bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated molecular testing of saliva for SARS-CoV-2 detection
Authors: Matic Nancy , Lawson Tanya , Ritchie Gordon , Stefanovic Aleksandra , Leung Victor , Champagne Sylvie , Romney Marc G. , Lowe Christopher F. 
Published: August 2020

AbstractWith surging global demand for increased SARS-CoV-2 testing capacity, clinical laboratories seek automated, high-throughput molecular solutions, particularly for specimen types which do not rely upon supply of specialized collection devices or viral transport media (VTM). Saliva was evaluated as a diagnostic specimen for SARS-CoV-2 using the cobas® SARS-CoV-2 Test on the cobas® 6800 instrument. Saliva specimens submitted from various patient populations under investigation for COVID-19 from March-July 2020 were processed in the laboratory with sterile phosphate-buffered saline in a 1:2 dilution and vortexed with glass beads. The processed saliva samples were tested using a commercial assay for detection of the SARS-CoV-2 E gene (LightMix®) in comparison to the cobas® SARS-CoV-2 Test. 22/64 (34.4%) of the saliva samples were positive for SARS-CoV-2. Positive and negative concordance between the LightMix® and cobas® assays were 100%. There was no cross-contamination of samples observed on the cobas® 6800. The overall invalid rate for saliva on the cobas® 6800 (1/128, 0.78%) was similar to the baseline invalid rate observed for nasopharyngeal swabs/VTM and plasma samples. Saliva is a feasible specimen type for SARS-CoV-2 testing on the cobas® 6800, with potential to improve turnaround time and enhance testing capacity.
Local protection bubbles: an interpretation of the decrease in the velocity of coronavirus’s spread in the city of São Paulo
Authors: Pinto José Paulo Guedes , Magalhães Patrícia Camargo , Figueiredo Gerusa Maria , Alves Domingos , Segura-Angel Diana Maritza 
Published: August 2020

AbstractAfter four months of dealing with the pandemic, the city of São Paulo entered a phase of relaxed social-distancing measures in July 2020, and saw its social isolation rate fall at the same time as the number of cases, deaths, and hospital bed occupation declined. We use a calibrated multi-agent model to describe these dynamics. We assert here that this phenomenon can be understood as the result of local protective bubbles formed in the city’s sub-environments at the same time that there was an exhaustion of contagion networks. Both reduce the velocity of the virus’s spread, causing temporary reductions in the epidemic curve, albeit in an unstable equilibrium. These local bubbles can burst anytime and anywhere due to the reintroduction of a few infected people at the same time that there is a reduction in non-pharmaceutical interventions (NPI), such as social-distancing practices. It is important to stress that this hypothesis aligns with the dynamics of the virus’s spread observed so far, without needing ad hoc suppositions about natural collective immunity thresholds or heterogeneity in the population’s transmission rate, which come with the risk of making mistaken predictions that may could lead to the loss of many lives. The safe way to move ahead is to continue doing all we can to avoid new infections until a vaccine is found that properly and safely creates herd immunity.
To what extent physical distancing and other COVID-19 preventive measures being implemented among people in Arba Minch town, Southern Ethiopia: exploring evidences for an urgent call for action?
Authors: Asfaw Mekuria Asnakew , Yohannes Tsegaye , Churko Chuchu , Bekele Alemayehu , Wegayehu Teklu 
Published: August 2020

