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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jonathan Gray; maxalbert; James Harrison; Thingus; +8 Authors

    Changed Upgraded Python dependencies What's Changed Bump deps by @jc-harrison in https://github.com/Flowminder/FlowKit/pull/6442 Release 1.21.1 by @jc-harrison in https://github.com/Flowminder/FlowKit/pull/6443 Bump cryptography from 41.0.7 to 42.0.0 in /flowkit_jwt_generator by @dependabot in https://github.com/Flowminder/FlowKit/pull/6444 Bump cryptography from 41.0.7 to 42.0.0 in /deployment by @dependabot in https://github.com/Flowminder/FlowKit/pull/6446 Full Changelog: https://github.com/Flowminder/FlowKit/compare/1.21.0...1.21.1

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      ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Kuzmin Alexander; Orekhov Philipp; Astashkin Roman; Gordeliy Valentin; +1 Authors

    The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of 1) unmodified (NoPTM_POPC_Martini3b: 0.5 & 2.5 μs); 2) palmitoylated (CYSP40, CYSP43, CYSP 44, CYSP40/43, CYSP 40/44, CYSP 43/44, CYSP40/43/44_POPC_Martini3b: 0.5 μs); 3) glycosylated (ASNG66: 0.5 μs) SARS-CoV-2 E protein in the monomeric form in a POPC bilayer. The trajectories of CG MD (TMD;H2H3_NoPTM_POPC_Martini3b: 0.5 μs) of systems containing artificial proteins consisting of only transmembrane domain (TMD) or only cytoplasmic domain (H2H3) in a POPC bilayer. The trajectory of CG MD (4xNoPTM_POPC_Martini3b: 0.5 mks) of the system containing 4 proteins with centers of mass fixed in the plane of the POPC bilayer (XY). The trajectories of CG MD of systems containing 2 proteins in the membranes buckled in a single direction (CurvedMembrane1;2X_2xNoPTM_POPC_Martini3b: 1 μs) and in the membrane buckled in both directions (CurvedMembraneXY_2xNoPTM_POPC_Martini3b: 1 μs). Simulations have been performed using the beta version of Martini 3 (CG) force field, running with the GROMACS 2020.1 under the conditions reported in bioRxiv 2021.03.10.434722.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Claudio, Kleucio; Thomazini, Luis Fernando Viviani; Silva-Santos, Carlos Henrique da; Sasaki, Eduardo Noboru;

    Correlations in pandemic world are calculated between Covid-19 deaths and ABO/Rh blood groups. The initial results from this code are shown in SSRN: ABO/Rh Blood Groups and COVID-19: Temporal Analyses Point Out Rh-negative with the Greatest Correlations. Studies from temporal analyzes suggest COVID-19 pandemic characterization parameters. Current results (2022) has been prepared to new version of the SSRN article above.

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      ZENODO
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    Authors: Kuzmin Alexander; Orekhov Philipp; Astashkin Roman; Gordeliy Valentin; +1 Authors

    The trajectories of all-atom (AA) MD simulations (NoPTM-1;2;3;4_POPC;Mix_CHARMM36m: 0.1x3 μs) were obtained based on 4 starting representative conformations from the coarse-grained simulation (10.5281/zenodo.4740706). For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol). Simulations have been performed using the CHARMM36m (AA) force field, running with the GROMACS 2019.5 package on the supercomputer JURECA at Forschungszentrum Jülich.

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    ZENODO
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      ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jonathan Gray; maxalbert; James Harrison; Thingus; +8 Authors

