Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (51)

ProteinN (19)

NSP5 (11)

ComplexRdRp (9)

ProteinE (6)


SARS-CoV-2 Proteins
    displaying 31 - 40 records in total 1322
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    Probabilistic combination of eigenlungs-based classifiers for COVID-19 MESHD diagnosis in chest CT images

    Authors: Juan E. Arco; Andrés Ortiz; Javier Ramírez; Francisco J. Martínez-Murcia; Yu-Dong Zhang; Jordi Broncano; M. Álvaro Berbís; Javier Royuela-del-Val; Antonio Luna; Juan M. Górriz

    id:2103.02961v1 Date: 2021-03-04 Source: arXiv

    The outbreak of the COVID-19 MESHD ( Coronavirus disease 2019 MESHD) pandemic has changed the world. According to the World Health Organization (WHO), there have been more than 100 million confirmed cases of COVID-19 MESHD, including more than 2.4 million deaths. It is extremely important the early detection of the disease, and the use of medical imaging such as chest X-ray (CXR) and chest Computed Tomography (CCT) have proved to be an excellent solution. However, this process requires clinicians to do it within a manual and time-consuming task, which is not ideal when trying to speed up the diagnosis. In this work, we propose an ensemble classifier based on probabilistic Support Vector Machine (SVM) in order to identify pneumonia MESHD patterns while providing information about the reliability of the classification. Specifically, each CCT scan is divided into cubic patches and features contained in each one of them are extracted by applying kernel PCA. The use of base classifiers within an ensemble allows our system to identify the pneumonia MESHD patterns regardless of their size or location. Decisions of each individual patch are then combined into a global one according to the reliability of each individual classification: the lower the uncertainty, the higher the contribution. Performance is evaluated in a real scenario, yielding an accuracy of 97.86%. The large performance obtained and the simplicity of the system (use of deep learning in CCT images would result in a huge computational cost) evidence the applicability of our proposal in a real-world environment.

    Self-supervised deep convolutional neural network for chest X-ray classification

    Authors: Matej Gazda; Jakub Gazda; Jan Plavka; Peter Drotar

    id:2103.03055v2 Date: 2021-03-04 Source: arXiv

    Chest radiography is a relatively cheap, widely available medical procedure that conveys key information for making diagnostic decisions. Chest X-rays are almost always used in the diagnosis of respiratory diseases MESHD such as pneumonia MESHD or the recent COVID-19 MESHD. In this paper, we propose a self-supervised deep neural network that is pretrained on an unlabeled chest X-ray dataset. The learned representations are transferred to downstream task - the classification of respiratory diseases MESHD. The results obtained on four public datasets show that our approach yields competitive results without requiring large amounts of labeled training data.

    Hope, Depression, Anxiety MESHD and Associated Factors Among Parents of Retinoblastoma MESHD Patients During the Pneumonia Epidemic in COVID-19 MESHD: A Cross-Sectional Study

    Authors: Changjuan Zeng; Wenting Cao; Ting Zhao; Li Li; Lili Hou

    doi:10.21203/ Date: 2021-03-04 Source: ResearchSquare

    BackgroundThe 2019 coronavirus disease MESHD ( COVID-19 MESHD) is a global public health emergency. So far, only a limited number of studies have investigated the impact of the pneumonia MESHD pandemic in COVID-19 MESHD on the mental health of parents having children with cancer MESHD. This study investigated the hope, depression MESHD, anxiety MESHD, and relevant influencing factors among parents of retinoblastoma MESHD patients during the pneumonia epidemic in COVID-19 MESHD.MethodsA total of 317 parents having children with retinoblastoma MESHD admitted to the Ninth People’s Hospital affiliated with the Shanghai Jiao Tong University, School of Medicine, and Qilu Children’s Hospital of Shandong University were investigated by cross-sectional investigation and convenient sampling. The survey tools included a Demographic Questionnaire, Herth Hope Index (HHI), The Generalized Anxiety Disorder MESHD (GAD-7), and The Patient Health Questionnaires (PHQ)-2. ResultsThe hope level score of the parents of retinoblastoma MESHD patients was (35.36 ±4.42), which was at the medium level. The highest dimension of the hope score was to take positive action (12.07± 1.57), and the lowest dimension was to maintain a close relationship with others (11.50± 1.64). The incidence rates of anxiety MESHD and depression MESHD were 41.32% (131/317) and 29.97% (95/317), respectively. Hope level was negatively correlated with anxiety and depression MESHD. Monoculus or binoculus disease, sleep quality, health status, having anxiety/depression MESHD or not, had a statistically significant effect on the research subjects' hope level (p<0.05). Multiple linear regression analysis revealed that the course of the disease, education level, and depression MESHD were independent influencing factors (p<0.05), which could explain 22.60% of the variation in hope level.ConclusionDuring the COVID-19 MESHD outbreak, medical staff should formulate targeted intervention measures according to the different characteristics of eye disease MESHD, the course of the disease, the parents' educational level, health status, and emotional state so as to improve parents' hope level.

