bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocol for a Feasibility study incorporating a Randomised Pilot Trial with an Embedded Process Evaluation and Feasibility Economic Analysis of ThinkCancer!: A primary care intervention to expedite cancer diagnosis in Wales
Authors: Disbeschl Stefanie , Surgey Alun , Roberts Jessica L , Hendry Annie , Lewis Ruth , Goulden Nia , Hoare Zoe , Williams Nefyn , Anthony Bethany Fern , Edwards Rhiannon Tudor , Law Rebecca-Jane , Hiscock Julia , Carson-Stevens Andrew , Neal Richard D , Wilkinson Clare 
Published: December 2020

ABSTRACTBackgroundRelative to the rest of Europe, the UK has relatively poor cancer outcomes, with late diagnosis and a slow referral process being major contributors. General practitioners (GPs) are often faced with patients presenting with a multitude of non-specific symptoms that could be cancer. Safety netting can be used to manage diagnostic uncertainty by ensuring patients with vague symptoms are appropriately monitored, which is now even more crucial due to the ongoing Covid-19 pandemic and its major impact on cancer referrals. The ThinkCancer! Workshop is an educational behaviour change intervention aimed at the whole general practice team, designed to improve primary care approaches to ensure timely diagnosis of cancer. The workshop will consist of teaching and awareness sessions, the appointment of a Safety Netting Champion and the development of a bespoke Safety Netting Plan, and has been adapted so it can be delivered remotely. This study aims to assess the feasibility of the ThinkCancer! Intervention for a future definitive randomised controlled trial.MethodsThe ThinkCancer! study is a randomised, multisite feasibility trial, with an embedded process evaluation and feasibility economic analysis. Twenty-three to 30 general practices will be recruited across Wales, randomised in a ratio of 2:1 of intervention versus control who will follow usual care. The workshop will be delivered by a GP educator and will be adapted iteratively throughout the trial period. Baseline practice characteristics will be collected via questionnaire. We will also collect Primary Care Intervals (PCI), Two Week Wait (2WW) referral rates, conversion rates and detection rates at baseline and six months post-randomisation. Participant feedback, researcher reflections and economic costings will be collected following each workshop. A process evaluation will assess implementation using an adapted Normalisation Measure Development (NoMAD) questionnaire and qualitative interviews. An economic feasibility analysis will inform a future economic evaluation.DiscussionThis study will allow us to test and further develop a novel evidenced-based complex intervention aimed at general practice teams to expedite the diagnosis of cancer in primary care. The results from this study will inform the future design of a full-scale definitive phase III trial.Trial registratiointended registry: clinicaltrials.gov
The Impact of Coronavirus Disease 2019 Pandemic on People with Diabetes in Indonesia: A Cross Sectional National Scale Web-Survey
Authors: Kshanti Ida Ayu , Epriliawati Marina , Mokoagow Md Ikhsan , Nasarudin Jerry , Magfira Nadya 
Published: December 2020

ABSTRACTBackgroundAs the country with the 7th largest number of People with Diabetes (PWD) in the world, the COVID-19 pandemic, and the Large Social Scale Restriction (LSSR) policy taken by the Indonesian government to reduce the number of COVID-19 transmissions is estimated to interfere diabetes management and will increase the incidence of diabetes complications. This study aims to determine the difficulties of diabetes management and its impact on diabetes morbidity during the COVID-19 pandemic in Indonesia.MethodologyThis study is a cross-sectional study using a national scale web survey. This research was conducted in Indonesia enrolling 1,124 PWD aged 18 years or older. Diabetes complications are defined as any incidence of hypoglycaemia, or Diabetic Foot Ulcer (DFU), or hospital admission experienced by PWD in Indonesia during the COVID-19 pandemic. The correlation between diabetes management difficulties and diabetes-related complications was measured using a modified cox regression test.ResultsDiabetes management difficulties were experienced by 69.8% of PWD in Indonesia. The difficulties include attending diabetes consultation 30.1%, access to diabetes medication 12.4%, checking blood sugar levels 9.5%, controlling diet 23.8%, and performing regular exercise 36.5%. Diabetes-related complications occurred in 24.6% of subjects. Those who had diabetes management difficulties during the COVID-19 pandemic are prone to have diabetes complications by 1.4 times greater (PR: 1.41, 95% CI: 1.09-1.83) than those who did not.ConclusionThe COVID-19 pandemic and LSSR have a substantial impact on diabetes management and indirectly increased diabetes morbidity in Indonesia.
Correlation between adult tobacco smoking prevalence and mortality of Coronavirus Disease-19 across the world
Authors: Magfira Nadya , Helda  
Published: December 2020

