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opencc-by-4.0Apr 2022View details →

ClinSpEn Corpus: Parallel English-Spanish COVID-19 Clinical Cases, Terminology and Ontology Concepts

ClinSpEn Parallel Corpus Collection This repository contains the complete ClinSpEn corpus collection, which was used for the <a href="https://temu.bsc.es/clinspen">ClinSpEn shared task</a> at Biomedical WMT 2022. ClinSpEn is a collection of Gold Standard EN-ES parallel corpora of different types of clinical data: case reports, medical controlled vocabularies/ontologies, and clinical terms and entities extracted from medical content. It includes development and test data translated by professional medical translators that can be used to train and benchmark clinical EN-ES machine translation systems. Additionally, monolingual background data is provided so that the systems' performance can be analyzed in unseen data. If you use this dataset, please cite: <blockquote> <pre><code>inproceedings{biowmt22, title={Findings of the WMT 2022 Biomedical Translation Shared Task: Monolingual Clinical Case Reports}, author={Neves, Mariana and Yepes, Antonio Jimeno and Siu, Amy and Roller, Roland and Thomas, Philippe and Navarro, Maika Vicente and Yeganova, Lana and Wiemann, Dina and Di Nunzio, Giorgio Maria and Vezzani, Federica and others}, booktitle={WMT22-Seventh Conference on Machine Translation}, pages={694--723}, year={2022} } </code></pre> </blockquote> Data Description ClinSpEn proposes three different sub-tracks, each based on a different type of clinical data: 1. Clinical Cases: Parallel EN-ES COVID-19 clinical case reports. The direction of this sub-track is EN>ES. The dataset’s case reports were carefully selected to cover a wide range of aspects related to the disease: different types of patients (children, adults, elderly and pregnant people, babies), different comorbidities (cancer, mental health issues, immunosuppressed patients) and symptomatology (mild and severe presentations, dermatologic, immunologic and psychiatric manifestations, thrombosis, ...). The reports were translated from English to Spanish by a professional medical translator on a first step and revised by a clinical expert on a second step. The sample (dev) set and test set are made up of parallel txt files (50 and 152 documents each, respectively), with the Spanish version having a “.es” extension and the English files having a “.en” extension. Each report has been parallelized so that every sentence’s line number corresponds to the same sentence’s line number in both languages. The background data (9,804 files) is made up of a TSV file with four columns: filename, document number, line number and English line. The clinical cases themselves include COVID-19 case reports as well as diverse content extracted from PubMed. If you need to map the entries in the join test + background document provided in earlier versions, you may use the "clinspen_clinicalcases_test-set_filename_mapping.tsv" file. 2. Clinical Terminology: Parallel EN-ES clinical terms extracted from medical literature and clinical records, with particular focus on diseases, symptoms, findings, procedures and professions and translated and revised by professional medical translators. The direction of this sub-track is ES>EN. The sample (dev) set contains 7,000 terms as a tab-separated file (TSV), with the first column corresponding to English terms and the second column to Spanish terms. The test data (12,128 terms) is made up of a TSV file with three columns: term number, English term and Spanish term. The background data (201,890 terms) is made up of a TSV file with two columns: term number and Spanish term. The term number columns can be used to map the entries in the join test + background document provided in earlier versions. 3. Ontology Concepts: Parallel EN-ES concepts extracted from various open biomedical ontologies and taxonomies and then manually translated by a professional medical translator. The direction of this sub-track is EN>ES. The sample (dev) data includes 400 concepts. The terms are presented as tab-separated file (TSV), with the first column corresponding to English terms and the second column to Spanish terms. The third column includes the term’s origin ontology and its correspondent ID (separated by an underscore), while the fourth one includes a link to the concept in OBO Library. The test data (1,789 concepts) is made up of a TSV file with five columns: term number, English term, Spanish term, ontology id and OBO library URL. The background data (299,408 concepts) is made up of a TSV file with four columns: term number, English term, ontology id and OBO library URL. The term number columns can be used to map the entries in the join test + background document provided in earlier versions.   Related Links: <ul> <li> ClinSpEn website with more information: <a href="https://temu.bsc.es/clinspen/">https://temu.bsc.es/clinspen/</a> </li> <li> WMT website: <a href="https://www.statmt.org/wmt22/">https://www.statmt.org/wmt22/</a> </li> </ul> License This work is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>. Contact If you have any question or suggestion, please contact us at the following addresses: - Salvador Lima-López (<salvador [dot] limalopez [at] gmail [dot] com>) - Darryl Estrada (<darrylestrada97 [at] gmail [dot] com>) - Martin Krallinger (<krallinger [dot] martin [at] gmail [dot] com>)

