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opencc-zeroJul 2020View details →

Data from: Pediatric intensive care unit admissions for COVID-19: insights using state-level data

Introduction Intensive care has played a pivotal role during the COVID-19 pandemic as many patients developed severe pulmonary complications. The availability of information in pediatric intensive care (PICUs) remains limited. The purpose of this study is to characterize COVID-19 positive admissions (CPAs) in the United States and to determine factors that may impact those admissions. Materials and Methods This is a retrospective cohort study using data from the COVID-19 dashboard virtual pediatric system) containing information regarding respiratory support and comorbidities for all CPAs between March and April 2020. The state level data contained 13 different factors from population density, comorbid conditions and social distancing score. The absolute CPAs count was converted to frequency using the state's population. Univariate and multivariate regression analyses were performed to assess the association between CPAs frequency and endpoints. Results A total of 205 CPAs were reported by 167 PICUs across 48 states. The estimated CPAs frequency was 2.8 per million children. A total of 3,235 tests were conducted with 6.3% positive tests. Children above 11 years of age comprised 69.7% of the total cohort and 35.1% had moderated or severe comorbidities. The median duration of a CPA was 4.9 days [1.25-12.00 days]. Out of the 1,132 total CPA days, 592 [52.2%] were for mechanical ventilation. The inpatient mortalities were 3 [1.4%]. Multivariate analyses demonstrated an association between CPAs with greater population density [beta-coefficient 0.01, p<0.01] and increased percent of children receiving the influenza vaccination [beta-coefficient 0.17, p=0.01]. Conclusions Inpatient mortality during PICU CPAs is relatively low at 1.4%. CPA frequency seems to be impacted by population density while characteristics of illness severity appear to be associated with ultraviolet index, temperature, and comorbidities such as Type 1 diabetes. These factors should be included in future studies using patient-level data.

opencc-zeroJul 2020View details →

Data from: Early spread of COVID-19 in Romania

This individual-level dataset describes (a) the early spread of the novel coronavirus (COVID-19) and (b) the first human-to-human transmission networks, in Romania. Specifically, in the first set of data (a), we profile the first 147 cases referring to: whether an individual is an index case, place of residence, sex, age, probable citizenship, probable country and place of infection, arrival date to a Romanian county, COVID-19 confirmation date as well as the sources of information. Also, the second set of data (b) contains the first observed human-to-human COVID-19 transmission networks (attributes of the nodes and the direction of COVID-19 transmission, i.e. who infects whom). Networks embed 159 nodes and 203 transmission ties. Indirect identifiers are masked / de-identified.

opencc-by-4.0Jul 2020View details →

Aerosol light absorption in Nanjing, China during the 2020 COVID-19 lockdown period

This file contains the data in aerosol light absorption measured by Aethalometer AE33 in Nanjing, China from January 3 to March 31, 2020.

opencc-by-4.0Jul 2020View details →

Uncertainty in times of COVID-19: Raw survey data

Data from a survey of consumer expectations From April 24, 2020, through June 22, 2020, Fabian Lange and Lars Vilhuber conducted the survey "Uncertainty in COVID-19 times". The survey is a single-question survey focusing on people's anticipation about social distancing rules and firm closures during the 2020 COVID-19 health crisis.

opencc-by-4.0Aug 2020View details →

Analysis of factors influencing the network teaching effect of college students in a medical school during the COVID-19 epidemic

Analysis of factors influencing the network teaching effect of college students in a medical school during the COVID-19 epidemic

opencc-by-4.0Jul 2020View details →

Air pollution 01.2014 - 05.2020 (including COVID-19 lockdown) data from Graz, Austria

