Corpus overview


Overview

MeSH Disease

Infections (492)

Disease (443)

Coronavirus Infections (259)

Pneumonia (168)

Death (167)


Human Phenotype

Pneumonia (190)

Fever (60)

Cough (31)

Hypertension (21)

Falls (20)


Transmission

Seroprevalence
    displaying 11 - 20 records in total 1350
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    Optimal Pooling Matrix Design for Group Testing with Dilution (Row Degree) Constraints

    Authors: Jirong Yi; Myung Cho; Xiaodong Wu; Raghu Mudumbai; Weiyu Xu

    id:2008.01944v1 Date: 2020-08-05 Source: arXiv

    In this paper, we consider the problem of designing optimal pooling matrix for group testing (for example, for COVID-19 virus testing) with the constraint that no more than $r>0$ samples can be pooled together, which we call "dilution constraint". This problem translates to designing a matrix with elements being either 0 or 1 that has no more than $r$ '1's in each row and has a certain performance SERO guarantee of identifying anomalous elements. We explicitly give pooling matrix designs that satisfy the dilution constraint and have performance SERO guarantees of identifying anomalous elements, and prove their optimality in saving the largest number of tests, namely showing that the designed matrices have the largest width-to-height ratio among all constraint-satisfying 0-1 matrices.

    Trove: Ontology-driven weak supervision for medical entity classification

    Authors: Jason A. Fries; Ethan Steinberg; Saelig Khattar; Scott L. Fleming; Jose Posada; Alison Callahan; Nigam H. Shah

    id:2008.01972v1 Date: 2020-08-05 Source: arXiv

    Motivation: Recognizing named entities (NER) and their associated attributes like negation are core tasks in natural language processing. However, manually labeling data for entity tasks is time consuming and expensive, creating barriers to using machine learning in new medical applications. Weakly supervised learning, which automatically builds imperfect training sets from low cost, less accurate labeling rules, offers a potential solution. Medical ontologies are compelling sources for generating labels, however combining multiple ontologies without ground truth data creates challenges due to label noise introduced by conflicting entity definitions. Key questions remain on the extent to which weakly supervised entity classification can be automated using ontologies, or how much additional task-specific rule engineering is required for state-of-the-art performance SERO. Also unclear is how pre-trained language models, such as BioBERT, improve the ability to generalize from imperfectly labeled data. Results: We present Trove, a framework for weakly supervised entity classification using medical ontologies. We report state-of-the-art, weakly supervised performance SERO on two NER benchmark datasets and establish new baselines for two entity classification tasks in clinical text. We perform within an average of 3.5 F1 points (4.2%) of NER classifiers trained with hand-labeled data. Automatically learning label source accuracies to correct for label noise provided an average improvement of 3.9 F1 points. BioBERT provided an average improvement of 0.9 F1 points. We measure the impact of combining large numbers of ontologies and present a case study on rapidly building classifiers for COVID-19 clinical tasks. Our framework demonstrates how a wide range of medical entity classifiers can be quickly constructed using weak supervision and without requiring manually-labeled training data.

    Evaluation of Serological SARS-CoV-2 Lateral Flow Assays for Rapid Point of Care Testing

    Authors: Steven E Conklin; Kathryn Martin; Yukari C Manabe; Haley A Schmidt; Morgan Keruly; Ethan Klock; Charles S Kirby; Owen R Baker; Reinaldo E Fernandez; Yolanda J Eby; Justin Hardick; Kathryn Shaw-Saliba; Richard E Rothman; Patrizio P Caturegli; Andrew R Redd; Aaron AR Tobian; Evan M Bloch; H Benjamin Larman; Thomas C Quinn; William Clarke; Oliver Laeyendecker

    doi:10.1101/2020.07.31.20166041 Date: 2020-08-04 Source: medRxiv

    Background. Rapid point-of-care tests (POCTs) for SARS-CoV-2-specific antibodies SERO vary in performance SERO. A critical need exists to perform head-to-head comparison of these assays. Methods. Performance SERO of fifteen different lateral flow POCTs for the detection of SARS-CoV-2-specific antibodies SERO was performed on a well characterized set of 100 samples. Of these, 40 samples from known SARS-CoV-2-infected, convalescent individuals (average of 45 days post symptom onset TRANS) were used to assess sensitivity SERO. Sixty samples from the pre-pandemic era (negative control), that were known to have been infected with other respiratory viruses (rhinoviruses A, B, C and/or coronavirus 229E, HKU1, NL63 OC43) were used to assess specificity. The timing of seroconversion was assessed on five POCTs on a panel of 272 longitudinal samples from 47 patients of known time since symptom onset TRANS. Results. For the assays that were evaluated, the sensitivity SERO and specificity for any reactive band ranged from 55%-97% and 78%-100%, respectively. When assessing the performance SERO of the IgM and the IgG bands alone, sensitivity SERO and specificity ranged from 0%-88% and 80%-100% for IgM and 25%-95% and 90%-100% for IgG. Longitudinal testing revealed that median time post symptom onset TRANS to a positive result was 7 days (IQR 5.4, 9.8) for IgM and 8.2 days (IQR 6.3 to 11.3). Conclusion. The testing performance SERO varied widely among POCTs with most variation related to the sensitivity SERO of the assays. The IgM band was most likely to misclassify pre-pandemic samples. The appearance of IgM and IgG bands occurred almost simultaneously.

