Corpus overview


MeSH Disease

Infections (545)

Disease (455)

Death (395)

Coronavirus Infections (272)

Pneumonia (108)

Human Phenotype

Pneumonia (112)

Fever (108)

Cough (87)

Fatigue (27)

Hypertension (20)


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    Deep Learning Models for Early Detection and Prediction of the spread of Novel Coronavirus (COVID-19)

    Authors: Devante Ayris; Kye Horbury; Blake Williams; Mitchell Blackney; Celine Shi Hui See; Syed Afaq Ali Shah

    id:2008.01170v1 Date: 2020-07-29 Source: arXiv

    SARS-CoV2, which causes coronavirus disease MESHD (COVID-19) is continuing to spread globally and has become a pandemic. People have lost their lives due to the virus and the lack of counter measures in place. Given the increasing caseload and uncertainty of spread, there is an urgent need to develop machine learning techniques to predict the spread of COVID-19. Prediction of the spread can allow counter measures and actions to be implemented to mitigate the spread of COVID-19. In this paper, we propose a deep learning technique, called Deep Sequential Prediction Model (DSPM) and machine learning based Non-parametric Regression Model (NRM) to predict the spread of COVID-19. Our proposed models were trained and tested on novel coronavirus 2019 dataset, which contains 19.53 Million confirmed cases TRANS of COVID-19. Our proposed models were evaluated by using Mean Absolute Error and compared with baseline method. Our experimental results, both quantitative and qualitative, demonstrate the superior prediction performance SERO of the proposed models.

    Predicting Critical State after COVID-19 Diagnosis Using Real-World Data from 20152 Confirmed US Cases TRANS

    Authors: Mike Domenik Rinderknecht; Yannick Klopfenstein

    doi:10.1101/2020.07.24.20155192 Date: 2020-07-27 Source: medRxiv

    The global COVID-19 pandemic caused by the virus SARS-CoV-2 has led to over 10 million confirmed cases TRANS, half a million deaths MESHD, and is challenging healthcare systems worldwide. With limited medical resources, early identification of patients with a high risk of progression to severe disease MESHD or a critical state is crucial. We present a prognostic model predicting critical state within 28 days following COVID-19 diagnosis trained on data from US electronic health records (EHR) within IBM Explorys, including demographics, comorbidities, symptoms, laboratory test results, insurance types, and hospitalization. Our entire cohort included 20152 COVID-19 cases, of which 3160 patients went into critical state or died. Random, stratified train-test splits were repeated 100 times to obtain a distribution of performance SERO. The median and interquartile range of the areas under the receiver operating characteristic curve (ROC AUC) and the precision recall SERO curve (PR AUC) were 0.863 [0.857, 0.866] and 0.539 [0.526, 0.550], respectively. Optimizing the decision threshold lead to a sensitivity SERO of 0.796 [0.775, 0.821] and a specificity of 0.784 [0.769, 0.805]. Good model calibration was achieved, showing only minor tendency to over-forecast probabilities above 0.6. The validity of the model was demonstrated by the interpretability analysis confirming existing evidence on major risk factors (e.g., higher age TRANS and weight, male TRANS gender TRANS, diabetes, cardiovascular disease MESHD disease, and chronic kidney HP kidney disease MESHD). The analysis also revealed higher risk for African Americans and "self-pay patients". To the best of our knowledge, this is the largest dataset based on EHR used to create a prognosis model for COVID-19. In contrast to large-scale statistics computing odds ratios for individual risk factors, the present model combining a rich set of covariates can provide accurate personalized predictions enabling early treatment to prevent patients from progressing to a severe or critical state.

