bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 detection in setting of viral swab scarcity: are MRSA swabs and viral swabs equivalent?
Authors: Federman Daniel G. , Gupta Shaili , Stack Gary , Campbell Sheldon M. , Peaper David R. , Dembry Louise M. , Fisher Ann , Tarabar Asim F. , Kozal Michael , Ruser Christopher B. 
Published: May 2020

AbstractBackgroundThe global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown.MethodsWe compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay.ResultsOf the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%).ConclusionWe found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.
Meat consumption and risk of 25 common conditions: outcome-wide analyses in 475,000 men and women in the UK Biobank study
Authors: Papier Keren , Fensom Georgina K , Knuppel Anika , Appleby Paul N , Tong Tammy YN , Schmidt Julie A , Travis Ruth C , Key Timothy J , Perez-Cornago Aurora 
Published: May 2020

AbstractBackgroundThere is limited prospective evidence on the association between meat consumption and many common, non-cancerous health outcomes. We examined associations of meat intake with risk of 25 common conditions (other than cancer).MethodsWe used data from 474 998 middle-aged men and women recruited into the UK Biobank study between 2006 and 2010 and followed-up until 2017 (mean follow-up of 8.0 years) with available information on meat intake at baseline (collected via touchscreen questionnaire), and linked hospital admissions and mortality data. For a large sub-sample, dietary intakes were re-measured using an online, 24-hour questionnaire.ResultsIn multi-variable adjusted (including body mass index (BMI)) Cox regression models corrected for multiple testing, a higher consumption of red and processed meat combined was associated with higher risks of ischaemic heart disease (HR per 70 g/day higher intake 1.14, 95% CI 1.06-1.22), pneumonia (1.28,1.15-1.41), diverticular disease (1.18,1.10-1.26), colon polyps (1.09,1.04-1.13), and diabetes (1.29,1.19-1.40), and a lower risk of iron deficiency anaemia (IDA), driven by a higher consumption of red meat (HR per 50g/day higher intake 0.77,0.69-0.86). Higher poultry meat intake was associated with higher risks of gastro-oesophageal reflux disease (HR per 30g/day higher intake 1.14, 1.06-1.23), gastritis and duodenitis (1.10,1.04-1.16), diverticular disease (1.09,1.04-1.16), and diabetes (1.13,1.06-1.20), and a lower risk of IDA (0.80,0.73-0.87).ConclusionsHigher red, processed, and poultry meat consumption was associated with higher risks of several common conditions; higher BMI accounted for a substantial proportion of these increased risks. Higher red and poultry meat consumption was associated with lower IDA risk.
Health Care Workers’ Mental Health During the First Weeks of the SARS-CoV-2 Pandemic in Switzerland – A Cross-Sectional Study
Authors: Weilenmann Sonja , Ernst Jutta , Petry Heidi , Pfaltz Monique C. , Sazpinar Onur , Gehrke Samuel , Paolercio Francesca , von Känel Roland , Spiller Tobias R. 
Published: May 2020

AbstractBackgroundThe current SARS-CoV-2 pandemic poses various challenges for health care workers (HCWs), which may impair their mental health. First evidence from China suggests that HCWs are at risk for anxiety and depression. However, generalizability to western countries is limited. The current study aimed at exploring HCWs’ mental health during the SARS-CoV-2 pandemic in Switzerland. In addition, we conducted a network analysis to investigate the independent effect of risk and protective factors on HCWs’ mental health and their interplay.MethodsIn an exploratory, cross-sectional, nation-wide online survey, we assessed demographics, work characteristics, COVID-19 exposure, and anxiety, depression, and burnout in 857 physicians and 553 nurses during the pandemic in Switzerland. At the time of data collection, Switzerland had among the highest per capita rate of COVID-19 cases in the world.ResultsOverall symptom levels of anxiety, depression, and burnout were elevated. Women, nurses, frontline staff and HCWs exposed to COVID-19 patients reported more symptoms than their peers. However, these effects were all small and, in the network analysis, most of them did not remain significant after controlling for the other factors. Whereas COVID-19 exposure was only partially associated with mental health, perceived support by the employer independently predicted anxiety and burnout.ConclusionsOur finding that HCWs had elevated levels of anxiety, depression, and burnout underscores the importance to systematically monitor HCWs’ mental health during this ongoing pandemic. Because perceived support and mental health impairments were negatively related, we encourage the implementation of supportive measures for HCWs’ well-being during this crisis.
Analysis of SARS-CoV-2 transmission in different settings, among cases and close contacts from the Tablighi cluster in Brunei Darussalam
Authors: Chaw Liling , Koh Wee Chian , Jamaludin Sirajul Adli , Naing Lin , Alikhan Mohammad Fathi , Wong Justin 
Published: May 2020

