bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sampling bias minimization in disease frequency estimates
Authors: Shtossel Oshrit , Louzoun Yoram 
Published: May 2021

An accurate estimate of the number of infected individuals in any disease is crucial. Current estimates are mainly based on the fraction of positive samples or the total number of positive samples. However, both methods are biased and sensitive to the sampling depth. We here propose an alternative method to use the attributes of each sample to estimate the change in the total number of positive patients in the total population. We present a Bayesian estimator assuming a combination of condition and time-dependent probability of being positive, and mixed implicit-explicit solution for the probability of a person with conditions i at time t of being positive. We use this estimate to predict the total probability of being positive at a given day t.We show that these estimate results are smooth and not sensitive to the properties of the samples. Moreover, these results are a better predictor of future mortality.
Rare GATA6 variants associated with risk of congenital heart disease phenotypes in 200,000 UK Biobank exomes
Authors: Williams Simon G. , Byrne Dominic , Keavney Bernard D. 
Published: May 2021

AbstractSeveral genes have been associated with congenital heart disease (CHD) risk in previous GWAS and sequencing studies, but studies involving larger numbers of case samples remain needed to facilitate further understanding of what remains a complex and largely uncharacterised genetic etiology. Here we use whole exome sequencing data from 200,000 samples in the UK Biobank to assess ultra-rare and potentially pathogenic variation associated with increased risk of CHD. Our findings indicate that rare variants in GATA6, presumably with a lesser effect on gene function than those causing severe CHD phenotypes, or buffered by other genetic and environmental effects during development, are also associated with minor CHD conditions, specifically bicuspid aortic valve, the most common CHD condition.
COVID-19 susceptibility variants associate with blood clots, thrombophlebitis and circulatory diseases
Authors: Papadopoulou Areti , Musa Hanan , Sivaganesan Mathura , McCoy David , Deloukas Panos , Marouli Eirini 
Published: May 2021

AbstractObjectiveEpidemiological studies suggest that individuals with comorbid conditions including diabetes, chronic lung diseases and others, are at higher risk of adverse COVID-19 outcomes. Genome-wide association studies have identified several loci associated with increased susceptibility and severity for COVID-19. However, it is not clear whether these associations are genetically determined or not. We used a Phenome-Wide Association (PheWAS) approach to investigate the role of genetically determined COVID-19 susceptibility on disease related outcomes.Approach and ResultsPheWAS analyses were performed in order to identify traits and diseases related to COVID-19 susceptibility and severity, evaluated through a predictive COVID-19 risk score. We utilised phenotypic data in up to 400,000 individuals from the UK Biobank, including Hospital Episode Statistics and General Practice data. We identified a spectrum of associations between both genetically determined COVID-19 susceptibility and severity with a number of traits. COVID-19 risk was associated with increased risk for phlebitis and thrombophlebitis (OR = 1.11, p = 5.36e-08). We also identified significant signals between COVID-19 susceptibility with blood clots in the leg (OR= 1.1, p = 1.66e-16) and with increased risk for blood clots in the lung (OR = 1.12, p = 1.45 e-10).ConclusionsOur study identifies significant association of genetically determined COVID-19 with increased blood clot events in leg and lungs. The reported associations between both COVID-19 susceptibility and severity and other diseases adds to the identification and stratification of individuals at increased risk, adverse outcomes and long-term effects.
Vaccination strategies when vaccines are scarce: On conflicts between reducing the burden and avoiding the evolution of escape mutants
Authors: Geoffroy Félix , Traulsen Arne , Uecker Hildegard 
Published: May 2021

