Table 2.

Significant Partial Rank Correlation Coefficients (PRCCs) for inflammation outcomes. List of all the parameters/mechanisms (rows) that have a significant (i.e., p < 10⁻³) PRCC with respect to outputs of the model that are directly related to some markers of infection (columns). See Appendix B for a detailed description of the outcomes analyzed here. A + (or −) indicates a positive (or negative) correlation between the parameter and the infection level outcome. The magnitude/strength of the correlation is given by the number of + (or −). The table recapitulates, whenever possible, the dynamics over time. The outputs with * are selected as examples to illustrate PRCC time courses (see Figure 5). Ext Mtb means extracellular bacteria that is not inside DCs or macrophages, Tot Mtb means total bacteria intracellular and extracellular, Gran size means actual measure of the granuloma diameter. The parameters τ define thresholds for T cell recruitment at each vascular source (in terms of number of molecules). The parameter λ represents the frequency of Mtb-specific Naïve T cells in the blood/LN (see Appendix A for details on all the parameters listed below).

	INFECTION (LUNG)
Parameters	Tot Mtb*	Ext Mtb	Total Infected Macs*	Total Infected DCs*	Gran Size*
growthRateIntMtb	+ + +	+ + +	+ + +	+1
lungExitInterval				+ + +
${\tau }_{{\mathrm{T}}_{\gamma }-\mathrm{CC}}$—chemokine threshold for Tγ recruitment			++
τTreg−TNF—tumor necrosis factor (TNF) threshold for Treg recruitment
k4—CD4+ T precursorproliferation	− − −	− − −		− −
k13—CD8+ T precursorproliferation	− − −	− − −	− − −	− − −	early + then − − −
scalingMDC—Scaling to host factor representing the number of granulomas developing in the whole lung at time of infection
k11—Naïve CD8+ T priming	− −	− −	− −	− −	− −
% of Resident DCs				+ +	−
λ		− −

¹This PRCC is below 0.3, so it is not shown in Figure 5c.