Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm)

This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three examples are used as illustrations: the first example is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second example contains NMR-metabonomics data, measured on urine samples of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.     

Use of a partial filling technique and reverse migrating micelles in the study of N-methylcarbamate pesticides by micellar electrokinetic chromatography-electrospray ionization mass spectrometry

This study describes three ways to couple micellar electrokinetic chromatography (MEKC) on-line with electrospray ionization mass spectrometry (ESI-MS) for the analysis of N-methylcarbamate pesticides. The methods involved the use of a partial filling (PF) technique under basic conditions and the use of reverse migrating micelles (RMMs) under acidic and basic conditions. The use of RMMs in basic electrolyte solutions required coated capillaries with low electroosmotic flows, and capillaries coated with anionic poly(sodium 2-acrylamide-2-methylpropanesulfonate) were selected for the purpose. Before the on-line MEKC-ESI-MS coupling, the MEKC and MS conditions were separately optimized under off-line conditions. The methods were compared in terms of detection limits and the stability of the electrospray process. The PF method offered good separation but poorer stability of the electrospray relative to the other methods. A more stable electrospray performance was obtained with use of RMMs in acidic electrolyte solutions, but some of the analytes were protonated and could not be detected due to the increase in their retention factors. However, with the use of anionic polymer-coated capillaries and RMMs at pH 8.5, all analytes were successfully separated. The high-salt stacking method was applied to improve the sensitivity of MEKC-ESI-MS and the detection limits were in the range of 0.04-2.0 microg/ml.     

Electron impact mass spectra of 2-(2-pyridyl)methylene-1,3-dicarbonyl compounds: Unusual abundance of the [M + 1]+ ion and the effect of stereochemistry

Electron impact mass spectra of 2-(2-pyridyl)methylene-1,3-dicarbonyl compounds and related heteroaryl species have been investigated. In 3-(2-pyridyl)methylene-2,4-pentanedione, its 6′-methyl and 6′-methoxycarbonyl derivatives and in E- and Z-ethyl 3-oxo-2-(2-pyridyl)methylenebutanoates the base peak arises from the loss of methyl radical from the molecular ion to produce a 3-oxo-3H-indolizinium ion. A marked difference is observed in the behaviour of the geometric isomers of the keto esters. The diketones and E-keto ester carrying a 2-pyridyl substituent and ketone functionality on the same side of the carbon-carbon double bond exhibit an unusually high [M + 1]⁺/[M]^+˙ ratio (about 2.5) under normal ionization conditions (pressure 10–100 μPa). This abnormality is a function of pressure only and independent of temperature. In the case of the Z-keto ester, the corresponding malonate, 3- and 4-(2-pyridyl)methylene-2,4-pentanediones, and 2-furyl, 2-thienyl and phenyl diketone analogues, the ratio does not differ much from that due to the natural isotope abundance. Results for 1,1,1,5,5,5-hexadeuterio-2-(2-pyridyl)-methylene-2,4-pentanedione (strong M + 2 peak) suggest one mass unit transfer as an intermolecular proton shift from a methyl group to give a 3-hydroxy-3-methyl-3H-indolizinium ion. This real mass spectrometric phenomenon is a unique example of low pressure self-chemical ionization.     

Semi-rotating cryogenic modulator for comprehensive two-dimensional gas chromatography

A laboratory-made cryogenic modulator for comprehensive two-dimensional gas chromatography (GCxGC) was constructed and evaluated. Analytes were trapped with carbon dioxide and desorbed with heated GC oven air. The GCxGC system included a non-polar first-dimension column and a semi-polar second-dimension column connected to a flame ionisation detector. A laboratory-written Matlab-based program was used for the data analysis. Peak widths at half height for n-alkanes, obtained with use of new modulator, were at narrowest 60 ms.     

