bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shedding of infectious SARS-CoV-2 from airways in hospitalized COVID-19 patients in relation to serum antibody responses
Authors: Glans Hedvig , Gredmark-Russ Sara , Olausson Mikaela , Falck-Jones Sara , Varnaite Renata , Christ Wanda , Maleki Kimia T. , Karlberg Maria Lind , Broddesson Sandra , Falck-Jones Ryan , Bell Max , Johansson Niclas , Färnert Anna , Smed-Sörensen Anna , Klingström Jonas , Bråve Andreas 
Published: September 2020

AbstractTo understand the risk of transmission of SARS-CoV-2 in hospitalized COVID-19 patients we simultaneously assessed the presence of SARS-CoV-2 RNA, live infectious virus in the airways, and virus-specific IgG and neutralizing antibodies in sera in 36 hospitalized COVID-19 patients. SARS-CoV-2 could be cultured from four patients, all with low or undetectable antibody response. Our data suggests that the level of SARS-CoV-2 antibodies may correlate to risk for shedding live SARS-CoV-2 virus in hospitalized COVID-19 patients.
Neural markers of suppression in impaired binocular vision
Authors: Lygo Freya A. , Richard Bruno , Wade Alex R. , Morland Antony B. , Hess Robert F. , Baker Daniel H. 
Published: September 2020

AbstractObjective/PurposeEven after conventional patching treatment, individuals with a history of amblyopia typically lack good stereo vision. This is often attributed to atypical suppression between the eyes, yet the specific mechanism is still unclear. Guided by computational models of binocular vision, we tested explicit predictions about how neural responses to contrast might differ in individuals with impaired binocular vision.DesignA 5 × 5 factorial repeated measures design was used, in which all participants completed a set of 25 conditions (stimuli of different contrasts shown to the left and right eyes).Participants25 individuals with a history of amblyopia, and 19 control participants with typical visual development, participated in the study.MethodsNeural responses to different combinations of contrast in the left and right eyes, were measured using both electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). Stimuli were sinusoidal gratings with a spatial frequency of 3c/deg, flickering at 4Hz. In the fMRI experiment, we also ran population receptive field and retinotopic mapping sequences, and a phase-encoded localiser stimulus, to identify voxels in primary visual cortex (V1) sensitive to the main stimulus.Main outcome measuresThe main outcome measures were the signal-to-noise ratio of the steady state visual evoked potential, and the fMRIβweights from a general linear model.ResultsNeural responses generally increased monotonically with stimulus contrast. When measured with EEG, responses were attenuated in the weaker eye, consistent with a fixed tonic suppression of that eye. When measured with fMRI, a low contrast stimulus in the weaker eye substantially reduced the response to a high contrast stimulus in the stronger eye. This effect was stronger than when the stimulus-eye pairings were reversed, consistent with unbalanced dynamic suppression between the eyes.ConclusionsMeasuring neural responses using different methods leads to different conclusions about visual differences in individuals with impaired binocular vision. Both of the atypical suppression effects may relate to binocular perceptual deficits, e.g. in stereopsis, and we anticipate that these measures could be informative for monitoring the progress of treatments aimed at recovering binocular vision.
Temporal Analysis of COVID-19 Peak Outbreak
Authors: Tewari Amit 
Published: September 2020

AbstractIntent of this research is to explore how mathematical models, specifically Susceptible-Infected-Removed (SIR) model, can be utilized to forecast peak outbreak timeline of COVID-19 epidemic amongst a population of interest starting from the date of first reported case. Till the time of this research, there was no effective and universally accepted vaccine to control transmission and spread of this infection. COVID-19 primarily spreads in population through respiratory droplets from an infected person’s cough and sneeze which infects people who are in proximity. COVID-19 is spreading contagiously across the world. If health policy makers and medical experts could get early and timely insights into when peak infection rate would occur after first reported case, they could plan and optimize medical personnel, ventilators supply, and other medical resources without over-taxing the infrastructure. The predictions may also help policymakers devise strategies to control the epidemic, potentially saving many lives. Thus, it can aid in critical decision-making process by providing actionable insights into COVID-19 outbreak by leveraging available data.
Seroprevalence and Correlates of SARS-CoV-2 Antibodies in Healthcare Workers in Chicago
Authors: Wilkins John T. , Gray Elizabeth L. , Wallia Amisha , Hirschhorn Lisa R. , Zembower Teresa R. , Ho Joyce , Kalume Naomi , Agbo Ojoma , Zhu Alex , Rasmussen-Torvik Laura J. , Khan Sadiya S. , Carnethon Mercedes , Huffman Mark , Evans Charlesnika T. 
Published: September 2020

