bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy and performance of the WHO 2015 and WHO 2019 HIV testing strategies across epidemic settings
Authors: Eaton Jeffrey W , Sands Anita , Barr-DiChiara Magdalena , Jamil Muhammad S , Baggaley Rachel , Tippett Barr Beth A , Kalua Thokozani , Jahn Andreas , Maheu-Giroux Mathieu , Johnson Cheryl C 
Published: April 2021

AbstractBackgroundWHO 2019 HIV testing guidelines recommended a standard HIV testing strategy consisting of three consecutively HIV-reactive test results on serology assays to diagnose HIV infection. National HIV programmes in high prevalence settings currently using the strategy consisting of only two consecutive HIV-reactive tests should consider when to implement the new guideline recommendations.Methods and FindingsWe implemented a probability model to simulate outcomes of WHO 2019 and the two strategies recommended by WHO 2015 guidelines on HIV testing services. Each assay in the strategy was assumed independently 99% sensitivity and 98% specificity, the minimal thresholds required for WHO prequalification. For each strategy and positivity ranging 20% to 0.2%, we calculated the number of false-negative, false-positive, and inconclusive results; positive and negative predictive value (PPV, NPV); number of each assay used, and testing programme costs. We found that the NPV was above 99.9% for all scenarios modelled. Under the WHO 2015 two-test strategy, the PPV was below the 99% target threshold when positivity fell below 5%. For the WHO 2019 strategy, the PPV was above 99% for all positivity levels. The number reported ‘inconclusive’ was higher under the WHO 2019 strategy. Implementing the WHO 2019 testing strategy in Malawi, would require around 89,000 A3 tests in 2021, compared to 175,000 A2 tests and over 4.5 million A1 tests per year. The incremental cost of the WHO 2019 strategy was less than 2% in 2021 and declined to 0.9% in 2025.ConclusionsAs positivity among persons testing for HIV reduces below 5% in nearly all settings, implementation of the WHO 2019 testing strategy will ensure that positive predictive value remains above the 99% target threshold, averting misdiagnoses and ART initiations among HIV uninfected people. The incremental cost of implementing the WHO 2019 HIV testing strategy compared to the two-test strategy is negligible because the third assay accounts for a small and diminishing share of total HIV tests.
Replication of LZTFL1 gene region as a susceptibility locus for COVID-19 in Latvian population
Authors: Rescenko Raimonds , Peculis Raitis , Ustinova Monta , Ansone Laura , Terentjeva Anna , Litvina Helena Daiga , Birzniece Liga , Megnis Kaspars , Kolesova Oksana , Rozentale Baiba , Viksna Ludmila , Rovite Vita , Klovins Janis 
Published: April 2021

AbstractThe severity of COVID-19 disease is partly determined by host genetic factors that have been reported by GWAS. We evaluated nine previously reported genome-wide significant associations regardless of the disease severity in a representative sample from the population of Latvia. Our cohort consisted of 475 SARS-CoV-2 positive cases, from which 146 were hospitalized individuals and 2217 controls. We found three variants from Neanderthal introgression event at the 3p21.31 region to be significantly associated with increased risk of SARS-CoV-2 infection and hospitalization status. The strongest association was displayed by rs71325088 with Bonferroni adjusted P=0.007, OR=1.46 [95% CI 1.17-1.81]. We performed fine-mapping by exploring 1 Mb region at 3p21.31 locus and identified 9 SNPs with even lower p-values with the strongest association estimated for rs2191031 P=5e-05, OR = 1.40[CI 95% 1.19-1.64] located in the LZTFL1. We show clear replication of 3p.21.31 locus in an independent cohort which favors further functional investigation of leading variants.
Smoking and COVID-19: A two-sample Mendelian randomization study
Authors: Zheng Bing-Kun , Li Na 
Published: April 2021

