bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the impact of high-risk human papillomavirus on oropharyngeal squamous cell carcinomas in Taiwan: A retrospective cohort study
Authors: Hiles Guadalupe Lorenzatti , Chang Kai-Ping , Bellile Emily L. , Wang Chun-I , Yen Wei-Chen , Goudsmit Christine M. , Briggs Hannah L. , Thomas Trey B. , Peters Lila , Afsari Macy A. , Pinatti Lisa M. , Morris Anna C. , Jawad Nadine , Carey Thomas E. , Walline Heather M. 
Published: October 2020

AbstractBackground and ObjectivesHuman papillomavirus (HPV)-driven oropharyngeal squamous cell carcinoma (OPSCC) is increasing globally. In Taiwan, HPV-positive OPSCC is obscured by tobacco, alcohol, and betel quid use. We investigated the role of high-risk HPV (hrHPV) in a large retrospective Taiwan OPSCC cohort.Methods and ResultsThe cohort of 541 OPSCCs treated at Chang Gung Memorial Hospital from 1998-2016 consisted of 507 men (94%) and 34 women (6%). Most used tobacco (81%), alcohol (51%), and betel quid (65%). Formalin-fixed, paraffin-embedded tissue was used for p16 staining (a surrogate marker for HPV) and testing for HPV DNA presence and type by Multiplex HPV PCR-MassArray. HPV DNA and/or p16 staining (HPV-positive) was found in 28.4% (150/528) tumors. p16 and HPV DNA were strongly correlated (F < 0.0001). HPV16 was present in 82.8%, and HPV58 in 7.5% of HPV-positive tumors. HPV was associated with higher age (55.5 vs. 52.7 years, p = 0.004), lower T-stage (p = 0.008) better overall survival (OS) (hazard ratio [HR] 0.58 [95% CI 0.42-0.81], p = 0.001), and disease-free survival (DFS) (HR 0.54 [95% CI 0.40-0.73], p < 0.0001). Alcohol was strongly associated with recurrence and death (OS: HR 2.06 [95% CI 1.54-2.74], p < 0.0001; DFS: HR 1.72 [95% CI 1.33-2.24], p < 0.0001). OS and DFS in HPV-positive cases decreased for alcohol users (p < 0.0001). Obscured by the strong alcohol effect, predictive associations were not found for tobacco or betel quid.ConclusionsAs with HPV-positive OPSCC globally, HPV is an increasingly important etiological factor in Taiwanese OPSCC. HPV-positive OPSCC has considerable survival benefit, but that is reduced by alcohol, tobacco, and betel quid use. hrHPV is a cancer risk factor in males and females. Vaccinating both sexes with a multivalent vaccine including HPV58, combined with alcohol and tobacco cessation policies will be effective cancer-prevention public health strategies in Taiwan.
Emergence of Clade III Candida auris of African Origin in Los Angeles
Authors: Price Travis K. , Mirasol Ruel , Ward Kevin W. , Dayo Ayrton J. , Chandrasekaran Sukantha , Garner Omai B. , de St Maurice Annabelle , Yang Shangxin 
Published: October 2020

ABSTRACTCandida auris is an emerging multi-drug resistant yeast responsible for invasive infections among hospitalized patients. We described a case series of C. auris isolated in the Los Angeles area from an ongoing outbreak. Genomic analysis showed a single Clade III lineage of African origin in all 6 cases since 2019.
Predicting the impact of COVID-19 interruptions on transmission of gambiense human African trypanosomiasis in two health zones of the Democratic Republic of Congo
Authors: Aliee Maryam , Castaño Soledad , Davis Christopher N , Patel Swati , Miaka Erick Mwamba , Spencer Simon EF , Keeling Matt J , Chitnis Nakul , Rock Kat S 
Published: October 2020

