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Following Penner et al. [ 125] a total of 100 ENMs were calculated and replicated using sub-sampling (70% model training and 30% model testing) and finally three average models were derived: maximum, mean and minimum prediction gained.
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The mean number of cells for each insert was calculated and three replicates were obtained for each condition.
The mean of all replicates was calculated and is shown±S.D. of all replicates.
Abundance estimates for each T. gondii gene were calculated and the three biological replicates for each time point were averaged before differential expression analysis was performed using Cuffdiff, a Cufflinks program.
The relative fold-change between the various ligation conditions (+kinase vs kinase at 5% PEG, 12.5% PEG vs 5% PEG, 15% PEG vs 5% PEG, 12.5% PEG/+kinase vs 5% PEG/-kinase and 15% PEG/+kinase vs 5% PEG/-kinase) were calculated and plotted for five replicate experiments, along with the standard error of the mean.
18 The percentage of replicate trees in which the associated sequences cluster together in the bootstrap test (1000 replicates) were calculated, and branches with <50% bootstrap cutoff were collapsed.
Relative electrophoretic mobilities (Rf) of the peptide marker from three technical replicates were calculated and plotted against log10 of their molecular weights to generate a standard curve17.
Water temperatures were monitored using a handheld digital thermometer (HH21, Omega Engineering, Inc., Stamford, CT, USA), and the average treatment temperatures across all replicates were calculated and used in the LT50 analyses.
The mean predictive ability across the 200 replicates was calculated and bootstrap confidence intervals.
log2(Rnr3-GFP/tdTomato) values were calculated and LOESS normalized for each replicate experiment.
Ratios between mutant and wild type expression were calculated and levels for the four replicates were averaged.
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