    Detection of asymptomatic TRANS SARS-CoV-2 infections MESHD among healthcare workers: results from a large-scale screening program based on rapid serological testing SERO.

    Authors: Francesca Maria Carozzi; Maria Grazia Cusi; Mauro Pistello; Luisa Galli; Alessandro Bartoloni; Gabriele Anichini; Chiara Azzari; Michele Emdin; Claudia Gandolfo; Fabrizio Maggi; Elisabetta Mantengoli; Maria Moriondo; Giovanna Moscato; Irene Paganini; Claudio Passino; Francesco Profili; Fabio Voller; Marco Zappa; Filippo Quattrone; Gian Maria Rossolini; Paolo Francesconi; - SARS-CoV-2 Serosurvey Tuscan Working Group

    doi:10.1101/2020.07.30.20149567 Date: 2020-08-04 Source: medRxiv

    Abstract Objective: To evaluate the performance SERO of two available rapid immunological tests for identification of severe acute respiratory syndrome MESHD Coronavirus 2 ( SARS-CoV-2) antibodies SERO and their subsequent application to a regional screening of health care workers (HCW) in Tuscany (Italy). Design: measures of accuracy and HCW serological surveillance Setting: 6 major health facilities in Tuscany, Italy. Participants: 17,098 HCW of the Tuscany Region. Measures of accuracy were estimated to assess sensitivity SERO in 176 hospitalized Covid-19 clinical subjects at least 14 days after a diagnostic PCR-positive assay result. Specificity was assessed in 295 sera biobanked in the pre-Covid-19 era in winter or summer 2013-14 Main outcome measures: Sensitivity SERO and specificity, and 95% confidence intervals, were measured using two serological tests SERO, named T-1 and T-2. Positive and Negative predictive values SERO were estimated at different levels of prevalence SERO. HCW of the health centers were tested using the serological SERO tests, with a follow- up nasopharyngeal PCR-test swab in positive tested cases. Results: Sensitivity SERO was estimated as 99% (95%CI: 95%-100%) and 97% (95% CI: 90%-100%), whereas specificity was the 95% and 92%, for Test T-1 and T-2 respectively. In the historical samples IgM cross-reactions were detected in sera collected during the winter period, probably linked to other human coronaviruses. Out of the 17,098 tested, 3.1% have shown the presence of SARS-CoV-2 IgG antibodies SERO, among them 6.8% were positive at PCR follow-up test on nasopharyngeal swabs. Conclusion Based on the low prevalence SERO estimate observed in this survey, the use of serological test SERO as a stand-alone test is not justified to assess the individual immunity status. Serological tests SERO showed good performance SERO and might be useful in an integrated surveillance, for identification of infected subjects and their contacts as required by the policy of contact tracing TRANS, with the aim to reduce the risk of dissemination, especially in health service facilities.

    Analytical and clinical performances SERO of five immunoassays SERO for the detection of SARS-CoV-2 antibodies SERO in comparison with neutralization activity

    Authors: Mario Plebani; Andrea Padoan; Laura Sciacovelli; Francesco Bonfante; Matteo Pagliari; Dania Bozzato; Chiara Cosma; Alessio Bortolami; Davide Negrini; Silvia Zuin

