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  • Open Access
    Authors: 
    Pulliam, Juliet R.C.; van Schalkwyk, Cari; Lombard, Belinda; Govender, Nevashan; von Gottberg, Anne; Cohen, Cheryl; Groome, Michelle J.; Dushoff, Jonathan; Mlisana, Koleka; Moultrie, Harry;
    Publisher: Zenodo
    Project: WT | Characterization of SARS-... (221003), WT | Characterization of SARS-... (221003)

    This version contains a single file, with time series data for the most recent monthly report on SARS­-CoV-­2 Reinfection Trends in South Africa: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) Note: There may be some inconsistencies with the numbers of infections through time in earlier versions of this data set due to back-filling of late-arriving data. Note: Earlier versions of this data set included data files for Pulliam, JRC, C van Schalkwyk, B Lombard, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. DOI: 0.1126/science.abn4947 For code and more details see: https://github.com/jrcpulliam/reinfections/releases/tag/v3.0 or 10.5281/zenodo.6108448 The version of this data set associated with the publication (available via the links above) included the following files: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) demog_data.csv - counts of individuals eligible for reinfection (total), who have 0 suspected reinfections (no_reinf) or >0 suspected reinfections (reinf) by province (province), age group (5-year bands, agegrp5), and sex (M = Male, F = Female, U = Unknown, sex) posterior_90_null.RData - posterior samples from the MCMC fitting procedure (as used in the manuscript) sim_90_null.RDS - simulation results (as used in the manuscript) emp_haz_sens_an.RDS - output of sensitivity analysis of relative empirical hazard estimation to assumed observation probabilities (as used in the manuscript) The data provided here cover the period from 2021-03-04 to 2022-11-02.

  • Open Access
    Authors: 
    Robin A. Corey; Noah Harrison; Phillip J. Stansfeld; Mark S. P. Sansom; Anna L. Duncan;
    Publisher: Zenodo
    Project: UKRI | Triggering assembly of th... (MR/S009213/1), UKRI | Functional dynamics of th... (BB/R002517/1), UKRI | The UK High-End Computing... (EP/R029407/1), UKRI | The Lipoprotein Biogenesi... (BB/P01948X/1), WT | LipID: A Lipid Annotation... (208361), UKRI | Nano to Meso and Back Aga... (BB/R00126X/1), UKRI | Hydrophobic Gating in Mem... (EP/R004722/1), UKRI | Assembly and Dynamics of ... (BB/S003339/1)

    Coarse-grained structure (gro) and trajectory (xtc) files for yeast, mouse, and human respiratory supercomplexes in a membrane containing either cardiolipin (CL) or monolysocardiolipin (MLCL). Atomistic structure (gro) and trajectory (xtc) files for the yeast respiratory supercomplex in a membrane containing either CL or MLCL. Three repeats of each simulation are present in each case.

  • Open Access English
    Authors: 
    Menger, Katja E.; Chapman, James; Diaz-Maldonado, Hector; Khazeem, Mushtaq M.; Deen, Dasha; Erdinc, Direnis; Casement, John W.; Di Leo, Valeria; Pyle, Angela; Rodriguez-Luis, Alejandro; +4 more
    Publisher: Zenodo
    Project: WT | Mitochondrial DNA mainten... (213464)

    Raw image data from the article "Two type I topoisomerases maintain DNA topology in human mitochondria" by Katja E. Menger et al. Funding also from the Rosetrees and Stoneygate Trust, ref. M811.

  • Open Access English
    Authors: 
    Lucinde, Ruth Khadembu; Abdi, Abdirahman; Orindi, Benedict; Mwakio, Stella; Gathuri, Henry; Onyango, Edwin; Chira, Salome; Ogero, Morris; Isaaka, Lynda; Shangala, Jimmy; +32 more
    Publisher: Zenodo
    Project: WT | Core Support for the East... (203077)

    These files contain the SPIRIT checklist and study flow diagram for the SONIA Trial. This trial is a pragmatic randomized controlled trial of standard care versus steroids plus standard care for treatment of pneumonia in adults admitted to Kenyan hospitals.

  • Open Access
    Authors: 
    Pulliam, Juliet R.C.; van Schalkwyk, Cari; Lombard, Belinda; Govender, Nevashan; von Gottberg, Anne; Cohen, Cheryl; Groome, Michelle J.; Dushoff, Jonathan; Mlisana, Koleka; Moultrie, Harry;
    Publisher: Zenodo
    Project: WT | Characterization of SARS-... (221003)

    This version contains a single file, with time series data for the most recent monthly report on SARS­-CoV-­2 Reinfection Trends in South Africa: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) Note: There may be some inconsistencies with the numbers of infections through time in earlier versions of this data set due to back-filling of late-arriving data. Note: Earlier versions of this data set included data files for Pulliam, JRC, C van Schalkwyk, B Lombard, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. DOI: 0.1126/science.abn4947 For code and more details see: https://github.com/jrcpulliam/reinfections/releases/tag/v3.0 or 10.5281/zenodo.6108448 The version of this data set associated with the publication (available via the links above) included the following files: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) demog_data.csv - counts of individuals eligible for reinfection (total), who have 0 suspected reinfections (no_reinf) or >0 suspected reinfections (reinf) by province (province), age group (5-year bands, agegrp5), and sex (M = Male, F = Female, U = Unknown, sex) posterior_90_null.RData - posterior samples from the MCMC fitting procedure (as used in the manuscript) sim_90_null.RDS - simulation results (as used in the manuscript) emp_haz_sens_an.RDS - output of sensitivity analysis of relative empirical hazard estimation to assumed observation probabilities (as used in the manuscript)

