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The number of escape mutations from non-wild type was small, and therefore not included in the comparative analysis.
The number of escape mutations from non-wild type was too small for analysis within subsets, and therefore only major groups were included in the comparative analysis.
Viral load was reduced about 1.0 log10 around 400 days p/s, and was accompanied by reverse mutations at Gag positions 207, 292, 451 (Figure 3B), escape mutations from the wild type at positions 90 and 129 (Figure 3C), and escape mutations from non-wild type at positions 186 and 223 (Figure 3D).
Time to completeness for escape mutations from non-wild type (median (IQR) of 243 (211–427) days p/s) was significantly longer than for reverse mutations (p = 0.001) but did not differ from escape mutations from the wild type (p = 0.27).
The time of reaching dominance for escape mutations from non-wild type (median (IQR) of 230 (150–389) days p/s) was later than that for reverse mutations (p<0.001), but did not significantly differ from the time to dominance for escape mutations from the wild type (p = 0.14).
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The increase of viral RNA load around 200 days p/s was accompanied by escape mutations from wild type such as at amino acid positions 147 and 441 (Figure 4C), and escape mutation from non-wild type at position 28 (Figure 4D).
Kinetics of viral RNA load, proviral DNA load, and CD4+ T cell count in subject D-5018 are presented in Figure 3A, while dynamics of Gag mutations are shown in Figures 3B (reverse mutations), 3C (escape mutations from consensus), and 3D (escape from non-wild type).
The time of first appearance of escape mutations from the non-wild type (median (IQR) of 188 (103–309) days p/s) was later than that of reverse mutations (p<0.001) but earlier than that of escape mutations from the wild type (p<0.001).
Two types of escape mutation were distinguished: escape from the wild type (Figure 2A, position 242), and escape from non-wild type (Fig. 2A, position 28).
By captive this means non-wild, not necessarily in a cage and never captured from the wild - see "Warnings" below.
The distribution of mutation frequencies observed for a given spot in the control arrays was assumed to be noise for all non-wild type nucleotides.
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