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Analysis of nuclear alignment was also used to determine how cell direction was influenced by the features.
The primary applications of this probe are preparation and quality assurance of 13C and 15N hyperpolarized contrast agents using PASADENA (parahydrogen and synthesis allow dramatically enhanced nuclear alignment) and other parahydrogen-based methods of hyperpolarization.
Image analysis showed that anisotropic tissue constructs cultured on microfabricated ECM lines possessed a high degree of nuclear alignment similar to that found in vivo; nuclei in isotropic tissues were polymorphic in shape with an apparently random orientation.
Nuclear alignment was significantly increased when cells were cultured on grooved substrates (*** p < 0.001), (see Fig. 2).
We also used the GARD method [ 45] to detect potential signs of recombination in each nuclear alignment.
The nuclear alignment was divided into two data sets: (1) each of the 17 intron loci and (2) combined sequences of all introns.
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Due to the presence of ambiguous areas in the nuclear alignments, we excluded the alignment ambiguities using Gblocks 0.91b [ 79] with default parameters (allowed gap positions = all).
We confirmed that the selected samples produced the same arrangements of evolutionary lineages as the entire plastid and nuclear alignments by generating maximum likelihood (ML) trees using the GTR+ G + I and GTR+ G models, respectively (data not shown).
The combined mitochondrial and nuclear alignments contained 396 variable sites and 195 of these were parsimony informative with 0.015 (SE = 0.001) of average p-distance and TrN+G was determined as the best-fit evolutionary model.
A separate analysis of all mitochondrial and nuclear loci (Alignment 2&3) resulted in high congruent phylogenies.
The 475 bp nuclear ITS alignment contained five distinct haplotypes (Table 3; Figure 3; GenBank sequence accession numbers HQ864695- HQ864699).
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