bluuebunny/crossref_metadata_2025_split huggingface dataset:
One to host them all: genomics of the diverse bacterial endosymbionts of the spiderOedothorax gibbosus
Authors: Halter Tamara , Köstlbacher Stephan , Rattei Thomas , Hendrickx Frederik , Manzano-Marín Alejandro , Horn Matthias 
Published: June 2022

AbstractBacterial endosymbionts of the groupsWolbachia, CardiniumandRickettsiaceaeare well-known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analyzed a unique system in which the dwarf spiderOedothorax gibbosusis co-infected with up to five different endosymbionts affiliated withWolbachia, ‘CandidatusTisiphia’ (formerly Torix groupRickettsia), Cardinium,andRhabdochlamydia.Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed amongO. gibbosuspopulations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome resolved level, we used long-read sequencing to reconstruct closed genomes of theWolbachia, ‘Ca.Tisiphia’ andCardiniumendosymbionts. We provide insights in the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of theCardinium, ‘Ca.Tisiphia’ andWolbachiaendosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on earth and show the usefulness of transposable elements as an evolutionary “contact-tracing” tool.Data summaryAll supporting data, code and protocols have been provided within the article or through supplementary data files. Seven supplementary figures and seven supplementary tables are available with the online version of this article. Sequencing data used in this study was generated and previously published by Hendrickxet al.,2021. Genome assemblies generated in this study have been deposited under the project PRJEB52003 at DDBJ/ENA/GenBank. The MAG ofR. oedothoracisOV001 was deposited at DDBJ/ENA/GenBank under the sample SAMN28026840. The genome of‘CandidatusRhabdochlamydia oedothoracis W744×776’ was previously published by Halteret al.,2022 and is available at DDBJ/ENA/GenBank (accession:CP075587-CP075588). The collection of genomes and proteomes, all files for phylogenetic analyses including gene alignments, concatenated alignments, and tree files, and original output files of the HGT and SNP predictions used in this study are available at zenodo (https://doi.org/10.5281/zenodo.6362846).
A comparison of sleep-wake patterns among school-age children and adolescents in Hong Kong before and during the COVID-19 pandemic
Authors: Chau Steven WH , Hussain Samara , Chan Sandra SM , Wong Oscar WH , Zhang Jihui , Feng Hongliang , Lai Kelly YC , Ma Suk Ling , So Suzanne HW , Tsoi Kelvin KF , Wing Yun Kwok , Hung Se Fong , Leung Patrick WL 
Published: June 2022

AbstractBackgroundLifestyle of children and adolescents have changed extensively during the COVID-19 pandemic due to school suspension and social distancing measures, which can affect their sleep health. Existing studies in the area used convenient samples and focused on the initial months of the pandemic.MethodAs part of a territory-wide epidemiological study in Hong Kong, this cross-sectional study recruited primary and secondary school students by stratified random sampling. We investigated the pandemic’s effects on sleep parameters using multivariate regression, adjusting for age, sex, household income, seasonality and presence of mental disorders, and the effects’ moderators and mediators.FindingsBetween September 1, 2019 and June 2, 2021, 791 primary and 442 school students were recruited and analysed. After correcting for multiple testing, being assessed during COVID predicted a longer sleep latency in primary and secondary school students in school days (95% CI = 1.0–5.2 minutes, adjusted p-value = 0.010; and 95% CI= 3.9–13.0 minutes, adjusted p-value =0.004, respectively) and non-school days (95% CI = 1.7–7.2 minutes, adjusted p-value = 0.005; 95% CI = 3.4–13.7 minutes, adjusted p-value = 0.014, respectively). Low household income was a moderator for later bedtime (adjusted p-value = 0.032) and later sleep onset (adjusted p-value = 0.043) during non-school days among secondary school students. Sex and digital leisure time were not moderator and mediator of the pandemic’s effect on sleep parameters, respectively.InterpretationChanges associated with the COVID-19 pandemic have a widespread and enduring effect on sleep health of school-aged students in Hong Kong. Household income play a role in adolescents’ sleep health’s resilience against these changes, and anti-epidemic measures effects on the health gap of the youth should be considered.FundingGovernment of the Hong Kong Special Administrative Region, Food and Health Bureau, Health and Medical Research Fund (Ref. No.: MHS-P1(Part 1)-CUHK).
LIVER-RELATED AND OTHER-CAUSE MORTALITY RISK IN EXCESSIVE DRINKERS: ANALYSIS OF DATA FROM THE UK BIOBANK
Authors: Whitfield John B , Seth Devanshi , Morgan Timothy R ,   GenomALC Consortium
Published: June 2022

