bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the Impact of the COVID-19 Pandemic for the Low- and Middle-Income Countries
Authors: Ding Zhiwei , Sha Feng , Kong Jing , Li Bingyu , Zhang Yi , Yip Paul , Yang Zhouwang 
Published: August 2020

AbstractThis study predicts the maximum hospital demand and number of infections for the LMICs in the first wave of COVID-19 pandemic. The epidemic is estimated to impose health care burden excessively exceeding the current capacity of hospitals in many LMICs, especially in Honduras, Central African Republic and Colombia.
A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English Primary Schools with application of Structured Expert Judgement
Authors: Sparks R.S.J. , Aspinall W.P. , Brooks-Pollock E. , Cooke R.M. , Danon L. , Barclay J. , Scarrow J.H. , Cox J.H. 
Published: August 2020

AbstractBackgroundContact patterns are the drivers of close-contacts infections, such as COVID-19. In an effort to control COVID-19 transmission in the UK, schools were closed on 23 March 2020. With social distancing in place, Primary Schools were partially re-opened on 1 June 2020, with plans to fully re-open in September 2020. The impact of social distancing and risk mitigation measures on children’s contact patterns is not known.MethodsWe conducted a structured expert elicitation of a sample of Primary Headteachers to quantify contact patterns within schools in pre-COVID-19 times and how these patterns were expected to change upon re-opening. Point estimates with uncertainty were determined by a formal performance-based algorithm. Additionally, we surveyed school Headteachers about risk mitigation strategies and their anticipated effectiveness.ResultsExpert elicitation provides estimates of contact patterns that are consistent with contact surveys. We report mean number of contacts per day for four cohorts within schools along with a range at 90% confidence for the variations of contacts among individuals. Prior to lockdown, we estimate that, mean numbers per day, younger children (Reception and Year 1) made 15 contacts [range 8..35] within school, older children (Year 6) 18 contacts [range 5.. 55], teaching staff 25 contacts [range 4.. 55) and non-classroom staff 11 contacts [range 2.. 27]. Compared to pre-COVID times, after schools re-opened the mean number of contacts were reduced by about 53% for young children, about 62% for older children, about 60% for classroom staff and about 64% for other staff. Contacts between teaching and non-teaching staff reduced by 80%, which is consistent with other independent estimates. The distributions of contacts per person are asymmetric indicating a heavy tail of individuals with high contact numbers.ConclusionsWe interpret the reduction in children’s contacts as a consequence of efforts to reduce mixing with interventions such as forming groups of children (bubbles) who are organized to learn together to limit contacts. Distributions of contacts for children and adults can be used to inform COVID-19 transmission modelling. Our findings suggest that while official DfE guidelines form the basis for risk mitigation in schools, individual schools have adopted their own bespoke strategies, often going beyond the guidelines.
Has COVID-19 Hurt Resident Education? A network-wide resident survey on education and experience during the pandemic
Authors: Ostapenko Alexander , McPeck Samantha , Liechty Shawn , Kleiner Daniel 
Published: August 2020

ABSTRACTPurposeAs the COVID-19 pandemic continues to evolve, the healthcare system has been forced to adapt in myriad ways. Residents have faced significant changes in work schedules, deployment to COVID-19 units, and alterations to didactics. This study aims to identify the effects of the COVID-19 pandemic on resident perception of their own education within the Nuvance Health Network.MethodsWe conducted an observational study assessing resident perception of changes in education and lifestyle during the COVID-19 pandemic. A survey was developed to assess the quality and quantity of resident education during this time and administered anonymously to all residents within the healthcare network.ResultsEighty-four (68%) residents responded to the survey from five different specialties, including general surgery, internal medicine, obstetrics and gynecology, pathology, and radiology. The average change in hours per week performing clinical work was −5.6 hours (SD=16.8), in time studying was +0.02 hours (SD=4.6), in weekly didactics was −1.7 hours (SD=3.1), and in attending involvement was −1.2 hours (SD=2.3). Additionally, 32% of residents expressed concern that the pandemic has diminished their preparedness to become an attending, 13% expressed concern about completing graduation requirements, and 3% felt they would need an additional year of training.ConclusionsDuring the COVID-19 pandemic thus far, residents perceived that time spent on organized didactics/conferences decreased and that attending physicians are less involved in education. Furthermore, the majority of residents felt that the quality of didactic education diminished as a result of the pandemic. Surprisingly, while many residents expressed concerns about being prepared to become an attending, few were concerned about completing graduation requirements or needing an extra year of education. In light of these findings, it is critical to devote attention to the effects of the pandemic on residents’ professional trajectories and create innovative opportunities for improving education during this challenging time.
Twelve-year changes in protein profiles in patients with and without gastric bypass surgery
Authors: Yousri Noha A. , Engelke Rudolf , Sarwath Hina , McKinlay Rodrick D. , Simper Steven C. , Adams Ted D. , Schmidt Frank , Suhre Karsten , Hunt Steven C. 
Published: August 2020