AbstractMany control programmes against neglected tropical diseases have been interrupted due to COVID-19 pandemic, including those that rely on active case finding. In this study we focus on gambiense human African trypanosomiasis (gHAT), where active screening was suspended in the Democratic Republic of Congo (DRC) due to the pandemic. We use two independent mathematical models to predict the impact of COVID-19 interruptions on transmission and reporting, and the achievement of 2030 elimination of transmission (EOT) goal for gHAT in two moderate-risk regions of DRC. We consider different interruption scenarios, including reduced passive surveillance in fixed health facilities, and whether this suspension lasts until the end of 2020 or 2021. Our models predict an increase in the number of new infections in the interruption period only if both active screening and passive surveillance were suspended, and with slowed reduction - but no increase - if passive surveillance remains fully functional. In all scenarios, the EOT may be slightly pushed back if no mitigation such as increased screening coverage is put in place. However, we emphasise that the biggest challenge will remain in the higher prevalence regions where EOT is already predicted to be behind schedule without interruptions unless interventions are bolstered.
COVID-19 symptoms at hospital admission vary with age and sex: ISARIC multinational study
Authors: Pritchard Mark G ,   ISARIC Clinical Characterisation Group
Published: October 2020

AbstractBackgroundThe ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms.MethodsInternational, prospective observational study of 60⍰109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms.Results‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30-to 60-year-olds (respectively 80%, 79%, 69%; at least one 95%). They were reported less frequently in children (≤18 years: 69%, 48%, 23%; 85%), older adults (≥70 years: 61%, 62%, 65%; 90%), and women (66%, 66%, 64%; 90%; vs men 71%, 70%, 67%; 93%). The most common atypical presentation under 60 years of age was nausea and vomiting, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country.InterpretationAdults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men.SummaryAdults over 60 and children admitted to hospital with COVID-19 are less likely to have typical symptoms. Nausea and vomiting are common atypical presentations under 30 and confusion over 60. Women are less likely to experience typical symptoms than men.
Intention to have the seasonal influenza vaccination during the COVID-19 pandemic among eligible adults in the UK
Authors: Sherman Susan M. , Sim Julius , Amlôt Richard , Cutts Megan , Dasch Hannah , Rubin G James , Sevdalis Nick , Smith Louise E. 
Published: October 2020

AbstractWe investigated likelihood of having the seasonal influenza vaccination in 645 participants who were eligible for the vaccination in the UK. 55.8% indicated they were likely to have the vaccination. Previous research suggests that increasing uptake of the influenza vaccination may help contain a COVID-19 outbreak, so steps need to be taken to convert intention into behaviour and to reach the 23.9% who were unlikely to have the vaccination and the 20.3% who were unsure.
Hyper-Exponential Growth of COVID-19 during Resurgence of the Disease in Russia
Authors: Baruah Hemanta K. 
Published: October 2020

AbstractIn Russia, COVID-19 has currently been growing hyper-exponentially. This type of a spread pattern was not seen during the first wave of the pandemic the world over. Indeed when the disease had first appeared, in the accelerating stage the spread pattern was observed to have followed a highly nonlinear pattern that could be said to be approximately exponential or sub-exponential. As to why in the resurgence the growth has become hyper-exponential is another matter. But this has been happening in Europe and how long this would continue cannot be predicted. It may so happen that in the countries in which retardation has already been taking place, there may be resurgence of the disease. It was observed that in the World as a whole, retardation was on the threshold during the second half of September. But if the resurgence happens to follow the hyper-exponential growth pattern in different countries, there may be resurgence in the World as a whole.
Altered hippocampal functional connectivity patterns in patients with cognitive impairments following ischaemic stroke: a resting-state fMRI study
Authors: Jung JeYoung , Laverick Rosanna , Nader Kurdow , Wilson Martin , Auer Dorothee P. , Rotshtein Pia , Hosseini Akram A. 
Published: October 2020

