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The observed time course is in agreement with the predicted loss of nuclear p65 (Fig. 4C), implying that NF-κB continuously exports out to the cytoplasm in an IκBα-independent manner.
The absence of some computationally predicted scenarios (clusters 1, 3, 4, and 6) from the experimentally observed time course profiles could be partly due to some unrealistic combinations of parameter values in our variation analysis.
These experiments showed that the increase in E7 mRNA and reduction of both p38 phosphorylation and activity levels started approximately 2 3 hrs after tet removal, which is in agreement with the previously observed time course for the appearance of E7 mRNA and protein [48].
The simulation-based model evaluation comparing observed time course of dropout and the model predicted showed a reasonable description of the data (results not shown).
The data and references used in the prospective predictions can be found in Supplementary Table S2. Figure 2i shows the predicted and observed time course for the change from baseline in 4βHC following administration of carbamazepine (CYP3A4 inducer) for 24 weeks.
We note, however, that the observed time course is roughly consistent with the time scale of "fast" adaptation in cones, which restores a large part of the light-sensitive current initially turned off at the peak of the response to a step of light[19].
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Thus, a background model for the Fourier score F was generated by fitting autoregressive processes of the order 1 (AR (1)) to the observed time courses and subsequent calculation of F for the generated random expression vectors.
The observed time courses exhibited biphasic behavior and were best fit to a double exponential equation.
The direct measurement of nicking kinetics, using quench flow, suggests that both thermodynamic equilibria and kinetics play a part in the observed time courses (Table 1).
As can be seen in Figure 4, this equation fits the observed time courses in both H and D isotopic buffers very well; the rate parameters are listed in Table 4.
We provide RJMCMC sampling algorithms for both fully observed and partially observed time-course observation data.
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