Find research datasets worth reusing

opencc-by-4.0Jun 2023View details →

Exploring the HONO source during the COVID-19 pandemic in a megacity in China

HONO concentrations were measured using an atmospheric HONO online detector (TiH300, Focused Photonics., China). An automatic weather station (QXZ1.0, Yigu Technologies, China) was used to observe temperature, relative humidity, wind direction, and wind speed. PM2.5 was analyzed using a tapered element oscil-lating microbalance (Model 1400a, Thermo Electron, USA). Ozone (O3) was monitored using UV absorption (TE, Model 49i, Waltham, USA), while carbon monoxide (CO) was quantified using a gas filter correlation/non-dispersive infrared analyzer (TE, Model 48i, Waltham,USA). Nitrogen oxides (NO-NO2-NOx) were measured using an ammonia analyzer (AQMS-650, Focused Photonics, China). Photolysis rates of HCHO, NO2, H2O2, NO–3, and HONO were measured using an atmospheric photolysis rate analyzer (PFS-100, Focused Photonics, China). An ambient ion monitor (URG-9000D, Thermo Fisher Scientific, USA) was used to obtain the hourly mass concentrations of NO–3.

opencc-by-4.0Jun 2023View details →

Pharmacokinetic dataset of a randomized controlled trial investigating the efficacy and safety of intravenous imatinib mesylate (Impentri®) in subjects with acute respiratory distress syndrome induced by COVID-19

Abstract Background The coronavirus disease 2019 (COVID-19) pandemic has led to a disruptive increase in the number of intensive care unit (ICU) admissions with acute respiratory distress syndrome (ARDS). ARDS is a severe, life-threatening medical condition characterized by widespread inflammation and vascular leak in the lungs. Although there is no proven therapy to reduce pulmonary vascular leak in ARDS, recent studies demonstrated that the tyrosine kinase inhibitor imatinib reinforces the endothelial barrier and prevents vascular leak in inflammatory conditions, while leaving the immune response intact. Methods This is a randomized, double-blind, parallel-group, placebo-controlled, multicenter clinical trial of intravenous (IV) imatinib mesylate in 90 mechanically ventilated subjects with COVID-19-induced ARDS. Subjects are 18 years or older, admitted to the ICU for mechanical ventilation, meeting the Berlin criteria for moderate-severe ARDS with a positive polymerase chain reaction test for SARS-CoV2. Participants will be randomized in a 1:1 ratio to either imatinib (as mesylate) 200 mg bis in die (b.i.d.) or placebo IV infusion for 7 days, or until ICU discharge or death. The primary study outcome is the change in Extravascular Lung Water Index (EVLWi) between day 1 and day 4. Secondary outcome parameters include changes in oxygenation and ventilation parameters, duration of invasive mechanical ventilation, number of ventilator-free days during the 28-day study period, length of ICU stay, and mortality during 28 days after randomization. Additional secondary parameters include safety, tolerability, and pharmacokinetics. Discussion The current study aims to investigate the efficacy and safety of IV imatinib in mechanically ventilated subjects with COVID-19-related ARDS. We hypothesize that imatinib decreases pulmonary edema, as measured by extravascular lung water using a PiCCO catheter. The reduction in pulmonary edema may reverse hypoxemic respiratory failure and hasten recovery. As pulmonary edema is an important contributor to ARDS, we further hypothesize that imatinib reduces disease severity, reflected by a reduction in 28-day mortality, duration of mechanical ventilation, and ICU length of stay.

opencc-by-4.0Jun 2023View details →

A Pilot Randomized Controlled Trial of Distance Laughter Therapy for Mothers' Level of Depression, Anxiety, and Parental Stress during the COVID-19 Pandemic

Presented here are both quantitative and qualitative datasets from a study titled 'A Pilot Randomized Controlled Trial of Distance Laughter Therapy for Mothers’ Level of Depression, Anxiety, and Parental Stress during the COVID-19 Pandemic.' The COVID-19 pandemic has necessitated significant lifestyle modifications globally, leading to heightened psychological stressors, notably depression and anxiety. Concurrently, the exigencies of parental care have escalated, thereby amplifying the risk of caregiver exhaustion and potential child maltreatment. This study sought to assess the efficacy and feasibility of utilizing distance laughter therapy for mothers who are looking after young children during these challenging times. The primary objective was to alleviate symptoms of depression, anxiety, and parental stress.

