MOESM2 of PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization

Additional file 2. Protein Microarray Analyser source code archive. This archive includes the Protein Microarray Analyser source code, the executable jar file, the default settings, and the necessary (raw data folder, .gal file) and generated (results folder) files for a worked example

MOESM1 of PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization

Additional file 1. A worked example of Protein Microarray Analyser. This example includes a step-by-step description using a real dataset generated with our custom protein array

The sensitivity and specificity (and 95% confidence intervals (%); top panel of table) and positive and negative predictive value (middle panel of table) of smear-microscopy alone, urine LAM alone, and a combination of urine LAM and smear-microscopy.

<p>The bottom panel of the table shows the test sensitivity in smear negative culture positive TB patients. For sensitivity calculations the definite TB group (n = 141) was used whilst specificity calculations were performed using the non-TB group (n = 172) as a reference.</p

Clinical and demographic characteristics of 440 evaluable TB suspects, stratified by HIV status.

<p>*Irreconcilable ambiguity on the request form precluding processing of sample, or patient consented but did not turn up for the test.</p><p>**Excludes 42 (9.5%) patients who refused HIV testing and 11 (2.5%) patients who had no data.</p

LAM positivity (> zero OD units = positive for LAM after subtraction of the negative control i.e. cutpoint is zero) in cultures of oral mouth flora (oral flora) and in organism-specific cultures (various Actinobacteria, including different strains of Nocardia and Streptomyces, and <i>C. albicans</i>, <i>T. paurometabolum</i>, and <i>C. neoformans</i> inoculated into normal broth culture [containing yeast extract] and Todd-Hewitt culture media [without yeast extract].

<p>Normal oral flora from six different healthy control subjects was also cultured).</p

Flow chart of patients recruited to the study stratified by patient subgroup, smear microscopy, HIV status, and CD4 T cell count.

<p>Flow chart of patients recruited to the study stratified by patient subgroup, smear microscopy, HIV status, and CD4 T cell count.</p

The effect of aerosol hydration on particle size distribution.

<p>The graph shows APS measurements of “wet” and “dry” releases of <i>M</i>. <i>smegmatis</i>::<i>gfp</i>. (see text for details).</p

Isolation and visualization of viable mycobacteria in the RASC.

<p>(A) <i>M</i>. <i>smegmatis</i>::<i>gfp</i> growth on solid 7H10 agar plates from the Six-Stage Viable Andersen Cascade Impactor after wet release of 200 μl diluted culture into the RASC (30 000, 3000 and 300 colony forming units—CFU). The columns indicate the particle sizes captured on each plate across the 6 stages of the impactor, and the rows indicate the estimated total number of CFU passing through the impactor. Each release was repeated three times and the mean and SD for each plate are presented below the typical growth pattern distribution seen in the particle release. In all the releases the sampling was run for 5 minutes at 28 l/min resulting in the potential total capture of 3000, 300 and 30 CFU respectively. (B) SEM (left) and fluorescent microscopy (right) of <i>M</i>. <i>smegmatis</i>::<i>gfp</i> isolated on a PM10 impactor following experimental release.</p

Particle production as a function of respiration in a clinical TB patient.

<p>CO₂ concentration (solid line and left ordinate) and particle counts (dots and right ordinate) in the 1–2.5 μm size range for a TB patient.</p

The Respiratory Aerosol Sampling Chamber (RASC).

<p>(A) Photograph of the RASC (with the door open) on site in a community TB clinic (1) aerodynamic particle sizer (2) Filter samplers (3) Andersen impactor (4) Mixing fan (5) CO2, temperature and RH (6) PM10 impactor (7) Chair for participant. (B) Block diagram depicting the fluidic and electronic configuration of the RASC. Thick connecting lines indicate airflow and aerosol paths; thin lines indicate electronic connections. All air leaving the RASC is HEPA filtered.</p