindberg Samantha K. , Willsey Graham G. , Mantis Nicholas J. 
Published: December 2024

ABSTRACTThe O5-specific monoclonal IgA antibody, Sal4, mediates the conversion ofSalmonella entericaserovar Typhimurium (STm) from virulent, free-swimming cells to non-motile, multicellular aggregates in solution (“flocs”) as well as biofilm-like associations at the air-liquid interface (ALI). We hypothesize that the rapid transition from an invasive to a non-invasive state reflects an adaptation of STm to Sal4 IgA exposure. In this report, we performed a genome-wide CRISPRi screen to identify STm genes that influence multicellular aggregate formation in response to Sal4 IgA treatment. From a customized library of >36,000 spacers, ∼1% (373) were enriched at ALI after two consecutive rounds of Sal4 IgA treatment. The enriched spacers mapped to a diversity of targets, including genes involved in O-antigen modification, cyclic-di-GMP metabolism, outer membrane biosynthesis/signaling, and invasion/virulence, with the most frequently targeted gene beingfimW, which encodes a negative regulator of Type 1 Fimbriae (T1F) expression. Generation of a STm ΔfimWstrain confirmed that the loss of FimW results in a hyperfimbriated phenotype and evasion of Sal4 IgA-mediated agglutination in solution. Closer examination of thefimWmutant revealed its propensity to form biofilms at the ALI specifically in response to Sal4 exposure, suggesting that T1F “primes” STm to transition from a planktonic to a sessile state possibly by facilitating bacterial attachment to abiotic surfaces. These findings shed light on the mechanism by which protective secretory IgA antibodies influence STm virulence in the intestinal environment.