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@@ -7,9 +7,9 @@ datasets. |
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+ [X] Install Rstudio |
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+ [X] Install packages described in [[README.md]] |
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- [-] Learning R and loading data |
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- [X] Learning R and loading data |
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+ [X] Read 'R for Data Science' |
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+ [ ] Read 'Discovering Statistics with R |
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+ [X] Read 'Discovering Statistics with R |
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+ [X] Set current working directory in http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/02-load-data.Rmd#L13 |
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+ [X] Read file in http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/02-load-data.Rmd#L27 |
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+ [X] Some data attributes and simple plot in http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/02-load-data.Rmd#L62 |
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@@ -25,7 +25,7 @@ datasets. |
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+ [X] Describe datasets in http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/01-datasets.md |
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+ [ ] Assess new dataset with covariates |
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- [-] Modelling |
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- [-] Modeling |
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+ [X] Schizont/ELISA vs time to diagnosis, see https://biogems.info/KEMRI/Malaria/03-using-tidyverse.html |
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+ [X] Merge cytokines with covariates |
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+ [ ] Explore cytokines responses with groups |
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@@ -50,7 +50,12 @@ Francis Ndungu & Pjotr Prins |
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units) |
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+ ELISA maps to Schizont column (log10 transformed) |
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+ anti-schizont antibody is measured before infection |
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- lumefantrine log10 too |
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- Lumefantrine log10 too. Lumefantrine is an antimalarial drug. It is |
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only used in combination with artemether. The term "co-artemether" |
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is sometimes used to describe this combination. Lumefantrine has a |
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much longer half-life compared to artemether, and is therefore |
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thought to clear any residual parasites that remain after |
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combination treatment. |
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- Treg_freq – The frequency of Tregs as a proportion of CD4+ T cells |
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- Treg_Ki67_FC – The fold change in the number of Tregs expressing |
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Ki-67 (a proliferation marker) between C-1 and C+14 |
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@@ -62,6 +67,8 @@ Francis Ndungu & Pjotr Prins |
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cell marker) |
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- Cytokine_status_cm1 – Detectable level of pro-inflammatory cytokines |
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at C-1 (1 = yes, 0 = no) |
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- Measured cytokines [[https://en.wikipedia.org/wiki/Interferon_type_I][IFNa]], [[https://en.wikipedia.org/wiki/Interferon_gamma][IFNg]], [[https://en.wikipedia.org/wiki/Interleukin_1_beta][IL1.b]], [[https://en.wikipedia.org/wiki/Interleukin_2][IL.2]], [[https://en.wikipedia.org/wiki/Interleukin_4][LI.4]], [[https://en.wikipedia.org/wiki/Interleukin_17][IL.17]], [[https://en.wikipedia.org/wiki/Tumor_necrosis_factor][TNFa]], |
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[[https://en.wikipedia.org/wiki/Transforming_growth_factor_beta][TGFb]], [[https://en.wikipedia.org/wiki/Interleukin_10][IL10]]. |
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- Screening PCR – Whether the volunteer had detectable parasitaemia at |
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screening by qPCR (1 = yes, 0 = no) |
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- Symptoms_DoD – (Treated group only) whether the volunteer was |
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@@ -71,3 +78,46 @@ Francis Ndungu & Pjotr Prins |
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yes, 0 = no) |
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- IL10_DoD – Whether the volunteer had detectable IL-10 at the day of |
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Diagnosis (1 = yes, 0 = no) |
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* Notes |
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** Cytokines |
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Cytokines are a broad and loose category of small proteins (~5–20 kDa) |
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important in cell signaling. Cytokines are peptides and cannot cross |
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the lipid bilayer of cells to enter the cytoplasm. A given cytokine |
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may be produced by more than one type of cell. They act through |
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cell surface receptors and are especially important in the immune |
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system; cytokines modulate the balance between humoral and cell-based |
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immune responses. |
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For malaria the relative balance between Th1 and Th2 cytokines appears |
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crucial. Th1 cytokines, interleukin-12 (IL-12) and gamma interferon |
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(IFN-γ), and anti-inflammatory Th2 cytokines, IL-4 and IL-10 play a |
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role. |
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Interleukin 10 (IL-10), also known as human cytokine synthesis |
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inhibitory factor (CSIF), is an anti-inflammatory cytokine. In humans, |
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interleukin 10 is encoded by the IL10 gene. IL-10 downregulates the |
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expression of Th1 cytokines, MHC class II antigens, and co-stimulatory |
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molecules on macrophages. It also enhances B cell survival, |
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proliferation, and antibody production. IL-10 can block NF-κB |
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activity, and is involved in the regulation of the JAK-STAT signaling |
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pathway. IL-10 counteracts the hyperactive immune response in the |
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human body. |
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* T helper cells (CD4+) |
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The T helper cells (Th cells), also known as CD4+ cells, are a type of |
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T cell that play an important role in the immune system, particularly |
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in the adaptive immune system. They help the activity of other immune |
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cells by releasing T cell cytokines. These cells help suppress or |
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regulate immune responses. |
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* Regulatory T cells (Tregs) |
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The regulatory T cells (Tregs /ˈtiːrɛɡ/ or Treg cells), formerly known |
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as suppressor T cells, are a subpopulation of T cells that modulate |
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the immune system, maintain tolerance to self-antigens, and prevent |
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autoimmune disease. Tregs are immunosuppressive and generally suppress |
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or downregulate induction and proliferation of effector T cells. |