AbstractWe report the transmission dynamics of SARS-CoV-2 across different settings from the initial COVID-19 cluster in Brunei, arisen from 19 attendees at the Malaysian Tablighi Jama’at gathering and resulted in 52 locally transmitted cases. Highest non-primary attack rates(ARs) were observed at a subsequent local religious gathering (14.8% [95%CI: 7.1,27.7]) and in the household (10.6% [95%CI: 7.3,15.1]. Household ARs of symptomatic cases were higher (14.4% [95%CI: 8.8,19.9]) than asymptomatic (4.4% [95%CI: 0.0,10.5]) or presymptomatic cases (6.1% [95%CI: 0.3,11.8]). Low ARs (<1%) were observed for workplace and social settings. Our analysis highlights that SARS-CoV-2 transmission varies depending on environmental, behavioural and host factors. We identify ‘red flags’ of potential super-spreading events, namely densely populated gatherings for prolonged periods in enclosed settings, presence of individuals with recent travel history, and group behaviours such as communal eating, sleeping and sharing of personal hygiene facilities. We propose differentiated testing strategies that account for transmission risk.Article summary lineWe highlight the variability of SARS-CoV-2 transmission across different settings, identify settings at highest risk, and characterize the role of environmental, behavioural, and host factors in driving SARS-CoV-2 transmission.
The impact of same-day antiretroviral therapy initiation under the WHO Treat-All policy
Authors: Kerschberger Bernhard , Boulle Andrew , Kuwengwa Rudo , Ciglenecki Iza , Schomaker Michael 
Published: May 2020

ABSTRACTBackgroundRapid initiation of antiretroviral therapy (ART) is recommended for people living with HIV, with the option to start treatment on the day of diagnosis (same-day-ART). However, the effect of same-day-ART remains unknown in realistic public sector settings.MethodsWe established a cohort of ≥16-year-old patients who initiated first-line ART under Treat-All in Eswatini between 2014-2016, either on the day of HIV care enrolment (same-day-ART) or 1–14 days thereafter (early-ART). Directed acyclic graphs, flexible parametric survival analysis and targeted maximum likelihood estimation (TMLE) were used to estimate the effect of same-day-ART initiation on the composite unfavourable treatment outcome (loss to follow-up;death;viral failure).ResultsOf 1328 patients, 839 (63.2%) initiated same-day ART. The adjusted hazard ratio of the unfavourable outcome was increased by 1.48 (95% CI:1.16–1.89) for same-day-ART compared with early-ART. TMLE suggested that after 1 year, 28.9% of patients would experience the unfavourable outcome under same-day-ART compared with 21.2% under early-ART (difference: 7.7%; 1.3–14.1%). This effect was driven by loss to follow-up and varied over time, with a higher hazard during the first year after HIV care enrolment and a similar hazard thereafter.ConclusionsWe found an increased risk with same-day-ART. A limitation was possible silent transfers that were not captured.
Search for the trend of COVID-19 infection following Farr’s law, IDEA model and power law
Authors: Bhattacharya Srijit , Islam Moinul , De Alokkumar 
Published: May 2020