AbstractBackgroundThe number of confirmed Coronavirus disease 2019 (COVID-19) cases surge substantially in resource-poor settings within the fragile health system. Since there are no proven vaccine and treatment in place against the disease, controlling strategy mainly rely on preventive measures. However, data on the extent of implementing physical distancing and other preventive measures were under estimated. This study, therefore, investigated these gaps among people in Arba Minch town, southern Ethiopia.MethodsWe conducted a community based cross-sectional study in Arba Minch town; from 15-30 June 2020. Data were collected using interviewer administered questionnaire and checklist. Then, data were cleaned, coded and entered to EpiData version 4.4.2, and exported to SPSS version 20 for analysis.ResultsOf the total participants (459), 43.6% achieved above the mean score (6±1.97) on preventive measures of COVID-19. Only 29.8% of participants kept the recommended physical distance, and surprisingly, in all public gathering places the distance was not kept totally. In addition, of the total participants, only 37.7% had face-mask use practice; 20.5% had hand sanitizer use practice, and 13.1% were measuring their body temperature every two weeks. Moreover, 42.5% of participants avoided attendance in public gatherings; 44.7% stopped touching their nose, eye and mouth; 55.6% practiced stay-at-home; and 60% had frequent hand washing practice. Majority of participants (66.7%) practiced covering their mouth and nose while coughing or sneezing; 68.2% had treatment seeking behavior if they experience flue like symptoms; 69.1% practiced isolating themselves while having flue like symptoms; and 89.3% avoided hand shaking.ConclusionsThe findings of this study suggest that physical distancing and other COVID-19 preventive measures were inadequately implemented among people in Arba Minch town. Thus, an urgent call for action is demanding to mitigate the spread of the COVID-19 as early as possible before it brings a devastating impact.
Data Resource Profile: Understanding the patterns and determinants of health in South Asians - South Asia Biobank
Authors: Song Peige , Gupta Ananya , Goon Ian Y , Hasan Mehedi , Mahmood Sara , Page Polly , Pradeepa Rajendra , Siddiqui Samreen , Silva Wnurinham , Aarthi Garudam R , Afzal Saira , Day Sophie E , Frost Gary S , Holmes Bridget A , Kamalesh Rajan , Kusuma Dian , Miraldo Marisa , Pineda Elisa , Hersch Fred , Rai Baldeesh K , Sarker Malabika , Sassi Franco , Valabhji Jonathan , Wareham Nick J , Ahmed Sajjad , Anjana Ranjit M , Brage Soren , Forouhi Nita G , Jha Sujeet , Kasturiratne Anuradhani , Katulanda Prasad , Khawaja Khadija I , Loh Marie , Mridha Malay K , Wickremasinghe Ananda R , Kooner Jaspal S , Chambers John C 
Published: August 2020

AbstractBackground and aimsThis paper describes the data resource profile of South Asia Biobank (SAB), which was set up in South Asia from November 2018 to March 2020, to identify the risk factors and their complex interactions underlying the development of type-2 diabetes mellitus, cardiovascular disease and other chronic diseases in South Asians.Data resource basicsThis cross-sectional population-based study has recruited 52713 South Asian adults from 118 surveillance sites at five centres of excellence in South Asia (Bangladesh, North India, South India, Pakistan and Sri Lanka). Structured assessments of participants included six complementary domains: i). Registration and consent; ii). Questionnaire (information on behavioural risk factors, personal and family medical history, medications, socioeconomic status); iii). Physical measurements (height, weight, waist and hip circumference and bio-impedance for body fat composition, blood pressure, cardiac evaluation, retinal photography, respiratory evaluation); iv). Biological samples (blood and urine); v). Physical activity monitoring and vi). Dietary intake by a 24-hour recall. Aliquots of whole blood, serum, plasma, and urine were put into storage at −80°C for further analysis.Key resultsThe prevalence of obesity is 6.6% in Bangladesh, 19.7% in India, 33.9% in Pakistan and 15.7% in Sri Lanka. The prevalence of diabetes is 11.5%, 27.7%, 25.3%, and 24.8%, and the prevalence of hypertension is 26.7%, 36.9%, 44.5%, 35.0% in Bangladesh, India, Pakistan and Sri Lanka respectively.Collaboration and data accessSAB is the first comprehensive biobank of South Asian individuals. Collected data are available to the global scientific community upon request.
OpenSAFELY: Do adults prescribed non-steroidal anti-inflammatory drugs have an increased risk of death from COVID-19?
Authors:   The OpenSAFELY Collaborative, Wong Angel YS , MacKenna Brian , Morton Caroline E , Schultze Anna , Walker Alex J , Bhaskaran Krishnan , Brown Jeremy P , Rentsch Christopher T , Williamson Elizabeth , Drysdale Henry , Croker Richard , Bacon Seb , Hulme William , Bates Chris , Curtis Helen J , Mehrkar Amir , Evans David , Inglesby Peter , Cockburn Jonathan , McDonald Helen I , Tomlinson Laurie , Mathur Rohini , Wing Kevin , Forbes Harriet , Parry John , Hester Frank , Harper Sam , Evans Stephen JW , Smeeth Liam , Douglas Ian J , Goldacre Ben 
Published: August 2020

