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Malaria Infant Study

Summary

This repository includes the data and code necessary for reproducing the analysis in our malaria infant study manuscript.

Data File

The data file, MIS_master_data_sheet_long.csv, is a 119x30 data frame which has the following column names, where each row represents one individual at either acute infection or 4 weeks post-treatment. A reformatted companion file, MIS_master_data_sheet_wide.csv, is also included for convenience.

The covariates for each subject are given in the first six columns:

  • Subject_ID (factor): The unique subject ID.

  • Sample (factor): The unique subject ID and visit number (1 or 2).

  • age.years (numeric): The age of each subject, which ranges from <1 year to 70 years.

  • Age (factor): The age group of each subject, A (adults) or I (infants and young children).

  • Sex (factor): The sex of each subject, F (female) or M (male).

  • Visit (integer): The visit number, 1 for acute infection (first visit), or 2 for post-treatment (second visit).

The levels of nine analytes are given in the following columns, in pg/ml:

  • GMCSF (numeric): granulocyte-macrophage colony-stimulating factor.

  • IFNg (numeric): interferon gamma.

  • IL10 (numeric): interleukin 10.

  • IL12p40 (numeric): interleukin 12 p40.

  • IL12p70 (numeric): interleukin 12 p70.

  • sCD40L (numeric): soluble CD40-ligand.

  • IL1b (numeric): interleukin 1 beta.

  • IL6 (numeric): interleukin 6.

  • TNFa (numeric): tumor necrosis factor alpha.

Additional phenotypes:

  • Nitrate.570 (numeric): Nitric oxide metabolite concentration, given in micromolar.

  • malaria.Ab (numeric): Absorbance values used to determine malaria.Ab.result.

  • malaria.Ab.result (factor): Three levels of antibody test results: grey (uncertain), neg (negative), pos (positive).

  • CD33.live (numeric): Percent of live cells that are CD33+.

  • mDC.live (numeric): Percent of live cells that are myeloid dendritic cells (CD11c+ HLA−DR+).

  • monocytes.live (numeric): Percent of live cells that are monocytes.

  • inflam.CD163 (numeric): Percent of monocytes that are inflammatory monocytes (CD3- CD20- CD14+ CD16++).

  • patrol.CD163 (numeric): Percent of monocytes that are patrolling monocytes (CD3- CD20- CD14++ CD16+).

  • trad.CD163 (numeric): Percent of monocytes that are traditional monocytes (CD3- CD20- CD14++ CD16-).

  • low.traditional (numeric): Percent of monocytes that are CD14low.

  • Hb (numeric): The level of hemoglobin, in grams per decaliter.

  • pfs25 (numeric): Pfs25-expressing gametocytes/ul.

  • pfs16 (integer): Pfs16-expressing gametocytes/ul.

  • pfs230 (integer): Pfs230-expressing gametocytes/ul.

  • parasites (numeric): Parasites per ul blood.