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The concordance index of the prognostic nomogram for predicting OS in the training set and validation set were 0.70 and 0.66, respectively. Our data showed that the PBC EBV DNA load was an independent and robust survival biomarker, which remained significant even after adjusting for plasma EBV DNA loads in a subset of 205 patients of the cohort (HR 1.88; = 0.025). Importantly, a combination of PBC EBV DNA load and plasma EBV DNA load improved the predicted OS. The EBV-DNA load in PBCs may be an independent prognosis marker for NPC patient