AbstractBackgroundIdentifying factors associated with SARS-CoV-2 infection among healthcare workers (HCW)s may help health systems optimize SARS-CoV-2 infection control strategies. Methods: We conducted a cross-sectional analysis of baseline data from the Northwestern HCW SARS-CoV-2 Serology Cohort Study. The Abbott Architect Nucleocapsid IgG assay was used to determine seropositivity. Logistic regression models (unadjusted and adjusted for demographics and self-reported community exposure to COVID-19) were fit to quantify the associations between occupation group, healthcare delivery tasks, and community exposure and seropositive status.Results6,510 HCWs, including 1,794 nurses, and 904 non-patient facing administrators participated. The majority were women (79.6%), 74.9% were white, 9.7% were Asian, 7.3% were Hispanic and 3.1% were Black. The crude prevalence rate of seropositivity was 4.8% (95% confidence interval (CI): 4.6%-5.2%). Out-of-hospital exposure to COVID-19 occurred in 9.3% of HCWs and was strongly associated with seropositivity (OR=4.7, 95% CI: 3.5-6.4). When compared to administrators, nursing was the only occupation group with a significantly higher adjusted-odds (OR: 1.9, 95% CI: 1.3-2.9) of seropositivity. Exposure to COVID-19 patients was reported by 37.8% of participants and was associated with higher positivity than those not exposed (OR= 2.2, 95% CI: 1.6-3.0). Being exposed to patients receiving high-flow oxygen therapy, and hemodialysis also remained significantly associated with a 45% and 57% higher odds for seropositive status, respectively.ConclusionsExposure to COVID-19 patients, and longer duration patient therapies were each associated with higher risk for seropositive status; however, the community burden of COVID-19 remains a significant source of exposure to SARS CoV-2 infection among HCWs in Chicago.
Anakinra and Intravenous IgG versus Tocilizumab in the Treatment of COVID-19 Pneumonia
Authors: Zantah Massa , Castillo Eduardo Dominguez , Gangemi Andrew J. , Patel Maulin , Chowdhury Junad , Verga Steven , Abramian Osheen , Zheng Matthew , Lu Kevin , Lau Arthur , Levinson Justin , Zhao Hauquing , Criner Gerard J. , Caricchio Roberto ,   for the Temple University COVID-19 Research Group
Published: September 2020

AbstractBackgroundCOVID-19 can lead to acute respiratory failure and an exaggerated inflammatory response. Studies have suggested promising outcomes using monoclonal antibodies targeting IL-1β (Anakinra) or IL6 (Tocilizumab), however no head to head comparison was done between the two treatments. Herein, we report our experience in treating COVID-19 pneumonia associated with cytokine storm with either subcutaneous Anakinra given concomitantly with intravenous immunoglobulin (IVIG), or intravenous Tocilizumab.MethodsComprehensive clinical and laboratory data from patients with COVID-19 pneumonia admitted at our hospital between March and May 2020 were collected. Patients who received either Anakinra/ IVIG or Tocilizumab were selected. Baseline characteristics including oxygen therapy, respiratory status evaluation using ROX index, clinical assessment using NEWS score and laboratory data were collected. Outcomes included mortality, intubation, ICU admission and length of stay. In addition, we compared the change in ROX index, NEWS score and inflammatory markers at days 7 and 14 post initiation of therapy.Results84 consecutive patients who received either treatment (51 in the Anakinra/ IVIG group and 33 in the Tocilizumab group) were retrospectively studied. Baseline inflammatory markers were similar in both groups. There was no significant difference regarding to death (21.6% vs 15.2%, p 0.464), intubation (15.7% vs 24.2%, p 0.329), ICU need (57.1% vs 48.5%, p 0.475) or length of stay (13+9.6 vs 14.9+11.6, p 0.512) in the Anakinra/IVIG and Tocilizumab, respectively. Additionally, the rate of improvement in ROX index, NEWS score and inflammatory markers was similar in both groups at days 7 and 14. Furthermore, there was no difference in the incidence of superinfection in both groups.ConclusionTreating COVID-19 pneumonia associated with cytokine storm features with either subcutaneous Anakinra/IVIG or intravenous Tocilizumab is associated with improved clinical outcomes in most subjects. The choice of treatment does not appear to affect morbidity or mortality. Randomized controlled trials are needed to confirm our study findings.FundingNone.
Cohort profile: St. Michael’s Hospital Tuberculosis Database (SMH-TB), a retrospective cohort of electronic health record data and variables extracted using natural language processing
Authors: Landsman David , Abdelbasit Ahmed , Wang Christine , Guerzhoy Michael , Joshi Ujash , Mathew Shaun , Pou-Prom Chloe , Dai David , Pequegnat Victoria , Murray Joshua , Chokar Kamalprit , Banning Michaelia , Mamdani Muhammad , Mishra Sharmistha , Batt Jane 
Published: September 2020

