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The first class includes windows with 5 or less mutations, the second class includes highly mutable regions (6 to 18 mutations).
The first condition imposes the assumption that the smallest number of mutations consistent with the observed sequences is a good approximation to the true accumulated set of mutations; the second condition correlates the edge weights to the observed data.
The first set were predicted as stop gain and stop-loss mutations; the second was a mutation set predicted as frame shift and in-frame mutations, which were classified as loss of function variants.
The first is identification of pathways significantly enriched in genes containing non-synonymous mutations; the second uses pathways so identified to find groups that are functionally related in the largest number of samples.
The first class includes windows with 4 or less mutations, the second class includes highly mutable windows with 5 to 11 mutations per window, and the third class comprises obvious hypermutable windows (number of mutations 14, 15, 17, and 22).
Little et al. [ 128] fitted a generalization of the Armitage-Doll model to the Japanese atomic bomb survivor and IRSCC leukaemia data which allowed for two cell populations at birth, one consisting of normal stem cells carrying no mutations, the second a population of cells each of which has been subject to a single mutation.
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The software predicted a damaging effect for all four missense mutations, the fifth being a 1 bp frame shift deletion.
Furthermore, Alfred Knudson [ 388] hypothesized that hereditary retinoblastoma involves two mutations, the first one in the germ line.
The first mutation is a null-mutation; the second mutation results in an amino acid change affecting a residue poorly conserved amongst species.
Researchers were rather on a quest for the opposite situation, where one crippling mutation is rescued by a second, intragenic, suppressor mutation, the second restoring the function lost due to the first mutation [ 19, 20].
Progression to frank and active disease would require a second somatic mutation (the second "hit") in the remaining allele in the affected tissue type.
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