    Epidemiological investigation and prevention control analysis of longitudinal distribution of COVID-19 in Henan province, China

    Authors: Xianguang Yang; Xuelin Chen; Cuihong Ding; Zhibo Bai; Jingyi Zhu; Gege Sun; Guoying Yu

    doi:10.1101/2020.07.25.20161844 Date: 2020-07-27 Source: medRxiv

    Objective: To analyze the vertical distribution of six cities in Henan Province,China from January 21, 2020 to June17, 2020: Xinyang City (including Gushi County), Nanyang City (including Dengzhou City), Zhumadian City (including XincaiCounty), Zhengzhou City (including Gongyi City), Puyang City and Anyang City (including Hua County) corona virus disease MESHD 2019(COVID-19) epidemiological characteristics and local prevention and control measures.Methods: Data were collected and analyzed through the COVID-19 information published on the official websites of health commissions of Henan Province and six cities.Results: As of June 17, 2020, the cumulative incidence rate of COVID-19 in Henan province was 1.33/100,000, the cumulative cure rate was 98.27%, the cumulative mortality rate was 1.73%, the age TRANS range of diagnosed cases was 5days-85years old, and the male TRANS to female TRANS ratio was 1.09:1.The confirmed cases TRANS of COVID-19 in Henan province were mainly imported cases from Hubei, accounting for 87.74%, of which the highest number was 70.50% in Zhumadian. The contact cases and local cases increased in a fluctuating manner over time.Significance: In this paper, epidemiological characteristics of COVID-19 in Henan province from the outbreak to the effective control within 60 days were analyzed, and effective and distinctive prevention and control measures in various cities were summarized, so as to provide a favorable reference for the further formulation and implementation of epidemic prevention and control and a valuable theoretical basis for effectively avoiding the second outbreak.

    Power Law in COVID-19 Cases in China

    Authors: Behzod B. Ahundjanov; Sherzod B. Akhundjanov; Botir B. Okhunjanov

    doi:10.1101/2020.07.25.20161984 Date: 2020-07-27 Source: medRxiv

    The novel coronavirus (COVID-19) was first identified in China in December 2019. Within a short period of time, the infectious disease MESHD disease has spread TRANS has spread far and wide. This study focuses on the distribution of COVID-19 confirmed cases TRANS in China---the original epicenter of the outbreak. We show that the upper tail of COVID-19 cases in Chinese cities is well described by a power law distribution, with exponent less than one, and that a random proportionate growth model predicated by Gibrat's law is a plausible explanation for the emergence of the observed power law behavior. This finding is significant because it implies that COVID-19 cases in China is heavy-tailed and disperse, that a few cities account for a disproportionate share of COVID-19 cases, and that the distribution has no finite mean or variance. The power-law distributedness has implications for effective planning and policy design as well as efficient use of government resources.

    The Socio-Spatial Determinants of COVID-19 Diffusion: The Impact of Globalisation, Settlement Characteristics and Population

    Authors: Thomas Sigler; Sirat Mahmuda; Anthony Kimpton; Julia Loginova; Pia Wohland-Jakhar; Elin Charles-Edwards; Jonathan Corcoran

    doi:10.21203/ Date: 2020-07-26 Source: ResearchSquare

    Background: COVID-19 is an emergent infectious disease MESHD disease that has spread TRANS that has spread geographically to become a global pandemic. While much research focuses on the epidemiological and virological aspects of the COVID-19 transmission TRANS, there remains a gap in knowledge regarding the drivers of geographical diffusion between places. Here, we use quantile regression to model the roles of globalisation, human settlement and population characteristics as socio-spatial determinants of COVID-19 diffusion over a six-week period in March and April 2020. Results: The quantile regression model suggest that globalisation and settlement population characteristics related to high human mobility predict disease MESHD diffusion. Human development level (HDI) and total population predict COVID-19 diffusion in countries with a high number of total confirmed cases TRANS per million whereas larger household size, older populations, and globalisation tied to human interaction predict COVID-19 diffusion in countries with a low number of total confirmed cases TRANS per million.  Conclusions: The analysis confirms that globalisation, settlement and population characteristics lead to greater disease MESHD diffusion, and primarily variables tied to high human mobility. These outcomes serve to inform policies around ‘flattening the curve’, particularly as they related to anticipated relocation diffusion from more- to less-developed countries and regions, and hierarchical diffusion from countries with higher population and density. Epidemiological strategies must be tailored to suit the range of human mobility patterns, as well as the variety of settlement and population characteristics.

