bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Computer Vision Syndrome Among University Students and Faculty During COVID-19 Pandemic
Authors: Al Ashkar Ihab Fouad , Alhammadi Amna Sayah , Bayram Ola Salam , Ammari Maria , Binashour Aisha Saleh , Mohamed Ahmed , Hussein A. , Talaat I 
Published: December 2024

AbstractIntroductionThe COVID-19 lockdown drastically increased screen time among students and faculty members due to online learning. Previous studies suggested increased screen time causes computer vision syndrome (CVS). This study aims to compare the prevalence of CVS among students and faculty in the UAE during the COVID-19 pandemic.MethodsA descriptive cross-sectional study was conducted among 386 university students and faculty members across the UAE. A self-administered questionnaire was distributed online to collect socio-demographic data, symptoms of CVS, its associated factors, and the use of preventive measures. Informed consent was obtained, and participants who met the inclusion criteria were enrolled in the study. The indicated data were identified and analyzed using the 25th version of the SPSS program.ResultsFemales were more likely to have computer vision syndrome, neck pain, back pain, and wrist pain. Students had a higher total screen time and a greater prevalence of Computer vision syndrome, 85.8% compared to faculty members. The prevalence of CVS was highest among students at the College of Science, 91.7%. Subjects who spent more time using the screen had more CVS symptoms than those who spent less time on screens (P= 0.039). Using laptops for more than 5 hours daily had a higher CVS prevalence of 90.6% (p=0.022). Wearing corrective eyeglasses was associated with increased CVS prevalence while taking breaks from the screen, which showed decreased prevalence. 52.5% of those with CVS experienced reduced productivity.ConclusionCVS was most prevalent in students; they also had higher screen time levels than faculty members.
Steps on the path to clinical translation – a survey of the UK MRI community
Authors: Markus Julia E , Hubbard Cristinacce Penny L , Punwani Shonit , O’Connor James PB , Mills Rebecca , Lopez Maria Yanez , Grech-Sollars Matthew , Fasano Fabrizio , Waterton John C , Thrippleton Michael J , Hall Matt G , Francis Susan T , Statton Ben , Murphy Kevin , So Po-Wah , Hyare Harpreet 
Published: December 2024

AbstractPurposeOur goal was to understand the barriers and challenges to clinical translation of quantitative MR (qMR) as perceived by stakeholders un the UK.MethodsWe conducted an electronic survey on 7 key areas related to clinical translation of qMR, developed at the BIC-ISMRM workshop: “Steps on the path to clinical translation”. Based on the 7 areas identified: (i) clinical workflow, (ii) changes in clinical practice, (ii) improving validation, (iv) standardisation of data acquisition and analysis, (v) sharing of data and code, (vi) improving quality management, and (vii) end-user engagement, a 40-question survey was developed. Members of BIC-ISMRM, MR-PHYSICS, BSNR and institutional mailing lists were invited to respond to the online survey over a 5-week period between September and October 2022. The responses were analysed via descriptive statistics of multiple-choice questions, Likert scores and a thematic analysis of free text questions.ResultsA total of 69 responses were received from predominantly research imaging scientists (69%) in numerous centres across the UK. Three main themes were identified: 1) the need to develop Consensus in terminology, decision making and validation; 2) an appreciation of uniqueness of each clinical situation and the need for Context Dependency; and 3) the importance of developing a Product Profile as early in development as possible.ConclusionEffective translation of qMR imaging and spectroscopic biomarkers to achieve their full clinical in the UK and internationally must address the differing needs and expectations of a wide range of stakeholders.
MAETi: Mild acid elution in a tip enables immunopeptidome profiling from 25,000 cells
Authors: Beyrle Julian , Distler Ute , Gomez-Zepeda David , Tenzer Stefan 
Published: December 2024

