bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of masks, testing and contact tracing in preventing COVID-19 resurgences: a case study from New South Wales, Australia
Authors: Stuart RM , Abeysuriya Romesh G. , Kerr Cliff C. , Mistry Dina , Klein Daniel J. , Gray Richard , Hellard Margaret , Scott Nick 
Published: October 2020

AbstractObjectivesThe early stages of the COVID-19 pandemic illustrated that SARS-CoV-2, the virus that causes the disease, has the potential to spread exponentially. Therefore, as long as a substantial proportion of the population remains susceptible to infection, the potential for new epidemic waves persists even in settings with low numbers of active COVID-19 infections, unless sufficient countermeasures are in place. We aim to quantify vulnerability to resurgences in COVID-19 transmission under variations in the levels of testing, tracing, and mask usage.SettingThe Australian state of New South Wales, a setting with prolonged low transmission, high mobility, non-universal mask usage, and a well-functioning test-and-trace system.ParticipantsNone (simulation study)ResultsWe find that the relative impact of masks is greatest when testing and tracing rates are lower (and vice versa). Scenarios with very high testing rates (90% of people with symptoms, plus 90% of people with a known history of contact with a confirmed case) were estimated to lead to a robustly controlled epidemic, with a median of ∼180 infections in total over October 1 – December 31 under high mask uptake scenarios, or 260–1,200 without masks, depending on the efficacy of community contact tracing. However, across comparable levels of mask uptake and contact tracing, the number of infections over this period were projected to be 2-3 times higher if the testing rate was 80% instead of 90%, 8-12 times higher if the testing rate was 65%, or 30-50 times higher with a 50% testing rate. In reality, NSW diagnosed 254 locally-acquired cases over this period, an outcome that had a low probability in the model (4-7%) under the best-case scenarios of extremely high testing (90%), near-perfect community contact tracing (75-100%), and high mask usage (50-75%), but a far higher probability if any of these were at lower levels.ConclusionsOur work suggests that testing, tracing and masks can all be effective means of controlling transmission. A multifaceted strategy that combines all three, alongside continued hygiene and distancing protocols, is likely to be the most robust means of controlling transmission of SARS-CoV-2.Strengths and limitations of this studyA key methodological strength of this study is the level of detail in the model that we use, which allows us to capture many of the finer details of the extent to which controlling COVID-19 transmission relies on the balance between testing, contact tracing, and mask usage.Another key strength is that our model is stochastic, so we are able to quantify the probability of different epidemiological outcomes under different policy settings.A key limitation is the shortage of publicly-available data on the efficacy of contact tracing programs, including data on how many people were contacted for each confirmed index case of COVID-19.
Large-scale Testing for SARS-CoV-2 using Tapestry Pooling
Authors: Chakravarthy Anirudh , Krishna Srikar , Ghosh Sumana , Tomar Ajay , Varahan Sriram , Rajwade Ajit , Ghosh Sabyasachi , Gupta Nimay , Agarwal Rishi , Payal Himanshu , Chakraborty Prantik , Vemula Krishna Vishal , Vyas Akanksha , Goru Ritesh , Krishna Sandeep , Palakodeti Dasaradhi , Gopalkrishnan Manoj 
Published: October 2020

AbstractWe have previously described Tapestry Pooling, a scheme to enhance the capacity of RT-qPCR testing, and provided experimental evidence with spiked synthetic RNA to show that it can help to scale testing and restart the economy. Here we report on validation studies with Covid19 patient samples for the Tapestry Pooling scheme with prevalence in the range of 1% to 2%. We pooled RNA extracted from patient samples that were previously tested for Covid19, sending each sample to three pools. Following three different pooling schemes, we pipetted 320 samples into 48 pools with pool size of 20 at prevalence rate of 1.6%, 500 samples into 60 pools with pool size of 25 at prevalence rate of 2%, and 961 samples into 93 pools with pool size of 31 at prevalence rate of 1%. Of the 191 RT-qPCR experiments that we performed, only one pool was incorrect (false negative). Our recovery algorithm correctly called results for the individual samples, with a 100% sensitivity and a 99.9% specificity, with only one false positive across all the 1,781 blinded results required to be called. We show up to 10X savings in number of tests required at a range of prevalence rates and pool sizes. These experiments establish that Tapestry Pooling is robust enough to handle the diversity of sample constitutions and viral loads seen in real-world samples.
Occurrence of Four Dengue Virus Serotypes and Chikungunya Virus in Kilombero, Tanzania during Dengue Outbreak in 2018
Authors: Chipwaza Beatrice , Sumaye Robert David , Weisser Maja , Gingo Winfrid , Yeo Nicholas Kim-Wah , Amrun Siti Naqiah , Okumu Fredros O. , Ng Lisa F.P. 
Published: October 2020

