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Third, glycemic variability might have a true deleterious biological effect in critically ill patients.
Since all missense mutations retained transactivation activity, only 1 of 84 (1.2%) was considered a true deleterious mutation.
This may relate to increased survival of the cells in vivo or, given the clinical worsening of disease, a true deleterious effect of allogeneic MSCs on arthritis progression in an inflammatory environment.
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(2) Q 2 = TP + TN TP + TN + FP + FN ⋅ 100%% (3) R = TP TP + FN ⋅ 100%% (4) P = TP TP + FP ⋅ 100%% (5) MCC = TP ⋅ TN − FP ⋅ FN TP + FN TP + FP TN + FP TN + FN where TP are true positives (deleterious mutations), TN – true negatives (benign mutations), FP – false positives, and FN – false negatives.
Unfortunately, this conclusion is true only for deleterious mutations and further investigation is needed for cases where beneficial mutations also occur.
As each synthesized data set was created with known global parameters [ κ = 2, π* = (0.25), and τ = 0] and site-specific fitnesses, the true proportion of deleterious, neutral, and advantageous mutations is also known.
For example, considering U SDM = 0.5, a value that might closely reflect the true haploid genomic deleterious mutation rate (see Methods), we expect an extinction time of less than 10 Kyr (~6 × 104 generations, assuming an average 60 day generation time in nature) for a range of critical selection coefficients sc between about 0.0003 and 0.09.
After applying this exclusion criterion, 15 CYPs remained with 270 variants that were used to generate vectors, including 73 benign (true negative) and 197 deleterious (true positive) mutations.
This is especially true for scenarios in which deleterious and protective variants are present.
Given that most of these mutations are likely to be passengers, we evaluated whether this was true for non-synonymous or overtly deleterious mutations (nonsense, frameshift, essential splice site).
If true, this could lessen the signal of deleterious mutation accumulation in selfers and potentially explain the weaker signal found in the Jamaican genotype.
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