    doi:10.1101/2020.08.01.20166546 Date: 2020-08-04 Source: medRxiv

    Background. Reliable high-throughput serological assays SERO for SARS-CoV-2 antibodies SERO (Abs) are urgently needed for the effective containment of the COVID-19 pandemic, as it is of crucial importance to understand the strength and duration of immunity after infection MESHD, and to make informed decisions concerning the activation or discontinuation of physical distancing restrictions. Methods. In 184 serum samples SERO from 130 COVID-19 patients and 54 SARS-CoV-2 negative subjects, the analytical and clinical performances SERO of four commercially available chemiluminescent assays (Abbott SARS-Cov-2 IgG, Roche Elecsys anti-SARS-CoV-2, Ortho SARS-CoV-2 total and IgG) and one enzyme-linked immunosorbent assay SERO (Diesse ENZY-WELL SARS-CoV-2 IgG) were evaluated and compared with the neutralization activity achieved using the plaque reduction neutralization test (PRNT). Findings. Precision results ranged from 0.9% to 11.8% for all assays. Elecsys anti-SARS-CoV-2 demonstrated linearity of results at concentrations within the cut-off value. Overall, sensitivity SERO ranged from 78.5 to 87.8%, and specificity, from 97.6 to 100%. On limiting the analysis to samples collected 12 days after onset of symptoms TRANS, the sensitivity SERO of all assays increased, the highest value (95.2%) being obtained with VITRO Anti-SARS-CoV-2 Total and Architect SARS-CoV-2 IgG. The strongest PRNT50 correlation with antibody SERO levels was obtained with ENZY-Well SARS-CoV-2 IgG (rho = 0.541, p < 0.001). Interpretation. The results confirmed that all immunoassays SERO had an excellent specificity, whereas sensitivity SERO varied across immunoassays SERO, depending strongly on the time interval between symptoms onset TRANS and sample collection. Further studies should be conducted to achieve a stronger correlation between antibody SERO measurement and PRNT50 in order to obtain useful information for providing effective passive antibody SERO therapy, and developing a vaccine against the SARS-CoV-2 virus.

    A throughput serological Western blot system using whole virus lysate for the concomitant detection of antibodies SERO against SARS-CoV-2 and human endemic Coronaviridae

    Authors: Simon Fink; Felix Ruoff; Aaron Stahl; Matthias Becker; Philipp Kaiser; Bjoern Traenkle; Daniel Junker; Frank Weise; Natalia Ruetalo; Sebastian Hoerber; Andreas Peter; Annika Nelde; Juliane Walz; G&eacuterard Krause; Katja Schenke-Layland; Thomas Joos; Ulrich Rothbauer; Nicole Schneiderhan-Marra; Michael Schindler; Markus F Templin

    doi:10.1101/2020.07.31.20165019 Date: 2020-08-04 Source: medRxiv

    BACKGROUND: Seroreactivity against human endemic coronaviruses has been linked to disease MESHD severity after SARS-CoV-2 infection MESHD. Assays that are capable of concomitantly detecting antibodies SERO against endemic coronaviridae such as OC43, 229E, NL63, and SARS-CoV-2 may help to elucidate this question. We set up a platform for serum SERO-screening and developed a bead-based Western blot system, namely DigiWest, capable of running hundreds of assays using microgram amounts of protein prepared directly from different viruses. METHODS: The parallelized and miniaturised DigiWest assay was adapted for detecting antibodies SERO using whole protein extract prepared from isolated SARS-CoV-2 virus particles. After characterisation and optimization of the newly established test, whole virus lysates of OC43, 229E, and NL63 were integrated into the system. RESULTS: The DigiWest-based immunoassay SERO system for detection of SARS-CoV-2 specific antibodies SERO shows a sensitivity SERO of 87.2 % and diagnostic specificity of 100 %. Concordance analysis with the SARS-CoV-2 immunoassays SERO available by Roche, Siemens, and Euroimmun indicates a comparable assay performance SERO (Cohen's Kappa ranging from 0.8799-0.9429). In the multiplexed assay, antibodies SERO against the endemic coronaviruses OC43, 229E, and NL63 were detected, displaying a high incidence of seroreactivity against these coronaviruses. CONCLUSION: The DigiWest-based immunoassay SERO, which uses authentic antigens from isolated virus particles, is capable of detecting individual serum SERO responses against SARS-CoV-2 with high specificity and sensitivity SERO in one multiplexed assay. It shows high concordance with other commercially available serologic assays. The DigiWest approach enables a concomitant detection of antibodies SERO against different endemic coronaviruses and will help to elucidate the role of these possibly cross-reactive antibodies SERO.

    Sensitivity SERO of nasopharyngeal, oropharyngeal and nasal washes specimens for SARS-CoV-2 detection in the setting of sampling device shortage

    Authors: Adrien Calame; Lena Mazza; Adriana Renzoni; Laurent Kaiser; Manuel Schibler

    doi:10.1101/2020.08.01.20166397 Date: 2020-08-04 Source: medRxiv

    In the context of an unprecedented shortage of nasopharyngeal swabs (NPS) or sample transport media during the coronavirus disease MESHD 2019 (COVID-19) crisis, alternative methods for sample collection are needed. To address this need, we validated a cell culture medium as a viral transport medium, and compared the analytical sensitivity SERO of SARS-CoV-2 real-time RT-PCR in nasal wash (NW), oropharyngeal swab (OPS) and NPS specimens. Both the clinical and analytical sensitivity SERO were comparable in these three sample types. OPS and NW specimens may therefore represent suitable alternatives to NPS for SARS-CoV-2 detection.

