The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods

Biological experiments often produce enormous amount of data, which are usually analyzed by data clustering. Cluster analysis refers to statistical methods that are used to assign data with similar properties into several smaller, more meaningful groups. Two commonly used clustering techniques are introduced in the following section: principal component analysis (PCA) and hierarchical clustering. PCA calculates the variance between variables and groups them into a few uncorrelated groups or principal components (PCs) that are orthogonal to each other. Hierarchical clustering is carried out by separating data into many clusters and merging similar clusters together. Here, we use an example of human leukocyte antigen (HLA) supertype classification to demonstrate the usage of the two methods. Two programs, Generating Optimal Linear Partial Least Square Estimations (GOLPE) and Sybyl, are used for PCA and hierarchical clustering, respectively. However, the reader should bear in mind that the methods have been incorporated into other software as well, such as SIMCA, statistiXL, and R.

Oblique matching pursuit

A method for selecting a suitable subspace for discriminating signal components through an oblique projection is proposed. The selection criterion is based on the consistency principle introduced by Unser and Aldroubi and extended by Elder. An effective implementation of this principle for the purpose of subspace selection is achieved by updating of the dual vectors yielding the corresponding oblique projector. © 2007 IEEE.

Power-controlled phase-matching and instability of CW propagation in multicore optical fibers with a central core

We present modulation instability analysis including azimuthal perturbations of steady-state continuous wave (CW) propagation in multicore-fiber configurations with a central core. In systems with a central core, a steady CW evolution regime requires power-controlled phase matching, which offers interesting spatial-division applications. Our results have general applicability and are relevant to a range of physical and engineering systems, including high-power fiber lasers, optical transmission in multicore fiber, and systems of coupled nonlinear waveguides. © 2013 Optical Society of America.

Peptide binding to the HLA-DRB1 supertype:a proteochemometrics analysis

A proteochemometrics approach was applied to a set of 2666 peptides binding to 12 HLA-DRB1 proteins. Sequences of both peptide and protein were described using three z-descriptors. Cross terms accounting for adjacent positions and for every second position in the peptides were included in the models, as well as cross terms for peptide/protein interactions. Models were derived based on combinations of different blocks of variables. These models had moderate goodness of fit, as expressed by r2, which ranged from 0.685 to 0.732; and good cross-validated predictive ability, as expressed by q2, which varied from 0.678 to 0.719. The external predictive ability was tested using a set of 356 HLA-DRB1 binders, which showed an r2(pred) in the range 0.364-0.530. Peptide and protein positions involved in the interactions were analyzed in terms of hydrophobicity, steric bulk and polarity.

Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide:can the α3 and β2m domains be neglected?

Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histo-compatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVY-DGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histocompatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVYDGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available for this study allow us to compare directly differences in the behavior of very large molecular models; in this case, the entire extracellular portion of the peptide–MHC complex vs. the isolated peptide binding domain. Comparison of the results from the partial and the whole system simulations indicates that the peptide is less tightly bound in the partial system than in the whole system. From a detailed study of conformations, solvent-accessible surface area, the nature of the water network structure, and the binding energies, we conclude that, when considering the conformation of the α1–α2 domain, the α3 and β2m domains cannot be neglected. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1803–1813, 2004

A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily

Epitope identification is the basis of modern vaccine design. The present paper studied the supermotif of the HLA-A3 superfamily, using comparative molecular similarity indices analysis (CoMSIA). Four alleles with high phenotype frequencies were used: A*1101, A*0301, A*3101 and A*6801. Five physicochemical properties—steric bulk, electrostatic potential, local hydro-phobicity, hydrogen-bond donor and acceptor abilities—were considered and ‘all fields’ models were produced for each of the alleles. The models have a moderate level of predictivity and there is a good correlation between the data. A revised HLA-A3 supermotif was defined based on the comparison of favoured and disfavoured properties for each position of the MHC bound peptide. The present study demonstrated that CoMSIA is an effective tool for studying peptide–MHC interactions.

The HLA-A2-supermotif:a QSAR definition

Identification of epitopes capable of binding multiple HLA types will significantly rationalise the development of epitope-based vaccines. A quantitative method assessing the contribution of each amino acid at each position was applied to over 500 nonamer peptides binding to 5 MHC alleles — A*0201, A*0202, A*0203, A*0206 and A*6802 — which together define the HLA-A2-like supertype. FXIGXI (L)IFV was identified as a supermotif for the A2-supertype based on the contributions of the common preferred amino acids at each of the nine positions. The results indicate that HLA-A*6802 is an intermediate allele standing between A2 and A3 supertypes: at anchor position 2 it is closer to A3 and at anchor position 9 it is nearer to A2. Models are available free on-line at http://www.jenner.ac.uk/MHCPred and can be used for binding affinity prediction.