AbstractBackground and aimCoronavirus disease 2019 (COVID-19) is a global pandemic spreading worldwide. Limited studies showed that smokers were at higher risk of having severe complications and higher mortality. This study aims to analyze the possible correlation between adult tobacco smoking prevalence and COVID-19 mortality all over the world.MethodsThis is a correlation study, we conducted a linear regression to analyse the correlation between smoking prevalence data in adults and COVID-19 Case Fatality Ratio (CFR) in countries with 1000 confirmed COVID-19 cases on May 3, 2020.ResultsSeventy-five country included with median CFR 3.66%. There are no relationships between adult male or female smoking prevalence with COVID-19 mortality in all over the countries. The multivariate analysis showed p-values of 0.823 and 0.910 for male and female smoking prevalence respectively. However, in lower-middle-income countries (LMIC), there is a positive correlation between the prevalence of adult male smoking with the lethality of COVID-19. Each percentage point increase in adult male smoking prevalence caused a CFR of COVID-19 increase by 0.08% (95% CI 0.00%-0.15%, p=0.041).ConclusionsA correlation was found between the prevalence of adult male smoking and the CFR of COVID-19 in lower middle-income countries. Based on these findings, strengthening tobacco control policies is needed to reduce the impact of the COVID-19 pandemic especially in LMIC. Further researches are still needed.
Which COVID policies are most effective? A Bayesian analysis of COVID-19 by jurisdiction
Authors: Wibbens Phebo , Koo Wesley Wu-Yi , McGahan Anita M. 
Published: December 2020

AbstractThis paper reports the results of a Bayesian analysis on large-scale empirical data to assess the effectiveness of eleven types of COVID-control policies that have been implemented at various levels of intensity in 40 countries and U.S. states since the onset of the pandemic. The analysis estimates the marginal impact of each type and level of policy as implemented in concert with other policies. The purpose is to provide policymakers and the general public with an estimate of the relative effectiveness of various COVID-control strategies. We find that a set of widely implemented core policies reduces the spread of virus but not by enough to contain the pandemic except in a few highly compliant jurisdictions. The core policies include the cancellation of public events, restriction of gatherings to fewer than 100 people, recommendation to stay at home, recommended restrictions on internal movement, implementation of a partial international travel ban, and coordination of information campaigns. For the median jurisdiction, these policies reduce growth rate in new infections from an estimated 270% per week to approximately 49% per week, but this impact is insufficient to prevent eventual transmission throughout the population because containment occurs only when a jurisdiction reduces growth in COVID infection to below zero. Most jurisdictions must also implement additional policies, each of which has the potential to reduce weekly COVID growth rate by 10 percentage points or more. The slate of these additional high-impact policies includes targeted or full workplace closings for all but essential workers, stay-at-home requirements, and targeted school closures.
High efficacy of saliva in detecting SARS-CoV-2 by RT-PCR in adults and children
Authors: Huber Michael , Schreiber Peter W. , Scheier Thomas , Audigé Annette , Buonomano Roberto , Rudiger Alain , Braun Dominique L. , Eich Gerhard , Keller Dagmar I. , Hasse Barbara , Böni Jürg , Berger Christoph , Günthard Huldrych F. , Manrique Amapola , Trkola Alexandra 
Published: December 2020

