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Total tag density of histone modifications was calculated as described above in average profile calculation over the CVM genes and 500 ring expressed genes in a stage-specific manner.
The number of binding events or posttranslational modifications was calculated for each RNA/protein isoform and then combined nonredundantly for each gene.
The relative enrichment of histone modifications was calculated by ddCt method [fold change of enrichment = 2 delta (Ct-ChIP) – (Ct- input)].
The autocorrelation of the histone modifications was calculated by the following steps: 1. Pre-process the overlapping gene pairs and genes not covered by the probes.
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Based on experiment data, the minimum stiffness modifications were calculated.
Energy modifications are calculated at constant intervals as waves transform over the forereef platform along a series of reef profile transects running into the atoll centre.
In our model, synaptic plasticity modifications are calculated as hebbian and anti-hebbian law, simulating long term potentiation (LTP) and long term depression (LTD), respectively.
Relative association of chromatin-bound protein or histone modifications were calculated using the formula 2- ΔCt)*100, where ΔCt is Ct(output) - Ct(input), output is the immuno-precipitated DNA and input is the purified genomic DNA from starting material of the ChIP assay.
Enrichment of histone modifications were calculated as described in [ 5], requiring >2-fold enrichment over input for both replicates.
Relative quantities of histone modifications were calculated by taking the fold enrichment relative to the IgG background, normalized to input or H3 enrichment: (CtIgG-Ctmodification)/(CtIgG – CtH3).
Basing on the measurements of the contact angles of the three liquids, and according to the Young equation and the Lifshitz van der Waals and Lewis acid base theory, the BAPC surface energy after the modification was calculated.
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