Or with the “Foxp3 Fixation/Permeabilization” kit from eBioscience prior to quantify the intracellular FoxP3 detection. Samples were finally fixed in PBS+1 paraformaldehyde, kept at 4uC. A multilaser CyFlow ML flow cytometer (Partec GmbH, Mu nster, Germany) was used to acquire the samples, and the ?data were analyzed using FloMax (Partec) and FlowJo v8.8.(Tree Star Inc., Ashland, OR, USA) softwares. Single staining and “Fluorescence Minus One” (FMO) 18325633 controls were performed, and gates defining the positive and negative expression of cell surface antigens were combined by boolean gating strategy, as described [32]. Simplified Presentation of Incredibly Complex Evaluations (SPICE) software (kindly provided by Dr. Mario Roederer, Vaccine Research Center, NIAID, NIH) was used to graphically depict polychromatic flow cytometry data [33]. For T cell function analysis, we put a threshold of 0.02 on the basis of the distribution of negative values generated after background subtraction, with a minimum of 10 events [34].Biomarkers of HIV Control after PHIFigure 2. Trends of CD8+ T and CD4+ T cell response to gag- and MedChemExpress CI 1011 nef-derived peptides. Boxes indicate median values with 25th and 75th percentiles, whiskers show minimum and maximum. Figure shows the total response to viral peptides, i.e., the sum of all cells positive for at least one of the markers studied (IL-2, IFN-c, CD154 and CD107a). Patients were studied at month 1 (M1), month 2 (M2), month 3 (M3), month 4 (M4), and month 6 (M6) after PHI. The values of nonparametric analysis of variance (Skillings-Mack, and p values) are reported in figures. Stars in graphs indicate the significant differences of pairwise comparisons between the indicated months, performed by Tukey-Kramer test. doi:10.1371/journal.pone.0050728.gBiomarkers of HIV Control after PHIFigure 3. Characterization of the T cell response to gag-derived peptides. Pie charts show the qualitative composition of total gag-specific CD4+ or CD8+ T cell response; each pie slice represents the mean proportion of the total CD4+ T cell response contributed by a single functional pattern, as indicated in the bottom legend. Arcs designed outside the pies represent the fraction of total cells expressing a particular marker, irrespectively of the positive or negative expression of other markers (blue: CD154; red: CD107a; green: IFN-c; black: IL-2). doi:10.1371/journal.pone.0050728.gBiomarkers of HIV Control after PHIFigure 4. Characterization of the T cell response to nef-derived peptides. Pie charts show the qualitative composition of total gag-specific CD4+ or CD8+ T cell response; each pie slice represents the mean proportion of the total CD4+ T cell response contributed by a single functional pattern, as indicated in the bottom legend. Arcs designed outside the pies represent the fraction of total cells expressing a particular marker, 15755315 irrespectively of the positive or negative expression of other markers (blue: CD154; red: CD107a; green: IFN-c; black: IL-2). doi:10.1371/journal.pone.0050728.gStatistical analysesThe time-dependent behavior of T lymphocyte activation, Tregs and gag- or 
nef-specific responses were analyzed by the nonparametric analysis of variance using the Skillings-Mack test to address the presence of missing data. Tukey-Kramer testwas 
used for pairwise comparisons between the months. Differences were considered statistically significant when p,0.05. Linear regressions were performed to investigate the PS 1145 site associations bet.Or with the “Foxp3 Fixation/Permeabilization” kit from eBioscience prior to quantify the intracellular FoxP3 detection. Samples were finally fixed in PBS+1 paraformaldehyde, kept at 4uC. A multilaser CyFlow ML flow cytometer (Partec GmbH, Mu nster, Germany) was used to acquire the samples, and the ?data were analyzed using FloMax (Partec) and FlowJo v8.8.(Tree Star Inc., Ashland, OR, USA) softwares. Single staining and “Fluorescence Minus One” (FMO) 18325633 controls were performed, and gates defining the positive and negative expression of cell surface antigens were combined by boolean gating strategy, as described [32]. Simplified Presentation of Incredibly Complex Evaluations (SPICE) software (kindly provided by Dr. Mario Roederer, Vaccine Research Center, NIAID, NIH) was used to graphically depict polychromatic flow cytometry data [33]. For T cell function analysis, we put a threshold of 0.02 on the basis of the distribution of negative values generated after background subtraction, with a minimum of 10 events [34].Biomarkers of HIV Control after PHIFigure 2. Trends of CD8+ T and CD4+ T cell response to gag- and nef-derived peptides. Boxes indicate median values with 25th and 75th percentiles, whiskers show minimum and maximum. Figure shows the total response to viral peptides, i.e., the sum of all cells positive for at least one of the markers studied (IL-2, IFN-c, CD154 and CD107a). Patients were studied at month 1 (M1), month 2 (M2), month 3 (M3), month 4 (M4), and month 6 (M6) after PHI. The values of nonparametric analysis of variance (Skillings-Mack, and p values) are reported in figures. Stars in graphs indicate the significant differences of pairwise comparisons between the indicated months, performed by Tukey-Kramer test. doi:10.1371/journal.pone.0050728.gBiomarkers of HIV Control after PHIFigure 3. Characterization of the T cell response to gag-derived peptides. Pie charts show the qualitative composition of total gag-specific CD4+ or CD8+ T cell response; each pie slice represents the mean proportion of the total CD4+ T cell response contributed by a single functional pattern, as indicated in the bottom legend. Arcs designed outside the pies represent the fraction of total cells expressing a particular marker, irrespectively of the positive or negative expression of other markers (blue: CD154; red: CD107a; green: IFN-c; black: IL-2). doi:10.1371/journal.pone.0050728.gBiomarkers of HIV Control after PHIFigure 4. Characterization of the T cell response to nef-derived peptides. Pie charts show the qualitative composition of total gag-specific CD4+ or CD8+ T cell response; each pie slice represents the mean proportion of the total CD4+ T cell response contributed by a single functional pattern, as indicated in the bottom legend. Arcs designed outside the pies represent the fraction of total cells expressing a particular marker, 15755315 irrespectively of the positive or negative expression of other markers (blue: CD154; red: CD107a; green: IFN-c; black: IL-2). doi:10.1371/journal.pone.0050728.gStatistical analysesThe time-dependent behavior of T lymphocyte activation, Tregs and gag- or nef-specific responses were analyzed by the nonparametric analysis of variance using the Skillings-Mack test to address the presence of missing data. Tukey-Kramer testwas used for pairwise comparisons between the months. Differences were considered statistically significant when p,0.05. Linear regressions were performed to investigate the associations bet.
