Grayscale and colour image Codec based on matching pursuit in the spatio-frequency domain

This report presents and evaluates a novel idea for scalable lossy colour image coding with Matching Pursuit (MP) performed in a transform domain. The benefits of the idea of MP performed in the transform domain are analysed in detail. The main contribution of this work is extending MP with wavelets to colour coding and proposing a coding method. We exploit correlations between image subbands after wavelet transformation in RGB colour space. Then, a new and simple quantisation and coding scheme of colour MP decomposition based on Run Length Encoding (RLE), inspired by the idea of coding indexes in relational databases, is applied. As a final coding step arithmetic coding is used assuming uniform distributions of MP atom parameters. The target application is compression at low and medium bit-rates. Coding performance is compared to JPEG 2000 showing the potential to outperform the latter with more sophisticated than uniform data models for arithmetic coder. The results are presented for grayscale and colour coding of 12 standard test images.

Interocular suppression is gated by interocular feature matching

We present a new form of contrast masking in which the target is a patch of low spatial frequency grating (0.46 c/deg) and the mask is a dark thin ring that surrounds the centre of the target patch. In matching and detection experiments we found little or no effect for binocular presentation of mask and test stimuli. But when mask and test were presented briefly (33 or 200 ms) to different eyes (dichoptic presentation), masking was substantial. In a 'half-binocular' condition the test stimulus was presented to one eye, but the mask stimulus was presented to both eyes with zero-disparity. This produced masking effects intermediate to those found in dichoptic and full-binocular conditions. We suggest that interocular feature matching can attenuate the potency of interocular suppression, but unlike in previous work (McKee, S. P., Bravo, M. J., Taylor, D. G., & Legge, G. E. (1994) Stereo matching precedes dichoptic masking. Vision Research, 34, 1047) we do not invoke a special role for depth perception. © 2004 Elsevier Ltd. All rights reserved.

HLA-DP2 binding prediction by molecular dynamics simulations

Major histocompatibility complex (MHC) II proteins bind peptide fragments derived from pathogen antigens and present them at the cell surface for recognition by T cells. MHC proteins are divided into Class I and Class II. Human MHC Class II alleles are grouped into three loci: HLA-DP, HLA-DQ, and HLA-DR. They are involved in many autoimmune diseases. In contrast to HLA-DR and HLA-DQ proteins, the X-ray structure of the HLA-DP2 protein has been solved quite recently. In this study, we have used structure-based molecular dynamics simulation to derive a tool for rapid and accurate virtual screening for the prediction of HLA-DP2-peptide binding. A combinatorial library of 247 peptides was built using the "single amino acid substitution" approach and docked into the HLA-DP2 binding site. The complexes were simulated for 1 ns and the short range interaction energies (Lennard-Jones and Coulumb) were used as binding scores after normalization. The normalized values were collected into quantitative matrices (QMs) and their predictive abilities were validated on a large external test set. The validation shows that the best performing QM consisted of Lennard-Jones energies normalized over all positions for anchor residues only plus cross terms between anchor-residues.

Peptide binding prediction for the human class II MHC allele HLA-DP2:a molecular docking approach

MHC class II proteins bind oligopeptide fragments derived from proteolysis of pathogen antigens, presenting them at the cell surface for recognition by CD4+ T cells. Human MHC class II alleles are grouped into three loci: HLA-DP, HLA-DQ and HLA-DR. In contrast to HLA-DR and HLA-DQ, HLA-DP proteins have not been studied extensively, as they have been viewed as less important in immune responses than DRs and DQs. However, it is now known that HLA-DP alleles are associated with many autoimmune diseases. Quite recently, the X-ray structure of the HLA-DP2 molecule (DPA*0103, DPB1*0201) in complex with a self-peptide derived from the HLA-DR a-chain has been determined. In the present study, we applied a validated molecular docking protocol to a library of 247 modelled peptide-DP2 complexes, seeking to assess the contribution made by each of the 20 naturally occurred amino acids at each of the nine binding core peptide positions and the four flanking residues (two on both sides).

Colour image coding with matching pursuit in the spatio-frequency domain

We present and evaluate a novel idea for scalable lossy colour image coding with Matching Pursuit (MP) performed in a transform domain. The idea is to exploit correlations in RGB colour space between image subbands after wavelet transformation rather than in the spatial domain. We propose a simple quantisation and coding scheme of colour MP decomposition based on Run Length Encoding (RLE) which can achieve comparable performance to JPEG 2000 even though the latter utilises careful data modelling at the coding stage. Thus, the obtained image representation has the potential to outperform JPEG 2000 with a more sophisticated coding algorithm.

Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102:a bioinformatic approach to the prediction of new epitopes

Predictive models of peptide-Major Histocompatibility Complex (MHC) binding affinity are important components of modern computational immunovaccinology. Here, we describe the development and deployment of a reliable peptide-binding prediction method for a previously poorly-characterized human MHC class I allele, HLA-Cw*0102.

Contrast matching and discrimation in human vision

The aim of this work was to investigate human contrast perception at various contrast levels ranging from detection threshold to suprathreshold levels by using psychophysical techniques. The work consists of two major parts. The first part deals with contrast matching, and the second part deals with contrast discrimination. Contrast matching technique was used to determine when the perceived contrasts of different stimuli were equal. The effects of spatial frequency, stimulus area, image complexity and chromatic contrast on contrast detection thresholds and matches were studied. These factors influenced detection thresholds and perceived contrast at low contrast levels. However, at suprathreshold contrast levels perceived contrast became directly proportional to the physical contrast of the stimulus and almost independent of factors affecting detection thresholds. Contrast discrimination was studied by measuring contrast increment thresholds which indicate the smallest detectable contrast difference. The effects of stimulus area, external spatial image noise and retinal illuminance were studied. The above factors affected contrast detection thresholds and increment thresholds measured at low contrast levels. At high contrast levels, contrast increment thresholds became very similar so that the effect of these factors decreased. Human contrast perception was modelled by regarding the visual system as a simple image processing system. A visual signal is first low-pass filtered by the ocular optics. This is followed by spatial high-pass filtering by the neural visual pathways, and addition of internal neural noise. Detection is mediated by a local matched filter which is a weighted replica of the stimulus whose sampling efficiency decreases with increasing stimulus area and complexity. According to the model, the signals to be compared in a contrast matching task are first transferred through the early image processing stages mentioned above. Then they are filtered by a restoring transfer function which compensates for the low-level filtering and limited spatial integration at high contrast levels. Perceived contrasts of the stimuli are equal when the restored responses to the stimuli are equal. According to the model, the signals to be discriminated in a contrast discrimination task first go through the early image processing stages, after which signal dependent noise is added to the matched filter responses. The decision made by the human brain is based on the comparison between the responses of the matched filters to the stimuli, and the accuracy of the decision is limited by pre- and post-filter noises. The model for human contrast perception could accurately describe the results of contrast matching and discrimination in various conditions.

Identification of the HLA-DM/HLA-DR interface

Human leukocyte antigen (HLA)-DM is a critical participant in antigen presentation that catalyzes the dissociation of the Class II-associated Invariant chain-derived Peptide (CLIP) from the major histocompatibility complex (MHC) Class II molecules. There is competition amongst peptides for access to an MHC Class II groove and it has been hypothesised that DM functions as a 'peptide editor' that catalyzes the replacement of one peptide for another within the groove. It is established that the DM catalyst interacts directly with the MHC Class II but the precise location of the interface is unknown. Here, we combine previously described mutational data with molecular docking and energy minimisation simulations to identify a putative interaction site of >4000A2 which agrees with known point mutational data for both the DR and DM molecule. The docked structure is validated by comparison with experimental data and previously determined properties of protein-protein interfaces. A possible dissociation mechanism is suggested by the presence of an acidic cluster near the N terminus of the bound peptide.

Colour image coding with wavelets and matching pursuit

This thesis considers sparse approximation of still images as the basis of a lossy compression system. The Matching Pursuit (MP) algorithm is presented as a method particularly suited for application in lossy scalable image coding. Its multichannel extension, capable of exploiting inter-channel correlations, is found to be an efficient way to represent colour data in RGB colour space. Known problems with MP, high computational complexity of encoding and dictionary design, are tackled by finding an appropriate partitioning of an image. The idea of performing MP in the spatio-frequency domain after transform such as Discrete Wavelet Transform (DWT) is explored. The main challenge, though, is to encode the image representation obtained after MP into a bit-stream. Novel approaches for encoding the atomic decomposition of a signal and colour amplitudes quantisation are proposed and evaluated. The image codec that has been built is capable of competing with scalable coders such as JPEG 2000 and SPIHT in terms of compression ratio.

Simulation in the supply chain context:matching the simulation tool to the problem

The supply chain can be a source of competitive advantage for the firm. Simulation is an effective tool for investigating supply chain problems. The three main simulation approaches in the supply chain context are System Dynamics (SD), Discrete Event Simulation (DES) and Agent Based Modelling (ABM). A sample from the literature suggests that whilst SD and ABM have been used to address strategic and planning problems, DES has mainly been used on planning and operational problems., A review of received wisdom suggests that historically, driven by custom and practice, certain simulation techniques have been focused on certain problem types. A theoretical review of the techniques, however, suggests that the scope of their application should be much wider and that supply chain practitioners could benefit from applying them in this broader way.

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.