AbstractBackgroundTuberculosis (TB) is a major cause of death worldwide. TB research draws heavily on clinical cohorts which can be generated using electronic health records (EHR), but granular information extracted from unstructured EHR data is limited. The St. Michael’s Hospital TB database (SMHTB) was established to address gaps in EHR-derived TB clinical cohorts and provide researchers and clinicians with detailed, granular data related to TB management and treatment.MethodsWe collected and validated multiple layers of EHR data from the TB outpatient clinic at St. Michael’s Hospital, Toronto, Ontario, Canada to generate the SMH-TB database. SMH-TB contains structured data directly from the EHR, and variables generated using natural language processing (NLP) by extracting relevant information from free-text within clinic, radiology, and other notes. NLP performance was assessed using recall, precision and F1 score averaged across variable labels. We present characteristics of the cohort population using binomial proportions and 95% confidence intervals (CI), with and without adjusting for NLP misclassification errors.ResultsSMH-TB currently contains retrospective patient data spanning 2011 to 2018, for a total of 3298 patients (N=3237 with at least 1 associated dictation). Performance of TB diagnosis and medication NLP rulesets surpasses 93% in recall, precision and F1 metrics, indicating good generalizability. We estimated 20% (95% CI: 18.4-21.2%) were diagnosed with active TB and 46% (95% CI: 43.8-47.2%) were diagnosed with latent TB. After adjusting for potential misclassification, the proportion of patients diagnosed with active and latent TB was 18% (95% CI: 16.8-19.7%) and 40% (95% CI: 37.8-41.6%) respectivelyConclusionSMH-TB is a unique database that includes a breadth of structured data derived from structured and unstructured EHR data. The data are available for a variety of research applications, such as clinical epidemiology, quality improvement and mathematical modelling studies.
Genetic variation in RCOR1 is associated with tinnitus in UK Biobank
Authors: Wells Helena R.R. , Zainul Abidin Fatin N. , Freidin Maxim B. , Williams Frances M.K. , Dawson Sally J. 
Published: September 2020

AbstractTinnitus is a prevalent condition in which perception of sound occurs without an external stimulus. It is often associated with pre-existing hearing loss or noise-induced damage to the auditory system. In some individuals it occurs frequently or even continuously and leads to considerable distress and difficulty sleeping. There is little knowledge of the molecular mechanisms involved in tinnitus which has hindered the development of treatments. Evidence suggests that tinnitus has a heritable component although previous genetic studies have not established specific risk factors. We performed a case-control genome-wide association study for self-reported tinnitus in 172,608 UK Biobank volunteers. Three variants in close proximity to the RCOR1 gene reached genome wide significance: rs4906228 (p=1.7E-08), rs4900545 (p=1.8E-08) and 14:103042287_CT_C (p=3.50E-08). RCOR1 encodes REST Corepressor 1, a component of a co-repressor complex involved in repressing neuronal gene expression in non-neuronal cells. Eleven other independent genetic loci reached a suggestive significance threshold of p<1E-06.
Characteristics of anti-SARS-CoV-2 antibodies in recovered COVID-19 subjects
Authors: Huynh Angela , Arnold Donald M. , Smith James W. , Moore Jane C. , Zhang Ali , Chagla Zain , Harvey Bart J. , Stacey Hannah D. , Ang Jann C. , Clare Rumi , Ivetic Nikola , Chetty Vasudhevan T. , Bowdish Dawn ME , Miller Matthew S. , Kelton John G. , Nazy Ishac 
Published: September 2020

