bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carers using assistive technology in dementia care: an explanatory sequential mixed methods study
Authors: Sriram Vimal , Jenkinson Crispin , Peters Michele 
Published: April 2021

AbstractINTRODUCTIONInformal carers support persons with dementia to live at home, even with deteriorating physical and cognitive issues. The purpose of this explanatory sequential mixed methods study is to examine the experiences and impact of Assistive Technology (AT) on carers, providing care for a person with dementia.METHODSThe quantitative phase was a survey carried out with carers of persons with dementia in the UK, who used AT. The qualitative phase involved in-depth telephone interviews with a purposive sample of survey respondents. Data was analysed using hermeneutic phenomenology to develop, compare and explain the findings of the survey.RESULTSThe survey included data from 201 carers. Smartphones and tablet computers were the most frequently used AT. Multiple AT were used in the care of persons with dementia predominantly for safety, communication, and reminders. The Short Form-12 questions in the survey showed that carers in the 46-65 age group and carers who were not extremely satisfied with AT had lower mental component scores and carers who lived with the person with dementia and older carers had lower physical component scores. Twenty-three carers participated in the interviews, and 5 themes with 14 sub-themes were identified. The interviews helped confirm data from the survey on the impact of AT on the physical, mental and social wellbeing of the carers. It helped describe reasons for satisfaction with AT; how AT was used in daily life and strengthened caring relationships; and how wider support systems enhanced the care of a person with dementia using AT.CONCLUSIONSThis study describes the use of AT in the real-world context. AT supplements the care provided to a person with dementia in the community. Appropriate use, access to AT and abilities of the carer can enhance the support provided through AT to both carers and the person with dementia.
Prevention of COVID-19 by mRNA-based vaccines within the general population of California
Authors: Andrejko Kristin L. , Pry Jake , Myers Jennifer F. , Jewell Nicholas P. , Openshaw John , Watt James , Jain Seema , Lewnard Joseph A. 
Published: April 2021

ABSTRACTBackgroundEstimates of COVID-19 vaccine effectiveness under real-world conditions, and understanding of barriers to uptake, are necessary to inform vaccine rollout.MethodsWe enrolled cases (testing positive) and controls (testing negative) from among the population whose SARS-CoV-2 molecular diagnostic test results from 24 February-29 April 2021 were reported to the California Department of Public Health. Participants were matched on age, sex, and geographic region. We assessed participants’ self-reported history of COVID-19 vaccine receipt (BNT162b2 and mRNA-1273). Participants were considered fully vaccinated two weeks after second dose receipt. Among unvaccinated participants, we assessed willingness to receive vaccination, when eligible. We measured vaccine effectiveness (VE) via the matched odds ratio of prior vaccination, comparing cases with controls.ResultsWe enrolled 1023 eligible participants aged ≥18 years. Among 525 cases, 71 (13.5%) received BNT162b2 or mRNA-1273; 20 (3.8%) were fully vaccinated with either product. Among 498 controls, 185 (37.1%) received BNT162b2 or mRNA-1273; 86 (16.3%) were fully vaccinated with either product. Two weeks after second dose receipt, VE was 86.8% (95% confidence interval: 68.6-94.7%) and 85.6% (69.1-93.9%) for BNT162b2 and mRNA-1273, respectively. Fully vaccinated participants receiving either product experienced 91.3% (79.7-96.3%) and 68.3% (28.5-86.0%) VE against symptomatic and asymptomatic infection, respectively. Among unvaccinated participants, 42.4% (159/375) residing in rural regions and 23.8% (67/281) residing in urban regions reported hesitancy to receive COVID-19 vaccination.ConclusionsAuthorized mRNA vaccines are effective at reducing documented SARS-CoV-2 infections within the general population of California. Vaccine hesitancy presents a barrier to reaching coverage levels needed for herd immunity.Brief pointsVaccination is preventing documented SARS-CoV-2 infection in California, with 68% and 91% effectiveness against asymptomatic and symptomatic infection, respectively.Vaccine effectiveness was equivalent for BNT126b2 and mRNA-1273.Only 66% of unvaccinated participants were willing to receive the vaccine when eligible.
Spike protein antibodies mediate the apparent correlation between SARS-CoV-2 nucleocapsid antibodies and neutralization test results
Authors: Perkmann Thomas , Koller Thomas , Perkmann-Nagele Nicole , Klausberger Miriam , Duerkop Mark , Holzer Barbara , Hartmann Boris , Mucher Patrick , Radakovics Astrid , Ozsvar-Kozma Maria , Wagner Oswald F , Binder Christoph J , Haslacher Helmuth 
Published: April 2021