opencc-by-4.0Mar 2021View details →

International E-Conference On Post Covid-19 Situation

International E-Conference On Post Covid-19 Situation organized by Anjuman Islam Janjira Degree College of Science, Murud on 30th March 2021

opencc-by-4.0Apr 2023View details →

Data - Positive and Negative Affect Schedule in early COVID-19 pandemic

Data of a Positive and Negative Affect Schedule (PANAS) study done in early COVID-19 pandemic. The dataset has 4 sheets. The first one and the second one have 334 rows and 45 columns. The third and the fourth have 87 rows and 2 columns. Note that the first sheet includes a comment about the data in column 5, rows 336-341. Sheets 1 and 2 present the same information, but in different language: sheet one is in English and sheet 2 is in Spanish. Sheets 3 and 4 also have the same content, again: sheet 3 in English and sheet 4 in Spanish. SPANISH: Datos de estudio con escala Positive and Negative Affect Schedule (PANAS) realizado en los inicio de la pandemia COVID-19. El dataset incluye 4 hojas. La primera y la segunda contienen 334 filas y 45 columnas. La tercera y la cuarta tienen 87 filas y 2 columnas. Nótese que la primera hoja incluye un comentario sobre los datos en la columna 5, filas 336-341. Las hojas 1 y 2 contienen la misma información, pero en distinto idioma: la hoja 1 en inglés y la hoja 2 en español. Las hojas 3 y 4 también contienen la misma información, de nuevo: la hoja 3 en inglés y la hoja 4 en español.

opencc-by-4.0Jul 2023View details →

Assessment of the Quality of Life and Resilience in Ventilated Patients with COVID-19: Findings One year After Hospital Discharge

Assessment of the Quality of Life and Resilience in Ventilated Patients with COVID-19: Findings One year After Hospital Discharge This dataset was collected in a prospective cohort study to evaluate the quality of life and resilience of patients managed with invasive mechanical ventilation due to severe COVID-19, one year after hospital discharge. Methodology Design A prospective cohort study was conducted, and the present study received approval from the Ethics Committee of Universidad del Rosario (DVO005-1957- CV1534). Informed consent was obtained from each patient or their legal caregiver, which was given via telephone. Patients/Population Data were collected from patients who received MV support for respiratory failure secondary to critical illness due to COVID-19. The study included consecutively patients discharged alive from the Hospital Universitario Mayor Méderi located in the city of Bogota, Colombia from March 19, 2020, to April 30, 2021. Patients who passed away after discharge, those with whom telephone communication was not feasible, individuals with cognitive impairment preventing them from responding to the survey without obtaining information from a caregiver, and those who declined to participate in the study (as indicated by the patient and/or caregiver) were excluded from the final analysis. Intervention/Measurement Participants were administered a structured questionnaire that included three scales: PCFS (Post-COVID-19 functional Status Scale), EQ-5D-3L (EuroQol 5 dimensions 3 levels) (administered via telephone application), and CD-RISC (Connor-Davidson Resilience Scale). Permission for the non-commercial use of the EQ-5D-3L scale was obtained from the EuroQol Customer Portal (Registration No. 55265). Statistical Analysis The general characteristics of the population and the results of the PCFS, EQ-5D-3L, and CD-RISC were described. Continuous variables were presented as mean and standard deviation (SD) or median and interquartile range (IQR) depending on the data distribution. Categorical variables were described using absolute and relative frequencies. The PCFS was reported using a grading system ranging from Grade 0, indicating patients who were able to resume their daily activities without limitations, to Grade 4, representing severe functional limitations. The five dimensions of the EQ-5D-3L were considered as numerical variables and scored as follows: 1 for no alteration, 2 for moderate alteration, and 3 for severe alteration. The total score was computed by summing the scores from each dimension, ranging from 5 (indicating optimal quality of life) to 15 (indicating severely compromised quality of life). To assess the usefulness of the PCFS in measuring QoL, Pearson correlations were performed between the total score of the EQ-5D-3L and each individual dimension with the PCFS score. The CD-RISC and its 25 dimensions were evaluated as well. Each dimension was treated as a numerical variable and scored as follows: 0 for no alteration, 1 for mild alteration, 2 for moderate alteration, 3 for severe alteration, and 4 for critical alteration. The total CD-RISC score ranged from 0 (indicating no resilience) to 100 (indicating the best possible resilience). Furthermore, it was hypothesized that patients with higher resilience, as measured by the CD-RISC scale, would have better quality of life (QoL). Pearson correlations were examined between the PCFS score and the total CD-RISC score.

