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SARS-CoV-2 proteins

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    Automatic identification of risk factors for SARS-CoV-2 positivity and severe clinical outcomes of COVID-19 MESHD using Data Mining and Natural Language Processing

    Authors: Verena Schoening; Evangelia Liakoni; Juergen Drewe; Felix Hammann

    doi:10.1101/2021.03.25.21254314 Date: 2021-03-26 Source: medRxiv

    Objectives: Several risk factors have been identified for severe clinical outcomes of COVID-19 MESHD caused by SARS-CoV-2. Some can be found in structured data of patients' Electronic Health Records. Others are included as unstructured free-text, and thus cannot be easily detected automatically. We propose an automated real-time detection of risk factors using a combination of data mining and Natural Language Processing ( NLP HGNC). Material and methods: Patients were categorized as negative or positive for SARS-CoV-2, and according to disease severity (severe or non-severe COVID-19 MESHD). Comorbidities were identified in the unstructured free-text using NLP HGNC. Further risk factors were taken from the structured data. Results: 6250 patients were analysed (5664 negative and 586 positive; 461 non-severe and 125 severe). Using NLP HGNC, comorbidities, i.e. cardiovascular and pulmonary conditions, diabetes MESHD, dementia MESHD and cancer MESHD, were automatically detected (error rate [≤]2%). Old age, male sex, higher BMI, arterial hypertension MESHD, chronic heart failure MESHD, coronary heart disease MESHD, COPD MESHD, diabetes MESHD, insulin HGNC only treatment of diabetic MESHD patients, reduced kidney and liver function were risk factors for severe COVID-19 MESHD. Interestingly, the proportion of diabetic MESHD patients using metformin but not insulin HGNC was significantly higher in the non-severe COVID-19 MESHD cohort (p<0.05). Discussion and conclusion: Our findings were in line with previously reported risk factors for severe COVID-19 MESHD. NLP HGNC in combination with other data mining approaches appears to be a suitable tool for the automated real-time detection of risk factors, which can be a time saving support for risk assessment and triage, especially in patients with long medical histories and multiple comorbidities.

    Clinical Characteristics of Severe COVID-19 MESHD in China: A Case Series and Meta-analysis

    Authors: Geling Teng; Hua Hu; Xia Wang; Junsheng Wang; Hongmei Zhang; Ying Chen

    doi:10.21203/rs.3.rs-186426/v1 Date: 2021-01-29 Source: ResearchSquare

    Background: There have been inconsistent reports regarding the unique manifestations of severe coronavirus disease 2019 MESHD ( COVID-19 MESHD) occurring in China. This study analyzed the clinical manifestation of 13 severe COVID-19 MESHD cases at a single institution and compared the data to previously reported characteristics of severe COVID-19 MESHD in China. Methods: This retrospective case study included patients with severe COVID-19 MESHD who were admitted to the isolation ward of the Shandong Chest Hospital from January 2020 to February 2020. The clinical signs and symptoms, laboratory examination results, imaging features, treatment strategies, and patient prognoses were summarized. A database search was then conducted for studies published through December 2020 documenting characteristics of severe COVID-19 MESHD cases in China. The pooled results for severe COVID-19 MESHD patients in China were calculated by using the random-effects model.Results: A total of 4 severe and 9 critical patients were included from Shandong Chest Hospital. The average patient age was 55.3 (range 23-88) years, and 61.5% of patients were male. Chest computed tomography for all patients showed multiple lesions as ground-glass shadows in both lungs. All patients presented bacterial infection MESHD and various degrees of liver and myocardial injury MESHD. The treatment strategies for patients included antibiotics, immunoglobulin, and glucocorticoids, and mechanical ventilation was used in all patients for respiratory failure MESHD. Two patients died, and 11 recovered. In the pooled data for severe COVID-19 MESHD patients, the most common comorbidities were hypertension MESHD, diabetes mellitus MESHD, and coronary heart disease MESHD. The common signs in these patients were fever MESHD, cough MESHD, fatigue MESHD, chest tightness MESHD, and a leukocyte count > 10. Conclusions: Older males with hypertension MESHD, diabetes mellitus MESHD, and coronary heart disease MESHD may be at higher risk of developing severe COVID-19 MESHD. Patients should be assessed for concomitant bacterial infections MESHD. Cardiac and liver enzymes, fever MESHD, cough MESHD, fatigue MESHD, chest tightness MESHD, and leukocytosis MESHD should be monitored for signs of disease progression. 

