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In order to test whether we can detect a temporal signal in the ancient P. infestans mtDNA sequences compared to modern strains, that is, shorter branches in the ancient strains compared to the modern ones, we calculated the nucleotide distance as the number of substitutions between HERB-1, haplotype Ia and haplotype Ib mtDNA genomes to the outgroup P17777.
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For the former ones we calculate their Shannon entropy [45] (H), thus evaluating their informational content.
The fact that spots, lacking a test and reference signal, are valued as poorly performing, instead of potentially representing divergent genes explains why previously reported specificities and sensitivities were slightly higher than the ones we calculate in the current study[ 16].
This half-life of 19 My is very different from the one we calculated based on the global size of the copies because it does not take into account selection against TE insertions and has to be considered as a quasi-neutral deletion rate estimate.
This is a factor of seven times larger than the one we calculated when no neutron signal was observed.
For one, we calculated overall averages across all periods and years lumped together and applied the "Treatment + Region" model to these.
When taking this into account the sample size may have been five times as large than the one we calculated.
Based on the reported cumulative incidence of the nth infection at 6, 12, and 24 month intervals (table 1), we calculated one month hazard rates and converted these to one month transition probabilities corresponding to the appropriate age interval and number of previous infections.
For each one, we calculate the Euclidean distances to all the SIFT features in the resized image, and record the shortest distance, then sum up all of the shortest distances, and define a mean of the sum as the distance between two images to evaluate the distortion of resized image.
We thus decided to present two different pieces of information on urinary osmolality: on the one hand, we calculated urinary salt osmolality (i.e., twice the sum of urinary sodium and potassium), which was available in all patients; on the other hand, for the subgroup of patients in which this was available, we also calculated, with a standard formula, total urinary osmolality.
On the one hand, we calculated correlations without considering phylogeny at all, and thus obtained the value r = 0.89 cited above.
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