AbstractImportanceThere has been speculation that non-steroidal anti-inflammatory drugs (NSAIDs) may negatively affect coronavirus disease 2019 (COVID-19) outcomes, yet clinical evidence is limited.ObjectiveTo assess the association between NSAID use and deaths from COVID-19 using OpenSAFELY, a secure analytical platform.DesignTwo cohort studies (1stMarch-14thJune 2020).SettingWorking on behalf of NHS England, we used routine clinical data from >17 million patients in England linked to death data from the Office for National Statistics.ParticipantsStudy 1: General population (people with an NSAID prescription in the last three years). Study 2: people with rheumatoid arthritis/osteoarthritis.ExposuresCurrent NSAID prescription within the 4 months before 1stMarch 2020.Main Outcome and MeasureWe used Cox regression to estimate hazard ratios (HRs) for COVID-19 related death in people currently prescribed NSAIDs, compared with those not currently prescribed NSAIDs, adjusting for age, sex, comorbidities and other medications.ResultsIn Study 1, we included 535,519 current NSAID users and 1,924,095 non-users in the general population. The crude HR for current use was 1.25 (95% CI, 1.07–1.46), versus non-use. We observed no evidence of difference in risk of COVID-19 related death associated with current use (HR, 0.95, 95% CI, 0.80–1.13) in the fully adjusted model.In Study 2, we included 1,711,052 people with rheumatoid arthritis/osteoarthritis, of whom 175,631 (10%) were current NSAID users. The crude HR for current use was 0.43 (95% CI, 0.36–0.52), versus non-use. In the fully adjusted model, we observed a lower risk of COVID-19 related death (HR, 0.78, 95% CI, 0.65–0.94) associated with current use of NSAID versus non-use.Conclusion and RelevanceWe found no evidence of a harmful effect of NSAIDs on COVID-19 related deaths. Risks of COVID-19 do not need to influence decisions about therapeutic use of NSAIDs.
Examining face-mask usage as an effective strategy to control COVID-19 spread
Authors: Catching Adam , Capponi Sara , Yeh Ming Te , Bianco Simone , Andino Raul 
Published: August 2020

AbstractCOVID-19’s high virus transmission rates have caused a pandemic that is exacerbated by the high rates of asymptomatic and presymptomatic infections. These factors suggest that face masks and social distance could be paramount in containing the pandemic. We examined the efficacy of each measure and the combination of both measures using an agent-based model within a closed space that approximated real-life interactions. By explicitly considering different fractions of asymptomatic individuals, as well as a realistic hypothesis of face masks protection during inhaling and exhaling, our simulations demonstrate that a synergistic use of face masks and social distancing is the most effective intervention to curb the infection spread. To control the pandemic, we show that practicing social distance is less efficacious than the widespread usage of face masks and that wearing face masks provides optimal protection even if only a small portion of the population comply with social distance. Finally, the face mask effectiveness in curbing the viral spread is not reduced if a large fraction of population is asymptomatic. Our findings have important implications for policies that dictate the reopening of social gatherings.Author summaryThe COVID-19 outbreak has created an enormous burden on the worldwide population. Among the various ways of preventing the spread of the virus, face masks have been proposed as a main way of reducing transmission. Yet, the interplay between the usage of face mask and other forms of Non-Pharmaceutical Intervention is still not completely clear. In this paper we introduce a stochastic individual-based model which aims at producing realistic scenarios of disease spread when mask wearing with different inward and outward efficacy and social distancing are enforced. The model elucidates the conditions that makes the two forms of intervention synergistic in preventing the spread of the disease.
Circulating-tumor DNA from Two Types of Blood Collection Tubes for Monitoring Tumor Burden Validated with Esophageal Squamous Cell Carcinoma Patients
Authors: Endo Fumitaka , Iwaya Takeshi , Sasaki Yasushi , Chiba Takehiro , Yaegashi Mizunori , Kume Kohei , Sato Kei , Arisue Atsuhiro , Kawagishi Ryoko , Matuo Teppei , Akiyama Yuji , Sasaki Akira , Suzuki Yuji , Tokino Takashi , Masuda Mari , Yamada Tesshi , Nakagawa Hidewaki , Nishizuka Satoshi S. 
Published: August 2020