    Health-related quality of life of COVID-19 MESHD survivors at 6 months after hospital discharge: a cohort study

    Authors: MeiXuan Lin; Liqun Huang; Danwen Zheng; Linjie Zhang; Bing Feng; Yuntao Liu; Jiajun Hu; Qiaoli Lin; Xiaotu Xi; Xiaohua Xu; Qian Wang; Xin Zhou; Zehui He; Heng Weng; Banghan Ding; Qiuying Deng; Jianwen Guo; Zhongde Zhang

    doi:10.21203/rs.3.rs-176489/v1 Date: 2021-01-28 Source: ResearchSquare

    Background: COVID-19 MESHD is a multi-systemic disease MESHD that is highly contagious and pathogenic. The long-term consequences of it are not yet clear, as is whether society and life can return to a healthy state. Long-term assessment of their health-related quality of life (HRQoL) is essential. This study aimed to investigate HRQoL and its risk factors in COVID-19 MESHD survivors at a follow-up of 6-month. Methods: A multicenter cross-sectional survey was conducted among 192 COVID-19 MESHD patients with confirmed age ≥ 18 years who were discharged from various hospitals in Wuhan from January to April 2020. The demographic characteristics, clinical characteristics, and laboratory results of the study subjects were obtained from the hospital's medical records. Survivors' HRQoL was assessed using the Short Form 36 (SF-36), cognition was assessed using the ascertain dementia MESHD eight-item informant questionnaire (AD8), and survivors' pulmonary function were examined. All participants in this study completed the survey and testing at Hubei Provincial Hospital of Chinese and Western Medicine. SF-36 scores were compared with the Chinese norm, and logistic regression and multivariate analysis were used to investigate the factors affecting HRQoL in COVID-19 MESHD survivors. Results: SF-36 showed significant differences in HRQoL between COVID-19 MESHD survivors and the general Chinese population ( P< 0.05).Multiple linear regression demonstrated that age was negatively correlated with physical functioning (PF), role-physical limitation (RP) and social functioning (SF) ( P <0.05). Bodily pain MESHD (BP), vitality (VT), SF and role-emotional limitation (RE) were negatively correlated with females ( P <0.05). Length from discharge to follow‐up was positively correlated with PF and RP ( P <0.05). Abnormal cognitive function MESHD was negatively correlated with PF, RP, general health (GH), VT, SF, RE and mental health (MH) ( P <0.05). Abnormal Carbon Monoxide Diffusing Capacity (DLCO%<80%) was significantly negatively correlated with PF and SF ( P <0.05).In addition, there was a significant negative correlation between Coronary heart disease MESHD and RP MESHD, GH, VT and RE ( P <0.05).Logistic regression analysis demonstrated that age(OR 1.032) and AD8 scores (OR 1.203)were risk factors associated with a low physical component summary (PCS) score. Length from discharge to follow‐up (OR 0.971) was the protective factor for PCS score. Abnormal cognitive function MESHD (OR 1.543) was a significant determinant associated with a mental component summary (MCS)<50 in COVID-19 MESHD patients. Conclusions: The HRQoL of COVID-19 MESHD survivors remains to be improved at six-month follow-up. Future studies should track HRQoL in older adults, women, patients with abnormal DLCO, and abnormal cognitive function MESHD for a long time and provide them with rehabilitation advice and guidance.