AbstractWhen vaccine supply is limited but population immunisation urgent, the allocation of the available doses needs to be carefully considered. One aspect of dose allocation is the time interval between the primer and the booster injections in two-dose vaccines. By stretching this interval, more individuals can be vaccinated with the first dose more quickly. Even if the level of immunity of these ‘half-vaccinated’ individuals is lower than that of those who have received both shots, delaying the second injection can be beneficial in reducing case numbers, provided a single dose is sufficiently effective. On the other hand, there has been concern that intermediate levels of immunity in partially vaccinated individuals may favour the evolution of vaccine escape mutants. In that case, a large fraction of half-vaccinated individuals would pose a risk – but only if they encounter the virus. This raises the question whether there is a conflict between reducing the burden and the risk of vaccine escape evolution or not. We develop a minimal model to assess the population-level effects of the timing of the booster dose. We set up an SIR-type model, in which more and more individuals become vaccinated with a two-dose vaccine over the course of a pandemic. As expected, there is no trade-off when vaccine escape evolves at equal probabilities in unvaccinated and half-vaccinated patients. If vaccine escape evolves more easily in half-vaccinated patients, the presence or absence of a trade-off depends on the reductions in susceptibility and transmissibility elicited by the primer dose.
Assessing COVID-19 Pandemic Risk Perception and Response Preparedness in Veterinary and Animal Care Workers
Authors: Dalton Kathryn R. , Guyer Kimberly M. , Schiaffino Francesca , Ferradas Cusi , Falke Jacqueline R. , Beasley Erin A. , Meza Kayla , Laughlin Paige , Agnew Jacqueline , Barnett Daniel J. , Nuzzo Jennifer B. , Davis Meghan F. 
Published: May 2021

AbstractVeterinary and animal care workers (VACW) perform critical functions in biosecurity and public health, yet little has been done to understand the unique needs and barriers these workers face when responding during a pandemic crisis. This study evaluated VACWs’ perceived risks and roles during COVID-19, and explored barriers and facilitators in their readiness, ability, and willingness to respond during a pandemic. We deployed a survey targeting U.S. veterinary medical personnel, animal shelter and control workers, zoo and wildlife workers, plus other animal care workers. Data were collected on participants’ self-reported job and demographic factors, perceptions of risk and job efficacy, and readiness, ability, and willingness to respond during the pandemic. We found that leadership roles and older age had the strongest association with decreased perceived risk and improved job efficacy and confidence, and that increased reported contact level with others (both co-workers and the public) was associated with increased perceived risk. We determined that older age and serving in leadership positions were associated with improved readiness, willingness, and ability to respond. VACWs’ dedication to public health response, reflected in our findings, will be imperative if more zoonotic vectors of SARS-CoV-2 arise. Response preparedness in VACW can be improved by targeting younger workers not in leadership roles in support programs that center on improving job efficacy and confidence in safety protocols. These findings can be used to target intervention and training efforts to support the most vulnerable within this critical, yet often overlooked, workforce.
Visual Exploratory Data Analysis of COVID-19 Pandemic: One Year After the Outbreak
Authors: Nazir Amril , Ulusoy Suleyman , Lotfi Lujaini 
Published: May 2021

AbstractBackgroundGovernments across the globe have taken different measures to handle the Covid-19 outbreak since it began in early 2020. Countries implemented various policies and restrictive measures to prevent transmission of the virus, reduce the impacts of the outbreak (i.e., individual, social, and economic), and provide effective control measures. Although it has been over one year since the outbreak started, few studies have examined the long-term effects of the pandemic. Furthermore, researchers need to examine which government intervention variables are the most, and least, effective. Such analysis is critical to determine the best practices in support of policy decisions.MethodsVisual exploratory data analysis (V-EDA) offers a user-friendly data visualization model to evaluate the impact of the pandemic. It allows one to observe visual patterns of trends. The V-EDA was conducted on one year data for the COVID-19 Pandemic, one year after the outbreak between 1 January and 31 December, 2020. The data were analyzed using the student’s t-test to verify if there was a statistical difference between two independent groups, and the Spearman test was also used to analyze the correlation coefficient between two quantitative datasets and their positive or negative inclination.FindingsWe found that high-testing countries had more cases per million than low-testing countries. For low-testing countries, however, there was a positive correlation between the testing level and the number of cases per million. This suggests that high-testing countries tested in a preventive manner while low-testing countries may have a higher number of cases than those confirmed. The poorest developing countries have reduced testing which can coincide with the reduction in new cases, which we did not observe in the high-testing countries. Among the restrictive measures analyzed, a higher population aged 70 or older and lower GDP per capita was related to a higher case fatality ratio. Restrictive measures reduce the number of new cases after four weeks, indicating the minimum time required for the measures to have a positive effect. Finally, public event cancellation, international travel control, school closing, contact tracing, and facial coverings were the most important measures to reduce virus spread. We observed that countries with the lowest number of cases had a higher stringency index.
Identification of risk and protective human leukocyte antigens in COVID-19 using genotyping and structural modeling
Authors: Shen Yiran , Ostrov David A. , Rananaware Santosh , Jain Piyush K , Nguyen Cuong Q. 
Published: May 2021

AbstractCOVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. Since innate and adaptive immune responses are elicited in COVID-19 patients, we genotyped 94 Florida patients with confirmed COVID-19 and 89 healthy controls. We identified an HLA gene, HLA-DPA1, in which specific alleles were associated with the risk of SARS-CoV-2 positivity and COVID-19 disease. HLA-DPA1*01:03 was associated with reduced incidence of SARS-CoV-2 positivity, whereas HLA-DPA1*03:01 was associated with increased risk of SARS-CoV-2 positivity. These data suggest a model in which COVID-19 severity is influenced by immunodominant peptides derived from SARS-CoV-2 preferentially presented by specific HLA-DP molecules to either protective (for asymptomatic COVID-19) or pathogenic T cells (in severe COVID-19). Although this study is limited to comparing SARS-CoV-2 positive and negative subjects, these data suggest that HLA typing of COVID-19 patients stratified for disease severity may be informative for identifying biomarkers and disease mechanisms in high-risk individuals.
Population-level management of Type 1 diabetes via continuous glucose monitoring and algorithm-enabled patient prioritization: Precision health meets population health
Authors: Ferstad Johannes O. , Vallon Jacqueline J. , Jun Daniel , Gu Angela , Vitko Anastasiya , Morales Dianelys P. , Leverenz Jeannine , Lee Ming Yeh , Leverenz Brianna , Vasilakis Christos , Osmanlliu Esli , Prahalad Priya , Maahs David M , Johari Ramesh , Scheinker David 
Published: May 2021

AbstractObjectiveTo develop and scale algorithm-enabled patient prioritization to improve population-level management of type 1 diabetes (T1D) in a pediatric clinic with fixed resources, using telemedicine and remote monitoring of patients via continuous glucose monitor (CGM) data review.Research Design and MethodsWe adapted consensus glucose targets for T1D patients using CGM to identify interpretable clinical criteria to prioritize patients for weekly provider review. The criteria were constructed to manage the number of patients reviewed weekly and identify patients who most needed provider contact. We developed an interactive dashboard to display CGM data relevant for the patients prioritized for review.ResultsThe introduction of the new criteria and interactive dashboard was associated with a 60% reduction in the mean time spent by diabetes team members who remotely and asynchronously reviewed patient data and contacted patients, from 3.2±0.20 to 1.3±0.24 minutes per patient per week. Given fixed resources for review, this corresponded to an estimated 147% increase in weekly clinic capacity. Patients who qualified for and received remote review (n=58) have associated 8.8 percentage points (pp) (95% CI = 0.6–16.9pp) greater time-in-range (70-180 mg/dL) glucoses compared to 25 control patients who did not qualify at twelve months after T1D onset.ConclusionsAn algorithm-enabled prioritization of T1D patients with CGM for asynchronous remote review reduced provider time spent per patient and was associated with improved time-in-range.
Teletherapy for children with developmental disorders during the COVID-19 pandemic in the Philippines: a mixed-methods evaluation from the perspectives of parents and therapists
Authors: Eguia Kathlynne F. , Capio Catherine M. 
Published: May 2021

