Proportion and Absolute Count of CSF Populations.

*<p>calculated using Mann-Whitney U-test.</p

Flow cytometry gating strategy to define blood and CSF white blood cell (WBC) populations.

<p>Data was compensated and gated using FlowJo to define TruCOUNT™ beads, (i) from both blood (left panel) and CSF (right panel) data. Remaining events were displayed in a CD45 vs FSC plot (ii) to gate out debris and define a total WBC population. CD14 was used to gate monocytes (iii) from the total WBC gate, and CD14− cells were displayed on a CD45 vs SSC plot (iv) to define lymphocyte and granulocyte gates. Lymphocytes were subdivided into CD3+ T cells and CD3− lymphocytes (v), CD3− lymphocytes were displayed on a CD19 vs CD56&16 (vi) plot to define B cells and NK cells respectively. CD3+ T cells were displayed on a CD4 vs CD8 plot (vii) to define CD4+ and CD8+ T cells.</p

HIV-infected and uninfected subjects have distinct blood and CSF lymphocyte proportions and counts.

<p>Proportions of CD3+, CD4+ and CD8+ T cells; B cells; and NK cells present in the blood (A) and CSF (B) of HIV-uninfected (HIV-) and HIV-infected (HIV+) subjects are depicted as a percentage of total lymphocyte population. Absolute CSF cell counts of lymphocyte subsets for HIV-uninfected and HIV infected (C) subjects are shown. Median and interquartile range for each cell population are shown in the box plots. Whiskers are set at 10–90%. Mean values are indicated by (+).</p

ART influences the absolute lymphocyte subset counts present in the CSF of HIV-infected subjects.

<p>Absolute number of CSF monocytes (A), CD3+ T (B), CD4+ T (C), CD8+ T (D), B (E) and NK (F) cell subsets present in CSF of the 4 patient subgroups <i>(Off, Rx Viremic, Rx VL<500</i> and <i>HIV-uninfected)</i> are shown. Median and interquartile range for each cell population are shown in the box plots. Whiskers are set at 10–90%. Mean values are indicated by (+). ANOVA for significant overall differences between the 3 HIV-infected treatment groups was conducted, with the p value depicted at the top of each panel. Post-hoc analysis using Dunn’s test comparing differences between pairs of groups, if statistically significant, are as indicated in each panel.</p

Background Characteristics of Study Subjects.

<p>SD = standard deviation.</p><p>IQR = interquartile range.</p><p>NA = Not applicable.</p

Parameters associated with CD4 T cell count loss among patients with partially-controlled drug resistant viremia using a mixed effects model.

<p>The model shows that CD4 T cell count decreased over time. Across all subjects higher levels of CD4 T cell activation were associated with lower levels of CD4 T cell counts controlling for log plasma HIV-1 viremia. Higher replication capacity was also associated with lower CD4 counts.</p

Spectral analysis estimated parameters for CD8 T cell activation.

<p>For each individual, the mean and standard deviations for wave components for CD8 T cell activation is presented.</p

Parameters associated with log HIV viremia among a subset of patients with partially controlled drug resistant viremia using a non-linear mixed-effects model.

<p>The model found evidence of an oscillatory signal in patients whose regimens did not include a protease inhibitor.</p

Spectral analysis estimated parameters for CD4 T-cell activation.

<p>For each individual, the mean and standard deviations for wave components for CD4 T cell activation is presented.</p

Parameters associated with log HIV viremia among patients with partially controlled drug resistant viremia using a mixed-effects model.

<p>The model suggests that increases in CD8 T cell activation was associated with increases in log HIV viremia.</p