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The percentage of positive tumor cells was evaluated, and the expression was classified into 2 categories: low expression (less than 10% positive cells) or high expression (more than 10% positive cells) for CD9 expression and negative (no positive cells) or positive for CD82 expression.
Nucleolin expression was classified as nucleolin-high or nucleolin-low using the median nucleolin labeling index of 3.5% as cutoff.
Previously known HCRT co-expressed genes were not reported in our analysis either because they were not listed within the top 100 SAM ranked candidates (NPTX2, GAL (galanin), and CART (cocaine and amphetamine regulated transcript), or expression was classified as "absent" (PDYN) using the microarray suite software (MAS) 5.0 algorithm.
These transcripts were not identified in our human array analysis as they either were expressed in other areas of the brain, leading to a low SAM ranking (NPTX2, GAL, CART) or because the expression was classified as absent in most samples (PDYN, ENTPD3), although the QRT-PCR analysis indicated moderately decreased expression of these genes in narcolepsy (see results).
Any other pattern of p16 expression was classified as p16.
Expression was classified in a qualitative manner as present or absent.
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Transcripts with different patterns of expression were classified with J-Express 2012 software package (54) using Euclidean distance based k-means clustering.
The colon cancer specimens with positive Ct-OATP1B3 mRNA expression were classified into two groups by the degree of differentiation, well-differentiated (n = 10), and moderately differentiated (n = 18).
Functional categories of genes with altered expression were classified using gene ontology programs.
High ANLN protein expression were classified as tumours with a staining intensity >1, and low expression classified as tumours with a staining intensity ≤1.
Strains that showed single and multiple bonding were classified as S and M strains, while strains without explicit GbpB expression were classified as N type.
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