3AbstractThe identification of MHC class I presented ligands by mass spectrometry (MS)-based immunopeptidomics is an essential tool to characterize antigen processing pathways and to define targets for tumor immunotherapies. However, existing sample preparation workflows typically require large sample inputs, limiting the applicability in high throughput drug screenings, kinetic immunopeptidome studies and for scare samples in clinical contexts. To address this challenge, we developed Mild Acid Elution in a Tip (MAETi), an antibody-free approach for low input MHC-1 immunopeptidome profiling. Using an optimized β-alanine MAE-buffer for MAETi reduces background interferences, enhances peptide coverage, and boosts reproducibility. Comparing bulk β-alanine-based MAE with bulk immunoprecipitation (IP), achieves similar or complementary immunopeptidome depth. Using two protocol layouts we further profiled initial inputs from 25,000 to 1 Million cells with HLA-tailored DDA- and DIA-PASEF schemes yielding on average over 1,000 and 3,000 predicted binders, respectively (DIA). This renders MAETi a facile, fast and scalable method enabling robust MS-based immunopeptidomics for minimal sample inputs.2Main messages / HighlightsMAETi is a simplified and optimized MAE workflow enabling MHC1-ligandomics profiling from sub-million cell samples down to 25,000 cellsWe present a minimal, simplified sample preparation protocol termed Mild Acid Elution in a Tip (MAETi) enabling the MHC-1 ligandome analysis using 25,000 to 100,000,000 cells per sample as initial inputReplacing citric acid in the elution buffer by β-alanine reduced unspecific contaminants, resulted in cleaner LC-MS chromatograms and boosted 8-13mer identifications by over 50% in MAEti samples.Bulk β-alanine-based MAE provides similar coverage of MHC class 1 ligands compared to bulk immunoprecipitation
Uncovering sex differences in Parkinson’s Disease through metaanalysis of single cell transcriptomic studies
Authors: Gordillo-González Fernando , Soler-Sáez Irene , Galiana-Roselló Cristina , Hidalgo Marta R. , Gómez-Cabañes Borja , Grillo-Risco Rubén , Dolader-Rabinad Beatriz , del Rey Díez Natalia , Virués-Morales Alejandro , Yanguas-Casás Natalia , Ferrer Franc Casanova , García-García Francisco 
Published: December 2024

AbstractAbundant evidence supports the significant impact of biological sex on various aspects of Parkinson Disease (PD), including incidence, progression, symptoms or response to treatment. The incidence and prevalence of the disease is higher in males, while its age of onset is earlier than in females. There are also sex differences in the symptomatology, both motor and non-motor. In female PD, tremor, pain, depression and dysphagia are predominant, whereas in male PD, freezing of gait, camptocormia, cognitive impairment and urinary dysfunction are more common. Likewise, there are sex differences in the pathophysiology of the disease, related to most of the pathological processes of PD, as is the case of the greater activation of microglia in males or the lower oxidative stress in females. All these findings support the idea that different molecular mechanisms may be involved in PD depending on the sex of the patient. Some explanations for these events are related to biological, genetic, hormonal or environmental factors, such as the possible anti-inflammatory and neuroprotective effect of estrogens. However, the underlying molecular mechanisms have not yet been fully described. Our results show sex differences in gene expression, cell-cell communication and pathway activation in all major brain cell types, highlighting the presence of greater neuroinflammation in men and greater neurodegeneration in the SNpc in men, with the latter appearing to be inverted between sexes when observed in the cortical zone. Finally, we have made all the results available in a publicly accessible webtool, in order to allow the exploration of results to other researchers and to broaden the molecular-level understanding of PD sex differences.
Global diversity of putative functional viral auxiliary metabolic genes and their relationship with soil organic carbon stocks
Authors: Merges Dominik 
Published: December 2024

