TABLE I.

Model States

State	Description	Initial No. of Cells
Phenotypes
memT	Resting CD4+ memory T cell	1·103
Th	Active CD4+ T helper cell	0
iTreg	Induced T regulatory cell	0
nTreg	Active natural T regulatory cell	0
mem_nTreg	Resting natural T regulatory cell	0
iDCs	Immature ’sampling’ DC in the superficial LP with access to the Lumen	1000
iDCLP	Immature dendritic cell in the LP	1000
eDC	Effector dendritic cell in the LP	0
tDC	Tolerogenic dendritic cell in the LP	0
eDCL	Effector sDC in the lumen	0
tDCL	Tolerogenic sDC dendritic cell in the lumen	0
DC Anergic	Anergic dendritic cell	0
M0	Undifferentiated macrophage	1·103
Ml	Activated inflammatory macrophage	0
M12	M2 recently transitioned from Ml	0
M21	Ml recently transitioned from M2	0
M2	Activated regulatory macrophage	0
EC	Healthy epithelial cell	104 [40]
pEC	Damaged or pro-inflammatory epithelial Cell	0
MASource	monocytes: MA precursor	105
DCSource	monocytes: DC precursor	105
Mem T Source	memory T cell in blood	104
ThSource	Potential child cell from a proliferating Th	5·105
iTregSource	Potential child cell from a proliferating iTreg	5·105
Locations
B_lumen	Commensal bacterium in the lumen	1000
Bf_lumen	Foreign bacterium in the lumen	30
B_LP	Commensal bacterium in the LP	0
Bf_LP	Foreign bacterium in the LP	0
Death
Edead	Killed epithelial cell	0
B_dead	Killed commensal bacterium	0
Bf_dead	Killed foreign bacterium	0