Simulation space.

<p>The ellipsoid lattice resemble the typical shape of a lymph node. Entities interact within voxels. Typical simulations consist of 5 of volume discretized on voxels and populated by about cells.</p

Virological rebound after stopping HAART.

<p>Virological rebound at 1, 2, 4 and 8 weeks after therapy interruption for different starting time points of HAART (). Dots represent the results of thousands simulations. The fitting lines are given by the Richards' curve in equation 1. Standard deviation is about 0.1 for all points.</p

Clinical and simulated data.

<p>Statistical summary of clinical and simulated for both <i>very-early</i> and <i>late</i> settings. Panel A shows how the data is distributed. In panel B the “whiskers” indicate the lower, median and upper quartile while largest and smaller values are shown by dashed lines. Outliers are shown as small circles. Panel C shows the cumulative distribution functions for the two groups. Panel D reports the normal probability plots (or quantile-quantile plots) for comparison to normal distributions. Legend: SVE  =  simulated very early, PzVE  =  patients very early; SL  =  simulated late, PzL  =  patients late.</p

Contingency table.

<p>Contingency table for simulated data where the expected frequency count for each cell of the table is at least 5. The rows represent the average viremia after 4 weeks from treatment interruption in logarithmic scale. The columns represent the two groups in which HAART starts during chronic phase (<i>late</i>) or within the first 20 days (<i>very-early</i>). The null hypothesis states that knowing the start timing does not help to predict . That is, the events are independent. Support for the alternative hypothesis suggests that the two events are related. The value found rejects the null hypothesis.</p

Simulations of treated and untreated case.

<p>Comparing simulations of the treated and untreated cases. All simulations share the same parameter settings with the only difference that therapy starts at day 0 in the <i>very-early</i>, at day 40 in the <i>early</i> and at day 200 in the <i>late</i> settings. The duration of simulated therapy is one year.</p

Size and mean gene distances on chromosomes.

<p>BP size = size in base pairs = number of nucleotides.</p

The bp-distance between genes and is denoted as .

<p>The ppi-distance is the shortest path between nodes of the corresponding PPI network indicated by . In this example the internode distance is equal to one so that is greater than .</p

Z-score values for each chromosomes for MINT network, computed by equation 5, are reported as function of the threshold

<p>.</p

Percentage of gene couples distances for the whole network (red plot) and for the same chromosome (green plot) for both networks considered: BIOGRID (lower panel) and MINT (upper panel).

<p>Percentage of gene couples distances for the whole network (red plot) and for the same chromosome (green plot) for both networks considered: BIOGRID (lower panel) and MINT (upper panel).</p

Distributions of of shortest path distances for chromosomes 1–16 (from left top to right bottom) for both networks considered: BIOGRID (blue lines) and MINT (red lines).

<p>Distributions of of shortest path distances for chromosomes 1–16 (from left top to right bottom) for both networks considered: BIOGRID (blue lines) and MINT (red lines).</p