AbstractGlobal biodiversity decline has prompted extensive research and debate on how biodiversity loss affects ecosystem functioning. Microbial taxonomic and functional diversity loss can impair critical processes such as plant biomass degradation or nitrogen fixation. Biotic interactions, especially those involving microbes and their viruses, are increasingly recognized as drivers of such processes. Microbial viruses carry auxiliary metabolic genes (AMGs), functional genes acquired from bacterial hosts, that mediate processes like carbon and nitrogen cycling, positioning viruses as potential reservoirs of essential ecosystem functions. To investigate the putative contribution of viral AMGs to microbial functional diversity and ecosystem functioning in soils, the global dataset of soil viral genomes, comprising 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units from 2,953 soil metagenomes, was mined for carbon (C) and nitrogen (N) cycling genes. For C cycling, 301 viral genomes with AMGs from glycoside hydrolase (GH) families (n cellulase = 182; n hemicellulase = 119) were detected. The viruses containing cellulase and hemicellulase AMGs were distributed across most major ecosystem types, including agricultural, forest, grassland, and permafrost soils, but were absent from deserts, salt marshes, and shrublands. Forest ecosystems harbored the highest abundance of cellulase and hemicellulase AMGs. The ratio of cellulase to hemicellulase AMGs varied by ecosystem, showing near parity in forests but cellulase dominance in agricultural, grassland, and permafrost soils. Relating AMGs to ecosystem functioning, sites with cellulase and hemicellulase AMGs showed significantly lower soil organic carbon (SOC) content in agricultural soils, whereas no significant differences were observed in forest, grassland, or permafrost soils. These results suggest that viral AMGs may influence SOC dynamics, particularly in agricultural systems, and highlight the need for deeper investigation into their functional roles in soil ecosystems. This study underscores the importance of viral contributions to ecosystem functioning, emphasizing the potential of microbial viruses to serve as mutualistic agents in global biogeochemical cycles.
A Palette of Bridged Bicycle-Strengthened Fluorophores
Authors: Zhang Junwei , Zhang Kecheng , Wang Kui , Wang Bo , Zhu Siyan , Qian Hongping , Ma Yumiao , Zhang Mengling , Liu Tianyan , Chen Peng , Shen Yuan , Fu Yunzhe , Fang Shilin , Zhang Xinxin , Zou Peng , Deng Wulan , Mu Yu , Chen Zhixing 
Published: December 2024

AbstractOrganic fluorophores are the keystone of advanced biological imaging. The vast chemical space of fluorophores has been extensively explored in seek of molecules with ideal properties. However, within the current molecular constraints, there appears to be a trade-off between high brightness, robust photostability, and tunable biochemical properties. Herein we report a general strategy to systematically boost the performance of donor-acceptor-type fluorophores by leveraging SO2and O-substituted azabicyclo[3.2.1] octane auxochromes. These bicyclic heterocycles give rise to a collection of ‘Bridged’ dyes (BD) spanning the UV and visible range with top-notch quantum efficiencies, enhanced water solubility, and tunable cell-permeability. Notably, these azabicyclic fluorophores showed remarkable photostability than its tetramethyl or azatidine analogue, at the same time completely resistant to oxidative photobluing rendered by the Bredt’s rule. Functionalized BD dyes are tailored for applications in single-molecule imaging, super-resolution imaging (STED and SIM) in fixed or live mammalian cells and plant cells, and live zebrafish imaging or chemigenetic voltage imaging. Synergizing with advanced imaging methods, the bridge bicycle dyes represent a versatile palette for biological researches.
Sparse Multitask group Lasso for Genome-Wide Association Studies
Authors: Nouira Asma , Azencott Chloé-Agathe 
Published: December 2024

