bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring the proportion infected by SARS-CoV-2 from age-stratified hospitalisation and serological data
Authors: Hozé Nathanaël , Paireau Juliette , Lapidus Nathanaël , Kiem Cécile Tran , Salje Henrik , Severi Gianluca , Touvier Mathilde , Zins Marie , Lamballerie Xavier de , Lévy-Bruhl Daniel , Carrat Fabrice , Cauchemez Simon 
Published: January 2021

AbstractBackgroundRegional monitoring of the proportion infected by SARS-CoV-2 is important to guide local management of the epidemic, but is difficult in the absence of regular nationwide serosurveys.MethodsWe developed a method to reconstruct in real-time the proportion infected by SARS-CoV-2 and the proportion of infections being detected from the joint analysis of age-stratified seroprevalence, hospitalisation and case data. We applied our approach to the 13 French metropolitan regions.FindingsWe estimate that 5.7% [5.1%-6.4%] of adults in metropolitan France had been infected by SARS-CoV-2 by May 2020. This proportion remained stable until August and increased to 12.6% [11.2%-14.3%] by the end of November. With 23.8% [21.2%-26.8%] infected in the Paris region compared to 4.0% [3.5% - 4.6%] in Brittany, regional variations remained large (Coefficient of Variation CV: 0.53) although less so than in May (CV: 0.74). The proportion infected was twice higher (17.6% [13.4%-22.7%]) in 20-49 y.o. than in 50+ y.o (8.0% [5.7% - 11.5%]). Forty percent [33.7% - 45.4%] of infections in adults were detected in June-August compared to 55.7% [48.7% - 63.1%] in September-November. Our method correctly predicted seroprevalence in 11 regions in which only hospitalisation data were used.InterpretationIn the absence of contemporary serosurvey, our real-time monitoring indicates that the proportion infected by SARS-CoV-2 may be above 20% in some French regions.FundingEU RECOVER, ANR, Fondation pour la Recherche Médicale, Inserm.
Early detection of prostate gland and breast cancer risk based on routine check-up data using survival analysis trees for left-truncated and right-censored data
Authors: Coster Dan , Fisher Eyal , Shenhar-Tsarfaty Shani , Menes Tehillah , Berliner Shlomo , Rogowski Ori , Zeltser David , Shapira Itzhak , Halperin Eran , Rosset Saharon , Gorfine Malka , Shamir Ron 
Published: January 2021

ABSTRACTObjectiveTo predict breast cancer (BC) and prostate gland cancer (PGC) risk among healthy individuals by analyzing routine laboratory measurements, vital signs and age.Materials and MethodsWe analyzed electronic medical records of 20,317 healthy individuals who underwent routine checkups, encompassing more than 600 parameters per visit, and identified those who later developed cancer. We developed a novel ensemble method for risk prediction of multivariate time series data using a random forest model of survival trees for left truncated and right-censored data.ResultsUsing cross-validation, our method predicted future PGC and BC 6 months before diagnosis, achieving an area under the ROC curve of 0.62±0.05 and 0.6±0.03 respectively, better than standard random forest, Cox-regression model and a single survival tree. Our method can complement existing screening tests such as clinical breast examination and mammography for BC, and help in detection of subjects that were missed by these tests.DiscussionComputational analysis of results of routine checkups of healthy individuals can improve the detection of those at risk of cancer development.ConclusionOur method may assist in early detection of breast and prostate gland cancer.
Hospital load and increased COVID-19 related mortality - a nationwide study in Israel
Authors: Rossman Hagai , Meir Tomer , Somer Jonathan , Shilo Smadar , Gutman Rom , Arie Asaf Ben , Segal Eran , Shalit Uri , Gorfine Malka 
Published: January 2021

AbstractThe spread of Coronavirus disease 19 (COVID-19) has led to many healthcare systems being overwhelmed by the rapid emergence of new cases within a short period of time. We explore the ramifications of hospital load due to COVID-19 morbidity on COVID-19 in-hospital patient mortality. We address this question with a nationwide study based on the records of all 22,636 COVID-19 patients hospitalized in Israel from mid-July 2020 to mid-January 2021. We show that even under moderately heavy patient load (>500 countrywide hospitalized severely-ill patients; the Israeli Ministry of Health defined 800 severely-ill patients as the maximum capacity allowing adequate treatment), in-hospital mortality rate of patients with COVID-19 significantly increased compared to periods of lower patient load (250-500 severely-ill patients): 14-day mortality rates were 22.1% (Standard Error 3.1%) higher (mid-September to mid-October) and 27.2% (Standard Error 3.3%) higher (mid-December to mid-January). We further show this higher mortality rate cannot be attributed to changes in the patient population during periods of heavier load.
The Relationship between Democracy embracement and COVID-19 reported casualties worldwide
Authors: Hussein Muhammad R. , AlSulaiman Thamer , Habib Mohamed , Awad Engy A. , Morsi Islam , Herbold John R. 
Published: January 2021