opencc-by-4.0Mar 2023View details →

The use of digital technologies among older adults during the COVID-19 Pandemic: A descriptive study in Turkey

Data set from the article "The use of digital technologies among older adults during the COVID-19 Pandemic: A descriptive study in Turkey"

opencc-by-4.0Mar 2023View details →

Global misinformation spillovers in the online vaccination debate before and during COVID-19 - ex

The dataset includes all the ids of the tweets analysed in the paper "Global misinformation spillovers in the online vaccination debate before and during COVID-19", divided by lang. They are all the tweets containing vaccines keywords in 18 different European languages, spanning the period October 2019 - March 2021 (excluded 2020 Jan - 2020 Jun). Note that a large fraction of the tweets can't be retrieved because of the suspension of the accounts and the removal of the posts by the users, so the study is only partially reproducible. The unzipped dataset has a dimension of 8,0G. The authors of the paper are: Lenti J, Mejova Y, Kalimeri K, Panisson A, Paolotti D, Tizzani M, Starnini M.

opencc-by-4.0Sep 2022View details →

Effects of COVID-19 in Endocrine Patients: A Cross-Sectional Study.

Abstract: Introduction: Home confinement due to COVID-19 lockdown led to changes in daily routines, including social interactions, as well as restrictions on the possibility of playing sports and eating habits. These changes could have a greater impact on patients suffering from chronic diseases, such as endocrine patients, especially in emotional and behavioral dimensions. Materials and Methods: This study aimed to assess the effects of COVID-19-induced quarantine on daily habits in a group of patients with endocrine disorders, focusing on food consumption, eating habits and sleep during the confinement. Eighty-five endocrine patients were enrolled. A structured interview was administered to investigate socio-demographic information, general medical conditions, and habits adopted during quarantine. All patients underwent the Spielberger State Anxiety Inventory (STAI-Y1) to assess state anxiety. Result: Results showed that subjects mainly had a sedentary lifestyle. We found a significant increase in the number of cigarettes in smokers and in meals consumed during confinement, as well as a high rate of sleep disturbance, especially insomnia. Notably, physical well-being resulted to be a predictive factor (OR = 0.38; 95%CI = [0.95,0.66]), whereas anxiety was a risk factor for sleep disorder (OR = 1.22; 95%CI = [1.10,1.40]), as was working in public and private offices and being a student. Conclusions: Changes in daily habits were likely due to the alterations in routine, resulting in greater boredom and inactivity during the day. In addition, future research should focus on the importance of patient adherence to therapy.

opencc-zeroMar 2023View details →

Visual policy narrative messaging and COVID-19 vaccine uptake

In the face of vaccine hesitancy, public health officials are seeking more effective risk communication approaches to increase vaccination rates. We test the influence of visual policy narratives on COVID-19 vaccination behavior through a panel survey experiment conducted in early 2021 (n=3900) and then eight weeks later (n=2268). We examine the effects of three visual policy narrative messages that test the narrative mechanism of character selection (yourself, your circle, and your community) and a non-narrative control on COVID-19 vaccine behavior. Visual risk messages that use narratives positively influence COVID-19 vaccination through serial mediation of affective response to the messages and motivation to get the COVID-19 vaccination. Additionally, character selection matters, as messages focusing on protecting others (i.e., your circle and your community) perform stronger than that of yourself. Political ideology moderated some of the effects, with conservative respondents in the non-narrative control condition having a higher probability of vaccination in comparison to the protect yourself condition. Taken together, these results suggest that public health officials should use narrative-based visual communication messages that emphasize communal benefits of vaccinations.