Dataset for publication: "Using explainable machine learning to interpret the effects of policies on air pollution: COVID-19 lockdown in London"

This online repository offers supplementary datasets supporting the findings in the research article titled "Using explainable machine learning to interpret the effects of policies on air pollution: COVID-19 lockdown in London," published in Environmental Science & Technology. The dataset contains air quality data from different monitoring sites in London between 2016 and 2020 and weather data for the same period. Additionally, the dataset incorporates 136 features relating to London's Middle Layer Super Output Areas (MSOAs) in the year 2019, which can be used to identify the key factors contributing to the heterogeneous changes in air quality levels at different spatial locations during the pandemic. Please refer to the metadata file for detailed data sources and descriptions.

Validation of the EQ-5D-3L in Patients with Severe COVID-19 One Year After Hospital Discharge

This is a prospective cohort study database aimed at validating the EQ-5D-3L in patients with COVID-19 who underwent invasive mechanical ventilation, assessing their quality of life one year after hospital discharge.

Sounding Covid-19 Repository

The Covid-19 pandemic has caused cities to become sparsely populated, significantly changing urban sound environments with different restrictions placed. By capturing audio recordings at various points during lockdowns, we can sonically observe the impact of Covid-19 constraints and how these places have transformed over time.  The repository holds 91 sound compositions from 27 separate locations, focusing on the effects of Covid-19 during Belfast, Northern Ireland's Lockdowns (1-3 in 2020-2021), Exit Strategies (Summer 2020 and 2021), Lifted Restrictions (2022), and a Lockdown visit to Montreal, Canada, in 2020-2021.  This project explores the auditory and sonic art perspectives of how cities sound without the presence of humans or the usual level of human density in popular public spaces in Belfast and a few areas in Montreal. It focuses on field recordings, soundwalking experiences, soundscape composition, and sound map contributions. Folders contain audio and images, categorised as: 1-Sounding Covid-19_Belfast-Northern Ireland <ul> <li>1-Lockdown 1 + Exit Strategies-2020</li> <li>2-Lockdown 2-2020</li> <li>3-Lockdown 3 + Exit Strategies-2021</li> <li>4-Lifted Restrictions-2022</li> </ul> 2-Sounding Covid-19_Montreal-Canada

opencc-zeroAug 2023View details →

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Biofilm formation and plasmid-mediated quinolone resistance genes at varying quinolone inhibitory concentrations in quinolone-resistant bacteria superinfecting COVID-19 inpatients