AbstractBackgroundThe COVID-19 toll of cases and deaths followed an uneven pattern across the world. The literature has partly explained the observed discrepancy between the different countries by country-specific and systemic patterns worldwide. In this study, we propose an additional explanation that the magnitude of COVID-19 toll reported to the WHO could be influenced by the level of free speech and Democracy in the reporting countries.MethodsWe constructed a longitudinal dataset including the daily COVID-19 count of cases and deaths worldwide and each country’s respective score on the Freedom in the World index. We applied two Generalized Estimating Equation models to investigate if a country’s reported toll count of COVID-19 cases and deaths is related to that country’s freedom level. We controlled for factors identified in the current literature to affect the pandemic’s spread.ResultsA country’s score on the Freedom In the World Index was associated with its reported COVID-19 cases count (57028.43, 95% CI 985.3619 - 113071.5, P= 0.0461) and deaths count (3473.273, 95% CI1217.12-5729.42, P=.002). Also, despite having almost equal shares of the world’s population, countries at the bottom category of the Freedom index reported 21% and 11% of the COVID-19 toll cases and death counts reported by countries of highest scores on the index, respectively.ConclusionsThe known magnitude of the COVID-19 pandemic’s morbidity and mortality appears to be as transparent as the reporting countries uphold free speech and Democracy. This pattern could potentially misguide international aid and global vaccine distribution plans.
A Scoping Review of the Experience of Implementing Population Testing for SARS-CoV-2
Authors: Foster Clare R , Campbell Fiona , Blank Lindsay , Cantrell Anna , Black Michelle , Lee Andrew C K 
Published: January 2021

AbstractBackgroundThe SARS-CoV-2 pandemic has led to the swift introduction of population testing programmes in many countries across the world, using testing modalities such as drive-through, walk-through, mobile and home visiting programmes. Here, we provide an overview of the literature describing the experience of implementing population testing for SARS-CoV-2.MethodsWe conducted a scoping review using Embase, Medline and the Cochrane Library in addition to a grey literature search. We identified indicators relevant to process, quality and resource outcomes related to each testing modality.Results2,999 titles were identified from the academic literature and the grey literature search, of which 22 were relevant. Most studies were from the USA and the Republic of Korea. Drive-through testing centres were the most common testing modality evaluated and these provided a rapid method of testing whilst minimising resource use.ConclusionsThe evidence base for population testing lacks high quality studies, however, the literature provides evaluations of the advantages and limitations of different testing modalities. There is a need for robust evidence in this area to ensure that testing is deployed in a safe and effective manner in response to the Covid-19 pandemic.
Seroprevalence of Chagas in urban and rural indigenous populations of the south of Gran Chaco
Authors: Colussi Carlina , Stafuza Mariana , Nepote Marcelo , Mendicino Diego 
Published: January 2021

AbstractBackground & objectivesIn Latin America, Chagas disease is endemic, with high prevalence in rural indigenous communities and increasing prevalence in urban areas due to migration from rural areas with active vector transmission. The objective of the work was to assess differences in the prevalence of Chagas disease in urban and rural moqoit communities of the south of Gran Chaco, Santa Fe province, Argentina.MethodsA seroprevalence study was conducted in six moqoit populations. Belonging to an urban community was considered as an exposure variable, whereas seropositivity for Chagas disease was considered as an outcome variableResultsThe results showed that 9.26% of the 702 volunteers evaluated and 3.50% of women of childbearing potential were seropositive. The prevalence of Chagas disease in urban communities was 6.41 times higher than in rural communities.Interpretation & conclusionsThe seroprevalence found in the moqoit community is higher than that estimated for the general population of the same region, with greater impact in the urban area than in the rural area. The decline of vector transmission in the rural area could be related to the conservation of ancestral practices and the expansion of the agricultural model.
Labeling self-tracked menstrual health records with hidden semi-Markov models
Authors: Symul Laura , Holmes Susan 
Published: January 2021

