Prediction of Candidate Primary Immunodeficiency Disease Genes Using a Support Vector Machine Learning Approach

Screening and early identification of primary immunodeficiency disease (PID) genes is a major challenge for physicians. Many resources have catalogued molecular alterations in known PID genes along with their associated clinical and immunological phenotypes. However, these resources do not assist in identifying candidate PID genes. We have recently developed a platform designated Resource of Asian PDIs, which hosts information pertaining to molecular alterations, protein-protein interaction networks, mouse studies and microarray gene expression profiling of all known PID genes. Using this resource as a discovery tool, we describe the development of an algorithm for prediction of candidate PID genes. Using a support vector machine learning approach, we have predicted 1442 candidate PID genes using 69 binary features of 148 known PID genes and 3162 non-PID genes as a training data set. The power of this approach is illustrated by the fact that six of the predicted genes have recently been experimentally confirmed to be PID genes. The remaining genes in this predicted data set represent attractive candidates for testing in patients where the etiology cannot be ascribed to any of the known PID genes.

Thermoelectric power in ultrathin films, quantum wires and carbon nanotubes under classically large magnetic field: Simplified theory and relative comparison

We study the thermoelectric power under classically large magnetic field (TPM) in ultrathin films (UFs), quantum wires (QWs) of non-linear optical materials on the basis of a newly formulated electron dispersion law considering the anisotropies of the effective electron masses, the spin-orbit splitting constants and the presence of the crystal field splitting within the framework of k.p formalism. The results of quantum confined III-V compounds form the special cases of our generalized analysis. The TPM has also been studied for quantum confined II-VI, stressed materials, bismuth and carbon nanotubes (CNs) on the basis of respective dispersion relations. It is found taking quantum confined CdGeAs2, InAs, InSb, CdS, stressed n-InSb and Bi that the TPM increases with increasing film thickness and decreasing electron statistics exhibiting quantized nature for all types of quantum confinement. The TPM in CNs exhibits oscillatory dependence with increasing carrier concentration and the signature of the entirely different types of quantum systems are evident from the plots. Besides, under certain special conditions, all the results for all the materials gets simplified to the well-known expression of the TPM for non-degenerate materials having parabolic energy bands, leading to the compatibility test. (C) 2009 Elsevier B.V. All rights reserved.

Hamilton's theory of turns revisited

We present a new approach to Hamilton's theory of turns for the groups SO(3) and SU(2) which renders their properties, in particular their composition law, nearly trivial and immediately evident upon inspection. We show that the entire construction can be based on binary rotations rather than mirror reflections.

CAE-based prediction of projectile residual velocity for impact on single and multi-layered metallic armour plates

The present, paper deals with the CAE-based study Of impact of jacketed projectiles on single- and multi-layered metal armour plates using LS-DYNA. The validation of finite element modelling procedure is mainly based on the mesh convergence study using both shell and solid elements for representing single-layered mild steel target plates. It, is shown that the proper choice of mesh density and the strain rate-dependent material properties are essential for all accurate prediction of projectile residual velocity. The modelling requirements are initially arrived at by correlating against test residual velocities for single-layered mild steel plates of different depths at impact velocities in the ran.-c of approximately 800-870 m/s. The efficacy of correlation is adjudged, in terms of a 'correlation index', defined in the paper: for which values close to unity are desirable. The experience gained for single-layered plates is next; used in simulating projectile impacts on multi-layered mild steel target plates and once again a high degree of correlation with experimental residual velocities is observed. The study is repeated for single- and multi-layered aluminium target plates with a similar level of success in test residual velocity prediction. TO the authors' best knowledge, the present comprehensive study shows in particular for the first time that, with a. proper modelling approach, LS-DYNA can be used with a great degree of confidence in designing perforation-resistant single and multi-layered metallic armour plates.

