Automatic internal calibration in liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry of protein digests

Accurately measured peptide masses can be used for large-scale protein identification from bacterial whole-cell digests as an alternative to tandem mass spectrometry (MS/MS) provided mass measurement errors of a few parts-per-million (ppm) are obtained. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) routinely achieves such mass accuracy either with internal calibration or by regulating the charge in the analyzer cell. We have developed a novel and automated method for internal calibration of liquid chromatography (LC)/FTICR data from whole-cell digests using peptides in the sample identified by concurrent MS/MS together with ambient polydimethyl-cyclosiloxanes as internal calibrants in the mass spectra. The method reduced mass measurement error from 4.3 +/- 3.7 ppm to 0.3 +/- 2.3 ppm in an E. coli LC/FTICR dataset of 1000 MS and MS/MS spectra and is applicable to all analyses of complex protein digests by FTICRMS. Copyright (c) 2006 John Wiley & Sons, Ltd.

A method of synthesis of silicious inorganic ordered materials (MCM-41-SBA-1) employing polyacrylic acid-C(n)TAB-TEOS nanoassemblies

In this work we describe the synthesis of a variety of MCM-41 type hexagonal and SBA-1 type cubic mesostructures and mesoporous silicious materials employing a novel synthesis concept based on polyacrylic acid (Pac)-C(n)TAB complexes as backbones of the developing structures. The ordered porosity of the solids was established by XRD and TEM techniques. The synthesis concept makes use of Pac-C(n)TAB nanoassemblies as a preformed scaffold, formed by the gradual increase of pH. On this starting matrix the inorganic precursor species SiO2 precipitate via hydrolysis of TEOS under the influence of increasing pH. The molecular weight (MW) of Pac, as well as the length of carbon chain in C,TAB, determine the physical and structural characteristics of the obtained materials. Longer chain surfactants (C(16)TAB) lead to the formation of hexagonal phase, while shorter chain surfactants (C(14)TAB, C(12)TAB) favor the SBA-1 phase. Lower MW of Pac (approximate to2000) leads to better-organized structures compared to higher MW ( 450,000), which leads to worm-like mesostructures. Cell parameters and pore size increase with increasing polyelectrolyte and/or surfactant chain, while at the same time SEM photography reveals that the particle size decreases. Conductivity experiments provide some insight into the proposed self-assembling pathway. (C) 2003 Elsevier Inc. All rights reserved.

Impact damage characterisation of thermoplastic matrix composites using transmission transient thermography

In this work, IR thermography is used as a non-destructive tool for impact damage characterisation on thermoplastic E-glass/polypropylene composites for automotive applications. The aim of this experimentation was to compare impact resistance and to characterise damage patterns of different laminates, in order to provide indications for their use in components. Two E-glass/polypropylene composites, commingled ®Twintex (with three different weave structures: directional, balanced and 3-D) and random reinforced GMT, were in particular characterised. Directional and balanced Twintex were also coupled in a number of hybrid configurations with GMT to evaluate the possible use of GMT/Twintex hybrids in high-energy absorption components. The laminates were impacted using a falling weight tower, with impact energies ranging from 15 J to penetration. Using IR thermography during cooling down following a long pulse (3 s), impact damaged areas were characterised and the influence of weave structure on damage patterns was studied. IR thermography offered good accuracy for laminates with thickness not exceeding 3.5 mm: this appears to be a limit for the direct use of this method on components, where more refined signal treatment would probably be needed for impact damage characterisation.

A method of weighting indicators in building energy efficiency assessment

This paper identifies the indicators of energy efficiency assessment in residential building in China through a wide literature review. Indicators are derived from three main sources: 1) The existing building assessment methods; 2)The existing Chinese standards and technology codes in building energy efficiency; 3)Academia research. As a result, we proposed an indicator list by refining the indicators in the above sources. Identified indicators are weighted by the group analytic hierarchy process (AHP) method. Group AHP method is implemented following key steps: Step 1: Experienced experts are selected to form a group; Step 2: A survey is implemented to collect the individual judgments on the importance of indicators in the group; Step 3: Members’ judgments are synthesized to the group judgments; Step 4: Indicators are weighted by AHP on the group judgments; Step 5: Investigation of consistency estimation shows that the consistency of the judgment matrix is accepted. We believe that the weighted indicators in this paper will provide important references to building energy efficiency assessment.

