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H NMR spectra of urine were acquired on a Bruker DRX600 spectrometer operating at 600.13 MHz H observation frequency using the BEST (Bruker Efficient Sample Transfer) 5 mm flow-injection probe for sample delivery and analysis.
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Watermelon provides a number of QC steps including the use of SNP probes for sample relatedness and identification of possible sample mix-ups.
These needs have generated a variety of device designs from microelectrodes for fast scan cyclic voltammetry (FSCV) and electrophysiology to microdialysis probes for sampling and detecting various neurochemicals.
To obtain supervised data on signal-intensity ratios for different copy numbers, as in the previous study (4), we measured the signal intensities of probes for samples with different numbers of X chromosomes in triplicate and used GIM to obtain the signal-intensity ratios of nX (representing each of the X chromosomes, where n = 1, 2, …, 5) to 2X.
The radioactive signal for the mt-tRNAGlu probe was normalized to that of the tRNALeu UUR) probe for each sample.
Text files containing the signal and detection P-values per probe for each sample were imported into FlexArray software v.1.6.2 (McGill University and Genome Quebec Innovation Centre; http://gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e).
Figures 2B 2D show the relationship of power to the various model parameters (e.g. number of associated probes, R2) for sample size of n = 100.
We used the same HF probe for all samples (type D, approximately 80 μm integration width, see Fig. 1 – Wassenberg et al. 2015b).
Bead summary data was imported into GenomeStudio to remove control probes and to produce a text file containing the signal and detection p-values per probe for all samples.
Interview guides typically contained 10-12 sample questions and 4-6 probes for each sample question.
Each array slide was in 8 × 60K format, which tested eight separate samples with approximate 60,000 probes for each sample.
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