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For each of the 35 genes, we determined a range in HC fold change gene expression, defined by the HC mean ± 1 standard deviation (SD).
Based on the analysis of differentially expressed genes, we determined that genes of the plant hormone signal transduction pathway was significantly enriched, suggesting that these pathways were modulated in the transgenic plants.
To further examine factors which directly regulate mtDNA encoded genes, we determined TFAM, TFB1M and TFB2M expression.
For SNPs in protein coding genes, we determined whether they caused synonymous or non-synonymous codon substitutions, or resided in UTR regions (Tables S1 and S2, Figure S1).
To gain insight into the biological processes associated with the regulated genes, we determined which GO annotation terms were over-represented.
In addition, by using reporter genes we determined that the low-Mg2+ concentration, acidic media and PhoP regulator induce mgtC expression in S. Typhi.
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For each of the four genes we determine its connection with neighboring genes with maximum mutual information that is also statistically significant, resulting in j c = (3, 1, 1, 1).
Using a downstream Fus1-lacZ reporter gene, we determined that PCSTE3 does not recognize a- or α-factor pheromones as ligands for the receptor.
To facilitate future genetic studies of this important gene, we determined haplotype frequencies and performed linkage disequilibrium (LD) analysis of four different polymorphisms at the PTHR1 locus.
In samples positive for ROP18 gene, we determined by an allele specific PCR, if patients got the upstream insertion positive ROP18 sequence Toxoplasma strain (mouse avirulent strain) or the upstream insertion negative ROP18 sequence Toxoplasma strain (mouse virulent strain).
Secondly, for each gene, we determined an EV occurrence parameter corresponding to the number of time the gene was found to vary in the same way among donors.
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