AbstractBackgroundDengue and Chikungunya viruses can cause large-scale epidemics with attack rates exceeding 80%. In Tanzania, there have been repeated outbreaks of dengue fever, the most recent one in 2018 and 2019 mostly reported in coastal areas. Despite its importance, there is limited knowledge on epidemiology of dengue (DENV) and chikungunya (CHIKV) in Tanzania. This study was conducted to investigate the prevalence of DENV and CHIKV in Kilombero district, South-Eastern Tanzania.MethodsA cross-sectional study was conducted at Kibaoni Health Center, in Kilombero district, in the rainy and dry seasons of 2018. Febrile patients of any age and gender were enrolled. Blood samples were taken and screened for DENV and CHIKV viral RNA by real-time RT-PCR assays.ResultsA total of 294 patients were recruited. Most were females (65%), and aged between 14⍰25 years (33%). DENV and CHIKV were detected in 29 (9.9%) and 3 (1.0%) patients, respectively. DENV was detected across all age groups and during both dry and rainy seasons. Although all four DENV serotypes were detected, serotypes 1 and 3 dominated and were present in 14 patients (42.4%) each. Additionally, the study showed DENV-1 and DENV-3 co-infections.ConclusionThis study reveals the co-circulation of all four DENV serotypes and CHIKV in Kilombero district. Importantly, we report the first occurrence of DENV-4 in Tanzania. Unlike previous DENV outbreaks caused by DENV-2, the 2018 outbreak was dominated by DENV-1 and DENV-3. Occurrence of all serotypes suggests the possibility of having severe clinical outcomes in future DENV epidemics in Tanzania.
Migration, Infectious Diseases and Drug Addiction in Russia
Authors: Lifshits Marina , Neklyudova Natalia 
Published: October 2020

AbstractThe aim of the paper is to analyze the possible impact of various aspects of internal and external migration in Russia’s regions on the prevalence of the following social dangerous diseases: HIV, active tuberculosis, syphilis, drug addiction, acute and chronic viral hepatitis B and C. We analyzed the papers that concern the impact of migration on the health of the host territory population. The main research methods are econometric and correlation analysis. We constructed panel models for each disease. The models tested various socioeconomic indicators (including education level, cash income, housing improvements and the incidence of alcoholism), as well as climatic, geographical and demographic indicators. Influence of disease incidence in the neighbouring regions is also considered. Five various indicators of migration were tested. They characterize labour immigration, internal and external migration inflows to the regions and share of people born outside the region. We tried to track changes of factors that influence spread of diseases over time. It allowed us to correct the conclusions drawn earlier. In the course of the research, positive significant statistical correlation of the following indicators of migration and disease incidence was established:foreign citizens employment and incidence of syphilis in 2005;share of internal migrants and incidence of drug addiction in 2005;foreign citizens employment and incidence of drug addiction in 2006-2016;foreign citizens inflow and detection of chronic viral hepatitis in 2010;foreign citizens inflow and detection of acute hepatitis C in 2011-2016.JEL F22; I1; R23
Development and evaluation of a new IgM/IgG rapid diagnostic test for SARS-CoV-2
Authors: Ducrest P.J. 
Published: October 2020

AbstractThere is an urgent need in rapid diagnostic test (RDT) to detect antibodies against SARS-CoV-2. We have developed a rapid and simple point-of-care lateral flow immunoassay (LFIA) detecting IgM and IgG against SARS-CoV-2 in 10 minutes. The aim of this study is to evaluate the diagnostic performance of this RDT. RT-PCR positive plasma samples (n=35) for SARS-CoV-2 and 97 negative control samples were studied. Diagnostic performance of IgG/IgM RDT was assessed using both gold standard RT-PCR and Electro-chemiluminescence immunoassay (ECLIA) Elecsys®Anti-SARS-CoV-2 total Ig. Overall, RDT sensitivity was 100% (95% confidence interval [95%CI]: 88-100%) and specificity 93% (95% CI: 85-97%). This IgG/IgM RDT done in plasma displays a high diagnostic accuracy for SARS-CoV-2 IgG/IgM in high COVID-19 prevalence settings. Its use could be considered in the absence of routine diagnostic serology facilities for samples collected between 10 and 180 days after symptoms onset.
Analysis of the potential for a malaria vaccine to reduce gaps in malaria intervention coverage
Authors: Unwin H. Juliette T. , Mwandigha Lazaro , Winskill Peter , Ghani Azra C. , Hogan Alexandra B. 
Published: October 2020