The likelihood of treatment failure in COVID-19 patients with bacterial superinfection stems from phenotypic, viz., biofilms, and genotypic mechanisms. This cross-sectional study aimed to determine the inhibitory concentrations of quinolones—nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and levofloxacin—in biofilm formers [minimum biofilm inhibitory concentration (MBIC)] and non-formers [minimum inhibitory concentration (MIC)] as well as correlate the quinolones' folds with the presence of plasmid-mediated quinolone-resistance (PMQR) genes in quinolone-resistant bacteria isolated from COVID-19 inpatients. Quinolone-resistant isolates (n=193), verified through disc diffusion, were tested for quinolone inhibitory concentrations and biofilm formation with broth microdilution and microtiter plate methods, respectively. Polymerase chain reaction was used to detect PMQR genes. MIC to MBIC median increase in folds for ciprofloxacin, ofloxacin, and levofloxacin was 128 (2-8,192), 64 (4-1,024), and 32 (4-512) in gram-positive cocci (GPC), respectively, while it was 32 (4-8,192), 32 (4-2,048), and 16 (2-1,024) in fermentative-gram-negative bacilli (F-GNB), and 16 (4-4,096), 64 (2-64), and 16 (8-512) in non-fermentative-gram-negative bacilli (NF-GNB). Biofilm-forming F-GNB (32/126) and NF-GNB (10/24) harbored qnrB [11/32 versus (vs.) 3/10], aac(6')-Ib-cr (10/32 vs. 4/10), and qnrS (9/32 vs. 0/10) genes, respectively. A 32-fold median increase in ciprofloxacin was significantly associated with qnrA and qnrS in F-GNB and NF-GNB, respectively. F-GNB and NF-GNB biofilms were significantly associated with aac(6')-Ib-cr and qnrS genes, respectively. Nearly one-third of the superinfecting bacteria in COVID-19 patients formed biofilms, and had at least one PMQR gene, increasing the need for quinolone inhibitory concentrations.

Adverse childhood events and clinical manifestation of anxiety symptoms in Greek adolescents during COVID-19 pandemic

Background: Adverse Childhood Experiences (ACEs) are linked to the development of Anxiety in Adolescence. According to recent studies, the pandemic COVID-19 is a novel ACE that has increased Anxiety among adolescents. This study aims to investigate the relationship between Adverse Childhood Experiences (ACEs) and COVID-19 in the development of Anxiety in Adolescence. Methods: A cross-sectional study with a community sample of 248 boys and girls aged 12 to 15 years (Mean: 13.50 years) from five High Schools in Eastern Attica were conducted. A total of four questionnaires were used: 1) Demographic Questionnaire, 2) State-Trait-Anxiety-Inventory for Children – STAIC, 3) Adverse Childhood Experiences Scale, and 4) COVID-19 Impact Scale. Results: The results demonstrated a strong correlation between the total number of adverse childhood experiences (ACEs) and Anxiety (Trait and State) in adolescence (Trait Anxiety: rho=.37, p0.001; State Anxiety: rho=.29, p0.001). Girls scored substantially higher on Trait Anxiety (U = 4353, p 0.001) and State Anxiety (U = 5822.5, p = 0.014) than boys. Girls also demonstrated more significant Anxiety than boys. The number of adverse childhood experiences was found to be significantly related to the impact of COVID-19 (=0.025, p 0.001). Conclusions: The present study's findings can be used to design and implement future effective, preventive, and therapeutic programs for adolescents with anxiety symptoms who were exposed to a variety of Adverse Childhood Experiences and the COVID-19 pandemic during their adolescence.

opencc-zeroAug 2023View details →

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Recognizing the importance of near-home contact with nature for mental well-being based on the COVID-19 lockdown experience

Several urban landscape planning solutions have been introduced around the world to find a balance between developing urban spaces, maintaining and restoring biodiversity, and enhancing quality of human life. Our global mini-review, combined with analysis of big data collected from Google Trends at global scale, reveals the importance of enjoying day-to-day contact with nature and engaging in such activities as nature observation and identification and gardening for the mental well-being of humans during the COVID-19 pandemic. Home-based activities, such as watching birds from one's window, identifying species of plants and animals, backyard gardening, and collecting information about nature for citizen science projects, were popular during the first lockdown in spring 2020, when people could not easily venture out of their homes. In our mini-review, we found 37 articles from 28 countries with a total sample of 114,466 people. These papers suggest that home-based engagement with nature was an entertaining and pleasant distraction that helped preserve mental well-being during a challenging time. According to Google Trends, interest in such activities increased during lockdown compared to the previous five years. Millions of people worldwide are chronically or temporarily confined to their homes and neighborhoods because of illness, childcare chores, or elderly care responsibility, which makes it difficult for them to travel far to visit such places as national parks, created through land sparing, where people go to enjoy nature and relieve stress. This article posits that for such people, living in an urban landscape designed to facilitate effortless contact with small natural areas is a more effective way to receive the mental health benefits of contact with nature than visiting a sprawling nature park on rare occasions.

