Methods for prediction of peptide binding to MHC molecules: A comparative study

Background: A variety of methods for prediction of peptide binding to major histocompatibility complex (MHC) have been proposed. These methods are based on binding motifs, binding matrices, hidden Markov models (HMM), or artificial neural networks (ANN). There has been little prior work on the comparative analysis of these methods. Materials and Methods: We performed a comparison of the performance of six methods applied to the prediction of two human MHC class I molecules, including binding matrices and motifs, ANNs, and HMMs. Results: The selection of the optimal prediction method depends on the amount of available data (the number of peptides of known binding affinity to the MHC molecule of interest), the biases in the data set and the intended purpose of the prediction (screening of a single protein versus mass screening). When little or no peptide data are available, binding motifs are the most useful alternative to random guessing or use of a complete overlapping set of peptides for selection of candidate binders. As the number of known peptide binders increases, binding matrices and HMM become more useful predictors. ANN and HMM are the predictive methods of choice for MHC alleles with more than 100 known binding peptides. Conclusion: The ability of bioinformatic methods to reliably predict MHC binding peptides, and thereby potential T-cell epitopes, has major implications for clinical immunology, particularly in the area of vaccine design.

On entanglement and Lorentz transformations

We study the transformation of maximally entangled states under the action of Lorentz transformations in a fully relativistic setting. By explicit calculation of the Wigner rotation, we describe the relativistic analog of the Bell states as viewed from two inertial frames moving with constant velocity with respect to each other. Though the finite dimensional matrices describing the Lorentz transformations are non-unitary, each single particle state of the entangled pair undergoes an effective, momentum dependent, local unitary rotation, thereby preserving the entanglement fidelity of the bipartite state. The details of how these unitary transformations are manifested are explicitly worked out for the Bell states comprised of massive spin 1/2 particles and massless photon polarizations. The relevance of this work to non-inertial frames is briefly discussed.

Neighborhood and Efficiency in Manufacturing in Brazilian Regions: A Spatial Markov Chain Analysis

This paper analyzes the geography of regional competitiveness in manufacturing in Brazil. The authors estimate stochastic frontiers to calculate regional efficiency of representative firms in 137 regions in the period 2000-2006, in four sectors defined by technological intensity. The efficiency results are analyzed using Markov Spatial Transition Matrices to provide insights into the transition of regions between efficiency levels, considering their local spatial context. The results indicate that geography plays an important role in manufacturing competitiveness. In particular, regions with more competitive neighbors are more likely to improve their relative efficiency (pull effect) over time, and regions with less competitive neighbors are more likely to lose relative efficiency (drag effect). The authors find that the pull effect is stronger than the drag effect.

A comparative study of similarity measures for manufacturing cell formation

We introduced a spectral clustering algorithm based on the bipartite graph model for the Manufacturing Cell Formation problem in [Oliveira S, Ribeiro JFF, Seok SC. A spectral clustering algorithm for manufacturing cell formation. Computers and Industrial Engineering. 2007 [submitted for publication]]. It constructs two similarity matrices; one for parts and one for machines. The algorithm executes a spectral clustering algorithm on each separately to find families of parts and cells of machines. The similarity measure in the approach utilized limited information between parts and between machines. This paper reviews several well-known similarity measures which have been used for Group Technology. Computational clustering results are compared by various performance measures. (C) 2008 The Society of Manufacturing Engineers. Published by Elsevier Ltd. All rights reserved.

A spectral clustering algorithm for manufacturing cell formation

A graph clustering algorithm constructs groups of closely related parts and machines separately. After they are matched for the least intercell moves, a refining process runs on the initial cell formation to decrease the number of intercell moves. A simple modification of this main approach can deal with some practical constraints, such as the popular constraint of bounding the maximum number of machines in a cell. Our approach makes a big improvement in the computational time. More importantly, improvement is seen in the number of intercell moves when the computational results were compared with best known solutions from the literature. (C) 2009 Elsevier Ltd. All rights reserved.

Calcium Carbonate Particle Growth Depending on Coupling among Adjacent Layers in Hybrid LB/LbL Films

There are practical and academic situations that justify the study of calcium carbonate crystallization and especially of systems that are associated with organic matrices and a confined medium. Despite the fact that many different matrices have been studied, the use of well-behaved, thin organic films may provide new knowledge about this system. In this work, we have studied the growth of calcium carbonate particles on well-defined organic matrices that were formed by layer-by-layer (LbL) polyelectrolyte films deposited on phospholipid Langmuir-Blodgett films (LB). We were able to change the surface electrical charge density of the LB films by changing the proportions of a negatively charged lipid, the sodium salt of dimyristoyl-sn-glycero-phosphatidyl acid (DMPA), and a zwitterionic lipid. dimyristoyl-sn-glycero-phosphatidylethanolamine (DMPE). This affects the subsequent polyelectrolyte LbL film deposition, which also changes the the nature of the bonding (electrostatic interaction or hydrogen bonding). This approach allowed for the formation of calcium carbonate particles of different final shapes, roughnesses, and sizes. The masses of deposited lipids, polyelectrolytes, and calcium cabonate were quantified by the quartz crystal microbalance technique. The structures of obtained particles were analyzed by scanning electron microscopy.

Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications

Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes. (C) 2004 Elsevier Inc. All rights reserved.

Self-assembled films from WO(3): Electrochromism and lithium ion diffusion

WO(3)/chitosan and WO(3)/chitosan/poly(ethylene oxide) (PEO) films were prepared by the layer-by-layer method. The presence of chitosan enabled PEO to be carried into the self-assembled structure, contributing to an increase in the Li(+) diffusion rate. On the basis of the galvanostatic intermittent titration technique (GITT) and the quadratic logistic equation (QLE), a spectroelectrochemical method was used for determination of the ""optical"" diffusion coefficient (D(op)), enabling analysis of the Li(+) diffusion rate and, consequently, the coloration front rate in these host matrices. The D(op) values within the WO(3)/chitosan/PEO film were significantly higher than those within the WO(3)/chitosan film, mainly for higher values of injected charge. The presence of PEO also ensured larger accessibility to the electroactive sites, in accordance with the method employed here. Hence, this spectroelectrochemical method allowed us to separate the contribution of the diffusion process from the number of accessible electroactive sites in the materials, thereby aiding a better understanding of the useful electrochemical and electrochromic properties of these films for use in electrochromic devices. (C) 2010 Elsevier B.V. All rights reserved.

Rifampicin determination in plasma by stir bar-sorptive extraction and liquid chromatography

A sensitive and reproducible stir bar-sorptive extraction and high performance liquid chromatography-UV detection (SBSE/HPLC-UV) method for therapeutic drug monitoring of rifampicin in plasma samples is described and compared with a liquid:liquid extraction (LLE/HPLC-UV) method. This miniaturized method can result in faster analysis, higher sample throughput, lower solvent consumption and less workload per sample while maintaining or even improving sensitivity. Important factors in the optimization of SBSE efficiency such as pH, temperature, extraction time and desorption conditions (solvents, mode magnetic stir, mode ultrasonic stir, time and number of steps) were optimized recoveries ranging from 75 to 80%. Separation was obtained using a reverse phase C(8) column with UV detection (254 nm). The mobile phase consisted of methanol:0.25 N sodium acetate buffer, pH 5.0 (58:42, v/v). The SBSE/HPLC-UV method was linear over a working range of 0.125-50.0 mu g mL(-1). The intra-assay and inter-assay precision and accuracy were studied at three concentrations (1.25, 6.25 and 25.0 mu g mL(-1)). The intra-assay coefficients of variation (CVs) for all compounds were less than 10% and all inter-CVs were less than 10%. Limits of quantification were 0.125 mu g mL(-1). Stability studies showed rifampicin was stable in plasma for 12 h after thawing; the samples were also stable for 24 h after preparation. Based on the figures of merit results, the SBSE/HPLC-UV proved to be adequate to the rifampicin analyses from therapeutic to toxic levels. This method was successfully applied to the analysis of real samples and was as effective as the LLE/HPLC-UV method. (C) 2009 Elsevier B.V. All rights reserved.

Effect of mesoporosity of vanadium oxide prepared by sol-gel process as cathodic material evaluated by cyclability during Li(+) insertion/deinsertion

The effect of pore structure on the behavior of lithium intercalation into an electrode containing porous V(2)O(5) film has been investigated and compared with the electrode containing a non-porous V(2)O(5) film. X-ray diffraction patterns indicate a lamellar structure for both materials. Nitrogen adsorption isotherms, t-plot method, and Scanning Electronic Microscopy show that the route employed for the preparation of mesoporous V(2)O(5) was successful. The electrochemical performance of these matrices as lithium intercalation cathode materials was evaluated. The porous material reaches stability after several cycles more easily compared with the V(2)O(5) xerogel. Lithium intercalation into the porous V(2)O(5) film electrode is crucially influenced by pore surface and film surface irregularity, in contrast with the non-porous surface of the V(2)O(5) xerogel.