    Point-of-care ultrasound for COVID-19 pneumonia MESHD pneumonia HP patients in the ICU

    Authors: zouheir bitar; Mohammed Shamsah; Omar Bamasood; Ossama Maadrani; Huda Al foudri

    doi:10.21203/ Date: 2020-07-26 Source: ResearchSquare

    BackgroundPoint-of-care ultrasound (POCUS) has a major role in the management of patients with acute hypoxic respiratory and circulatory failure and guides hemodynamic management. There is scarce literature on POCUS assessment characteristics in COVID-19 pneumonia MESHD pneumonia HP with hypoxic respiratory failure HP.MethodsThe study is an observational, prospective, single‐center study conducted in the intensive care unit of Adan General Hospital from May 1st, 2020, to June 25, 2020. The study included adults TRANS suspected to have COVID-19 transferred to the intensive care unit (ICU) with fever MESHD fever HP or suspected respiratory infection MESHD. Patients were transferred to the ICU directly from the ED or general medical wards after reverse transcriptase-polymerase chain reaction (RT-PCR) testing. A certified intensivist in critical care ultrasound who was blinded to the RT-PCR results, if available at the time of examination, performed the lung ultrasound and echocardiology within 12 hours of the patient’s admission to the ICU. We calculated the E/e’, E/A ratio, left ventricular ejection fraction EF, IVC diameter, RV size and systolic function. We performed ultrasound in 12 chest areas.ResultsOf 92 patients with suspected COVID-19 pneumonia MESHD pneumonia HP, 77 (84%) cases were confirmed TRANS. The median age TRANS of the patients was 53 (82-36) years, and 71 (77%) were men.In the group of patients with confirmed COVID-19 pneumonia MESHD pneumonia HP, echocardiographic findings showed normal E/e’, deceleration time (DT), and transmittal E/A ratio in comparison to the non-COVID19 patients (P .001 for both). The IVC diameter was <2 cm with > 50% collapsibility in 62 (81%) patients with COVID-19 pneumonia MESHD pneumonia HP; a diameter of > 2 cm and < 50% collapsibility in all patients, with a P value of 0.001, was detected among those with non-COVID-19 pneumonia MESHD pneumonia HP. There were 3 cases of myocarditis MESHD myocarditis HP with poor EF (5.5%), severe RV dysfunction was seen in 9 cases (11.6%), and 3 cases showed RV thrombus.Chest US revealed four signs suggestive of COVID-19 pneumonia MESHD pneumonia HP in 77 patients (98.6%) ( sensitivity SERO 96.9%, CI 85%‐99.5%) when compared with RT-PCR results.ConclusionPOCUS plays an important role in bedside diagnosis, hemodynamic assessment and management of patients with acute hypoxic respiratory and circulatory failure in patients with COVID-19 pneumonia MESHD pneumonia HP.

    Seroprevalence SERO of SARS-CoV-2 IgG Antibodies SERO in Utsunomiya City, Greater Tokyo, after first pandemic in 2020 (U-CORONA): a household- and population-based study

    Authors: Nobutoshi Nawa; Jin Kuramochi; Shiro Sonoda; Yui Yamaoka; Yoko Nukui; Yasunari Miyazaki; Takeo Fujiwara