Development of a liquid chromatographic time-of-flight mass spectrometric method for the determination of unlabelled and deuterium-labelled alpha-tocopherol in blood components

A method is described for the analysis of deuterated and undeuterated alpha-tocopherol in blood components using liquid chromatography coupled to an orthogonal acceleration time-of-flight (TOF) mass spectrometer. Optimal ionisation conditions for undeuterated (d0) and tri- and hexadeuterated (d3 or d6) alpha-tocopherol standards were found with negative ion mode electrospray ionisation. Each species produced an isotopically resolved single ion of exact mass. Calibration curves of pure standards were linear in the range tested (0-1.5 muM, 0-15 pmol injected). For quantification of d0 and d6 in blood components following a standard solvent extraction, a stable-isotope-labelled internal standard (d3-alpha-tocopherol) was employed. To counter matrix ion suppression effects, standard response curves were generated following identical solvent extraction procedures to those of the samples. Within-day and between-day precision were determined for quantification of d0- and d6-labelled alpha-tocopherol in each blood component and both averaged 3-10%. Accuracy was assessed by comparison with a standard high-performance liquid chromatography (HPLC) method, achieving good correlation (r(2) = 0.94), and by spiking with known concentrations of alpha-tocopherol (98% accuracy). Limits of detection and quantification were determined to be 5 and 50 fmol injected, respectively. The assay was used to measure the appearance and disappearance of deuterium-labelled alpha-tocopherol in human blood components following deuterium-labelled (d6) RRR-alpha-tocopheryl acetate ingestion. The new LC/TOFMS method was found to be sensitive, required small sample volumes, was reproducible and robust, and was capable of high throughput when large numbers of samples were generated. Copyright (C) 2003 John Wiley Sons, Ltd.

Absorption of isoflavones in humans: effects of food matrix and processing

If soy isoflavones are to be effective in preventing or treating a range of diseases, they must be bioavailable, and thus understanding factors which may alter their bioavailability needs to be elucidated. However, to date there is little information on whether the pharmacokinetic profile following ingestion of a defined dose is influenced by the food matrix in which the isoflavone is given or by the processing method used. Three different foods (cookies, chocolate bars and juice) were prepared, and their isoflavone contents were determined. We compared the urinary and serum concentrations of daidzein, genistein and equol following the consumption of three different foods, each of which contained 50 mg of isoflavones. After the technological processing of the different test foods, differences in aglycone levels were observed. The plasma levels of the isoflavone precursor daidzein were not altered by food matrix. Urinary daidzein recovery was similar for all three foods ingested with total urinary output of 33-34% of ingested dose. Peak genistein concentrations were attained in serum earlier following consumption of a liquid matrix rather than a solid matrix, although there was a lower total urinary recovery of genistein following ingestion of juice than that of the two other foods. (c) 2006 Elsevier Inc. All rights reserved.

Characterisation of blends based on hydroxyethylcellulose and maleic acid-alt-methyl vinyl ether

Hydrophilic polymeric films based on blends of hydroxyethylcellulose and maleic acid-co-methyl vinyl ether were produced by casting from aqueous solutions. The physicochemical properties of the blends have been assessed using Fourier transform infrared spectroscopy, thermal gravimetric analysis, differential scanning calorimetry, dielectric spectroscopy, etc. The pristine films exhibit complete miscibility due to the formation of intermacromolecular hydrogen bonding. The thermal treatment of the blend films leads to cross-linking via intermacromolecular esterification and anhydride formation. The cross-linked materials are able to swell in water and their swelling degree can be easily controlled by temperature and thermal treatment time. The formation of the crosslinks is apparent in the dynamic properties of the blends as observed through the mechanical relaxation and dielectric relaxation spectra. The dielectric characteristics of the material are influenced by the effects of change in the local structure of the blend on the ionic conduction processes and the rate of dipolar relaxation. Separation of these processes is attempted using the dielectric modulus method. Significant deviations from a simple additive rule of mixing on the activation energy are observed consistent with hydrogen bonding and crosslinking of the matrix. This paper indicates a method for the creation of films with good mechanical and physical characteristics by exposing the blends to a relatively mild thermal treatment.

Finding the smallest eigenvalue by the inverse Monte Carlo method with refinement

Finding the smallest eigenvalue of a given square matrix A of order n is computationally very intensive problem. The most popular method for this problem is the Inverse Power Method which uses LU-decomposition and forward and backward solving of the factored system at every iteration step. An alternative to this method is the Resolvent Monte Carlo method which uses representation of the resolvent matrix [I -qA](-m) as a series and then performs Monte Carlo iterations (random walks) on the elements of the matrix. This leads to great savings in computations, but the method has many restrictions and a very slow convergence. In this paper we propose a method that includes fast Monte Carlo procedure for finding the inverse matrix, refinement procedure to improve approximation of the inverse if necessary, and Monte Carlo power iterations to compute the smallest eigenvalue. We provide not only theoretical estimations about accuracy and convergence but also results from numerical tests performed on a number of test matrices.

Monte Carlo methods for matrix computations on the grid

Many scientific and engineering applications involve inverting large matrices or solving systems of linear algebraic equations. Solving these problems with proven algorithms for direct methods can take very long to compute, as they depend on the size of the matrix. The computational complexity of the stochastic Monte Carlo methods depends only on the number of chains and the length of those chains. The computing power needed by inherently parallel Monte Carlo methods can be satisfied very efficiently by distributed computing technologies such as Grid computing. In this paper we show how a load balanced Monte Carlo method for computing the inverse of a dense matrix can be constructed, show how the method can be implemented on the Grid, and demonstrate how efficiently the method scales on multiple processors. (C) 2007 Elsevier B.V. All rights reserved.