ABSTRACTObjectiveTo evaluate long-term whole blood (WB) storage at room temperature (RT), plasma and peripheral blood mononuclear cell (PBMC) DNA was collected simultaneously using BD Vacutainer® CPTTM Mononuclear Cell Preparation Tubes (CPT) and Streck Cell-Free DNA Blood Collection Tubes (BCT®).MethodsPlasma DNA was isolated from both types of tubes at various time points at RT. DNA from PBMCs was extracted using CPT from WB stored in BCT. The extracted DNA was used to monitor esophageal cancer treatment.ResultsBCT maintained steady levels of plasma DNA for up to nine days. After transfer of BCT-stored WB to CPT, PBMC-DNA were yielded with suitable quality for up to seven days. ctDNA from esophageal cancer patients carrying TP53 mutations reflected treatment efficacy.ConclusionBCT/CPT combinatory procedure allows storage of blood samples for up to seven days at RT for valid clinical assays using ctDNA.
First report of tocilizumab use in a cohort of Latin American patients hospitalized for severe COVID-19 pneumonia
Authors: Valenzuela Omar , Ibáñez Sebastián , Poli María , Roessler Patricia , Aylwin Mabel , Roizen Gigia , Iruretagoyena Mirentxu , Agar Vivianne , Donoso Javiera , Fierro Margarita , Montes José 
Published: August 2020

AbstractIntroduction/objectivesAn interleukin-6 inhibition strategy could be effective in selected COVID-19 patients. The objective is to present our experience of tocilizumab use in patients with severe COVID-19.MethodsObservational retrospective cohort study. Hospitalized patients were evaluated by our multidisciplinary team for eventual use of tocilizumab. Patients with progressive ventilatory impairment and evidence of a hyperinflammatory state despite usual treatment received tocilizumab 8 mg/kg intravenous (maximum dose 800 mg), in addition to standard treatment. The use and time of use of mechanical ventilation (MV), the change of the Alveolar-arterial (A-a) gradient, of the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) and of inflammation laboratory parameters after 72 hours of tocilizumab use was evaluated.Results29 patients received tocilizumab. 93.1% were men, 37.9% were obese, and 34.5% had hypertension. Of the 20 patients who were not on MV when receiving tocilizumab, 11 required non-invasive MV, for an average of five days, and one of them required intubation. A-a gradient, PaO2/FiO2, and inflammation parameters improved significantly. A better lymphocyte count, which improved significantly after tocilizumab use, was significantly associated with less use of MV. Five patients presented positive culture samples after tocilizumab, three being of clinical significance. A lower lymphocyte count was associated with having a positive culture. No other significant adverse events were seen.ConclusionOur study suggests the utility and shows the safety of tocilizumab use in COVID-19 patients who have respiratory failure and evidence of hyperinflammation. Lymphocyte improvement was a predictor of good response.Key-pointsThe use of tocilizumab in patients with severe COVID-19 was safe.Most of the patients presented a good response in terms of ventilatory and inflammatory parameters.Lymphocyte improvement after using tocilizumab was the main predictor of a good outcome.
Comprehensive analysis of the key epidemiological parameters to evaluate the impact of BCG vaccination on COVID-19 pandemic
Authors: Datta Niloy R. , Datta Sneha 
Published: August 2020

AbstractGlobally, the heterogenous coronavirus disease 2019 (COVID-19) case fatality rate (CFR) could be influenced by various epidemiological parameters. Identifying these could help formulate effective public health strategies. Incidence and mortality of COVID-19 for each of the 220 countries as on July 30, 2020 were evaluated against key epidemiological variables, namely - BCG vaccination (ongoing vs. discontinued/never undertaken), %population aged ≥65 years, incidences of ischemic heart disease (IHD), hypertensive heart disease (HHD), cancer, malaria, and diabetes; human development index (HDI) and population density. These were retrieved from the public domains of WHO, UN, World Bank and published reports. The COVID-19 CFRs ranged between 0.0% and 28.3% (mean ± SD: 3.05% ± 3.48). The influence of the individual epidemiological parameters on CFR were evaluated through the event rate estimations. A significantly lower event rate was observed in countries with ongoing BCG vaccination program (ER: with vs without ongoing BCG vaccination: 0.020 vs 0.034, p<0.001). The type of BCG strains used also influenced the ER; this being 0.018, 0.031 and 0.019 for early, late and mixed strains respectively (p=0.008). The epidemiological variables significantly associated with higher COVID-19 event rate were countries with higher %population aged ≥65 years (p<0.001), greater incidence of IHD (p<0.001) and cancer (p=0.003) and better HDI (p=0.003). Incidences of malaria, HHD and diabetes along with population density had no significant impact on COVID-19 CFR. Further, BCG vaccination significantly lowered the COVID-19 ER in each of the high-risk population subgroups - countries with >7.1% population aged ≥65 years (p=0.008), >0.737 HDI (p=0.001), IHD >1171/105 population (p=0.004) and cancer incidence >15726 (p<0.001). The results supports BCG induced “trained immunity” leading to heterologous immunoprotection against COVID-19. Thus BCG vaccination with early strains could provide a cost-effective prophylaxis, especially in high-risk individuals and bridge the gap till an effective vaccine against SARS-CoV-2 is freely available globally.
Assessing the risk of COVID-19 importation and the effect of quarantine
Authors: Arino Julien , Bajeux Nicolas , Portet Stéphanie , Watmough James 
Published: August 2020

