Canonical correlation analysis (CCA) and partial least squares (PLS) are well-known techniques for feature extraction from two sets of multidimensional variables. The fundamental difference between CCA and PLS is that CCA maximizes the correlation while PLS maximizes the covariance. Although both CCA and PLS have been applied successfully in various applications, the intrinsic relationship betw...

The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinati...

INTRODUCTION Gastrodia elata tuber (GET) has been widely used in China as a famous herbal medicine. However, the quality control markers (QCMs) for GET still need further investigation. OBJECTIVE To develop a rational strategy based on fingerprint-efficacy relationship modelling to discover the efficacy-related QCMs, using GET as a case study. METHODOLOGY The high-performance liquid chromat...

MOTIVATION DNA microarray analysis is characterized by obtaining a large number of gene variables from a small number of observations. Cluster analysis is widely used to analyze DNA microarray data to make classification and diagnosis of disease. Because there are so many irrelevant and insignificant genes in a dataset, a feature selection approach must be employed in data analysis. The perform...

BACKGROUND Lipidomic analysis was performed to explore differences in lipid profiles between plasma from lean and obese subjects, followed by in vitro methods to examine a role for the identified lipids in endothelial cell pathophysiology. METHODS Plasma was collected from 15 morbidly obese and 13 control subjects. Lipids were extracted from plasma and analyzed using LC/MS, and MS/MS to chara...

We provide an overview of how the underlying philosophy of chemometrics is integrated throughout metabonomic studies. Four steps are demonstrated: (1) definition of the aim, (2) selection of objects, (3) sample preparation and characterization, and (4) evaluation of the collected data. This includes the tools applied for linear modeling, for example, Statistical Experimental Design (SED), Princ...

Clinical features and investigations lack predictive value when diagnosing pneumonia, especially when patients are ventilated and when patients develop ventilator associated pneumonia (VAP). New tools to aid diagnosis are important to improve outcomes. This pilot study examines the potential for metabolic profiling to aid the diagnosis in critical care. In this prospective observational study v...

In this work we present a set of force fields for nine synthetically relevant and/or structurally interesting N-heterocyclic carbenes, including imidazol-, thiazol-, triazol-, imidazolidin-, and pyridine-ylidenes. The bonding parameters were calculated by using a series of geometry optimizations by ab initio methods. For fitting the non-bonding interactions, a water molecule was employed as a p...

The OPLS-AA all-atom force field and the Analytical Generalized Born plus Non-Polar (AGBNP) implicit solvent model, in conjunction with torsion angle conformational search protocols based on the Protein Local Optimization Program (PLOP), are shown to be effective in predicting the native conformations of 57 9-residue and 35 13-residue loops of a diverse series of proteins with low sequence iden...