    Impact of Early Corticosteroids on 60-day Mortality in Critically MESHD Ill Patients with COVID-19 MESHD: A Multicenter Cohort Study of the OUTCOMEREA Network

    Authors: Claire Dupuis; Etienne de Montmollin; Niccolò Buetti; Dany Goldgran-Toledano; Jean Reignier; Carole Schwebel; Julien Domitile; Mathilde Neuville; Moreno Ursino; Shidasp Siami; Stéphane Ruckly; Corinne Alberti; Bruno Mourvillier; Sebastien Bailly; Virginie Laurent; Marc Gainnier; Bertrand Souweine; Jean-François Timsit

    doi:10.21203/ Date: 2021-03-03 Source: ResearchSquare

    ObjectivesIn severe COVID-19 MESHD pneumonia MESHD, the appropriate timing and dosing of corticosteroids(CS) is not known. Patient subgroups for which CS could be more beneficial also need appraisal. The aim of this study was to assess the effect of early CS in COVID-19 MESHD pneumonia MESHD patients admitted to the ICU on the occurrence of 60-day mortality, ICU-acquired-bloodstream infections(ICU-BSI), and hospital-acquired pneumonia MESHD and ventilator-associated pneumonia MESHD(HAP-VAP).MethodsWe included patients with COVID-19 MESHD pneumonia MESHD admitted to 11 ICUs belonging to the French OutcomeReaTM network from January to May 2020. We used survival models with ponderation with inverse probability of treatment weighting (IPTW). Inflammation MESHD was defined as Ferritin >1000 µg/l or D-Dimers >1000 µg/l or C-Reactive Protein HGNC >100 mg/dL.ResultsThe study population comprised 302 patients having a median age of 61.6(53-70) years of whom 78.8% were male and 58.6% had at least one comorbidity. The median SAPS II MESHD was 33(25-44). Invasive mechanical ventilation was required in 34.8% of the patients. Sixty-six (21.8%) patients were in the Early-CS-subgroup. Most of them (n=55, 83.3%) received high doses of steroids. Overall, 60-day mortality was 29.4%. The risks of 60-day mortality (IPTWHR =0.88;95% CI 0.55 to 1.39, p=0.58), ICU-BSI and HAP-VAP were similar in the two groups. Importantly, early CS treatment was associated with a lower mortality rate in patients aged 60 years or more (IPTWHR, 0.51;95% CI, 0.29 – 0.91; p=0.02). But, CS was associated with an increased risk of death for the patients younger than 60 years without inflammation MESHD on admission (IPTWHR =8.17;95% CI, 1.76, 37.85; p=0.01).ConclusionFor patients with COVID-19 MESHD pneumonia MESHD, early CS treatment was not associated with patient survival. Interestingly, inflammation MESHD and age can significantly influence the effect of CS.

    Low-dose lung radiotherapy for COVID-19 MESHD lung disease MESHD: a pre-clinical efficacy study in a bleomycin model of pneumonitis MESHD.