AbstractBackgroundIschemic stroke with cognitive impairment is a considerable risk factor for developing dementia. Identifying imaging markers of cognitive impairment following ischemic stroke will help to develop prevention strategies against post-stroke dementia.MethodsHere, we investigated the hippocampal functional connectivity (FC) pattern following ischemic stroke, using resting-state fMRI (rs-fMRI). Thirty-three cognitively impaired patients after ischemic stroke and sixteen age-matched controls with no known history of neurological disorder, were recruited for the study. Importantly, no patient had a direct ischaemic insult to hippocampus on examination of brain imaging. Seven subfields of hippocampus were used as a seed region for FC analyses.ResultsAcross all hippocampal subfields, FC with the inferior parietal lobe in patients was reduced as compared with healthy controls. This decreased FC included both supramarginal gyrus and angular gyrus. The FC of hippocampal subfields with cerebellum was increased. Importantly, the degree of the altered FC between hippocampal subfields and IPL was associated with their impaired memory function.ConclusionOur results demonstrated that decreased hippocampal-IPL connectivity was associated with cognitive impairment in patients with ischemic stroke. These findings provide novel insights into the role of hippocampus in cognitive impairment following ischemic stroke.
Reliability and Validity of Cognitive Workload in Older Adults
Authors: Devos Hannes , Gustafson Kathleen , Ahmadnezhad Pedram , Liao Ke , Mahnken Jonathan D. , Brooks William M. , Burns Jeffrey M. 
Published: October 2020

AbstractCognitive workload (mental effort) is a measure of attention allocation to a task, which can be administered through self-report or physiological measures. Cognitive workload is increasingly recognized as an important determinant of performance in cognitive tests and daily life activities. However, the reliability and validity of these measures have not been established in older adults with a wide range of cognitive ability. The aim of this study was to establish the test-retest reliability of the NASA-Task Load Index (NASA-TLX) and Index of Cognitive Activity (ICA), extracted from pupillary size. The convergent validity of these measures against event-related potentials (ERPs) was also investigated. A total of 38 individuals with scores on the Montreal Cognitive Assessment ranging between 17 and 30 completed a working memory test (n-back) with three levels of difficulty at baseline and two-week follow-up. Intraclass correlation coefficients (ICC) values of the NASA-TLX ranged between 0.71 and 0.81, demonstrating good to excellent reliability. Mean ICA scores showed fair to good reliability, with ICC’s ranging between 0.56 and 0.73. Mean ICA and NASA-TLX scores showed significant and moderate correlations (Pearson r range between 0.30 and 0.33) with P3 ERP at the midline channels. We conclude that ICC and NASA-TLX are reliable measures of cognitive workload in older adults. Further research is needed in dissecting the subjective and objective constructs of cognitive workload.
SARS-CoV-2 seroprevalence and detection fraction in Utah urban populations from a probability-based sample
Authors: Samore Matthew H. , Looney Adam , Orleans Brian , Greene Tom , Seegert Nathan , Delgado Julio C , Presson Angela , Zhang Chong , Ying Jian , Zhang Yue , Shen Jincheng , Slev Patricia , Gaulin Maclean , Yang Mu-Jeung , Pavia Andrew T. , Alder Stephen C. 
Published: October 2020

ABSTRACTThis project’s aim was to generate an unbiased estimate of the incidence of SARS-CoV-2 infection in four urban counties in Utah. A multi-stage sampling design was employed to randomly select community-representative participants 12 years and over. Between May 4 and June 30, 2020, surveys were completed and sera drawn from 8,108 individuals belonging to 5,125 households. A qualitative chemiluminescent microparticle immunoassay was used to detect the presence of IgG antibody to SARS-CoV-2. The overall prevalence of IgG antibody to SARS-CoV-2 was estimated at 0.8%. The estimated seroprevalence-to-case count ratio was 2.4, corresponding to a detection fraction of 42%. Only 0.2% of individuals who had a nasopharyngeal swab collected were reverse transcription polymerase chain reaction (RT-PCR) positive. The prevalence of antibodies to SARS-CoV-2 in Utah urban areas between May and June was low and the prevalence of positive RT-PCR even lower. The detection fraction for COVID-19 in Utah was comparatively high.Article SummaryProbability-based sampling provides an effective method for robust estimates of community-based SARS-CoV-2 seroprevalence and detection fraction among urban populations in Utah.
Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank
Authors: Naseri Ardalan , Zhi Degui , Zhang Shaojie 
Published: October 2020