AbstractCoronavirus Disease 2019 (COVID-19) is a global pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While detection of SARS-CoV-2 by polymerase chain reaction with reverse transcription (RT-PCR) is currently used to diagnose acute COVID-19 infection, serological assays are needed to study the humoral immune response to SARS-CoV-2. SARS-CoV-2 IgG/A/M antibodies against SARS-CoV-2 spike (S) protein and its receptor-binding domain (RBD) were characterized using an enzyme-linked immunosorbent assay (ELISA) and assessed for their ability to neutralize live SARS-CoV-2 virus in recovered subjects who were RT-PCR-positive (n=153), RT-PCR-negative (n=55), and control samples collected pre-COVID-19 (n=520). Anti-SARS-CoV-2 antibodies were detected in 90.9% of resolved subjects up to 180 days post-symptom onset. Anti-S protein and anti-RBD IgG titers correlated (r= 0.5157 and r = 0.6010, respectively) with viral neutralization. Of the RT-PCR-positive subjects, 22 (14.3%) did not have anti-SARS-CoV-2 antibodies; and of those, 17 had RT-PCR cycle threshold (Ct) values >27, raising the possibility that these indeterminate results are from individuals who were not infected, or had mild infection that failed to elicit an antibody response. This study highlights the importance of serological surveys to determine population-level immunity based on infection numbers as determined by RT-PCR.
Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis
Authors: Chen Xinhua , Chen Zhiyuan , Azman Andrew S. , Deng Xiaowei , Chen Xinghui , Lu Wanying , Zhao Zeyao , Yang Juan , Viboud Cecile , Ajelli Marco , Leung Daniel T. , Yu Hongjie 
Published: September 2020

AbstractBackgroundA rapidly increasing number of serological surveys for anti-SARS-CoV-2 antibodies have been reported worldwide. A synthesis of this large corpus of data is needed.PurposeTo evaluate the quality of serological studies and provide a global picture of seroprevalence across demographic and occupational groups, and to provide guidance for conducting better serosurveys.Data sourcesPubMed, Embase, Web of Science, medRxiv, bioRxiv, SSRN and Wellcome were searched for English-language papers published from December 1, 2019 to August 28, 2020.Study selectionSerological studies that evaluated seroprevalence of SARS-CoV-2 infections in humans.Data extractionTwo investigators independently extracted data from included studies.Data SynthesisMost of 178 serological studies, representing tests in >800,000 individuals, identified were of low quality. Close contacts and high-risk healthcare workers had higher seroprevalence of 22.9% (95% CI: 11.1-34.7%) and 14.9% (4.8-25.0%), compared to low-risk healthcare workers and general population of 5.5% (4.6-6.4%) and 6.3% (5.5-7.1%). Generally, young people (0-20 yrs) were less likely to be seropositive compared to the middle-aged (21-55 yrs) populations (RR, 0.8, 95% CI: 0.7-0.8). Seroprevalence correlated with clinical COVID-19 reports with 10 (range: 2 to 34) infections per confirmed COVID-19 case.LimitationsSome heterogeneity cannot be well explained quantitatively.ConclusionsThe overall quality of seroprevalence studies examined was low. The relatively low seroprevalence among general populations suggest that in most settings, antibody-mediated herd immunity is far from being reached. Given that ratio of infections to confirmed cases is on the same order of magnitude across different locales, reported case numbers may help provide insights into the proportion of the population infected.Primary Funding sourceNational Science Fund for Distinguished Young Scholars (PROSPERO: CRD42020198253).
Taste alteration in COVID-19: a rapid review with data synthesis reveals significant geographical differences
Authors: Cirillo Nicola 
Published: September 2020

AbstractTo facilitate a timely understanding of the differences in the prevalence of gustatory disturbances (GD) in individuals infected with SARS-CoV-2, we undertook a rapid systematic review of articles published in the repository of the National Library of Medicine (MEDLINE/PubMed) and medRxiv from their inception until September 3, 2020. The minimum requirements for completing a restricted systematic review were met. Of the 431 articles retrieved, 61 eligible studies (28,374 confirmed COVID-19 cases) from 20 countries were included in the analysis. The results show strong significant differences in the overall reported prevalence of GD between East Asia [13%, 95% CI 0.14-26.06%], Middle East [38.83%, 95% CI 27.47-50.19%], Europe [57.18%, 95% CI 52.35-62.01%], and The Americas [66.78%, 95% CI 54.77-78.79%]. There were no trends showing differences of GD prevalence in the available literature between February and August, 2020. These data show that there is a distinct geographical distribution of GD in COVID-19 patients and this may explain the differences of diagnostic criteria for COVID-19 case definition.
Factors associated with limited access to condoms and sources of condoms during the COVID-19 pandemic in South Africa
Authors: Bolarinwa Obasanjo Afolabi 
Published: September 2020

