Composition for personal growth : program design and evaluation.

<p>Two categories were used for cross-validation of the model, either type 1 or type 2. Clinical isolates were treated as an unknown class and cross-validated sensitivity, specificity, and class error were based on their classification prediction score with their respective reference strain control class. CV, cross-validated.</p><p>Cross-validated PLS-DA modeling statistics for the prediction performance for NA-SERS typing of individual type 1 and 2 <i>M</i>. <i>pneumoniae</i> clinical isolates.</p

NA-SERS specificity spectra

Wavenumber and intensity values for 521 spectra of Mycoplasma pneumoniae, other mycoplasmas, and background controls

Principle component analysis of <i>M</i>. <i>pneumoniae</i> strain typing and other human commensal and pathogenic <i>Mollicutes</i> species.

<p>For all panels, each individual shape represents a single sample spectrum. PC scores plots of 1 vs. 2 vs. 3 of: <b>(A)</b><i>M</i>. <i>pneumoniae</i> reference strains and all 13 other type 1 clinical isolates; <b>(B)</b><i>M</i>. <i>pneumoniae</i> reference strains and all 11 other type 2 clinical isolates; <b>(C)</b><i>M</i>. <i>pneumoniae</i> type 1 reference strain, type 2 reference strain, and all six type 2V clinical isolates; and <b>(D)</b> growth medium control, all <i>M</i>. <i>pneumoniae</i> strains, and all 12 other human commensal and pathogenic <i>Mollicutes</i> species. For panels A-C, dark gray diamonds represent type 1 sample spectra whereas open squares represent the type 2 sample spectra. In panel C, type 2V clinical isolate spectra are represented by light gray triangles. For panel D, growth medium control spectra are represented by dark gray diamonds, <i>M</i>. <i>pneumoniae</i> spectra by open squares, and all 12 other <i>Mollicutes</i> species by light gray triangles. For panels A-D, clustering of samples is indicated by black circles or brackets.</p

Comparison of averaged, baseline-corrected, and normalized SERS spectra for type 1, type 2, and type 2V genotypes.

<p>Raw spectra of all type 1 (n = 155), type 2 (n = 135), and type 2V (n = 60) clinical isolates and controls were averaged, baseline-corrected, and normalized using GRAMS32/A1 spectral software package (Galactic Industries, Nashua, NH). Red, average spectrum of all type 1 <i>M</i>. <i>pneumoniae</i> strains; green, average spectrum of all type 2 <i>M</i>. <i>pneumoniae</i> strains; blue, average spectrum of all type 2V <i>M</i>. <i>pneumoniae</i> strains. Peaks unique to a specific genotype of <i>M</i>. <i>pneumoniae</i> are indicated by arrows and identified above the spectral fingerprint. Type 1 peaks, red arrows; type 2 peaks, green arrows; and type 2V peaks, blue arrows. Inset at top right of image depicts zoomed-in view of the type 2 doublet at 767 and 778 cm^-1.</p

PLS-DA distinguishing <i>M</i>. <i>pneumoniae</i> strains from other human commensal and pathogenic <i>Mollicutes</i> species.

<p>Each panel represents a cross-validated class prediction score for <b>(A)</b> class 1, growth medium control; <b>(B)</b> class 2, all <i>M</i>. <i>pneumoniae</i> strains; and <b>(C)</b> class 3, all other human commensal and pathogenic <i>Mollicutes</i> samples. For panels A-C, each individual shape represents a single pre-processed NA-SERS spectrum. The growth medium control spectra are represented by gray diamonds, the <i>M</i>. <i>pneumoniae</i> spectra by open shapes that differ by cluster to indicate the different individual strains and isolates, and the human commensal and pathogenic <i>Mollicutes</i> species are represented by light gray shapes that differ by cluster to indicate the individual species. The red-dotted line indicates the classification threshold line for positive class prediction, and the black-dotted line indicates the 95% confidence interval. Cross-validated sensitivity, specificity, and class error for the panels were as follows: <b>(A)</b> growth medium control: 1.00, 1.00, and 0, respectively; for <b>(B)</b> All <i>M</i>. <i>pneumoniae</i> samples: 1.00, 1.00, and 0, respectively; and for <b>(C)</b> All 12 <i>Mollicutes</i> species: 1.00, 1.00, and 0, respectively. Cross-validated statistics were obtained using Venetian blinds with 10 data splits to represent the prediction performance of the PLS-DA model for <i>M</i>. <i>pneumoniae</i> detection.</p

PLS-DA for NA-SERS typing of type 1 and 2 <i>M</i>. <i>pneumoniae</i> strains.

