On the forced matching numbers of bipartite graphs

Let G be a graph that admits a perfect matching. A forcing set for a perfect matching M of G is a subset S of M, such that S is contained in no other perfect matching of G. This notion has arisen in the study of finding resonance structures of a given molecule in chemistry. Similar concepts have been studied for block designs and graph colorings under the name defining set, and for Latin squares under the name critical set. There is some study of forcing sets of hexagonal systems in the context of chemistry, but only a few other classes of graphs have been considered. For the hypercubes Q(n), it turns out to be a very interesting notion which includes many challenging problems. In this paper we study the computational complexity of finding the forcing number of graphs, and we give some results on the possible values of forcing number for different matchings of the hypercube Q(n). Also we show an application to critical sets in back circulant Latin rectangles. (C) 2003 Elsevier B.V. All rights reserved.

Potent T cell response to a class I-binding 13-mer viral epitope and the influence of HLA micropolymorphism in controlling epitope length

The BZLF1 antigen of Epstein-Barr virus includes three overlapping sequences of different lengths that conform to the binding motif of human leukocyte antigen (HLA) B*3501. These 9-mer ((56)LPOGQLTAy(64)), 11-mer ((54)EPLPQGQLTAy(64)), and 13-mer ((52)LPEPLPQGQLTAY(64)) peptides all bound well to B*3501; however, the CTL response in individuals expressing this HILA allele was directed strongly and exclusively towards the 11-mer peptide. In contrast, EBV-exposed donors expressing HLA B*3503 showed no significant CTL response to these peptides because the single amino acid difference between B*3501 and B*3503 within the F pocket inhibited HLA binding by these peptides. The extraordinarily long 13-mer peptide was the target for the CTL response in individuals expressing B*3508, which differs from B*3501 at a single position within the D pocket (B*3501, 156 Leucine; B*3508, 156 Arginine). This minor difference was shown to enhance binding of the 13-mer peptide, presumably through a stabilizing interaction between the negatively charged glutamate at position 3 of the peptide and the positively charged arginine at HLA position 156. The 13-mer epitope defined in this study represents the longest class I-binding viral epitope identified to date as a minimal determinant. Furthermore, the potency of the response indicates that peptides of this length do not present a major structural barrier to CTL recognition.

Complete modulational-instability gain spectrum of nonlinear quasi-phase-matching gratings

We consider plane waves propagating in quadratic nonlinear slab waveguides with nonlinear quasi-phase-matching gratings. We predict analytically and verify numerically the complete gain spectrum for transverse modulational instability, including hitherto undescribed higher-order gain bands. (C) 2004 Optical Society of America.

Applying machine learning to catalogue matching in astrophysics

We present the results of applying automated machine learning techniques to the problem of matching different object catalogues in astrophysics. In this study, we take two partially matched catalogues where one of the two catalogues has a large positional uncertainty. The two catalogues we used here were taken from the H I Parkes All Sky Survey (HIPASS) and SuperCOSMOS optical survey. Previous work had matched 44 per cent (1887 objects) of HIPASS to the SuperCOSMOS catalogue. A supervised learning algorithm was then applied to construct a model of the matched portion of our catalogue. Validation of the model shows that we achieved a good classification performance (99.12 per cent correct). Applying this model to the unmatched portion of the catalogue found 1209 new matches. This increases the catalogue size from 1887 matched objects to 3096. The combination of these procedures yields a catalogue that is 72 per cent matched.

Edge-to-edge matching model for predicting orientation relationships and habit planes-the improvements

The edge-to-edge matching model has been further developed along with the Cu/Cr system as an example. The conditions for zigzag atom rows to be matching directions are included and the critical value of interatomic spacing misfit along matching directions and the critical value of d-value mismatch between matching planes are proposed in the new version of the model. (c) 2005 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Crystallographic study of grain refinement in aluminum alloys using the edge-to-edge matching model

The edge-to-edge matching model for describing the interfacial crystallographic characteristics between two phases that are related by reproducible orientation relationships has been applied to the typical grain refiners in aluminum alloys. Excellent atomic matching between Al3Ti nucleating substrates, known to be effective nucleation sites for primary Al, and the Al matrix in both close packed directions and close packed planes containing these directions have been identified. The crystallographic features of the grain refiner and the Al matrix are very consistent with the edge-to-edge matching model. For three other typical grain refiners for Al alloys, TiC (when a = 0.4328 nm), TiB2 and AIB(2), the matching only occurs between the close packed directions in both phases and between the second close packed plane of the Al matrix and the second close packed plane of the refiners. According to the model, it is predicted that Al3Ti is a more powerful nucleating substrate for Al alloy than TiC, TiB2 and AlB2. This agrees with the previous experimental results. The present work shows that the edge-to-edge matching model has the potential to be a powerful tool in discovering new and more powerful grain refiners for Al alloys. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Comments on edge-to-edge matching and the equivalence of the invariant line, Delta g and Moire fringe approaches to the crystallographic features of precipitates

Three apparently distinct and different approaches have been proposed to account for the crystallographic features of diffusion-controlled precipitation. These three models are based on (a) an invariant line in the habit plane, (b) the parallelism of a pair of Deltags that are perpendicular to the habit plane and (c) the parallelism of a pair of Moire fringes that are in turn parallel to the habit plane. The purpose of the present paper is to show that these approaches are in fact absolutely equivalent and that when certain conditions are satisfied they are essentially the same as the recent edge-to-edge matching model put forward by the authors. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Edge-to-edge matching and its applications - Part I. Application to the simple HCP/BCC system

