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    Development and Validation of a Deep Learning MESHD Model for Prediction of Severe Outcomes in Suspected COVID-19 MESHD Infection

    Authors: Varun Buch; Aoxiao Zhong; Xiang Li; Marcio Aloisio Bezerra Cavalcanti Rockenbach; Dufan Wu; Hui Ren; Jiahui Guan; Andrew Liteplo; Sayon Dutta; Ittai Dayan; Quanzheng Li

    id:2103.11269v1 Date: 2021-03-21 Source: arXiv

    COVID-19 MESHD patient triaging with predictive outcome of the patients upon first present to emergency department (ED) is crucial for improving patient prognosis, as well as better hospital resources management and cross-infection MESHD control. We trained a deep feature fusion model to predict patient outcomes, where the model inputs were EHR data including demographic information, co-morbidities, vital signs and laboratory measurements, plus patient's CXR images. The model output was patient outcomes defined as the most insensitive oxygen therapy required. For patients without CXR images, we employed Random Forest method for the prediction. Predictive risk scores for COVID-19 MESHD severe outcomes ("CO-RISK" score) were derived from model output and evaluated on the testing dataset, as well as compared to human performance. The study's dataset (the "MGB COVID Cohort") was constructed from all patients presenting to the Mass General Brigham (MGB) healthcare system from March 1 HGNCst to June 1st, 2020. ED visits with incomplete or erroneous data were excluded. Patients with no test order for COVID or confirmed negative test results were excluded. Patients under the age of 15 were also excluded. Finally, electronic health record (EHR) data from a total of 11060 COVID-19 MESHD confirmed or suspected patients were used in this study. Chest X-ray (CXR) images were also collected from each patient if available. Results show that CO-RISK score achieved area under the Curve (AUC) of predicting MV/death (i.e. severe outcomes) in 24 hours of 0.95, and 0.92 in 72 hours on the testing dataset. The model shows superior performance to the commonly used risk scores in ED (CURB-65 and MEWS). Comparing with physician's decisions, CO-RISK score has demonstrated superior performance to human in making ICU/floor decisions.

    Deaths for Hospital Acquired Infections in Intensive Care Units and COVID Departments in Italy That May Be Biased for Coronavirus Caused Mortality. Warning for Science and Politics and Further Suggestions

    Authors: Salvatore Chirumbolo; Vincenzo Simonetti; Marianno Franzini; Luigi Valdenassi; Dario Bertossi; Sergio Pandolfi

    doi:10.21203/rs.3.rs-298862/v1 Date: 2021-03-04 Source: ResearchSquare

    Background Hospital acquired infections (HAIs) are a serious concern for COVID-19 pandemic MESHD and its emergency in hospitals and healthcare units in Italy. The incidence of nosocomial infections MESHD in the clinical outcomes of COVID-19 MESHD is a quite dismissed feature in the crowded debate about how addressing and managing COVID-19 MESHD outbreak in Italy. Methods Statistical methods using Kaplan-Meier plots, Bayesian calculation on RR and Or, regression calculation and confounder ANCOVA tests were applied on publicly data from the Italian Ministry of Health to highlight the rate of HAIs on COVID diagnosis. Results RR value to die in hospitals during COVID-19 pandemic MESHD because of nosocomial infections MESHD in 2020, taking into account the number of deaths provided by the Italian Ministry of Health on December 31st 2020 and values about HAIs in current literature, leads to RR = 8.47 (CI95 = 8.38-8.56, odds ratio (OR) = 8.55). Hospitalized people have more probability to be healed (median, Me = 35.92) respect to non hospitalized ones (Me = 30.28), whereas hospitalization increased the median of deaths (Me = 29.37) respect to non hospitalized people (Me =24.26). Conclusions Nosocomial infections MESHD may exert a major role, as a confounder, in increasing the dramatic amount of deceases so far accounted to exclusively SARS-CoV2 infections MESHD. If such, politics should be much more aware of this concern. 

