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The use of a much more stringent cut off (p < 0.00001) still identified 219 to 229 transcripts.
At a more stringent cut off level, still 63% of the sequences could be determined within ±10○C and 6% within ±5○C.
Since a 20% alteration in gene expression for many genes, such as transcription factors, can have dramatic cellular and biological responses [ 26, 32], a more stringent cut off (e.g. 2×) was not used in the current study.
As a result, we believe there is little significant biology lost by using a conservative cut off (consistent with literature precedent) of 0.125 (i.e., one mRNA per 8 cells) vs a more stringent cut off of 0.05 (one mRNA per 20 cells).
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With the more stringent cut-off limit of 90%, 20.8% of all mtDNAs were designated Finn-characteristic.
A more stringent cut-off limit of 90% also was applied to the data, and the results obtained with the different data sets were compared.
For this view we used a more stringent cut-off, based on the overall structural similarities of the 10,000 structures generated, and calculated separately for each sequence as follows.
The value of nHI/nH did not essentially change when a more stringent cut-off E-value was used (nHI/nH was 0.027 and 0.032 for the E-values of 1e-5 and 1e-10, respectively).
We expected that a less stringent cut-off (e.g., 40%) would allow too many negative sequences in the phyloPWM, and that a more stringent cut-off (e.g., 90%) would not introduce enough variability.
Indeed, our re-analysis of their published data indicates that even more "targets" are found when this same cut-off is applied to the control experiment involving an untagged strain, and this is true even when more stringent cut-offs are used (Table 1).
Therefore, we used more stringent cut-off levels resulting in a negative outcome.
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