Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Semi-Supervised Classification Using Sparse Gaussian Process Regression

Gaussian Processes (GPs) are promising Bayesian methods for classification and regression problems. They have also been used for semi-supervised learning tasks. In this paper, we propose a new algorithm for solving semi-supervised binary classification problem using sparse GP regression (GPR) models. It is closely related to semi-supervised learning based on support vector regression (SVR) and maximum margin clustering. The proposed algorithm is simple and easy to implement. It gives a sparse solution directly unlike the SVR based algorithm. Also, the hyperparameters are estimated easily without resorting to expensive cross-validation technique. Use of sparse GPR model helps in making the proposed algorithm scalable. Preliminary results on synthetic and real-world data sets demonstrate the efficacy of the new algorithm.

Path integral quantisation of topological field theories

Conditions for quantum topological invariance of classically topological field theories in the path integral formulation are discussed. Both the three-dimensional Chern-Simons system and a Witten-type topological field theory are shown to satisfy these conditions.

Sediment Volume Tests for Expansive Soil Identification and Classification

Equilibrium sediment volume tests are conducted on field soils to classify them based on their degree of expansivity and/or to predict the liquid limit of soils. The present technical paper examines different equilibrium sediment volume tests, critically evaluating each of them. It discusses the settling behavior of fine-grained soils during the soil sediment formation to evolve a rationale for conducting the latest version of equilibrium sediment volume test. Probable limitations of equilibrium sediment volume test and the possible solution to overcome the same have also been indicated.

Euclideanization, topological theories, higher dimensions and all that

It is shown that the euclideanized Yukawa theory, with the Dirac fermion belonging to an irreducible representation of the Lorentz group, is not bounded from below. A one parameter family of supersymmetric actions is presented which continuously interpolates between the N = 2 SSYM and the N = 2 supersymmetric topological theory. In order to obtain a theory which is bounded from below and satisfies Osterwalder-Schrader positivity, the Dirac fermion should belong to a reducible representation of the Lorentz group and the scalar fields have to be reinterpreted as the extra components of a higher dimensional vector field.

Evidence of gate-tunable topological excitations in two-dimensional electron systems

We report experimental observations of a new mechanism of charge transport in two-dimensional electron systems (2DESs) in the presence of strong Coulomb interaction and disorder. We show that at low enough temperature the conductivity tends to zero at a nonzero carrier density, which represents the point of essential singularity in a Berezinskii-Kosterlitz-Thouless-like transition. Our experiments with many 2DESs in GaAs/AlGaAs heterostructures suggest that the charge transport at low carrier densities is due to the melting of an underlying ordered ground state through proliferation of topological defects. Independent measurement of low-frequency conductivity noise supports this scenario.

Quenching across quantum critical points: Role of topological patterns

We introduce a one-dimensional version of the Kitaev model consisting of spins on a two-legged ladder and characterized by Z(2) invariants on the plaquettes of the ladder. We map the model to a fermionic system and identify the topological sectors associated with different Z2 patterns in terms of fermion occupation numbers. Within these different sectors, we investigate the effect of a linear quench across a quantum critical point. We study the dominant behavior of the system by employing a Landau-Zener-type analysis of the effective Hamiltonian in the low-energy subspace for which the effective quenching can sometimes be non-linear. We show that the quenching leads to a residual energy which scales as a power of the quenching rate, and that the power depends on the topological sectors and their symmetry properties in a non-trivial way. This behavior is consistent with the general theory of quantum quenching, but with the correlation length exponent nu being different in different sectors. Copyright (C) EPLA, 2010

Interdiffusion study on Co(W) solid solution and topological close-packed mu phase in Co-W system

An interdiffusion study is conducted on the Co-W system by a diffusion couple technique. The interdiffusion coefficient of the Co(W) solid solution and the Co7W6 mu phase is determined. The activation energy is found to increase with the W content of the Co(W) solid solution. (C) 2010 Elsevier Ltd. All rights reserved.

Fluorescence and topological gap of conjugated phenylene polymers

We propose that strong fluorescence in conjugated polymers requires a dipole-allowed state to be the lowest singlet. Hückel theory for para-conjugated phenyl rings yields an extended, topologically one-dimensional ?-system with increased alternation, states localized on each ring, and charge-transfer excitations between them. Exact Pariser�Parr�Pople results and molecular spectra for oligomers support a topological contribution and a lowest dipole-allowed singlet in phenylene polymers.

A classification of homogeneous operators in the Cowen-Douglas class

An explicit construction of all the homogeneous holomorphic Hermitian vector bundles over the unit disc D is given. It is shown that every such vector bundle is a direct sum of irreducible ones. Among these irreducible homogeneous holomorphic Hermitian vector bundles over D, the ones corresponding to operators in the Cowen-Douglas class B-n(D) are identified. The classification of homogeneous operators in B-n(D) is completed using an explicit realization of these operators. We also show how the homogeneous operators in B-n(D) split into similarity classes. (C) 2011 Elsevier Inc. All rights reserved.

Chance constrained uncertain classification via robust optimization

This paper studies the problem of constructing robust classifiers when the training is plagued with uncertainty. The problem is posed as a Chance-Constrained Program (CCP) which ensures that the uncertain data points are classified correctly with high probability. Unfortunately such a CCP turns out to be intractable. The key novelty is in employing Bernstein bounding schemes to relax the CCP as a convex second order cone program whose solution is guaranteed to satisfy the probabilistic constraint. Prior to this work, only the Chebyshev based relaxations were exploited in learning algorithms. Bernstein bounds employ richer partial information and hence can be far less conservative than Chebyshev bounds. Due to this efficient modeling of uncertainty, the resulting classifiers achieve higher classification margins and hence better generalization. Methodologies for classifying uncertain test data points and error measures for evaluating classifiers robust to uncertain data are discussed. Experimental results on synthetic and real-world datasets show that the proposed classifiers are better equipped to handle data uncertainty and outperform state-of-the-art in many cases.

Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Two-mode quantum systems: Invariant classification of squeezing transformations and squeezed states

A general analysis of squeezing transformations for two-mode systems is given based on the four-dimensional real symplectic group Sp(4, R). Within the framework of the unitary (metaplectic) representation of this group, a distinction between compact photon-number-conserving and noncompact photon-number-nonconserving squeezing transformations is made. We exploit the U(2) invariant squeezing criterion to divide the set of all squeezing transformations into a two-parameter family of distinct equivalence classes with representative elements chosen for each class. Familiar two-mode squeezing transformations in the literature are recognized in our framework and seen to form a set of measure zero. Examples of squeezed coherent and thermal states are worked out. The need to extend the heterodyne detection scheme to encompass all of U(2) is emphasized, and known experimental situations where all U(2) elements can be reproduced are briefly described.

Studies in crystal engineering: Effect of fluorine substitution in crystal packing and topological photodimerization of styryl coumarins in the solid state

Styryl coumarins generally yield centrosymmetric (alpha-mode, anti-HT) photodimers when subjected to irradiation in the solid state, However, the substitution of fluorine dramatically alters the packing mode and steers the molecules 4-(4-fluorostyryl)coumarin 1 and 4-(2-fluorostyryl)coumarin 2 to form a stereospecific photodimer, beta-mode, syn-HH across the styrenic double bond (yield 78-85%). The stereochemistry of the photodimer 2a has been established by X-ray crystallography. There is no evidence for the presence of C-H ... F interactions. The true nature of the weak atom-atom interactions called into play when fluorine is substituted is not clear, It is observed that the fluoro substituted compounds have greater crystal density than the corresponding unsubstituted ones.