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Cluster 1 included both baseline samples and all PBL samples derived from subjects at 24 hours after endotoxin.
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However, when a non-pairwise SAM method was used (i.e. two unmatched groups: (i) all baseline samples and (ii) all three-month samples), XPN correction of the integrated data was essential (Additional file 3B&C).
A strong positive correlation was present between serum IL-6 and IL-17 levels both in the 98 baseline samples and when all samples were considered (r = 0.6508, P <0.0001; and r = 0.618, P <0.0001, respectively).
Patient samples selected for sequencing included all baseline samples and samples from patients with virologic failure.
Toxicity was present in all of the baseline samples and was removed in the ammonia purged samples.
A case control study was performed on baseline samples for all 53 subjects with virologic failures (VF) at Week 48 and 95 subjects with virologic successes (VS) randomly selected and matched by CD4 count and viral load.
This is one of the limitations of this study regarding the representativeness of baseline samples across all age groups.
Surprisingly, however, low but detectable concentrations of 25(OH)D2 (ranging from 0·6 to 2·5 nmol/l) were found in all baseline samples from all subjects.
Panel A of Figure 3 shows a heat map of the Pearson correlations between all biological replicates of baseline samples, for all methods.
To investigate further the relation between inflammation and citrullination, we analyzed the correlation between the presence of total and intracellular CP, as well as PAD enzymes, and the degree of local inflammation in baseline samples obtained from all RA patients and healthy individuals (n = 34).
All measurements from the single-antigen ELISAs were combined with the measurements from the bead-array cytokine assay for integrated analysis of cytokine and autoantibody profiles in baseline samples derived from all three cohorts of etanercept new-start RA patients.
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