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Antinuclear antibody or myeloperoxidase-antineutrophil cytoplasmic antibody (ANCA) was not detected, but proteinase 3 (PR3 -ANCA was detected at a low titer (24 enzyme-linked immunosorbant assay unit).
Across the entire dataset, β values for the HM27 differentially methylated probe and assay unit CpG_10 were significantly correlated (r = 0.70, p = 0.0008).
A limiting dilution analysis was applied to the data to estimate the number of viable Leishmania expressed as Limiting Dilution Assay Unit.
Across the entire dataset, β values for the HM27 DMP and assay unit CpG_14.15 were significantly correlated (r = 0.92, p <0.0001).
We quantitatively measured methylation at 11 CpG dinucleotides within 8 assay units at MRPL28 (Additional file 1: Figure S3), including the HM27 differentially-methylated probe (DMP) site (assay unit CpG_14.15).
Figure 3A presents boxplots of methylation values obtained from the array probe in the discovery case-control samples, and from Sequenom assay unit CpG_14.15 in the discovery and replication case-control samples.
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To obtain sufficient numbers of CD19+/IgM+ B cells for each ChIP assay, units were pooled prior to stimulation.
We also quantitatively measured methylation at 10 CpG sites within 9 assay units at the pro-inflammatory cytokine gene IL32.
For all Sequenom assay units, mean β values were lower in cases than controls, consistent with the direction of difference observed by HM27.
Large case-control Δβ values were observed for several Sequenom CpG assay units, especially those lying in close proximity to the HM27 probe (Additional file 1: Table S3).
Absorbances for all four tests were read at a wavelength of 450 nm. Assay units were ng/mL for LCN2, CLU, and sTNFR, and pg/mL for IL-6.
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