AbstractObjectivesSARS-CoV-2 infection induces the formation of different antibodies. However, not all of which might prevent the virus from entering the cell, although their concentrations correlate with the titers of viral neutralization tests (NTs). Antibodies against the viral nucleocapsid (NC), e.g., can be classified as such. We aimed to prove the hypothesis that the apparent correlation between NC-antibody levels and NT-titers is mediated by simultaneously occurring antibodies against viral spike-protein components.MethodsWe included 64 individuals with previous SARS-CoV-2 infection (>14d after symptom onset). SARS-CoV-2 antibodies against the NC (Roche total antibody ECLIA, Abbott IgG CMIA) and spike-protein (Technozym RBD ELISA, DiaSorin S1/S2 CLIA) were measured, and neutralization tests were performed. The effect of spike-protein antibodies on the correlation between NC-antibodies and NT-titers was evaluated by partial correlation and mediation analyses.ResultsBoth tested assays assessing antibodies against the NC correlated significantly with NT titers: Abbott ρ=0.742, P<0.0001; Roche ρ=0.365, P<0.01. However, when controlling the rank correlations for the presence of RBD or S1/S2 antibodies, correlation coefficients dropped to ρ=0.318/ρ=0.329 (P<0.05/P<0.01), respectively for Abbott and vanished for Roche. As a result, only a maximum of 11% of NT titer variability could be explained by NC-antibody levels.ConclusionsOur data suggest that the apparent correlation between NC antibodies and NT titers is strongly mediated by co-occurring RBD antibody concentrations. To avoid falsely implied causal relationships, all correlation analyses of non-spike-associated antibody assays and neutralization assays should include a partial correlation analysis to exclude a possible mediator effect of spike-associated antibodies.
COVID-19 outcomes among hospitalized men with or without exposure to alpha-1-adrenergic receptor blocking agents
Authors: Li Shilong , Jun Tomi , Wang Zichen , Kao Yu-Han , Schadt Emilio , Konig Maximilian F. , Bettegowda Chetan , Vogelstein Joshua T. , Papadopoulos Nickolas , Parsons Ramon E. , Chen Rong , Schadt Eric E. , Li Li , Oh William K. 
Published: April 2021

AbstractImportanceAlpha-1-adrenergic receptor antagonists (α1-blockers) can abrogate pro-inflammatory cytokines and may improve outcomes among patients with respiratory infections. Repurposing readily available drugs such as α1-blockers could augment the medical response to the COVID-19 pandemic.ObjectiveTo evaluate the association between α1-blocker exposure and COVID-19 mortalityDesignReal-world evidence studySettingPatient level data with 32,355 records tested for SARS-CoV-2 at the Mount Sinai Health System including 8,442 laboratory-confirmed cases extracted from five member hospitals in the New York City metropolitan area.Participants2,627 men aged 45 or older admitted with COVID-19 between February 24 and May 31, 2020Exposuresα1-blocker use as an outpatient or while admitted for COVID-19Main Outcomes and MeasuresIn-hospital mortalityResultsMen exposed to α1-blockers (N=436) were older (median age 73 vs. 64 years, P<0.001) and more likely to have comorbidities than unexposed men (N=2,191). Overall, 758 (28.9%) patients died in hospital, 1,589 (60.5%) were discharged, and 280 (10.7%) were still hospitalized as of May 31, 2020. Outpatient exposure to α1-blockers was not associated with COVID-19 hospital outcomes, though there was a trend towards significance (OR 0.749, 95% CI 0.527-1.064; P=0.106). Conversely, inpatient use of α1-blockers was independently associated with improved in-hospital mortality in both multivariable logistic (OR 0.633, 95% CI 0.434-0.921; P=0.017) and Cox regression analyses (HR 0.721, 95% CI 0.572-0.908; P=0.006) adjusting for patient demographics, comorbidities, and baseline vitals and labs. Age-stratified analyses suggested greater benefit from inpatient α1-blocker use among younger age groups: Age 45-65 OR 0.384, 95% CI 0.164-0.896 (P=0.027); Age 55-75 OR 0.511, 95% CI 0.297-0.880 (P=0.015); Age 65-89 OR 0.810, 95% CI 0.509-1.289 (P=0.374).Conclusions and RelevanceInpatient α1-blocker use was independently associated with improved COVID-19 mortality among hospitalized men. Clinical trials to assess the therapeutic value of α1-blockers in COVID-19 are warranted.
Genomic sequence characteristics and the empiric accuracy of short-read sequencing
Authors: Marin Maximillian , Vargas Roger , Harris Michael , Jeffrey Brendan , Epperson L. Elaine , Durbin David , Strong Michael , Salfinger Max , Iqbal Zamin , Akhundova Irada , Vashakidze Sergo , Crudu Valeriu , Rosenthal Alex , Farhat Maha Reda 
Published: April 2021

