bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing COVID-19 Risk, Vulnerability and Infection Prevalence in Communities
Authors: Kiaghadi Amin , Rifai Hanadi S. , Liaw Winston
Published: May 2020

Background

The spread of coronavirus in the United States with nearly one million confirmed cases and over 53,000 deaths has strained public health and health care systems. While many have focused on clinical outcomes, less attention has been paid to vulnerability and risk of infection. In this study, we developed a planning tool that examines factors that affect vulnerability to COVID-19.

Methods

Across 46 variables, we defined five broad categories: 1) access to medical, 2) underlying health conditions, 3) environmental exposures, 4) vulnerability to natural disasters, and 5) sociodemographic, behavioral, and lifestyle factors. We also used reported rates for morbidity, hospitalization, and mortality in other regions to estimate risk at the county (Harris County) and census tract levels.

Analysis

A principal component analysis was undertaken to reduce the dimensions. Then, to identify vulnerable census tracts, we conducted rank-based exceedance and K-means cluster analyses.

Results

Our study showed a total of 722,357 (~17% of the County population) people, including 171,403 between the ages of 45-65 (~4% of County’s population), and 76,719 seniors (~2% of County population), are at a higher risk based on the aforementioned categories. The exceedance and K-means cluster analysis demonstrated that census tracts in the northeastern, eastern, southeastern and northwestern regions of the county are at highest risk. The results of age-based estimations of hospitalization rates showed the western part of the County might be in greater need of hospital beds. However, cross-referencing the vulnerability model with the estimation of potential hospitalized patients showed that part of the County has the least access to medical facilities.

Conclusion

Policy makers can use this planning tool to identify neighborhoods at high risk for becoming hot spots; efficiently match community resources with needs, and ensure that the most vulnerable have access to equipment, personnel, and medical interventions.
Protocol for a systematic review of qualitative and quantitative effects of cardiovascular disease risk communication using ‘heart age’ concepts
Authors: Bonner Carissa , Batcup Carys , Cornell Samuel , Fajardo Michael Anthony , Doust Jenny , McGeechan Kevin , Trevena Lyndal
Published: May 2020

Introduction

The concept of ‘heart age’ is increasingly used for health promotion and alongside clinical guidelines for cardiovascular disease (CVD) prevention. These tools have been used by millions of consumers around the world, and many health organisations promote them as a way of encouraging lifestyle change. However, heart age tools vary widely in terms of their underlying risk models and display formats, the effectiveness of these tools compared to other CVD risk communication formats remains unclear, and doctors have raised concerns over their use to expand testing of healthy low risk adults.

Methods and analysis

We aim to systematically review both qualitative and quantitative evidence of the effects of heart age when presented to patients or consumers for the purpose of CVD risk communication. Four electronic databases will be search until April 2020 and reference lists from similar review articles will be searched. Studies will be considered eligible if they meet the following criteria: (1) published from the inception of the database to April 2020, in peer-reviewed journals, (2) used an adult population (over 18 years of age) or, if not explicit regarding age, are clear that participants were not children, (3) present the concept of ‘heart age’ to patients or consumers for the purpose of CVD risk communication, (4) report qualitative themes or quantitative outcomes relating to psychological and/or behavioural responses to heart age. Two reviewers will perform study selection, data extraction and quality assessment. Reporting of the review will be informed by Preferred Reporting Items for Systematic Review and Meta-Analysis guidance.

Ethics and dissemination

Ethical approval is not required as it is a protocol for a systematic review. Findings will be disseminated through peer-reviewed publications and conference presentations.
A comparative meta andin silicoanalysis of differentially expressed genes and proteins in canine and human bladder cancer
Authors: Gambim Victoria Vitti , Laufer-Amorim Renee , Alves Ricardo Fonseca , Grieco Valeria , Fonseca-Alves Carlos Eduardo
Published: May 2020

Canine and human bladder cancer present several similar anatomical, morphological and molecular characteristics and dogs can be considered a model for human bladder cancer. However, the veterinary literature lacks information regarding cross validation analysis between human and canine large-scale data. Therefore, this research aimed to perform a meta-analysis of the previous canine literature on bladder cancer, identifying genes and protein previously evaluated in these studies. Besides that, we also performed a cross validation of the canine transcriptome data and the human data from The Cancer Genome Atlas (TCGA) to identify potential markers for both species. It was performed a meta-analysis using the following indexing terms “bladder” AND “carcinoma” AND “dog” in different international databases and 385 manuscripts were identified in our initial search. Then, several inclusion criteria were applied and only 25 studies met these criteria. Among these studies, five presented transcriptome data and 20 evaluated only isolated genes or proteins.