    A Prospective Clinical Evaluation of a Patient Isolation Hood During the COVID-19 Pandemic MESHD

    Authors: Forbes McGain; Samantha Bates; Jung Hoon Lee; Patrick Timms; Marion Kainer; Craig French; Jason Monty

    doi:10.1101/2021.02.19.21251739 Date: 2021-02-23 Source: medRxiv

    Background: Healthcare workers have frequently become infected with SARS-CoV-2 whilst treating patients with COVID-19 MESHD. A variety of novel devices have been proposed to reduce COVID-19 MESHD cross contamination. Objective: To test whether a novel patient isolation hood was safe and comfortable, and could potentially reduce HCW COVID-19 MESHD infections. Methods: Prospective cohort study of 20 patients, entailing staff/patient questionnaires, and safety aspects of prototype isolation hoods. Prospective collection of HCW COVID-19 MESHD data. Assessment of isolation hood safety and practicality, and adverse event reporting. Outcome Measures: Questionnaires responses, adverse events reporting, rates of HCW infections MESHD during study period (20/6/2020 - 21/7/2020). HCW COVID-19 MESHD infections reported until last recorded HCW COVID-19 MESHD diagnosis (20/6/2020 - 27/9/2020). Results: Of the 60 (of 64) eligible individual staff surveys, 60 favoured isolation hood use. Staff were unanimous in: perceiving the hood as safe (60/60), preferring its use (56/56), and understanding its potential COVID-19 MESHD cross-contamination minimisation (60/60). All eight patients who completed the questionnaire thought the isolation hood helped prevent COVID-19 MESHD cross-infection MESHD, was safe, and comfortable. There were no reported patient safety adverse events. The overall attack COVID-19 MESHD attack rate from 20/6/2020-27/9/2020 among registered nurses was 3.4% (102/2994): ICUs 2.2% (3/138), Geriatric wards 13.2% (26/197), and COVID-19 MESHD Wards 18.3% (32/175). The COVID-19 MESHD attack rate among medical staff was: all junior medical staff 2.1% (24/932), senior medical staff 0.7% (4/607), aged care/rehabilitation 6.7% (2/30), and ICU all medical staff 8.6% (3/35). Conclusions: The isolation hood was strongly endorsed by staff and patients, and post-study became part of standard ICU therapy. ICU nurse COVID-19 MESHD infection rates were low. ICU HCWs feel safer when treating patients with COVID-19 MESHD using an isolation hood.

    Changes in Prevalence of Nosocomial Infection Pre- and Post- COVID-19 pandemic MESHD from a Tertiary Hospital in China

    Authors: Chunmei Su; Zhiqin Zhang; Xu Zhao; Hanlin Peng; Yi Hong; Lili Huang; Jie Huang; Xiangming Yan; Shuiyan Wu; Zhenjiang Bai

    doi:10.21203/rs.3.rs-228202/v1 Date: 2021-02-10 Source: ResearchSquare

    Background: Nosocomial infections MESHD ( NIs MESHD) are an important cause of mortality, and increasing evidence reveals that the prevalence of NIs MESHD can be reduced through effective prevention and control measures. The aim of this study was to investigate the impact of the prevention and control measures for the COVID-19 pandemic MESHD on NIs MESHD.Methods: A retrospective study was conducted to analyze the prevalence of NIs MESHD before and after COVID-19 pandemic MESHD for six months in the Children’s Hospital of Soochow University.Results: A total of 39,914 patients in 2019 and 34,645 patients in 2020 were admitted to the hospital during the study. There were 1.39% (481/34645) of patients with NIs MESHD in 2020, which was significantly lower than the 2.56% (1021/39914) of patients in 2019. The rate of critical and fatal cases was also decreased. Except for the ICU, the prevalence of nosocomial infection MESHD in most departments decreased from 2019 to 2020. Regarding the source of infections, a significant reduction was mainly observed in respiratory (0.99% vs 0.42%, p=0.000) and digestive tract (0.63% vs 0.14%, p=0.000). The microorganism analysis of respiratory infections MESHD indicated an obvious decline in acinetobacters and fungi. The most significant decline of pathogens in gastrointestinal infections MESHD was observed for rotavirus. The comparison of catheter-related nosocomial infections between 2019 and 2020 did not show significant differences. Conclusions: The prevention and control measures for the COVID-19 pandemic MESHD have reduced the nosocomial infection MESHD in almost all departments, except the ICU, mainly regarding respiratory, gastrointestinal, and oral infections MESHD, while catheter-related infections did not show any differences.  