AbstractEvidence from observational studies suggested that smokers are at increased risk of coronavirus disease 2019 (COVID-19). We aimed to assess the causal effect of smoking on risk for COVID-19 susceptibility and severity using two-sample Mendelian randomization method. Smoking-associated variants were selected as instrument variables from two largest genetic studies. The latest summary data of COVID-19 that shared on Jan 18, 2021 by the COVID-19 Host Genetics Initiative was used. The present Mendelian randomization study provided genetic evidence that smoking was a causal risk factor for COVID-19 susceptibility and severity. In addition, there may be a dose-effect relationship between smoking and COVID-19 severity.
Risk quantification for SARS-CoV-2 infection through airborne transmission in university settings
Authors: Ambatipudi Mythri , Gonzalez Paola Carrillo , Tasnim Kazi , Daigle Jordan T. , Kulyk Taisa , Jeffreys Nicholas , Sule Nishant , Trevino Rafael , He Emily M. , Mooney David J. , Koh Esther 
Published: April 2021

ABSTRACTThe COVID-19 pandemic has significantly impacted learning as many institutions switched to remote or hybrid instruction. An in-depth assessment of the risk of infection that takes into account environmental setting and mitigation strategies is needed to make safe and informed decisions regarding reopening university spaces. A quantitative model of infection probability that accounts for space-specific parameters is presented to enable assessment of the risk in reopening university spaces at given densities. The model uses local positivity rate, room capacity, mask filtration efficiency, air exchange rate, room volume, and time spent in the space as parameters to calculate infection probabilities in teaching spaces, dining halls, dorms, and shared bathrooms. The model readily calculates infection probabilities in various university spaces, with mask filtration efficiency and air exchange rate being among the dominant variables. When applied to university spaces, this model demonstrated that, under specific conditions that are feasible to implement, in-person classes could be held in large lecture halls with an infection risk over the semester < 1%. Meal pick-ups from dining halls and the use of shared bathrooms in residential dormitories among small groups of students could also be accomplished with low risk. The results of applying this model to spaces at Harvard University (Cambridge and Allston campuses) and Stanford University are reported. Finally, a user-friendly web application was developed using this model to calculate infection probability following input of space-specific variables. The successful development of a quantitative model and its implementation through a web application may facilitate accurate assessments of infection risk in university spaces. In light of the impact of the COVID-19 pandemic on universities, this tool could provide crucial insight to students, faculty, and university officials in making informed decisions.
Racial Disparities in the SOFA Score Among Patients Hospitalized with COVID-19
Authors: Tolchin Benjamin , Oladele Carol , Galusha Deron , Kashyap Nitu , Showstark Mary , Bonito Jennifer , Salazar Michelle C. , Herbst Jennifer L. , Martino Steve , Kim Nancy , Nash Katherine A. , Nguemeni Tiako Max Jordan , Roy Shireen , Jubanyik Karen 
Published: April 2021

AbstractBackgroundSequential Organ Failure Assessment (SOFA) score predicts probability of in-hospital mortality. Many crisis standards of care use SOFA score to allocate medical resources during the COVID-19 pandemic.Research QuestionAre SOFA scores disproportionately elevated among Non-Hispanic Black and Hispanic patients hospitalized with COVID-19, compared to Non-Hispanic White patients?Study Design and MethodsRetrospective cohort study conducted in Yale New Haven Health System, including 5 hospitals with total of 2681 beds. Study population drawn from consecutive patients aged ≥18 admitted with COVID-19 from March 29thto August 1st, 2020. Patients excluded from the analysis if not their first admission with COVID-19, if they did not have SOFA score recorded within 24 hours of admission, if race and ethnicity data were not Non-Hispanic Black, Non-Hispanic White, or Hispanic, or if they had other missing data. The primary outcomes was SOFA score, with peak score within 24 hours of admission dichotomized as <6 or ≥6.ResultsOf 2982 patients admitted with COVID-19, 2320 met inclusion criteria and were analyzed, of whom 1058 (45.6%) were Non-Hispanic White, 645 (27.8%) were Hispanic, and 617 (26.6%) were Non-Hispanic Black. Median age was 65.0 and 1226 (52.8%) were female. In univariate logistic screen and in full multivariate model, Non-Hispanic Black patients but not Hispanic patients had greater odds of an elevated SOFA score ≥6 when compared to Non-Hispanic White patients (OR 1.49, 95%CI 1.11-1.99).InterpretationCrisis standards of care utilizing the SOFA score to allocate medical resources would be more likely to deny these resources to Non-Hispanic Black patients.
Global-scale analysis and longitudinal assessment of COVID-19 incidence in the first six months
Authors: Ghosh Sujoy , Roy Saikat Sinha 
Published: April 2021

