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To investigate which EMCs are enhanced in the pykF knockout mutant, we calculated the part of Eqs.
Based on the distribution of CR hybridization signal in the Col ddm1-2 mutant, we calculated CR DNA methylation indices by measuring the percentage of hybridization signal in each lane that corresponded to restriction fragments larger than 1 kb.
To investigate how the number of integrated enzyme activities affects the estimated fluxes in the pykF mutant, we calculated the model error profile defined by Eq. (21) for all combinations of the enzymes as shown in Figure 5.
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To quantify the adjustment of the starch degradation rates in the mutants, we calculated the ratio R between the degradation rates (normalized by the respective end-of-light period starch content) during the normal and the early night.
To evaluate similarities between morphologic changes in drug-treated wild-type cells and mutant strains, we calculated the Pearson product-moment correlation coefficient R and the associated P value for the 104 principal component scores from the two samples (Figure 1 III).
To display the effect of receipt of SP on mutant females, we calculated effect sizes, as the standardized mean difference (Cohen's d) over a pooled estimator of the standard deviation as the denominator.
In order to assess the larger between-replicate expression variability in mutant long-day, we calculated for all genes the absolute differences between the log2 FPKM + 1) expression level in the two replicates.
To further analyse the mutants' growth properties, we calculated the relative maximum biomass increase as an indicator for growth rate (Fig. 6B).
As plasma albumin levels were unchanged between mutant and WT littermates, we calculated bilirubin/albumin (B/A) ratio.
We calculated mutant fractions as the number of surviving colonies divided by the total number of cells plated after correction for any nonspecific killing due to complement alone.
We calculated the mutant phenotype similarity between each nonhit and known regulators (see Methods for details).
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