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The following results are related to COVID-19. Are you interested to view more results? Visit OpenAIRE - Explore.
39,452 Research products, page 1 of 3,946

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  • Open Access English
    Authors: 
    de Bock, Ellen; Herman, Eline S.; Bastian, Okan W.; Filipe, Mando D.; Vriens, Menno R.; Richir, Milan C.;

    Background: To provide for Coronavirus Disease 2019 (COVID-19) healthcare capacity, (surgical oncology) guidelines were established, forcing to alter the timing of performing surgical procedures. It is essential to determine whether these guidelines have led to disease progression. This study aims to give an insight into the number of surgical oncology procedures performed during the pandemic and provide information on short-term clinical outcomes. Materials and methods: A systematic literature search was performed on all COVID-19 articles including operated patients, published before March 21, 2022. Meta-analysis was performed to visualize the number of performed surgical oncology procedures during the pandemic compared to the pre-pandemic period. Random effects models were used for evaluating short-term clinical outcomes. Results: Twenty-four studies containing 6762 patients who underwent a surgical oncology procedure during the pandemic were included. The number of performed surgical procedures for an oncological pathology decreased (−26.4%) during the pandemic. The number of performed surgical procedures for breast cancer remained stable (+0.3%). Moreover, no difference was identified in the number of ≥T2 (OR 1.00, P = 0.989), ≥T3 (OR 0.95, P = 0.778), ≥N1 (OR 1.01, P = 0.964) and major postoperative complications (OR 1.55, P = 0.134) during the pandemic. Conclusion: The number of performed surgical oncology procedures during the COVID-19 pandemic decreased. In addition, the number of performed surgical breast cancer procedures remained stable. Oncological staging and major postoperative complications showed no significant difference compared to pre-pandemic practice. During future pandemics, the performed surgical oncology practice during the first wave of the COVID-19 pandemic seems appropriate for short-term results.

  • Open Access English
    Authors: 
    Norddahl, Gudmundur L.; Melsted, Páll; Gunnarsdottir, Kristbjorg; Halldórsson, Gísli Hreinn; Olafsdottir, Thorunn; Gylfason, Arnaldur; Kristjánsson, Már; Magnusson, Olafur T.; sulem, patrick; Gudbjartsson, Daniel Fannar; +3 more
    Country: Iceland

    By the end of July 2021, the majority of the Icelandic population had received vaccination against COVID-19. In mid-July a wave of SARS-CoV-2 infections, dominated by the Delta variant, spread through the population, followed by an Omicron wave in December. A booster vaccination campaign was initiated to curb the spread of the virus. We estimate the risk of infection for different vaccine combinations using vaccination data from 276,028 persons and 963,557 qPCR tests for 277,687 persons. We measure anti-Spike-RBD antibody levels and ACE2-Spike binding inhibitory activity in 371 persons who received one of four recommended vaccination schedules with or without an mRNA vaccine booster. Overall, we find different antibody levels and inhibitory activity in recommended vaccination schedules, reflected in the observed risk of SARS-CoV-2 infections. We observe an increased protection following mRNA boosters, against both Omicron and Delta variant infections, although BNT162b2 boosters provide greater protection against Omicron than mRNA-1273 boosters. Publisher Copyright: © 2022, The Author(s). Peer reviewed

  • Open Access French
    Authors: 
    Astruc, Lisa; Lemaire, Emilie; Golaz, Valérie; Gastineau, Bénédicte;
    Country: France

    Comme lors de la première vague épidémique de Covid-19 en 2020, les communications du Ministère de la santé et la presse nous alertent sur le fait que les hôpitaux de France sont saturés ou sur le point de l’être. Dans plusieurs régions françaises, des opérations chirurgicales sont déprogrammées. Les soignants, remobilisés même lorsqu’ils sont malades, montrent des signes d’épuisement, voire se mettent en grève. Que savons-nous de la tension hospitalière ? L’objectif de cette note est de clarifier la manière dont elle est mesurée, de clarifier comment l’indicateur de tension hospitalière est construit, à partir de l’analyse de ses tendances nationales et régionales. Cela nous amène à mettre en lumière le rôle de cet indicateur dans les politiques mises en place en période épidémique. Pour cela, nous allons aborder quatre questions. Comment a évolué la tension hospitalière depuis le début de la pandémie ? Connait-elle de grandes disparités régionales ? Comment la tension hospitalière est-elle calculée ? Que ne dit pas cet indicateur de tension hospitalière ?