AbstractBackgroundRT-PCR of nasopharyngeal swabs (NPS) is the acknowledged gold standard for the detection of SARS-CoV-2 infection. Rising demands for repetitive screens and mass-testing necessitate, however, the development of additional test strategies. Saliva may serve as an alternative to NPS as its collection is simple, non-invasive and amenable for mass- and home-testing but rigorous validation of saliva particularly in children is missing.MethodsWe conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and nasopharyngeal swab (NPS) of 1270 adults and children reporting to outpatient test centers and an emergency unit for an initial SARS-CoV-2 screen. The saliva collection strategy developed utilizes common, low-cost plastic tubes, does not create biohazard waste at collection and was tailored for self-collection and suitability for children.ResultsIn total, 273 individuals were tested SARS-CoV-2 positive in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (Overall Percent Agreement = 97.8%). Despite lower viral loads in saliva of both adults and children, detection of SARS-CoV-2 in saliva compared well to NPS (Positive Percent Agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (Positive Predictive Value = 84.8%), underlining that NPS sampling in children can be challenging.ConclusionsThe comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2 with particular advantages for testing children that is readily applicable to increase and facilitate repetitive and mass-testing in adults and children.Article Summary Main PointsComparison with nasopharyngeal swabs in a large test center-based study confirms that saliva is a reliable and convenient material for the detection of SARS-CoV-2 by RT-PCR in adults and increases detection efficacy in children.
Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater
Authors: Whitney Oscar N. , Kennedy Lauren C. , Fan Vinson , Hinkle Adrian , Kantor Rose , Greenwald Hannah , Crits-Christoph Alexander , Al-Shayeb Basem , Chaplin Mira , Maurer Anna C. , Tjian Robert , Nelson Kara L. 
Published: December 2020

ABSTRACTWastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods’ sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled “Sewage, Salt, Silica and SARS-CoV-2” (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol and silica RNA capture matrices to recover 6-fold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, both suitable as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and could be performed in approximately 3 hours. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.SYNOPSISThe 4S method for measuring SARS-CoV-2 in wastewater is promising for effective, economical, and accessible wastewater-based epidemiology.ABSTRACT ART
Designing and validating a Markov model for hospital-based addiction consult service impact on 12-month drug and non-drug related mortality
Authors: King Caroline A. , Englander Honora , Korthuis P. Todd , Barocas Joshua A. , McConnell K. John , Morris Cynthia D. , Cook Ryan 
Published: December 2020

AbstractIntroductionAddiction consult services (ACS) engage hospitalized patients with opioid use disorder (OUD) in care and help meet their goals for substance use treatment. Little is known about how ACS affect mortality for patients with OUD. The objective of this study was to design and validate a model that estimates the impact of ACS care on 12-month mortality among hospitalized patients with OUD.MethodsWe developed a Markov model of referral to an ACS, post-discharge engagement in SUD care, and 12-month drug-related and non-drug related mortality among hospitalized patients with OUD. We populated our model using Oregon Medicaid data and validated it using international modeling standards.ResultsThere were 6,654 patients with OUD hospitalized from April 2015 through December 2017. There were 114 (1.7%) drug-related deaths and 408 (6.1%) non-drug related deaths at 12 months. Bayesian logistic regression models estimated four percent (4%, 95% CI= 2%, 6%) of patients were referred to an ACS. Of those, 47% (95% CI= 37%, 57%) engaged in post-discharge OUD care, versus 20% not referred to an ACS (95% CI= 16%, 24%). The risk of drug-related death at 12 months among patients in post-discharge OUD care was 3% (95% CI= 0%, 7%) versus 6% not in care (95% CI = 2%, 10%). The risk of non-drug related death was 7% (95% CI =1%, 13%) among patients in post-discharge OUD treatment, versus 9% not in care (95% CI= 5%, 13%).DiscussionOur novel Markov model reflects trajectories of care and survival for patients hospitalized with OUD. This model can be used to evaluate the impact of other clinical and policy changes to improve patient survival.
Implications of delayed reopening in controlling the COVID-19 surge in Southern and West-Central USA
Authors: Dandekar Raj , Wang Emma , Barbastathis George , Rackauckas Chris 
Published: December 2020