Regarding the studies involving isolated protein analysis, HER-2 protein was the most studied (3/20), followed by TAG-72 (2/20), COX-2 (2/2), Survivin (2/2) and CK7 (2/2). Regarding the cross-validation analysis of human and canine transcriptome data, we identified 35 deregulated genes, includingERBB2, TP53, EGFRandE2F2. Our results demonstrated that the previous canine literature on bladder cancer was focused on the evaluation of isolated markers with no association with patient’s survival. Besides that, the lack of information regarding tumor muscle-invasion can be considered an important limitation when comparing human and canine bladder tumors. Our in-silico analysis involving canine and human transcriptome data provided several genes with potential to be markers for both human and canine bladder tumors and these genes should be considered for future studies on canine bladder cancer.
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

Background

The 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.

Methods

We 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.

Results

Of 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%).

Conclusion

We 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

Background

There 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).

Methods

We 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.

Results

In 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).

Conclusions

Higher 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.
Determinants of Severity in Cancer Patients with COVID-19 Illness
Authors: Robilotti Elizabeth V. , Babady N. Esther , Mead Peter A. , Rolling Thierry , Perez-Johnston Rocio , Bernardes Marilia , Bogler Yael , Caldararo Mario , Ortiz Cesar J. Figueroa , Glickman Michael S. , Joanow Alexa , Kaltsas Anna , Lee Yeon Joo , Bianchi Anabella Lucca , Mariano Amanda , Morjaria Sejal , Nawar Tamara , Papanicolaou Genovefa A. , Predmore Jacqueline , Redelman-Sidi Gil , Schmidt Elizabeth , Seo Susan K. , Sepkowitz Kent , Shah Monika , Wolchok Jedd D. , Hohl Tobias M. , Taur Ying , Kamboj Mini
Published: May 2020

New York State had 180,458 cases of SARS-CoV-2 and 9385 reported deaths as of April 10th, 2020. Patients with cancer comprised 8.4% of deceased individuals1. Population-based studies from China and Italy suggested a higher COVID-19 death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-19 disease4. This information is critical to balance the competing safety considerations of reducing SARS-CoV-2 exposure and cancer treatment continuation. Since March 10th, 2020 Memorial Sloan Kettering Cancer Center (MSKCC) performed diagnostic testing for SARS-CoV-2 in symptomatic patients. Overall, 40% out of 423 patients with cancer were hospitalized for COVID-19 illness, 20% developed severe respiratory illness, including 9% that required mechanical ventilation, and 9% that died. On multivariate analysis, age ≥ 65 years and treatment with immune checkpoint inhibitors (ICI) within 90 days were predictors for hospitalization and severe disease, while receipt of chemotherapy within 30 days and major surgery were not. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. Association between ICI and COVID-19 outcomes will need interrogation in tumor-specific cohorts.
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

Background

The 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.

Methods

In 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.

Results

Overall 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.

Conclusions

Our 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

We 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 line

We 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

Background

Rapid 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.

Methods

We 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).

Results

Of 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.

Conclusions

We 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

Following 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

Clinically 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

Purpose

Given 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.

Methods

Using 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.

Results

Nearly 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.

Conclusions

Nearly 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

Abstract

Background

Bacterial 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.

Methods

South 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.

Results

SAHPRA 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.

Conclusion

Navigation 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 registration

This 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

Deaths 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

Objective

The subjective experiences were assessed of cochlear implant (CI) users either wearing or not wearing a hearing aid (HA) at the contralateral ear.

Design

Unilateral 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 sample

Twenty-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).

Results

Comparisons 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.