A kinematic theory for radially foldable planar linkages

By using the algebraic locus of the coupler curve of a PRRP planar linkage, in this paper, a kinematic theory is developed for planar, radially foldable closed-loop linkages. This theory helps derive the previously invented building blocks, which consist of only two inter-connected angulated elements, for planar foldable structures. Furthermore, a special case of a circumferentially actuatable foldable linkage (which is different from the previously known cases) is derived from the theory, A quantitative description of some known and some new properties of planar foldable linkages, including the extent of foldability, shape-preservation of the interior polygons, multi-segmented assemblies and heterogeneous circumferential arrangemants, is also presented. The design equations derived here make the conception of even complex planar radially foldable linkages systematic and straightforward. Representative examples are presented to illustrate the usage of the design equations and the construction of prototypes. The current limitations and some possible extensions of the theory are also noted. (c) 2007, Elsevier Ltd. All ri-hts reserved.

Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment

We report the binding energy of various nucleobases (guanine (G), adenine (A), thymine (T) and cytosine (C)) with (5,5) single-walled carbon nanotube (SWNT) calculated using first-principle Hartre–Fock method (HF) together with classical force field. The binding energy without including the solvation effects of water decreases in the order G>A>T>C. The inclusion of solvation energy changes the order of binding preference to be G>T>A>C. Using isothermal titration (micro) calorimetry experiments, we also show the relative binding affinity to be T>A>C, in agreement with our calculations.

An elementary introduction to solar dynamo theory

The cyclically varying magnetic field of the Sun is believed to be produced by the hydromagnetic dynamo process. We first summarize the relevant observational data pertaining to sunspots and solar cycle. Then we review the basic principles of MHD needed to develop the dynamo theory. This is followed by a discussion how bipolar sunspots form due to magnetic buoyancy of flux tubes formed at the base of the solar convection zone. Following this, we come to the heart of dynamo theory. After summarizing the basic ideas of a turbulent dynamo and the basic principles of its mean field formulation, we present the famous dynamo wave solution, which was supposed to provide a model for the solar cycle. Finally we point out how a flux transport dynamo can circumvent some of the difficulties associated with the older dynamo models.

Critical test for Altshuler-Aronov theory: Evolution of the density of states singularity in double perovskite Sr2FeMoO6 with controlled disorder

With high-resolution photoemission spectroscopy measurements, the density of states (DOS) near the Fermi level (E-F) of double perovskite Sr2FeMoO6 having different degrees of Fe/Mo antisite disorder has been investigated with varying temperature. The DOS near E-F showed a systematic depletion with increasing degree of disorder, and recovered with increasing temperature. Altshuler-Aronov (AA) theory of disordered metals well explains the dependences of the experimental results. Scaling analysis of the spectra provides experimental indication for the functional form of the AA DOS singularity.

Thermoelectric Power Under Strong Magnetic Field in Quantum Dots and Quantized Superlattices: Simplified Theory and Relative Comparison

In this paper, we study the thermoelectric power under strong magnetic field (TPSM) in quantum dots (QDs) of nonlinear optical, III-V, II-VI, GaP, Ge, Te, Graphite, PtSb2, zerogap, Lead Germanium Telluride, GaSb, stressed materials, Bismuth, IV-VI, II-V, Zinc and Cadmium diphosphides, Bi2Te3 and Antimony respectively. The TPSM in III-V, II-VI, IV-VI, HgTe/CdTe quantum well superlattices with graded interfaces and effective mass superlattices of the same materials together with the quantum dots of aforementioned superlattices have also been investigated in this context on the basis of respective carrier dispersion laws. It has been found that the TPSM for the said quantum dots oscillates with increasing thickness and decreases with increasing electron concentration in various manners and oscillates with film thickness, inverse quantizing magnetic field and impurity concentration for all types of superlattices with two entirely different signatures of quantization as appropriate in respective cases of the aforementioned quantized structures. The well known expression of the TPSM for wide-gap materials has been obtained as special case for our generalized analysis under certain limiting condition, and this compatibility is an indirect test of our generalized formalism. Besides, we have suggested the experimental method of determining the carrier contribution to elastic constants for nanostructured materials having arbitrary dispersion laws.