AbstractA critical hurdle in Genome-Wide Association Studies (GWAS) involves population stratification, wherein differences in allele frequencies among subpopulations within samples are influenced by distinct ancestry. This stratification implies that risk variants may be distinct across populations with different allele frequencies. This study introduces Sparse Multitask Group Lasso (SMuGLasso) to tackle this challenge. SMuGLasso is based on MuGLasso, which formulates this problem using a multitask group lasso framework in which tasks are subpopulations, and groups are population-specific Linkage-Disequilibrium (LD)-groups of strongly correlated Single Nucleotide Polymorphisms (SNPs). The novelty in SMuGLasso is the incorporation of an additional 𝓁1-norm regularization for the selection of population-specific genetic variants. As MuGLasso, SMuGLasso uses a stability selection procedure to improve robustness and gap-safe screening rules for computational efficiency.We evaluate MuGLasso and SMuGLasso on simulated data sets as well as on a case-control breast cancer data set and a quantitative GWAS inArabidopsis thaliana. We show that SMuGLasso is well suited to addressing linkage disequilibrium and population stratification in GWAS data, and show the superiority of SMuGLasso over MuGLasso in identifying population-specific SNPs. On real data, we confirm the relevance of the identified loci through pathway and network analysis, and observe that the findings of SMuGLasso are more consistent with the literature than those of MuGLasso. All in all, SMuGLasso is a promising tool for analyzing GWAS data and furthering our understanding of population-specific biological mechanisms.Author summaryGenome-Wide Association Studies (GWAS) scan thousands of genomes to identify loci associated with a complex trait. However, population stratification, which is the presence in the data of multiple subpopulations with differing allele frequencies, can lead to false associations or mask true population-specific associations. We recently proposed MuGLasso, a new computational method to address this issue. However, MuGLasso relied on an ad-hoc post-processing of the results to identify population-specific associations. Here, we present SMuGLasso, which directly identifies both global and population-specific associations.We evaluate both MuGLasso and SMuGLasso on several datasets, including both case-control (such as breast cancer vs. controls) and quantitative (for example, plant flowering time) traits, and show on simulations that SMuGLasso is better suited than MuGLasso for the identification of population-specific associations. In addition, SMuGLasso’s findings on real case studies are more consistant with the literature than that of MuGLasso, which is possibly due to false discoveries of MuGLasso. These results show that SMuGLasso could be applied to other complex traits to better elucidate the underlying biological mechanisms.
Polyolefin colonization and partial degradation byGordoniasp., andArthrobactersp. isolated from wetlands and compost
Authors: Coughlin Scott A. , McFall Adam , Kelly Stephen A. , Megaw Julianne 
Published: December 2024

AbstractPlastics and microplastics constitute an ever-increasing pollutant in the biosphere. There is clear evidence that environmental microbes possess enzyme systems and metabolic apparatus to degrade natural high molecular weight polymers, which substantially overlap with those involved in the biodegradation of plastics. This study investigated the presence and activities of plastic-degrading microbes in environments with a high abundance of plant-derived polymers, including cellulosic, chitinous, or lignin-derived compounds. Microbes were enriched in a minimal medium, with low-density polyethylene (LDPE), polypropylene (PP), poly(ethylene terephthalate) (PET), or polystyrene (PS) as the sole carbon source, resulting in 12 bacterial isolates. Plastic mass loss and cell viability were measured over a 28-day incubation period, in addition to assessment of biofilm formation.Gordoniasp. iso11 displayed mass loss of PP of up to 22.8% and formed a viable dense biofilm (109CFU cm-2) on a PP film. A putative alkane-1-monoxygenase (AlkB) was identified from genome sequence analysis, which aligned with a known LDPE-degrading enzyme. Furthermore, reductions in the contact angle of medium supernatant fromGordoniasp. iso11 provided evidence of biosurfactant production which may enhance the bioavailability of the synthetic plastic. To our knowledge, this is the first demonstration of PP degradation byGordonia.
MRS-Sim: Open-Source Framework for Simulating In Vivo-like Magnetic Resonance Spectra
Authors: LaMaster John , Oeltzschner Georg , Li Yan 
Published: December 2024