AbstractFollowing power law, Farr’s law and IDEA model, we analyze the data of COVID-19 pandemic for India up to 2 May, 2020 and for Germany, France, Italy, the USA, Singapore, China and Denmark up to 26 April, 2020. The cumulative total number of infected persons as a function of elapsed time has been fitted with power law to find the scaling exponent (γ). The reduction in γ in different countries signals the reduction in the growth of infection, possibly, due to long-term Government intervention. The extent of infection and reproduction rate R0 of the same are also examined using Farr’s law and IDEA model. The new cases per day with time assume Gaussian bell shaped curve, obeying the rule that faster rise follows faster decay. In India and Singapore, the peak of the bell shaped curve is still elusive. It is found that, till date, countries such as Denmark and India implementing sooner lockdown have underwent lower number of new cases of infection. Daily variation shows, R0 of all the countries is reducing, ushering in fresh hopes to combat COVID-19. Finally, we try to make a prediction as to the date on which the different countries will come down to daily cases of infection as low as one hundred (100).
Risk Factors for Clinically Relevant Postoperative Pancreatic Fistula (CR-POPF) after Distal Pancreatectomy: A Single Center Experience
Authors: Wang Gao Qing , Yadav Dipesh Kumar , Jiang Wei , Hua Yong Fei , De Lu Cai 
Published: May 2020

AbstractClinically relevant postoperative pancreatic fistula (CR-POPF) is the considerable contributor to major complications after pancreatectomy. The purpose of this study was to evaluate the potential risk factor contributing to CR-POPF following distal pancreatectomy (DP) and discussed the risk factors of pancreatic fistula in order to interpret the clinical importance. All the patients who underwent DP in between January 2011 and January 2020 were reviewed retrospectively in accordance with relevant guidelines and regulations. The univariate and multivariate analysis was performed was performed to test an independent risk factors for pancreatic fistula. P<0.05 was considered statistically significant. In all of the 263 patients with DP, pancreatic fistula was the most common surgical complication 19.0%. The univariate analysis of 18 factors showed that the patients with a malignant tumor, soft pancreas, and patient without ligation of the main pancreatic duct are more likely to develop pancreatic fistula. However, on multivariate analysis the soft texture of the pancreas (OR= 2.381, P= 0.001) and the ligation of main pancreatic duct (OR= 0.388, P= 0.002) were only an independent influencing factor for CR-POPF. As a conclusion, pancreatic fistula was the most common surgical complication after DP, and the texture of pancreas and ligation of main pancreatic duct can influence an incidence of CR-POPF.
Assessing Differential Impacts of COVID-19 on Black Communities
Authors: Millett Gregorio A. , Jones Austin T. , Benkeser David , Baral Stefan , Mercer Laina , Beyrer Chris , Honermann Brian , Lankiewicz Elise , Mena Leandro , Crowley Jeffrey S. , Sherwood Jennifer , Sullivan Patrick 
Published: May 2020

AbstractPurposeGiven incomplete data reporting by race, we used data on COVID-19 cases and deaths in US counties to describe racial disparities in COVID-19 disease and death and associated determinants.MethodsUsing publicly available data (accessed April 13, 2020), predictors of COVID-19 cases and deaths were compared between disproportionately (≥13%) black and all other (<13% black) counties. Rate ratios were calculated and population attributable fractions (PAF) were estimated using COVID-19 cases and deaths via zero-inflated negative binomial regression model. National maps with county-level data and an interactive scatterplot of COVID-19 cases were generated.ResultsNearly ninety-seven percent of disproportionately black counties (656/677) reported a case and 49% (330/677) reported a death versus 81% (1987/2,465) and 28% (684/ 2465), respectively, for all other counties. Counties with higher proportions of black people have higher prevalence of comorbidities and greater air pollution. Counties with higher proportions of black residents had more COVID-19 diagnoses (RR 1.24, 95% CI 1.17-1.33) and deaths (RR 1.18, 95% CI 1.00-1.40), after adjusting for county-level characteristics such as age, poverty, comorbidities, and epidemic duration. COVID-19 deaths were higher in disproportionally black rural and small metro counties. The PAF of COVID-19 diagnosis due to lack of health insurance was 3.3% for counties with <13% black residents and 4.2% for counties with ≥13% black residents.ConclusionsNearly twenty-two percent of US counties are disproportionately black and they accounted for 52% of COVID-19 diagnoses and 58% of COVID-19 deaths nationally. County-level comparisons can both inform COVID-19 responses and identify epidemic hot spots. Social conditions, structural racism, and other factors elevate risk for COVID-19 diagnoses and deaths in black communities.
Results from the first South African Health Products Regulatory Authority-approved randomised trial evaluating supplementation of standard antibiotic therapy with a commercially available probiotic in South African women with bacterial vaginosis
Authors: Happel Anna-Ursula , Singh Ravesh , Mitchev Nireshni , Mlisana Koleka , Jaspan Heather B. , Barnabas Shaun L. , Passmore Jo-Ann S. 
Published: May 2020