ObjectivesAs a response to the lockdown associated with COVID-19 in the Philippines, therapy services for children with developmental disorders shifted to telehealth (i.e., teletherapy). This study evaluated the delivery of teletherapy from the perspectives of parents and therapists.MethodsParticipants consisted of parents (n = 47) and therapists (n = 102) of children with developmental disorders who were receiving teletherapy during the lockdown. A mixed-methods triangulation design-convergence model was adopted; participants were invited to respond to an online survey with closed- and open-ended questions. Quantitative data were analyzed using descriptive and non-parametric inferential tests, while qualitative data were examined using thematic analysis.ResultsOverall satisfaction with teletherapy was positive, with parents reporting significantly higher satisfaction compared to therapists. Satisfaction was positively associated with the frequency of teletherapy sessions for parents, and with their years of experience for therapists. The top enabling factors were family participation and effective communication. The main challenges were time constraints and difficulty with instruction and monitoring associated with the two-dimensional nature of teletherapy. The benefits included parents’ empowerment and enhanced understanding of their children’s needs.DiscussionThe shift to teletherapy facilitated a heightened focus on family-centered care. The evaluation findings suggest that the general satisfaction with teletherapy and the benefits associated with family-centered care will likely promote teletherapy as a service delivery mode to continue beyond the pandemic.
Impact of National and Regional Lockdowns on Growth of COVID-19 Cases in COVID-Hotspot City of Pune in Western India: A Real-World Data Analysis
Authors: Mave Vidya , Shaikh Arsh , Monteiro Joy Merwin , Bogam Prasad , Pujari Bhalchandra S , Gupte Nikhil 
Published: May 2021

AbstractBackgroundReal-world data assessing the impact of lockdowns on COVID-19 cases remain limited from resource-limited settings. We examined growth of incident confirmed COVID-19 cases before, during and after lockdowns in Pune, a city in western India with 3.1 million population that reported the largest COVID-19 burden at the peak of the pandemic.MethodsUsing anonymized individual-level data captured by Pune’s public health surveillance program between February 1st and September 15th 2020, we assessed weekly incident COVID-19 cases, infection rates, and epidemic curves by lockdown status (overall and by sex, age, and population density) and modelled the natural epidemic using the 9-compartmental model INDSCI-SIM. Effect of lockdown on incident cases was assessed using multilevel Poisson regression. We used geospatial mapping to characterize regional spread.FindingsOf 241,629 persons tested for SARS-CoV-2, the COVID-19 disease rate was 267.0 (95% CI 265.3 – 268.8) per 1000 persons. Epidemic curves and geospatial mapping showed delayed peak of the cases by approximately 8 weeks during the lockdowns as compared to modelled natural epidemic. Compared to a subsequent unlocking period, incident COVID-19 cases 43% lower (IRR 0.57, 95% CI 0.53 – 0.62) during India’s nationwide lockdown and 22% (IRR 0.78, 95% CI 0.73 – 0.84) during Pune’s regional lockdown and was uniform across age groups and population densities.ConclusionLockdowns slowed the growth of COVID-19 cases in population dense, urban region in India. Additional analysis from rural and semi-rural regions of India and other resource-limited settings are needed.
SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 epidemic in Lombardy, Italy (March – June 2020)
Authors: Castiglioni Sara , Schiarea Silvia , Pellegrinelli Laura , Primache Valeria , Galli Cristina , Bubba Laura , Mancinelli Federica , Marinelli Marilisa , Cereda Danilo , Ammoni Emanuela , Pariani Elena , Zuccato Ettore , Binda Sandro 
Published: May 2021

AbstractWastewater-based viral surveillance is a promising approach to monitor the circulation of SARS-CoV-2 in the general population. The aim of this study was to develop an analytical method to detect SARS-CoV-2 RNA in urban wastewater, to be implemented in the framework of a surveillance network in the Lombardy region (Northern Italy). This area was the first hotspot of COVID-19 in Europe. Composite 24h samples were collected weekly in eight cities from end-March to mid-June 2020 (first peak of the epidemic). The method developed and optimized, involved virus concentration, using PEG centrifugation, and one-step real-time RT-PCR for analysis. SARS-CoV-2 RNA was identified in 65 (61%) out of 107 samples, and the viral concentrations (up to 2.1 E +05 copies/L) were highest in March-April. By mid-June, wastewater samples tested negative in all the cities. Viral loads were used for inter-city comparison and Brembate, Ranica and Lodi had the highest. The pattern of decrease of SARS-CoV-2 in wastewater was closely comparable to the decline of active COVID-19 cases in the population, reflecting the effect of lock-down. Wastewater surveillance of SARS-CoV-2 can integrate ongoing virological surveillance of COVID-19, providing information from both symptomatic and asymptomatic individuals, and monitoring the effect of health interventions.
The COVID-19 pandemic storm in India
Authors: Nesteruk Igor 
Published: May 2021

