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Quantitative real-time PCR confirmed a statistically significant increase of comparable entity in the expression of the fabI gene of clinical isolates when compared to reference strains (using gyrA as housekeeping control).
Among the established pathogenic markers, no significant change was observed in the Indian isolates when compared to other H1N1pdm viruses.
Three amino acid substitutions showed decreased proportions in treatment-experienced subtype B isolates when compared to drug-naïve isolates (I326V, T470N, and K512R).
Thus, emm typing provides a useful tool for identifying isolates when compared to traditional M typing.
The modified/corrected rapid real-time PCR typing method of Mäkinen et al. [ 28] correctly identified all 46 of the isolates when compared to full gene sequencing.
In line with our discovery of a greater overall abundance of variants in the SSTI isolates we saw a significantly larger number of both synonymous and non-coding variants in the SSTI isolates when compared to the severe isolates.
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For isoniazid, inhA was wildtype in all isolates, and katG mutated in all resistant isolates when comparing to Bactec MGIT susceptibility (Table 3).
For patient 1, the rifampicin mono-resistant isolate harboured numerous heterogeneous variants, all of which were unique to this isolate when compared to its paired MDR isolate.
The paired MDR isolate, R1210, showed a total of 8 heterogeneous variants to be unique to this isolate when compared to R912, two of which were fixed within the population of R912.
In addition, there is higher identity (98.3%–99.0%) among other aMPV-C isolates than when compared to isolate JC (96.0% 96.7%).
Specifically, supercontigs 6, 7, 8, 9, 10, 13, 14, 15, and 16 showed a greater chromosome copy number in the JEL427-P9 isolate compared with the JEL427-P39 isoland, and when compared to the average of other isolates studied to date (Rosenblum et al. 2013; Figure 2).
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