Doctoral researchers Covid-19 experiences, collaborative autoethnography dataset.

Data provided here consists of the summaries of Covid 19 pandemic experiences of doctoral researchers at Brighton and Sussex Medical School under the Social Sciences for Severely Stigmatising Skin diseases (5S Foundation) in Ethiopia, Rwanda, and Sudan.  Conducting doctoral research is a challenging endeavour, a challenge which as the growing literature on the subject has shown, the COVD-19 pandemic has made even more so. For some doctoral researchers, however, the pandemic has also been accompanied by political unrest and military conflict, putting them and their networks at risk and making their research especially difficult to sustain. We have written about how we navigated doing doctoral studies during the period of the pandemic and socio-political unrest.

Defining neutralization and allostery by antibodies against COVID-19 variants

The changing landscape of mutations in the SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. A major factor that contributes to the functional activity of neutralizing antibodies are the intrinsic quaternary changes that occur as a result of antibody-Spike trimer interactions. In this study, we reveal the conformational dynamics and allosteric perturbations linked to binding of human monoclonal antibodies and the viral Spike protein. We identify epitope hotspots of known and novel antibodies, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants of concern (VoCs) on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Our comparative analyses of the antibody-footprints on Spike variants reveal how antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects. These differences have important implications for neutralization efficacy and for developing new antibodies targeting emerging variants. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19, and provide a foundation for the design of effective antiviral strategies.

Estigma en hombres homosexuales en el contexto social colombiano durante la pandemia del COVID-19

Los trastornos de salud mental (TSM) son una preocupación global que incluye condiciones como la depresión, el trastorno afectivo bipolar, la esquizofrenia y la demencia, con un impacto significativo en Colombia. La comunidad LGBT+ está especialmente en riesgo, sufriendo discriminación, estrés debido a la ocultación de su sexualidad y violencia emocional y física, lo que contribuye a una mayor prevalencia de depresión y ansiedad en esta población. El estigma ha sido identificado como uno de los principales factores que contribuyen al aumento de los TSM en esta población, afectando su salud tanto a nivel individual como social. El estigma, la discriminación y la violencia experimentadas por personas LGBT+ se acentuaron durante la pandemia de COVID-19 debido a barreras en el acceso a la atención médica y experiencias estigmatizantes. Para abordar esta problemática, se realiza una investigación con enfoque cualitativo centrada en hombres homosexuales mayores de 18 años en Colombia, analizando mediante entrevistas semiestructuradas sus experiencias de estigma, discriminación y violencia tanto antes como durante la pandemia. Para el análisis se utiliza la teoría del estrés de minorías como marco teórico para comprender estas vivencias y respaldar la formulación de políticas públicas que promueven la justicia social en el país. Las narraciones corroboran las principales categorías descritas por la teoría del estrés de minorías. Es fundamental generar evidencia científica que tenga en cuenta las características socio estructurales de Colombia y brinde apoyo a esta comunidad vulnerable, buscando mejorar su bienestar social y psicológico en un contexto desafiante.