ABSTRACTThe sharp increase in the number of new COVID-19 patients in India in the second half of April 2021 has caused alarm around the world. A detailed analysis of this pandemic storm is still ahead. We present the results of anterior analysis using a generalized SIR-model (susceptible-infected-removed). The final size of this pandemic wave and its duration are predicted. Obtained results show that the COVID-19 pandemic will be a problem for mankind for a very long time.
Quantifying the relationship between SARS-CoV-2 viral load and infectiousness
Authors: Marc Aurélien , Kerioui Marion , Blanquart François , Bertrand Julie , Mitjà Oriol , Corbacho-Monné Marc , Marks Michael , Guedj Jérémie 
Published: May 2021

AbstractThe relationship between SARS-CoV-2 viral load and infectiousness is not known. Using data from a prospective cohort of index cases and high-risk contact, we reconstructed by modelling the viral load at the time of contact and the probability of infection. The effect of viral load was particularly large in household contacts, with a transmission probability that increased to as much as 37% when the viral load was greater than 10 log10 copies per mL. The transmission probability peaked at symptom onset in most individuals, with a median probability of transmission of 15%, that hindered large individual variations (IQR: [8, 37]). The model also projects the effects of variants on disease transmission. Based on the current knowledge that viral load is increased by 2 to 4-fold on average, we estimate that infection with B1.1.7 virus could lead to an increase in the probability of transmission by 8 to 17%.
Comparing Patient Reported Outcomes to Objective Measures of Function in patients with Chronic Pain: Using the SF-12, 2 minute walk test and Elevation and Movement Lift test
Authors: Gupta Gaurav , Paquet-Proulx Emilie , Besemann LCol Markus , Burton Kira , Lalonde Sasha , Minerbi Amir 
Published: May 2021

AbstractIntroductionAn Ideal battery of testing for function would be inexpensive, easily administered, standardized and validated for multiple health issues. This would also be sensitive to change over time and able to extrapolate avocational and vocational tasks. The data collection exercise for this study included both subjective and objective measures which include the Short Form Health Survey 12 (SF-12), the 2 minute walk test (2MWT) and a newly developed upper extremity strength/conditioning activity called the Elevation and Movement Lift test (EMLi).MethodsA convenience sample of 102 patients with chronic pain. They were seen in the Canadian Forces Health Services Unit (CFHSU (O)) Physiatry Clinic between January-September 2019 and were asked to complete the data intake protocol. This included: completing a questionnaire with the Numeric Rating Pain Scale (NRS) covering the previous 7 days, the SF-12, and completed the 2 MWT and EMLi.ResultsFor the 2MWT heart rate, perceived exertion and number of steps were all increased for patients with chronic pain compared to the control group. There was no difference noted between patients with upper/lower body pain. In patients with chronic pain SF-12 physical function score negatively correlated with perceived exertion but not performance. As for the EMLI test, all groups had similar perceived exertion and heart rate outcomes but a reduced performance was noted with the upper extremity group.DiscussionFor the 2MWT, the individual’s performance related to effort and not their pain state, PE and SF-12. This suggests a higher capacity for walking then the patients realise. As for the EMLi, individual’s performance was poorer for same level of effort. This correlates to their perceived function as seen on the SF-12 which might measure pain related dysfunction.ConclusionThe 2MWT performance was effort dependent and not correlated with perceived abilities. Therefore it can be used to challenge patient performance. EMLi performance correlated with perception and upper extremity pain. This could be used to set clinical training targets and monitor each individual’s progress.