<p>Cross-validated class prediction scores for <b>(A)</b> all 13 type 1 clinical isolates, and <b>(B)</b> all 11 type 2 clinical isolates. For panels A and B, each individual shape represents a single pre-processed NA-SERS spectrum. <i>M</i>. <i>pneumoniae</i> type 1 reference strain control and other clinical isolates are represented by dark gray diamonds, while the type 2 reference strain control and other clinical isolates are represented by open shapes. Shapes differ by cluster to indicate the individual clinical isolates and samples, and the strain/isolate designation is indicated above the brackets for each cluster. The red-dotted line indicates the classification threshold line for positive class prediction, and the black-dotted line indicates the 95% confidence interval. The cross-validated sensitivity, specificity and class error were obtained using Venetian blinds with 10 data splits to represent the prediction performance of models for classification of <b>(A)</b> type 1 strains: 0.968, 0.96, and 0.04, respectively and for <b>(B)</b> type 2 strains: 1.00, 0.993, and 0.004, respectively.</p

PLS-DA for NA-SERS typing of type 2V <i>M</i>. <i>pneumoniae</i> clinical isolates.

<p>Cross-validated class prediction scores for <b>(A)</b> class 1, the type 1 reference strain control; <b>(B)</b> class 2, the type 2 reference strain control; and <b>(C)</b> class 3, all six type 2V clinical isolates. For the panels A-C, each individual shape represents a single pre-processed NA-SERS spectrum. The <i>M</i>. <i>pneumoniae</i> type 1 reference strain control is represented by dark gray diamonds, the type 2 reference strain control is represented by open squares, and the type 2V clinical isolates are represented by light gray shapes. The light gray shapes differ by cluster to indicate the individual clinical isolates, and the strain/isolate designation is indicated above the brackets for each cluster. The red-dotted line indicates the classification threshold line for positive class prediction, and the black-dotted line indicates the 95% confidence interval. The cross-validated sensitivity, specificity and class error for panels A-C were obtained using Venetian blinds with 10 data splits to represent the prediction performance of <b>(A)</b> type 1 strains: 1.00, 0.988, and 0.006, respectively; for <b>(B)</b> type 2 strains: 0.92, 0.906, and 0.08, respectively; and for <b>(C)</b> type 2V strains: 1.00, 1.00, and 0, respectively.</p

Cross-validated PLS-DA modeling statistics for the prediction performance for species discrimination between <i>M</i>. <i>pneumoniae</i> and nine other human commensal and pathogenic mycoplasma species individually.

<p>For species discrimination, three categories were incorporated to cross-validate the model: either category 1: growth medium control (GMC); category 2: <i>M</i>. <i>pneumoniae</i> (M129); or category 3: other mycoplasma species in question. Eight spectra from each category were of known class and two spectra from each category were treated as unknowns to generate a cross-validated prediction model. Cross-validated sensitivity, specificity, and class error were based on the classification prediction score for each category.</p><p>Cross-validated PLS-DA modeling statistics for the prediction performance for species discrimination between <i>M</i>. <i>pneumoniae</i> and nine other human commensal and pathogenic mycoplasma species individually.</p

Quality control and sample information for <i>Mollicutes</i> species and <i>M</i>. <i>pneumoniae</i> control cultures.

<p>^aGenome sizes obtained from published sources [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131831#pone.0131831.ref035" target="_blank">35</a>] and known G+C contents from the GenBank database</p><p>Quality control and sample information for <i>Mollicutes</i> species and <i>M</i>. <i>pneumoniae</i> control cultures.</p

PLS-DA of 32 <i>M</i>. <i>pneumoniae</i> clinical isolates, including reference strains M129 and FH.

<p>Each panel represents a cross-validated class prediction score for <b>(A)</b> class 1, substrate background; <b>(B)</b> class 2, growth medium control; and <b>(C)</b> class 3, all <i>M</i>. <i>pneumoniae</i> strains. For panels A-C, each individual shape represents a single pre-processed NA-SERS spectrum. The substrate background spectra are represented by gray diamonds, the growth medium control spectra by solid black squares, and the <i>M</i>. <i>pneumoniae</i> spectra by open shapes that differ by cluster to indicate the different individual strains and isolates. The red-dotted line indicates the classification threshold line for positive class prediction, and the black-dotted line indicates the 95% confidence interval. Cross-validated sensitivity, specificity, and class error for the panels were as follows: <b>(A)</b> nanorod substrate background: 1.00, 1.00, and 0, respectively; for <b>(B)</b> growth medium control: 1.00, 1.00, and 0, respectively; and for <b>(C)</b><i>M</i>. <i>pneumoniae</i>: 1.00, 1.00, and 0, respectively. Cross-validated statistics were obtained using Venetian blinds with 10 data splits to represent the prediction performance of the PLS-DA model for <i>M</i>. <i>pneumoniae</i> detection.</p