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A multitrait analysis was conducted on the analysis population to validate the structure of the FGVS created using the previous analyses.
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Fluid elasticity of pure and diluted fluids (10 fluids from 10 young pitchers from the seven plants used in the previous analyses) was investigated using capillary break-up extensional rheometry [26].
We used Preassembler with the same PacBio data that was used in the previous analyses.
In order to investigate this issue, we used two approaches that are more sensitive than those used in the previous analyses – fluorescent in situ hybridization (FISH) and quantitative reverse-transcription PCR (qRT-PCR).
Because many of the same subjects were used in the previous analyses, the results of the present analyses of signal intensity are similar.
The possibility of this result arising from artifacts during the experimental procedure has been considered by performing an "ad hoc" experiment in which serum samples from two closely related, but clearly differentiated patients were mixed in equal proportions and the resulting mixture was subjected to the same experimental procedure used in the previous analyses.
This bias may have resulted from the inadequacy of the linear and logit models used in the previous analyses, as neither emerges from epidemiological theory and the appropriate link function was yet unknown.
Thus, it is difficult to capture the characteristics of individual samples using the previous correlation-based network analyses.
Since the dominance effects of HLA-DRB1 are known to be highly genotype dependent, we chose to model the effects of HLA-DRB1 genotypes, rather than alleles [13], as has been done in the previous analyses using these same data.
As in the previous analyses using MrBayes, posterior probability (PP) values greater than 0.95 were considered strong support.
To test for robustness of the significant regions identified by the previous analyses using the whole data set, we performed a half-split reliability analysis in the time domain.
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