opencc-by-4.0Mar 2023View details →

SHIFT OF ONLINE CONSUMER PURCHASING BEHAVIOR IN VIETNAM DURING THE COVID-19 AND IN THE NEW NORMAL CONTEXT

The study’s findings contribute to clarify shift of online consumer purchasing behavior and factors affecting the frequency of consumers’ online purchases in pandemic and after the pandemic’s demise, in order to help business to developeffective marketing strategies and enhance their presence in the e-commerce sector.

opencc-zeroApr 2023View details →

Data for: Evaluation of antibody kinetics and durability in health individuals vaccinated with inactivated COVID-19 vaccine (CoronaVac): a cross-sectional and cohort study in Zhejiang, China

Background: Although inactivated COVID-19 vaccines are proven to be safe and effective in the general population, the dynamic response and duration of antibodies after vaccination in the real world should be further assessed. Methods: We enrolled 1067 volunteers who had been vaccinated with one or two doses of CoronaVac in Zhejiang Province, China. Another 90 healthy adults without previous vaccinations were recruited and vaccinated with three doses of CoronaVac, 28 days and 6 months apart. Serum samples were collected from multiple timepoints and analyzed for specific IgM/IgG and neutralizing antibodies (NAbs) for immunogenicity evaluation. Antibody responses to the Delta and Omicron variants were measured by pseudovirus-based neutralization tests. Results: Our results revealed that binding antibody IgM peaked 14–28 days after one dose of CoronaVac, while IgG and NAbs peaked approximately 1 month after the second dose and then declined slightly over time. Antibody responses had waned by month 6 after vaccination and became undetectable in the majority of individuals at 12 months. Levels of NAbs to live SARS-CoV-2 were correlated with anti-SARS-CoV-2 IgG and NAbs to pseudovirus, but not IgM. Homologous booster around 6 months after primary vaccination activated anamnestic immunity and raised NAbs 25.5-fold. The neutralized fraction subsequently rose to 36.0% for Delta (p=0.03) and 4.3% for Omicron (p=0.004), and the response rate for Omicron rose from 7.9% (7/89) to 17.8% (16/90). Conclusions: Two doses of CoronaVac vaccine resulted in limited protection over a short duration. The inactivated vaccine booster can reverse the decrease of antibody levels to prime strain, but it does not elicit potent neutralization against Omicron; therefore, the optimization of booster procedures is vital.

embargoedcc-zeroApr 2023View details →

Monocentric retrospective cohort of 30,423 COVID-19 patients

Population and design: Monocentric cohort comparing COVID-19 patients exposed or not exposed to the treatment hydroxychloroquine (HCQ)+azithromycin (AZ) used as a standard of care in our center (Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France). The inclusion period was from 2 March 2020 to 31 December 2021, with a follow-up period of 6 weeks. Inclusion and exclusion criteria: Data included were those of patients ≥ 18 years of age with PCR-proven COVID-19 disease regardless of symptoms (asymptomatic or symptomatic) and treated in our centre, i.e. having had a medical examination by one of the doctors in our centre (Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France) either as outpatients or as inpatients, i.e. hospitalized on the day of the visit in our outpatient unit following evaluation or directly transferred from another medical ward except intensive care unit. The reasons for exclusion were an erroneous patient identification (identity surveillance and duplicates), lack of available medical data, lack of COVID-19 after checking the medical record (including patients without COVID-19 consulting for a post-COVID-19 syndrome), expression of opposition to the use of their medical data for research purposes (in accordance with European General Data Protection Regulation), and data from patients hospitalized in our center after intensive care. Data from COVID-19 outpatients left without medical advice were excluded.

opencc-by-4.0Apr 2023View details →

COVID-19 PBMC sample information and the VCF file of variants around OAS1 gene.