Please cite: <a href="https://doi.org/10.1016/j.envpol.2020.114587">https://doi.org/10.1016/j.envpol.2020.114587</a> Air quality by means of  NO2, PM10 and O3 was measured at five sites in Graz, Austria (Süd (eng. South) - S, Nord (eng. North) - N, West (eng. West) - W, Don Bosco – D, Ost (eng. East) – O). In addition weather conditions like temperature, percipitation, relative humidity, pressure, wind speed and direction are added. The authors created binary temporal variables like weekday, month, season, year and day of year (numerical). The data consist of 2343 rows and 53 columns with a timestamp from January 2014 to May 2020 in a daily frequency. More details on measurement and the sites are available in Moser et al. [1] and [2]. The environmental data was provided by the Austrian government under the following license:  CC-BY-4.0: Land Steiermark - data.steiermark.gv.at __________________ [1] Moser F, Kleb U, Katz H (2019) Statistische Analyse der Luftqualitätin Graz anhand von Feinstaub und Stickstoffdioxid. Graz [2] <a href="https://www.umwelt.steiermark.at/cms/ziel/2060750/DE/">https://www.umwelt.steiermark.at/cms/ziel/2060750/DE/</a>

opencc-by-4.0Aug 2020View details →

Comparative Study of the Restorative effects of Forest and Urban Videos during Covid-19 Lockdown: Intrinsic and Benchmark Value

Article: "Comparative Study of the Restorative effects of Forest and Urban Videos during Covid-19 Lockdown: Intrinsic and Benchmark Value" Video S1:  forest environment  Video S2: urban environment

opencc-by-4.0Sep 2020View details →

Finland COVID-19 R-value estimate March - August

This dataset contains the time-dependent effective reproduction number Rt of the COVID-19 epidemic in Finland for the period Feb 27th 2020 - August 14th 2020. The reproduction number was estimated using the daily new coronavirus cases in <a href="https://thl.fi/en/web/thlfi-en/statistics/statistical-databases/open-data/confirmed-corona-cases-in-finland-covid-19-">the infectious diseases registry of Finland</a> with an unscented RTS smoother and the SEIR epidemic model. The SEIR model was defined as \(S(t+1) = S(t) - \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} + \omega_{S}\\ E(t+1) = E(t) + \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} - \frac{E(t)}{T_e} + \omega_{E}\\ I(t+1) = I(t) + \frac{E(t)}{T_e}-\frac{I(t)}{T_i} + \omega_{I} \\ R_t(t+1) = R_t(t) + \omega_{R_t}\) with S, E, and I being the susceptible, exposed, and infective populations, Rt the time-dependent effective reproduction number, and ωs are normally distributed random numbers with zero mean and small (1e-8) variance except for ωRt whose variance was set to 0.00025. The exposed state duration was set to Te=3 days and infective state duration Ti=5 days. The measurement model (from the SEIR state to observed daily new cases) was defined as \(P_\text{new cases}(k) \propto \mathcal{N}\left[ \alpha \frac{R_t(t-5 days)}{T_i}I(t-5\text{days}) \frac{S(t-5\text{days})}{N}, \sigma_\text{new cases}^2(t) \right]\), i.e., via a time-delayed gaussian process whose variance was computed by the observed daily new cases with a 7-day rolling mean. Here the detection rate α is set to 10%, but has no significant affect on the computed R-values.   The data is a CSV-format file with the columns <ul> <li>date = ISO 8601 date string</li> <li>Rt = maximum a posteriori estimate of Rt</li> <li>Rt_lower50 = lower limit of the 50% credible interval for Rt</li> <li>Rt_upper50 = upper limit of the 50% credible interval for Rt</li> <li>Rt_lower90 = lower limit of the 90% credible interval for Rt</li> <li>Rt_upper90 = upper limit of the 90% credible interval for Rt</li> </ul>

Data from: Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19

Human behavior (movement, social contacts) plays a central role in the spread of pathogens like SARS-CoV-2. The rapid spread of SARS-CoV-2 was driven by global human movement, and initial lockdown measures aimed to localize movement and contact in order to slow spread. Thus, movement and contact patterns need to be explicitly considered when making reopening decisions, especially regarding return to work. Here, as a case study, we consider the initial stages of resuming research at a large research university, using approaches from movement ecology and contact network epidemiology. First, we develop a dynamical pathogen model describing movement between home and work; we show that limiting social contact, via reduced people or reduced time in the workplace are fairly equivalent strategies to slow pathogen spread. Second, we develop a model based on spatial contact patterns within a specific office and lab building on campus; we show that restricting on-campus activities to labs (rather than labs and offices) could dramatically alter (modularize) contact network structure and thus, potentially reduce pathogen spread by providing a workplace mechanism to reduce contact. Here we argue that explicitly accounting for human movement and contact behavior in the workplace can provide additional strategies to slow pathogen spread that can be used in conjunction with ongoing public health efforts.