ABSTRACTBackground and AimsHigh alcohol intake is associated with increased mortality. We aimed to identify factors affecting mortality in people drinking extreme amounts.Approach and ResultsInformation was obtained from the UK Biobank on approximately 500,000 participants aged 40-70 years at baseline assessment in 2006-2010. Habitual alcohol intake, lifestyle and physiological data, laboratory test results, and hospital diagnoses and death certificate data (to June 2020) for 5136 men (2.20% of male participants) and 1504 women (0.60%) who reported taking ≥80 g/day or ≥50g/day, respectively, were used in survival analysis. Compared to all other participants, their mortality HRs were 9.40 (95% CI 7.00-12.64) for any liver disease (ICD-10 K70-K76), 2.02 (1.89-2.17) for all causes, 1.89 (1.69-2.12) for any cancer (C00-C99), and 1.87 (1.61-2.17) for any circulatory disease (I00-I99). Liver disease diagnosis or abnormal liver function tests predicted not only deaths attributed to liver disease but also those from cancers or circulatory diseases. Mortality among excessive drinkers was also associated with quantitative alcohol intake, diagnosed alcohol dependence (ICD-10 F10.2), and current smoking at assessment.ConclusionsPeople with chronic excessive alcohol intake experience decreased average survival but there is substantial variation in their mortality, with liver abnormality and alcohol dependence each associated with worse prognosis. Clinically, patients with these risk factors as well as high alcohol intake should be considered for early or intensive management. Research can usefully focus on the factors predisposing to dependence or liver abnormality.
Intrapersonal predictors of internalized stigma among school going adolescents living with HIV in southwestern Uganda
Authors: Kirabira Joseph , Ashaba Scholastic , Favina Allain , Maling Samuel , Nansera Denis , Zanoni Brian C. 
Published: June 2022

AbstractBackgroundHIV is one of the most stigmatized conditions globally significantly affecting the quality of life of people living with HIV. Stigma particularly affects adolescents living with HIV (ALHIV) due to challenges associated with developmental stage including physical and psychological changes and the need to build peer relationships. The effect of intrapersonal factors including resilience, health locus of control, self-efficacy, and empowerment on HV stigma among ALHIV in Uganda has not been studied. This study aimed at assessing the association between internalized HIV stigma and resilience, health locus of control, coping self-efficacy and empowerment among ALHIV.MethodsWe conducted a cross-sectional study between August and October 2020 among 173 adolescents who were attending the HIV clinic at Mbarara Regional Referral Hospital. We measured HIV stigma (the internalized AIDS Related Stigma scale), health locus of control (the 18-item Form C version of the Multi-Dimensional Health Locus of Control measure), resilience (25-item Resilience Scale), self-efficacy (the coping self-efficacy scale), and empowerment (the 28-item empowerment scale). Linear regression models were run to determine the association between HIV stigma and intrapersonal factors and adjusted for sociodemographic characteristics.ResultsThe median age of participants was 16 (IQR 15-18) years and the median HIV stigma score was 3 (IQR 2-4). There was a negative correlation between HIV stigma and internal health locus of control (b= -0.08, p<0.001), resilience (b= -0.03p<0.001) and coping self-efficacy (b= -0.02, p<0.001) while empowerment score was positively correlated (b= 0.05, p=0.003). However, after mutually adjusting for the intrapersonal factors (resilience, internal locus of control, empowerment and coping self-efficacy), and sociodemographic characteristics, only internal health locus of control (p=0.008) and coping self-efficacy (p<0.001) remained significantly associated with HIV stigma.ConclusionInternal health locus of control, resilience, coping self-efficacy and empowerment are strong intrapersonal predictors of internalized stigma among ALHIV. Designing interventions focusing on strengthening these factors among the adolescents may be a significant step in the fight against internalized HIV stigma.
Effective conservation decisions require models designed for purpose: a case study for boreal caribou in Ontario’s Ring of Fire
Authors: Dyson Matt , Endicott Sarah , Simpkins Craig , Turner Julie W. , Avery-Gomm Stephanie , Johnson Cheryl A. , Leblond Mathieu , Neilson Eric W. , Rempel Rob , Wiebe Philip A. , Baltzer Jennifer L. , Hughes Josie , Stewart Frances E.C. 
Published: June 2022

