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Reads were assembled into transcripts, their abundance estimated and tests for differential expression and regulation between the tissue samples were performed.
Processing of the data and computation of the gene expression ratios between the tissue samples and the common reference was carried out in the R statistical programming environment version 2.3.0 [http://www.r-project.org/] using various Bioconductor packages [30].
Staining discrepancies were observed between the tissue samples and the corresponding cell lines (Table 4).
Of note, we observed discrepant expression of miR-1246 betheen tissuesamplesmples and serum obtained from ESCC patients.
Negative controls consisted of extracted 5-μm-thick slices of paraffin blocks containing no tissue and cut in between the tissue samples.
The use of synthetic RNAs and SAMstrt in normalization enabled comparison of gene expression levels in the highly heterogenous samples and facilitated discovery of differences between the tissue samples and cultured cells.
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In addition, the distances from the center of the tissue to the white spots are examined to identify the artifacts in crescent form which resulted from the small gaps between the tissue sample and the circle fitted to the sample.
To identify these incomplete lumens, we model an entire tissue sample as a circle, and the white spots between the tissue sample and the circle are the candidate incomplete lumens.
Immunohistochemical analysis of uterine tissue samples for MHC II+ cells revealed significant differences (P < 0.05) between the control and semen-treated ligated portions of the horns, as well as between the tissue sample of uterine wall and that from the utero-tubal junction, but there were no significant differences for CD4+ cells.
Immunohistochemical analysis of uterine tissue samples for MHC class II-positive cells revealed significant differences between the control and semen-treated (higher values) horns (Table 1), as well as between the tissue sample of uterine wall and that from the utero-tubal junction (higher values).
There are significant differences in the optical properties of the tissue samples between different wavelengths of laser (P < 0.01).
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