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Eleven risk indices were selected and five thousand samples were created for training and testing.
Aβ1 40 baseline samples were created for each time-point by pooling all replicates (see Supplementary material, Fig. S1a).
To test the sensitivity of the results to the minimum growth rate threshold, separate Monte Carlo samples were created for each minimum threshold ranging from 50%to100%0% at 5% increments.
For the 'Schäfer' data set, CN and GE values are drawn from a normal mixture where two components represent aberrations of different extent for each locus; 100 samples were created for each input with mixing proportions of either 10% or 90% for the affected and normal regions.
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Transverse sections of the sample were created for each y-position of the field of view and the reconstruction was repeated slice by slice to create the 3D volumes (supplementary material Movie 2).
Plants in each block were sampled at medium stalk position and a pooled sample was created for each block and analyzed by Inductively Coupled Plasma Mass Spectrometry (ICP-MS) for Cd content in leaves.
cDNA libraries for all samples were created using the TruSeq® RNA Sample Prep Kit v2 48, Set B (Illumina®, cat. no. RS-122-2002), as per the TruSeq® RNA Sample Preparation v2 Guide, Low-Throughput Protocol.
A catalogue and a questionnaire for all the samples were created that included the information from the printed labels of the product packages.
Separate sampling frames were created for maternal and newborn charts.
Based on these settings, analysis sets for each of the individual infected sample cohorts were created for a representative gel using the normalized parameters to identify qualitative changes and a 2-fold increase/decrease to identify quantitative changes.
Variable Number of samples was created to account for possible differences in the amount of data analysed for each object.
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