Predicting survival from microarray data--a comparative study

MOTIVATION: Survival prediction from gene expression data and other high-dimensional genomic data has been subject to much research during the last years. These kinds of data are associated with the methodological problem of having many more gene expression values than individuals. In addition, the responses are censored survival times. Most of the proposed methods handle this by using Cox's proportional hazards model and obtain parameter estimates by some dimension reduction or parameter shrinkage estimation technique. Using three well-known microarray gene expression data sets, we compare the prediction performance of seven such methods: univariate selection, forward stepwise selection, principal components regression (PCR), supervised principal components regression, partial least squares regression (PLS), ridge regression and the lasso. RESULTS: Statistical learning from subsets should be repeated several times in order to get a fair comparison between methods. Methods using coefficient shrinkage or linear combinations of the gene expression values have much better performance than the simple variable selection methods. For our data sets, ridge regression has the overall best performance. AVAILABILITY: Matlab and R code for the prediction methods are available at http://www.med.uio.no/imb/stat/bmms/software/microsurv/.     

CGH-Explorer: a program for analysis of array-CGH data

SUMMARY: CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.     

The capsule polysaccharide structure and biogenesis for non-O1 Vibrio cholerae NRT36S: genes are embedded in the LPS region

Background  

In V. cholerae, the biogenesis of capsule polysaccharide is poorly understood. The elucidation of capsule structure and biogenesis is critical to understanding the evolution of surface polysaccharide and the internal relationship between the capsule and LPS in this species. V. cholerae serogroup O31 NRT36S, a human pathogen that produces a heat-stable enterotoxin (NAG-ST), is encapsulated. Here, we report the covalent structure and studies of the biogenesis of the capsule in V. cholerae NRT36S.     

Reproducibility and repeatability of measuring the electrical impedance of the pregnant human cervix-the effect of probe size and applied pressure

Background  

The utility of cervical electrical impedance spectroscopy (EIS) as a diagnostic tool is being investigated in clinical trials. We sought to assess the reliability of two different sizes of tetrapolar probes used in measuring cervical impedance.     

Comparison of human uterine cervical electrical impedance measurements derived using two tetrapolar probes of different sizes

Background  

We sought to compare uterine cervical electrical impedance spectroscopy measurements employing two probes of different sizes, and to employ a finite element model to predict and compare the fraction of electrical current derived from subepithelial stromal tissue.     

Circulating levels of matrix proteases and their inhibitors in pregnant women with and without a history of recurrent pregnancy loss

Background  

We have recently shown that serum relaxin-2 levels are attenuated in women with a history of recurrent pregnancy loss (RPL). We sought to determine whether a history of RPL is also associated with changes in serum matrix metalloproteases (MMPs) and tissue inhibitors of matrix metalloproteases (TIMP) -1 and -2.