Fuzzy-logic-based health monitoring and residual-life prediction for composite helicopter rotor

A health-monitoring and life-estimation strategy for composite rotor blades is developed in this work. The cross-sectional stiffness reduction obtained by physics-based models is expressed as a function of the life of the structure using a recent phenomenological damage model. This stiffness reduction is further used to study the behavior of measurable system parameters such as blade deflections, loads, and strains of a composite rotor blade in static analysis and forward flight. The simulated measurements are obtained using an aeroelastic analysis of the composite rotor blade based on the finite element in space and time with physics-based damage modes that are then linked to the life consumption of the blade. The model-based measurements are contaminated with noise to simulate real data. Genetic fuzzy systems are developed for global online prediction of physical damage and life consumption using displacement- and force-based measurement deviations between damaged and undamaged conditions. Furthermore, local online prediction of physical damage and life consumption is done using strains measured along the blade length. It is observed that the life consumption in the matrix-cracking zone is about 12-15% and life consumption in debonding/delamination zone is about 45-55% of the total life of the blade. It is also observed that the success rate of the genetic fuzzy systems depends upon the number of measurements, type of measurements and training, and the testing noise level. The genetic fuzzy systems work quite well with noisy data and are recommended for online structural health monitoring of composite helicopter rotor blades.

Energy identities in water wave theory for free-surface boundary condition with higher-order derivatives

A modified form of Green's integral theorem is employed to derive the energy identity in any water wave diffraction problem in a single-layer fluid for free-surface boundary condition with higher-order derivatives. For a two-layer fluid with free-surface boundary condition involving higher-order derivatives, two forms of energy identities involving transmission and reflection coefficients for any wave diffraction problem are also derived here by the same method. Based on this modified Green's theorem, hydrodynamic relations such as the energy-conservation principle and modified Haskind–Hanaoka relation are derived for radiation and diffraction problems in a single as well as two-layer fluid.

Hanle-Zeeman redistribution matrix. I. Classical theory expressions in the laboratory frame

Polarized scattering in spectral lines is governed by a 4; 4 matrix that describes how the Stokes vector is scattered and redistributed in frequency and direction. Here we develop the theory for this redistribution matrix in the presence of magnetic fields of arbitrary strength and direction. This general magnetic field case is called the Hanle- Zeeman regime, since it covers both of the partially overlapping weak- and strong- field regimes in which the Hanle and Zeeman effects dominate the scattering polarization. In this general regime, the angle-frequency correlations that describe the so-called partial frequency redistribution (PRD) are intimately coupled to the polarization properties. We develop the theory for the PRD redistribution matrix in this general case and explore its detailed mathematical properties and symmetries for the case of a J = 0 -> 1 -> 0 scattering transition, which can be treated in terms of time-dependent classical oscillator theory. It is shown how the redistribution matrix can be expressed as a linear superposition of coherent and noncoherent parts, each of which contain the magnetic redistribution functions that resemble the well- known Hummer- type functions. We also show how the classical theory can be extended to treat atomic and molecular scattering transitions for any combinations of quantum numbers.

Experimental study on shrinkage behaviour and prediction of shrinkage magnitudes of residual soils

The present study examines the shrinkage behaviour of residually derived black cotton (BC) soil and red soil compacted specimens that were subjected to air-drying from the swollen state. The soil specimens were compacted at varying dry density and moisture contents to simulate varied field conditions. The void ratio and moisture content of the swollen specimens were monitored during the drying process and relationship between them is analyzed. Shrinkage is represented as reduction in void ratio with decrease in water content of soil specimens. It is found to occur in three distinct stages. Total shrinkage magnitude depends on the type of clay mineral present. Variation in compaction conditions effect marginally total shrinkage magnitudes of BC soil specimens but have relatively more effect on red soil specimens. A linear relation is obtained between total shrinkage magnitude and volumetric water content of soil specimens in swollen state and can be used to predict the shrinkage magnitude of soils.

Memory-efficient spatial prediction image compression scheme

In prediction phase, the hierarchical tree structure obtained from the test image is used to predict every central pixel of an image by its four neighboring pixels. The prediction scheme generates the predicted error image, to which the wavelet/sub-band coding algorithm can be applied to obtain efficient compression. In quantization phase, we used a modified SPIHT algorithm to achieve efficiency in memory requirements. The memory constraint plays a vital role in wireless and bandwidth-limited applications. A single reusable list is used instead of three continuously growing linked lists as in case of SPIHT. This method is error resilient. The performance is measured in terms of PSNR and memory requirements. The algorithm shows good compression performance and significant savings in memory. (C) 2006 Elsevier B.V. All rights reserved.

How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.