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Recently, Kundo [14] has reported a set of tight biding parameters based on fitting to a first principle calculation but more directly related to the physical quantities of interest.
These results were based on fitting to 2 transfusion associated cases up to 2006, whereas here we are fitting to 3 cases up to 2009, taking into account a number of years during which no transfusion associated cases have been observed.
Figure 3 shows the residual surfaces based on fitting to 2 individual noise-free data sets and to the same 2 data sets together.
For each of the available data sets, variation in systemic concentration eliciting a toxic response was represented by a geometric SD (GSD) for population toxicodynamic variability based on fitting to a log-normal distribution [Tables A4.5 and A4.6 in IPCS (2014)].
Our results show a substantial decrease in the uncertainty of the future course of the primary epidemic in the susceptible genotype (MM-homozygous at codon 129 of the prion protein gene), with a best estimate of 40 future deaths (95% prediction interval 9 540) based on fitting to the vCJD case data alone.
Based on fitting to the vCJD case data alone (which is comparable to previous analyses [ 9, 10]), the upper limit of the 95% prediction interval (PI) for future cases has decreased from approximately 7,000 cases last year to just 540 cases.
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The final ensemble is obtained by subsequent optimization using PHENIX and filtering based on fit-to-data, measured using a cross-validation parameter R free; lower R free implies better fit-to-data.
Subsequent to the automated model building, we manually deleted ill-fitting waters and edited alternative protein side chain conformations based on fit to the electron density in Coot (Emsley et al., 2010) and refinement with phenix.refine.refine
The proper scaling relationship for each of the hindered diffusion models is evaluated based on fits to experimental data.
The fault geometry for inversion (strike 15° and dip 18°) was estimated by slightly modifying the gCMT solution (strike 18° and dip 18°) based on fit to teleseismic waveforms.
Our in silico predictions are based on fits to Suc-LLVY-MCA and Bz-VGR-MCA degradation by mouse proteasome.
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