    Authors: Mark R Jackson; Katrina Stevenson; Sandeep K Chahal; Emer Curley; George Finney; Rodrigo Gutierrez-Quintana; Evarest Onwubiko; Angelika F Rupp; Karen Strathdee; Megan KL MacLeod; Charles McSharry; Anthony J Chalmers

    doi:10.1101/2021.03.03.433704 Date: 2021-03-03 Source: bioRxiv

    Purpose: Low-dose whole lung radiotherapy ( LDLR HGNC) has been proposed as a treatment for patients with acute respiratory distress syndrome MESHD associated with SARS-CoV-2 infection MESHD and clinical trials are underway. There is an urgent need for preclinical evidence to justify this approach and inform dose, scheduling and mechanisms of action. Materials and methods: Female C57BL/6 mice were treated with intranasal bleomycin sulphate (7.5 or 11.25 units/kg, day 0) then exposed to whole lung radiation therapy (0.5, 1.0, 1.5 Gy or sham, day 3). Bodyweight was measured daily and lung tissue harvested for histology and flow cytometry on day 10. Computed tomography (CT) lung imaging was performed pre-radiation (day 3) and pre-endpoint (day 10). Results: Bleomycin caused pneumonitis MESHD of variable severity which correlated with weight loss MESHD. LDLR at 1.0 Gy was associated with a significant increase in the proportion of mice recovering to 98% of initial bodyweight; many of these mice exhibited less severe histopathological lung changes. Mice experiencing moderate initial weight loss MESHD were more likely to respond to LDLR than those experiencing severe initial weight loss MESHD. LDLR (1.0 Gy) significantly reduced bleomycin induced increases in interstitial macrophages, CD103+ dendritic cells and neutrophil-DC hybrids. Pre-radiation, bleomycin treated mice exhibited significantly higher percentages of non-aerated lung in left than right lungs; LDLR (1.0 Gy) prevented further reductions in aerated lung volume in right but not left lungs. LDLR doses of 0.5 and 1.5 Gy did not modulate bodyweight or flow cytometric readouts of bleomycin pneumonitis MESHD. Conclusions: Our data support the concept that LDLR can ameliorate acute inflammatory lung injury MESHD, identify 1.0 Gy as the most effective dose and provide preliminary evidence that it is more effective in the context of moderate than severe pneumonitis MESHD. Mechanistically, LDLR significantly suppressed bleomycin induced accumulation of interstitial macrophages, CD103+ dendritic cells and neutrophil-DC hybrids in the lung.

    Learning Invariant Representations across Domains and Tasks

    Authors: Jindong Wang; Wenjie Feng; Chang Liu; Chaohui Yu; Mingxuan Du; Renjun Xu; Tao Qin; Tie-Yan Liu

    id:2103.05114v1 Date: 2021-03-03 Source: arXiv

    Being expensive and time-consuming to collect massive COVID-19 MESHD image samples to train deep classification models, transfer learning is a promising approach by transferring knowledge from the abundant typical pneumonia MESHD datasets for COVID-19 MESHD image classification. However, negative transfer may deteriorate the performance due to the feature distribution divergence between two datasets and task semantic difference in diagnosing pneumonia MESHD and COVID-19 MESHD that rely on different characteristics. It is even more challenging when the target dataset has no labels available, i.e., unsupervised task transfer learning. In this paper, we propose a novel Task Adaptation Network (TAN) to solve this unsupervised task transfer problem. In addition to learning transferable features via domain-adversarial training, we propose a novel task semantic adaptor that uses the learning-to-learn strategy to adapt the task semantics. Experiments on three public COVID-19 MESHD datasets demonstrate that our proposed method achieves superior performance. Especially on COVID-DA dataset, TAN significantly increases the recall and F1 score by 5.0% and 7.8% compared to recently strong baselines. Moreover, we show that TAN also achieves superior performance on several public domain adaptation benchmarks.