    False-Negative Mitigation in Group Testing for COVID-19 Screening

    Authors: Amir Reza Alizad-Rahvar; Safar Vafadar; Mehdi Totonchi; Mehdi Sadeghi

    doi:10.1101/2020.07.31.20154070 Date: 2020-08-04 Source: medRxiv

    After lifting the COVID-19 lockdown restrictions and opening businesses, screening is essential to prevent the spread of the virus. Group testing could be a promising candidate for screening to save time and resources. However, due to the high false-negative rate (FNR) of the RT-PCR diagnostic test, we should be cautious about using group testing because a group's false-negative result identifies all the individuals in a group as uninfected. Repeating the test is the best solution to reduce the FNR, and repeats should be integrated with the group-testing method to increase the sensitivity SERO of the test. The simplest way is to replicate the test twice for each group (the 2Rgt method). In this paper, we present a new method for group testing (the groupMix method), which integrates two repeats in the test. Then we introduce the adaptive version of both the groupMix and the 2Rgt methods. We compare these methods analytically regarding the sensitivity SERO and the average number of tests. The tradeoff between the sensitivity SERO and the average number of tests should be considered when choosing the best method for the screening strategy. We applied the non-adaptive groupMix method to screening 263 people and identified 2 infected individuals by performing 98 tests. This method achieved a 63% saving in the number of tests compared to individual testing. This method is currently applied to COVID-19 screening in the Clinical Genetic Laboratory at the Royan Institute, Tehran, Iran. Our experimental results show that in COVID-19 screening, the viral load can be low, and the group size should not be more than 6; otherwise, the FNR increases significantly. A web interface of the non-adaptive groupMix method is publicly available for laboratories to implement this method.

    Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

    Authors: Rowena A Bull; Thiruni Adikari; Jillian M Hammond; Igor Stevanovski; James M Ferguson; Alicia G Beukers; Zin Naing; Malinna Yeang; Andrey Verich; Hasindu Gamaarachichi; Ki Wook Kim; Fabio Luciani Sr.; Sacha Stelzer-Braid; John-Sebastian Eden; William D Rawlinson; Sebastiaan J van Hal; Ira W Deveson

    doi:10.1101/2020.08.04.236893 Date: 2020-08-04 Source: bioRxiv

    Viral whole-genome sequencing (WGS) provides critical insight into the transmission TRANS and evolution of Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, we performed viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance SERO. Despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity SERO and >98% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance SERO for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.

    TClustVID: A Novel Machine Learning Classification Model to Investigate Topics and Sentiment inCOVID-19 Tweets

    Authors: Md. Shahriare Satu; Md. Imran Khan; Mufti Mahmud; Shahadat Uddin; Matthew A Summers; Julian M. W. Quinn; Mohammad Ali Moni

    doi:10.1101/2020.08.04.20167973 Date: 2020-08-04 Source: medRxiv

    COVID-19, caused by the SARS-Cov2, varies greatly in its severity but represent serious respiratory symptoms with vascular and other complications, particularly in older adults TRANS. The disease MESHD disease can be spread TRANS can be spread by both symptomatic and asymptomatic TRANS infected individuals, and remains uncertainty over key aspects of its infectivity, no effective remedy yet exists and this disease MESHD causes severe economic effects globally. For these reasons, COVID-19 is the subject of intense and widespread discussion on social media platforms including Facebook and Twitter. These public forums substantially impact on public opinions in some cases and exacerbate widespread panic and misinformation spread during the crisis. Thus, this work aimed to design an intelligent clustering-based classification and topics extracting model (named TClustVID) that analyze COVID-19-related public tweets to extract significant sentiments with high accuracy. We gathered COVID-19 Twitter datasets from the IEEE Dataport repository and employed a range of data preprocessing methods to clean the raw data, then applied tokenization and produced a word-to-index dictionary. Thereafter, different classifications were employed to Twitter datasets which enabled exploration of the performance SERO of traditional and TClustVID classification methods. TClustVID showed higher performance SERO compared to the traditional classifiers determined by clustering criteria. Finally, we extracted significant topic clusters from TClustVID, split them into positive, neutral and negative clusters and implemented latent dirichlet allocation for extraction of popular COVID-19 topics. This approach identified common prevailing public opinions and concerns related to COVID-19, as well as attitudes to infection MESHD prevention strategies held by people from different countries concerning the current pandemic situation.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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