AbstractStudies examining factors responsible for COVID-19 incidence have mostly focused at the national or sub-national level. Here we undertake an analysis of COVID-19 cases at the global scale to identify key factors associated with disease incidence. A regression modeling framework was used to identify key variables associated with COVID-19 incidence, and to assess longitudinal trends in reported incidence at the country-level. New COVID-19 case dynamics in response to lockdowns was characterized via cluster analysis. Eleven variables were found to be independently associated with COVID-19 infections (p<1e-05) and a 4-variable model adequately explained global variations in COVID-19 cases (p<0.01). COVID-19 case trajectories for most countries followed the log-logistic curve. Six predominant country clusters summarized the differences in individual country’s response to lockdowns. Globally, economic and meteorological factors are important determinants of COVID-19 incidence. Analysis of longitudinal trends and lockdown effects on COVID-19 caseloads further highlights important nuances in country-specific responses to the pandemic. These findings on the first six months of the pandemic has important implications for additional phases of the disease currently underway in many countries.
Increasing concentration of COVID-19 by socioeconomic determinants and geography in Toronto, Canada: an observational study
Authors: Mishra Sharmistha , Ma Huiting , Moloney Gary , Yiu Kristy CY , Darvin Dariya , Landsman David , Kwong Jeffrey C. , Calzavara Andrew , Straus Sharon , Chan Adrienne K , Gournis Effie , Rilkoff Heather , Xia Yiqing , Katz Alan , Williamson Tyler , Malikov Kamil , Kustra Rafal , Maheu-Giroux Mathieu , Sander Beate , Baral Stefan D 
Published: April 2021

ABSTRACTBackgroundInequities in the burden of COVID-19 observed across Canada suggest heterogeneity within community transmission.ObjectivesTo quantify the magnitude of heterogeneity in the wider community (outside of long-term care homes) in Toronto, Canada and assess how the magnitude in concentration evolved over time (January 21 to November 21, 2020).DesignRetrospective, population-based observational study using surveillance data from Ontario’s Case and Contact Management system.SettingToronto, Canada.ParticipantsLaboratory-confirmed cases of COVID-19 (N=33,992).MeasurementsWe generated epidemic curves by SDOH and crude Lorenz curves by neighbourhoods to visualize inequities in the distribution of COVID-19 cases by social determinants of health (SDOH) and estimated the crude Gini coefficient. We examined the correlation between SDOH using Pearson correlation coefficients.ResultsThe Gini coefficient of cumulative cases by population size was 0.41 (95% CI: 0.36-0.47) and were estimated for: household income (0.20, 95%CI: 0.14-0.28); visible minority (0.21, 95%CI: 0.16-0.28); recent immigration (0.12, 95%CI: 0.09-0.16); suitable housing (0.21, 95%CI: 0.14-0.30); multi-generational households (0.19, 95%CI: 0.15-0.23); and essential workers (0.28, 95% CI: 0.23-0.34). Most SDOH were highly correlated.Locally acquired cases were concentrated in higher income neighbourhoods in the early phase of the epidemic, and then concentrated in lower income neighbourhoods. Mirroring the trajectory of epidemic curves by income, the Lorenz curve shifted over time from below to above the line of equality with a similar pattern across SDOH.LimitationsStudy relied on area-based measures of the SDOH and individual case counts of COVID-19. We cannot infer concentration of cases by specific occupational exposures given limitation to broad occupational categories.ConclusionCOVID-19 is increasingly concentrated by SDOH given socioeconomic inequities and structural racism.Primary Funding SourceCanadian Institutes of Health Research.
The association of ABO blood group with the asymptomatic COVID-19 cases in India
Authors: Singh Prajjval Pratap , Srivastava Abhishek K , Upadhyay Sudhir K , Singh Ashish , Gupta Pranav , Maurya Sanjeev , Upadhyay Shashank , Pandey Rudra Kumar , Srivastava Anshika , Dev Priya , Singh Vanya , Mishra Rahul , Shukla Manoj Kumar , Chaubey Govind , Kumar Pradeep , Rai Vandana , Tripathi Yamini B , Pathak Abhishek , Mishra Vijay Nath , Mallick Chandana Basu , Shrivastava Pankaj , Chaubey Gyaneshwer 
Published: April 2021

