Short communication: Impact of directly observed sputum collection on sputum culture contamination rates

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Elucidating Novel Serum Biomarkers Associated with Pulmonary Tuberculosis Treatment

In an unbiased approach to biomarker discovery, we applied a highly multiplexed proteomic technology (SOMAscan, SomaLogic, Inc, Boulder, CO) to understand changes in proteins from paired serum samples at enrollment and after 8 weeks of TB treatment from 3

Elucidating Novel Serum Biomarkers Associated with Pulmonary Tuberculosis Treatment

In an unbiased approach to biomarker discovery, we applied a highly multiplexed proteomic technology (SOMAscan, SomaLogic, Inc, Boulder, CO) to understand changes in proteins from paired serum samples at enrollment and after 8 weeks of TB treatment from 3

Feature separation by KS distance for 1,030 measured proteins, with corresponding significance levels shown as q-values.

<p>Feature separation by KS distance for 1,030 measured proteins, with corresponding significance levels shown as q-values.</p

Changes in expression of non-specific markers for active TB, including acute phase reactants SAA (A) and CRP (B), and albumin (C), between baseline and week 8 of therapy.

<p>Changes in expression of non-specific markers for active TB, including acute phase reactants SAA (A) and CRP (B), and albumin (C), between baseline and week 8 of therapy.</p

Scatter plot of the separation of baseline and week 8 samples using the two markers with the largest KS distances.

<p>Scatter plot of the separation of baseline and week 8 samples using the two markers with the largest KS distances.</p

Paired analysis of markers with largest change between baseline and week 8 of TB therapy in <i>n</i> = 39 patients, ranked by the median intra-subject fold-change.

<p>Paired analysis of markers with largest change between baseline and week 8 of TB therapy in <i>n</i> = 39 patients, ranked by the median intra-subject fold-change.</p

Empirical cumulative distribution functions showing Log RFU for the eight proteins with largest KS distances between baseline and week 8.

<p>Empirical cumulative distribution functions showing Log RFU for the eight proteins with largest KS distances between baseline and week 8.</p

Unpaired analysis of proteins showing differential expression between baseline and week 8 in <i>n</i> = 39 TB patients.

<p>A total of 60 proteins were differentially expressed using the KS test and 0.01% false discovery rate (q <10⁻⁴; for all 116 proteins with q <10⁻³ see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061002#pone.0061002.s007" target="_blank">Table S4</a>). The shift in expression is shown as the signed KS-distance, with a positive KS value indicating up-regulation of the protein after 8 weeks of TB therapy. Also shown are the raw p-value and resulting FDR corrected “q-value”.</p>*<p>Swiss Prot is a large protein sequence database widely used for protein resources.</p