Analysis of measles-mumps-rubella (MMR) titers of recovered COVID-19 patients

The measles-mumps-rubella (MMR) vaccine has been theorized to provide protection against COVID-19. Our aim was to determine whether any MMR IgG titers are inversely correlated with severity in recovered COVID-19 patients previously vaccinated with MMR II. We divided 80 subjects into two groups, comparing MMR titers to recent COVID-19 severity. The MMR II group consisted of 50 subjects who would primarily have MMR antibodies from the MMR II vaccine, and a comparison group of 30 subjects who would primarily have MMR antibodies from sources other than MMR II, including prior measles, mumps, and/or rubella illnesses. There was a significant inverse correlation (rs = -0.71, P < .001) between mumps titers and COVID-19 severity within the MMR II group. There were no correlations between mumps titers and severity in the comparison group, between mumps titers and age in the MMRII group, or between severity and measles or rubella titers in either group. Within the MMR II group: mumps titers of 134 to 300 AU/ml (n=8) were only found in those who were functionally immune or asymptomatic; all with mild symptoms had mumps titers below 134 AU/ml (n=17); all with moderate symptoms had mumps titers below 75 AU/ml (n=11); all who had been hospitalized and required oxygen had mumps titers below 32 AU/ml (n=5). Our results demonstrate that there is a significant inverse correlation between mumps titers from MMR II and COVID-19 severity.

opencc-zeroDec 2019View details →

COVID-19 clinician moral injury survey

Background Moral injury is an emerging explanation of burnout and suicidality, but remains poorly quantified in at-risk practitioners. We hypothesized that COVID-19 pandemic-related moral injury differs between frontline clinicians, genders, age, and country of practice. Methods We conducted an online cross-sectional survey of international physicians, nurses, nurse practitioners, paramedics and respiratory therapists between April and June 2020. We included the adapted version of the Expressions of Moral Injury Scale (EMIS). The primary outcome was differences in moral injury scores between clinician roles. Results Three hundred and two clinicians participated, including physicians (61% [n=184]), nurses (28% [n=85]), and nurse practitioners (5% [n=14]). The median age was 39 (IQR 32-76), females comprised 54% of the respondents, and the majority resided in Canada (n =183 [61%]) or the United States (US; n = 106 [35%]). Emergency medicine (88% [n=265]), and intensive care (6% [n=17]) were the main specialties responding. Median moral injury scores across multiple domains were higher for nurses compared to physicians, as well as for younger, and female respondents. Moral injury scores were also significantly higher for respondents from the United States, the United Kingdom and Australia, compared to Canada. Conclusions Our research suggests that during COVID-19, measures of moral injury differ across roles, gender and place of work. Future research is warranted to better understand the impact of moral injury on clinicians' psychological well-being during the COVID-19 pandemic.

Impact of coronavirus disease 2019 (COVID-19) outbreak on radiology research: an Italian survey

This article reports the results of a national survey, which had the purpose of understanding how COVID-19 pandemic has changed the scientific activity of Italian radiology researchers. A total of 327 Italian radiologists took part in the survey (mean age: 49±12 years). The majority of participants (245/327, 74.9%) was not working for or in agreement with a University and most of them were hospital staff radiologists (222/327, 67.9%). More than two-thirds of surveyed radiologists (231/327, 71%) was working in a public institution, which mostly was a general hospital (188/327, 57.5%); 86/327 (26.3%) participants declared to work in a university hospital.  After national lockdown, the working-flow came back to normal in the vast majority of cases (285/327, 87.2%). Participants reported that a total of 462 radiological trials were recruiting patients at their institutions prior to COVID-19 outbreak, of which 332 (71.9%) were stopped during the emergency. On the other hand, 252 radiological trials have been started during the pandemic, of which 156 were non-COVID-19 trials (61.9%) and 96 were focused on COVID-19 patients (38.2%). Participants reported a significant increase of the number of hours per week spent for research purposes during national lockdown (mean 4.5±8.9 hours during lockdown vs. 3.3±6.8 hours before lockdown; p=.046), followed by a significant drop after lockdown (3.2±6.5 hours per week, p=.035). Notably, 60% of participants reported that they do not spend any time on research. During national lockdown, 15.6% of participants started new review articles and completed old papers, 14.1% completed old works, and 8.9% started new review articles. Ninety-six surveyed radiologists (29.3%) declared to have submitted at least one article during COVID-19 emergency. This study confirms the need to be prepared to future challenging scenarios like COVID-19 emergency in order to support radiology researchers, thereby allowing them to push forward their activity.

