Corpus overview


MeSH Disease

Human Phenotype

Obesity (1)

Hypertension (1)

Fever (1)

Cough (1)

Pneumonia (1)


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    Performance SERO of AV1 Real-Time Mode

    Authors: Ludovic Roux; Alexandre Gouaillard

    id:2009.14165v1 Date: 2020-09-29 Source: arXiv

    With COVID-19, the interest for digital interaction has raised, putting in turn real-time or low-latency codecs into a new light. Most of the codec ecosystem, including AV1, has been focusing on coding efficiency which is the main sought after improvement for Video On Demand use case. Very little literature exist on real-time codecs. This work focuses on explaining the differences between the VOD and the interactive use cases from the codec point of view. It makes the difference between latency and throughput, and show that reducing the former to achieve interactive latency is orthogonal to achieving maximum coding efficiency. Measurements are made on encoding of Full HD MESHD video sequences from the literature to compare %1/ the speed of AV1 real-time and default AV1, 2/ the respective performances SERO of H.264, VP8, VP9 and AV1 all in real-time mode.

    Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

    Authors: Anna Pavlova; Diane L. Lynch; Laura Zanetti-Polzi; Micholas Dean Smith; Chris Chipot; Daniel W. Kneller; Andrey Kovalevsky; Leighton Coates; Andrei A. Golosov; Callum J. Dickson; Camilo Velez-Vega; José S. Duca; Josh V. Vermaas; Yui Tik Pang; Atanu Acharya; Jerry M Parks; Jeremy C. Smith; James C. Gumbart; Tom P Gordon; Amy W Chung; Miles P Davenport; Stephen J Kent

    doi:10.1101/2020.09.07.286344 Date: 2020-09-10 Source: bioRxiv

    The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins MESHD. In addition to the catalytic dyad His41-Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV Mpro MESHD, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N{delta} ( HD MESHD) and N{epsilon} (HE) protonation of His41 and His164, respectively, the -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.

    SARS-Coronavirus-2 nucleocapsid protein measured in blood SERO using a Simoa ultra-sensitive immunoassay SERO differentiates COVID-19 infection MESHD with high clinical sensitivity SERO.

    Authors: Dandan Shan; Joseph M Johnson; Syrena C Fernandes; Muriel Mendes; Hannah Suib; Marcella Holdridge; Elaine M Burke; Katie G Beauregard; Ying Zhang; Megan Cleary; Samantha Xu; Xiao Yao; Purvish P Patel; Tatiana Plavina; David H Wilson; Lei Chang; Kim M Kaiser; Jacob Natterman; Susanne V Schmidt; Eicke Latz; Kevin Hrusovsky; Dawn Mattoon; Andrew J Ball; Saurabh Gombar; Robert Tibshirani; Benjamin A Pinsky; Scott D Boyd

    doi:10.1101/2020.08.14.20175356 Date: 2020-08-17 Source: medRxiv

    The COVID-19 pandemic continues to have an unprecedented impact on societies and economies worldwide. Despite rapid advances in diagnostic test development and scale-up, there remains an ongoing need for SARS-CoV-2 tests which are highly sensitive, specific, minimally invasive, cost-effective and scalable for broad testing and surveillance. Here we report development of a highly sensitive single molecule array (Simoa) immunoassay SERO on the automated HD MESHD-X platform for the detection of SARS-CoV-2 Nucleocapsid protein (N-protein) in venous and capillary blood SERO (fingerstick). In pre-pandemic and clinical sample sets, the assay has 100% specificity and 97.4% sensitivity SERO for serum SERO / plasma SERO samples. The limit of detection (LoD) estimated by titration of inactivated SARS-CoV-2 virus is 0.2 pg/ml, corresponding to 0.05 Median Tissue Culture Infectious Dose (TCID50) per ml, > 2000 times more sensitive than current EUA approved antigen tests. No cross-reactivity to other common respiratory viruses, including hCoV229E, hCoVOC43, hCoVNL63, Influenza A or Influenza B, was observed. We detected elevated N-protein concentrations in symptomatic, asymptomatic TRANS, and pre-symptomatic PCR+ individuals using capillary blood SERO from a finger-stick collection device. The Simoa SARS-CoV-2 N-protein assay has the potential to detect COVID-19 infection via antigen in blood SERO with similar or better performance SERO characteristics of molecular tests, while also enabling at home and point of care sample collection.

    Impact of COronaVirus Disease MESHD -2019 (COVID-19) pandemic on Haemodialysis care delivery pattern in Karnataka, India- a cross-sectional, questionnaire based survey.

    Authors: Anupama Y J; Arvind Conjeevaram; Ravindra Prabhu A; Manjunath Doshetty; Sanjay Srinivasa; Venkatesh Moger

    doi:10.1101/2020.07.25.20151225 Date: 2020-07-27 Source: medRxiv

    The COVID-19 pandemic has disrupted health care delivery globally. Patients on in-centre haemodialysis( HD MESHD) are particularly affected due to their multiple hospital visits and the need for uninterrupted care for their well-being and survival. We studied the impact of the pandemic and the national policy for pandemic control on the HD MESHD care delivery in Karnataka state in India in April 2020, when the first and second national lockdown were in place. An online, questionnaire based survey of dialysis facilities was conducted and the responses analysed. The questions were pertaining to the key areas such as changes in number of dialysis treatments, frequency, duration, expenses, transportation to and from dialysis units, impact on availability of consumables, effect on dialysis personnel and on machine maintenance. 62 centres participated. Median of dialysis treatments for the months of March and April 2020 were 695.5 and 650 respectively. Reduction in dialysis treatments was noted in 29(46.8%) facilities , decreased frequency reported by 60 centres. In at least 35(56.5%) centres, dialysis patients had to bear increased expenses. Cost and availability of dialysis consumables were affected in 40(64.5%) and 55(88.7%) centres respectively. Problems with transportation and movement restriction were the two key factors affecting both patients and dialysis facilities.This survey documents the collateral impact of COVID -19 on the vulnerable group of patients on HD MESHD, even when not affected by COVID. It identifies the key areas of challenges faced by the patients and the facilities and implores the care-providers for finding newer avenues for mitigation of the problems. Key words: COVID-19, India, Haemodialysis , dialysis care delivery, questionnaire-based survey