AbstractGastric bypass surgery results in long-term weight loss due to re-routing of the gastro-intestinal anatomy and dietary intake alterations. Studies have examined protein change during rapid weight loss (up to 1 year post-surgery), but whether protein changes are maintained long-term after weight stabilization is unknown. To identify proteins and pathways involved with the long-term beneficial effects of weight loss, abundances of 1297 blood-circulating proteins were measured at baseline, 2 and 12 years after Roux-en-Y gastric bypass surgery. Protein changes were compared between 234 surgery and 144 non-surgery subjects with severe obesity, with discovery and replication subgroups. Seventy-one protein changes were associated with 12-year BMI changes and 58 (7 unique) with surgical status. Protein changes, including ApoM, were most strongly associated with long-term changes in lipids (HDL-C and triglycerides). Inflammation, adipogenesis, cellular signaling, and complement pathways were implicated. Short-term improvements in protein levels were maintained long-term, even after some weight regain.
Sero-prevalence Findings from Metropoles in Pakistan: Implications for Assessing COVID-19 Prevalence and Case-fatality within a Dense, Urban Working Population
Authors: Javed Wajiha , Baqar Jaffer Bin , Abidi Syed Hussain Baqar , Farooq Wajiha 
Published: August 2020

AbstractPopulation-level serologic testing has demonstrated groundbreaking results in monitoring the prevalence and case-fatality of COVID-19 within a population. In Pakistan, Getz Pharma conducted a sero-prevalence survey on a sample of 24,210 individuals using the IgG/IgM Test Kit (Colloidal gold) with follow-up and sequential testing after every 15-20 days on a sub-sample. This is the first of its kind, large scale census conducted on a dense, urban, working population in Pakistan. The study results reveal that from 24,210 individuals screened, 17.5% tested positive, with 7% IgM positive, 6.0% IgG positive and 4.5% combined IgM and IgG positive. These findings have been extrapolated to the rest of the urban, adult, working population of Pakistan, and as of 6th July, 2020, 4.11 million people in Pakistan have been infected with COVID-19, which is 17.7 times higher than the current number of 231,818 symptom-based PCR cases reported by the government which exclude asymptomatic cases.
Inequality indices to monitor geographic differences in incidence, mortality and fatality rates over time during the COVID-19 pandemic
Authors: Manz Kirsi , Mansmann Ulrich 
Published: August 2020

AbstractBackgroundIt is of interest to explore the variability in how the COVID-19 pandemic evolved geographically during the first twelve months. To this end, we apply inequality indices over regions to incidences, infection related mortality, and infection fatality rates. If avoiding of inequality in health is an important political goal, a metric must be implemented to track geographical inequality over time.MethodsThe relative and absolute Gini index as well as the Theil index are used to quantify inequality. Data are taken from international data bases. Absolute counts are transformed to rates adjusted for population size.ResultsComparing continents, the absolute Gini index shows an unfavorable development in four continents since February 2020. In contrast, the relative Gini as well as the Theil index support the interpretation of less inequality between European countries compared to other continents. Infection fatality rates within the EU as well as within the U.S. express comparable improvement towards more equality (as measured by both Gini indices).ConclusionsThe use of inequality indices to monitor changes in geographic in-equality over time for key health indicators is a valuable tool to inform public health policies. The absolute and relative Gini index behave complementary and should be reported simultaneously in order to gain a meta-perspective on very complex dynamics.
COVID-19 vaccination intention in the UK: Results from the ‘COVID-19 Vaccination Acceptability Study’ (CoVAccS), a nationally representative cross-sectional survey
Authors: Sherman Susan M. , Smith Louise E. , Sim Julius , Amlôt Richard , Cutts Megan , Dasch Hannah , Rubin G James , Sevdalis Nick 
Published: August 2020