We investigated our recently published PBMC scRNA-seq data (Stephenson et al. 2021 Nat Med) obtained from 112 donors, including 84 COVID-19 positive individuals, and profiled using the CITE-seq approach, as an independent in vivo validation of OAS1 eQTL colocalisation with GWAS locus for COVID-19 susceptibility. The dataset includes both sample information and genotype information of variants around OAS1 gene (chr12:111906777-113906777) as in VCF format. The whole variant data of the COVID-19 PBMC samples is available upon request.

opencc-zeroApr 2023View details →

The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic

A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019, with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.

opencc-by-4.0Jan 2023View details →

Post COVID-19 trends in simulation use within diagnostic radiography and radiation therapy education.

The authors developed and deployed an online survey among diagnostic radiography and/or radiation therapy educators with experience in pre-registration training (academic, clinical or combined).The aim of this study was to capture global trends and activity on simulation-based education (SBE) in medical imaging and radiation therapy education. Simulation is a well-established component of medical radiation science training that embraces a wide range of activities and resources all aiming to provide a safe environment in which to practice clinical skills. The survey instrument design was informed by a prior review of the literature, a previous international survey conducted by members of the research team1 and experience within the research team. It comprised two open and 27 closed questions designed to ascertain data across four domains: type of training environment of the respondent (n=13), access to and use of simulation within the participants’ institution (n=13) and possible future trends in simulation (n=3). Data captured in this study was compared with similar data from Bridge and colleagues previous survey in 2020.1 There is an opportunity for this dataset to add to the evidence base on the evolving landscape of the use of SBE in radiography/radiation therapy education. Such information has the potential to inform future practices and to create best-practice standards in the adoption of simulation-based educational resources and activities in diagnostic radiography and radiation therapy. Reference: <ol> <li>Bridge P, Shiner N, Bolderston A, et al. International audit of simulation use in pre-registration medical radiation science training. Radiography (Lond). Nov 2021;27(4):1172-1178. doi:10.1016/j.radi.2021.06.011</li> </ol>

Data for "Human judgement forecasting of COVID-19 in the UK" by Bosse et. al (2023)

Data used in the paper "Human judgement forecasting of COVID-19 in the UK" by Bosse et. al (2023). All code for the paper can be found at https://github.com/epiforecasts/uk-crowd-forecasting-challenge.

Neuro COVID-19

Incidence of neurological manifestations and complications in patients with COVID-19 infection: a propensity score matching analysis

PRISMA DIAGRAM FOR ARTICLE: Lessons learned during the health crisis caused by COVID-19 in the work of the nursing professional: A systematic review

PRISMA DIAGRAM FOR ARTICLE: Lessons learned during the health crisis caused by COVID-19 in the work of the nursing professional: A systematic review

opencc-by-4.0Jul 2022View details →

COVID-19 and Traffic Safety: Exploring Exposure, Crash Frequency and Severity, and Roadway and Network Design

Early COVID-19 lockdowns in the first half of 2020 largely kept people at home, thereby reducing motor vehicle traffic levels. Theoretically, reduced traffic exposure should have resulted in reduced motor vehicle crashes. However, a variety of factors may have complicated this relationship. In order to better understand the impact of COVID-19 lockdowns on traffic safety outcomes, we explore fatalities, injuries, and total crashes before and during the lockdowns on both the national and state levels. We provide descriptive statistics and create negative binomial regressions exploring the role of vehicle, user, and built environment factors on traffic safety outcomes. Findings suggest that crash counts in Region 6 were 35%-50% lower in 2020 during the COVID-19 lockdowns. Crashes that occurred during the COVID-19 lockdowns were more likely to be more severe. Fatal pedestrian crashes across the U.S. decreased during COVID-19 (although not as much as overall fatal crashes) and fatal bicyclist crash counts increased. Drunk drivers were less prevalent in nationwide fatalities but more prevalent in overall Region 6 crashes. Overall, crashes were more likely single-vehicle fixed-object or rollover crashes involving unsafe speeds. In Texas, suburban areas saw the most crashes before and during COVID-19, although they also saw the greatest decrease. Rural Texas crashes were most likely to result in a fatality or serious injury, and that likelihood got worse during the COVID-19 lockdowns. While Texas freeways and arterials saw the largest decreases in crash counts, these functional classifications still had the most crashes. Urban interstates and rural local roads in Texas were notable because these two functional classifications actually saw increases in the number of fatal and serious injury crashes during COVID-19 lockdowns.