  • Open Access
    Authors: 
    oishee-hoque;
    Publisher: Zenodo

    No description provided.

  • Open Access
    Authors: 
    Davoodi Monfared, Mansoor; Senapati, Abhishek; Mertel, Adam; Schlechte-Welnicz, Weronika; Calabrese, Justin;
    Publisher: Rodare

    Codes for "Optimal workplace occupancy strategies during the COVID-19 pandemic"

  • Research software . 2022
    Open Access
    Authors: 
    O'Neil, Shawn; Beasley, William Howard;
    Publisher: Zenodo

    Research with the National COVID Cohort Collaborative (N3C)

  • Research software . 2022
    Open Access
    Authors: 
    O'Neil, Shawn; Beasley, William Howard;
    Publisher: Zenodo

    Research with the National COVID Cohort Collaborative (N3C) If you use this software, please cite it as below

  • Open Access
    Authors: 
    Leaman, Robert;
    Publisher: Zenodo

    A significant percentage of COVID-19 survivors experience ongoing multisystemic symptoms that often affect daily living, a condition known as Long Covid or post-acute-sequelae of SARS-CoV-2 infection. However, identifying scientific articles relevant to Long Covid is challenging since there is no standardized or consensus terminology. We developed an iterative human-in-the-loop machine learning framework combining data programming with active learning into a robust ensemble model, demonstrating higher specificity and considerably higher sensitivity than other methods. This dataset contains the source code (python and shell scripts) used to create the Long Covid collection, along with a snapshot of processed data and predictions. This research was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health.

  • Open Access
    Authors: 
    Kikstra, Jarmo S.;
    Publisher: Zenodo

    This repository contains data for the main text figures plus some supplementary information in the pre-print: Kikstra et al., 2022, GMD, "The IPCC Sixth Assessment Report WGIII climate assessment of mitigation pathways: from emissions to global temperatures" DOI: tbd This work should be cited as: Kikstra et al. (2022). Scripts for climate mitigation scenarios with persistent COVID-19 related energy demand changes. DOI: 10.5281/zenodo.6610604. The data that these scripts use need to be downloaded from the AR6 and SR15 Scenario Database hosted by IIASA. N.B. the used input data files cannot be rehosted due to the AR6 and SR15 scenario database licenses. In future versions the input data will be simplified to use the specific download file format of the scenario explorer. The scenarios that were used for the IPCC Sixth Assessment Report, Working Group III contribution on Climate Change Mitigation (AR6 WGIII) have been made available at https://data.ene.iiasa.ac.at/ar6. The scenarios that were used for the IPCC Special Report on 1.5C warming (SR1.5) have been made available at https://data.ece.iiasa.ac.at/iamc-1.5c-explorer/. Questions Please send any questions to kikstra@iiasa.ac.at

