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Peaks 1 5 of the ABR in mice are generally considered to arise approximately from the cochlear origins (peak 1), from the cochlear nucleus (peak 2), the superior olivary complex (peak 3), the lateral lemniscus (peak 4) and the inferior colliculus (peak 5) (Henry 1979).
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For each profile, there are N predicted origins (peaks) that we ask how many of them are real origins.
To determine the overlap of γH2AX with putative replication origins, peaks were converted to the hg19 human genome assembly with liftOver (http://genome.ucsc.edu/cgi-bin/hgLiftOver).
The slope of the line connecting an origin (peak) and a termination zone (valley) shows the direction and the rate of the fork migration.
Crystals of ROCK (535 709) formed in space group P1 and displayed strong non-origin peaks in its Native Patterson map.
We therefore developed a composite average conservation score around the highest point of the origin peaks (peak heights with at least 1 or 1.5 log2-fold changes).
A t-test comparison at TSS for the random sample and the origin peaks demonstrated a highly significant difference (p<10−41, Fig. S3).
In contrast, a t-test performed to compare the average conservation score at origin peaks versus random locations was found to be highly significant (p = 1.1×10−14).
To examine the relationship of replication initiation with transcription, we initially compared the location of known transcription start sites (TSS) contained in our array to the pattern of origin peaks obtained in MCF-7.
Because origin peaks were not confined to genes or their 5'ends, we sought to determine if other features of the genome were significantly related to their localization in intergenic regions.
To ascertain if the correlation between origin peaks and conserved sequences also held for non-genic regions, we selected for analysis intergenic regions that were separated by at least 1000 bp from the nearest genes on either end of the gene free segment (an illustration of such region is shown in Supporting Figure S12).
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