Sex-disaggregated Analysis of Risk Factors of COVID-19 Mortality Rates in India

This Zenodo resource contains the data used to perform analysis in the article "Sex-disaggregated Analysis of Risk Factors of COVID-19 Mortality Rates in India". Data The data is organized in the form of tables. hypothesis-test-data This table contains data used to perform the two tailed hypothesis test on gender mortality in different regions. <pre><code>* Region * Male_Deaths - Number of male COVID-19 deaths in region. * Female_Deaths - Number of female COVID-19 deaths in region. * Male_cases - Number of male COVID-19 positive in region. * Female_cases - Number of female COVID-19 positive in region. </code></pre> lasso-covid19India This table contains data used for analysis on cases throughout India. Columns from COVID-19 India data <pre><code>* State_Code * State * District * Confirmed * Active * Recovered * Deceased </code></pre> Columns taken from NFHS data <pre><code>* Sex_ratio_of_the_total_population_females_per_1000_males * Women_whose_Body_Mass_Index_BMI_is_below_normal_BMI__185_kgm214_ * Men_whose_Body_Mass_Index_BMI_is_below_normal_BMI__185_kgm2_ * Women_who_are_overweight_or_obese_BMI__250_kgm214_ * Men_who_are_overweight_or_obese_BMI__250_kgm2_ * All_women_age_1549_years_who_are_anaemic_ * Men_age_1549_years_who_are_anaemic_130_gdl_ * Women_Blood_sugar_level__high_140_mgdl_ * Men_Blood_sugar_level__high_140_mgdl_ * Women_Very_high_Systolic_180_mm_of_Hg_andor_Diastolic_110_mm_of_Hg_ * Men_Very_high_Systolic_180_mm_of_Hg_andor_Diastolic_110_mm_of_Hg_ </code></pre> lasso-KA+TN-bulletin This table contains data used for analysis on the sub-cohort of Karnataka and Tamil Nadu. Data from Media Bulletin <pre><code>* District * Total_Positives * total_deaths * male_deaths * female_deaths * Male_cases_in_data * Female_cases_in_data </code></pre> Calculated Data <pre><code>* Estimated_Male_cases - Estimated male cases using total positives column and existing case data * Estimated_Female_Cases - Estimated female cases using total positives column and existing case data * Male_Mortality - Estimated Male Cases / male_deaths * Female_Mortality - Estimated Female Cases / female_deaths </code></pre> Columns taken from NFHS data <pre><code>* Sex_Ratio_females_every_1000_males * State Women_whose_Body_Mass_Index_BMI_is_below_normal_BMI__185_kgm214_ * Men_whose_Body_Mass_Index_BMI_is_below_normal_BMI__185_kgm2_ * Women_who_are_overweight_or_obese_BMI__250_kgm214_ * Men_who_are_overweight_or_obese_BMI__250_kgm2_ * All_women_age_1549_years_who_are_anaemic_ * Men_age_1549_years_who_are_anaemic_130_gdl_ * Women_Blood_sugar_level__high_140_mgdl_ * Men_Blood_sugar_level__high_140_mgdl_ * Women_Very_high_Systolic_180_mm_of_Hg_andor_Diastolic_110_mm_of_Hg_ * Men_Very_high_Systolic_180_mm_of_Hg_andor_Diastolic_110_mm_of_Hg_ </code></pre> Code The code is available at this <a href="https://github.com/harishpb26/Sex-disaggregated-Analysis-of-Risk-Factors-of-COVID-19-Mortality-Rates-in-India">Github Repository</a>.