    doi:10.1101/2020.07.20.20155945 Date: 2020-07-26 Source: medRxiv

    Background: The number of confirmed cases TRANS of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infections MESHD in Japan are substantially lower in comparison to the US and UK, potentially due to the under-implementation of polymerase chain reaction (PCR) tests. Studies reported that more than half of the SARS-CoV-2 infections are asymptomatic MESHD asymptomatic TRANS, confirming the importance for conducting seroepidemiological studies. Although the seroepidemiological studies in Japan observed a reported prevalence SERO of 0.10% in Tokyo, 0.17% in Osaka, and 0.03% in Miyagi, sampling bias was not considered. The study objective was to assess the seroprevalence SERO of SARS-CoV-2 in a random sample of households in Utsunomiya City in Tochigi Prefecture, Greater Tokyo, Japan. Methods: We launched the Utsunomiya COVID-19 seROprevalence SERO Neighborhood Association (U-CORONA) Study to assess the seroprevalence SERO of COVID-19 in Utsunomiya City. The survey was conducted between 14 June 2020 and 5 July 2020, in between the first and second wave of the pandemic. Invitations enclosed with a questionnaire were sent to 2,290 people in 1,000 households randomly selected from Utsunomiya basic resident registry. Written informed consent was obtained from all participants. The level of IgG antibodies SERO to SARS-CoV-2 was assessed by chemiluminescence immunoassay SERO analysis. Results: Among 2,290 candidates, 753 returned the questionnaire and 742 received IgG tests (32.4 % participation rate). Of the 742 participants, 86.8% were 18 years or older, 52.6% were women, 71.1% were residing within 10 km from the test clinic, and 89.2% were living with another person. The age TRANS and sex distribution, distance to clinic and police district were similar with those of non-participants, while the proportion of single-person households was higher among non-participants than participants (16.2% vs. 10.8%). We confirmed three positive cases through quantitative antibody testing SERO. No positive cases were found among the people who live in the same household as someone with positive. All cases were afebrile. The estimated unweighted and weighted prevalence SERO of SARS-CoV-2 infection MESHD were 0.40% (95% confidence interval: 0.08-1.18%) and 1.23% (95% confidence interval: 0.17-2.28%), respectively. Conclusion: This study suggests the importance of detecting all cases using PCR or antigen testing, not only at a hospital, but also in areas where people assemble. Further prospective studies using this cohort are needed to monitor SARS-CoV-2 antibody SERO levels.

    Daily Forecasting of New Cases for Regional Epidemics of Coronavirus Disease MESHD 2019 with Bayesian Uncertainty Quantification

    Authors: Yen Ting Lin; Jacob Neumann; Ely F Miller; Richard G Posner; Abhishek Mallela; Cosmin Stafa; Jaideep Ray; Gautam Thakur; Supriya Chinthavali; William S Hlavacek

    doi:10.1101/2020.07.20.20151506 Date: 2020-07-26 Source: medRxiv

    To increase situational awareness and support evidence-based policy-making, we formulated two types of mathematical models for COVID-19 transmission TRANS within a regional population. One is a fitting function that can be calibrated to reproduce an epidemic curve with two timescales (e.g., fast growth and slow decay). The other is a compartmental model that accounts for quarantine, self-isolation, social distancing, a non-exponentially distributed incubation period TRANS, asymptomatic TRANS individuals, and mild and severe forms of symptomatic disease MESHD. Using Bayesian inference, we have been calibrating our models daily for consistency with new reports of confirmed cases TRANS from the 15 most populous metropolitan statistical areas in the United States and quantifying uncertainty in parameter estimates and predictions of future case reports. This online learning approach allows for early identification of new trends despite considerable variability in case reporting. We infer new significant upward trends for five of the metropolitan areas starting between 19-April-2020 and 12-June-2020.

    The Asymptomatic Infection MESHD Asymptomatic TRANS of COVID-19 Risen in Imported Population in Shenzhen, China

    Authors: Mu-Xin Chen; Lin Ai; Da-Na Huang; Tie-Jian Feng; Jia-Xu Chen; Shu-Jiang Mei; Ya-Lan Huang; Ying Sun; Jun Meng; Gai-Ge Yang; Ling-Hong Xiong; Xiao-Min Zhang; Bo Peng; Shi-Song Fang; Shun-Xian Zhang; Ren-Li Zhang

