Mean (and 95% confidence intervals) for mRNA copy numbers estimated by mixed-effects modeling for IL-4, IL-6, and IL-8.

<p>Data represent back-transformed results of log₁₀-transformed data. Values in columns with the same letter indicate absence of statistical significance between groups for a given age. Values in rows with differing superscripted numbers indicate significant (P<0.05) differences among ages within group.</p><p>Mean (and 95% confidence intervals) for mRNA copy numbers estimated by mixed-effects modeling for IL-4, IL-6, and IL-8.</p

Schematic diagram representing the distribution of the total population into the 3 subgroups (<i>R. equi</i> pneumonia foals [clinical], subclinical foals, and unaffected foals), and by genome-wide association studies versus PCR genotyping for TRPM2 SNP.

<p>The 3 comparisons among groups are also summarized.</p

Boxplots of log₁₀ values of mRNA copy numbers by age and treatment group: blue boxes are data from the control (saline) group and red boxes are data from the CpG-treated foals.

<p>The triangles in the middle of boxes represent the median value; the bottom and top of the boxes represent the 25^th and 75^th percentiles, respectively. The vertical lines extending from the boxes to horizontal lines represent multiples of 1.75 of the respective interquartile distance. Numbers above boxes represent within-treatment group differences among ages: within treatment group, ages with different numbers differed significantly (P<0.05) between groups. Asterisks denote days on which values were significantly (P<0.05) different between the control and Cp-G-treated foals. Arrows along the horizontal axis indicate ages when treatment (saline or CpG) was administered.</p

Mean (and 95% confidence intervals) for neutrophil parameters determined using flow cytometry (please see text for details) and estimated by mixed-effects modeling.

<p>Values in columns with the same letter indicate absence of statistical significance between groups for a given age. Values in rows with differing superscripted numbers indicate significant (P<0.05) differences among ages within group.</p><p>Mean (and 95% confidence intervals) for neutrophil parameters determined using flow cytometry (please see text for details) and estimated by mixed-effects modeling.</p

Joint analysis of <i>TRPM2</i> SNP UKUL3936.

<p>*Median (range) reported for frequency of allele A, along with the proportion of A alleles among all alleles represented for each group. Joint analysis includes genotypes derived from SNP array and PCR genotyping.</p

Boxplots of values of liberated 4-methylumbelliferone (4-MU) measured fluorometrically by age and treatment group: blue boxes are data from the control (saline) group and red boxes are data from the CpG-treated foal (see <b>Figure 1</b> for boxplot description).

<p>Numbers above boxes represent within-treatment group differences among ages: within treatment group, ages with different numbers differed significantly (P<0.05) between groups. Asterisks denote days on which values were significantly (P<0.05) different between the control and Cp-G-treated foals. Arrows along the horizontal axis indicate ages when treatment (saline or CpG was administered.</p

Manhattan plots of standard chi-squared significance values for the 3 genome-wide association studies.

<p>Manhattan plots for (A) comparison 1, (B) comparison 2, and (C) comparison 3; (D) Mixed effects-model analysis of comparison 3.</p

Top 5 CNV regions identified using logistic regression for the association of <i>R. equi</i> with either the binary variable presence or absence of a CNV identified in the region (Presence columns) or the log₂ ratio of intensity values of the CNVs (Intensity columns).

<p>CNVR identification numbers are provided in Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098710#pone-0098710-t001" target="_blank">Table 1</a>.</p

CNVs identified in the each clinical group.

<p>CNVs: median (range; sum); Kruskal-Wallis test.</p

Mean ratios of total and <i>R. equi</i>-specific IgA in naso-pharyngeal samples.

<p>Relative quantities on day 32 relative to day 2 (log₁₀-transformed) of IgA from 34 foals in 4 treatment groups as described in Fig. 2. Bars with differing letters indicate significant (P<0.05) differences among groups. A) Mean ratio (95% confidence interval) concentration total IgA; B) Mean ratio OD <i>R. equi</i>-specific IgA; C) Proportion of foals with increase in total IgA from day 32 relative to day 2; D) Proportion of foals with increase in <i>R. equi</i>-specific IgA from day 32 relative to day 2.</p