AbstractGlobally, millions of women track their menstrual cycle and fertility via smartphone-based health apps, generating multivariate time series with frequent missing data. To leverage data from self-tracking tools in epidemiological studies on fertility or the menstrual cycle’s effects on diseases and symptoms, it is critical to have methods for identifying reproductive events, e.g. ovulation, pregnancy losses or births. We present two coupled hidden semi-Markov models that adapt to changes in tracking behavior, explicitly capture variable– and state– dependent missingness, allow for variables of different type, and quantify uncertainty. The accuracy on synthetic data reaches 98% with no missing data, 90% with realistic missingness, and 94% accuracy on our partially labeled real-world time series. Our method also accurately predicts cycle length by learning user characteristics. It is publicly available (HiddenSemiMarkov R package) and transferable to any health time series, including self-reported symptoms and occasional tests.
National interest may require distributing COVID-19 vaccines to other countries
Authors: Rotesi Tiziano , Pin Paolo , Cucciniello Maria , Malik Amyn A. , Paintsil Elliott E. , Bokemper Scott E. , Willebrand Kathryn , Huber Gregory A. , Melegaro Alessia , Omer Saad B. 
Published: January 2021

AbstractAs the clinical trials for COVID-19 vaccine progress, understanding how to distribute the initially scarce doses is of paramount importance and a quantitative analysis of the trade-offs involved in domestic-only versus cooperative distribution is still missing. In this study we use a network Susceptible-Infected-Removed (SIR) model to show under which circumstances it is in a country’s self-interest to ensure other countries can also obtain a COVID-19 vaccine rather than focusing only on vaccination of their own residents. In particular, we focus our analysis on the US’s decision and estimate the internal burden of COVID-19 disease under different scenarios about vaccine cooperation. We show that in scenarios in which the US has reached the threshold for domestic herd immunity, the US may find it optimal to donate doses to other countries with lower vaccination coverage, as this would allow for a sharp reduction in the inflow of infected individuals from abroad.
The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants
Authors: Bradshaw William J. , Huggins Jonathan H. , Lloyd Alun L. , Esvelt Kevin M. 
Published: January 2021

AbstractThe SARS-CoV-2 variant B.1.1.7 reportedly exhibits substantially higher transmission than the ancestral strain and may generate a major surge of cases before vaccines become widely available, while the P.1 and B.1.351 variants may be equally transmissible and also resist vaccines. All three variants can be sensitively detected by RT-PCR due to an otherwise rare del11288-11296 mutation in orf1ab; B.1.1.7 can also be detected using the common TaqPath kit. Testing, contact tracing, and isolation programs overwhelmed by SARS-CoV-2 could slow the spread of the new variants, which are still outnumbered by tracers in most countries. However, past failures and high rates of mistrust may lead health agencies to conclude that tracing is futile, dissuading them from redirecting existing tracers to focus on the new variants. Here we apply a branching-process model to estimate the effectiveness of implementing a variant-focused testing, contact tracing, and isolation strategy with realistic levels of performance. Our model indicates that bidirectional contact tracing can substantially slow the spread of SARS-CoV-2 variants even in regions where a large fraction of the population refuses to cooperate with contact tracers or to abide by quarantine and isolation requests.
Increased mortality associated with uncontrolled diabetes mellitus in patients with Pulmonary Cryptococcosis — a single U.S. cohort study
Authors: Archuleta Solana , Gharamti Amal A. , Sillau Stefan , Castellanos Paula , Chadalawada Sindhu , Mundo William , Bandali Mehdi , Oñate Jose , Martínez Ernesto , Chastain Daniel , DeSanto Kristen , Shapiro Leland , Schwartz Ilan S. , Franco-Paredes Carlos , Henao-Martínez Andrés F. 
Published: January 2021