An edge-based matching kernel through discrete-time quantum walks

In this paper, we propose a new edge-based matching kernel for graphs by using discrete-time quantum walks. To this end, we commence by transforming a graph into a directed line graph. The reasons of using the line graph structure are twofold. First, for a graph, its directed line graph is a dual representation and each vertex of the line graph represents a corresponding edge in the original graph. Second, we show that the discrete-time quantum walk can be seen as a walk on the line graph and the state space of the walk is the vertex set of the line graph, i.e., the state space of the walk is the edges of the original graph. As a result, the directed line graph provides an elegant way of developing new edge-based matching kernel based on discrete-time quantum walks. For a pair of graphs, we compute the h-layer depth-based representation for each vertex of their directed line graphs by computing entropic signatures (computed from discrete-time quantum walks on the line graphs) on the family of K-layer expansion subgraphs rooted at the vertex, i.e., we compute the depth-based representations for edges of the original graphs through their directed line graphs. Based on the new representations, we define an edge-based matching method for the pair of graphs by aligning the h-layer depth-based representations computed through the directed line graphs. The new edge-based matching kernel is thus computed by counting the number of matched vertices identified by the matching method on the directed line graphs. Experiments on standard graph datasets demonstrate the effectiveness of our new kernel.

A stable graph-based representation for object recognition through high-order matching

Many Object recognition techniques perform some flavour of point pattern matching between a model and a scene. Such points are usually selected through a feature detection algorithm that is robust to a class of image transformations and a suitable descriptor is computed over them in order to get a reliable matching. Moreover, some approaches take an additional step by casting the correspondence problem into a matching between graphs defined over feature points. The motivation is that the relational model would add more discriminative power, however the overall effectiveness strongly depends on the ability to build a graph that is stable with respect to both changes in the object appearance and spatial distribution of interest points. In fact, widely used graph-based representations, have shown to suffer some limitations, especially with respect to changes in the Euclidean organization of the feature points. In this paper we introduce a technique to build relational structures over corner points that does not depend on the spatial distribution of the features. © 2012 ICPR Org Committee.

Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0:a quantitative molecular docking study

Background: HLA-DPs are class II MHC proteins mediating immune responses to many diseases. Peptides bind MHC class II proteins in the acidic environment within endosomes. Acidic pH markedly elevates association rate constants but dissociation rates are almost unchanged in the pH range 5.0 - 7.0. This pH-driven effect can be explained by the protonation/deprotonation states of Histidine, whose imidazole has a pKa of 6.0. At pH 5.0, imidazole ring is protonated, making Histidine positively charged and very hydrophilic, while at pH 7.0 imidazole is unprotonated, making Histidine less hydrophilic. We develop here a method to predict peptide binding to the four most frequent HLA-DP proteins: DP1, DP41, DP42 and DP5, using a molecular docking protocol. Dockings to virtual combinatorial peptide libraries were performed at pH 5.0 and pH 7.0. Results: The X-ray structure of the peptide - HLA-DP2 protein complex was used as a starting template to model by homology the structure of the four DP proteins. The resulting models were used to produce virtual combinatorial peptide libraries constructed using the single amino acid substitution (SAAS) principle. Peptides were docked into the DP binding site using AutoDock at pH 5.0 and pH 7.0. The resulting scores were normalized and used to generate Docking Score-based Quantitative Matrices (DS-QMs). The predictive ability of these QMs was tested using an external test set of 484 known DP binders. They were also compared to existing servers for DP binding prediction. The models derived at pH 5.0 predict better than those derived at pH 7.0 and showed significantly improved predictions for three of the four DP proteins, when compared to the existing servers. They are able to recognize 50% of the known binders in the top 5% of predicted peptides. Conclusions: The higher predictive ability of DS-QMs derived at pH 5.0 may be rationalised by the additional hydrogen bond formed between the backbone carbonyl oxygen belonging to the peptide position before p1 (p-1) and the protonated ε-nitrogen of His 79β. Additionally, protonated His residues are well accepted at most of the peptide binding core positions which is in a good agreement with the overall negatively charged peptide binding site of most MHC proteins. © 2012 Patronov et al.; licensee BioMed Central Ltd.