    Impact of COVID-19 Pandemic MESHD on Inpatient Rehabilitation and the Original Infection Control Measures for Rehabilitation Team

    Authors: Yukimasa Igawa; Takahiro Sugimoto; Hiromasa Horimoto; Yusuke Moriya; Masaki Okada; Yasuyuki Yamada

    doi:10.1101/2021.01.20.21250145 Date: 2021-01-26 Source: medRxiv

    Objective: This study aimed to investigate the impact of the coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic on inpatient rehabilitation, and to determine the effectiveness of the original infection control measures implemented for the rehabilitation team. Methods: In this single-center, retrospective, observational study, we calculated multiple rehabilitation indices of patients discharged from our rehabilitation ward between February 28 and May 25, 2020 when Hokkaido was initially affected by COVID-19 MESHD, and compared them with those calculated during the same period in 2019. The Fisher exact test and the Mann-Whitney U test were used for statistical analysis. We also verified the impact of implementing the original infection control measures for the rehabilitation team on preventing nosocomial infections MESHD. Results: A total of 93 patients (47 of 2020 group, 46 of 2019 group) were included. The median age was 87 and 88 years, respectively, with no differences in age, sex, and main disease between the groups. Training time per day in the ward in 2020 was significantly lower than that in 2019 (p = 0.013). No significant differences were found in the qualitative evaluation indices of Functional Independence Measure (FIM) score at admission, FIM gain, length of ward stay, FIM efficiency, and rate of discharge to home. None of the patients or staff members had confirmed COVID-19 MESHD during the study period. Conclusions: Early COVID-19 pandemic MESHD in Hokkaido affected the quantitative index for inpatient rehabilitation but not the qualitative indices. No symptomatic nosocomial COVID-19 MESHD infections were observed with our infection control measures.

    The burden of nosocomial covid-19 MESHD: results from the Wales multi-centre retrospective observational study of 2518 hospitalised adults.

    Authors: Mark J Ponsford; Rhys Jefferies; Chris Davies; Daniel Farewell; Ian R Humphreys; Stephen Jolles; Sara Fairbairn; Keir Lewis; Daniel Menzies; Amit Benjamin; Favas Thaivalappil; Simon M Barry

    doi:10.1101/2021.01.18.21249433 Date: 2021-01-20 Source: medRxiv

    Objectives: To define the burden of nosocomial (hospital-acquired) novel pandemic coronavirus ( covid-19 MESHD) infection among adults hospitalised across Wales. Design: Retrospective observational study of adult patients with polymerase chain reaction (PCR) confirmed SARS-CoV-2 infection MESHD between 1st March to 1st July 2020 with a recorded hospital admission within the subsequent 31 days. Outcomes were collected up to 20th November using a standardised online data collection tool. Setting: Service evaluation performed across 18 secondary or tertiary care hospitals. Participants: 4112 admissions with a positive SARS-CoV-2 PCR result between 1st March to 1st July 2020 were screened. Anonymised data from 2518 participants were returned, representing over 60% of adults hospitalised across the nation of Wales. Main outcome measures: The prevalence and outcomes ( death MESHD, discharge) for nosocomial covid19 MESHD, assessed across of a range of possible case definitions. Results: Inpatient mortality rates for nosocomial covid19 MESHD ranged from 38% to 42% and remained consistently higher than participants with community acquired infection (31% to 35%) across a range of case definitions. Participants with nosocomial-acquired infection MESHD were an older, frailer, and multi-morbid population than those with community-acquired infection. Based on the Public Health Wales case definition, 50% of participants had been admitted for 30 days prior to diagnostic testing. Conclusions: This represents the largest assessment of clinical outcomes for patients with nosocomial covid-19 MESHD in the UK to date. These findings suggest that inpatient mortality rates from nosocomial-infection MESHD are likely higher than previously reported, emphasizing the importance of infection control measures, and supports prioritisation of vaccination for covid-19 MESHD negative admissions and trials of post-exposure prophylaxis in inpatient cohorts. Trial registration: This project was approved and sponsored by the Welsh Government, as part of a national audit and quality improvement scheme for patients hospitalised covid-19 MESHD across Wales.