Spectroelectrochemical Properties and Lithium Ion Storage in Self-Assembled Nanocomposites from TiO(2)

Layer-by-layer (LbL) nanocomposite films from TiO(2) nanoparticles and tungsten-based oxides (WO(x)H(y)), as well as dip-coating films of TiO(2) nano particles, were prepared and investigated by electrochemical techniques under visible light beams, aiming to evaluate the lithium ion storage and chromogenic properties. Atomic force microscopy (AFM) images were obtained for morphological characterization of the Surface of the materials, which have similar roughness. Cyclic voltammetry and chronoamperometry measurements indicated high storage capacity of lithium ions in the LbL nanocomposite compared with the dip-coating film, which was attributed to the faster lithium ion diffusion rate within the self-assembled matrix. On the basis of the data obtained from galvanostatic intermittent titration technique (GITT), the values of lithium ion diffusion coefficient (D(Li)) for TiO(2)/WO(x)H(y) were larger compared with those for TiO(2). The rate of the coloration front in the matrices was investigated using a spectroelectrochemical method based oil GITT, allowing the determination of the ""optical"" diffusion coefficient (D(op)) as a function of the amount of lithium ions previously inserted into the matrices. The Values of D(Li) and D(op) suggested the existence of phases with distinct contribution to lithium ion diffusion rates and electrochromic efficiency. Moreover, these results aided a better understanding of the temporal change of current density and absorbance during the ionic electro-insertion, which is important for the possible application of these materials in lithium ion batteries and electrohromic devices.

HPLC-FLD methods to quantify chloroaluminum phthalocyanine in nanoparticles, plasma and tissue: application in pharmacokinetic and biodistribution studies

Analytical and bioanalytical methods of high-performance liquid chromatography with fluorescence detection (HPLC-FLD) were developed and validated for the determination of chloroaluminum phthalocyanine in different formulations of polymeric nanocapsules, plasma and livers of mice. Plasma and homogenized liver samples were extracted with ethyl acetate, and zinc phthalocyanine was used as internal standard. The results indicated that the methods were linear and selective for all matrices studied. Analysis of accuracy and precision showed adequate values, with variations lower than 10% in biological samples and lower than 2% in analytical samples. The recoveries were as high as 96% and 99% in the plasma and livers, respectively. The quantification limit of the analytical method was 1.12 ng/ml, and the limits of quantification of the bioanalytical method were 15 ng/ml and 75 ng/g for plasma and liver samples, respectively. The bioanalytical method developed was sensitive in the ranges of 15-100 ng/ml in plasma and 75-500 ng/g in liver samples and was applied to studies of biodistribution and pharmacokinetics of AlClPc. (C) 2011 Elsevier B.V. All rights reserved.

Non-diagonal solutions of the reflection equation for the trigonometric A((1)) (n-1) vertex model

We obtain a class of non-diagonal solutions of the reflection equation for the trigonometric A(n-1)((1)) vertex model. The solutions can be expressed in terms of intertwinner matrix and its inverse, which intertwine two trigonometric R-matrices. In addition to a discrete (positive integer) parameter l, 1 less than or equal to l less than or equal to n, the solution contains n + 2 continuous boundary parameters.

Drinfield twists and alegebraic Bethe ansatz of the supersymmetric t-J model

We construct the Drinfeld twists (factorizing F-matrices) for the supersymmetric t-J model. Working in the basis provided by the F-matrix (i.e. the so-called F-basis), we obtain completely symmetric representations of the monodromy matrix and the pseudo-particle creation operators of the model. These enable us to resolve the hierarchy of the nested Bethe vectors for the gl(2\1) invariant t-J model.

Pt/TiO(2)/poly(vinyl sulfonic acid) Layer-by-Layer Films for Methanol Electrocatalytic Oxidation

One major challenge for the widespread application of direct methanol fuel cells (DMFCs) is to decrease the amount of platinum used in the electrodes, which has motivated a search for novel electrodes containing platinum nanoparticles. In this study, platinum nanoparticles were electrodeposited on layer-by-layer (LbL) films from TiO(2) and poly(vinyl sulfonic) (PVS), by immersing the films into a H(2)PtCl(6) solution and applying a 100 mu A current during different electrode position times. Scanning tunnel microscopy (STM) and atomic force microscopy (AFM) images showed increased platinum particle size and electrode roughness for increasing electrodeposition times. The potentiodynamic profile of the electrodes indicated that oxygen-like species in 0.5 mol L(-1) H(2)SO(4) were formed at less positive potentials for the smallest platinum particles. Electrochemical impedance spectroscopy measurements confirmed the high reactivity for the water dissociation and the large amount of oxygen-like species adsorbed on the smallest platinum nanoparticles. This high oxophilicity of the smallest nanoparticles was responsible for the electrocatalytic activity of Pt-TiO(2)/PVS systems for methanol electrooxidation, according to the Langmuir-Hinshelwood bifunctional mechanism. Significantly, the approach used here combining platinum electrodeposition and LbL matrices allows one to both control the particle size and optimize methanol electrooxidation, being therefore promising for producing membrane-electrode assemblies of DMFCs.