AbstractBackgroundDiabetes mellitus is an established risk factor for bacterial infections, but its role in Cryptococcosis is unclear. The study aimed to determine whether uncontrolled diabetes (HbA1c >7%) was an independent risk factor for mortality in cryptococcosis.MethodsA retrospective case-control study partially matched by age and gender was performed in patients tested forCryptococcusinfection at the University of Colorado Hospital from 2000-2019. A multivariable logistic regression model was used to identify mortality predictors. Cox proportional hazard model was used for survival analysis.ResultsWe identified 96 cases of Cryptococcosis and 125 controls. Among cases, cryptococcal meningitis (49.0%) and pneumonia (36.5%) constituted most infections. Cases with pulmonary cryptococcosis had a higher mortality at 10 weeks (50% vs 7%, p=0.006) and one year (66.7% vs 13.8%, p=0.005). Unadjusted Cox proportional hazard model found an increased rate of death for uncontrolled diabetes at 10-weeks (hazard ratio 8.4, CI: 1.4-50.8, p=0.02), and 1-year (hazard ratio 7.0, CI: 1.7-28.4, p=0.007) among pulmonary cryptococcosis cases. Multivariable analysis showed a significantly increased odds of 10-weeks (OR=4.3, CI: 1.1-16.5, p=0.035) and one-year (OR=5.9, CI: 2.2-15.8, p=0.014) mortality for uncontrolled diabetes among pulmonary cryptococcosis cases. After adjustment for gender, age, and case/control, for every 1% increase in HbA1c levels, the odds of pulmonary cryptococcosis mortality at one-year increased by 11% (OR = 1.6, CI 95%: 1.1-2.3, p= 0.006).ConclusionUncontrolled diabetes is associated with worse outcomes in pulmonary cryptococcosis, including a 4-fold and 6-fold increased odds of death at 10-weeks and 1-year, respectively. Glucose control interventions should be explored to improve clinical outcomes in patients with pulmonary cryptococcosis.
ADAM10- and presenilin 1/γ-secretase-dependent cleavage of PTPRT mitigates neurodegeneration of Alzheimer’s disease
Authors: Liu Siling , Zhang Zhongyu , Li Lianwei , Yao Li , Ma Zhanshan , Li Jiali 
Published: January 2021

AbstractPTPRT (receptor-type tyrosine-protein phosphatase T), as a brain-specific type 1 transmembrane protein, plays an important function in neurodevelopment and synapse formation. However, whether PTPRT-dependent signaling is involved in Alzheimer’s disease (AD) remains elusive. Here, we identified that PTPRT intracellular domain (PICD), which was released from ADAM10- and presenilin 1-/γ-secretase-dependent cleavage of PTPRT, efficiently translocated to the nucleus via a conserved nuclear localization signal. Inhibition of nuclear localization of PICD via the mutation of its nuclear localization signal (NLS) leads to accumulation of phosphorylated signal transducer and activator of transcription 3 (pSTAT3), which is a substrate of PTPRT and eventually resulted in neuronal cell death. Consistently, RNA sequencing reveals that expression of the PICD alone can profoundly alter the expression of genes associated with synapse function and dephosphorylation, phosphatase and cell adhesion. Unexpectedly, the downregulated levels ofPtprtmRNA and protein were found in both human and mouse AD brains. Finally, overexpression of PICD alone not only significantly decreases the level of phosph-STAT3Y705and Aβ deposition in the hippocampus of APP/PS1 mice, but also improves synaptic function and behavioral deficits in APP/PS1 mice. Our findings suggest that a novel role of the ADAM 10- and presenilin 1-/γ-secretase-dependent cleavage of PTPRT in the events can mitigate neurodegeneration of AD and moderate Alzheimer’s pathogenesis.
VeloSim: Simulating single cell gene-expression and RNA velocity
Authors: Zhang Ziqi , Zhang Xiuwei 
Published: January 2021

ABSTRACTThe availability of high throughput single-cell RNA-Sequencing data allows researchers to study the molecular mechanisms that drive the temporal dynamics of cells during differentiation or development. Recent computational methods that build upon single-cell sequencing technology, such as trajectory inference or RNA-velocity estimation, provide a way for researchers to analyze the state of each cell during a continuous dynamic process. However, with the surge of such computational methods, there is still a lack of simulators that can model the cell temporal dynamics, and provide ground truth data to benchmark the computational methods.Hereby we presentVeloSim, a simulation software that can simulate the gene-expression kinetics in cells along continuous trajectories.VeloSimis able to take any trajectory structure composed of basic elements including “linear” and “cycle” as input, and outputs unspliced mRNA count matrix, spliced mRNA count matrix, cell pseudo-time and true RNA velocity of the cells. We demonstrate howVeloSimcan be used to benchmark trajectory inference and RNA-velocity estimation methods with different amounts of biological and technical variation within the datasets.VeloSimis implemented into an R package available athttps://github.com/PeterZZQ/VeloSim.
Cutibacterium acnesclonal complexes display various growth rates in blood-culture bottles used for diagnosing orthopedic device-related infections
Authors: Sayed Faten El , Camernik Petra , Roux Anne-Laure , Papst Lea , Bauer Thomas , Nkam Lionelle , Sivadon-Tardy Valérie , Noussair Latifa , Herrmann Jean-Louis , Gaillard Jean-Louis , Jeverica Samo , Rottman Martin 
Published: January 2021