    Efficacy of Colchicine in Non-Hospitalized Patients with COVID-19 MESHD

    Authors: Jean-Claude Tardif; Nadia Bouabdallaoui; Philippe L L'Allier; Daniel Gaudet; Binita Shah; Michael H Pillinger; Jose Lopez-Sendon; Protasio da Luz; Lucie Verret; Sylvia Audet; Jocelyn Dupuis; Andre Y Denault; Martin Pelletier; Philippe A Tessier; Sarah Samson; Denis Fortin; Jean-Daniel Tardif; David Busseuil; Elisabeth Goulet; Chantal Lacoste; Anick Dubois; Avni Y Joshi; David D Waters; Priscilla Hsue; Norman E Lepor; Frederic Lesage; Nicolas Sainturet; Eve Roy-Clavel; Zohar Bassevitch; Andreas Orfanos; Jean C Gregoire; Lambert Busque; Christian Lavallee; Pierre-Olivier Hetu; Jean-Sebastien Paquette; Sylvie Levesque; Marieve Cossette; Anna Nozza; Malorie Chabot-Blanchet; Marie-Pierre Dube; Marie-Claude Guertin; Guy Boivin

    doi:10.1101/2021.01.26.21250494 Date: 2021-01-27 Source: medRxiv

    Background Evidence suggests the role of an inflammatory storm in COVID-19 MESHD complications. Colchicine is an orally administered, anti-inflammatory medication beneficial in gout MESHD, pericarditis MESHD and coronary disease MESHD. Methods We performed a randomized, double-blind trial involving non-hospitalized patients with COVID-19 MESHD diagnosed by polymerase chain reaction (PCR) testing or clinical criteria. The patients were randomly assigned to receive colchicine (0.5 mg twice daily for 3 days and once daily thereafter) or placebo for 30 days. The primary efficacy endpoint was the composite of death MESHD or hospitalization for COVID-19 MESHD. Results A total of 4488 patients were enrolled. The primary endpoint occurred in 4.7% of the patients in the colchicine group and 5.8% of those in the placebo group (odds ratio, 0.79; 95.1% confidence interval (CI), 0.61 to 1.03; P=0.08). Among the 4159 patients with PCR-confirmed COVID-19 MESHD, the primary endpoint occurred in 4.6% and 6.0% of patients in the colchicine and placebo groups, respectively (odds ratio, 0.75; 95% CI, 0.57 to 0.99; P=0.04). In these patients with PCR-confirmed COVID-19 MESHD, the odds ratios were 0.75 (95% CI, 0.57 to 0.99) for hospitalization due to COVID-19 MESHD, 0.50 (95% CI, 0.23 to 1.07) for mechanical ventilation, and 0.56 (95% CI, 0.19 to 1.66) for death MESHD. Serious adverse events were reported in 4.9% and 6.3% in the colchicine and placebo groups (P=0.05); pneumonia MESHD occurred in 2.9% and 4.1% of patients (P=0.02). Diarrhea MESHD was reported in 13.7% and 7.3% in the colchicine and placebo groups (P<0.0001). Conclusion Among non-hospitalized patients with COVID-19 MESHD, colchicine reduces the composite rate of death MESHD or hospitalization. (COLCORONA ClinicalTrials.gov number: NCT04322682)

    Immunological and cardio-vascular pathologies associated with SARS-CoV-2 infection MESHD in golden syrian hamster

    Authors: John F Fullard; Hao-chih Lee; Georgios Voloudakis; Shengbao Suo; Zhiping Shao; Cyril Peter; Behnam Javidfar; Wen Zhang; Shan Jiang; Andre Corvelo; Emma Woodoff-Leith; Dushyant P Purohit; Gabriel E Hoffman; Schahram Akbarian; Mary Fowkes; John Crary; Guo-Cheng Yuan; Panos Roussos; Garth Huberty; Fyodor D. Urnov; Petros Giannikopoulos; Jennifer A. Doudna; Tiannan Guo