    Initial Study on TMPRSS2 HGNC p.Val160Met Genetic Variant in COVID-19 MESHD patients

    Authors: Laksmi Wulandari; Berliana Hamidah; Cennikon Pakpahan; Nevy Shinta Damayanti; Neneng Dewi Kurniati; Christophorus Oetama Adiatmaja; Monica Rizky Wigianita; Soedarsono Soedarsono; Dominicus Husada; Damayanti Tinduh; Cita Rosita Sigit Prakoeswa; Anang Endaryanto; Ni Nyoman Tri Puspaningsih; Maria Inge Lusida; Kazufumi Shimizu; Delvac Oceandy

    doi:10.21203/ Date: 2021-03-03 Source: ResearchSquare

    Background Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is a global health problem that causes millions of deaths worldwide. The clinical manifestation of COVID-19 MESHD widely varies from asymptomatic infection to severe pneumonia MESHD and systemic inflammatory disease MESHD. It is thought that host genetic variability may affect the host's response to the virus infection MESHD and thus cause severity of the disease. The SARS-CoV-2 virus requires interaction with its receptor complex in the host cells before infection. The transmembrane protease serine 2 HGNC ( TMPRSS2 HGNC) has been identified as one of the key molecules involved in SARS-CoV-2 virus receptor binding and cell invasion. Therefore, in this study we investigated the correlation between a genetic variant within the human TMPRSS2 HGNC gene and COVID-19 MESHD severity and viral load.ResultsWe genotyped 95 patients with COVID-19 MESHD hospitalized in Dr Soetomo General Hospital and Indrapura Field Hospital (Surabaya, Indonesia) for the TMPRSS2 p HGNC.Val160Met polymorphism. Polymorphism was detected using a TaqMan assay. We then analysed the association between the presence of the genetic variant and disease severity and viral load. We did not observe any correlation between the presence of TMPRSS2 HGNC genetic variant with the severity of the disease. However, we identified significant association between the p.Val160Met polymorphism and the SARS-CoV-2 viral load, as estimated by the Ct value of the diagnostic nucleic acid amplification test. Furthermore, we observed a trend of association between the presence of the C allele and the mortality rate in patients with severe COVID-19 MESHD. ConclusionOur data indicate a possible association between TMPRSS2 HGNC p.Val160Met polymorphism and SARS-CoV-2 infectivity MESHD and the outcome of Covid-19 MESHD

    SARS-CoV-2 And Other Human Coronavirus Show Genome Patterns Previously Associated to Reduced Viral Recognition and Altered Immune Response

    Authors: Giovanni Franzo

    doi:10.21203/ Date: 2021-03-01 Source: ResearchSquare

    A new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia MESHD. Initial evidence suggests that dysregulation of the immune response could contribute to the pathogenesis, as previously demonstrated for SARS-CoV MESHD. The presence of genome composition features involved in delaying viral recognition is herein investigated for human coronaviruses (HCoVs), with a special emphasis on SARS-CoV-2. A broad collection of HCoVs polyprotein, envelope, matrix, nucleocapsid and spike coding sequences was downloaded and several statistics representative of genome composition and codon bias were investigated. A model able to evaluate and test the presence of a significant under- or over-representation of dinucleotide pairs while accounting for the underlying codon bias and protein sequence was also implemented. The study revealed the significant under-representation of CpG dinucleotide pair in all HcoV, but especially in SARS-CoV MESHD and even more in SARS-CoV-2. The presence of forces acting to minimize CpG content was confirmed by relative synonymous codon usage pattern. Codons containing the CpG pair were severely under-represented, primarily in the polyprotein and spike coding sequences of SARS-CoV-2. Additionally, a significant under-representation of the TpA pair was observed in the N and S region of SARS-CoV and SARS-CoV-2 MESHD. Increasing experimental evidence has proven that CpG and TpA are targeted by innate antiviral host defences, contributing both to RNA degradation and RIG-1 HGNC mediated interferon production. The low content of these dinucleotides could contribute to a delayed interferon production, dysregulated immune response, higher viral replication and poor outcome. Significantly, the RIG-1 HGNC signalling pathway was proven to be defective in elderlies, suggesting a likely interaction between limited viral recognition and lower responsiveness in interferon production that could justify the higher disease severity and mortality in older patients.