Conclusions

Bimodal 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

Abstract

With 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

Observational 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.
WMHs AND HOMOCYSTEINE LEVELS AS CANDIDATE BIOMARKER FOR COGNITIVE IMPAIRMENT
Authors: Misra Vivek , Krishnamoorthy Ennapadam S. , Balaji Shruti , Kuppan Jayandrakumar , Nagarajan K
Published: May 2020

The aim of this pilot study was to test the hypotheses that a) WMHs would be a biological marker in South Indian patients who present with either cognitive impairment, dementia or depression and b) presence of WMHs would be related to other blood biochemical markers. A significant positive correlation was present between temporal WMHs and increased homocysteine levels. A significant inverse correlation was obtained between MMSE scores and frontal caps. Association between temporal WMHs and elevated plasma homocysteine levels implies that this can serve as a biological marker for cognitive impairment and possibly for therapy.
Multivariate Prediction Network Model for epidemic progression to study the effects of lockdown time and coverage on a closed community on theoretical and real scenarios of COVID-19
Authors: Abramov Dimitri Marques , Junior Saint-Clair Gomes
Published: May 2020

The aim of this study was to develop a realistic network model to predict the relationship between lockdown duration and coverage in controlling the progression of the incidence curve of an epidemic with the characteristics of COVID-19 in two scenarios (1) a closed and non-immune population, and (2) a real scenario from State of Rio de Janeiro from May 6th 2020.

Effects of lockdown time and rate on the progression of an epidemic incidence curve in a virtual population of 10 thousand subjects. Predictor variables were reproductive values established in the most recent literature (R0 =2.7 and 5.7, and Re = 1.28 from Rio de Janeiro State at May 6th), without lockdown and with coverages of 25%, 50%, and 90% for 21, 35, 70, and 140 days in up to 13 different scenarios for each R0/Re, where individuals remained infected and transmitters for 14 days. We estimated model validity in theoretical and real scenarios respectively by applying an exponential model on the incidence curve with no lockdown with growth rate coefficient observed in realistic scenarios, and (2) fitting real data series from RJ upon simulated data, respectively.

For R0=5.7, the flattening of the curve occurs only with long lockdown periods (70 and 140 days) with a 90% coverage. For R0=2.7, coverages of 25 and 50% also result in curve flattening and reduction of total cases, provided they occur for a long period (70 days or more). For realistic scenario in Rio de Janeiro, lockdowns +25% or more from May 6th during 140 days showed expressive flattening and number of COVID cases two to five times lower. If a more intense coverage lockdown (about +25 to +50% as much as the current one) will be implemented until June 6th during at least 70 days, it is still possible reduce nearly 40-50% the impact of pandemy in state of Rio de Janeiro.

These data corroborate the importance of lockdown duration regardless of virus transmission and sometimes of intensity of coverage, either in realistic or theoretical scenarios of COVID-10 epidemics. Even later, the improvement of lockdown coverage can be effective to minimize the impact of epidemic.
Urban Air Pollution May Enhance COVID-19 Case-Fatality and Mortality Rates in the United States
Authors: Liang Donghai , Shi Liuhua , Zhao Jingxuan , Liu Pengfei , Schwartz Joel , Gao Song , Sarnat Jeremy , Liu Yang , Ebelt Stefanie , Scovronick Noah , Chang Howard H
Published: May 2020

Background

The novel human coronavirus disease 2019 (COVID-19) pandemic has claimed more than 240,000 lives worldwide, causing tremendous public health, social, and economic damages. While the risk factors of COVID-19 are still under investigation, environmental factors, such as urban air pollution, may play an important role in increasing population susceptibility to COVID-19 pathogenesis.

Methods

We conducted a cross-sectional nationwide study using zero-inflated negative binomial models to estimate the association between long-term (2010-2016) county-level exposures to NO2, PM2.5 and O3 and county-level COVID-19 case-fatality and mortality rates in the US. We used both single and multipollutant models and controlled for spatial trends and a comprehensive set of potential confounders, including state-level test positive rate, county-level healthcare capacity, phase-of-epidemic, population mobility, sociodemographic, socioeconomic status, behavior risk factors, and meteorological factors.