A sparse parallel hybrid Monte Carlo algorithm for matrix computations

In this paper we introduce a new algorithm, based on the successful work of Fathi and Alexandrov, on hybrid Monte Carlo algorithms for matrix inversion and solving systems of linear algebraic equations. This algorithm consists of two parts, approximate inversion by Monte Carlo and iterative refinement using a deterministic method. Here we present a parallel hybrid Monte Carlo algorithm, which uses Monte Carlo to generate an approximate inverse and that improves the accuracy of the inverse with an iterative refinement. The new algorithm is applied efficiently to sparse non-singular matrices. When we are solving a system of linear algebraic equations, Bx = b, the inverse matrix is used to compute the solution vector x = B(-1)b. We present results that show the efficiency of the parallel hybrid Monte Carlo algorithm in the case of sparse matrices.

Comparison of the computational cost of a Monte Carlo and deterministic algorithm for computing bilinear forms of matrix powers

In this paper we consider bilinear forms of matrix polynomials and show that these polynomials can be used to construct solutions for the problems of solving systems of linear algebraic equations, matrix inversion and finding extremal eigenvalues. An almost Optimal Monte Carlo (MAO) algorithm for computing bilinear forms of matrix polynomials is presented. Results for the computational costs of a balanced algorithm for computing the bilinear form of a matrix power is presented, i.e., an algorithm for which probability and systematic errors are of the same order, and this is compared with the computational cost for a corresponding deterministic method.

An Exponentially Convergent Nonpolynomial Finite Element Method for Time-Harmonic Scattering from Polygons

In recent years nonpolynomial finite element methods have received increasing attention for the efficient solution of wave problems. As with their close cousin the method of particular solutions, high efficiency comes from using solutions to the Helmholtz equation as basis functions. We present and analyze such a method for the scattering of two-dimensional scalar waves from a polygonal domain that achieves exponential convergence purely by increasing the number of basis functions in each element. Key ingredients are the use of basis functions that capture the singularities at corners and the representation of the scattered field towards infinity by a combination of fundamental solutions. The solution is obtained by minimizing a least-squares functional, which we discretize in such a way that a matrix least-squares problem is obtained. We give computable exponential bounds on the rate of convergence of the least-squares functional that are in very good agreement with the observed numerical convergence. Challenging numerical examples, including a nonconvex polygon with several corner singularities, and a cavity domain, are solved to around 10 digits of accuracy with a few seconds of CPU time. The examples are implemented concisely with MPSpack, a MATLAB toolbox for wave computations with nonpolynomial basis functions, developed by the authors. A code example is included.

Random orthogonal matrix simulation

This paper introduces a method for simulating multivariate samples that have exact means, covariances, skewness and kurtosis. We introduce a new class of rectangular orthogonal matrix which is fundamental to the methodology and we call these matrices L matrices. They may be deterministic, parametric or data specific in nature. The target moments determine the L matrix then infinitely many random samples with the same exact moments may be generated by multiplying the L matrix by arbitrary random orthogonal matrices. This methodology is thus termed “ROM simulation”. Considering certain elementary types of random orthogonal matrices we demonstrate that they generate samples with different characteristics. ROM simulation has applications to many problems that are resolved using standard Monte Carlo methods. But no parametric assumptions are required (unless parametric L matrices are used) so there is no sampling error caused by the discrete approximation of a continuous distribution, which is a major source of error in standard Monte Carlo simulations. For illustration, we apply ROM simulation to determine the value-at-risk of a stock portfolio.

A method for merging flow-dependent forecast error statistics from an ensemble with static statistics for use in high resolution variational data assimilation

The background error covariance matrix, B, is often used in variational data assimilation for numerical weather prediction as a static and hence poor approximation to the fully dynamic forecast error covariance matrix, Pf. In this paper the concept of an Ensemble Reduced Rank Kalman Filter (EnRRKF) is outlined. In the EnRRKF the forecast error statistics in a subspace defined by an ensemble of states forecast by the dynamic model are found. These statistics are merged in a formal way with the static statistics, which apply in the remainder of the space. The combined statistics may then be used in a variational data assimilation setting. It is hoped that the nonlinear error growth of small-scale weather systems will be accurately captured by the EnRRKF, to produce accurate analyses and ultimately improved forecasts of extreme events.

A robust controller design method for feedback substitution schemes using genetic algorithms

Controllers for feedback substitution schemes demonstrate a trade-off between noise power gain and normalized response time. Using as an example the design of a controller for a radiometric transduction process subjected to arbitrary noise power gain and robustness constraints, a Pareto-front of optimal controller solutions fulfilling a range of time-domain design objectives can be derived. In this work, we consider designs using a loop shaping design procedure (LSDP). The approach uses linear matrix inequalities to specify a range of objectives and a genetic algorithm (GA) to perform a multi-objective optimization for the controller weights (MOGA). A clonal selection algorithm is used to further provide a directed search of the GA towards the Pareto front. We demonstrate that with the proposed methodology, it is possible to design higher order controllers with superior performance in terms of response time, noise power gain and robustness.