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To model free full-length CD95 receptor as envisaged on a plasma membrane the CD95 ECD and TM domains were modeled as described above and the model of CD95 DD domain was based on the NMR structure of CD95 DD in solution (PDB ID 1ddf, [51]) added.
The model of the complete CD95 DISC core structure was assembled on the crystal structure of Apo2L/TRAIL in a complex with death receptor 5 (PDB ID 1dog [52]): CD95 ECD and TM domains were modeled as described above and the model of the CD95 DD domain was based on the CD95 DD crystal structure from the CD95/FADD DDs complex (PDB ID 3ezq [16]).
Finally, local anakinra (Supplementary Information Equations 10,11) and IL-1β (Supplementary Information Equations 12,13) concentrations were modeled as described in the Results (section "Anakinra treatment assumed to result in rapid and near-complete suppression of local IL-1β"), while local endogenous IL-1Ra levels (Supplementary Information Equation 14) were assumed constant.
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In the two series case, one series was modeled as described and the second was modeled as a flat profile.
The path loss is modeled as described in [44].
In other words, the execution order of the tasks related to some functionality was modeled as described in the system specification.
We examine a WB neuron with zero external drive, resting at its stable fixed point at time zero, and then subject to weak excitatory synaptic pulses at times k Δ, k = 1, 2, 3, … , with Δ > 0. The synaptic pulses are modeled as described in Sect.
The log-ratios of genes are modeled as described in the HMM approach.
The CaM and CaMKII reactions are modeled as described by Saucerman [ 16].
The C-terminal tail of Eco PolIIIα that is lacking in the crystal structure (2HNH) was modeled as described in (Toste Rêgo et al., 2013).
Inheritance of genetic traits was modeled as described above, and the sex of each individual was drawn randomly from a Bernoulli trial with the probability of 0.5.
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