    doi:10.1101/2021.01.11.426080 Date: 2021-01-11 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection MESHD in golden Syrian hamster (GSH) causes lungs pathology and resembles to human corona virus disease MESHD ( Covid-19 MESHD). Extra-pulmonary pathologies and immunological parameters of SARS-CoV-2 infection MESHD remained undefined in GSH. Using in silico modelling, we identified the similarities between human and hamster angiotensin-converting enzyme-2 (ACE-2), neuropilin-1 (NRP-1) that bind to receptor-binding domain (RBD) and S1 fragment of spike protein PROTEIN of SARS-CoV-2. SARS-CoV-2 infection MESHD led to lung pathologies, and cardiovascular complications MESHD ( CVC MESHD) marked by interstitial coronary fibrosis MESHD and acute inflammatory response. Serum lipidomic and metabolomic profile of SARS-CoV-2-infected MESHD GSH revealed changes in serum triglycerides (TG) and low-density lipoprotein (LDL), and alterations in metabolites that correlated with Covid19 MESHD. Together, we propose GSH as an animal model to study SARS-CoV-2 infection MESHD and its therapy associated with pulmonary and extra-pulmonary pathologies.

    Clinical features of COVID-19 MESHD patients with comorbid coronary heart disease MESHD

    Authors: Hang Yang; RUI GUO; Lincheng Yang; Ruitao Zhang; Yunpeng Ling; Qinggang Ge

    doi:10.21203/rs.3.rs-129449/v1 Date: 2020-12-15 Source: ResearchSquare

    Background: In addition to the lungs, the coronavirus disease 2019 MESHD ( COVID-19 MESHD) also affects multiple organs throughout the body. The relationship between COVID-19 MESHD infection and cardiovascular disease MESHD, and the mechanisms by which this disease causes damage to the cardiovascular system are unclear. Coronary heart disease MESHD ( CHD MESHD) is one of the common comorbidities of COVID-19 MESHD, but there is insufficient evidence for its clinical features and impact on clinical outcomes. The aim of this study was to analyze the clinical characteristics of COVID-19 MESHD patients with comorbid CHD MESHD and the possible risk factors for the occurrence of critical illness. Methods: A single-center, retrospective study was conducted to analyze COVID-19 MESHD patients admitted to the Sino-French New City Campus of Tongji Hospital in Wuhan, Hubei Province and treated by the Peking University National Medical Assistance Team between January 29 and March 10 HGNC, 2020. Patients testing positive for SARS-CoV-2 viral nucleic acid in nasopharyngeal swab specimens and who had comorbid CHD MESHD, were included in the study. Clinical data and laboratory test results of eligible patients were collected, and the factors associated with the occurrence of critical illness among these patients were evaluated. Results: A total of 205 patients were enrolled in this study, including 20 CHD MESHD patients and 185 non- CHD MESHD patients. The mean age was 66.7 years. Compared to non- CHD MESHD patients, more CHD MESHD patients had comorbid hypertension MESHD and diabetes MESHD (P < 0.05). In terms of laboratory tests, the CHD MESHD group did not differ significantly from the non- CHD MESHD group in blood routine, blood chemistry, and various inflammatory cytokines. More CHD MESHD patients experienced myocardial injury MESHD (25% vs 8.1% P < 0.031) and CHD MESHD patients were more likely to progress to critical illness MESHD (40% vs 16.8%P = 0.012). Univariate logistic regression analysis indicated that a history of CHD MESHD, occurrence of myocardial injury MESHD, high white blood cell (WBC) count, low lymphocyte count, and elevated levels of Cr, ferritin, IL-2R HGNC, IL-8 HGNC at admission were factors associated with the occurrence of critical illness. Multivariate regression analysis found that a history of CHD MESHD(OR=3.529, 95% CI =1.032-12.075, P =0.044),high WBC count(OR=1.289, 95% CI =1.136-1.463, P<0.001) and low lymphocyte count(OR=0.215, 95% CI =0.075-0.616, P =0.004)were independent factors for the occurrence of critical illness among COVID-19 MESHD patients. Conclusion: COVID-19 MESHD patients with comorbid CHD MESHD commonly exhibited myocardial injury MESHD and were prone to developing critical illness. Among COVID-19 MESHD patients, a history of CHD MESHD,high WBC count and low lymphocyte count were independent risk factors for the occurrence of critical illness. Greater attention and vigilance are needed in this regard during clinical practice.