AbstractRuns of homozygosity (ROH) segments, contiguous homozygous regions in a genome were traditionally linked to families and inbred populations. However, a growing literature suggests that ROHs are ubiquitous in outbred populations. Still, most existing genetic studies of ROH in populations are limited to aggregated ROH content across the genome, which does not offer the resolution for mapping causal loci. This limitation is mainly due to a lack of methods for efficient identification of shared ROH diplotypes. Here, we present a new method, ROH-DICE, to find large ROH diplotype clusters, sufficiently long ROHs shared by a sufficient number of individuals, in large cohorts. ROH-DICE identified over 1 million ROH diplotypes that span over 100 SNPs and shared by more than 100 UK Biobank participants. Moreover, we found significant associations of clustered ROH diplotypes across the genome with various self-reported diseases, with the strongest associations found between the extended HLA region and autoimmune disorders. We found an association between a diplotype covering the HFE gene and haemochromatosis, even though the well-known causal SNP was not directly genotyped nor imputed. Using genome-wide scan, we identified a putative association between carriers of an ROH diplotype in chromosome 4 and an increase of mortality among COVID-19 patients. In summary, our ROH-DICE method, by calling out large ROH diplotypes in a large outbred population, enables further population genetics into the demographic history of large populations. More importantly, our method enables a new genome-wide mapping approach for finding disease-causing loci with multi-marker recessive effects at population scale.
Age-adjusted Charlson comorbidity index score is the best predictor for severe clinical outcome in the hospitalized patients with COVID-19 infection: a result from nationwide database of 5,621 Korean patients
Authors: Kim Do Hyoung , Park Hayne Cho , Cho Ajin , Kim Juhee , Yun Kyu-sang , Kim Jinseog , Lee Young-Ki 
Published: October 2020

ABSTRACTAged population with comorbidities demonstrated high mortality rate and severe clinical outcome in the patients with coronavirus disease 2019 (COVID-19). However, whether age-adjusted Charlson comorbidity index score (CCIS) predict fatal outcomes remains uncertain. This retrospective, nationwide cohort study was performed to evaluate patient mortality and clinical outcome according to CCIS among the hospitalized patients with COVID-19 infection. We included 5,621 patients who had been discharged from isolation or had died from COVID-19 by April 30, 2020. The primary outcome was composites of death, admission to intensive care unit (ICU), use of mechanical ventilator or extracorporeal membrane oxygenation. The secondary outcome was mortality. Multivariate Cox proportional hazard model was used to evaluate CCIS as the independent risk factor for death. Among 5,621 patients, the high CCIS (≥3) group showed higher proportion of elderly population and lower plasma hemoglobin and lower lymphocyte and platelet counts. The high CCIS group was an independent risk factor for composite outcome (HR 3.63, 95% CI 2.45-5.37, P < 0.001) and patient mortality (HR 22.96, 95% CI 7.20-73.24, P < 0.001). The nomogram demonstrated that the CCIS was the most potent predictive factor for patient mortality. The predictive nomogram using CCIS for the hospitalized patients with COVID-19 may help clinicians to triage the high-risk population and to concentrate limited resources to manage them.
DAGBagM: Learning directed acyclic graphs of mixed variables with an application to identify prognostic protein biomarkers in ovarian cancer
Authors: Chowdhury Shrabanti , Wang Ru , Yu Qing , Huntoon Catherine J. , Karnitz Larry M. , Kaufmann Scott H. , Gygi Steven P. , Birrer Michael J. , Paulovich Amanda G. , Peng Jie , Wang Pei 
Published: October 2020