AbstractBackgroundShort-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias, reduce the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. For the clonal pathogen Mycobacterium tuberculosis (Mtb), researchers frequently exclude 10.7% of the genome believed to be repetitive and prone to erroneous variant calls. To benchmark short-read variant calling, we used 36 diverse clinical Mtb isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically study the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias, and GC content. åResultsReference based Illumina variant calling had a recall ≥89.0% and precision ≥98.5% across parameters evaluated. The best balance between precision and recall was achieved by tuning the mapping quality (MQ) threshold, i.e. confidence of the read mapping (recall 85.8%, precision 99.1% at MQ ≥ 40). Masking repetitive sequence content is an alternative conservative approach to variant calling that maintains high precision (recall 70.2%, precision 99.6% at MQ≥40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52 of the 168 PE/PPE genes (34.5%). We present a refined list of low confidence regions and examine the largest sources of variant calling error.ConclusionsOur improved approach to variant calling has broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems, and more generally for WGS applications in other organisms.
Biotext: Exploiting Biological-Text Format for Text Mining
Authors: de Jesus Soares Machado Diogo , De Pierri Camilla Reginatto , Santos Letícia Graziela Costa , Scapin Leonardo , da Silva Filho Antonio Camilo , Perico Camila Pereira , de Oliveira Pedrosa Fabio , Raittz Roberto Tadeu 
Published: April 2021

ABSTRACTThe large amount of existing textual data justifies the development of new text mining tools. Bioinformatics tools can be brought to Text Mining, increasing the arsenal of resources. Here, we present BIOTEXT, a package of strategies for converting natural language text into biological-like information data, providing a general protocol with standardized functions, allowing to share, encode and decode textual data for amino acid and DNA. The package was used to encode the arbitrary information present in the headings of the biological sequences found in a BLAST survey. The protocol implemented in this study consists of 12 steps, which can be easily executed and/ or changed by the user, depending on the study area. BIOTEXT empowers users to perform text mining using bioinformatics tools. BIOTEXT is freely available athttps://pypi.org/project/BIOTEXT/(Python package) andhttps://sourceforge.net/projects/BIOTEXTtools/files/AMINOcode_GUI/(Standalone tool).
Sensitive and specific spectral library searching with COSS and Percolator
Authors: Shiferaw Genet Abay , Gabriels Ralf , Bouwmeester Robbin , Van Den Bossche Tim , Vandermarliere Elien , Martens Lennart , Volders Pieter-Jan 
Published: April 2021

ABSTRACTMaintaining high sensitivity while limiting false positives is a key challenge in peptide identification from mass spectrometry data. Here, we therefore investigate the effects of integrating the machine learning-based post-processor Percolator into our spectral library searching tool COSS. To evaluate the effects of this post-processing, we have used forty data sets from two different projects and have searched these against the NIST and MassIVE spectral libraries. The searching is carried out using two spectral library search tools, COSS and MSPepSearch with and without Percolator post-processing, and using sequence database search engine MS-GF+ as a baseline comparator. The addition of the Percolator rescoring step to COSS is effective and results in a substantial improvement in sensitivity and specificity of the identifications. COSS is freely available as open source under the permissive Apache2 license, and binaries and source code are found athttps://github.com/compomics/COSS
MetaRNN: Differentiating Rare Pathogenic and Rare Benign Missense SNVs and InDels Using Deep Learning
Authors: Li Chang , Zhi Degui , Wang Kai , Liu Xiaoming 
Published: April 2021

AbstractWith advances in high-throughput DNA sequencing, numerous genetic variants have been discovered in the human genome. One challenge we face is interpreting these variants to help in disease screening, diagnosis, and treatment. While multiple computational approaches have been proposed to improve our understanding of genetic variants, their ability to identify rare pathogenic variants from rare benign ones is still lacking. Using context annotations and deep learning methods, we present pathogenicity prediction models, MetaRNN and MetaRNN-indel, to help identify and prioritize rare non-synonymous single nucleotide variants (nsSNVs) and non-frameshift insertion/deletions (nfINDELs). A recurrent neural network incorporating a +/- 1 codon window around the affected codon was combined with 28 high-level annotation scores and allele frequency features to develop the two proposed models. We use independent test datasets to demonstrate that these new models outperform state-of-the-art competitors and achieve a more interpretable score distribution. Importantly, prediction scores from the nsSNV-based and the nfINDEL-based models are comparable, enabling easy adoption of integrated genotype-phenotype association analysis methods. In addition, we provide pre-computed MetaRNN scores for all possible human nsSNVs and a Linux executable file for a fast one-stop annotation of nsSNVs and nfINDELs. All the resources are available athttp://www.liulab.science/MetaRNN.
Happy Cow or Thinking Pig? WUR Wolf – Facial Coding Platform for Measuring Emotions in Farm Animals
Authors: Neethirajan Suresh 
Published: April 2021