    Impact of COVID-19 MESHD and Associated Preventive Measures on Cardiometabolic Risk Factors in South Korea: An Observational Study

    Authors: Minji Sohn; Bo Kyung Koo; Soo Lim; Ho Il Yoon; Kyoung-Ho Song; Eu Suk Kim; Hong Bin Kim

    doi:10.21203/rs.3.rs-127499/v1 Date: 2020-12-12 Source: ResearchSquare

    Background: During the COVID-19 pandemic MESHD, people have been required to follow preventive measures such as social distancing or staying at home, which can lead to an unhealthy lifestyle. We investigated the effect of these preventive measures on metabolic parameters in individuals with cardiometabolic risk factors.Methods: Using data for patients who visited a tertiary hospital in South Korea at least twice a year for the past 4 years, changes in clinical and biochemical data from the COVID-19 pandemic MESHD (2019–2020) were compared with changes in the same data at the same annual time points during the three previous seasons of 2016–2019.Results: Among 7,094 patients, data for 1,485 were included. Systolic blood pressure increased by 2.6 ± 18.2 mmHg in the COVID-19 pandemic MESHD period compared with the 2018–2019, 2017–2018, and 2016–2017 seasons: –1.4 ± 16.5 mmHg, –2.8 ± 14.3 mmHg, and –0.7 ± 14.3 mmHg, respectively; all p < 0.05. The body mass index increased by 0.09 ± 1.16 kg/m2 in the 2019–2020 pandemic season whereas it changed by –0.39 ± 3.03 kg/m2 in 2018–2019 and by –0.34 ± 2.18 kg/m2 in 2017–2018 (both p <0.05). Total cholesterol, triglycerides, high-density lipoprotein-cholesterol, and low-density lipoprotein-cholesterol levels worsened in the pandemic season compared with the previous three. Fasting glucose and glycated hemoglobin levels also showed increasing tendencies during the pandemic, but without significance. During the COVID-19 pandemic MESHD, the number of patients whose metabolic syndrome MESHD worsened increased significantly by 21% compared with the 2018–2019 season. The 10-year coronary heart disease MESHD risk calculated using the Framingham risk score also increased significantly.Conclusions: Comorbidity and mortality arising from cardiometabolic disorders MESHD as collateral damage during COVID-19 MESHD infections and preventive procedures could have major impacts on human health in the future. Nationwide strategies to reverse the aggravation of cardiometabolic health during a pandemic should be implemented in countries attempting to cope with it.

    Research on Recognition Method of COVID-19 MESHD Images Based on Deep Learning

    Authors: dongshen ji; yanzhong zhao; zhujun zhang; qianchuan zhao

    doi:10.1101/2020.12.09.20246371 Date: 2020-12-11 Source: medRxiv

    In view of the large demand for new coronary pneumonia MESHD covid19 MESHD image recognition samples,the recognition accuracy is not ideal.In this paper,a new coronary pneumonia positive image recognition method proposed based on small sample recognition. First, the CT image pictures are preprocessed, and the pictures are converted into the picture formats which are required for transfer learning. Secondly, perform small-sample image enhancement and expansion on the converted picture, such as miscut transformation, random rotation MESHD and translation, etc.. Then, multiple migration models are used to extract features and then perform feature fusion. Finally,the model is adjusted by fine-tuning.Then train the model to obtain experimental results. The experimental results show that our method has excellent recognition performance in the recognition of new coronary pneumonia MESHD images,even with only a small number of CT image samples.

