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Protein spots exhibiting statistically significant changes in abundance across the 14 gels in the experiment were identified using a student's t-test with applied false discovery rate (FDR) and a p-value threshold of p<0.05.
Genes showing differential expression across the time points of the experiment were identified using SAM (multi-class) analysis [75] implemented in the MEV program of the TM4 microarray data analysis suite (http://TM4.org).
Differential genes from each experiment were identified using the same method used for our own data.
Differentially expressed genes between batches within each experiment were identified using one-way ANOVA within GENESPRING with an FDR corrected p-value threshold of 0.05.
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Component analysis of the corresponding products after electrical explosion experiment is identified using XPS.
The location of the Z-line and M-band in each experiment was identified using monoclonal antibodies that detect α-actinin (Z-line) and myomesin (M-band).
Features commonly differentially expressed in all experiments were identified using a Venn diagram.
Transcripts that were absent across all experiments were identified using Absent/Present calls (Microarray Suite 5.0) and filtered for transcripts that were not expressed in any experiment.
The reaction products formed during our temperature-programmed QMS/MB experiments were identified using a non-line-of-sight quadrupole mass spectrometer in single ion counting mode (Hiden HAL511/PIC), which is connected to the UHV system.
Flame and recirculation-zone structures and soot in the experiments are identified using direct photographs taken with and without Mie scattering from soot particles as well as laser-induced-incandescence (LII) measurements.
For both types of experiment peptides were identified using MASCOT 2.3 to search a custom database containing SWISSPROT human and bovine sequences and randomised versions thereof (bovine sequences were included as the secretomes will inevitably contain traces of FCS).
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