AbstractBackgroundBacterial vaginosis (BV) increases HIV risk and adverse reproductive outcomes in women. The standard-of-care (SOC) for BV is antibiotic treatment; however, cure rates are low and recurrence frequent. In South Africa, no trial comparing probiotics to SOC for BV has been approved by the South African Health Products regulatory Authority (SAHPRA). We aimed to explore the South African regulatory and ethics environment to evaluate adjunctive probiotics for improvement of BV treatment in a randomized single-blinded trial of a locally sourced oral-vaginal-combination probiotic for vaginal health.MethodsSouth African women with symptomatic vaginal discharge were screened for BV and sexually transmitted infections (STIs) including Trichomonas vaginalis, Mycoplasma genitalium, Neisseria gonorrhoae and Chlamydia trachomatis. BV positive (by Nugent Scoring) STI negative women were randomized to Metrogel™ alone (n=12) or Metrogel™ followed by a commercially available South African oral/vaginal probiotic (Vagiforte PLUS® Combo Pack; n=18). BV cure at one month was the primary endpoint. Secondary endpoints were recurrence, symptoms, vaginal microbiota and genital inflammation over five months post-treatment, and acceptability of the administered probiotic.ResultsSAHPRA reviewed and acknowledged this trial. Overall, 44.8% of women cleared BV one month post-treatment. Despite confirmed viability of probiotic species contained in the commercial oral/vaginal probiotic, they did not appear to colonize the female genital tract of most women in the intervention group. No significant differences in BV cure rates, vaginal pH, microbiota nor IL-1α concentrations were found between SOC and intervention groups, although we were underpowered to detect small differences. Acceptability and adherence to the probiotic product was high.ConclusionNavigation of the SAHPRA registration process for evaluating a commercial probiotic in a randomised trial has laid the path for future trials of improved probiotic products for vaginal health in South Africa with adequate sample sizes. Acceptability of vaginally applied probiotics was high in South African women. Improvements in both the content and delivery of commercially available probiotic products for vaginal health should be considered.Trial registrationThis trial was registered on 17 October 2017 with the South African National Clinical Trial Register of the Department of Health (DOH-27-1117-5579).
Excess Mortality in the United States During the First Three Months of the COVID-19 Pandemic
Authors: Rivera R. , Rosenbaum J. E. , Quispe W. 
Published: May 2020

AbstractDeaths are frequently under-estimated during emergencies, times when accurate mortality estimates are crucial for emergency response. This study estimates excess all-cause, pneumonia, and influenza mortality during the COVID-19 pandemic using the September 11, 2020 release of weekly mortality data from the United States (U.S.) Mortality Surveillance System (MSS) from September 27, 2015 to May 9, 2020, using semiparametric and conventional time-series models in 13 states with high reported COVID-19 deaths and apparently complete mortality data: California, Colorado, Connecticut, Florida, Illinois, Indiana, Louisiana, Massachusetts, Michigan, New Jersey, New York, Pennsylvania, and Washington. We estimated greater excess mortality than official COVID-19 mortality in the U.S. (excess mortality 95% confidence interval (CI) (100013, 127501) vs. 78834 COVID-19 deaths) and 9 states: California (excess mortality 95% CI (3338, 6344) vs. 2849 COVID-19 deaths); Connecticut (excess mortality 95% CI (3095, 3952) vs. 2932 COVID-19 deaths); Illinois (95% CI (4646, 6111) vs. 3525 COVID-19 deaths); Louisiana (excess mortality 95% CI (2341, 3183) vs. 2267 COVID-19 deaths); Massachusetts (95% CI (5562, 7201) vs. 5050 COVID-19 deaths); New Jersey (95% CI (13170, 16058) vs. 10465 COVID-19 deaths); New York (95% CI (32538, 39960) vs. 26584 COVID-19 deaths); and Pennsylvania (95% CI (5125, 6560) vs. 3793 COVID-19 deaths). Conventional model results were consistent with semiparametric results but less precise. Significant excess pneumonia deaths were also found for all locations and we estimated hundreds of excess influenza deaths in New York.We find that official COVID-19 mortality substantially understates actual mortality, excess deaths cannot be explained entirely by official COVID-19 death counts. Mortality reporting lags appeared to worsen during the pandemic, when timeliness in surveillance systems was most crucial for improving pandemic response.
Self-Assessment of Unilateral and Bimodal Cochlear Implant Experiences in Daily Life
Authors: Devocht Elke M J , Janssen A. Miranda L , Chalupper Josef , Stokroos Robert J , Kingma Herman , George Erwin L J 
Published: May 2020

