MMC Comparisons.

<p>MMC Comparisons.</p

HVTN 068 trial design with repeated immunogenicity measurements–cellular and antibody responses—during the 52 weeks of follow-up.

<p>HVTN 068 trial design with repeated immunogenicity measurements–cellular and antibody responses—during the 52 weeks of follow-up.</p

Gating strategy for activation panel (upper) and memory panel (lower).

<p>The sequential gating to CD3+ T cells is the same for both panels as shown in the upper row for each panel. Gating on CD4+ and CD8+ T cells is shown in the lower left graph in each panel. Markers of interest for each panel for CD4+ and CD8+ T cells are shown in the remaining plots.</p

qPBMC Comparisons.

<p>qPBMC Comparisons.</p

Selected MMC data for: CD4+, CD8+, CD4+CCR5+, CD8+CCR5+, CD4+CD38+DR+, and CD8+CD38DR+ T cells (boxplots showing the median, quartiles, and range for each cell population).

<p>Selected MMC data for: CD4+, CD8+, CD4+CCR5+, CD8+CCR5+, CD4+CD38+DR+, and CD8+CD38DR+ T cells (boxplots showing the median, quartiles, and range for each cell population).</p

Modeling of IFN-γ producing cytotoxic CD8+ T cells (CD8+ IFN-γ+ T cells) as a function of IL-2 producing CD4+ helper T cells (CD4+ IL-2+ T cells) and time (model 1 and model 2) in the rAd5-rAd5 group, HVTN 068 trial.

<p>Modeling of IFN-γ producing cytotoxic CD8+ T cells (CD8+ IFN-γ+ T cells) as a function of IL-2 producing CD4+ helper T cells (CD4+ IL-2+ T cells) and time (model 1 and model 2) in the rAd5-rAd5 group, HVTN 068 trial.</p

Selected PBMC data for CD4+, CD8+, CD4+CCR5+, CD8+CCR5+, CD4+CD38+DR+, and CD8+CD38DR+ T cells (boxplots showing the median, quartiles, and range for each cell population).

<p>Selected PBMC data for CD4+, CD8+, CD4+CCR5+, CD8+CCR5+, CD4+CD38+DR+, and CD8+CD38DR+ T cells (boxplots showing the median, quartiles, and range for each cell population).</p

An overview of the OpenCyto infrastructure.

<p>When reproducing manual gating, raw FCS files and FlowJo workspace XML files are read into the R environment using <i>parseWorkspace</i>, creating a <i>GatingSet</i> object that represents the compensated, transformed and gated data stored in an <i>ncdfFlowSet</i> on disk. Cell populations annotated with gates can be visualized using <i>plotGate</i>, from the <i>flowViz</i> package Gating schemes can be visualized using <i>plot</i>. To perform automated gating, the user defines a <i>csv</i> representation of a gating tree, which is read by the <i>OpenCyto</i> package to generate a <i>gatingTemplate object</i>. This template can be applied to a <i>GatingSet</i> containing data, but no gates, provided the data uses the markers defined in the template. OpenCyto utilizes built-in automated gating methods, or external methods registered via a plug-in framework, to gate different cell subsets and populate the <i>GatingSet</i> with data-driven gate definitions for each sample. Manual and automated gating may be readily compared within a single framework. Cell populations and features can be extracted for further statistical analysis with other R and BioConductor software packages. Data (red boxes), software packages (blue boxes), framework functionality (gray boxes), and data flow/data structures (arrows/labeled arrows) are represented. <i>flowCore</i>, <i>flowStats</i>, and <i>flowViz</i>, are the <i>core</i> Bioconductor flow packages that benefit from the substantial infrastructure changes we have made to improve scalability and data visualization.</p

The average frequency of expression across two CyTOF samples for cytokine-producing cell subsets from four T-cell maturational states.

<p>Samples were stimulated with PMA-Ionomycin for 3 hours. Rows represent different maturational cell subsets (TN: naïve, TCM: central memory, TEF: effector, TEM: effector memory) and are clustered by Euclidean distance similarity. Columns represent different cytokine-producing cell subsets. The bottom legend defines the cell subset in a column. The legend is colored by degree of functionality of the cell subsets (light blue: degree 1, dark blue: degree 2, light green: degree 3, dark green: degree 4, salmon: degree 5, red: degree 6, orange: degree 7). The shading of individual blocks of the heatmap represents the average proportion of cells in the subset across the two samples, normalized to the total number of CD8 T-cells. Naïve cells have low polyfunctionality compared to effector, effector memory, and central memory cells.</p