AbstractMotivationDirected gene/protein regulatory networks inferred by applying directed acyclic graph (DAG) models to proteogenomic data has been shown effective for detecting causal biomarkers of clinical outcomes. However, there remain unsolved challenges in DAG learning to jointly model clinical outcome variables, which often take binary values, and biomarker measurements, which usually are continuous variables. Therefore, in this paper, we propose a new tool, DAGBagM, to learn DAGs with both continuous and binary nodes. By using appropriate models for continuous and binary variables, DAGBagM allows for either type of nodes to be parents or children nodes in the learned graph. DAGBagM also employs a bootstrap aggregating strategy to reduce false positives and achieve better estimation accuracy. Moreover, the aggregation procedure provides a flexible framework to robustly incorporate prior information on edges for DAG reconstruction.ResultsAs shown by simulation studies, DAGBagM performs better in identifying edges between continuous and binary nodes, as compared to commonly used strategies of either treating binary variables as continuous or discretizing continuous variables. Moreover, DAGBagM outperforms several popular DAG structure learning algorithms including the score-based hill climbing (HC) algorithm, constraint-based PC-algorithm (PC-alg), and the hybrid method max-min hill climbing (MMHC) even for constructing DAG with only continuous nodes. The HC implementation in the R package DAGBagM is much faster than that in a widely used DAG learning R package bnlearn. When applying DAGBagM to proteomics datasets from ovarian cancer studies, we identify potential prognostic protein biomarkers in ovarian cancer.Availability and implementationDAGBagMis made available as a github repositoryhttps://github.com/jie108/dagbagM.
Size-dependent tradeoffs in aggressive behavior towards kin
Authors: Fouilloux Chloe , Fromhage Lutz , Valkonen Janne K. , Rojas Bibiana 
Published: October 2020

AbstractAggression between juveniles can be unexpected, as their primary motivation is to survive until their reproductive stage. However, instances of aggression, which may escalate to cannibalism, can be vital for survival, although the factors (e.g. genetic or environmental) leading to cannibalism vary across taxa. While cannibalism can greatly accelerate individual growth, it may also reduce inclusive fitness when kin are consumed. As a solution to this problem, some cannibals demonstrate kin discrimination and preferentially attack unrelated individuals. Here, we used both experimental and modeling approaches to consider how physical traits (e.g. size in relation to opponent) and genetic relatedness mediate aggressive behavior in dyads of cannibalisticDendrobates tinctoriustadpoles. We paired sibling, half-sibling, and non-sibling tadpoles of different sizes together in an arena and recorded their aggression and activity. We found that the interaction between size and relatedness predicts aggressive behavior: large non-siblings are significantly more aggressive than large siblings. Unexpectedly, although siblings tended to attack less overall, in size mismatched pairs they attacked faster than in non-sibling treatments. Ultimately, it appears that larval aggression reflects a balance between relatedness and size where individuals trade-off their own fitness with that of their relatives.
A validated generally applicable approach using the systematic assessment of disease modules by GWAS reveals a multi-omic module strongly associated with risk factors in multiple sclerosis
Authors: Badam Tejaswi V.S. , de Weerd Hendrik A. , Martínez-Enguita David , Olsson Tomas , Alfredsson Lars , Kockum Ingrid , Jagodic Maja , Lubovac-Pilav Zelmina , Gustafsson Mika 
Published: October 2020

ABSTRACTBackgroundThere are few (if any) practical guidelines for predictive and falsifiable multi-omics data integration that systematically integrate existing knowledge. Disease modules are popular concepts for interpreting genome-wide studies in medicine but have so far not been systematically evaluated and may lead to corroborating multi-omic modules.MethodsWe assessed eight module identification methods in 57 previously published expression and methylation studies of 19 diseases using GWAS enrichment analysis. Next, we applied the same strategy for multi-omics integration of 19 datasets of multiple sclerosis (MS), and further validated the resulting module using both GWAS and risk-factor associated genes from several independent cohorts.ResultsOur benchmark of modules showed that in immune-associated diseases modules inferred from clique-based methods were the most enriched for GWAS-genes. The multi-omics case study using MS revealed the robust identification of a module of 220 genes. Strikingly, most genes of the module was differentially methylated upon the action of one or several environmental risk factors in MS (n = 217, P = 10-47) and were also independently validated for association with five different risk factors of MS, which further stressed the high genetic and epigenetic relevance of the module for MS.ConclusionWe believe our analysis provides a workflow for selecting modules and our benchmark study may help further improvement of disease module methods. Moreover, we also stress that our methodology is generally applicable for combining and assessing the performance of multi-omics approaches for complex diseases.