    Added FlowETL sensor NRowsPresentSensor which checks for a specified minimum number of rows. Changed ForeignStagingTableOperator will now error if the underlying file cannot be read or the command returns an error. #5763 Flowmachine now requires SQLAlchemy >= 2.0.0 #6066 What's Changed Bump cryptography from 42.0.0 to 42.0.2 in /flowkit_jwt_generator by @dependabot in https://github.com/Flowminder/FlowKit/pull/6450 Bump cryptography from 42.0.0 to 42.0.2 in /deployment by @dependabot in https://github.com/Flowminder/FlowKit/pull/6453 Fix no poke by @greenape in https://github.com/Flowminder/FlowKit/pull/6448 Bump cryptography from 42.0.2 to 42.0.4 in /flowkit_jwt_generator by @dependabot in https://github.com/Flowminder/FlowKit/pull/6457 Bump cryptography from 42.0.2 to 42.0.4 in /deployment by @dependabot in https://github.com/Flowminder/FlowKit/pull/6460 Bump es5-ext from 0.10.53 to 0.10.63 in /flowauth/frontend by @dependabot in https://github.com/Flowminder/FlowKit/pull/6462 Sqlalachemy 2 by @greenape in https://github.com/Flowminder/FlowKit/pull/6461 Bump ip from 1.1.5 to 1.1.9 in /flowauth/frontend by @dependabot in https://github.com/Flowminder/FlowKit/pull/6456 Bump deps by @greenape in https://github.com/Flowminder/FlowKit/pull/6463 Unpin examples from old jupyter by @greenape in https://github.com/Flowminder/FlowKit/pull/6464 Full Changelog: https://github.com/Flowminder/FlowKit/compare/1.21.1...1.22.0

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Kuzmin Alexander; Orekhov Philipp; Astashkin Roman; Gordeliy Valentin; +1 Authors

    The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of 1) unmodified (FeigLab_NMR; FeigLab_PentamerNoPTM_POPC_Martini3b: 5 μs; 5 μs); 2) palmitoylated (FeigLab_PentamerCYSP43; PentamerCYSP44_POPC_Martini3b: 5 μs; 5 μs); SARS-CoV-2 E protein pentamer in a POPC bilayer. The trajectory of CG MD of system containing 2 pentamers in the membrane buckled in a single direction (BuckledMembrane_FeigLab_2xPentamerNoPTM_POPC_Martini3b: 1 μs). FeigLab_Pentamer: https://github.com/feiglab/sars-cov-2-proteins/blob/master/Membrane/E_protein.pdb FeigLab_NMR_Pentamer is assembled based on the transmembrane domain determined by NMR (PDB ID: 7K3G) and FeigLab model for the rest.

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    Authors: Kleucio Claudio; noboru-sasaki;

    This is the version v0.3 of Temporal Analysis about correlations between blood groups (ABO, Rh) and Covid-19. The initial results from this code considering total cumulative deaths are shown in SSRN: http://dx.doi.org/10.2139/ssrn.3794044. A new structure was implemented, where the R/ folder contains the source code, Data/ contains country data on blood types and number of deaths and others, the Tests/ folder contains compressed files with the first results (08/2020) and the latest results from 02/2024, configuration files for simulations and scripts for installing dependencies. Refactoring and other advancements have been made, including using weekly data from 2024 owid-covid-data.

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    Authors: Claudio, Kleucio; Thomazini, Luis Fernando Viviani; Silva-Santos, Carlos Henrique da; Sasaki, Eduardo Noboru;

    Correlations in pandemic world are calculated between Covid-19 and ABO/Rh blood groups. The initial results from this code are shown in SSRN: ABO/Rh Blood Groups and COVID-19: Temporal Analyses Point Out Rh-negative with the Greatest Correlations . The code was implemented in R and the main file is TemporalAnalysis.R. The results are saved in the directory: Results(date of analysis)/ . The first version v0.0 has automatically downloaded data file from Our World in Data: https://github.com/owid/covid-19-data/raw/master/public/data/owid-covid-data.csv . Refactoring and others advances has been in progress. R programming was used in a structured language manner. Better practices of R programming language maybe implemented in the future. Current results (2022) has been prepared to new version of the SSRN article above. The PCA analysis is incomplete, but the preliminary results were consistent with correlations.

