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To further assess the convergence and sampling of both approaches for calculating the L eq ∗, we performed additional replica exchange (REX) simulations (Sugita and Okamoto, 1999).
We found that removal of the G418 selection at this step allowed the growth of cells lacking the knockout allele and so an additional replica plating to PMG plates with 200 mg/L G418 was performed.
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Once the number of considered replicas is sufficient to take into account multipath signals (, (b, c, d)), the estimation algorithm detects and properly tracks the additional replicas (light blue), and thus successfully mitigates the multipath errors.
A major error source for positioning comes from multipath, the reception of additional signal replicas due to reflections caused by the receiver environment.
Two additional non-flying replicas were used.
The Pearson's correlation coefficient was calculated to show a high degree of reproducibility of among the replicas (Additional file 1B).
Finally, 13 domains were detected with p-value lower than 0.05 in the 10 replicas (Additional file 3: Supplemental Data 2A).
The number of alignments mapped per gene was found to be strongly correlated among all three replicas (Additional file 1: Figure S1).
However, convergence speed is not slowed down to 0.5 (see Figure 7) since, with replica scheme, additional extrinsic information exchanges exist in the time interval of one iteration.
The induction kinetics of TNF-encoding mRNA levels exemplified the qualitatively good agreement of replica experiments (Additional file 1: Figure S2).
To demonstrate the efficient multistep parallel transfer of solutions, MMVs containing DNA and cells in desired patterns were fabricated and used to test replica generation (Additional file 4: Figure S3a and b).
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