Inverse relationship of IL1RA ELISA results with DSST scores.

<p>Scatter plot of IL1RA ELISA absolute concentrations (circles and dotted lines) and DSST scores (triangles and solid lines) over time across 6 HIV-positive individuals showing consistent inverse correlation. Sampling time points include 1 (the day participant presents to the methadone clinic and begins first dose), 2 and 3 (second and third sessions ∼35 and 36 days of methadone, respectively), and 4 (∼100 days on methadone). The Pearson product-moment correlation scores are shown in the lower left corner of each scatter plot.</p

Demographics.

1<p>Mean (SE).</p>2<p>[ ] percent of sample affected.</p>3<p>p = 0.04.</p

Overview of differentially abundant saliva proteins across methadone treatment.

<p>A) and B) Heat map of all differential protein abundances in the HIV⁺ and HIV⁻, heroin dependent cohorts respectively due to methadone treatment (see supplemental table 3 for complete list) at p value <0.05. Clustering is based upon a Pearson distance metric with K-means clustering (K:5). Protein abundance values were scaled for plotting. C) Venn diagram showing the overlap between the respective HIV ^+/− heat map results and the previous 58 DSST correlating saliva proteins.</p

A graphical representation of the overlap between 47 salivary proteins that demonstrated significant positive correlations with DSST scores in HIV⁺ heroin addicts and exosomal proteins identified in the ExoCarta database [73].

<p>Proteins are grouped by functional categories for visualization purposes, and not sub-exosomal localization. Adapted from Mathivanin et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089366#pone.0089366-Mathivanan2" target="_blank">[105]</a>.</p

Differences in HIV⁺ vs. HIV⁻ scatter plots of DSST/protein abundance correlation analyses results for four salivary proteins of interest.

<p>(A–D) Scatter plots showing the correlation of specific salivary protein abundance values against measured DSST scores in HIV⁺, heroin dependent individuals. The proteins include IL1RA (interleukin-1 receptor antagonist), CANX (calnexin), VCP (valosin-containing protein), and UBA1 (ubiquitin-like modifier-activating enzyme 1). All proteins, except for IL1RA, show significant direct correlation of DSST with salivary protein abundance at <i>P-</i>value<0.05. (E–H) Scatter plots showing the same comparison except against HIV⁻ heroin dependent individuals; however, no perceived correlation is observed, i.e., all p-values are well above 0.05. The linear regression is shown by a red line, and the Pearson product-moment correlation score (<i>r</i>) and Benjamini-Hochberg corrected <i>P</i>-values are indicated in the inlay boxes.</p

Overview of clinical saliva sample collection and proteomic analysis.

<p>A) Timeline of the three participant cohorts and their respective days of saliva sample collection and DSST testing. The control population was HIV⁻ and heroin independent so no methadone treatment was initiated at day 0. B) Graph of DSST correlation with all identified and quantified saliva proteins from each respective group after sample collection, processing, instrument and data analysis. Proteins shown in red are those which pass the Benjamini-Hochberg corrected <i>P</i>-value of <0.05.</p

Proteins showing a significant correlation between abundance and DSST score.

<p>Proteins showing a significant correlation between abundance and DSST score.</p

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Additional file 2: Table S2.  TMT labeling scheme for phosphoproteomics

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Additional file 1: Table S1.  TMT labeling scheme for expression proteomics

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Additional file 4: Table S4.  Table of specimen age and RTR