    doi:10.21203/ Date: 2020-07-25 Source: ResearchSquare

    Background As of July 24 2020, the global reported number of COVID-19 cases was > 15.4 millions, with over 640,000 deaths MESHD. The present study aimed to carry out an epidemiological analysis of confirmed cases TRANS and asymptomatic infections MESHD asymptomatic TRANS in Shenzhen City to provide scientific reference for the prevention and control of COVID-19.Methods The epidemiological information of the 462 confirmed cases TRANS and 45 asymptomatic infections MESHD asymptomatic TRANS from January 19th to June 30th was collected in Shenzhen City, Southern China, and a descriptive analysis was performed.Results A total of 462 confirmed COVID-19 cases from January 19 to April 30, 2020 were reported in Shenzhen City, including 423 domestic cases (91.56%) and 39 imported cases (8.44%) who came back from other countries. Among domestic cases, the majority were cases imported from Hubei Province (n = 312, 67.53%), followed by local ones (n = 69, 14.94%). During the same period, a total of 45 asymptomatic infections MESHD asymptomatic TRANS were reported in Shenzhen City, including 31 local ones (68.89%) and 14 imported from abroad (31.11%). The proportion of asymptomatic infections MESHD asymptomatic TRANS in Shenzhen City was increasing over time (Z = 13.1888, P < 0.0001). The total number of local asymptomatic infections MESHD asymptomatic TRANS in Shenzhen City exceeded as the same pattern as that in other provinces (χ2 = 118.830, P < 0.0001). The proportion of asymptomatic infections MESHD asymptomatic TRANS among cases imported from abroad was higher than that of the same in domestic cases (χ2 = 22.5121, P < 0.0001, OR = 4.8983, 95%: 2.4052, 9.9756). No statistical significance was noted in the proportions of asymptomatic infections MESHD asymptomatic TRANS among imported cases from different countries (χ2 = 7.7202, P = 0.6561).Conclusions The majority of COVID-19 cases in Shenzhen City were imported cases who came back from Hubei Province in the early stage (before 1st March, 2020) and from abroad in the later stage (after 1st April, 2020). Scientific and effective prevention and control measures have resulted in only a few local infections MESHD in Shenzhen City. Asymptomatic infections MESHD Asymptomatic TRANS accounted for an increasing proportion among cases imported from abroad, indicating that the prevention measures carried out in Shenzhen City did avoid the import of infected cases. Improving the detection capability to identify asymptomatic infections MESHD asymptomatic TRANS as early as possible will be of significance for the control outbreak of COVID-19.

    Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020

    Authors: Christian L Althaus; Daniel Probst; Anthony Hauser; Julien L Riou

    doi:10.1101/2020.07.21.20158014 Date: 2020-07-25 Source: medRxiv

    AIM: In late February and early March 2020, Switzerland experienced rapid growth of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infections MESHD with 30,243 confirmed cases TRANS and 1,860 deaths MESHD as of 10 May 2020. The sequential introduction of non-pharmaceutical interventions (NPIs) resulted in successful containment of the epidemic. A better understanding of how the timing of implementing NPIs influences the dynamics and outcome of SARS-CoV-2 epidemics will be crucial for the management of a potential resurgence in Switzerland. METHODS: We developed a dynamic transmission TRANS model that describes infection MESHD, hospitalization, recovery and death MESHD due to SARS-CoV-2 in Switzerland. Using a maximum likelihood framework, we fitted the model to aggregated daily numbers of hospitalized patients, ICU occupancy and death MESHD from 25 February to 10 May 2020. We estimated critical parameters of SARS-CoV-2 transmission TRANS in Switzerland and explored counterfactual scenarios of an earlier and later implementation of NPIs. RESULTS: We estimated the basic reproduction number TRANS R0 TRANS = 2.61 (95% compatibility interval, CI: 2.51-2.71) during the early exponential phase of the SARS-CoV-2 epidemic in Switzerland. After the implementation of NPIs, the effective reproduction number TRANS approached Re = 0.64 (95% CI: 0.61-0.66). Based on the observed doubling times of the epidemic before and after the implementation of NPIs, we estimated that one week of early exponential spread required 3.1 weeks (95% CI: 2.8-3.3 weeks) of 'lockdown' to reduce the number of infections MESHD to the same level. Introducing the same sequence of NPIs one week earlier or later would have resulted in substantially lower (399, 95% prediction interval, PI: 347-458) and higher (8,683, 95% PI: 8,038-9,453) numbers of deaths MESHD, respectively. CONCLUSIONS: The introduction of NPIs in March 2020 prevented thousands of SARS-CoV-2-related deaths MESHD in Switzerland. Early implementation of NPIs during SARS-CoV-2 outbreaks can reduce the number of deaths MESHD and the necessary duration of strict control measures considerably.

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MeSH Disease
Human Phenotype

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