Incidence and relative risks for active TB in HIV-infected individuals with positive TST, T-SPOT.TB and dual positive results, compared with individuals with negative results.

<p><i>Definition of abbreviations</i>: BCG = Bacille Calmette-Guérin; CI = confidence interval; IPT = isoniazid preventive therapy; PY = person-year; TST =  tuberculin skin test. RR =  relative risk.</p><p>*Relative risk was calculated by Poisson regression method and the cell with “zero case” was assigned to 0.5 for calculation.</p><p>Individuals with IPT were excluded.</p

Flow chart showing 909 HIV-infected individuals recruited for final analysis.

<p>T-SPOT.<i>TB</i>  = (commercial form of interferon-gamma release assay from Oxford Immunotec, Abingdon, UK); TST =  tuberculin skin test; IPT = isoniazid preventive therapy.</p

Agreement between T-SPOT.TB assay and Tuberculin Skin Tests, stratified by age and CD4+ lymphocyte counts groups and BCG vaccination status.

<p><i>Definition of abbreviations</i>: BCG = Bacille Calmette-Guérin; TST =  tuberculin skin test.</p><p>*A TST reaction ≧5 mm was considered as positive.</p

Demographic data of enrolled participants at time of simultaneous T-SPOT.TB and TST.

<p><i>Definition of abbreviations</i>: MSM = man who had sex with man; IDU = injecting drug use; ART = highly active antiretroviral therapy; BCG = Bacille Calmette-Guérin; TST =  tuberculin skin test.</p>#<p>83 cases missed data of BCG scars; 133 cases missed TB contact history.</p

Risk for active TB among patients with dual positive results of TST and T-SPOT.TB stratified by receiving IPT or not.

<p>The TB incidence was 4.9 case per 100 PY for participants without IPT vs. 0.66 case per 100 PY for participants received IPT, p<0.05 by log-rank test. TST =  tuberculin skin test; IPT = isoniazid preventive therapy.</p

Predictors of positive TST and T-SPOT.TB result in multivariate logistic regression analysis.

<p><i>Definition of abbreviations</i>: aOR = adjusted Odds ratio; CI = 95% confidence interval; MSM = man who had sex with man; IDU = injecting drug use; ART = highly active antiretroviral therapy; BCG = Bacille Calmette-Guérin; TST =  tuberculin skin test.</p><p>*use participants with dual negative results as the reference group.</p>#<p>duration over 6 months.</p><p>All variables were included in multiple logistic regression analysis for adjustment.</p

Characterization of the effects of a 7 amino-acid deletion in p6^gag to the HIV-1 proteins expression, release and maturation.

<p>MT2 cells were infected with wild type (wt) or deleted-type (7d) recombinant viruses. After 12, 24, 36 and 48 hours, supernatant was collected and pelleted by ultracentrifugation. (A) Western blot analysis of the cell lysates (left panel) and viral lysates (right panel) from cells infected with wt or 7d viruses. (B) The relative expression levels of PR and RT in the viral lysates of cells infected with wt or 7d virus. The total arbitrary densitometer units of PR and RT were standardized by p24 and normalized to those of wt in parallel experiments. The images were analyzed with Image J software. (C) The ratios of p24 vs. Pr55 (maturation index) in the viral lysates at different time points after infection were calculated. The total arbitrary densitometer units of each hours post infection were normalized to those of wt in parallel experiments. All results were representative of two independent experiments. (D) Electron microscopic (EM) examination of the viral particles of cells infected with wt or 7d recombinant viruses. MAGIC-5 cells were fixed and processed for transmission EM at different time points after they were infected with wt or 7d viruses. Scale bar indicates 200 nm. (E) Quantification of relative proportions of mature vs. immature virions released at different time points in the cells infected with wt or 7d viruses using EM. The method of virion quantification has been described previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114441#pone.0114441-Fujii1" target="_blank">[43]</a>.</p

Comparisons of the changes of CD4 cell count and HIV-1 viral loads after the first clinical visit among the following four groups of treatment naïve patients.

<p>Men who have sex with men (MSM, 357 patients for CD4 cell count and 371 patients for viral loads analysis) vs. injection drug users (IDUs, 129 patients for CD4 cell count and 128 patients for viral loads analysis) (Fig. 1A and 1B); patients infected with CRF07_BC vs. infected with subtype B (Figs. 1C and 1D). A generalized estimating equation model was used for the analyses.</p

V3 amino acid sequences and predicted phenotypes of different HIV-1 isolates in Taiwan.

<p>A dash indicated a deletion or lack of an insertion.</p>a<p>The phenotype prediction based on 2 amino acid insertion/deletion between position 14 and 15, as well as variable amino acid positions (11, 18, 19, 23, 24 and 25) of V3 regions.</p>b<p>Geno2pheno (<a href="http://coreceptor.bioinf.mpi-inf.mpg.de/index.php" target="_blank">http://coreceptor.bioinf.mpi-inf.mpg.de/index.php</a>), false-positive rate of 0.01.</p>c<p>Position-Specific Scoring Matrix (PSSM) (<a href="http://indra.mullins.microbiol.washington.edu/webpssm/" target="_blank">http://indra.mullins.microbiol.washington.edu/webpssm/</a>).</p><p>V3 amino acid sequences and predicted phenotypes of different HIV-1 isolates in Taiwan.</p

Demographic data, risk factors and clinical characteristics of HIV-1-infected patients recruited in the study.

<p>Demographic data, risk factors and clinical characteristics of HIV-1-infected patients recruited in the study.</p