MIA and NIR Chemical Imaging for pharmaceutical product characterization

[EN] This paper presents a three step methodology based on the use of chemical oriented models (MCR and CLS) for extracting out the chemical distribution maps (CDMs) from hyperspectral images, afterwards performing multivariate image analysis (MIA) on the CDMs, and !nally extracting 'channel' and textural features from the score images related to quality characteristics These features show complementary properties to those directly obtained from the CDMs, since they take advantage of their internal correlation structure. The approach has been successfully applied to the evaluation of homogeneity and cluster presence of API in a novel formulation developed to improve the dissolution of poorly soluble drugs. © 2012 Elsevier B.V. All rights reserved.Research in this study was partially supported by the Spanish Ministry of Science and Innovation and FEDER funds from the European Union through grant DPI2011-28112-C04-02, and also by NSF-Engineering Research Center for Structured Organic Particulate Systems (ERC-SOPS, EEC-0540855) and the program NSF-Major Research Instrumentation grant 0821113.Prats-Montalbán, JM.; Jerez-Rozo, J.; Romanach, R.; Ferrer Riquelme, AJ. (2012). MIA and NIR Chemical Imaging for pharmaceutical product characterization. Chemometrics and Intelligent Laboratory Systems. 117(117):240-249. https://doi.org/10.1016/j.chemolab.2012.04.002S24024911711

Preprocessing differential methylation hybridization microarray data

<p>Abstract</p> <p>Background</p> <p>DNA methylation plays a very important role in the silencing of tumor suppressor genes in various tumor types. In order to gain a genome-wide understanding of how changes in methylation affect tumor growth, the differential methylation hybridization (DMH) protocol has been developed and large amounts of DMH microarray data have been generated. However, it is still unclear how to preprocess this type of microarray data and how different background correction and normalization methods used for two-color gene expression arrays perform for the methylation microarray data. In this paper, we demonstrate our discovery of a set of internal control probes that have log ratios (M) theoretically equal to zero according to this DMH protocol. With the aid of this set of control probes, we propose two LOESS (or LOWESS, locally weighted scatter-plot smoothing) normalization methods that are novel and unique for DMH microarray data. Combining with other normalization methods (global LOESS and no normalization), we compare four normalization methods. In addition, we compare five different background correction methods.</p> <p>Results</p> <p>We study 20 different preprocessing methods, which are the combination of five background correction methods and four normalization methods. In order to compare these 20 methods, we evaluate their performance of identifying known methylated and un-methylated housekeeping genes based on two statistics. Comparison details are illustrated using breast cancer cell line and ovarian cancer patient methylation microarray data. Our comparison results show that different background correction methods perform similarly; however, four normalization methods perform very differently. In particular, all three different LOESS normalization methods perform better than the one without any normalization.</p> <p>Conclusions</p> <p>It is necessary to do within-array normalization, and the two LOESS normalization methods based on specific DMH internal control probes produce more stable and relatively better results than the global LOESS normalization method.</p

An improved method for detecting and delineating genomic regions with altered gene expression in cancer

A method is presented for identifying genomic regions with altered gene expression in gene expression maps