1SUMMARYIn the wake of the rapid surge in the Covid-19 infected cases seen in Southern and West-Central USA in the period of June-July 2020, there is an urgent need to develop robust, data-driven models to quantify the effect which early reopening had on the infected case count increase. In particular, it is imperative to address the question: How many infected cases could have been prevented, had the worst affected states not reopened early? To address this question, we have developed a novel Covid-19 model by augmenting the classical SIR epidemiological model with a neural network module. The model decomposes the contribution of quarantine strength to the infection timeseries, allowing us to quantify the role of quarantine control and the associated reopening policies in the US states which showed a major surge in infections. We show that the upsurge in the infected cases seen in these states is strongly co-related with a drop in the quarantine/lockdown strength diagnosed by our model. Further, our results demonstrate that in the event of a stricter lockdown without early reopening, the number of active infected cases recorded on 14 July could have been reduced by more than 40% in all states considered, with the actual number of infections reduced being more than 100, 000 for the states of Florida and Texas. As we continue our fight against Covid-19, our proposed model can be used as a valuable asset to simulate the effect of several reopening strategies on the infected count evolution; for any region under consideration.
Low-cost, Smartphone-based Specular Imaging and Automated Analysis of the Corneal Endothelium
Authors: Mantena Sreekar , Chandra Jay , Pecyna Eryk , Zhang Andrew , Garrity Dominic , Tone Stephan Ong , Sastry Srinivas , Uddaraju Madhu , Jurkunas Ula V. 
Published: December 2020

ABSTRACTPurposeSpecular and confocal microscopes are important tools to monitor the health of the corneal endothelium (CE), but their high costs significantly limit accessibility in low-resource environments. In our study, we developed and validated a low-cost, fully automated method to quantitatively evaluate the CE using smartphone-based specular microscopy.MethodsA OnePlus 7 Pro smartphone attached to a Topcon SL-D701 slit-lamp was used to image normal the central corneal endothelium using the specular reflection technique. Images were automatically processed on-device and endothelial cell density (ECD), percentage of hexagonal cells (HEX), and coefficient of variation (CV) values were determined using our novel image analysis algorithm. The morphometric parameters generated from the images taken by Tomey EM-4000 specular microscope were compared between the testing modalities.ResultsNo significant differences in ECD (2799 ± 156 cells/mm2 vs 2779 ± 166 cells/mm2; p=0.28) and HEX (52 ± 6% vs 53 ± 6%; p=0.50) computed by smartphone-based specular imaging and specular microscope, respectively, were found. A statistically significant difference in CV (34 ± 3% vs 30 ± 3%; p<0.01) was found between the two methods. The concordance achieved between the smartphone-based method and the Tomey specular microscope is very similar to the concordance between two specular microscopes reported in the literature.ConclusionsSmartphone-based specular imaging and automated analysis is a low-cost method to quantitatively evaluate the CE with accuracy comparable to the clinical standard.Translational RelevanceThis tool can be used to screen the CE in low-resource regions and reveal the need for further investigation of suspected corneal endotheliopathies.
Effect of Vitamin D deficiency on COVID-19 status: A systematic review
Authors: Das Pranta , Samad Nandeeta , Ahinkorah Bright Opoku , Peprah Prince , Mohammed Aliu , Seidu Abdul-Aziz 
Published: December 2020

