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Bimax uses an underlying binary data model which assumes two possible expression levels per gene.
This is not surprising as the focal parameters correspond to the lowest and highest possible expression levels.
These issues should be addressed separately for each host/marker combination; genetic constructs should be optimized to achieve the highest possible expression levels without toxicity or effects on virulence.
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Call Γ⊂ R q the set of all possible expression level profiles r(t) indexed by time t1,…, t q.
For a comparison with Gupta et al. (2006), in which raw data are available and to avoid possible expression level-dependent bias in expression ratios, the correlation between expression ratio and mean expression level was also analyzed without any normalization; the results are virtually identical.
All of the vectors have extensive multiple cloning sites, and versions are available for producing N- or C- terminal GFP fusions at each of the possible relative expression levels.
Although the detection of differential expression was possible, gene expression levels may have been underestimated as tag counts may have been incomplete.
Petrovics et al measured overexpression in cancer tissues relative to benign prostate, and it is possible that expression levels in the surrounding stroma are clinically relevant as well.
When possible, protein expression levels of sex steroid and growth factor receptors and their ligands were measured by western blot analysis as described previously [ 22].
It is of course possible that expression levels of our fusions are too low in this region to be detected by confocal microscopy.
While it remains possible that expression levels will ultimately account for the correlation between number of interactions and evolutionary rate once more accurate expression data are published, we find it far more likely that the vast majority of improvement will be in protein interaction data.
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