AbstractThe COVID-19 pandemic has resulted several waves of infection in many countries worldwide. The large variations in case fatality ratio among different geographical regions suggests that the human susceptibility against this virus varies substantially. Several studies from different parts of the world showed a significant association of ABO blood group and COVID-19 susceptibility. It was shown that individuals with blood group O are at the lower risk of coronavirus infection. To establish the association of ABO blood group in SARS-CoV-2 susceptibility, we for the first time analysed SARS-CoV-2 neutralising antibodies as well as blood groups among 509 random individuals from three major districts of Eastern Uttar Pradesh region of India.. Interestingly, we found neutralising antibodies in significantly higher percentage of people with blood group AB (0.36) followed by B (0.31), A (0.22) and lowest in people with blood group O (0.11). This indicates that people with blood group AB are at comparatively higher risk of infection than other blood groups. Further, in line to previous reports we too observed that people with blood group O have significantly decreased risk of SARS-CoV-2 infection. Thus, among the asymptomatic SARS-CoV-2 infected individuals with blood group AB has highest, whilst blood group O has lowest risk of infection.
A randomised control trial of the effects of home-based online attention training and working memory training on cognition and everyday function in a community stroke sample
Authors: Peers Polly V. , Punton Sarah F. , Murphy Fionnuala C. , Watson Peter , Bateman Andrew , Duncan John , Astle Duncan E. , Hampshire Adam , Manly Tom 
Published: April 2021

AbstractCognitive difficulties are common following stroke and can have widespread impacts on everyday functioning. Technological advances offer the possibility of individualised cognitive training for patients at home, potentially providing a low-cost, low-intensity adjunct to rehabilitation services. Using this approach, we have previously demonstrated post-training improvements in attention and everyday functioning in fronto-parietal stroke patients. Here we examine whether these benefits are observed more broadly in a community stroke sample. Patients were randomised to either 4 weeks of online adaptive attention training (SAT), working memory training (WMT) or waitlist (WL). Cognitive and everyday function measures were collected before and after intervention, and after 3months. During training, weekly measures of patients’ subjective functioning were collected. The training was well received and compliance good. No differences in standardised cognitive tests were observed for either intervention relative to controls. However, on patient reported outcomes, SAT participants showed greater levels of improvement in everyday functioning than WMT or WL participants. In line with our previous work, everyday functioning improvements were greatest for patients with spatial impairments and those who received SAT training. Whether attention training can be recommended for stroke survivors depends on whether cognitive test performance or everyday functioning is considered more relevant.
DRUL for School: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2
Authors: Frank Mayu O. , Blachere Nathalie E. , Parveen Salina , Hacisuleyman Ezgi , Fak John , Luna Joseph M. , Michailidis Eleftherios , Wright Samara , Stark Pamela , Campbell Ann , Foo Ashley , Sakmar Thomas P. , Huffman Virginia , Bergh Marissa , Goldfarb Audrey , Mansisidor Andres , Patriotis Agata L. , Palmquist Karl H. , Poulton Nicolas , Leicher Rachel , Vargas César D. M. , Duba Irene , Hurley Arlene , Colagreco Joseph , Pagane Nicole , Orange Dana E. , Mora Kevin , Rakeman Jennifer L. , Fowler Randall C. , Fernandes Helen , Lamendola-Essel Michelle F. , Didkovsky Nick , Silvera Leopolda , Masci Joseph , Allen Machelle , Rice Charles M. , Darnell Robert B. 
Published: April 2021