AbstractBackgroundThe RTS,S/AS01 malaria vaccine is currently being piloted in three African countries. We sought to identify whether vaccination could reach additional children who are at risk from malaria but do not currently have access to, or use, core malaria interventions.MethodsUsing data from household surveys we calculated the overlap between malaria intervention coverage and childhood vaccination (diphtheria-tetanus-pertussis dose 3, DTP3) uptake in 20 African countries with at least one first administrative level unit withPlasmodium falciparumparasite prevalence greater than 10%. We used multilevel logistic regression to explore patterns of overlap by demographic and socioeconomic variables. We also estimated the public health impact of delivering RTS,S/AS01 to those children who do not use an insecticide-treated net (ITN) but who received the DTP3 vaccine.ResultsUptake of DTP3 was higher than malaria intervention coverage in most countries. Overall, 34% of children did not use ITNs and received DTP3, while 35% of children used ITNs and received DTP3, although this breakdown varied by country. We estimated that there are 33 million children in these 20 countries who do not use an ITN. Of these, 23 million (70%) received the DTP3 vaccine. Vaccinating those 23 million children who receive DTP3 but do not use an ITN could avert an estimated 9.7 million clinical malaria cases each year. An additional 10.8 million cases could be averted by vaccinating those 24 million children who receive the vaccine and use an ITN. Children who had access to or used an ITN were 9 to 13% more likely to reside in rural areas compared to those who had neither intervention regardless of vaccination status. Mothers’ education status was a strong predictor of intervention uptake and was positively associated with use of ITNs and vaccination uptake and negatively associated with having access to an ITN but not using it. Wealth was also a strong predictor of intervention coverage.ConclusionsChildhood vaccination to prevent malaria has the potential to reduce inequity in access to existing malaria interventions and could substantially reduce the childhood malaria burden in sub-Saharan Africa, even in regions with lower existing DTP3 coverage.
The risk for a new COVID-19 wave – and how it depends on R0, the current immunity level and current restrictions
Authors: Britton Tom , Trapman Pieter , Ball Frank 
Published: October 2020

AbstractThe COVID-19 pandemic has hit different parts of the world differently: some regions are still in the rise of the first wave, other regions are now facing a decline after a first wave, and yet other regions have started to see a second wave. The current immunity level î in a region is closely related to the cumulative fraction infected, which primarily depends on two factors: a) the initial potential for COVID-19 in the region (often quantified by the basic reproduction number R0), and b) the timing, amount and effectiveness of preventive measures put in place. By means of a mathematical model including heterogeneities owing to age, social activity and susceptibility, and allowing for time-varying preventive measures, the risk for a new epidemic wave and its doubling time, and how they depend on R0, î and the overall effect of the current preventive measures, are investigated. Focus lies on quantifying the minimal overall effect of preventive measures pMin needed to prevent a future outbreak. The first result shows that the current immunity level î plays a more influential roll than when immunity is obtained from vaccination. Secondly, by comparing regions with different R0 and î it is shown that regions with lower R0 and low î may now need higher preventive measures (pMin) compared with other regions having higher R0 but also higher î, even when such immunity levels are far from herd immunity.
Antimicrobial Resistance, Evidences on Irrational Anti-microbial Prescribing and Consumption during COVID-19 Pandemic and Possible Mitigation Strategies: A Bangladesh Perspective
Authors: Parveen Monira , Yeasmin Mahmuda , Molla Md. Maruf Ahmed 
Published: October 2020