Determining the change of Brillouin frequency shift by using the similarity matching method

We have proposed a similarity matching method (SMM) to obtain the change of Brillouin frequency shift (BFS), in which the change of BFS can be determined from the frequency difference between detecting spectrum and selected reference spectrum by comparing their similarity. We have also compared three similarity measures in the simulation, which has shown that the correlation coefficient is more accurate to determine the change of BFS. Compared with the other methods of determining the change of BFS, the SMM is more suitable for complex Brillouin spectrum profiles. More precise result and much faster processing speed have been verified in our simulation and experiments. The experimental results have shown that the measurement uncertainty of the BFS has been improved to 0.72 MHz by using the SMM, which is almost one-third of that by using the curve fitting method, and the speed of deriving the BFS change by the SMM is 120 times faster than that by the curve fitting method.

Permanent matching of coupled optical bottle resonators with better than 0.16 GHz precision

The fabrication precision is one of the most critical challenges to the creation of practical photonic circuits composed of coupled high Q-factor microresonators. While very accurate transient tuning of microresonators based on local heating has been reported, the record precision of permanent resonance positioning achieved by post-processing is still within 1 and 5 GHz. Here we demonstrate two coupled bottle microresonators fabricated at the fiber surface with resonances that are matched with a better than 0.16 GHz precision. This corresponds to a better than 0.17 Å precision in the effective fiber radius variation. The achieved fabrication precision is only limited by the resolution of our optical spectrum analyzer and can be potentially improved by an order of magnitude.

Handwritten and machine-printed text discrimination using a template matching approach

We propose a novel template matching approach for the discrimination of handwritten and machine-printed text. We first pre-process the scanned document images by performing denoising, circles/lines exclusion and word-block level segmentation. We then align and match characters in a flexible sized gallery with the segmented regions, using parallelised normalised cross-correlation. The experimental results over the Pattern Recognition & Image Analysis Research Lab-Natural History Museum (PRImA-NHM) dataset show remarkably high robustness of the algorithm in classifying cluttered, occluded and noisy samples, in addition to those with significant high missing data. The algorithm, which gives 84.0% classification rate with false positive rate 0.16 over the dataset, does not require training samples and generates compelling results as opposed to the training-based approaches, which have used the same benchmark.

QoE-aware power management in vehicle-to-grid networks:a matching-theoretic approach

Frequency, time and places of charging and discharging have critical impact on the Quality of Experience (QoE) of using Electric Vehicles (EVs). EV charging and discharging scheduling schemes should consider both the QoE of using EV and the load capacity of the power grid. In this paper, we design a traveling plan-aware scheduling scheme for EV charging in driving pattern and a cooperative EV charging and discharging scheme in parking pattern to improve the QoE of using EV and enhance the reliability of the power grid. For traveling planaware scheduling, the assignment of EVs to Charging Stations (CSs) is modeled as a many-to-one matching game and the Stable Matching Algorithm (SMA) is proposed. For cooperative EV charging and discharging in parking pattern, the electricity exchange between charging EVs and discharging EVs in the same parking lot is formulated as a many-to-many matching model with ties, and we develop the Pareto Optimal Matching Algorithm (POMA). Simulation results indicates that the SMA can significantly improve the average system utility for EV charging in driving pattern, and the POMA can increase the amount of electricity offloaded from the grid which is helpful to enhance the reliability of the power grid.

Matching theory based travel plan aware charging algorithms in V2G smart grid networks

The frequency, time and places of charging have large impact on the Quality of Experience (QoE) of EV drivers. It is critical to design effective EV charging scheduling system to improve the QoE of EV drivers. In order to improve EV charging QoE and utilization of CSs, we develop an innovative travel plan aware charging scheduling scheme for moving EVs to be charged at Charging Stations (CS). In the design of the proposed charging scheduling scheme for moving EVs, the travel routes of EVs and the utility of CSs are taken into consideration. The assignment of EVs to CSs is modeled as a two-sided many-to-one matching game with the objective of maximizing the system utility which reflects the satisfactory degrees of EVs and the profits of CSs. A Stable Matching Algorithm (SMA) is proposed to seek stable matching between charging EVs and CSs. Furthermore, an improved Learning based On-LiNe scheduling Algorithm (LONA) is proposed to be executed by each CS in a distributed manner. The performance gain of the average system utility by the SMA is up to 38.2% comparing to the Random Charging Scheduling (RCS) algorithm, and 4.67% comparing to Only utility of Electric Vehicle Concerned (OEVC) scheme. The effectiveness of the proposed SMA and LONA is also demonstrated by simulations in terms of the satisfactory ratio of charging EVs and the the convergence speed of iteration.