Observed versus expected prevalence of pigs in the states of the fecal shedding model.

<p>The 5 states are labeled 1, 2, 3, 4, and 5, denoting: 1-latency; 2-continuous shedding; 3-intermittent non-shedding state; 4-intermittent shedding state; and 5-recovery. Full line indicates the observed, while dashed and dotted lines denote mean and 95% CI of the expected prevalence.</p

Observed versus expected prevalence of pigs in the states of the immune response model.

<p>Shown are prevalences for the models using the custom cut-offs (panel A) and manufacturer based cut-offs (for all serotypes except <i>S.</i> Yoruba; panel B). The states are labeled 1 and 2, denoting an immune response below and above the seroconversion level, respectively. Full line indicates the observed, while dashed and dotted lines denote mean and 95% CI of the expected prevalence.</p

Ratios of transition intensities out of a state in the fecal shedding model¹.

1<p>Reference groups: low dose and <i>S.</i> Cubana.</p>2<p>Notation i→j denotes transition from state <i>i</i> to <i>j</i> with intensity <i>q_ij</i>. The 5 states are labeled 1, 2, 3, 4 and 5, denoting: 1-latency; 2-continuous shedding; 3-intermittent non-shedding state; 4-intermittent shedding state; and 5-recovery.</p>3<p>Notations 6, 9, C, Y, D, and T denote the low dose, high dose, <i>S.</i> Cubana, <i>S.</i> Yoruba, <i>S.</i> Derby and <i>S.</i> Typhimurium, respectively.</p>4<p>SE standard errors of the mean ratios of transition intensities.</p

A multistate model describing transition of pigs through the states of shedding following challenge.

<p>At time t an individual is in state <i>i</i>. Its 5 states are labeled 1, 2, 3, 4, and 5, denoting: 1-latency: the individual has been challenged but has not yet started (or will never start) shedding; 2-continuous shedding state; 3-intermittent non-shedding state; 4-intermittent shedding state; and 5-recovery: clearance of <i>Salmonella</i> from feces. Gray shaded compartments denote the pigs that excrete detectable levels of <i>Salmonella</i> in feces.</p

Mean sojourn and the expected total times in days for transient states of the fecal shedding model¹.

1<p>Reference groups: low dose and <i>S.</i> Cubana.</p>2<p>Notations 6, 9, C, Y, D, T, 1, 2, 3, and 4 denote the low dose, high dose, <i>S.</i> Cubana, <i>S.</i> Yoruba, <i>S.</i> Derby, <i>S.</i> Typhimurium, 1-latency, 2-continuous shedding, 3-intermittent non-shedding state, and 4-intermittent shedding state, respectively.</p>3<p>SE standard errors of the mean sojourn times.</p

Changes in proportion of detectable cytokine levels from baseline to month 12 in participants receiving ART,

<p>Only cytokines analyzed as dichotomous variable are included in this table. Changes of proportion of women with detectable cytokines are compared between baseline and month 12 using McNemar. No significant differences were found. Results on cytokines analyzed as continuous variables are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127201#pone.0127201.g002" target="_blank">Fig 2</a>.</p><p>Changes in proportion of detectable cytokine levels from baseline to month 12 in participants receiving ART,</p

Changes of biological marker levels in the genital compartments between baseline and month 12 among study participants receiving anti-retroviral therapy.

<p>Changes of genital (GVL) and plasma viral loads (PVL), CD4 counts and cytokines levels analysed as continuous variables were compared between baseline and month 12 in patients receiving antiretroviral therapy. Thin broken lines represent the change in immune parameter of a study participant between the two measurement times and the thick solid line in red is the average change in the parameter between the two time points. P values were calculated using the paired t-test and are displayed inside each graph. GVL, PVL and CD4 counts changes were significant, whereas cytokines levels remained comparable at baseline and month 12.</p

Cohort profile.

<p>This flow chart provides information on the number of patients recruited, eligible for antiretroviral therapy and who had viral load and CD4 data available at baseline and at month 12. Patients were classified in groups of genital viral load (GVL) <40 RNA copies/ml and GVL ≥40 copies /mL.</p

Predictors of GVL at baseline and at month 12 among participants receiving ART.

<p>Predictors of genital viral load ≥40 copies/mL at baseline and at month 12 were determined. Ninety six women initiating ART were included in the analysis at baseline. Forty-nine women receiving ART had viral load data available at month 12 and were included in the analysis at month 12. The variables included were:</p><p>At baseline: Plasma viral load, CD4, age, IL-8, IP-10, MIP-1b, VEGF, IL-6, GCSF, IL-1β, <i>N</i>. <i>gonorrhoea</i>, <i>Chlamydia trachomatis</i>, <i>Trichomonas vaginalis</i>, HSV2</p><p>At month 12: Use of family planning method, marital status, <i>Trichomonas vaginalis</i> at baseline & month 12, IL-8 at baseline & month 12, IP-10 at baseline & month 12, MIP-1b at month 12, IL-1β at month 12, IL-1RA at month 12, IL-6 at month 12, Genital VL at baseline, plasma VL at month 12.</p><p>AIC: Aikaike Information criteria.</p><p>Predictors of GVL at baseline and at month 12 among participants receiving ART.</p

Characteristics of the study population.

<p>Groups of participants with genital viral load (GVL) < 40 HIV RNA copies/mL (N = 132) versus GVL≥40 HIV RNA copies/mL (N = 111) at baseline are compared. Comparison is made using t-test for continuous and Chi-square for dichotomous variables. Significant differences are highlighted with*.</p><p>Characteristics of the study population.</p