Teaching Development of Distributed Software during COVID-19: An experience report in Brazil

In 2020, the COVID-19 pandemic affected all sectors of society worldwide, including education. Due to the social isolation requirement, several educational institutions used the Emergency Remote Teaching (ERT) approach to keep their courses active, at least partially. This document provides an experience report about using ERT in two courses (Distributed Systems and Software Development for the Cloud) that deal with the Development of Distributed Software Systems. In these two courses, we used three main approaches: synchronous online classes, asynchronous learning videos, and online material available on a Git repository. In some classes, we also adopted active methodologies such as problem-based learning and flipped classroom. Students were evaluated by seminars, tests, and programming activities. In the end, we collected their feedback from an online survey. Forty-two (42) graduate and undergraduate students reported a good level of acceptance of our ERT model. Part of the students had difficulties in doing their programming homework, and the main obstacles reported by them were: (i) their psychological context and (ii) to reconcile the course activities with home tasks as well as the demands of their jobs. Once practical experiences in ERT will be essential for a while given the uncertainty about how long COVID-19 pandemic will remain active, we expect the highlights and drawbacks of our experience could help other professors in planning their courses.

The scale and dynamics of COVID-19 epidemics across Europe

The number of COVID-19 deaths reported from European countries has varied more than 100-fold. In terms of coronavirus transmission, the relatively low death rates in some countries could be due to low intrinsic (e.g. low population density) or imposed contact rates (e.g. non-pharmaceutical interventions) among individuals, or because fewer people were exposed or susceptible to infection (e.g. smaller populations). Here we develop a flexible empirical model (skew-logistic) to distinguish among these possibilities. We find that countries reporting fewer deaths did not generally have intrinsically lower rates of transmission and epidemic growth, and flatter epidemic curves. Rather, countries with fewer deaths locked down earlier, had shorter epidemics that peaked sooner, and smaller populations. Consequently, as lockdowns are eased we expect, and are starting to see, a resurgence of COVID-19 across Europe.

Impact of COVID-19 lockdown on glycemic control in adults with type 1 diabetes mellitus: information and standardized questions regarding follow-up during lockdown

Aim. To examine the impact of the lockdown caused by COVID-19 pandemic on both the glycemic control and the daily habits of a group of patients with type 1 diabetes mellitus (T1DM) using flash continuous glucose monitoring devices (Flash CGM). Methods. Retrospective analysis based on all the information gathered in virtual consultations from a cohort of 50 adult patients with T1DM with follow-up at our site. We compared their CGM metrics during lockdown with their own previous data before the pandemic occurred, as well as the potential psychological and therapeutic changes. Results. We observed a reduction of the average glucose: 160.26 ± 22.55 mg/dl vs. 150 ± 20.96 mg/dl, p=0.0009, estimated HbA1c: 7.21 ± 0.78% vs. 6.83 ± 0.71%, p=000.5, glucose management indicator (GMI) 7.15 ± 0.57 % vs. 6.88 ± 0.49 %, p=0.0003, and glycemic variability (CV): 40.74 ± 6.66 vs. 36.43 ± 6.09 p<0.0001. Time in range showed an improvement: 57.46 ± 11.85% vs a 65.76 ± 12.09%, p<0.0001, without an increase in percentage of time in hypoglycaemia. Conclusions: COVID-19 lockdown was associated with an improvement in glycemic control in patients with T1DM using CGM.