Results

1,027,799 COVID-19 cases and 58,489 deaths were reported in 3,122 US counties from January 22, 2020 to April 29, 2020, with an overall observed case-fatality rate of 5.8%. Spatial variations were observed for both COVID-19 death outcomes and long-term ambient air pollutant levels. County-level average NO2 concentrations were positively associated with both COVID-19 case-fatality rate and mortality rate in single-, bi-, and tri-pollutant models (p-values<0.05). Per inter-quartile range (IQR) increase in NO2 (4.6 ppb), COVID-19 case-fatality rate and mortality rate were associated with an increase of 7.1% (95% CI 1.2% to 13.4%) and 11.2% (95% CI 3.4% to 19.5%), respectively. We did not observe significant associations between long-term exposures to PM2.5 or O3 and COVID-19 death outcomes (p-values>0.05), although per IQR increase in PM2.5 (3.4 ug/m3) was marginally associated with 10.8% (95% CI: −1.1% to 24.1%) increase in COVID-19 mortality rate.

Discussions and Conclusions

Long-term exposure to NO2, which largely arises from urban combustion sources such as traffic, may enhance susceptibility to severe COVID-19 outcomes, independent of longterm PM2.5 and O3 exposure. The results support targeted public health actions to protect residents from COVID-19 in heavily polluted regions with historically high NO2 levels. Moreover, continuation of current efforts to lower traffic emissions and ambient air pollution levels may be an important component of reducing population-level risk of COVID-19 deaths.
Training deep learning algorithms with weakly labeled pneumonia chest X-ray data for COVID-19 detection
Authors: Rajaraman Sivaramakrishnan , Antani Sameer
Published: May 2020

The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused a pandemic resulting in over 2.7 million infected individuals and over 190,000 deaths and growing. Respiratory disorders in COVID-19 caused by the virus commonly present as viral pneumonia-like opacities in chest X-ray images which are used as an adjunct to the reverse transcription-polymerase chain reaction test for confirmation and evaluating disease progression. The surge places high demand on medical services including radiology expertise. However, there is a dearth of sufficient training data for developing image-based automated decision support tools to alleviate radiological burden. We address this insufficiency by expanding training data distribution through use of weakly-labeled images pooled from publicly available CXR collections showing pneumonia-related opacities. We use the images in a stage-wise, strategic approach and train convolutional neural network-based algorithms to detect COVID-19 infections in CXRs. It is observed that weakly-labeled data augmentation improves performance with the baseline test data compared to non-augmented training by expanding the learned feature space to encompass variability in the unseen test distribution to enhance inter-class discrimination, reduce intra-class similarity and generalization error. Augmentation with COVID-19 CXRs from individual collections significantly improves performance compared to baseline non-augmented training and weakly-labeled augmentation toward detecting COVID-19 like viral pneumonia in the publicly available COVID-19 CXR collections. This underscores the fact that COVID-19 CXRs have a distinct pattern and hence distribution, unlike non-COVID-19 viral pneumonia and other infectious agents.
Asthma and COVID-19 in children – a systematic review and call for data
Authors: Castro-Rodriguez Jose A. , Forno Erick
Published: May 2020

Rationale

Whether asthma constitutes a risk factor for COVID-19 is unclear.

Methods

We performed a systematic literature search in three stages: First, we reviewed PubMed, EMBASE and CINAHL for systematic reviews of SARS-CoC-2 and COVID-19 in pediatric populations, and reviewed their primary articles; next, we searched PubMed for studies on COVID-19 or SARS-CoV-2 and asthma/wheeze, and evaluated whether the resulting studies included pediatric populations; lastly, we repeated the second search in BioRxiv.org and MedRxiv.org to find pre-prints that may have information on pediatric asthma.

Results

In the first search, eight systematic reviews were found, of which five were done in pediatric population; after reviewing 67 primary studies we found no data on pediatric asthma as a comorbidity for COVID-19. In the second search, we found 25 results in PubMed, of which five reported asthma in adults, but none included data on children. In the third search, 14 pre-prints in MedRxiv were identified with data on asthma, but again none with pediatric data. We found only one report by the U.S. CDC stating that 40/345 (~11.5%) children with data on chronic conditions had “chronic lung diseases including asthma”.

