As expected in regard to the sequence simulation protocol (see above), initial multiple sequence alignments returned by MUSCLE are composed of approximately 50% phylogenetically informative characters (i.e. those characters that are not generated by Seq-Gen from the star tree).
The model conditions were a worst case simulation in regard to the effects of sputum viscosity, pooled secretion volumes, and bacterial concentrations in pooled secretions above the cuff.
In regard to the empirical research, the similarity of simulation results to empirical findings suggests that in empirical research of small group collaboration, learning and performance, closer attention should be paid to the individuals' expectations of their own and their peers' competencies and performances, and on how sensitive the individuals are to the outcomes of these comparisons.
This paper rebuts the claim by Kumar and Stathopoulos in this journal (Suresh Kumar and Stathopoulos, 1999) that EARPG(1)/UPS using structured phases is unnecessarily complicated and inefficient compared with their EPG considering phase whitening, which is misleading in regard to the new modeling concept and the major simulation capability.
Finally, in regard to the reviewers' suggestion to report the longest simulation at which 0% of misintegrated proteins is observed, we have included a table in Figure 3 figure supplement 2 that reports the amount of simulation time required for 50%, 90%, and 95% of the CG trajectories to reach fully integrated topologies for each mutant.
The results from the anisotropic and isotropic simulations illustrate similar qualitative behaviour in regard to the number of filaments and VF wave dynamics.
Furthermore, we perform simulation studies to validate the proposed mechanism in regard to the fairness of APs.
In many cases, the precautions, suggestions, or changes are done with regard to the simulation results.
In regards to this, the simulations where drug susceptible strains are less immunogenic and where MDR strains are more fit would be informative about how the presence of prevalent HIV could affect the model.
Mean squared error decreased as the sample size increased; otherwise, there was little change in mean squared error with regard to the other simulation parameters.
