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Further studies should be performed to determine how the viral factors of mutational load, mutation linkage (mutations within the same viral genome), and specific mutational patterns interact and impact treatment responses to the many different antiretroviral regimens now used in the clinic.
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However, if the connection weights for the various modules are genetically inherited, this raises the problem of genetic linkage: favorable mutations may fall on one portion of the genotype encoding one neural module and unfavorable mutations on another portion encoding another module.
Advances in labeling of pyrosequencing specimens will facilitate linkage TDR mutations across the pol gene making it possible to use this approach for TDR surveillance for mutations in both protease and reverse transcriptase.
Our SNP detection array provides little information on linkage among mutations or overall haplotype, which is also a problem common to many resequencing platforms that rely on relatively short reads.
In order to study the dynamics of replacement and the linkage between mutations in patients presenting a switch from the N155H to the Y143C/H/R pattern, we cloned and sequenced the viral populations from the three patients at baseline RAL and during follow-up.
Yet the linkage between mutations and subsequent pathology is unclear.
The importance of interference, caused by genetic linkage between mutations, has been noted in a range of experimental studies.
As reviewed below (section 6.6), these findings have focused much attention in the field of CuZnSOD on the linkage between mutations in human CuZnSOD and FALS.
For most fragments, we observed a consistent decrease of LD over the first 100 200 bps, with fragment 5 being an exception with linkage of mutations at longer distances.
The paired-end reads obtained correspond to inserts of up to 700bp in length and therefore provide information on linkage of mutations up to that distance.
In sexual populations, if recombination is sufficiently common it can break up the linkage between mutations and ensure that each is selected independently (P eters and O tto 2003).
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