Additional file 1: of Impaired function of endothelial progenitor cells in children with primary systemic vasculitis

Paediatric Vasculitis Activity Score. (PDF 51 kb

Additional file 2: of Impaired function of endothelial progenitor cells in children with primary systemic vasculitis

Glossary and scoring for PVAS. (PDF 61 kb

Steady-State Pool Size as a Function of Virus Infectivity <i>p</i>

<p>Steady-State Pool Size as a Function of Virus Infectivity <i>p</i></p

The Predicted Time Course of CD4⁺ Memory T Cell Numbers as They Decline to Their Steady State Level for Different Levels of Immune Activation <i>a*</i> in the Presence of HIV

<p>The Predicted Time Course of CD4⁺ Memory T Cell Numbers as They Decline to Their Steady State Level for Different Levels of Immune Activation <i>a*</i> in the Presence of HIV</p

The Predicted Steady-State Pool Size as a Function of Virus Infectivity p, in the Presence of Different Levels of Immune Activation <i>a*</i>

<p>The Predicted Steady-State Pool Size as a Function of Virus Infectivity p, in the Presence of Different Levels of Immune Activation <i>a*</i></p

ANOSIM R-statistic and null distribution.

<p>ANOSIM statistic for unseparated T cell samples from Male 1 compared with Female, p<0.001 (A); Male 1 compared with Male 2, p ≈ 0.001 (B); Naïve T cell sample compared with memory T cells from Male 1, p≈1 (C); repeated one week later, p≈1 (D); and unseparated T cell samples from Male 1 taken one week apart, p≈1 (E).</p

Expression variability of proposed biomarkers for sepsis.

<p>The gene expression changes of a selection of proposed biomarkers are shown, to demonstrate their variability over the time-course. Starting from (a) in clockwise direction: (a) GZMB and (b) CCL4 are up- or down-regulated compared to 0 hours at all time points (“common”); (c) IL8 is up- or down-regulated compared to 0 hours at 8, 12, 24, and 48 hours; (d) MMP8 is up- or down-regulated compared to 0 hours at 12, 24, and 48 hours; (e) CCL3 is up- or down-regulated compared to 0 hours at 24 and 48 hours; (f) SULF2 is up- or down-regulated compared to 0 hours at 48 hours only. Up- and down-regulation is filtered at ≥2-fold change compared to 0 hours.</p

Patient demographics for longitudinal analysis.

<p>PELOD, PEdiatric Logistic Organ Dysfunction Score; PRISM, Pediatric Risk of Mortality Score.</p>*<p>4-hour sample resulted in degraded RNA, not used for further array experiments.</p

Gene expression changes over time.

<p>(a) Plot of 28,869 genes with normalized intensity values against time for the 5 patients, from GeneSpring 11.5 analysis (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060501#s2" target="_blank">Methods</a>). Colors of plots are representative of genes' change in expression level compared to the corresponding gene's expression at 0 hours for patient 1. Blue is for upregulated expression, yellow is for no change in expression, and red is for downregulated expression compared to patient 1 at time 0. (b) Numbers of genes up- and down-regulated over time for each of the 5 patients, compared to each patient's gene expression at 0 hours. The top panel indicates numbers of up-regulated genes, the bottom panel indicates numbers of down-regulated genes, for patients 1 (•), 2 (▪), 3 (Δ), 4 (<b>x</b>), and 5 (*).</p

Temporal variation in gene expression changes.

<p>Numbers of genes that change at different time points as compared to their baseline gene expression level are shown. Expression levels were analyzed by pairwise comparisons between each of 5 time points (4, 8, 12, 24, and 48 hours) compared to each patient's corresponding 0 hour gene expression profiles, and expression levels of greater than 2-fold changes were noted. This was performed for all 5 patients (except in patient 4 where the 4-hour sample had degraded RNA), 24 pairwise comparisons in total. Numbers in the sections of the Venn diagram correspond to numbers of genes that were up- or down-regulated by ≥2-fold for at least 1 in the 5 patients; numbers in the outer sections correspond to the numbers of genes uniquely regulated at the corresponding time points, and the number in the middle corresponds to the number of genes differentially regulated at all time points during the time-course.</p