OxCOVID19 Database, a multimodal data repository for better understanding the global impact of COVID-19.
Ontology highlight
ABSTRACT:
SUBMITTER: Mahdi A
PROVIDER: S-EPMC8084933 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Purpose: This study aims to characterize the early innate and adaptive responses induced by SARS-CoV-2 infection in children and adults over time up to 8 weeks post symptoms onset (POS). We report the gene signature of COVID-19 over the course of the disease in both age groups. The kinetic of infection was divided in 5-time intervals according to the calculated days POS: interval 1 (0-5), interval 2 (6-14), interval 3 (15-22), interval 4 (23-35), and interval 5 (36-81). Methods: RNA extraction was performed automatically via the PAXgene Blood miRNA Kit and the QIAcube instrument (Qiagen) following the manufacturer’s protocol. RNA concentration and quality were assessed by using the Qubit instrument (Invitrogen) and the Agilent 2100 Bioanalyzer, respectively. The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation with 100 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM for clustering and sequenced on an Illumina HiSeq 4000 sequencer for a minimum of 30 million single-end 100 reads per sample. Main results: (I) we observed an antiviral-IFN-signature and innate-cell-activation within the first 5 days post symptoms onset (POS), while genes associated with CD4 T-cell responses, plasma cells and immunoglobulin were upregulated in both age groups during the first two weeks POS, indicative of SARS-CoV-2-specific adaptive immune responses; (II) in adults, genes associated with IFN antiviral responses and activated dendritic cells were maintained during the second week of disease, and subsided only after 14 days. By contrast, those transcriptome changes subsided already after 5 days in children.
2021-09-22 | GSE166190 | GEO
Project description:Spiders are a highly diversified group of arthropods and play an important role in terrestrial ecosystems as ubiquitous predators, which makes them a suitable group to test a variety of eco-evolutionary hypotheses. For this purpose, knowledge of a diverse range of species traits is required. Until now, data on spider traits have been scattered across thousands of publications produced for over two centuries and written in diverse languages. To facilitate access to such data, we developed an online database for archiving and accessing spider traits at a global scale. The database has been designed to accommodate a great variety of traits (e.g. ecological, behavioural and morphological) measured at individual, species or higher taxonomic levels. Records are accompanied by extensive metadata (e.g. location and method). The database is curated by an expert team, regularly updated and open to any user. A future goal of the growing database is to include all published and unpublished data on spider traits provided by experts worldwide and to facilitate broad cross-taxon assays in functional ecology and comparative biology. Database URL:https://spidertraits.sci.muni.cz/.
| S-EPMC8517500 | biostudies-literature
Project description:International scientific collaborations have always been regarded as critical actions to address global pandemics, however, there was an obvious uncertainty between international collaboration and the COVID-19 control. We aim to combine digital data-based strategies to produce meaningful and advanced insights into the imbalance between COVID-19 and international collaboration, as well as reveal possible influencing factors, and ultimately enhance global collaboration. We conducted three retrospective cohort studies using respectively COVID-19 data from WHO, a complete dataset of scientific publications on coronavirus-related research from WoS, and daily data from Google Trends (GT). The results of geovisualization and spatiotemporal analysis revealed that the global COVID19 pandemic still remains serious. The global issue of imbalance between international collaborations and pandemic does exit, and the nations with good pandemic control had their own characteristics in above-mentioned correlation. Digital epidemiology provides, at least in part, evidence-based assessment and scientific advice to understand the imbalance between international collaborations and COVID-19. Our investigation demonstrates that transdisciplinary conversation through digital data-based strategies can help us fully understand the complex factors influencing the effectiveness of international scientific collaboration, thus facilitating the global response to COVID-19.
| S-EPMC8016224 | biostudies-literature
Project description:In response to the unprecedented global healthcare crisis of the COVID-19 pandemic, the scientific community has joined forces to tackle the challenges and prepare for future pandemics. Multiple modalities of data have been investigated to understand the nature of COVID-19. In this paper, MIDRC investigators present an overview of the state-of-the-art development of multimodal machine learning for COVID-19 and model assessment considerations for future studies. We begin with a discussion of the lessons learned from radiogenomic studies for cancer diagnosis. We then summarize the multi-modality COVID-19 data investigated in the literature including symptoms and other clinical data, laboratory tests, imaging, pathology, physiology, and other omics data. Publicly available multimodal COVID-19 data provided by MIDRC and other sources are summarized. After an overview of machine learning developments using multimodal data for COVID-19, we present our perspectives on the future development of multimodal machine learning models for COVID-19.
