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Even when taking the additional parameters into account, the best model was the default model in which all parameters were allowed to vary.
We have found out that the additional parameters were estimated very close to 0. Median of the parameters changed between 0.8×10−5 and 0.4×10−7 in all of the schemes.
Only a maximum allowed volume of 150 ml was predefined by the study protocol; all additional parameters, including injection rate and volume, were to be determined by the investigators.
We show that the data may be fitted by a yield function which is similar to the Gurson Tvergaard Needleman (GTN) form, but which also depends on the determinant of the stress tensor, and all additional parameters may be expressed in terms of standard GTN-like parameters.
Parameters seqfile, outfile, and treefile were specified appropriately, and other parameters were set as follows: verbose = 1, seqtype = 1, CodonFreq = 2, aaDist = 0, model = 0, NSsites = 3, ncatG = 3, icode = 0, RateAncestor = 1, clock = 0, cleandata = 0, method = 0 (with all additional parameters being set to the codeml default settings, as described in the 2009 PAML version 4.3 user guide.
All additional parameters were used as default values.
Matlab scripts were developed for the calculation of all the additional fields corresponding to parameters of vulnerability.
consent_flag - '0|1' - sets the consent_flag to 0 or 1. consent_not_required - '0|1' - sets the consent_not_required flag to 0 or 1. am_set_info.php is used to insert a new record into the consent table, but only if all four of these additional parameters are present.
Log-likelihood profiling of all the model parameters and additional diagnostic plots (data not shown) all confirmed the acceptable performance of the final selected model.
For simulation, we used the CHARMM program with the param27 all-atom force field and additional parameters for Hyp.
Besides ILBP and MBP all extensions to the classic LBP have additional parameters.
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