Chemi-Inspired Silicon Allotropes—Experimentally Accessible Si9 Cages as Proposed Building Block for 1D Polymers, 2D Sheets,Single-Walled Nanotubes,and Nanoparticles

Numerous studies on silicon allotropes with three-dimensional networks or as materials of lower dimensionality have been carried out in the past. Herein, allotropes of silicon, which are based on structures of experimentally accessible [Si₉]⁴⁻ clusters known as stable anionic molecular species in neat solids and in solution, are predicted. Hypothetical oxidative coupling under the formation of covalent Si–Si bonds between the clusters leads to uncharged two-, one- and zero-dimensional silicon nanomaterials not suffering from dangling bonds. A large variety of structures are derived and investigated by quantum chemical calculations. Their relative energies are in the same range as experimentally known silicene, and some structures are even energetically more favorable than silicene. Significantly smaller relative energies are reached by the insertion of linkers in form of tetrahedrally connected Si atoms. A chessboard pattern built of Si₉ clusters bridged by tetrahedrally connected Si atoms represents a two-dimensional silicon species with remarkably lower relative energy in comparison with silicene. We discuss the structural and electronic properties of the predicted silicon materials and their building block nido-[Si₉]^4– based on density functional calculations. All considered structures are semiconductors. The band structures exclusively show bands of low dispersion, as is typical for covalent polymers.     

On- and off-resonance spin-lock MR imaging of normal human brain at 0.1 T: possibilities to modify image contrast

The aim of the present investigation was to determine spin lock (SL) relaxation parameters for the normal brain tissues and thus, to provide basis for optimizing the imaging contrast at 0.1 T. 68 healthy volunteers were included. On-resonance spin lock relaxation time (T_1ρ) and off-resonance spin lock relaxation parameters (T_1ρ^off, M_e/M_o), MT parameters (T_1sat, M_s/M_o), and T₁, T₂ were determined for the cortical gray matter, and for the frontal and parietal white matters. The T_1ρ for the frontal and parietal white matters ranged from 110 to 133 ms and from 122 to 155 ms with locking field strengths from 50 μT to 250 μT, respectively. Accordingly, the values for the gray matter ranged from 127 to 155 ms. With a locking field strength of 50 μT, T_1ρ^off for the frontal and parietal white matters were from 114 to 217 ms and from 126 to 219 ms, and for the gray matter from 136 to 267 ms with the angle between the effective magnetic field (B_eff) and the z-axis (θ) ranging from 60° to 15°, respectively. The T_1ρ of the white and gray matters increased significantly with increasing locking field amplitude (p < 0.001). The T_1ρ^off decreased significantly with increasing θ (p < 0.001). T_1ρ and T_1ρ^off with θ ≥ 30° were statistically significantly shorter in the frontal than in the parietal white matters (p < 0.05). The duration, amplitude and θ of the locking pulse provide additional parameters to optimize contrast in brain SL imaging.     

Conical upper density theorems and porosity of measures

We study how measures with finite lower density are distributed around (n−m)-planes in small balls in Rn. We also discuss relations between conical upper density theorems and porosity. Our results may be applied to a large collection of Hausdorff and packing type measures.     

Fast and accurate single-island charge pump: implementation of a cooper pair pump

We introduce a Cooper pair "sluice" for the implementation of a frequency-locked current source. The device consists of two mesoscopic SQUIDs and of a single superconducting island with a gate. We demonstrate theoretically that it is possible to obtain a current as high as 0.1 nA at better than ppm accuracy via periodically modulating both the gate charge and the effective Josephson coupling. We find that the device is tolerant against background charge noise and operates well even in a dissipative environment. The effect of the imperfect suppression of the Josephson coupling and the finite operating frequency are also investigated.     

Continuous two-dimensional field-flow fractionation: a novel technique for continuous separation and collection of macromolecules and particles

Instrumental techniques to analyse macromolecular and particulate materials have undergone rapid development in response to the need for high resolution, precise identification and characterization, and enrichment and collection for further analysis. Continuous two-dimensional field-flow fractionation (2D-FFF), which is described in this article, is a novel technique for separation and collection of macromolecules and particles. 2D-FFF is based on the conventional field-flow fractionation principle but with carrier flow in two-dimensions. This overview discusses the principle of the technique, describes the instrumentation and suggests potential applications and further extensions. An overview of the basic field-flow fractionation principle is presented.     

Non-Gaussianity from preheating

We consider a two-field model for inflation where the second order metric perturbations can be amplified by a parametric resonance during preheating. We demonstrate that there can arise a considerable enhancement of non-Gaussianity sourced by the local terms generated through the coupled perturbations. We argue that the non-Gaussianity parameter could be as large as f(NL) approximately 50. Our results may provide a useful test of preheating in future cosmic microwave background experiments.