    The Impact of COVID-19 Pandemic MESHD on Neonatal Admission: An Interrupted Time-Series Study

    Authors: Weiqin Liu; Qifen Yang; Zhen-e Xu; Ya Hu; Yongming Wang; Zhenqiu Liu; Qianqian Zhao; Zhuangcheng Wang; Hong Wei; Ziyu Hua

    id:202101.0403/v1 Date: 2021-01-20 Source: Preprints.org

    (1) Introduction: The unprecedented coronavirus disease 2019 MESHD ( COVID-19 MESHD) epidemic has caused millions of infections worldwide and represents a significant challenge facing modern health care systems. This study was conducted to investigate the impact of lockdown measures on regional neonate services, which might be used to predict the long-term effects of medical behavior. (2) Methods: Using hospital information system ( HIS MESHD) Statistics data from 4 January 2019 to 27 August 2020, an interrupted time-series analysis was employed to compare changes and trends in hospital admissions and disease spectrum before and after the lockdown interventions. Furthermore, this study was designed to evaluate whether the pandemic influenced newborns' healthcare behavior. (3) Results: Overall, 13,540 infants were admitted to the NICU during the pre-COVID period (n = 12082) and COVID-impacted period (n =4558). The patients' age at admission were younger than that of the pre- COVID-19 MESHD period (median age 5d vs. 6d after birth, p<0.001). The overall number of neonate visits consistently decreased from the first days of the lockdown measures (24 January 2020). The disease spectrum for respiratory system, infectious diseases MESHD, and gastrointestinal disease MESHD indicated no declined immediately after intervention(p =0.079, p =0.113, p =0.060, respectively). There was an immediate decline in the volume of Jaundice-related conditions (p<0.001) after lockdown measures. The percentage of patients who suffer from respiratory system and infectious diseases MESHD has decreased (p =0.005 and p =0.002). However, a relatively high percentage of patients admitted to the neonatal intensive care unit (NICU) presented with Jaundice MESHD-related conditions (p <0.001). (4) Conclusions: In summary, the COVID-19 pandemic MESHD profoundly impacted the regional neonate services. However, it is still unclear what might be the effect of long-term effects from pandemic.

    Reduction in transfer of micro-organisms between patients and staff using short-sleeved gowns and hand/arm hygiene in Intensive Care during the Covid pandemic: a simulation-based randomised trial.

    Authors: Laura Vincent; Mudathir Ibrahim; Joanne Kitchin; Claire Pickering; Enrico Sorrentino; Claudia Salvagno; Laurie Earl; Louise Ma; Kathryn Simpson; Rose Baker; Peter McCulloch

