Table 1.

Transition rates of the avian SBM. For details see Materials and Methods section and Hünniger et al. (17) and Lehnert et al. (28).

Transition rate	Description	State transition
ϕM	Phagocytosis by monocytes	Mi,j + PAE → Mi + 1, j
ϕHe	Phagocytosis by heterophils	Hei,j + PAE → Hei + 1, j
${\kappa }_M^P$	Intracellular killing of pathogens by monocytes	Mi,j → Mi − 1, j + 1
${\kappa }_{He}^P$	Intracellular killing of pathogens by heterophils	Hei,j → Hei − 1, j + 1
${\kappa }_{EK}^P(t)$	Extrallular killing by antimicrobial proteins that were released by first-time phagocytosis by heterophils. The rate depends on the activity of antimicrobial proteins ($\overline{{\kappa }_{EK}}$) and the decay of their activity (γ) as defined in Hünniger et al. (17) and Lehnert et al. (28)	PAE → PKEPAHy → PKHy
ρ	Acquire immune evasion against phagocytosis and/ or extracellular killing	PAE → PAIEPKE → PKIE
${\kappa }_{stress}^{He}$	Killing of heterophils by stress	Hei,j → iPAE + jPKE
${\kappa }_{EM}^M$	Killing of monocytes by extracellular mechanisms that are pathogen dependent	Mi,j → iPAE + jPKE
${\kappa }_{EM}^{He}$	Killing of heterophils by mechanisms that are not cellularly induced but pathogen dependent	Hei,j → iPAE + jPKE
o	Proliferation rate of bacteria	PAE → 2PAE Mi,j → Mi + 1, j Hei,j → Hei + 1, j
Ψ	Formation of fungal hyphae in extracellular space	PAE → PHy
${\kappa }_{EK}^P$	Extracellular killing by constant concentration of antimicrobials	PAE → PKE PAHy → PKHy
${\kappa }_{lysis}^M$	Killing of monocytes by pathogen-induced lysis	Fungal SBM: Mi,j → PHy + (i − 1)PAE + jPKE Bacterial SBM: Mi,j → iPAE + jPKE
${\kappa }_{lysis}^{He}$	Killing of heterophils by pathogen-induced lysis	Hei,j → PHy + (i − 1)PAE + jPKE Hei,j → iPAE + jPKE