  • Open Access English
    Authors: 
    Thiyagarajan, Sathish; Shuyuan Wang; Chew, Ting Gang; Junqi Huang; Kumar, Lokesh; Balasubramanian, Mohan K.; O'Shaughnessy, Ben;
    Publisher: Zenodo
    Project: WT | Using a permeabilized cel... (101885), NIH | Modeling Contractile Ring... (5R01GM086731-08), WT | Using a permeabilized cel... (101885), NIH | Modeling Contractile Ring... (5R01GM086731-08)

    This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R01GM086731 to B.O'S. M.K.B was supported by a senior investigator award from the Wellcome Trust (WT101885MA). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the Wellcome Trust, UK. We acknowledge computing resources from Columbia University's Shared Research Computing Facility project. Simulation and experimental data related to the preprint "Myosin turnover controls actomyosin contractile instability" (https://www.biorxiv.org/content/10.1101/2021.03.18.436017).

  • Open Access
    Authors: 
    Vancaester, Emmelien;
    Publisher: Zenodo
    Project: WT | Wellcome Trust Sanger Ins... (206194), WT | Darwin Tree of Life (218328)

    This dataset represents the assembly of 110 high-quality complete Wolbachia genomes, from 93 insect species, of which 77 were circular. These genomes are named using the schema Xyz_ToLID_§ where Xyz is the first three letters of the insect order of the host, ToLID is the identifier of the host species, and § indicates the supergroup.

  • Open Access English
    Authors: 
    Vincent, Crystal; Beckwith, Esteban J.; Dionne, Marc; Gilestro, Giorgio F.;
    Publisher: Zenodo
    Project: UKRI | Sickness behavior: causes... (BB/L020122/2), UKRI | The ninna nanna gene: an ... (BB/R018839/1), EC | SEX_FIGHT_SLEEP (705930), UKRI | MEF2 targets and their fu... (MR/L018802/2), UKRI | Innate immune regulation ... (MR/R00997X/1), WT | Connecting causes and imm... (207467)

    Ethoscope dataset for Vicent et al 2022, PLoS Pathogens Original preprint available at: https://www.biorxiv.org/content/10.1101/2021.08.24.457493v1

  • Open Access
    Authors: 
    Pulliam, Juliet R.C.; van Schalkwyk, Cari; Lombard, Belinda; Govender, Nevashan; von Gottberg, Anne; Cohen, Cheryl; Groome, Michelle J.; Dushoff, Jonathan; Mlisana, Koleka; Moultrie, Harry;
    Publisher: Zenodo
    Project: WT | Characterization of SARS-... (221003)

    This version contains a single file, with time series data for the most recent monthly report on SARS­-CoV-­2 Reinfection Trends in South Africa: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) Note: There may be some inconsistencies with the numbers of infections through time in earlier versions of this data set due to back-filling of late-arriving data. Note: Earlier versions of this data set included data files for Pulliam, JRC, C van Schalkwyk, B Lombard, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. DOI: 0.1126/science.abn4947 For code and more details see: https://github.com/jrcpulliam/reinfections/releases/tag/v3.0 or 10.5281/zenodo.6108448 The version of this data set associated with the publication (available via the links above) included the following files: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) demog_data.csv - counts of individuals eligible for reinfection (total), who have 0 suspected reinfections (no_reinf) or >0 suspected reinfections (reinf) by province (province), age group (5-year bands, agegrp5), and sex (M = Male, F = Female, U = Unknown, sex) posterior_90_null.RData - posterior samples from the MCMC fitting procedure (as used in the manuscript) sim_90_null.RDS - simulation results (as used in the manuscript) emp_haz_sens_an.RDS - output of sensitivity analysis of relative empirical hazard estimation to assumed observation probabilities (as used in the manuscript)

  • Open Access
    Authors: 
    Pulliam, Juliet R.C.; van Schalkwyk, Cari; Lombard, Belinda; Govender, Nevashan; von Gottberg, Anne; Cohen, Cheryl; Groome, Michelle J.; Dushoff, Jonathan; Mlisana, Koleka; Moultrie, Harry;
    Publisher: Zenodo
    Project: WT | Characterization of SARS-... (221003), WT | Characterization of SARS-... (221003)

    This version contains a single file, with time series data for the most recent monthly report on SARS­-CoV-­2 Reinfection Trends in South Africa: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) Note: There may be some inconsistencies with the numbers of infections through time in earlier versions of this data set due to back-filling of late-arriving data. Note: The previous version of this data set included data files for Pulliam, JRC, C van Schalkwyk, B Lombard, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. DOI: 0.1126/science.abn4947 For code and more details see: https://github.com/jrcpulliam/reinfections/releases/tag/v3.0 or 10.5281/zenodo.6108448 The previous version of this data set (available via the links above) included the following files: ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date) demog_data.csv - counts of individuals eligible for reinfection (total), who have 0 suspected reinfections (no_reinf) or >0 suspected reinfections (reinf) by province (province), age group (5-year bands, agegrp5), and sex (M = Male, F = Female, U = Unknown, sex) posterior_90_null.RData - posterior samples from the MCMC fitting procedure (as used in the manuscript) sim_90_null.RDS - simulation results (as used in the manuscript) emp_haz_sens_an.RDS - output of sensitivity analysis of relative empirical hazard estimation to assumed observation probabilities (as used in the manuscript)

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