    Invasive Mechanical Ventilation May Be an Important Factor of Mortality in Severe/Critical COVID-19 MESHD Pneumonia: A Retrospective Cohort Study

    Authors: Jing Wei; Lei Shi; Zhi Cheng; Xinye Jin; Wei Zhao; Ruyou Li; You Zheng; Zhihang Peng; Changming Niu; Tingrong Huang; Ningfei Ji; Mao Huang; Xiaolin Chen; Jiaxin Yan; Mingjing Wu; Kaili Deng; Lei Shu; Xueli Wang; Yang Cao; Ganzhu Feng

    doi:10.21203/rs.3.rs-105230/v1 Date: 2020-11-09 Source: ResearchSquare

    Background: Many of severe COVID-19 MESHD patients are admitted to the hospital or even to the Intensive Care Unit(ICU). The present study was aimed to investigated the risk factors in death from COVID-19 MESHD.Methods: In this retrospective study, all inpatients confirmed severe or critical COVID-19 MESHD from two tertiary hospital in Huangshi were included, who had been discharged or died by March19,2020. Demographic,clinical,treatment,laboratory data and information were extracted from electronic medical records and compared between survivors group and non-survivors group. The univariable and multivariable logistic regression analysis was used to analyze the risk factors associated with in-hospital death MESHD.Results: 81 patients were included in this study, of whom 55 were discharged and 26 died in hospital. In all patients, 36(44.4%) patients had comorbidity, including  hypertension MESHD(27[33.3%]), diabetes MESHD(11[13.6%]) and coronary heart disease MESHD ( CHD MESHD)(11[13.6%]), and 16(19.8%) patients accompanied with more than 2 kinds of underlying diseases. The proportion of CHD MESHD in non-survivors group was significantly higher than that in survivors group(26.9% vs 7.3%, P=0.032), but there were no differences in hypertension MESHD, diabetes MESHD and COPD between the non-survivors group and the survivors group. Multivariable logistic regression analysis showed increasing odds of in-hospital death associated with aspartate aminotransferase( AST HGNC) and invasive mechanical ventilation (IMV) (P<0.001)(P=0.017).Conclusions: Invasive Mechanical Ventilation may contribute to mortality of severe/critical COVID-19 MESHD pneumonia, and with higher AST HGNC at admission was one of the indicators of poor prognosis.Trial registration: Chinese Clinical Trial Registration; ChiCTR2000031494; Registered 02 April 2020; http://www.medresman.org

    A potential impact of physical distancing on physical and mental health. A rapid narrative umbrella review of meta-analyses on the link between social isolation and health

    Authors: Nexhmedin Morina; Ahlke Kip; Thole H Hoppen; Stefan Priebe; Thomas Meyer

    doi:10.1101/2020.10.06.20207571 Date: 2020-10-07 Source: medRxiv

    Background: The imperative for physical distancing during the coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic may deteriorate physical and mental health. We aimed at summarizing the strength of evidence in the published literature on the association of social isolation and loneliness with physical and mental health. Methods: We conducted a systematic search in April 2020 to identify meta-analyses using the Medline, PsycINFO, and Web of Science databases. The search strategy included terms of social isolation, loneliness, living alone, and meta-analysis. Eligible meta-analyses needed to report any sort of association between an indicator of social isolation and any physical or mental health outcome. The findings were summarized in a narrative synthesis. Results: Twenty-five meta-analyses met our criteria, of which 10 focused on physical health and 15 on mental health outcomes. A total of more than 3 million individuals had participated in the 692 primary studies. The results suggest that social isolation is associated with chronic physical symptoms, frailty, coronary heart disease MESHD, malnutrition MESHD, hospital readmission, reduced vaccine uptake, early mortality, depression MESHD, social anxiety MESHD, psychosis MESHD, cognitive impairment MESHD in later life, and suicidal ideation. Conclusions: The existing evidence clearly indicates that social isolation is associated with a range of poor physical and mental health outcomes. A potential negative impact on these outcomes needs to be considered in future decisions on physical distancing measures.

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MeSH Disease
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