SummaryMRS-Sim is a powerful, open-source framework for simulating in vivo-like magnetic resonance spectroscopy data. Its modularity allows it to model the complexities of MRS data for a variety of clinical scenarios. The underlying physical equations include spectral components commonly found in linear-combination fitting routines plus some novel components. The first is a 3DB0field map simulator to modelB0field inhomogeneities, ranging from slight variations to severe distortions. The second is a novel semi-parametric generator that mimics signals from poorly characterized residual water regions and baseline offset contributions. This framework can simulate everything from raw multi-coil transients to preprocessed coil-combined data.A repository of information has been compiled to help non-expert users with general simulations of MRS data. Simulating realistic clinical-like datasets requires appropriate ranges and distributions for the model parameters, which are best determined by analyzing the parameter estimates from fitting real clinical data. Therefore, accompanying tools within MRS-Sim allow for analyzing the range and distributions of those parameters from in vivo datasets fitted with Osprey. This allows simulations to be tailored to specific clinical datasets.The modularity of this framework allows for easy customization of simulations to suit a variety of clinical scenarios and encourages continued community development. Using a single framework for various scenarios overcomes the inconsistent protocols in current literature. By simulating in vivo-like data, this framework can aid in many tasks in MRS, including verifying spectral fitting protocols and reproducibility analyses. The accessibility of readily available, synthetic data will also assist deep learning research for MRS, particularly in cases where clinical data is insufficient or unavailable for training and, in general, will help address reproducibility issues and make MRS research more accessible to a wider audience.
Ocular Disease Prevalence in California Sea Lions In Human Care: Freshwater Versus Saltwater Housing
Authors: Brehm Ingrid , Herzner Silas , Baumgartner Katrin , Beckmann Jörg , Simon Ralph , von Fersen Lorenzo 
Published: December 2024

AbstractCalifornia sea lions (Zalophus californianus), are susceptible to various ocular diseases, with some literature suggesting a heightened risk for those kept in freshwater pools as opposed to saltwater. Given the potential implications of housing conditions on animal health, we wanted to analyze the ocular health of two distinct groups of sea lions kept at Nuremberg Zoo, one housed in freshwater and the other in saltwater. Data extracted from the animals’ medical records over a ten-year period were used to compare the incidence of eye conditions and other medical conditions observed. The results revealed no significant difference in the overall prevalence of eye diseases between the two environments. However, a distinct seasonal pattern was noted: sea lions kept in freshwater exhibited a peak in eye disorders during the summer months, while those in saltwater displayed a more uniform distribution of the occurrence of ocular diseases throughout the year. These findings suggest that sun exposure and water quality are potentially more influential factors in the development of ocular diseases in pinnipeds than salinity or UV radiation. Further studies are necessary to elucidate the underlying mechanisms and optimize care practices for these marine mammals.Simple SummaryThis study investigated the ocular health of California sea lions (Zalophus californianus) at Nuremberg Zoo, comparing those housed in freshwater pools to those in saltwater. An analysis of medical records over ten years showed no significant difference in the overall prevalence of eye diseases between the two groups. However, sea lions in freshwater experienced a peak of eye disorders in the summer, while those in saltwater had a more consistent occurrence throughout the year. These results imply that factors such as sun exposure and water quality may play a more crucial in ocular disease development than salinity or UV radiation. The study highlights the need for further research to understand these dynamics and improve care for marine mammals.
CESA: Cross-species Epitope Sequence Analysis for discovery of existing antibodies useful for phospho-specific protein detection in model species
Authors: Hu Yanhui , Gao Chenxi , Mckenna William , Xia Baolong , Ariss Majd , Mohr Stephanie , Perrimon Norbert 
Published: December 2024

AbstractSignaling pathways play key roles in many important biological processes such as cell division, differentiation, and migration. Phosphorylation site-specific antibodies specifically target proteins phosphorylated on a given tyrosine, threonine, or serine residue. Use of phospho-specific antibodies facilitates analysis of signaling pathway regulation and activity. Given the usefulness of phospho-specific antibodies, a number of collections of these antibodies have been generated, typically for detection of phosphorylated mammalian proteins. Anecdotal evidence shows that some of these are also useful for detection of phosphorylated forms of orthologous proteins in model organisms. We propose that anti-phospho-mammalian protein antibody collections comprise an untapped resource for research in other species. To systematically analyze the potential utility of anti-phospho-mammalian protein antibodies in other species, we developed the Cross-species Epitope Sequence Analysis software tool (CESA). CESA identifies and aligns orthologous proteins in model species, then analyzes conservation of antibody target sites. We used CESA to predict what phospho-specific antibodies in a collection from Cell Signaling Technology (CST) might be useful for studies inDrosophila melanogasterand other species. CESA predicts that more than 232 sites on 116Drosophilaproteins can potentially be targeted by the antibodies initially developed at CST to detect human, mouse, or rat phosphoproteins.