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    Authors: Claudio, K.; Thomazini, L.F.V.; Silva-Santos, C. H.; Sasaki, E. N.;

    This is the version v0.3 of Temporal Analysis about correlations between blood groups (ABO, Rh) and Covid-19. The initial results from this code considering total cumulative deaths are shown in SSRN: http://dx.doi.org/10.2139/ssrn.3794044. A new structure was implemented, where the R/ folder contains the source code, Data/ contains country data on blood types, number of deaths and others, the Tests/ folder contains compressed files with the first results (08/2020) and the latest results from 02/2024, configuration files for simulations and scripts for installing dependencies. Refactoring and other advancements have been made, including using weekly data from 2024 owid-covid-data.

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    Authors: Claudio, Kleucio; Thomazini, Luis Fernando Viviani; Silva-Santos, Carlos Henrique da; Sasaki, Eduardo Noboru;

    This is the version v0.2 of Temporal Analysis about correlations between ABO groups and Covid-19. The analyses of correlations between ABO groups and total deaths per million (tdpm) were added. The initial results from this code considering total cumulative deaths are shown in SSRN: http://dx.doi.org/10.2139/ssrn.3794044. In this version are included a file to configure simulations: conf-options.R. Some refactorings were done like changing filenames and new functions were created. Statistical interpretation of analyses from tdpm should take into account the normality and p-values.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jonathan Gray; maxalbert; James Harrison; Thingus; +8 Authors

    Changed Upgraded Python dependencies What's Changed Bump deps by @jc-harrison in https://github.com/Flowminder/FlowKit/pull/6442 Release 1.21.1 by @jc-harrison in https://github.com/Flowminder/FlowKit/pull/6443 Bump cryptography from 41.0.7 to 42.0.0 in /flowkit_jwt_generator by @dependabot in https://github.com/Flowminder/FlowKit/pull/6444 Bump cryptography from 41.0.7 to 42.0.0 in /deployment by @dependabot in https://github.com/Flowminder/FlowKit/pull/6446 Full Changelog: https://github.com/Flowminder/FlowKit/compare/1.21.0...1.21.1

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    Authors: Kuzmin Alexander; Orekhov Philipp; Astashkin Roman; Gordeliy Valentin; +1 Authors

    The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of 1) unmodified (NoPTM_POPC_Martini3b: 0.5 & 2.5 μs); 2) palmitoylated (CYSP40, CYSP43, CYSP 44, CYSP40/43, CYSP 40/44, CYSP 43/44, CYSP40/43/44_POPC_Martini3b: 0.5 μs); 3) glycosylated (ASNG66: 0.5 μs) SARS-CoV-2 E protein in the monomeric form in a POPC bilayer. The trajectories of CG MD (TMD;H2H3_NoPTM_POPC_Martini3b: 0.5 μs) of systems containing artificial proteins consisting of only transmembrane domain (TMD) or only cytoplasmic domain (H2H3) in a POPC bilayer. The trajectory of CG MD (4xNoPTM_POPC_Martini3b: 0.5 mks) of the system containing 4 proteins with centers of mass fixed in the plane of the POPC bilayer (XY). The trajectories of CG MD of systems containing 2 proteins in the membranes buckled in a single direction (CurvedMembrane1;2X_2xNoPTM_POPC_Martini3b: 1 μs) and in the membrane buckled in both directions (CurvedMembraneXY_2xNoPTM_POPC_Martini3b: 1 μs). Simulations have been performed using the beta version of Martini 3 (CG) force field, running with the GROMACS 2020.1 under the conditions reported in bioRxiv 2021.03.10.434722.

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    Authors: Claudio, Kleucio; Thomazini, Luis Fernando Viviani; Silva-Santos, Carlos Henrique da; Sasaki, Eduardo Noboru;

    Correlations in pandemic world are calculated between Covid-19 deaths and ABO/Rh blood groups. The initial results from this code are shown in SSRN: ABO/Rh Blood Groups and COVID-19: Temporal Analyses Point Out Rh-negative with the Greatest Correlations. Studies from temporal analyzes suggest COVID-19 pandemic characterization parameters. Current results (2022) has been prepared to new version of the SSRN article above.