opencc-zeroOct 2020View details →

Fear of COVID-19 during confinement in Mauritius: a survey-based study

Background: Fear has been a common response to the coronavirus disease 2019 (COVID-19) pandemic throughout the world. In Mauritius, the outbreak of COVID-19 has been an exceptional occurrence requiring stringent confinement of the population. In this study we have explored people's reactions to COVID-19 during confinement, with emphasis on fear and the impact of news on the level of fear. Methods: An anonymized online survey was carried out during confinement. Participation was voluntary. Participants reported fear level on a scale from 1 to 10, where no fear scored 1 and maximum fear scored 10. Participants reported the impact of news on their fear level on a scale of 1 to 10, where 1 represented no impact and 10 represented maximum impact. Participants reported the status of their information about COVID-19 on a scale of 1 to 10. Results: The self-rated level of fear during confinement had a mean of 5.09 with 95%CI [4.70, 5.47]. This increased to a mean of 6.39 with 95%CI [6.00-6.78] at the prospect of confinement being lifted. The difference was statistically significant (paired-sample T-test, p<0.05). With regard to the impact of news on fear of COVID-19, the mean for local news was 5.97 with 95%CI [5.59, 6.34] whereas that of worldwide news was 6.86 with 95%CI [6.50, 7.23]. Worldwide news had a more significant impact (paired-sample T-test, p<0.05). The information score about COVID-19 had a mean of 5.12 with 95%CI [4.71, 5.53]. Conclusions: Participants experienced a moderate level of fear of COVID-19 during confinement which increased at the prospect of confinement being lifted, implying that people felt safer during confinement. Their fear was influenced more by international news than by local news. Overall participants reported that they were moderately well informed about the COVID-19 pandemic. Keywords: COVID-19, fear, confinement, pandemic, impact of news, Mauritius

Depression and Stress among Bangladeshi Students during COVID-19 Lockdown

This data was collected during COVID-19 pandemic (lockdown) from Bangladesh. The dataset contains social, financial, educational and other information including "Depression" and "Stress" (DASS-21 Scale) questions form tertiary level students. It was collected via google forms (e-questionnaire).

First COVID-19 Genomic Patient Cluster was at PLA Hospital in Wuhan, China

A paper published on Zenodo (DOI 10.5281/zenodo.4119263) by Dr. Steven Quay, M.D., PhD., head of two COVID-19 therapeutic programs at Atossa Therapeutics, Inc. (NASDAQ: ATOS), illuminates new scientific observations and conclusions documenting that the SARS-CoV-2 pandemic began at the General Hospital of Central Theater Command of People’s Liberation Army (PLA Hospital) in Wuhan, China, located at 627 Wulon Road, Wuchang District, Wuhan. International biospecimen data repositories indicate as early as December 10, 2019 COVID patient records were being created by PLA personnel, weeks before the Chinese government informed the WHO of the pandemic.   This is a short presentation by the author explaining his research.

Rapid publishing for public health books against COVID-19

A YouTube version of the video is <a href="https://www.youtube.com/watch?v=v6WUUTv-GIc&t=3s&ab_channel=SimonWorthington">available here</a>. Presented are two case studies covering the barriers to be overcome to fully automate the production workflow for Open Access multi-format books, to produce and distribute the following – ebook, print-on-demand, screen PDF, webbook, website, and an interoperable source. The first case study involves producing eight book sprints for <a href="https://github.com/akademie-oeffentliches-gesundheitswesen">training manuals</a>, some with MOOC modules, for the Academy of Public Health in Dusseldorf (Germany) which was run as a <a href="https://github.com/TIBHannover/Rapid-Collaborative-Health-Publishing">research cooperation</a> with the Open Science Lab, TIB – German National Library of Science and Technology.  The second case study involves converting the existing reports of <a href="https://www.independentsage.org/">Independent SAGE</a> (UK) – as Open Access, multi-format, enabling multi-channel distribution, and deposing in academic repositories.  The indie_SAGE project involved creating a volunteer academic working group to carry out the work. Here it is important to add that I am acting as a private individual. The Independent Science Advisory Group for Emergencies (indie_SAGE) was formed in May 2020 by the former chief Scientific Adviser to the UK government Sir David King, quote, ‘on how to minimise deaths and support Britain’s recovery from the COVID-19 crisis’.  The <a href="https://github.com/Independent-SAGE/Technical-Publishing-Working-Group">working group</a> is newly formed and welcomes help and volunteers!