The edge-to-edge matching crystallographic model has been used to predict all the orientation relationships (OR) between crystals that have simple hexagonal close packed (HCP) and body-centered cubic (BCC) structures. Using the critical values for the interatomic spacing misfit along the matching directions and the cl-value mismatch between matching planes, the model predicted all the four common ORs, namely the Burgers OR, the Potter OR, the Pitsch-Schrader OR and the Rong Dunlop OR, together with the corresponding habit planes. Taking the c(H)/a(H) and a(H)/a(B) ratios as variables, where H and B denote the HCP and BCC structures respectively, the model also predicted the relationship between these variables and the four ORs. These predictions are perfectly consistent with the published experimental results. As was the case in the FCC/BCC system, the edge-to-edge matching model has been shown to be a powerful tool for predicting the crystallographic features of diffusion-controlled phase transformations. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Edge-to-edge matching and its applications - Part II. Application to Mg-Al, Mg-Y and Mg-Mn alloys

A model for the crystallography and morphology of diffusion-controlled phase transformations - edge-to-edge matching - has been used to predict the orientation relationships (OR) and habit planes of precipitates Mg17Al12 in Mg-Al alloy, Mg24Y5 in Mg-Y alloy and alpha-Mn in Mg-Mn alloy. Based on the crystal structures and lattice parameters only, the model predicts that the possible ORs between Mg17Al12 and Mg matrix are the near Burgers OR, the Potter OR, the Gjonnes-Ostmoe OR and the Crawley OR. In the Mg-Y alloy, the OR between Mg24Y5 precipitates and the Mg matrix is predicted to be the Burgers OR only. The model also predicts that there are no reproducible ORs between alpha-Mn and Mg in the Mg-Mn alloy. Combining the edge-to-edge matching model and W. Zhang's Deltag approach, the habit plane and side facets of the precipitate for each OR can be determined. All the predicted ORs and the corresponding habit planes in Mg-Al and Mg-Y alloys agree very well with the experimental results. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

The correspondence framework for 3D surface matching algorithms

Beyond the inherent technical challenges, current research into the three dimensional surface correspondence problem is hampered by a lack of uniform terminology, an abundance of application specific algorithms, and the absence of a consistent model for comparing existing approaches and developing new ones. This paper addresses these challenges by presenting a framework for analysing, comparing, developing, and implementing surface correspondence algorithms. The framework uses five distinct stages to establish correspondence between surfaces. It is general, encompassing a wide variety of existing techniques, and flexible, facilitating the synthesis of new correspondence algorithms. This paper presents a review of existing surface correspondence algorithms, and shows how they fit into the correspondence framework. It also shows how the framework can be used to analyse and compare existing algorithms and develop new algorithms using the framework's modular structure. Six algorithms, four existing and two new, are implemented using the framework. Each implemented algorithm is used to match a number of surface pairs. Results demonstrate that the correspondence framework implementations are faithful implementations of existing algorithms, and that powerful new surface correspondence algorithms can be created. (C) 2004 Elsevier Inc. All rights reserved.

MULTIPRED: A computational system for prediction of promiscuous HLA binding peptides

MULTIPRED is a web-based computational system for the prediction of peptide binding to multiple molecules ( proteins) belonging to human leukocyte antigens (HLA) class I A2, A3 and class II DR supertypes. It uses hidden Markov models and artificial neural network methods as predictive engines. A novel data representation method enables MULTIPRED to predict peptides that promiscuously bind multiple HLA alleles within one HLA supertype. Extensive testing was performed for validation of the prediction models. Testing results show that MULTIPRED is both sensitive and specific and it has good predictive ability ( area under the receiver operating characteristic curve A(ROC) > 0.80). MULTIPRED can be used for the mapping of promiscuous T-cell epitopes as well as the regions of high concentration of these targets termed T-cell epitope hotspots. MULTIPRED is available at http:// antigen.i2r.a-star.edu.sg/ multipred/.

A population of HLA-DR+ immature cells accumulates in the blood dendritic cell compartment of patients with different types of cancer

Dendritic cell (DC) defects are an important component of immunosuppression in cancer. Here, we assessed whether cancer could affect circulating DC populations and its correlation with tumor progression. The blood DC compartment was evaluated in 136 patients with breast cancer, prostate cancer, and malignant glioma. Phenotypic, quantitative, and functional analyses were performed at various stages of disease. Patients had significantly fewer circulating myeloid (CD11c(+)) and plasmacytoid (CD123(+)) DC, and a concurrent accumulation of CD11c(-)CD123(-) immature cells that expressed high levels of HLA-DR+ immature cells (DR+IC). Although DR+IC exhibited a limited expression of markers ascribed to mature hematopoietic lineages, expression of HLA-DR, CD40, and CD86 suggested a role as antigen-presenting cells. Nevertheless, DR+IC had reduced capacity to capture antigens and elicited poor proliferation and interferon-gamma secretion by T-lymphocytes. Importantly, increased numbers of DR+IC correlated with disease status. Patients with metastatic breast cancer showed a larger number of DR+IC in the circulation than patients with local/nodal disease. Similarly, in patients with fully resected glioma, the proportion of DR+IC in the blood increased when evaluation indicated tumor recurrence. Reduction of blood DC correlating with accumulation of a population of immature cells with poor immunologic function may be associated with increased immunodeficiency observed in cancer.