ABSTRACTDecision making in conservation science often relies on the best available information. This may include using models that were not designed for purpose and are not accompanied by an assessment of limitations. To begin addressing these issues, we sought to reproduce, and evaluate the suitability of, the best available models for predicting impacts of proposed mining on boreal woodland caribou (Rangifer tarandus caribou)resource selection and demography in northern Ontario. We then evaluated their suitability for projecting the impacts of development in the Ring of Fire region. To aid in accessibility, we developed an R package for data preparation, analyses of resource selection, and demographic parameters. We found existing models were either ill suited, or lacking, for ongoing regional planning. The specificity of the regional resource selection model limited its usefulness for predicting impacts of development, and the high variability across caribou ranges limited the usefulness of a national aspatial demographic model for predicting range-specific impacts. Variability in model coefficients across caribou ranges suggests selection responses vary with habitat availability (i.e. a functional response) while demographic responses continue to decline with increasing disturbance. Models designed for forecasting that are continuously updated by range-specific demographic and habitat information, are required to better inform conservation decisions and ongoing policy and planning practices in the Ring of Fire region.
Motor unit dysregulation following 15 days of unilateral lower limb immobilisation
Authors: Inns Thomas B. , Bass Joseph J. , Hardy Edward J.O. , Wilkinson Daniel J. , Stashuk Daniel W. , Atherton Philip J. , Phillips Bethan E. , Piasecki Mathew 
Published: June 2022

AbstractDisuse atrophy, caused by situations of unloading such as limb immobilisation, causes a rapid yet diverging reduction in skeletal muscle function compared to muscle mass. While mechanistic insight into the loss of mass is well studied, deterioration of muscle function with a focus towards the neural input to muscle remains underexplored. This study aimed to determine the role of motor unit adaptation in disuse-induced neuromuscular deficits. Ten young, healthy male volunteers underwent 15 days of unilateral lower limb immobilisation with intramuscular EMG (iEMG) recorded from the vastus lateralis during knee extensor contractions normalised to maximal voluntary contraction (MVC) pre and post disuse. Muscle cross-sectional area was determined by ultrasound. Individual MUs were sampled and analysed for changes in MU discharge and MU potential (MUP) characteristics. Vastus lateralis (VL) CSA was reduced by approximately 15% which was exceeded by a two-fold decrease of 31% in muscle strength in the immobilised limb, with no change in either parameter in the non-immobilised VL. Parameters of MUP size were largely reduced with immobilisation, while neuromuscular junction (NMJ) transmission instability increased, and MU firing rate decreased at several contraction levels. All adaptations were observed in the immobilised limb only. These findings highlight impaired neural input following immobilisation reflected by suppressed MU discharge rate and instability of transmission at the NMJ which may underpin the disproportionate reductions of strength relative to muscle size.Key pointsMuscle mass and function decline rapidly in situations of disuse such as bed rest and limb immobilisation.The reduction in muscle function commonly exceeds that of muscle mass, which may be associated with the dysregulation of neural input to the muscle.We have used intramuscular electromyography to sample individual motor unit and near fibre potentials from the vastus lateralis following 15 days of unilateral limb immobilisation. Following disuse, the disproportionate loss of muscle strength when compared to size was associated with suppressed motor unit firing rate and increased markers of neuromuscular junction transmission instability.These central and peripheral motor unit adaptations were observed at multiple contraction levels and in the immobilised limb only. Our findings demonstrate neural dysregulation as a key component of functional loss following muscle disuse in humans.
Complex chromosomal rearrangements induced by transposons in maize
Authors: Sharma Sharu Paul , Peterson Thomas 
Published: June 2022

ABSTRACTEukaryotic genomes are large and complex, and gene expression can be affected by multiple regulatory elements and their positions within the dynamic chromatin architecture. Transposable Elements (TEs) are known to play important roles in genome evolution, yet questions remain as to how TEs alter genome structure and affect gene expression. Previous studies have shown that genome rearrangements can be induced by Reversed Ends Transposition (RET) involving termini of Activator (Ac) and related TEs in maize and other plants. Here, we show that complex alleles can be formed by the rapid and progressive accumulation of Ac-induced duplications and rearrangements. The p1 gene enhancer in maize can induce ectopic expression of the nearby p2 gene in pericarp tissue when placed near it via different structural rearrangements. By screening for p2 expression, we identified and studied five cases in which multiple sequential transposition events occurred and increased the p1 enhancer copy number. We see active p2 expression due to multiple copies of the p1 enhancer present near p2 in all five cases. The p1 enhancer effects are confirmed by the observation that loss of p2 expression is correlated with transposition-induced excision of the p1 enhancers. We also performed a targeted Chromosome Conformation Capture (3C) experiment to test the physical interaction between the p1 enhancer and p2 promoter region. Together, our results show that transposon-induced rearrangements can accumulate rapidly, and progressively increase genetic variation important for genomic evolution.
Composition and Functional Properties of Hemp Seed Protein Isolates from Various Hemp Cultivars
Authors: Liu Martin , Toth Jacob A. , Childs Mackenzie , Smart Lawrence B. , Abbaspourrad Alireza 
Published: June 2022