    doi:10.1101/2021.01.16.21249221 Date: 2021-01-16 Source: medRxiv

    BackgroundCurrent PPE practices in UK intensive care units involve "sessional" gown use. This protects staff, but puts patients at risk of nosocomial infection MESHD via PPE gowns. Anecdotal reports of such infections in ITUs during Covid are frequent. We therefore explored the use of short-sleeved gowns with hand and arm hygiene as an alternative to sessional gowns. MethodsITU Staff were invited for simulation suite training in Covid intubation and proning. They were trained in a specific hand and arm washing technique before performing simulated tasks using both standard and modified (short sleeved) PPE. Fluorescent powder was used to simulate micro-organisms, and detected using standardised photos under U/V light. Teams of staff were randomised to use standard or modified PPE first. Individuals were questioned about their feeling of personal safety, comfort and the patients safety at 4 intervals. Results68 staff and 17 proning volunteers were studied in 17 sessions. Modified PPE completely prevented staff contamination during Covid intubation, which occurred in 30/67 staff wearing standard PPE (p = 0.0029, McNemar). Conversely, proning volunteers were contaminated by staff in 15/17 sessions with standard PPE and in 1/17 with modified PPE (P = 0.0227 McNemar). Impressions of staff comfort were superior with modified PPE (p< 0.001, t-test); personal safety scored higher with standard PPE, but the difference decreased during the session (p<0.001 start, 0.068 end). Impressions of patient safety were initially similar (p=0.87) but finished strongly in favour of modified PPE (p<0.001). ConclusionsModified PPE using short sleeves and hand/arm cleansing appears superior to standard PPE with sessional gowns in preventing transfer of contamination between staff and patients. A clinical trial of this strategy is merited.

    School and community reopening during the COVID-19 pandemic MESHD: a mathematical modeling study

    Authors: Pei Yuan; Elena Aruffo; Nicholas ogden; Yi Tan; Evgenia Gatov; Effie Gournis; Sarah Collier; Qi Li; Iain Moyles; Nasri Bouchra; Huaiping Zhu

    doi:10.1101/2021.01.13.21249753 Date: 2021-01-15 Source: medRxiv

    BackgroundThe closure of communities, including schools, has been adopted to control the coronavirus disease 2019 MESHD ( COVID-19 MESHD) epidemic in most countries. Operating schools safely during the pandemic requires a balance between health risks and the need for in-person learning. We use compartmental models to explore school reopening scenarios. MethodsUsing demographic and epidemiological data between July 31 and November 23, 2020 from the city of Toronto, we developed a Susceptible-Exposed-Asymptomatic-Infectious-Recovered-Hospitalized-Isolated model. Our model with age, household, and community transmission allow us to study the impact of schools open in September 2020. The model mimics the transmission in households, the community, and schools, accounting for differences in infectiousness between adults and children and youth and adults working status. We assessed the extent to which school opening may have contributed to COVID-19 MESHD resurgence in the fall and simulated scenarios for the safe reopening of schools up to May 31, 2021. We further considered the impact of the introduction of the new variant of concern. FindingsThough a slight increase in infections among adults (2.8%) and children (5.4%) is anticipated by the end of the year, safe school opening is possible with stringent nonpharmaceutical interventions (NPIs) decreasing the risk of transmission in the community and the household. We found that while school reopening was not the key driver in virus resurgence, but rather it was community spread that determined the outbreak trajectory, brief school closures did reduce infections when transmission risk within the home was low. When considered possible cross-infection MESHD amongst households, communities, and schools, we found that home transmission was crucial for mitigating the epidemic and safely operating schools. Simulating the introduction of a new strain with higher infectiousness, we observed substantial increases in infections, even when both schools and communities are closed. InterpretationSchools can open safely under strict maintenance of strict public health measures in the community. The gradual opening of schools and communities can only be achieved by maintaining NPIs and mitigating household transmission risk to avoid the broader escape of infections acquired in schools into the community via households. If the new COVID-19 MESHD strain is more infectious for children, public spaces, including schools, should be closed, and additional NPIs, including the use of masks, should be extended to toddlers. FundingThis research was supported by Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council of Canada, and York University Research Chair program. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThe design of a gradual school reopening strategy remains at the heart of decision-making on reopening after shut-downs to control the epidemic. Although available studies have assessed the risk of school reopening by modelling the transmission across schools and communities, it remains unclear whether the risk is due to increased transmission in adults or children and youth.We used GoogleScholar and PubMed searches to identify previous published works. We used te following terms: "school closure", "covid 19 school closure", "reopening schools", "reopening screening school", "school household second wave model". The search of the studies ended in January 2021. Papers in other languages than English and letters were excluded from the search. Two modelling studies examined the effects of screening and delayed school reopening, two other agent-based modelling studies explored the epidemic spread across different age groups. Added-value of this studyWe find that the resurgence of COVID-19 MESHD in Toronto in fall 2020 mainly resulted from the increase of contact rate among adults in the community, and that the degree of in-person attendance had the most significant impact on transmission in schools. To our knowledge, our work is the first to investigate the resurgence in infections following school reopening and the impact of risk mitigation measures in schools operation during the pandemic. Our novel and comprehensive model considers the age and household structure, but also considers three different settings, school, household and community. We further examined the effects of self-screening procedures, class size, and schooling days on transmission, which enabled us to compare scenarios of school reopening separately for both adults and children and youth, and model the cross-infection MESHD between them to avoid potential underestimation. We found that after schools opened, reducing household transmission was crucial for mitigating the epidemic since it can reduce cross-infection MESHD amongst households, communities and schools. Lastly, given the recent report of SARS-CoV-2 variant (VOC202012/01), we investigated the impact of the new variant that may be more infectious in children and youth. Implications of all the available evidenceOur analysis can inform policymakers of planning the safe reopening of schools during COVID-19 MESHD. We suggest that integrating strict NPIs and school control measures are crucial for safe reopening. When schools are open, reducing transmission risk at home and community is paramount in curbing the spread of COVID-19 MESHD. Lastly, if children are more susceptible to the new COVID-19 MESHD VOC, both schools and community must be closed, the time children spend in essential services locations minimized, and NPIs for those aged less than three years enforced.