Conclusion

There is scarcely any data on whether childhood asthma (or other pediatric respiratory diseases) constitute risk factors for SARS-CoV-2 infection or COVID-19 severity. Studies are needed that go beyond counting the number of cases in the pediatric age range.
The date predicted 200.000 cases of Covid-19 in Spain using SutteARIMA
Authors: Ahmar Ansari Saleh , del Val Eva Boj
Published: May 2020

The aim of this study is predicted 200.000 cases of Covid-19 in Spain. Covid-19 Spanish confirmed data obtained from Worldometer from 01 March 2020 – 17 April 2020. The data from 01 March 2020 – 10 April 2020 using to fitting with data from 11 April – 17 April 2020. For the evaluation of the forecasting accuracy measures, we use mean absolute percentage error (MAPE). Based on the results of SutteARIMA fitting data, the accuracy of SutteARIMA for the period 11 April 2020 - 17 April 2020 is 0.61% and we forecast 20.000 confirmed cases of Spain by the WHO situation report day 90/91 which is 19 April 2020 / 20 April 2020.
Trends in Perception of COVID-19 in Polish Internet
Authors: Jarynowski Andrzej , Wójta-Kempa Monika , Belik Vitaly
Published: May 2020

INTRODUCTION

Due to the spread of SARS CoV-2 virus responsible for COVID-19 disease, there is an urgent need to analyse COVID-2019 epidemic perception in Poland. This study aims to investigate social perception of coronavirus in the Internet media during the epidemic. It is a signal report highlighting the main issues in public perception and medical commutation in real time.

METHODS

We study the perception of COVID-2019 epidemic in Polish society using quantitative analysis of its digital footprints on the Internet on platforms: Google, Twitter, YouTube, Wikipedia and electronic media represented by Event Registry, from January 2020 to 29.04.2020 (before and after official introduction to Poland on 04.03.20). We present trend analysis with a support of natural language processing techniques.

RESULTS

We identified seven temporal major clusters of interest on the topic COVID-2019: 1) Chinese, 2) Italian, 3) Waiting, 4) Mitigations, 5) Social distancing and Lockdown, 6) Anti-crisis shield, 7) Restrictions releasing. There was an exponential increase of interest when the Polish government “declared war against disease” around 11/12.03.20 with a massive mitigation program. Later on, there was a decay in interest with additional phases related to social distancing and an anti-crisis legislation act with local peaks. We have found that declarations of mitigation strategies by the Polish prime minister or the minister of health gathered the highest attention of Internet users. So enacted or in force events do not affect interest to such extent. Traditional news agencies were ahead of social media (mainly Twitter) in dissemination of information. We have observed very weak or even negative correlations between a colloquial searching term ‘antiviral mask’ in Google, encyclopaedic definition in Wikipedia “SARS-CoV-2” as well official incidence series, implying different mechanisms governing the search for knowledge, panic related behaviour and actual risk of acquiring infection.

CONCLUSIONS

Traditional and social media do not only reflect reality, but also create it. Risk perception in Poland is unrelated to actual physical risk of acquiring COVID-19. As traditional media are ahead of social media in time, we advise to choose traditional news media for a quick dissemination of information, however for a greater impact, social media should be used. Otherwise public information campaigns might have less impact on society than expected.
A mathematically rigorous assessment of the efficiency of quarantining and contact tracing in curbing the COVID-19 epidemic
Authors: Lambert Amaury
Published: May 2020

In our model of the COVID-19 epidemic, infected individuals can be of four types, according whether they are asymptomatic (A) or symptomatic (I), and use a contact tracing mobile phone app (Y) or not (N). We denote by f the fraction of A’s, by y the fraction of Y’s and by R0 the average number of secondary infections from a random infected individual.

We investigate the effect of non-electronic interventions (voluntary isolation upon symptom onset, quarantining private contacts) and of electronic interventions (contact tracing thanks to the app), depending on the willingness to quarantine, parameterized by four cooperating probabilities.

For a given ‘effective’ R0 obtained with non-electronic interventions, we use nonnegative matrix theory and stopping line techniques to characterize mathematically the minimal fraction y0 of app users needed to curb the epidemic. We show that under a wide range of scenarios, the threshold y0 as a function of R0 rises steeply from 0 at R0= 1 to prohibitively large values (of the order of 60 – 70% up) whenever R0 is above 1.3. Our results show that moderate rates of adoption of a contact tracing app can reduce R0 but are by no means sufficient to reduce it below 1 unless it is already very close to 1 thanks to non-electronic interventions.