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.

Third post-Newtonian angular momentum flux and the secular evolution of orbital elements for inspiralling compact binaries in quasi-elliptical orbits

The angular-momentum flux from an inspiralling binary system of compact objects moving in quasi-elliptical orbits is computed at the third post-Newtonian (3PN) order using the multipolar post-Minkowskian wave generation formalism. The 3PN angular-momentum flux involves the instantaneous, tail, and tail-of-tails contributions as for the 3PN energy flux, and in addition a contribution due to nonlinear memory. We average the angular-momentum flux over the binary's orbit using the 3PN quasi-Keplerian representation of elliptical orbits. The averaged angular-momentum flux provides the final input needed for gravitational-wave phasing of binaries moving in quasi-elliptical orbits. We obtain the evolution of orbital elements under 3PN gravitational radiation reaction in the quasi-elliptic case. For small eccentricities, we give simpler limiting expressions relevant for phasing up to order e(2). This work is important for the construction of templates for quasi-eccentric binaries, and for the comparison of post-Newtonian results with the numerical relativity simulations of the plunge and merger of eccentric binaries.

Free vibration and wave propagation analysis of uniform and tapered rotating beams using spectrally formulated finite elements

This paper presents a formulation of an approximate spectral element for uniform and tapered rotating Euler-Bernoulli beams. The formulation takes into account the varying centrifugal force, mass and bending stiffness. The dynamic stiffness matrix is constructed using the weak form of the governing differential equation in the frequency domain, where two different interpolating functions for the transverse displacement are used for the element formulation. Both free vibration and wave propagation analysis is performed using the formulated elements. The studies show that the formulated element predicts results, that compare well with the solution available in the literature, at a fraction of the computational effort. In addition, for wave propagation analysis, the element shows superior convergence. (C) 2007 Elsevier Ltd. All rights reserved.

Trace element nutrition of the silkwormBombyx mori L. I. Effect of trace elements

Trace elements zinc, copper, manganese, molybdenum and cobalt have been shown to have varying effects on growth and trace element composition of the silkworm. Results indicate the important role of manganese in the normal metabolism of the insect. Cobalt has been shown to exert a very favourable effect on growth and silk yield.

Primary Structural Documentation of the Major Urinary Protein of the Indian Commensal Rat (Rattus rattus) Using a Proteomics Platform

Purpose: A number of proteome studies have been performed recently to identify pheromone-related protein expression and their molecular function using genetically modified rodents' urine. However, no such studies have used Indian commensal rodents; interestingly, in a previous investigation, we confirmed the presence of volatile molecules in commensal rodents urine and these molecules seem to be actively involved in pheromonal communication. Therefore, the present study aims to identify the major urinary protein [MUP] present in commensal rat urine, which will help us to understand the protein's expression pattern and intrinsic properties among the rodents globally. Experimental Design: Initially, the total urinary proteins were separated by 1-D and 2-D electrophoresis and then subsequently analyzed by Matrix Assisted Laser Desorption Ionization-Time of Flight and Mass Spectrometer (MALDI-TOF/MS). Furthermore, they were then fragmented with the aid of a Tandem Mass Spectrometer (TOF/TOF) and the identified sequences aligned and confirmed using similarity with the deduced primary structures of members of the lipocalin superfamily.Results: The SDS-PAGE protein profiles showed distinct proteins with molecular masses of 15, 22.4, 25, 28, 42, 50, 55, 68, and 91 kDa. Of these proteins, the 22.4 kDa protein was considered to be target candidate. When 2D electrophoresis was carried out, about similar to 50 spots were detected with different masses and various pI ranges. The 22.4 kDa protein was found to have a pI of about 4.9. This 22.4 kDa protein spot was digested and subjected to mass spectrometry; it was identified as rat MUP. The fragmented peptides from the rat MUP at 935, 1026, 1192, and 1303 m/z were further fragmented with the aid of MS/MS and generated de novo sequence and this confirmed this protein to be the MUP present in the urine of commensal rats.Conclusion: The present investigation confirms the presence of MUP with a molecular mass of 22.4 kDa in the urine of commensal rats. This protein may be involved in the binding of volatile molecules and opens up a discussion about how volatile and non-volatile molecules in the commensal rats' urine may contribute chemo-communication.

Holographic optical elements: State-of-the-art review: Part 2

This is the second part of a two part review on the state-of-the-art in holographic optical elements (HOEs). The aspects of fabrication, evaluation, and applications of HOEs, are discussed in this part. It details the direction of future efforts towards finding work-horse type recording media, developing new methods for the evaluation of HOE, and identifying the areas of application where HOEs are to be considered as indispensable components/tools. Finally a summary of all the suggestions for future work made in the two parts is displayed in Table 2 of this part of the review.

Holographic optical elements — State-of-the-art review:Part I

A state-of-the-art review on holographic optical elements (HOE) is presented in two parts. In Part I a conceptual overview and an assessment of the current status on the design of HOE have been included. It is pointed out that HOE development based on the use of squeezed light, speckle, non-linear recording, comparative studies between optics and communication approaches, are some of the promising directions for future research in this vital area of photonics.

Topology design of three-dimensional structures using hybrid finite elements

Conventional three-dimensional isoparametric elements are susceptible to problems of locking when used to model plate/shell geometries or when the meshes are distorted etc. Hybrid elements that are based on a two-field variational formulation are immune to most of these problems, and hence can be used to efficiently model both "chunky" three-dimensional and plate/shell type structures. Thus, only one type of element can be used to model "all" types of structures, and also allows us to use a standard dual algorithm for carrying out the topology optimization of the structure. We also address the issue of manufacturability of the designs.