Roles of regional transport and vertical mixing in aerosol pollution in Shanghai over the COVID-19 lockdown period observed above urban canopy

Abstract Regional transport and vertical mixing are important for aerosol pollution of megacities, but their roles are often challenging to assess via ground observations. In this study, we measured aerosol chemical composition simultaneously above urban canopy (Shanghai Tower, 609 m), a site representative of aerosols from regional scale, and a nearby ground site and investigated the roles of regional transport and vertical mixing over 2020 COVID-19 lockdown period (Jan.1-Apr. 18), when local emissions were first drastically reduced and then recovered. During the lockdown period, regional transport was the major source of most aerosol species (organics, NO3-, SO42-, and NH4+) at both heights according to the high correlation coefficients (R=0.81~0.87) between both heights. Correlation coefficients and vertical ratios (609 m/ground) of most aerosol components showed similar diurnal variations with the evolution of planetary boundary layer height, indicating the role of vertical mixing in aerosol pollution. Moreover, the concentrations of aerosol components at 609 m generally preceded those at ground level by 1~2 h, indicating that aerosols were first transported at upper boundary layer, and then were mixed downwards to ground level. At 609 m, highly oxidized oxygenated organic aerosol (OOA; a surrogate of secondary organic aerosol (SOA)) dominated in organic aerosol (≥75%). The high correlations (R=0.96) between OOA and hydrocarbon-like organic aerosol (HOA; a surrogate of primary organic aerosol (POA)) at 609 m indicated that they originated similarly from regional transport. This study highlights the importance of regional joint prevention and control of pollutant emissions and observation above urban canopy.   The data files are provided for readers to evaluate this research.

Development of a Predictive Model for In-Hospital Mortality in COVID-19 Patients Using CAR, IL-6, IL-6/LY, and NLR: A Single-Center Study in Indonesia

Figure 1. ROC Curve of CAR, IL-6, IL-6/LY, and NLR   Figure 2. Kaplan Meier curve of (a) CAR (b) IL-6 (c) IL-6/LY (d) NLR blue line represents group above cut off and green one represents group below cut-off

Effects of Covid-19 Vaccines on the Menstrual Cycle: A Cross-Sectional Study

Background: Prior clinical studies that sought to investigate the safety and efficacy of Covid-19 vaccines did not list menstrual cycle changes as a side-effect. However, following reported cases of menstrual cycle disturbances after vaccination, this study sought to examine the link between Covid-19 vaccination and post-vaccine menstrual cycle abnormalities in pre- and post-menopausal women. Methods: A cross-sectional research design approach using online surveys was employed to investigate the link between vaccination and changes in menstrual cycle. The participants consisted of a cohort of 657 pre- and post-menopausal women with the majority drawn from the reproductive age group (25-44 years). The inclusion criteria was that participants must have received any type of Covid-19 vaccine, not be pregnant and those that did not have a negative diagnosis in any gynecologic condition. Of the eligible sample size, only 344 participants met the inclusion criteria. The sociodemographic and menstrual cycle data was collected from an online survey. Data was analyzed using descriptive, inferential chi-square tests, logistic regression, and correlation. Results: The results partially confirmed the findings from prior studies that Covid-19 vaccination is associated with significant changes in the women’s menstrual cycle flow and menstrual period length even after controlling for age, Body Mass Index, and ethnicity. Other menstrual cycle disturbances such as missed periods, cycle regularity, and spotting/vaginal bleeding were noted to be less significant. However, the extent of menstrual cycle changes was less severe and decreased after the second dose vaccination. It was found that 11.1% and 37.5% of post-menopausal women reported menstrual symptoms after the first and the second dose cycle respectively. Conclusion: The study concludes that although Covid-19 vaccines tend to adversely affect women’s menstrual cycle, these changes are short-lived. The findings have important implications in enhancing the success of Covid-19 vaccination programs by reducing cases of vaccine hesitancy among reproductive-age women.

Cluster Interconnectedness maps of COVID-19 spread in India.

This project contains clustered maps from sample data on COVID-19 acquired from the Indian Council of Medical Research. Citation is required if anyone wishes to use the files for additional research.