AbstractBackgroundOne major micronutrient known to have a possible protective effect against COVID-19 disease is vitamin D. This systematic review sought to identify and synthesise available evidence to aid the understanding of the possible effect of vitamin D deficiency on COVID-19 status and health outcomes in COVID-19 patients.MethodsThree databases PubMed, ScienceDirect, and Google Scholar were searched systematically to obtain English language journal article published within 1/12/2019 and 3/11/2020. The search consisted of the terms (“Vitamin D,” OR “25□Hydroxyvitamin D,” OR “Low Vitamin D.”) AND (“COVID-19” OR “2019-nCoV” OR “Coronavirus” OR “SARS-CoV-2”) AND (“disease severity” OR “IMV” OR “ICU admission” OR “mortality” OR “hospitalization” OR “infection”). We followed the recommended PRISMA guidelines in executing this study. After going through the screening of the articles, eleven articles were included in the review.FindingsAlmost all the included studies reported a positive association between Vitamin D sufficiency and COVID-19 status and health outcomes. Vitamin D deficient patients (< 25 ng/mL) are 5.84 times [aOR=6.84, p=0.01] more likely to die from COVID-19 compared to the vitamin D sufficient people. Another study also found that Vitamin D deficiency is associated with higher risk of death with Hazard ratio (HR) 14.73, p<0.001. Vitamin D deficient (<12 ng/mL) people were 2.2 times [aOR=3.2, p=0.07] more likely to develop severe COVID-19 after adjusting for age, gender, obesity, cardiac disease, and kidney disease compared to the vitamin D sufficient people. One study found that after controlling for confounders, patients with low 25(OH)D (<30 ng/mL) level are more likely [aOR=1.45, p=<0.001] to be COVID-19 infected compared to the patients with 25(OH)D level >=30 ng/mL.ConclusionFindings from the study included suggest Vitamin D may serve as a mitigating effect for covid-19 infection, severity and mortality. We recommend the need to encourage people to eat foods rich in vitamin D such as fish, red meat, liver and egg yolks whiles at the same time providing vitamin D supplements for individuals with COVID-19 in order to boost their immune systems.
Vaginal Microbiome Topic Modelling of Laboring Ugandan Women With and Without Fever
Authors: Movassagh Mercedeh , Bebell Lisa M. , Burgoine Kathy , Hehnly Christine , Zhang Lijun , Moran Kim , Sheldon Kathryn , Sinnar Shamim A. , Mbabazi Edith , Kumbakumba Elias , Bazira Joel , Ochoa Moses , Mulondo Ronnie , Nsubuga Brian K. , Weeks Andrew , Gladstone Melissa , Olupot-Olupot Peter , Ngonzi Joseph , Roberts Drucilla J. , Meier Frederick A. , Irizarry Rafael , Broach James , Schiff Steven J. , Paulson Joseph N. 
Published: December 2020

AbstractThe composition of the maternal vaginal microbiome may influence the duration of pregnancy, onset of labor and even neonatal outcomes. Maternal microbiome research in sub Saharan-Africa has focused on non-pregnant and postpartum composition of the vaginal microbiome. We examined the vaginal microbiome composition of 99 laboring Ugandan women using routine microbiology and 16S ribosomal DNA sequencing from two hypervariable regions (V1-V2 and V3-V4), using standard hierarchical methods. We then introduce Grades of Membership (GoM) modeling for the vaginal microbiome, a method often used in the text mining machine learning literature. Leveraging GoM models, we create a basis composed of a small number of microbial ‘topic’s whose linear combination optimally represents each patient yielding more accurate associations. We identified relationships between defined communities and the presentation or absence of intrapartum fever. Using a random forest model we showed that by including novel microbial topic models we improved upon clinical variables to predict maternal fever. We also show by integrating clinical variables with a microbial topic model into this model found young maternal age, fever report earlier in the current pregnancy, and longer labors, as well as a more diverse, lessLactobacillusdominated microbiome were features of labor associated with intrapartum fever. These results better define relationships between presentation or absence of intrapartum fever, demographics, peripartum course, and vaginal microbial communities, and improve our understanding of the impact of the microbiome on maternal and neonatal infection risk.