AbstractHemp seed protein isolates (HPI) were extracted from the seeds of seven commercial hemp cultivars, a Cornell breeding line, and a commercial hemp heart product. The composition and functional properties of the resulting HPI were investigated. HPI were of high protein purity >96% and contained various ratios of the major protein classes edestin, vicilin, and albumin, depending on the source. Protein solubility varied across HPI, and there was a positive correlation between greater levels of vicilin and albumin and improved solubility. The isoelectric points of HPI ranged from 5.50 to 5.94 but did not show significant effects associated with major protein class ratio. Significant differences in HPI foam capacity (52.9–84.9%), foam stability (68.1–89.4%), water holding capacity (0.83–1.05 g water/g protein isolate), and oil holding capacity (1.28–1.81 g oil/g protein isolate) were observed. In general, the emulsions generated from HPI performed poorly in terms of emulsifying activity, stability, and emulsion particle size. The ratio of edestin, vicilin, and albumin was found to play a major role in HPI functionality, suggesting that certain hemp cultivars may be better suited for generating protein ingredients that can functionalize plant-based foods.
Multi-task learning from single-cell multimodal omics with Matilda
Authors: Liu Chunlei , Huang Hao , Yang Pengyi 
Published: June 2022

AbstractSingle-cell multimodal omics technologies enable multiple molecular programs to be simultaneously profiled at a global scale in individual cells, creating opportunities to study biological systems at a resolution that was previously inaccessible. However, the analysis of single-cell multimodal omics data is challenging due to the lack of methods that can integrate across multiple data modalities generated from such technologies. Here, we present Matilda, a multi-task learning method for integrative analysis of single-cell multimodal omics data. By leveraging the interrelationship among tasks, Matilda learns to perform data simulation, dimension reduction, cell type classification, and feature selection in a single unified framework. We compare Matilda with other state-of-the-art methods on datasets generated from some of the most popular single-cell multimodal omics technologies. Our results demonstrate the utility of Matilda for addressing multiple key tasks on integrative single-cell multimodal omics data analysis.
A metagenomic approach to the molecular analysis of bacterial communities in tailings of a gold mine
Authors: Parsania Somayeh , Mohammadi Parisa , Soudi Mohammad Reza , Gharavi Sara 
Published: June 2022

AbstractGold mine operations release arsenic pollutants in environment. The present study investigated the diversity of bacterial communities in the arsenic-contaminated tailings dam effluent (TDE) of Zarshuran gold mine, Takab, northwest of Iran. The bacterial communities were examined using the next-generation sequencing method (Illumina) targeting the V3-V4 region of 16S rRNA genes. Bacteroidetes (50.3%), Proteobacteria (45.49%), Actinobacteria (1.14%) and Firmicutes (1.08%) constituted dominant phyla in the TDE. Its diversity was analyzed, and compared with that of three previously-studied arsenic-contaminated groundwater (GW) microbiomes. The raw sequencing data were analyzed in QIIME2. The prevalent taxonomic groups observed in all of the samples belonged to Proteobacteria (8.06-45.49%), Bacteroidetes (1.85-50.32%), Firmicutes (1.00-6.2%), Actinobacteria (0.86-5.09%), Planctomycetes (0.05-9.37%) and Cyanobacteria (0.6-2.71%). According to Principal Coordinates Analysis (PCoA), the TDE and GW samples were divided into high and low groups, based on their arsenic content, respectively. The average numbers of observed alpha diversity indices, i.e. Pielou’s evenness and Faith’s phylogenetic diversity, were not significantly different (P=0.18, Kruskal-Wallis test). According to the beta diversity analysis (unweighted), the observed operational taxonomic units (OTUs) and the diversity of the bacterial populations were not significantly different in the TDE, compared to the GW samples (PERMANOVA, P=0.276, 999 Permutations).
Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021
Authors: Eales Oliver , Wang Haowei , Haw David , Ainslie Kylie E. C. , Walters Caroline E. , Atchison Christina , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Ashby Deborah , Donnelly Christl A. , Elliott Paul , Riley Steven 
Published: June 2022

AbstractBackgroundFollowing rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.AimWe characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence.MethodsOn average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions.ResultsFollowing an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was masked by the effects of vaccination and the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups.ConclusionHigh-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was highly effective at reducing risk of infection with school holidays/closures playing a significant part.