Patient characteristics, overall and stratified by timing of cART (early <i>versus</i> deferred); entries are n (%) unless otherwise stated.

<p>*Included the following events: oesophageal candidiasis (n = 59); toxoplasmosis (n = 29); cytomegalovirus (n = 23); cryptococcal meningitis (n = 15); cryptosporidiosis (n = 7); progressive multifocal leukoencephalopathy (n = 5), herpes simplex infections (n = 8).</p

Factors associated with clinical progression (a new AIDS event or death) (N = 584).

<p>*As patients may have experienced more than one of the specific AIDS-defining events, each event is treated as a separate binary covariate; therefore, patients with the event of interest are compared to those without that event (but who will have at least one of the other AIDS events).</p

Patient characteristics, overall and stratified by type of AIDS-defining event^*; entries are n (%) unless otherwise stated.

<p>*As patients may have experienced more than one of the specific AIDS-defining events, each event is treated as a separate binary covariate.</p><p>**Included the following events: oesophageal candidiasis (n = 75); toxoplasmosis (n = 50); cytomegalovirus (n = 36); cryptococcal meningitis (n = 19); cryptosporidiosis (n = 8); progressive multifocal leukoencephalopathy (n = 18), herpes simplex infections (n = 10).</p><p>***Based on patients with sufficient follow-up to be categorized into one of the two groups (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026009#s2" target="_blank">Methods</a>).</p>§<p>A small number of patients developed AIDS-defining conditions or died that did not fall into one of the five specific categories (e.g. wasting syndrome) – these patients are included in the total column but will not be in the subcolumns.</p

Longitudinal analyses of HIV-1-specific T cell responses in PBMC.

<p>The total magnitude (A) and breadth (B) of ELISpot responses at baseline (BL), week 24 (w24) and week 60 (w60) are shown for all subjects together (left panels) and for each study arm separately (right panels, crossed lines for control arm, circles for MVC arm). Horizontal lines represent median values of Spot-forming cells (SFC)/10⁶ PBMC and the IQR, respectively. Mann-Whitney test was used in all statistical analysis. Only p values with significance after Bonferroni correction was shown. The numbers in parenthesis below the x-axis represent the median value.</p

Longitudinal assessment in functional profile of HIV-specific CD8⁺ T cells during cART with MVC intensification.

<p>A. Correlation between the total HIV-specific responses determined by direct ex-vivo ELISpot analysis (as spot-forming cells (SFC)/10⁶ PBMC) and by ICS analysis (% of IFN-γ⁺ CD8⁺ T cells). Linear regression line, and correlation coefficient and p-values (Spearman's rank correlation test) are shown. B. The change in total HIV-specific CD8⁺ T cell frequency over time by ICS analysis. Horizontal lines indicate median values of all positive responses. P values were determined by Mann-Whitney tests and shown if the significance remains after Bonferroni correction. C, D. Effector function profiles of HIV-specific CD8⁺ T cells over time in controls and MVC treated subjects. (left, baseline; middle, week 24; right, week 60). The median and IQR are indicated by horizontal lines and boxes, respectively. Differences relative to baseline values in each arm were tested for statistic significance by Mann-Whitney tests, and shown as # for p<0.05, ## for p<0.01.</p

Characteristics of participants.

<p>a: data from the closest previous timpoint for VL, CD4, CD8. The gap was 14–35 days.</p><p>b: not analyzed in this study because of sample limitation.</p><p>c: not determined because of lost patients.</p

Differentiation status in CD4⁺ and CD8⁺ T cells.

<p>A. Changes of CD4⁺ and CD8⁺ T cell count in each subject. B. The proportion of naïve (CD45RA⁺/CCR7⁺), central memory (CM, CD45RA⁻/CCR7⁺), effector memory (EM, CD45RA⁻/CCR7⁻), and Terminal effector memory (T_EMRA, CD45RA⁺/CCR7⁻) cells among CD4⁺ and CD8⁺ T cells in the control (cross and hatched line) and MVC arm (circle and solid line). The median and interquartile range (vertical line) are shown. Stars (control) and hatches (MVC arm) above the lines indicate significant differences relative to baseline values (p<0.05).</p

Longitudinal assessment of HIV-specific T cell responses with <i>in vitro</i> expanded T cells.

<p>A. Relationship of the breadth between responses detected by direct ELISpot and ELISpot using <i>in vitro</i> expanded cells. Responses on the x-axes represent the total HIV-1-specific responses in direct ELISpot, and the y-axes indicate total HIV-1-specific responses in expanded ELISpot for samples taken at baseline (circle), week 24 (square), and week 60 (triangle). B. Relationship of the magnitude between direct ELISpot and expanded ELISpot at each time point. cross: control arm, circle: MVC arm. The lines in A and B show linear regression lines. C, D. Changes in magnitude and breadth of total HIV-specific T cell responses in expanded ELISpot are shown as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087334#pone-0087334-g002" target="_blank">Figure 2</a>.</p

Proportion (95% CI) receiving RHZ-based empiric therapy (a) and proportion (95%CI) with MDR-TB (b) in different countries and study regions.

<p>The intraregional differences in the use of RHZ-based empiric anti-TB treatment are shown in relation to the observed MDR-TB prevalence.</p

Factors associated with MDR-TB in multivariable logistic regression analysis.

<p>Factors associated with MDR-TB in multivariable logistic regression analysis.</p