| S-EPMC10362086 | biostudies-literature
Project description:The COVID-19 pandemic is producing significant economic and social cost globally. As a cure or a treatment is yet unavailable, social distancing is considered the key way to prevent it. Mobility restrictions and confinement measures implemented across the world are considered to help reduce air pollution. However, empirical examination of the link between public mobility changes and air pollution during the COVID-19 period remains unavailable. This paper examines the short and long run impacts of mobility changes on carbon monoxide (CO) emissions by employing three dynamic estimators on a panel of 35 countries covering daily data from 15 February to April 17, 2020 - a period when most countries went into strict lockdowns. Findings show a consistent evidence at the all-countries level and across regions that long-run indoor mobility increases reduce CO emissions, while outdoor mobility increases across places such as transit stations, workplaces, grocery & pharmacies, retail & recreation, and parks drive up emissions. Among the regions studied, Europe excluding the EU and the UK (-8.4%), followed by East Asia and the Pacific (-4.3%), sees a larger emissions reduction from increased indoor mobility. While short-run effects are limited in general, emissions in US-Canada respond to indoor and outdoor mobility changes in both the short (1.1%) and long run (-1.4%). Findings overall indicate that reducing unnecessary outdoor mobility could help in maintaining air quality in the post-pandemic world.
| S-EPMC8570089 | biostudies-literature
Project description:MotivationThe Cellular Phenotype Database (CPD) is a repository for data derived from high-throughput systems microscopy studies. The aims of this resource are: (i) to provide easy access to cellular phenotype and molecular localization data for the broader research community; (ii) to facilitate integration of independent phenotypic studies by means of data aggregation techniques, including use of an ontology and (iii) to facilitate development of analytical methods in this field.ResultsIn this article we present CPD, its data structure and user interface, propose a minimal set of information describing RNA interference experiments, and suggest a generic schema for management and aggregation of outputs from phenotypic or molecular localization experiments. The database has a flexible structure for management of data from heterogeneous sources of systems microscopy experimental outputs generated by a variety of protocols and technologies and can be queried by gene, reagent, gene attribute, study keywords, phenotype or ontology terms.Availability and implementationCPD is developed as part of the Systems Microscopy Network of Excellence and is accessible at http://www.ebi.ac.uk/fg/sym.Contactjes@ebi.ac.uk or ugis@ebi.ac.ukSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4528631 | biostudies-literature
Project description:BackgroundThere is concern that the COVID-19 pandemic has damaged global childhood tuberculosis management. Quantifying changes in childhood tuberculosis notifications could support more targeted interventions to restore childhood tuberculosis services. We aimed to use time-series modelling to evaluate the impact of COVID-19 on child tuberculosis notifications.MethodsAnnual tuberculosis case notification data reported to WHO by 215 countries were used to calculate annual notification counts for the years 2014-20, stratified by age groups (0-4, 5-14, and ≥15 years) and sex. We used time-series modelling to predict notification counts for 2020, and calculated differences between these predictions and observed notifications in 2020 for each of the six WHO regions and at the country level for 30 countries with high tuberculosis burden. We assessed associations between these differences and the COVID-19 stringency index, a measure of COVID-19 social impact.FindingsFrom 2014 to 2019, annual tuberculosis notification counts increased across all age groups and WHO regions. More males than females in the 0-4 years age group and ≥15 years age group had notifications in all years from 2014 to 2020 and in all WHO regions. In the 5-14 years age group, more females than males were notified globally in all years, although some WHO regions had higher notifications from males than females. In 2020, global notifications were 35·4% lower than predicted (95% prediction interval -30·3 to -39·9; 142 525 observed vs 220 794 predicted notifications [95% prediction interval 204 509 to 237 078]) for children aged 0-4 years, 27·7% lower (-23·4 to -31·5; 256 398 vs 354 578 [334 724 to 374 431]) in children aged 5-14 years, and 18·8% lower (-15·4 to -21·9; 5 391 753 vs 6 639 547 [6 375 086 to 6 904 007]) for people aged 15 years or older. Among those aged 5-14 years, the reduction in observed relative to predicted notifications for 2020 was greater in males (-30·9% [-24·8 to -36·1]) than females (-24·5% [-18·1 to -29·9]). Among 28 countries with high tuberculosis burden, no association was observed between the stringency of COVID-19 restrictions and the relative difference in observed versus predicted notifications.InterpretationOur findings suggest that COVID-19 has substantially affected childhood tuberculosis services, with the youngest children most affected. Although children have mostly had fewer severe health consequences from COVID-19 than have adults, they have been disproportionately affected by the effects of the pandemic on tuberculosis care. Observed sex differences suggest that targeted interventions might be required. As countries rebuild health systems following the COVID-19 pandemic, it is crucial that childhood tuberculosis services are placed centrally within national strategic plans.FundingMedical Research Council.
