Ensemble trajectories of neuraminidase study with intravenous infection data.

<p>Ensemble fits of each strain for lung pathogen (<i>P</i>_<i>L</i>), blood pathogen (<i>P</i>_<i>b</i>), epithelial damage (<i>D</i>), and activated phagocytic cells (<i>N</i>). The black line represents the median trajectory, the inner dark gray area represents the 25^th to 75^th quantiles of trajectories, and the outer light gray envelope represents 90% of the trajectories (5^th to 95^th quantiles). Data points with standard deviations are represented by the black triangles with error bars. Data were taken at 0, 3, 6, 24, and 48 hours post-infection with five mice in each group. Trajectories are simulated over two days, with infection occurring on day 0 in the blood. The top row shows ensembles for NanA⁻ bacteria, the middle row shows ensembles for NanB⁻ bacteria, and the bottom row shows ensembles for the wild-type (WT) bacteria.</p

Analysis of bacteria-dependent parameters in the neuraminidase study.

<p>(A) One-dimensional parameter distributions of bacteria-dependent parameters: <i>q</i>, <i>a</i>, <i>ν</i>, <i>ξ</i>_<i>nl</i>, <i>ξ</i>_<i>nb</i>. The top row (green) shows ensembles for NanA⁻ bacteria. The middle row (red) shows ensembles for NanB⁻ bacteria. The bottom row (blue) shows ensembles for wild-type (WT) bacteria. (B) Principal values computed from singular-value decomposition of ensembles for each bacterial strain. (C-E) Two-dimensional parameter correlations for NanA⁻ (C) NanB⁻ (D) and wild-type (E) bacteria.</p

Ensemble trajectories of neuraminidase study with intranasal infection data.

<p>Ensemble fits of each strain for lung pathogen (<i>P</i>_<i>L</i>), blood pathogen (<i>P</i>_<i>B</i>), epithelial damage (<i>D</i>), and activated phagocytic cells (<i>N</i>). The black line represents the median trajectory, the inner dark gray area represents the 25^th to 75^th quantiles of trajectories, and the outer light gray envelope represents 90% of the trajectories (5^th to 95^th quantiles). Data points with standard deviations are represented by the black triangles with error bars. Data were taken at 0, 2, 4, 6, 12, 24, and 48 hours post-infection with five mice in each group. Trajectories are simulated over two days, with infection occurring on day 0 in the lungs. The top row shows ensembles for NanA⁻ bacteria, the middle row shows ensembles for NanB⁻ bacteria, and the bottom row shows ensembles for the wild-type (WT) bacteria.</p

Analysis of bacteria-dependent parameters in the pneumolysin activity study.

<p>(A) One-dimensional parameter distributions of bacteria-dependent parameters: <i>h</i>, <i>q</i>, <i>ν</i>, <i>ξ</i>_<i>nl</i>, <i>ξ</i>_<i>nb</i>. The top row (green) shows ensembles for H+/C- bacteria. The middle row (red) shows ensembles for H2-/C+ bacteria. The bottom row (blue) shows ensembles for wild-type (WT) bacteria. (B) Principal values computed from singular-value decomposition of ensembles for each bacterial strain. (C-E) Two-dimensional parameter correlations for H+/C- (C) H2-/C+ (D) and wild-type (E) bacteria.</p

Summary of bacteria-strain-dependent parameters in each of the three studies presented.

<p>Summary of bacteria-strain-dependent parameters in each of the three studies presented.</p

Ensemble trajectories of serotype study.

<p>Ensemble fits of each strain for lung pathogen (<i>P</i>_<i>L</i>), blood pathogen (<i>P</i>_<i>B</i>), epithelial damage (<i>D</i>), and activated phagocytic cells (<i>N</i>). The black line represents the median trajectory, the inner dark gray area represents the 25^th to 75^th quantiles of trajectories, and the outer light gray envelope represents 90% of the trajectories (5^th to 95^th quantiles). Data points with standard deviations are represented by the black triangles with error bars. Data were taken at 12, 24, and 48 hours post-infection with three mice in each group. Trajectories are simulated over two days, with infection occurring on day 0 in the blood. The top row shows ensembles for 0100993 bacteria, the middle row shows ensembles for TIGR4 bacteria, and the bottom row shows ensembles for the D39 bacteria.</p

Analysis of bacteria-dependent parameters in the sesrotype study.

<p>(A) One-dimensional parameter distributions of bacteria-dependent parameters: <i>h</i>, <i>q</i>, <i>a</i>, <i>ν</i>, <i>ξ</i>_<i>nl</i>, <i>ξ</i>_<i>nb</i>. The top row (green) shows ensembles for 0100993 bacteria. The middle row (red) shows ensembles for TIGR4 bacteria. The bottom row (blue) shows ensembles for D39) bacteria. (B) Principal values computed from singular-value decomposition of ensembles for each bacterial strain. (C-E) Composition of the last principal component for 0100993 (C) TIGR4 (D) and wild-type (E) bacteria. Warm colors represent a negative contribution to sensitivity, and cool colors represent a positive contribution.</p

Analysis of bacteria-dependent parameters in the pneumolysin activity study.

<p>(A) One-dimensional parameter distributions of bacteria-dependent parameters: <i>h</i>, <i>q</i>, <i>ν</i>, <i>ξ</i>_<i>nl</i>, <i>ξ</i>_<i>nb</i>. The top row (green) shows ensembles for H+/C- bacteria. The middle row (red) shows ensembles for H2-/C+ bacteria. The bottom row (blue) shows ensembles for wild-type (WT) bacteria. (B) Principal values computed from singular-value decomposition of ensembles for each bacterial strain. (C-E) Two-dimensional parameter correlations for H+/C- (C) H2-/C+ (D) and wild-type (E) bacteria.</p

Full list of parameters of the model, their biological interpretations, and the ranges over which they are varied in the ensemble.

<p>Full list of parameters of the model, their biological interpretations, and the ranges over which they are varied in the ensemble.</p

Ensemble trajectories of pneumolysin activity study.

<p>Ensemble fits of each strain for lung pathogen (<i>P</i>_<i>L</i>), blood pathogen (<i>P</i>_<i>B</i>), epithelial damage (<i>D</i>), and activated phagocytic cells (<i>N</i>). The black line represents the median trajectory, the inner dark gray area represents the 25^th to 75^th quantiles of trajectories, and the outer light gray envelope represents 90% of the trajectories (5^th to 95^th quantiles). Data points with standard deviations are represented by the black triangles with error bars. Data were taken at 0, 3, 6, 12, 24, and 48 hours post-infection with ten mice in each group. Trajectories are simulated over two days, with infection occurring on day 0. The top row shows ensembles for H+/C- bacteria, the middle row shows ensembles for H2-/C+ bacteria, and the bottom row shows ensembles for the wild-type (WT) bacteria.</p