opencc-by-4.0Jan 2023View details →

COVID-19 vaccination single cell datasets

The datasets presented here comprise the sequencing data featured in the research paper titled: "Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection": https://www.nature.com/articles/s41590-023-01608-9 Peripheral Blood Mononuclear Cell (PBMC) samples utilized for both CITE-seq and ASAP-seq were systematically collected at four distinct time intervals: <ul> <li>Pre-vaccination (Day 0)</li> <li>Post-primary vaccination (Day 2 and Day 10.</li> <li>Seven days post-boost vaccination (Day 28).</li> </ul> The count matrix folder contains count matrices for each experimental type, specifically CITE-seq, ASAP-seq, and ECCITE-seq. In addition, we have included the fully integrated, processed Seurat objects for downstream analysis. Details of the content within the count matrix folder are as follows: <ul> <li>The RNA, ATAC, and TCR modality outputs were generated using the 10x Cellranger pipeline.</li> <li>HTO and ADT modalities were mapped with Alevin.</li> </ul> Outlined below are the three processed single-cell datasets: <ol> <li>PBMC_vaccine_CITE.rds: 3' RNA and surface proteins (173 TotalSeq-A antibodies)</li> <li>PBMC_vaccine_ASAP.rds: Chromatin accessibility and surface proteins (173 TotalSeq-A antibodies)</li> <li>PBMC_vaccine_ECCITE_TCR.rds: 5' RNA, surface proteins (137 TotalSeq-C antibodies), TCR and dextramer loaded with peptides of SARS-CoV-2 spike protein.</li> </ol> <ul> <li>antigen_module_genes.rds: This file contains the vaccine-induced gene sets.</li> <li>antigen_module_peaks.rds: This file contains the DE peaks specific for vaccine-induced cells. </li> </ul> To map the scRNA-seq query dataset onto our CITE-seq reference: <pre><code>library(Seurat) PBMC_CITE <- readRDS("/zenedo/PBMC_vaccine_CITE.rds") query_scRNA <- readRDS("/home/xx/your_own_data.rds") anchors <- FindTransferAnchors( reference = PBMC_CITE, query = query_scRNA, normalization.method = "SCT", k.anchor = 5, reference.reduction = "spca", dims = 1:50) query_scRNA <- MapQuery( anchorset = anchors, query = query_scRNA, reference = PBMC_CITE, refdata = list( l1 = "celltypel1", l2 = "celltypel2", l3 = "celltypel3"), reference.reduction = "spca", reduction.model = "wnn.umap") </code></pre> To use the scATAC-seq data, please run the commands below to update the path of the fragment file for the object.   <pre><code>Vaccine_ASAP <- readRDS("PBMC_vaccine_ASAP.rds") # remove fragment file information Fragments(Vaccine_ASAP) <- NULL # Update the path of the fragment file Fragments(Vaccine_ASAP) <- CreateFragmentObject(path = "download/PBMC_vaccine_ASAP_fragments.tsv.gz", cells = Cells(Vaccine_ASAP))</code></pre>

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Estimation of non-health Gross Domestic Product (NHGDP) loss due to COVID-19 deaths in West Bengal, India

This study estimates the economic losses (GDP), particularly the impact of COVID-19 deaths on non-health components of GDP in West Bengal state. The NHGDP losses were evaluated using cost-of-illness approach. Future NHGDP losses were discounted at 3%. Excess death estimates by the World Health Organisation (WHO) and Global Burden of Disease (GBD) were used. Sensitivity analysis was carried out by varying discount rates and Average Age of Death (AAD). 21,532 deaths in West Bengal since 17th March 2020 till 31st December 2022 decreased the future NHGDP by $0.92 billion. Nearly 90% of loss was due to deaths occurring in above 30 years age-group. The majority of the loss was borne among the 46–60 years age-group. The NHGDP loss/death was $42,646, however, the average loss/death declined with a rise in age. The loss increased to $9.38 billion and $9.42 billion respectively based on GBD and WHO excess death estimates. The loss increased to $1.3 billion by considering the lower age of the interval as AAD. At 5% and 10% discount rates, the losses reduced to $0.769 billion and $0.549 billion respectively. Results from the study suggest that COVID-19 contributed to major economic loss in West Bengal. The mortality and morbidity caused by COVID-19, the substantial economic costs at individual and population levels in West Bengal, and probably across India and other countries, is another argument for better infection control strategies across the globe to end the impact of this epidemic.

opencc-zeroSep 2023View details →

Factors associated with work engagement of nurses during the fifth wave of the COVID-19 pandemic in Japan: Web-based cross-sectional study

A cross-sectional survey using Google Form was conducted in a target population of 400 nurses working in acute care and psychiatric institutions in Chiba and Tokyo prefectures, Japan. A total of 209 nurses participated in the study. Of these participants, 25 participants with missing survey items were excluded, resulting in a final sample of 184 participants (valid response rate: 46.0%). The survey was conducted from August 8 to September 30, 2021, during the “fifth wave” of the COVID-19 pandemic, when the number of positive cases was increasing.

Raw data for manuscript: Use of immunology in news and YouTube videos in the context of COVID-19: politicization and information bubbles

Coding of newsarticles and videos related to immunology and COVID-19 in Italian and English