  • Open Access
    Authors: 
    Katherine Eaton;
    Publisher: Zenodo

    v0.6.0 Notes This is a major release that includes the following changes: Detection of all recombinants in Nextclade dataset 2022-10-27: XA to XBE. Implementation of recombinant sublineages (ex. XBB.1). Implementation of immune-related statistics (rbd_level, immune_escape, ace2_binding) from nextclade, the Nextstrain team, and Jesse Bloom's group: https://github.com/nextstrain/ncov/blob/master/defaults/rbd_levels.yaml https://jbloomlab.github.io/SARS-CoV-2-RBD_DMS_Omicron/epistatic-shifts/ https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/ https://doi.org/10.1093/ve/veac021 https://doi.org/10.1101/2022.09.15.507787 https://doi.org/10.1101/2022.09.20.508745 Dataset Issue #168: NULL collection dates and NULL country is implemented. controls was updated to in include 1 strain from XBB for a total of 22 positive controls. The 28 negative controls were unchanged from v0.5.1. controls-gisaid strain list was updated to include XA through to XBE for a total of 528 positive controls. This includes sublineages such as XBB.1 and XBB.1.2 which synchronizes with Nextclade Dataset 2022-10-19. The 187 negatives controls were unchanged from v0.5.1. Nextclade Issue #176: Upgrade Nextclade dataset to tag 2022-10-27 and upgrade Nextclade to v2.8.0. Issue #193: Use the nextclade dataset sars-cov-2-21L to calculate immune_escape and ace2_binding. RBD Levels Issue #193: Create new rule rbd_levels to calculate the number of key receptor binding domain (RBD) mutations. Lineage Tree Issue #185: Use nextclade dataset Auspice tree for lineage hierarchy. Previously, the phylogeny of lineages was constructed from the cov-lineages website YAML. Instead, we now use the tree provided with nextclade datasets, to better synchronize the lineage model with the output. Rather than creating the output tree in resources/lineages.nwk, the lineage tree will output to data/sars-cov-2_<DATE>/tree.nwk. This is because different builds might use different nextclade datasets, and so are dataset specific output. sc2rf Issue #179: Fix bug where sc2rf/recombinants.ansi.txt is truncated. Issue #180: Fix recombinant sublineages (ex. XAY.1) missing their derived mutations in the cov-spectrum_query. Previously, the cov-spectrum_query mutations were only based on the parental alleles (before recombination). This led to sublinaeges (ex. XAY.1, XAY.2) all having the exact same query. Now, the cov-spectrum_query will include all substitutions shared between all sequences in the cluster_id. Issue #187: Document bug that occurs if duplicate sequences are present, and the initial validation was skipped by not running scripts/create_profile.sh. Issue #191 and Issue #192: Reduce false positives by ensuring that each mode of sc2rf has at least one additional parental population that serves as the alternative hypothesis. Issue #195: Implement a filter on the ratio of intermissions to alleles. Sequences will be marked as false positives if the number of intermissions (i.e. alleles that conflict with the identified parental region) is greater than or equal to the number of alleles contributed by the minor parent. This ratio indicates that there is more evidence that conflicts with recombination than there is allele evidence that supports a recombinant origin. Linelist Issue #183: Recombinant sublineages. When nextclade calls a lineage (ex. XAY.1) which is a sublineage of a sc2rf lineage (XAY), we prioritize the nextclade assignment. Issue #193: Add immune-related statistics: rbd_levels, rbd_substitutions, immune_escape, and ace2_binding. Plot Issue #57: Include substitutions within breakpoint intervals for breakpoint plots. This is a product of Issue #180 which provides access to all substitutions. Issue #112: Fix bug where breakpoints plot image was out of bounds. Issue #188: Remove the breakpoints distribution axis (ex. breakpoints_clade.png) in favor of putting the legend at the top. This significant reduces plotting issues (ex. Issue #112). Issue #193: Create new plot rbd_level. Validate Designated Lineages Issue #85: XAY, updated controls Issue #178: XAY.1 Issue #172: XBB.1 Issue #175: XBB.1.1 Issue #184: XBB.1.2 Issue #173: XBB.2 Issue #174: XBB.3 Issue #181: XBC.1 Issue #182: XBC.2 Issue #171: XBD Issue #177: XBE Proposed Lineages Issue #198: proposed1229 Issue #199: proposed1268 Issue #197: proposed1296 Commits 2506e907 docs: update changelog and add v0.6.0 testing summary package 0cc421e0 docs: update all contributors cd9b6cbb resources: update issues 0fa2e3c1 docs: update readme 375c3a76 resources: add proposed lineages for #197 #198 #199 dad989e7 param: remove BQ.1 from sc2rf mode VOC as its too close to BA.5.3 d7cb005f docs: update issue template lineage-validation 1beac97e resources: add XBF to curated breakpoints for #196 fae7bfdb script: sc2rf implement intermission allele ratio for #195 89a41265 script: additional manual curation of lineage_tree ebd3ce1f resources: update validation strains for controls-gisaid d8bff572 script: add RBD Level slide to report c1879c1d script: catch errors in rbd_level plotting with no recombinants 63545a08 script: fix bug in linelist with cluster_privates c24a7179 resources: update issues d32d557f docs: update development notes 7f825a41 script: manual fix for CK in lineage_tree fdd6f66d workflow: implement rbd levels for #193 0058dd6e param: upgrade nextclade dataset to 2022-10-27 and reduce breakpoints of XA mode fb062c32 env: upgrade nextclade to v2.8.0 See CHANGELOG.md for additional commits.