AbstractTo address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 µl saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/µl in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75×106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.
An ecological niche model to predict the geographic distribution of Haemagogus janthinomys, Dyar, 1921 the yellow fever and Mayaro virus vector, in South America
Authors: Celone Michael , Pecor David , Potter Alexander , Richardson Alec , Dunford James , Pollet Simon 
Published: April 2021

AbstractYellow fever virus (YFV) has a long history of impacting human health in South America. Mayaro virus (MAYV) is an emerging arbovirus of public health concern in the Neotropics and its full impact is yet unknown. Both YFV and MAYV are primarily maintained via a sylvatic transmission cycle but can be opportunistically transmitted to humans by the bites of infected forest dwelling Haemagogus janthinomys Dyar, 1921. To better understand the potential risk of YFV and MAYV transmission to humans, a more detailed understanding of this vector species’ distribution is critical. This study compiled a comprehensive database of 170 unique Hg. janthinomys collection sites retrieved from the published literature, digitized museum specimens and publicly accessible mosquito surveillance data. Covariate analysis was performed to optimize a selection of environmental (topographic and bioclimatic) variables associated with predicting habitat suitability, and species distributions modelled across South America using a maximum entropy (MaxEnt) approach. Our results indicate that suitable habitat for Hg. janthinomys can be found across forested regions of South America including the Atlantic forests and interior Amazon.Author SummaryMayaro virus is a neglected tropical disease and there is insufficient evidence to define its geographic range. The mosquito Haemagogus janthinomys is a primary vector of Mayaro and its distribution is largely unknown at a sub-country scale. Building compendiums of collection data and creating ecological niche models provides a more precise estimation vector species potential habitat. Our dataset stands as one of the most expansive existing for collection data of this species combining data published in literature, publicly available data repositories and digitized museum specimen records. Comparing results of niche models with near real time environmental data can give even better predictions of areas where Mayaro virus exposure could occur. The methods and results of this study can be replicated for any disease/vector of interest so long as there is data discoverable through the scientific literature, public repositories, or other civilian and governmental agencies willing to share.
Feedback-related potentials and oscillations during trial and error learning in Parkinson’s disease
Authors: Viñales Laura , Procyk Emmanuel , Quilodran René 
Published: April 2021

AbstractElectrophysiological markers of performance monitoring are thought to reflect functioning of dedicated neural networks and neuromodulatory systems. Whether and how these markers are altered in neurological diseases and whether they can reflect particular cognitive deficits remains to be confirmed. Here we first tested whether the frontal medial feedback-related potential, evoked during a trial and error learning task, is changed in early Parkinson’s disease patients compared to control subjects. The potential was not changed in amplitude and discriminated negative and positive feedback as in controls. Feedback-related markers in Parkinson’s patients also appeared in time-frequency analyses, unaltered in theta (3-7 Hz) band but reduced in beta (20-30 Hz) oscillations for positive feedback. Beta oscillations power appeared to be dramatically globally reduced during the task. Overall, our results show that Beta oscillation markers of performance monitoring captured by EEG are selectively altered in Parkinson’s disease patients, and that they are accompanied by changes in task-related oscillatory dynamics.Significance StatementFrontal neural activity evoked by outcomes reveal the functioning of neural systems devoted to flexible behaviours. Modulations of such activity in Parkinson’s disease (PD) patients could reflect specific alterations of neural systems and cognitive processing. The goal is to evaluate whether such activity can serve as markers of the disease. Here, using EEG and a trial and error learning protocol, we show that mid-frontal midline performance feedback-related potentials for different types of feedback were similar in controls and early diagnosed PD patients. However, task-related oscillations revealed alterations in the beta range accompanied by more global beta activity alteration in PD compared to controls subjects. This study provides data relevant to the search for non-motor biomarkers in early stages of PD.