    Differential expression of COVID-19-related genes in European Americans and African Americans

    Authors: Urminder Singh; Eve Syrkin Wurtele

    doi:10.1101/2020.06.09.143271 Date: 2020-06-10 Source: bioRxiv

    The Coronavirus disease MESHD 2019 (COVID-19) pandemic has affected African American populations disproportionately in regards to both morbidity and mortality. A multitude of factors likely account for this discrepancy. Gene expression represents the interaction of genetics and environment. To elucidate whether levels of expression of genes implicated in COVID-19 vary in African Americans as compared to European Americans, we re-mine The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) RNA-Seq data. Multiple genes integral to infection, inflammation MESHD and immunity are differentially regulated across the two populations. Most notably, F8A2 and F8A3, which encode the HAP40 protein that mediates early endosome movement in Huntingtons Disease MESHD, are more highly expressed by up to 24-fold in African Americans. Such differences in gene expression can establish prognostic signatures and have critical implications for precision treatment of diseases such as COVID-19. We advocate routine inclusion of information such as postal code, education level, and profession (as a proxies for socioeconomic condition) and race in the metadata about each individual sampled for sequencing studies. This relatively simple change would enable large-scale data-driven approaches to dissect relationships among race, socio-economic factors, and disease.

    Early experience with COVD-19 patients at tertiary care teaching hospital in southwestern United states

    Authors: Rahul Shekhar; Shubhra Upadhyay; Abubaker Sheikh; Jeanette Atencio; Devika Kapuria

    doi:10.1101/2020.05.15.20094284 Date: 2020-05-18 Source: medRxiv

    Abstract Importance: There is limited information about presenting characteristics, treatment and outcomes of patients requiring hospitalization for coronavirus disease MESHD 2019 (COVID-19) serving underserved population in southwestern United states. Objective: To describe the clinical characteristics and outcomes of patients with COVID-19, hospitalized in a tertiary care teaching hospital in southwestern United states serving Underserved population. Methods: Case series of first 50 adults TRANS admitted at the University of New Mexico (UNM) Health Science center, the only tertiary care teaching hospital in the state of New Mexico between Jan 19th to April 24th 2020 via retrospective and prospective chart review. Main outcomes and measures: Clinical outcomes during hospitalization, such as invasive mechanical ventilation, kidney replacement therapy and death MESHD. Demographics, baseline comorbidities, presenting vital signs, and test results were also collected. Results: A total of 50 patients were included (median age TRANS, 55.5; 20-85-year-old, 54% were female TRANS). Obesity HP was the most common comorbidity in 20/39 (51%), followed by diabetes MESHD in 18/50 (36%) and hypertension HP hypertension MESHD 17/50(34%). Mean onset of symptoms TRANS duration before admission 7.39 days (range 1-21days). Most common symptoms on presentation included subjective fevers HP 40/42 (95.2%), cough HP 43/46 (93%) 43/46 and shortness of breath 40/46(87%). At triage only 24% were febrile and 46% patient did not have a single febrile episode throughout hospitalization, 56% had respiratory rate > 20 and 66% had a heart rate > 90. 80% patients required oxygen and 20%required intubation on presentation. On differential analysis 46% had elevated neutrophil counts, and 48% had low lymphocytes counts. Median D dimer, Ferritin, CRP, LDH were all elevated at presentation. 10% of patients had a negative initial chest x ray. 19.3% patients have coinfection with another respiratory viral pathogen. 34 (68%) patient required ICU level of care at some point during hospitalization. More than 70% of patients were treated with antibiotics mainly directed towards community acquired pneumonia HP pneumonia MESHD but 97.5% patient has negative blood SERO culture and 93.3% has negative sputum cultures. Of admitted patients, 34% (17/50) were directly admitted to ICU and. Of these ICU patients 82.4% (28/34) required invasive mechanical ventilation. Patients spent a median of 2 days on the floor prior to ICU transfer, median length of stay in the ICU was 7 days. On comparing characteristics of patients, patients with diabetes MESHD, and higher lactate dehydrogenase on admission were more likely to require ICU level of care. No patient deaths were reported on the floor. Of 34 patients in the ICU 13 died while 6 are still receiving care in the hospital, with an overall mortality of 30.2% (13/43). Out of 13 patients who died, 2 were on HD MESHD, 11/13(84%) patients had acute kidney injury HP acute kidney injury MESHD and required CRRT or HD MESHD. The median length of stay is 7 days (Range 1-31days), for floor patients 4 days and ICU patients 13 days. Out of 43 patients who completed their clinical course 24/43(58.1%) were discharged home, 5/43(11.6%) went to rehabilitation facilities and 30.2% died. 16/30(53.3%) required oxygen on discharge. Conclusion: This case series provides characteristics and early experience in treating patient admitted to tertiary care teaching hospital in state of NEW Mexico.

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MeSH Disease
Human Phenotype

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