AbstractObjectiveThe subjective experiences were assessed of cochlear implant (CI) users either wearing or not wearing a hearing aid (HA) at the contralateral ear.DesignUnilateral CI-recipients were asked to fill out a set of daily-life questionnaires on bimodal HA use, hearing disability, hearing handicap and general quality of life.Study sampleTwenty-six CI-recipients who regularly use a contralateral HA (bimodal group) and twenty-two CI-recipients who do not use a HA in the contralateral ear (unilateral group).ResultsComparisons between both groups (bimodal versus unilateral) showed no difference in self-rated disability, hearing handicap or general quality of life. However within the group of bimodal listeners, participants did report a significant benefit of bimodal hearing ability in various daily life listening situations.ConclusionsBimodal benefit in daily life can consistently be experienced and reported within the group of bimodal users.
Deep Learning for Screening COVID-19 using Chest X-Ray Images
Authors: Basu Sanhita , Mitra Sushmita , Saha Nilanjan 
Published: May 2020

AbstractWith the ever increasing demand for screening millions of prospective “novel coronavirus” or COVID-19 cases, and due to the emergence of high false negatives in the commonly used PCR tests, the necessity for probing an alternative simple screening mechanism of COVID-19 using radiological images (like chest X-Rays) assumes importance. In this scenario, machine learning (ML) and deep learning (DL) offer fast, automated, effective strategies to detect abnormalities and extract key features of the altered lung parenchyma, which may be related to specific signatures of the COVID-19 virus. However, the available COVID-19 datasets are inadequate to train deep neural networks. Therefore, we propose a new concept called domain extension transfer learning (DETL). We employ DETL, with pre-trained deep convolutional neural network, on a related large chest X-Ray dataset that is tuned for classifying between four classes viz. normal, other_disease, pneumonia and Covid — 19. A 5-fold cross validation is performed to estimate the feasibility of using chest X-Rays to diagnose COVID-19. The initial results show promise, with the possibility of replication on bigger and more diverse data sets. The overall accuracy was measured as 95.3% ± 0.02. In order to get an idea about the COVID-19 detection transparency, we employed the concept of Gradient Class Activation Map (Grad-CAM) for detecting the regions where the model paid more attention during the classification. This was found to strongly correlate with clinical findings, as validated by experts.
Collider bias undermines our understanding of COVID-19 disease risk and severity
Authors: Griffith Gareth J , Morris Tim T , Tudball Matt , Herbert Annie , Mancano Giulia , Pike Lindsey , Sharp Gemma C , Palmer Tom M , Smith George Davey , Tilling Kate , Zuccolo Luisa , Davies Neil M , Hemani Gibran 
Published: May 2020

AbstractObservational data on COVID-19 including hypothesised risk factors for infection and progression are accruing rapidly, often from non-random sampling such as hospital admissions, targeted testing or voluntary participation. Here, we highlight the challenge of interpreting observational evidence from such samples of the population, which may be affected by collider bias. We illustrate these issues using data from the UK Biobank in which individuals tested for COVID-19 are highly selected for a wide range of genetic, behavioural, cardiovascular, demographic, and anthropometric traits. We discuss the sampling mechanisms that leave aetiological studies of COVID-19 infection and progression particularly susceptible to collider bias. We also describe several tools and strategies that could help mitigate the effects of collider bias in extant studies of COVID-19 and make available a web app for performing sensitivity analyses. While bias due to non-random sampling should be explored in existing studies, the optimal way to mitigate the problem is to use appropriate sampling strategies at the study design stage.