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Among the 28 amino acids that we examined in this study, characteristic differences between the two clusters were found for ornithine, arginine, citrulline, threonine, lysine, serine, aspartate and glutamate (which were lower in cetaceans), and cystathionine, 3-MH, carnosine, urea and 1-MH (which were increased in cetaceans).
The survival analysis did not show any significant differences between the two clusters (data not shown).
Differences between the two clusters were evaluated using the Mann–Whitney- U Test and the Chi-squared Test.
We have further explored the biophysical basis of the observed differences between the two clusters of correlated sites.
The k-means clustering was performed using a predetermined number of clusters (k = 2) and a log-rank test was used to estimate significance of survival differences between the two clusters.
Again, there were no significant differences between the two clusters with regard to the SpA subtypes (12 AS, 21 USpA, 24 PsA, 3 inflammatory bowel disease, and 2 reactive arthritis in cluster 1 versus 7 AS, 3 USpA, 9 PsA, and 1 inflammatory bowel disease in cluster 2), indicating the absence of a relation between histopathology and disease phenotypes.
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A major difference between the two clusters of conditions was the context dependent function of BMP4.
When all profiles were considered, tumor and non-malignant samples clustered separately, with a significant difference between the two clusters.
The major difference between the two clusters was the presence or absence of specific MGEs, which also explained the difference in genome sizes.
The SasX gene was absent in the BJ cluster.> Another notable difference between the two clusters was the absence of the 43.4 kb prophage φSA1 in the BJ cluster.
The gene content difference between the two clusters is the presence of paaL, a phenylacetic acid transporter, and paaM, a phenylacetic acid specific porin, along with an additional gene not known to be involved in phenylacetate degradation.
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