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The crystallization behavior of δPPL blocks (i.e., PPL blocks to crystallize into δ-form) was similar to that of PE blocks without any detectable induction time, so simultaneous crystallization of PE and δPPL blocks was observed on quenching from a lamellar microdomain structure (LMS), yielding a largely distorted LMS (with the standard deviation of each lamella thickness ∼ 36%).
Widespread reduction of these active marks affecting >1 kb blocks was observed on many genes repressed by Hairy, including ftz and other segmentally expressed genes such as h and 18w.
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Large LD blocks were found on chromosomes 4, 6, 9, and 11 of Cluster 3, whereas a clear large LD block was observed on chromosome 11 in Cluster 4. Within each block, higher LD values were observed along with the oblong bars, and not diagonally.
No decrease in staining intensity on older paraffin blocks was observed.
Non-isogenic blocks were generally found as stretches of SNPs of coherent genotypes, whereas recombination within non-isogenic blocks was observed in a few cases only (e.g. blocks on chromosomes 3 and 6 in NIL pair 3.05_R40).
However, no single main effect of blocks was observed.
The biggest difference for the average LD block size was observed on the X chromosome, and there was about a 2∶1 ratio between the LD block sizes for the high-CEU and low-CEU groups.
The level of LD, measured as r 2, was calculated for the significant SNPs in the BS11-derived population and various LD blocks were observed depending on the particular cycle of selection.
The biggest block for the high-CEU group, 397 Kb, was observed on chromosome 10, whereas the biggest block for the low-CEU group was 273 Kb.
In HapMap CEU, nearly the entire region is in moderate LD, whereas in HapMap YRI two distinct LD blocks are observed (ESM Fig. 2) and lower (on average) r values are observed between rs625643 and downstream SNPs (0.78 for CEU and 0.5 for YRI).
Extension veins, which developed only in sandstone blocks, were observed.
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