ABSTRACTAimTo investigate factors associated with intention to be vaccinated against COVID-19.MethodsOnline cross-sectional survey of 1,500 UK adults, recruited from an existing online research panel. Data were collected between 14th and 17th July 2020. We used linear regression analyses to investigate associations between intention to be vaccinated for COVID-19 “when a vaccine becomes available to you” and socio-demographic factors, previous influenza vaccination, general vaccine attitudes and beliefs, attitudes and beliefs about COVID-19, and attitudes and beliefs about a COVID-19 vaccination.Results64% of participants reported being likely to be vaccinated against COVID-19; 27% were unsure and 9% reported being unlikely to be vaccinated. Personal and clinical characteristics, previous influenza vaccination, general vaccination beliefs, and beliefs and attitudes about COVID-19 and a COVID-19 vaccination explained 77% of the variance in vaccination intention. Intention to be vaccinated was associated with more positive general COVID-19 vaccination beliefs and attitudes, weaker beliefs that the vaccination would cause side effects or be unsafe, greater perceived information sufficiency to make an informed decision about COVID-19 vaccination, greater perceived risk of COVID-19 to others but not oneself, older age, and having been vaccinated for influenza last winter (2019/20).ConclusionsDespite uncertainty around the details of a COVID-19 vaccination, most participants reported intending to be vaccinated for COVID-19. Actual uptake will likely be lower. Vaccination intention reflects general vaccine beliefs and attitudes. Campaigns and messaging about a COVID-19 vaccination should emphasize the risk of COVID-19 to others and necessity for everyone to be vaccinated.
Assessing the efficacy and safety of angiotensinogen inhibition using human genetics
Authors: Bovijn Jonas , Censin Jenny C , Lindgren Cecilia M , Holmes Michael V 
Published: August 2020

AbstractBackgroundNovel angiotensinogen (AGT) inhibitors are in early clinical development for treatment of hypertension. Evidence that this therapeutic approach will safely reduce risk of cardiovascular outcomes in humans is limited. We leveraged genetic data from more than one million individuals to characterise the effects of AGT inhibition.MethodsWe identified a genetic instrument for AGT inhibition from systolic blood pressure (SBP) genome-wide association study data, and investigated its relationship withAGTgene expression and circulating AGT protein concentration. We examined the instrument’s association with cardiovascular and renal outcomes, and compared the effect of the instrument with that of genetic instruments for other renin-angiotensin system (RAS) components and the causal effect of SBP overall. We performed phenome-wide association analyses to identify unanticipated effects of AGT inhibition.ResultsThe AGT instrument (rs2478539; 0.49 mmHg lower SBP per G-allele) was strongly associated with hypertension, and showed evidence of colocalisation withAGTmRNA expression across various tissues. Scaled to a 10 mmHg lower SBP, the AGT instrument was associated with a 41% lower risk of major cardiovascular events, a composite of myocardial infarction, coronary revascularisation and stroke (111,549 cases; odds ratio 0.59, 95% confidence interval, 0.47 – 0.74;P= 3.1 × 10-6). There was little evidence of heterogeneity between the AGT vascular estimates when compared to equivalent estimates from other RAS targets and the effect of SBP lowering more broadly, and no strong evidence of potential target-mediated adverse effects.ConclusionOur findings suggest that inhibition of AGT safely reduces risk of major vascular events. These results support ongoing clinical development programmes for AGT inhibitors.
Bilirubin is not associated with urinary bladder cancer risk and prognosis: A Mendelian Randomization Study in the UK Biobank
Authors: Lipunova Nadezda , Bryan Richard T , Zeegers Maurice 
Published: August 2020

ABSTRACTBackgroundMutations in UGT1A gene have been associated with the development and prognosis of urinary bladder cancer (UBC). UGT1A proteins are involved in a spectrum of detoxification processes, hence the biological mechanism between UGT1A and UBC is difficult to elucidate. Concurrently, mild hyperbilirubinemia, caused by alterations in UGT1A, has been associated with multiple health outcomes. We have investigated the potential effect of mild hyperbilirubinemia on UBC risk and prognosis, using a Mendelian Randomization (MR) approach in the UK Biobank.MethodsData on 1,281 UBC patients and 4,071 controls was available for a two-stage least squares MR estimation with rs6742078 as an instrumental variable. First, linear regression was fitted to establish the relationship between the rs6742078 and bilirubin levels (total and unconjugated). Secondly, bilirubin values were used to predict tested outcomes under a logistic model. Both stages were adjusted for participant sex, smoking status, and age.ResultsMR analysis showed no significant effects of bilirubin levels on UBC risk (total bilirubin: OR=1.02, 95% CI: 0.99-1.04; unconjugated bilirubin: OR=1.02, 95% CI: 0.99-1.05). No effects were observed for events of UBC recurrence, progression, or survival.ConclusionOur study suggests mild hyperbilirubinemia is not associated with urinary bladder cancer risk and prognosis.
Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region
Authors: Thielen Peter M. , Wohl Shirlee , Mehoke Thomas , Ramakrishnan Srividya , Kirsche Melanie , Falade-Nwulia Oluwaseun , Trovão Nídia S. , Ernlund Amanda , Howser Craig , Sadowski Norah , Morris Paul , Hopkins Mark , Schwartz Matthew , Fan Yunfan , Gniazdowski Victoria , Lessler Justin , Sauer Lauren , Schatz Michael C. , Evans Jared D. , Ray Stuart C. , Timp Winston , Mostafa Heba H. 
Published: August 2020

