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The patients with protocol modifications showed a significantly (p = 0.02) worse outcome compared to those without modifications.
None of these histone modifications showed a significant change in Dicer-deficient ES cells (Additional files 3 and 4).
None of the modifications showed a significant difference in the mixed model analysis when comparing RTT samples and controls on all loci.
These histone modifications showed a distinct distribution pattern across the GAPDH gene consistent with previous genome-wide ChIP chip and ChIP seq analyses [ 16, 35, 36].
Nearly all modifications showed a classification accuracy of at least 55% (in H) and 75% (in IMR90), which is above the classification accuracy of 50% expected at chance (we verified that classification accuracy on randomly shuffling labels was found to be ∼50%).
We then also determined the XIC areas of these peptides in all patients, showing that the peptides containing both modifications showed a similar behavior to the peptides containing only the citrullination site (for example, more present in RA patients), whereas peptides containing only the phosphorylation site were equally abundant in all patients (Additional file 1, Figure S3B).
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Although changes in tri-H3K9 and acetyl-H3K9 amount were not statistically significant, the in situ analysis of H3K9 modifications showed an obvious increase in fluorescence intensity indicating recovery of conformational state.
Combinations of modifications showed an additive decrease in percentage cross-reactivity with the outcome for GTX1/4, which is modified at the R1, R2 and R3 positions, displaying the lowest percentage cross-reactivity at ≤ 1.0%.
In a statement, the head of the American Investment Council, the private equity trade group, said, "These common-sense, thoughtful modifications show a commitment to improving the regulatory structure for private funds".
Two other amino acid side chain modifications show a similar selectivity for single proteins.
At gene promoters, deposition of both the repressive H3K27me3 and activating H3K4me3 marks of histone modifications shows a dependence on HP1a.
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