Bearing capacity of interfering multiple strip footings by using lower bound finite elements limit analysis

The ultimate bearing capacity of a number of multiple strip footings, identically spaced and equally loaded to failure at the same time,is computed by using the lower bound limit analysis in combination with finite elements. The efficiency factor due to the component of soil unit weight, is computed with respect to changes in the clear spacing (xi(gamma)) between the footings. It is noted that the failure load for a footing in the group becomes always greater than that of a single isolated footing. The values of xi(gamma) for the smooth footings are found to be always lower than the rough footings. The values ofxi(gamma) are found to increase continuously with a decrease in the spacing between footings. As compared to the available theoretical and experimental results reported in literature, the present analysis provides generally a little lower values of xi(gamma). (C) 2010 Elsevier Ltd. All rights reserved.

Bicyclic Phosphazenes Derived from (Amino) Cyclotetraphosphazenes

Amination reactions of 2,6-bis(primary amino)cyclotetraphosphazenes yield not only the expected (amino)cyclotetraphosphazenes but also novel trans-annular bridged bicyclic phosphazenes by an intramolecular substitution pathway. In addition, resins are formed in some reactions by an intermolecular condensation. The effect of substituents attached to the phosphazene ring, the attacking nucleophile and solvent on the formation of the trans-annular P-N-P bridge is considered in detail in relation to plausible reaction mechanisms. Analytical separation of bicyclic phosphazenes by high performance liquid chromatography (HPLC) on a reverse phase silica column is demonstrated. Structural features of bicyclic phosphazenes and salient aspects of their NVR spectroscopic data are discussed.

Plasticity in the primary binding site of galactose/N-acetylgalactosamine-specific lectins - Implication of the C-H center dot center dot center dot O hydrogen bond at the specificity-determining C-4 locus of the saccharide in 4-methoxygalactose recognition by jacalin and winged bean (basic) agglutinin I

It is currently believed that an unsubstituted axial hydroxyl at the specificity-determining C-4 locus of galactose is indispensable for recognition by galactose/N-acetylgalactosamine-specific lectins. Titration calorimetry demonstrates that 4-methoxygalactose retains binding allegiance to the Moraceae lectin jacalin and the Leguminosae lectin, winged bean (basic) agglutinin (WBA I). The binding reactions were driven by dominant favorable enthalpic contributions and exhibited significant enthalpy-entropy compensation. Proton NMR titration of C-methoxygalactose with jacalin and WBA I resulted in broadening of the sugar resonances without any change in chemical shift. The alpha-and beta-anomers of 4-methoxygalactose were found to be in slow exchange with free and lectin-bound states. Both the anomers experience magnetically equivalent environments at the respective binding sites. The binding constants derived from the dependence of NMR line widths on 4-methoxygalactose concentration agreed well with those obtained from titration calorimetry. The results unequivocally demonstrate that the loci corresponding to the axially oriented C-4 hydroxyl group of galactose within the primary binding site of these lectins exhibit plasticity. These analyses suggest, for the first time, the existence of C-H ... O-type hydrogen-bond(s) in protein-carbohydrate interactions in general and between the C-4 locus of galactose derivative and the lectins jacalin and WBA I in particular.

Primary structure of belladonna mottle virus coat protein.

The coat protein of belladonna mottle virus (a tymovirus) was cleaved by trypsin and chymotrypsin, and the peptides were separated by high performance liquid chromatography using a combination of gel permeation, reverse phase, and ion pair chromatography. The peptides were sequenced manually using the 4-N, N-dimethylaminoazobenzene-4'-isothiocyanate/phenyl isothiocyanate double-coupling method. The chymotryptic peptides were aligned by overlapping sequences of tryptic peptides and by homology with another tymovirus, eggplant mosaic virus. The belladonna mottle virus is more closely related to eggplant mosaic virus than to turnip yellow mosaic virus, the type member of this group, as evident from the sequence homologies of 57 and 32%, respectively. The accumulation of basic residues at the amino terminus implicated in RNA-protein interactions in many spherical plant viruses was absent in all the three sequences. Interestingly, the amino-terminal region is the least conserved among the tymoviruses. The longest stretch of conserved sequence between belladonna mottle virus and eggplant mosaic virus was residues 34-44, whereas it was residues 96-102 in the case of belladonna mottle virus and turnip yellow mosaic virus. A tetrapeptide in the region (residues 154-157) was found to be common for all the three sequences. It is possible that these conserved regions (residues 34-44, 96-102, 154-157) are involved in either intersubunit or RNA-protein interactions.

Wave propagation analysis in carbon nanotube embedded composite using wavelet based spectral finite elements

In this paper, elastic wave propagation is studied in a nanocomposite reinforced with multiwall carbon nanotubes (CNTs). Analysis is performed on a representative volume element of square cross section. The frequency content of the exciting signal is at the terahertz level. Here, the composite is modeled as a higher order shear deformable beam using layerwise theory, to account for partial shear stress transfer between the CNTs and the matrix. The walls of the multiwall CNTs are considered to be connected throughout their length by distributed springs, whose stiffness is governed by the van der Waals force acting between the walls of nanotubes. The analyses in both the frequency and time domains are done using the wavelet-based spectral finite element method (WSFEM). The method uses the Daubechies wavelet basis approximation in time to reduce the governing PDE to a set of ODEs. These transformed ODEs are solved using a finite element (FE) technique by deriving an exact interpolating function in the transformed domain to obtain the exact dynamic stiffness matrix. Numerical analyses are performed to study the spectrum and dispersion relations for different matrix materials and also for different beam models. The effects of partial shear stress transfer between CNTs and matrix on the frequency response function (FRF) and the time response due to broadband impulse loading are investigated for different matrix materials. The simultaneous existence of four coupled propagating modes in a double-walled CNT-composite is also captured using modulated sinusoidal excitation.