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The procedures adopted in this study are consistent with those conducted in the preliminary validation of the PIPP in an Australian sample (for details see [ 9]; for a more detailed description of Rasch analysis procedures, see [ 32]).
The digested or undigested 30 kDa filtered SGH provided for MS/MS identification of 11 of the 15 peptides reported in additional file 2, while the front of the gel shown in Figure 1 allowed for identification of two peptides, also identified by MS/MS of the filtrated sample (for details see Methods section).
Both endogenous and exogenous N7-methyl-G and O-methyl-dG were analyzed using sensitive LC-MS/MS methods employing selected reaction monitoring with detection limits of one N7-methyl-G/10 dG and one O-methyl-dG/10 dG per sample (for details, see Supporting Information).
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The study population (n = 82) comprised 58 H. pylori infected patient samples (for details of number of cases analyzed in each category, please see Figure 3) obtained from cases reporting mainly to the Deccan College of Medical Sciences and Allied Hospitals, (DCMS), Hyderabad, and 24 clinically healthy donors.
Nine are common in the top 20 list of most expressed snoRNAs in the two respective samples (for details see Additional files 5 and 6).
Following preprocessing, the data consisted of 138 interventional single-gene deletion profiles and 67 observational wild type samples (for details on data preprocessing see Supplementary Materials Section 3.3).
The study used a cross-sectional survey design using multi-stage cluster sampling (for details on sampling see (Roberts et al., 2008)), and the sample population was adult (≥ 18 years old) male and female IDPs.
In this work, we used 1920 metagenomic samples from the project "Moving pictures of human microbiome" [ 26] to build the microbial matrix and similarity network (refer to section "Similarity measurements of metagenomic samples" for details).
An optional position-specific correction of reads (step 6) can be performed if standard samples are provided by the user (typically a single cloned allele amplified and sequenced along with the samples; for details see Supplementary Materials).
Inputs for the alignment software were chromatograms of ten different individuals analysed both spiked and non-spiked (see " Control samples" for details) and the set of parameters for peak detection and alignment.
We checked 18 randomly selected genes at 2 dpa in three biological replicates for homoeolog contributions to the transcriptome for domesticated G. hirsutum samples (for details of validation design, see Supplementary methods in Additional file 6).
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