AbstractBackgroundEvidence has shown that the prescribed lockdown and physical distancing due to the novel coronavirus disease 2019 (COVID-19) have made accessing essential health care services much more difficult in low-and middle-income countries. Access to contraception is an essential service and should not be denied, even in a global crisis, because of its associated health benefits. Therefore, it is important to maintain timely access to contraception without unnecessary barriers. Hence, this study examines the factors contributing to limited access to condoms and preferred source of condoms during the COVID-19 pandemic in South Africa.MethodsThis study used data from the National Income Dynamics Study-Coronavirus Rapid Mobile Survey (NIDS-CRAM) wave 1 survey. The NIDS-CRAM is a nationally representative survey of the National Income Dynamics Survey (NIDS), which involves a sample of South Africans from 2017 NIDS wave 5, who were then re□interviewed via telephone interview. This is the first secondary dataset on coronavirus from NIDS during the coronavirus pandemic. A total of 5,304 respondents were included in the study. Data were analysed using frequencies and percentages, chi-square test and binary logistic regression analysis.ResultsAlmost one-quarter (22.40%) of South Africans could not access condoms, and every 7 in 10 South Africans preferred public source of condoms. Those who were other population groups [aOR=0.37; 95% CI=0.19-0.74] and those who were in the third wealth quintile [aOR=0.60; 95% CI=0.38-0.93] had lower odds of having access to condoms while those respondents who were aged 25-34 [aOR=0.48; 95% CI=0.27-0.83] and those with a secondary level of education and above [aOR=0.24; 95% CI=0.08-0.71] were less likely to prefer public source of condom.ConclusionThis study concludes that there was limited access to condoms during the COVID-19 pandemic and that the preferred source of condoms was very skewed to public source in South Africa. Strategic interventions such as community distribution of free condoms to avert obstruction of condom access during the COVID-19 pandemic or any future pandemics should be adopted.
The major predictors of testing positive for COVID-19 among symptomatic hospitalized patients
Authors: Barasa Samson , Kiage-Mokaya Josephine , Luna Geraldine , Friedlander Michael 
Published: September 2020

AbstractIntroductionIncreasing corona virus disease 2019 (COVID-19) pre-test probability can minimize testing patients who are less likely to have COVID-19 and therefore reducing personal protective equipment and COVID-19 testing kit use. The aim of this study was to identify patients who were likely to test positive for COVID-19 among symptomatic patients suspected of having COVID-19 during hospitalization by comparing COVID-19 positive and negative patients.MethodWe conducted a retrospective chart review of patients who were ≥18 years old and underwent COVID-19 Polymerase chain reaction test because they presented with symptoms thought to be due to COVID-19. The Poisson regression analysis was conducted after clinical presentation, demographic, medical co-morbidities, laboratory and chest image data was retrieved from the medical records.ResultsCharts of 277 and 35 COVID-19 negative and positive patients respectively were analyzed. Dyspnea (61%) was the most common symptom among COVID-19 negative patients, while 83% and 77% COVID-19 positive patients had cough and fever respectively.COVID-19 positive patients were more likely to present initially with cough [1.082 (1.022 - 1.145)] and fever [1.066 (1.013 - 1.122)], besides being males [1.066 (1.013 - 1.123)] and 50 to 69 years old [1.090 (1.019 - 1.166)]. Dyspnea, weakness, lymphopenia and bilateral chest image abnormality were not associated with COVID-19 positivity.COVID-19 positive patients were less likely to have non-COVID-19 respiratory viral illness [0.934 (0.893 - 0.976)], human immunodeficiency virus [0.847 (0.763 - 0.942)] and heart failure history [0.945 (0.908 - 0.984)]. Other chronic medical problems (hypertension, diabetes mellitus, chronic obstructive pulmonary disease and coronary artery disease) were not associated with testing positive for COVID-19.ConclusionCough and fever are better predictors of symptomatic COVID-19 positivity during hospitalization. Despite published studies reporting a high prevalence of lymphopenia among COVID-19 positive patients, lymphopenia is not associated with the risk of testing positive for COVID-19.