Bayesian data integration and variable selection for pan‐cancer survival prediction using protein expression data

Accurate prognostic prediction using molecular information is a challenging area of research, which is essential to develop precision medicine. In this paper, we develop translational models to identify major actionable proteins that are associated with clinical outcomes, like the survival time of patients. There are considerable statistical and computational challenges due to the large dimension of the problems. Furthermore, data are available for different tumor types; hence data integration for various tumors is desirable. Having censored survival outcomes escalates one more level of complexity in the inferential procedure. We develop Bayesian hierarchical survival models, which accommodate all the challenges mentioned here. We use the hierarchical Bayesian accelerated failure time model for survival regression. Furthermore, we assume sparse horseshoe prior distribution for the regression coefficients to identify the major proteomic drivers. We borrow strength across tumor groups by introducing a correlation structure among the prior distributions. The proposed methods have been used to analyze data from the recently curated “The Cancer Proteome Atlas” (TCPA), which contains reverse‐phase protein arrays–based high‐quality protein expression data as well as detailed clinical annotation, including survival times. Our simulation and the TCPA data analysis illustrate the efficacy of the proposed integrative model, which links different tumors with the correlated prior structures.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/1/biom13132_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/2/biom13132.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/3/biom13132-sup-0003-supmat.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/4/biom13132-sup-0002-supplementary-v6-22Jul2019.pd

The monitoring system for the aerogel Cherenkov counter of the BELLE detector

We report on a design and performances of a monitoring system developed for the aerogel Cherenkov counters (ACC) of the BELLE detector. The system consists of blue LEDs, a diffuser box, and optical distributors which distribute the LED light to the ACC modules. The employed LED (NSPB series) has been observed to have high reliability on the long term stability and the temprature dependence. The diffuser box is employed to reduce the intrinsic non-uniformity of the LED light intensity. The overall performances of the present monitoring system on uniformity and intensity of the light output have been found to satisfy all the requirements for the monitoring.Comment: 24 pages, LaTeX, 13 eps figures, to be published in Nucl. Instrum. and Meth. A. Postscript file (4.5 MB) is available at http://www-hep.phys.saga-u.ac.jp/~murakami/paper/xxx_accmon.p

Effects of [NaBr] on the rate of intramolecular general base-assisted hydrolysis of N-(2 `-Hydroxyphenyl)phthalimide in the presence of cationic micelles: Kinetic evidence for the probable micellar structural transition

Pseudofirst-order rate constants for aqueous cleavage of N-(2'-hydroxyphenyl)phthalimide (1), obtained at 0.001 M NaOH, 2 x 10(-4) M 1, 2% v/v CH(3)CN, and 30 degrees C, show a nonmonotonic decrease with the increase in the total concentration of cetyltrimethylammonium bromide ([CTABr](T)) within its range >= 9 x 10(-5)-= 0.04 M CTABr and within a [NaBr] range of 0.0-0.005 M. These observations, in view of the pseudophase (PP) model of the micelle, reveal the presence of presumably spherical micelles at <= 3 x 10(-4) M CTABr in the presence of a constant concentration of NaBr within its range of 0.0-0.01 M. The average value of the CTABr micellar binding constant (K(S)) of ionized 1 (i.e., 1(-)), under these conditions, is (1.88 +/- 0.62) x 10(3) M(-1). The increase in [CTABr](T) at 4 x 10(-4) M causes a micellar structural transition from most likely spherical to cylindrical, which is evident from the increase in K(S) values from 3.46 x 10(3) to 11.4 x 10(3) M(-1) with the increase in [CTABr](T) from 4 x 10(-4) to similar to 1 x 10(-3) M in the absence of NaBr. The values of k(obs) at different [NaBr] and at a constant [CTABr](T) follow a kinetic relationship derived from an empirical equation coupled with a PP model of micelle. This relationship gives the value of a kinetic parameter, F(X/S), which represents the fraction of micellized S(-) (S(-) = 1(-)) transferred to the aqueous phase by the limiting concentration of X(-) (X(-) = Br(-)) through ion exchange X(-)/S(-). The value of F(Br/I) is 0.65 +/- 0.1