    Serologic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Infection MESHD in Hospital Health Care Workers

    Authors: Jonne J Sikkens; David T.P. Buis; Edgar J.G. Peters; Mireille Dekker; Michiel Schinkel; Tom D.Y. Reijnders; Alex R. Schuurman; Justin de Brabander; Ayesha Lavell; Jaap J Maas; Jelle Koopsen; Alvin X Han; Colin A. Russell; Janke Schinkel; Marcel Jonges; Sebastien P.F. Matamoros; Suzanne Jurriaans; Rosa van Mansfeld; W. Joost Wiersinga; Yvo M Smulders; Menno D. de Jong; Marije K Bomers

    doi:10.1101/2021.01.10.21249440 Date: 2021-01-12 Source: medRxiv

    BACKGROUND It is unclear how, when and where health care workers (HCW) working in hospitals are infected with SARS-CoV-2. METHODS Prospective cohort study comprising 4-weekly measurement of SARS-CoV-2 specific antibodies and questionnaires from March to June 2020. We compared SARS-CoV-2 incidence between HCW working in Covid-19 MESHD patient care, HCW working in non- Covid-19 MESHD patient care and HCW not in patient care. Phylogenetic analyses of SARS-CoV-2 samples from patients and HCW were performed to identify potential transmission clusters. RESULTS We included 801 HCW: 439 in the Covid-19 MESHD patient care group, 164 in the non- Covid-19 MESHD patient care group and 198 in the no patient care group. SARS-CoV-2 incidence was highest in HCW working in Covid-19 MESHD patient care (13.2%), as compared with HCW in non- Covid-19 MESHD patient care (6.7%, hazard ratio [HR] 2.2, 95% confidence interval [CI] 1.2 to 4.3) and in HCW not working in patient care (3.6%, HR 3.9, 95% CI 1.8 to 8.6). Within the group of HCW caring for Covid-19 MESHD patients, SARS-CoV-2 cumulative incidence was highest in HCW working on Covid-19 MESHD wards (25.7%), as compared with HCW working on intensive care units (7.1%, HR 3.6, 95% CI 1.9 to 6.9), and HCW working in the emergency room (8.0%, HR 3.3, 95% CI 1.5 to 7.1). Phylogenetic analyses on Covid-19 MESHD wards identified multiple potential HCW-to-HCW transmission clusters while no patient-to-HCW transmission clusters were identified. CONCLUSIONS HCW working on Covid-19 MESHD wards are at increased risk for nosocomial SARS-CoV-2 infection MESHD SARS-CoV-2 infection MESHD, with an important role for HCW-to-HCW transmission.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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