ABSTRACTBlood-culture bottles (BCBs) are widely used to improve the diagnosis of orthopedic device-related infections. Data is scarce on the growth ofCutibacterium acnesand its genotypes in BCBs under real-life clinical conditions.We studied 39 cases of revision arthroplasty for which at least one intraoperative sample yielded a pureC. acnesculture from anaerobic BCBs (BD Bactec Lytic/10 Anaerobic/F [Lytic Ana]) and/or solid media. Genotyping ofC. acnesisolates from the 39 cases allowed: i) the identification of 49 non-redundant isolates belonging to four clonal complexes (CCs): CC18, CC28, CC36, and CC53 and ii) the determination of infectant and contaminant strains. Under real-life clinical conditions, Lytic Ana alone was more often positive for contaminants than infectant strains (18/36 [50%]versus2/13 [15.4%]; p = 0.047). The time to detection (TTD) values in Lytic Ana were shorter for CC53 than other CCs (mean [SD] TTD: 77 [15]versus165 [71] hours; p = 0.02). CC53 was confirmed to grow faster than other CCs by studying an enlarged panel of 70 genotypedC. acnesstrains inoculatedin vitrointo Lytic Ana vials (mean [SD] TTD: 73 [13]versus122 [50] hours; p < 0.001).The use of Lytic Ana BCBs in orthopedics increases the recovery rate ofC. acnesbut leads to the isolation of proportionally more contaminants than true infectant strains. TTD values are much shorter for CC53 strains, irrespective of their being infectant or contaminant. TTD does not solely reflect the bacterial load of samples but also clonal complex-related traits.
Changes in the Health of Adolescent Athletes: A Comparison of Health Measures Collected Before and During the CoVID-19 Pandemic
Authors: McGuine Timothy A. , Biese Kevin , Hetzel Scott J. , Petrovska Labina , Kliethermes Stephanie , Reardon Claudia L. , Bell David R. , Brooks M. Alison , Watson Andrew M. 
Published: January 2021

ABSTRACTContextIn the spring of 2020, schools closed to in-person teaching and sports were cancelled to control the transmission of CoVID-19. The changes that took place to the physical and mental health among young athletes during this time remain unknown, however.ObjectiveIdentify changes in the health (mental health, physical activity and quality of life) of athletes that occurred during the CoVID-19 pandemic.DesignCross sectional study.SettingSample recruited via social media.Patients or Other Participants3243 Wisconsin adolescent athletes (age=16.2±1.2 yrs., female=58% female) completed an online survey in May 2020 (DuringCoVID-19). Health measures for this cohort were compared with previously reported data for Wisconsin adolescent athletes (n=5231, age=15.7±1.2, 47% female) collected in 2016–2018 (PreCoVID-19).Main Outcome Measure(s)Demographic information included: sex, grade and sports played. Health assessments included the Patient Health Questionnaire-9 Item (PHQ-9) to identify depression symptoms, the Pediatric Functional Activity Brief Scale (PFABS) for physical activity, and the Pediatric Quality of Life Inventory 4.0 (PedsQL) for health related quality of life (HRQoL). Univariable comparisons of these variables between groups were made via t-tests or chi-square tests. Means and 95% confidence intervals (CI) for each group were estimated by survey weighted ANOVA models.RESULTSCompared to PreCoVID-19, a larger proportion of the During-CoVID-19 participants reported rates of moderate to severe levels of depression (9.7% vs 32.9%, p<0.001). During-CoVID-19 participants reported 50% lower (worse) PFABS scores (mean:12.2 [95%CI: 11.9, 12.5] vs 24.7 [24.5, 24.9] p<0.001) and lower (worse) PedsQL total scores compared to the PreCoVID-19 participants (78.4 [78.0, 78.8] vs. 90.9 [90.5, 91.3] p<0.001).CONCLUSIONSDuring the CoVID-19 pandemic, adolescent athletes reported increased symptoms of depression, decreased physical activity and decreased quality of life compared to adolescent athletes in previous years.Key pointsAdolescent athletes during CoVID-19 were three times more likely to report moderate to severe symptoms of depression compared to data collected prior to CoVID-19.Adolescent athletes during CoVID-19 reported significantly lower physical activity and quality of life scores compared to high school athletes prior to the CoVID-19 pandemicPost CoVID-19 policies should be implemented to improve the health of adolescent athletes in the US.