Additional file 1: of Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens

Predicted HLA class II binding peptides in Mtb72F. (XLSX 15 kb

Additional file 3: of Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens

Predicted 9-mer HLA class I peptide binding regions in Mtb72F. (XLSX 13 kb

MOESM2 of A monoclonal antibody-based immunoassay to measure the antibody response against the repeat region of the circumsporozoite protein of Plasmodium falciparum

Additional file 2: Figure S1. Overview of the design of the two clinical vaccine studies from which the serum samples have been derived

Box plots for cytokine positive T cell frequencies on stimulation with CSP peptides pre-vaccination, 1 month after the last vaccination and 12 months after the last vaccination, shown by cytokine and by vaccination group.

<p>Box plots show medians and inter-quartile ranges, the whiskers show 5^th to 95^th centiles, and outliers are shown by circles. Vaccination group is indicated by “RTS” for RTS,S/AS01_E and “Ctl” for rabies control. T cell phenotype is indicated by + and − for the cytokines shown far left. Significance is indicated by a horizontal line at p<0.0003 (using a Bonferroni correction for multiple comparisons).</p

MOESM2 of The biological function of antibodies induced by the RTS,S/AS01 malaria vaccine candidate is determined by their fine specificity

Additional file 2. M1 versus M2: Scatterplot comparing M1 and M2 opsonization frequency and intensity

A representative example of the identification and quantitation of RTS,S/AS01_E induced CSP-peptide reactive CD4+ T cells producing various cytokines.

<p>A) CD4+/CD8+ T cells were gated off the side scatter (SCC) Vs CD3 gate, after gating on lymphocytes on the SSC vs forward scatter (FSC) density plot. B) Determination of the percentages of IL2+, TNF+ and IFNγ CD4+ T cells following <i>in vitro</i> stimulations with nothing (Media control), CSP and SEB. C) An example of a typical gating tree showing the identification and quantitation of CD4+ T cells producing various combinations of IL2, TNF and IFNγ, following stimulation with nothing (media control), CSP or SEB, is shown. The resultant data was expressed as percentages of cytokine positive CD4+ T cells.</p

Kaplan Meier plot showing fraction of the RTS,S/AS01_E vaccinees experiencing an episode of clinical malaria, divided according to antibody and TNF+ only CD4+ cell anti-CSP responses.

<p>The 4 groups are as follows; 1) anti-CSP antibody titers below 40 EU/ml, TNF+ only CD4+ cells on CSP stimulation below median; 2) anti-CSP antibody titers above 40 EU/ml, TNF+ only CD4+ cells on CSP-peptide stimulation below median; 2) anti-CS antibody titers below 40 EU/ml, TNF+ CD4+ cells on CSP-peptide stimulation above median; 2) anti-CSP antibody titers above 40 EU/ml, TNF+ only CD4+ cells on CSP-peptide stimulation above median. The anti-CSP antibody titers are applied as a time-varying covariate.</p

Geometric means and 95% confidence intervals for cellular responses to CSP by vaccination group and t-test on log-transformed values for significance of difference.

<p>Pre-vac = prior to vaccination, Vac+1 = 1 month after final vaccination, Vac+12 = 12 months after final vaccination.</p

Hazard Ratios (HR) and 95% Confidence intervals from Cox regression models for the effect of CD4+ cellular responses to CSP on clinical malaria episodes.

<p>Hazard Ratios are adjusted by age (as a continuous variable), distance from the dispensary (continuous variable), bednet use, location of residence (in 4 groupings) and, when all vaccinees are included in an analysis, by vaccination group.</p><p>“At least TNF+” refers to all cells producing TNF, including polyfunctional cells (i.e. producing TNF with IL2, TNF with IFNγ, or TNF with IFNγ and IL2). The parallel definition applies to “at least IL2+”. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052870#s2" target="_blank">Results</a> that are significant after a Bonferroni correction (i.e.<0.002) are shown in bold.</p

Multivariable logistic regression analysis for the effect avidity on clinical malaria.

<p>Multivariable logistic regression analysis for the effect avidity on clinical malaria.</p