AbstractThere are evidences that show increased antimicrobial consumption among COVID-19 patients. This has increased the burden on worsening situation of antimicrobial resistance (AMR) throughout the world. Bangladesh, one of the countries with highest numbers of COVID-19 cases, without effective regulation of antimicrobial prescription may suffer in future with study results showing a significant proportion of participants taking antimicrobial without proper indication and prescription from physicians. Suggested mitigation strategies include – strict regulation of over the counter (OTC) antimicrobial prescription, testing biochemical marker such as procalcitonin prior to initiation of antimicrobial therapy, introduction of color coded and tightly sealed bottled antimicrobial drugs, massive campaigning on social media, effective utilization of telemedicine and finally, raising awareness among physicians and patients regarding judicial use of antimicrobial.
Host transcriptional analysis to improve the diagnosis of group A streptococcal pharyngitis
Authors: Yu Jinsheng , Tycksen Eric , Yang Wei , Mariani Thomas J. , Bhattacharya Soumyaroop , Falsey Ann R. , Topham David J. , Storch Gregory A. 
Published: October 2020

AbstractCurrent diagnostic methods used to evaluate patients with pharyngitis for the presence of group AStreptococcus(GAS) do not discriminate between acute infection and asymptomatic carriage, potentially resulting in overuse of antibiotics. We hypothesized that host response as measured by the transcriptomic profile of peripheral blood leukocytes could make this distinction, and could also distinguish between GAS and viral infection. We used RNA sequencing to generate whole blood transcriptomes from 37 children, including 10 with acute GAS pharyngitis, 5 with asymptomatic GAS carriage, 3 with adenoviral pharyngitis, 3 with pharyngitis of unknown etiology, and 16 asymptomatic children negative for GAS. Transcriptional profiles from children with symptomatic GAS, GAS carriage, symptomatic adenoviral pharyngitis, and controls were each distinct. Of 15,185 genes with analyzable sequence, 1357 (8.9%) were differentially expressed in the children with symptomatic GAS compared to those with asymptomatic carriage, and 1336 (8.8%) compared to symptomatic adenovirus infection. A panel of 13 genes distinguished between children with acute GAS and all others with 91% accuracy. The gene encoding CD177, a marker of neutrophil activation, had a 152-fold increase in expression in children with acute GAS, and is a potential diagnostic biomarker. We conclude that measurement of host response is highly promising to improve the diagnosis of GAS pharyngitis and could help limit unnecessary antibiotic use.One Sentence SummaryThis study demonstrates that analysis of host gene expression can improve the diagnosis of group A streptococcal pharyngitis, which will limit unnecessary antibiotic therapy.
Mathematical Modeling of COVID-19 Pandemic in the African Continent
Authors: Aries Nawel , Ounis Houdayfa 
Published: October 2020

AbstractThe present work aims to give a contribution to the understanding of the highly infectious pandemic caused by the COVID-19 in the African continent. The study focuses on the modelling and the forecasting of COVID-19 spread in the most affected African continent, namely: Morocco, Algeria, Tunisia, Egypt and South Africa and for the sake of comparison two of the most affected European country are also considered, namely: France and Italy. To this end, an epidemiological SEIQRDP model is presented, which is an adaptation of the classic SIR model widely used in mathematical epidemiology. In order to better coincide with the preventive measures taken by the governments to deal with the spread of COVID-19, this model considers the quarantine. For the identification of the model’s parameters, official data of the pandemic up to August 1st, 2020 are considered. The results show that the number of infections due to the use of quarantine is expected to be very low provided the isolation is effective. However, it is increasing in some countries with the early lifting of containment. Finally, the information provided by the SEIQRDP model could help to establish a realistic assessment of the short-term pandemic situation. Moreover, this will help maintain the most appropriate and necessary public health measures after the lockdown lifting.
Electroconvulsive Therapy with a Memory Reactivation Intervention for Post-Traumatic Stress Disorder: A Randomized Controlled Trial
Authors: Tang Victor M. , Trought Kathleen , Gicas Kristina M. , Kozak Mari , Josselyn Sheena A. , Daskalakis Zafiris J. , Blumberger Daniel M. , Voineskos Daphne , Knyahnytska Yuliya , Chung Yuan , Zhou Young , Isserles Moshe , Wong Albert H.C. 
Published: October 2020

