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Our analyses refer to predictors of catch-up during a period when parental concerns around the safety of the vaccine were relatively high, and the incidence of measles relatively low; predictors of catch-up in families with young children today may be different.
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The research-based PAM50 intrinsic subtype and claudin-low predictors were used to assign intrinsic subtype to samples [ 17, 18].
Human claudin-low tumor samples were identified using either SigClust [ 22] or the nine-cell line claudin-low predictor.
Prediction of the claudin-low subtype was done using the claudin-low predictor developed in Prat et al [ 27].
Next, claudin-low cell lines were identified using the previously reported 9-cell line claudin-low predictor [ 1].
The nine-cell line claudin-low predictor identified 37 samples (~11%) as claudin-low, including the 28 claudin-low samples previously identified by hierarchical clustering.
Samples identified by SigClust [ 22] or the nine-cell line claudin-low predictor were called claudin-low, regardless of the PAM50 call.
Finally, from the claudin-low predictor, we evaluated the Euclidian distance of each sample to the claudin-low 9-cell line centroid.
Conversely, the nine-cell line claudin-low predictor identified the MaSC and stromal (CD49flow/EpCAM-) subpopulations of Lim et al. [ 24] as claudin-low, and as expected, both subpopulations showed the highest and lowest expression of the up- and downregulated genes that define the nine-cell line claudin-low predictor.
Overall, the nine-cell line claudin-low predictor showed 87.5% sensitivity, 97.0% specificity, and 75.7% and 98.7% positive and negative predictive values, respectively, if the SigClust-defined claudin-low group is considered the gold standard.
However, we acknowledge a potential caveat of the nine-cell line claudin-low predictor, which is that tumors with high stromal content might also be identified as claudin-low.
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CEO of Professional Science Editing for Scientists @ prosciediting.com