AbstractObjectivesDuring the early stage of COVID-19 spread, many governments and regional jurisdictions put in place travel restrictions and imposed quarantine after arrivals in an effort to slow down or stop the importation of cases. At the same time, they implemented non-pharmaceutical interventions (NPI) to curtail local spread. We assess the risk of importation of COVID-19 in locations that are at that point without infection or where local chains of transmission have extinguished, and evaluate the role of quarantine in this risk.MethodsA stochastic SLIAR epidemic model is used. The effect of the rate, size, and nature of importations is studied and compared to that of NPI on the risk of importation-induced local transmission chains. The effect of quarantine on the rate of importations is assessed, as well as its efficacy as a function of its duration.ResultsThe rate of importations plays a critical role in determining the risk that case importations lead to local transmission chains, more so than local transmission characteristics, i.e., strength of NPI. The latter influences the severity of the outbreaks. Quarantine after arrival in a location is an efficacious way to reduce the rate of importations.ConclusionsLocations that see no or low level local transmission should ensure that the rate of importations remains low. A high level of compliance with post-arrival quarantine followed by testing achieves this objective with less of an impact than travel restrictions or bans.
SelectStitch: Automated Frame Segmentation and Stitching to Create Composite Images from Otoscope Video Clips
Authors: Binol Hamidullah , Moberly Aaron C. , Niazi M. Khalid Khan , Essig Garth , Shah Jay , Elmaraghy Charles , Teknos Theodoros , Taj-Schaal Nazhat , Yu Lianbo , Gurcan Metin N. 
Published: August 2020

AbstractBackground and ObjectiveThe aim of this study is to develop and validate an automated image segmentation-based frame selection and stitching framework to create enhanced composite images from otoscope videos. The proposed framework, called SelectStitch, is useful for classifying eardrum abnormalities using a single composite image instead of the entire raw otoscope video dataset.MethodsSelectStitch consists of a convolutional neural network (CNN) based semantic segmentation approach to detect the eardrum in each frame of the otoscope video, and a stitching engine to generate a high-quality composite image from the detected eardrum regions. In this study, we utilize two separate datasets: the first one has 36 otoscope videos that were used to train a semantic segmentation model, and the second one, containing 100 videos, which was used to test the proposed method. Cases from both adult and pediatric patients were used in this study. A configuration of 4-levels depth U-Net architecture was trained to automatically find eardrum regions in each otoscope video frame from the first dataset. After the segmentation, we automatically selected meaningful frames from otoscope videos by using a pre-defined threshold, i.e., it should contain at least an eardrum region of 20% of a frame size. We have generated 100 composite images from the test dataset. Three ear, nose, and throat (ENT) specialists (ENT-I, ENT-II, ENT-III) compared in two rounds the composite images produced by SelectStitch against the composite images that were generated by the base processes, i.e., stitching all the frames from the same video data, in terms of their diagnostic capabilities.ResultsIn the first round of the study, ENT-I, ENT-II, ENT-III graded improvement for 58, 57, and 71 composite images out of 100, respectively, for SelectStitch over the base composite, reflecting greater diagnostic capabilities. In the repeat assessment, these numbers were 56, 56, and 64, respectively. We observed that only 6%, 3%, and 3% of the cases received a lesser score than the base composite images, respectively, for ENT-I, ENT-II, and ENT-III in Round-1, and 4%, 0%, and 2% of the cases in Round-2.ConclusionsFrame selection improves the diagnostic quality of composite images from otoscope video clips.