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    Authors: Kuzmin Alexander; Orekhov Philipp; Astashkin Roman; Gordeliy Valentin; +1 Authors

    The trajectories of all-atom (AA) MD simulations (NoPTM-1;2;3;4_POPC;Mix_CHARMM36m: 0.1x3 μs) were obtained based on 4 starting representative conformations from the coarse-grained simulation (10.5281/zenodo.4740706). For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol). Simulations have been performed using the CHARMM36m (AA) force field, running with the GROMACS 2019.5 package on the supercomputer JURECA at Forschungszentrum Jülich.

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    Authors: Jonathan Gray; maxalbert; James Harrison; Thingus; +8 Authors

    Added FlowETL sensor NRowsPresentSensor which checks for a specified minimum number of rows. Changed ForeignStagingTableOperator will now error if the underlying file cannot be read or the command returns an error. #5763 Flowmachine now requires SQLAlchemy >= 2.0.0 #6066 What's Changed Bump cryptography from 42.0.0 to 42.0.2 in /flowkit_jwt_generator by @dependabot in https://github.com/Flowminder/FlowKit/pull/6450 Bump cryptography from 42.0.0 to 42.0.2 in /deployment by @dependabot in https://github.com/Flowminder/FlowKit/pull/6453 Fix no poke by @greenape in https://github.com/Flowminder/FlowKit/pull/6448 Bump cryptography from 42.0.2 to 42.0.4 in /flowkit_jwt_generator by @dependabot in https://github.com/Flowminder/FlowKit/pull/6457 Bump cryptography from 42.0.2 to 42.0.4 in /deployment by @dependabot in https://github.com/Flowminder/FlowKit/pull/6460 Bump es5-ext from 0.10.53 to 0.10.63 in /flowauth/frontend by @dependabot in https://github.com/Flowminder/FlowKit/pull/6462 Sqlalachemy 2 by @greenape in https://github.com/Flowminder/FlowKit/pull/6461 Bump ip from 1.1.5 to 1.1.9 in /flowauth/frontend by @dependabot in https://github.com/Flowminder/FlowKit/pull/6456 Bump deps by @greenape in https://github.com/Flowminder/FlowKit/pull/6463 Unpin examples from old jupyter by @greenape in https://github.com/Flowminder/FlowKit/pull/6464 Full Changelog: https://github.com/Flowminder/FlowKit/compare/1.21.1...1.22.0

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    Authors: Kuzmin Alexander; Orekhov Philipp; Astashkin Roman; Gordeliy Valentin; +1 Authors

    The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of 1) unmodified (FeigLab_NMR; FeigLab_PentamerNoPTM_POPC_Martini3b: 5 μs; 5 μs); 2) palmitoylated (FeigLab_PentamerCYSP43; PentamerCYSP44_POPC_Martini3b: 5 μs; 5 μs); SARS-CoV-2 E protein pentamer in a POPC bilayer. The trajectory of CG MD of system containing 2 pentamers in the membrane buckled in a single direction (BuckledMembrane_FeigLab_2xPentamerNoPTM_POPC_Martini3b: 1 μs). FeigLab_Pentamer: https://github.com/feiglab/sars-cov-2-proteins/blob/master/Membrane/E_protein.pdb FeigLab_NMR_Pentamer is assembled based on the transmembrane domain determined by NMR (PDB ID: 7K3G) and FeigLab model for the rest.

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    Authors: Kleucio Claudio; noboru-sasaki;

    This is the version v0.3 of Temporal Analysis about correlations between blood groups (ABO, Rh) and Covid-19. The initial results from this code considering total cumulative deaths are shown in SSRN: http://dx.doi.org/10.2139/ssrn.3794044. A new structure was implemented, where the R/ folder contains the source code, Data/ contains country data on blood types and number of deaths and others, the Tests/ folder contains compressed files with the first results (08/2020) and the latest results from 02/2024, configuration files for simulations and scripts for installing dependencies. Refactoring and other advancements have been made, including using weekly data from 2024 owid-covid-data.

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      ZENODO
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      Data sources: ZENODO
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      This Research product is the result of merged Research products in OpenAIRE.

      You have already added works in your ORCID record related to the merged Research product.