AbstractBackgroundThe early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility.MethodsWe performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region.ResultsWe analyzed 620 samples from the Johns Hopkins Health System collected between March 11–31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belong to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades.ConclusionsWe established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.
Efficacy of Corticosteroids in COVID-19 Patients: A Systematic Review and Meta-Analysis
Authors: Tlayjeh Haytham , Mhish Olaa H. , Enani Mushira A. , Alruwaili Alya , Tleyjeh Rana , Thalib Lukman , Hassett Leslie , Arabi Yaseen M. , Kashour Tarek , Tleyjeh Imad M. 
Published: August 2020

AbstractBackgroundTo systematically review the literature about the effect of systemic corticosteroid therapy (CST) on outcomes of COVID-19 patients.MethodsWe searched Medline, Embase, EBM Reviews, Scopus, Web of Science, and preprints up to July 20, 2020. We included observational studies and randomized controlled trials (RCT) that assessed COVID-19 patients treated with CST. We pooled adjusted effect estimates of mortality and other outcomes using a random effect model, among studies at low or moderate risk for bias. We assessed the certainty of evidence for each outcome using the GRADE approach.ResultsOut of 1067 citations screened for eligibility, one RCT and 19 cohort studies were included (16,977 hospitalized patients). Ten studies (1 RCT and 9 cohorts) with 10,278 patients examined the effect of CST on short term mortality. The pooled adjusted RR was 0.92 (95% CI 0.69-1.22, I2=81.94 %). This effect was observed across all stages of disease severity. Four cohort studies examined the effect of CST on composite outcome of death, ICU admission and mechanical ventilation need. The pooled adjusted RR was 0.41(0.23-0.73, I2=78.69%). Six cohort studies examined the effect of CST on delayed viral clearance. The pooled adjusted RR was 1.47(95% CI 1.11-1.93, I2=43.38%).ConclusionHeterogeneous and low certainty cumulative evidence suggests that CST lacks efficacy in reducing short-term mortality while possibly delaying viral clearance in patients hospitalized with COVID-19. Because of the discordant results between the single RCT and observational studies, more research should continue to identify the clinical and biochemical characteristics of patients’ population that could benefit from CST.
Long-Term Exposure to Outdoor Air Pollution and COVID-19 Mortality: an ecological analysis in England
Authors: Feng Zhiqiang , Cherrie Mark , Dibben Chris 
Published: August 2020

AbstractThere is an urgent need to examine what individual and environmental risk factors are associated with COVID-19 mortality. This objective of this study is to investigate the association between long term exposure to air pollution and COVID-19 mortality. We conducted a nationwide, ecological study using zero-inflated negative binomial models to estimate the association between long term (2014-2018) small area level exposure to NOx, PM2.5, PM10 and SO2 and COVID-19 mortality rates in England adjusting for socioeconomic factors and infection exposure. We found that all four pollutant concentrations were positively associated with COVID-19 mortality. The increase in mortality risk ratio per inter quarter range increase was for PM2.5:11%, 95%CIs 6%-17%), PM10 (5%; 95%CIs 1%-11%), NOx (11%, 95%CIs 6%-15%) and SO2 (7%, 95%CIs 3%-11%) were respectively in adjusted models. Public health intervention may need to protect people who are in highly polluted areas from COVID-19 infections.
Timing HIV infection with nonlinear viral dynamics
Authors: Reeves Daniel , Rolland Morgane , Dearlove Bethany L , Li Yifan , Robb Merlin , Schiffer Joshua T , Gilbert Peter , Cardozo-Ojeda E Fabian , Mayer Bryan 
Published: August 2020

AbstractIn HIV prevention trials, precise identification of infection time is critical to quantify drug efficacy but difficult to estimate as trials may have relatively sparse visit schedules. The last negative visit does not guarantee a boundary on infection time because viral nucleic acid is not present in the blood during early infection. Here, we developed a framework that combines stochastic and deterministic within-host mathematical modeling of viral dynamics accounting for the early unobservable viral load phase until it reaches a high chronic set point. The infection time estimation is based on a population non-linear mixed effects (pNLME) framework that includes the with-in host modeling. We applied this framework to viral load data from the RV217 trial and found a parsimonious model capable of recapitulating the viral loads. When adding the stochastic and deterministic portion of the best model, the estimated infection time for the RV217 data had an average of 2 weeks between infecting exposure and first positive. We assessed the sensitivity of the infection time estimation by conducting in silico studies with varying viral load sampling schemes before and after infection. pNLME accurately estimates infection times for a daily sampling scheme and is fairly robust to sparser schemes. For a monthly sampling scheme before and after first positive bias increases to -7 days. For pragmatic trial design, we found sampling weekly before and monthly after first positive allows accurate pNLME estimation. Our estimates can be used in parallel with other approaches that rely on viral sequencing, and because the model is mechanistic, it is primed for future application to infection timing for specific interventions.