AbstractEmotions play an indicative and informative role in the investigation of farm animal behaviors. Systems that respond and can measure emotions provide a natural user interface in enabling the digitalization of animal welfare platforms. The faces of farm animals can be one of the richest channels for expressing emotions. We present WUR Wolf (Wageningen University & Research: Wolf Mascot)—a real-time facial expression recognition platform that can automatically code the emotions of farm animals. Using Python-based algorithms, we detect and track the facial features of cows and pigs, analyze the appearance, ear postures, and eye white regions, and correlate with the mental/emotional states of the farm animals. The system is trained on dataset of facial features of images of the farm animals collected in over 6 farms and has been optimized to operate with an average accuracy of 85%. From these, we infer the emotional states of animals in real time. The software detects 13 facial actions and 9 emotional states, including whether the animal is aggressive, calm, or neutral. A real-time emotion recognition system based on YoloV3, and Faster YoloV4-based facial detection platform and an ensemble Convolutional Neural Networks (RCNN) is presented. Detecting expressions of farm animals simultaneously in real time makes many new interfaces for automated decision-making tools possible for livestock farmers. Emotions sensing offers a vast amount of potential for improving animal welfare and animal-human interactions.
Shorter effective lifespan in laboratory populations ofD. melanogastermight reduce sexual selection
Authors: Mital Avani , Sarangi Manaswini , Nandy Bodhisatta , Pandey Neha , Joshi Amitabh 
Published: April 2021

AbstractThe role of sexual selection in mediating levels of sexual conflict has been demonstrated in many experimental evolution studies onDrosophilaspp. where competition among males for mating was the target of selection. Sexual selection has also been shown to affect the evolution of life-histories. However, the influence of divergent life-histories on reproductive strategies and, therefore, sexual selection and possibly sexual conflict, has been less well studied. We examinedD. melanogasterpopulations selected for a short development time and early age at reproduction for changes in reproductive behaviour and traits that are proxies of sexual selection. We report a large reduction in reproductive competition experienced by the males of these populations, compared to ancestral populations that are not consciously selected for rapid development or early reproduction, potentially leading to reduced sexual selection. We show that rapidly developing and early reproducing populations have very low levels of mating in their lifetime (females are more or less monandrous), low courtship levels, shorter copulation duration, and longer time from eclosion to first mating, compared to the controls. These results are discussed in the context of the previously demonstrated reduction of inter-locus sexual conflict in these populations. We show that life-history strategies might have a large and significant impact on sexual selection, with each influencing the other and contributing to the complexities of adaptation.Significance statementSexual conflict, often manifested as an arms-race between males and females trying to enhance their own reproductive success at some cost to the other, is of great evolutionary interest because it can maintain genetic variation in populations, prevent the independent optimization of male and female traits, and also promote speciation. Sexual selection, or variation in mating success, is well known to affect levels of sexual conflict. However, it is not so clear whether, and how, the regular evolution of life-histories also affects sexual selection. Here, we show that life-history evolution in fruit fly populations selected for traits not directly related to sexual conflict might, nevertheless, mediate the possible evolution of altered sexual conflict levels through effects on sexual selection. Populations that evolved to develop to adulthood fast, and reproduce relatively early in life, are shown to potentially experience less sexual selection, which can explain the low sexual conflict levels earlier observed in them.
Integrative systems biology approach identified crucial genes and transcription factors associated with gallbladder cancer pathogenesis
Authors: Roy Nabanita , Kshattry Mrinmoy , Mandal Susmita , Jolly Mohit Kumar , Bhattacharyya Dhruba Kumar , Barah Pankaj 
Published: April 2021

AbstractGallbladder cancer (GBC) has a lower incidence rate among the population relative to other cancer types but majorly contributes to the total cancer cases of the biliary tract system. GBC is distinguished from other malignancies due to its high mortality, marked geographical variation and poor prognosis. To date no systemic targeted therapy is available for GBC. The main objective of this study is to determine the molecular signatures correlated with GBC development using integrative system level approaches. We performed analysis of publicly available transcriptomic data to identify differentially regulated genes and pathways. Co-expression network analysis and differential regulatory network analysis identified hub genes and hub transcription factors (TFs) associated with GBC pathogenesis and progression. We then assessed the epithelial-mesenchymal transition (EMT) status of the hub genes using a combination of three scoring methods. The hub genes such as; CDC6, MAPK15, CCNB2, BIRC7, L3MBTL1 identified are regulators of cell cycle components which suggests that cell cycle regulatory genes are significantly linked to GBC pathogenesis and progression.
Abundance-occupancy relationships along taxonomic ranks reveal a consistency of niche differentiation in marine bacterioplankton with distinct lifestyles
Authors: Izabel-Shen Dandan , Höger Anna-Lena , Jürgens Klaus 
Published: April 2021

AbstractAbundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at the genus and phylum levels. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification.Subject Categorymicrobial population and community ecology