| S-EPMC9671550 | biostudies-literature
Project description:Screening programs have been associated with a substantial reduction in colorectal cancer (CRC) mortality through endoscopic resection of preneoplastic lesions and detection of early-stage invasive cancers.
In March 2020, the World Health Organization declared as a pandemic the outbreak of coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2. Since then, the SARS-CoV-2 have never stopped spreading, causing an unprecedented situation with highly restrictive considerations to be adopted by the majority of countries worldwide.
Health-care facilities have been making an enormous effort to assist patients affected by COVID-19, while adopting measures to maintain a safe environment for patients and healthcare professionals. As a result, the usual workflow in endoscopy departments changed dramatically, leading to an increase in cancelled procedures, probably increasing the future burden of Colorectal Cancer due to delays in diagnosis.
| 2358399 | ecrin-mdr-crc
Project description:The COVID-19 pandemic has sparked unprecedented public health and social measures (PHSM) by national and local governments, including border restrictions, school closures, mandatory facemask use and stay at home orders. Quantifying the effectiveness of these interventions in reducing disease transmission is key to rational policy making in response to the current and future pandemics. In order to estimate the effectiveness of these interventions, detailed descriptions of their timelines, scale and scope are needed. The Health Intervention Tracking for COVID-19 (HIT-COVID) is a curated and standardized global database that catalogues the implementation and relaxation of COVID-19 related PHSM. With a team of over 200 volunteer contributors, we assembled policy timelines for a range of key PHSM aimed at reducing COVID-19 risk for the national and first administrative levels (e.g. provinces and states) globally, including details such as the degree of implementation and targeted populations. We continue to maintain and adapt this database to the changing COVID-19 landscape so it can serve as a resource for researchers and policymakers alike.
| S-EPMC7453020 | biostudies-literature
Project description:To prevent the outbreak of the Coronavirus disease (COVID-19), many countries around the world went into lockdown and imposed unprecedented containment measures. These restrictions progressively produced changes to social behavior and global mobility patterns, evidently disrupting social and economic activities. Here, using maritime traffic data collected via a global network of Automatic Identification System (AIS) receivers, we analyze the effects that the COVID-19 pandemic and containment measures had on the shipping industry, which accounts alone for more than 80% of the world trade. We rely on multiple data-driven maritime mobility indexes to quantitatively assess ship mobility in a given unit of time. The mobility analysis here presented has a worldwide extent and is based on the computation of: Cumulative Navigated Miles (CNM) of all ships reporting their position and navigational status via AIS, number of active and idle ships, and fleet average speed. To highlight significant changes in shipping routes and operational patterns, we also compute and compare global and local vessel density maps. We compare 2020 mobility levels to those of previous years assuming that an unchanged growth rate would have been achieved, if not for COVID-19. Following the outbreak, we find an unprecedented drop in maritime mobility, across all categories of commercial shipping. With few exceptions, a generally reduced activity is observable from March to June 2020, when the most severe restrictions were in force. We quantify a variation of mobility between -5.62 and -13.77% for container ships, between +2.28 and -3.32% for dry bulk, between -0.22 and -9.27% for wet bulk, and between -19.57 and -42.77% for passenger traffic. The presented study is unprecedented for the uniqueness and completeness of the employed AIS dataset, which comprises a trillion AIS messages broadcast worldwide by 50,000 ships, a figure that closely parallels the documented size of the world merchant fleet.
| S-EPMC8433355 | biostudies-literature