    Discharge from the Emergency Department and Early Hospital Revaluation in Patients with COVID-19 MESHD Pneumonia: an Observational Study

    Authors: Massimo Mattioli; Devis Benfaremo; Francesca Fulgenzi; Silvia Gennarini; Luciano Mucci; Margherita Lambertini; Francesca Padiglione; Ramona Brugnera; Barbara Gabrielli; Flavia Giorgino; Maria Capalbo; Edoardo Berselli; Gianluca Moroncini; Gabriele Frausini; Umberto Gnudi

    doi:10.21203/ Date: 2021-03-01 Source: ResearchSquare

    Background Health National Systems world-wide are facing the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) pandemic. We purpose an outpatient management for patients affected by SARS-CoV-2 related pneumonia at risk of progression, after discharge from Emergency Department (ED).Methods This was a single-center prospective observational study. We enrolled patients with confirmed SARS-CoV-2 pneumonia MESHD, without hypoxemic respiratory failure MESHD, and at least one of the following: age ≥ 65 or presence of one or more comorbidities or pneumonia MESHD involvement > 25% on high resolution computed tomography (HRCT). The ambulatorial visit was performed after at least 48 hours, then patients could be discharged, admitted for hospitalization, or deferred for a further visit. As a control, we evaluated a historical cohort of patients hospitalized with comparable clinical and radiological features.Results A total of 84 patients were enrolled (51 M, mean age 62.8 y). Two-thirds of patients had at least one comorbidity and 41.6% had a lung involvement > 25% at HRCT; the mean duration of symptoms was 8 ± 3 days and the mean PaO2/FiO2 ratio 357.5 ± 38.6. At the end of the follow-up period, 69 patients had been discharged and 15 hospitalized (mean stay 6 days). Older age and higher NEWS2 were significant predictors of hospitalization at the first follow-up visit. One hospitalized patient died of septic shock MESHD. In the control group, the mean hospital stay was 8 days.Conclusions Adopting a “discharge and early revaluation” strategy appear to be safe and feasible. This approach may help to optimize hospital resources during the SARS-CoV-2 pandemic.

    An Evaluation of Thrombotic MESHD Tendency by Whole-Body Enhanced CT Scan for Critical COVID-19 MESHD Pneumonia: A Case Series Study

    Authors: Fumihiro Ogawa; Yasufumi Oi; Kento Nakajima; Reo Matsumura; Tomoki Nakagawa; Takao Miyagawa; Takeru Abe; Ichiro Takeuchi

    doi:10.21203/ Date: 2021-02-27 Source: ResearchSquare

    Background: Coronavirus disease ( COVID-19 MESHD) pneumonitis MESHD associated with severe respiratory failure MESHD has a high mortality rate. Based on recent reports, the most severely ill patients present with  coagulopathy MESHD, and disseminated intravascular coagulation MESHD (DIC)-like massive intravascular clot formation is frequently observed. Coagulopathy MESHD has emerged as a significant contributor to thrombotic complications MESHD. Although recommendations have been made for anticoagulant use for COVID-19 MESHD, no guidelines have been specified.Case presentation: We describe four cases of critical COVID-19 MESHD with thrombosis MESHD detected by enhanced CT scan. The CT findings of all cases demonstrated typical findings of COVID-19 MESHD and pulmonary embolism MESHD or deep venous thrombus MESHD without critical exacerbation. Two patients died of respiratory failure MESHD due to COVID-19 MESHD.Discussion: Previous reports have suggested coagulopathy MESHD with thrombotic MESHD signs as the main pathological feature of COVID-19 MESHD, but no previous reports have focused on coagulopathy MESHD evaluated by whole-body enhanced CT scan. Changes in hemostatic biomarkers, represented by an increase in D-dimer and fibrin/fibrinogen degradation products, indicated that the essence of coagulopathy MESHD was massive fibrin formation. Although there were no clinical symptoms related to their prognosis, critical COVID-19 MESHD-induced systemic thrombus MESHD formation was observed. Conclusions: Therapeutic dose anticoagulants should be considered for critical COVID-19 MESHD because of induced coagulopathy MESHD, and aggressive follow-up by whole body enhanced CT scan for systemic venous thromboembolism MESHD ( VTE MESHD) is necessary. 

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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