AbstractIntroductionPost-traumatic Stress Disorder (PTSD) often does not respond to available treatments. Memories are vulnerable to disruption during reconsolidation, and electroconvulsive therapy (ECT) has amnestic effects. We sought to exploit this phenomenon as a potential treatment for PTSD with a clinical trial of patients with PTSD receiving ECT.MethodsTwenty-eight participants with severe depression with comorbid PTSD referred for ECT treatment were randomly assigned to reactivation of a traumatic or non-traumatic memory using script driven imagery prior to each ECT treatment. Primary outcomes were change in scores on the Modified PTSD Symptom Scale - Self Report (MPSS-SR) and the Clinician-Administered PTSD Scale for DSM-5 (CAPS-5). Assessments were completed by blinded raters. Secondary outcomes included a comparison of the change in heart rate while listening to the script.ResultsTwenty-five patients who completed a post-ECT assessment were included in the analysis. No significant group differences were found in the MPSS-SR or CAPS-5 scores from pre-ECT to post-ECT or 3-month follow-ups. However, both groups improved at post-ECT and 3-month follow up. Partial eta squared estimates of effect size showed large effect sizes for all outcomes (η2 > 0.13). Changes in heart rate were not significantly different between groups or over time.ConclusionsIn this RCT, ECT paired with pre-treatment traumatic memory reactivation was not more effective for treating PTSD symptoms than ECT alone. While our primary hypothesis was not supported, our data provides further support for the efficacy of ECT for improving symptoms of PTSD with comorbid depression.ClinicalTrials.govhttps://clinicaltrials.gov/ct2/show/NCT04027452Identifier: NCT04027452
An Overview of Retraction Status and Reasons of Non-Cochrane Systematic Reviews in Medicine
Authors: Shi Qianling , Wang Zijun , Zhou Qi , Hou Ruizhen , Gao Xia , He Shaoe , Zhao Siya , Ma Yanfang , Zhang Xianzhuo , Guan Quanlin , Chen Yaolong 
Published: October 2020

AbstractBackgroundMany previous studies have analyzed the status of retracted publications from different perspectives, but so far no study has focused on systematic reviews (SRs). The purpose of this study is to analyze the retraction status and reasons of non-Cochrane SRs in the field of medicine.MethodsWe searched MEDLINE and Embase from their inception to April 18, 2020, as well as Retraction Watch Database and Google Scholar with no language restriction to find non-Cochrane SRs that were retracted for any reason. Two reviewers independently screened and extracted data. We describe the characteristic and reasons of retraction and the duration from publication to retraction.ResultsWe identified 150 non-Cochrane SRs in medicine retracted between 2004 and 2020. The majority of retracted SRs were led by authors from China and affiliated with hospitals. Most SRs were published in journals with an impact factor ≤3, and in journal ranked in the third quarter. The largest proportion of retraction notices were issued by the publisher and editor(s) jointly; seven did not report this information. Fraudulent peer-review was the most common reason for retraction, followed by unreliable data meaning errors in study selection or data analysis. The median time between publication and retraction was 14.0 months. SRs retracted due to research misconduct took longer to retract than SRs retracted because of honest error.ConclusionsThe situation with retracted SRs is critical globally, and in particular in China. The most common reasons for retraction are fraudulent peer-review and unreliable data, and in most cases the study is retracted more than a year after publication. Efforts should be made to improve the process of peer review and adherence to the COPE retraction guidance, while at the same time authors should strengthen their skills in SR methodology.
Outcomes of COVID-19: disparities by ethnicity
Authors: Ali Hamad , Alshukry Abdullah , Marafie Sulaiman K , AlRukhayes Monera , Ali Yaseen , Abbas Mohammad Bu , Al-Taweel Abdullah , Bukhamseen Yousef , Dashti Mohammad H , Al-Shammari Abdullah , Abu-Farha Mohammad , AbuBaker Jehad , Al-Mulla Fahd 
Published: October 2020

AbstractObjectivesTo investigate the role of ethnicity in COVID-19 outcome disparities in a cohort in Kuwait.MethodsThis is a retrospective analysis of 405 individuals infected with SARS-CoV-2 in Kuwait. Outcomes such as symptoms severity and mortality were considered. Multivariate logistic regression models were used to report the odds ratios (OR) for ICU admission and dying from COVID-19.ResultsThe cohort included 290 Arabs and 115 South Asians. South Asians recorded significantly higher COVID-19 death rates compared to Arabs (33% vs. 7.6%, P value<0.001). When compared to Arabs, South Asians also had higher odds of being admitted to the ICU (OR = 6.28, 95% CI: 3.34 – 11.80, p < 0.001). South Asian patients showed 7.62 (95% CI: 3.62 – 16.02, p < 0.001) times the odds of dying from COVID-19.ConclusionCOVID-19 patients with South Asians ethnicity are more likely to have worse prognosis and outcome when compared to patients with Arab ethnicity. This suggest a possible role for ethnicity in COVID-19 outcome disparities and this role is likely to be multifactorial.