CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

The evolution of shear bands of saturated soil

The development of the shear bands of saturated soil in coupling-rate- and pore-pressure-dependent simple shear has been discussed, using a simple model and a matching technique at the moving boundary of a shear band. Tt is shown that the development of shear bands are dominated by the coupling-rate and pore-pressure effect of the material. The strength of the soil acts as a destabilizer, whilst pore pressure diffusion makes the band expand. The theory is discussed and some computational solutions have been presented.

Evolutions of Compaction Bands of Saturated Soils

The development of compaction bands in saturated soils，which is coupling—rate，inertial and pore—pressure—dependent，under axisymmetric loading was discussed，using a simple model and a matching technique at the moving boundary of a band．It is shown that the development of compaction bands is dominated by the coupling rate and pore—pressure effects of materia1．The soil strength makes the band shrinking，whilst pore pressure diffusion makes the band expand．Numerical simulations were carried out in this paper ·

Análise de transição entre cabos coaxiais constituída por corrugações e desníveis angulares.

Esta dissertação apresenta um formalismo baseado no Método dos Elementos Finitos (MEF), adequado a análise de descontinuidades coaxiais com simetria axial, entre duas linhas coaxiais quaisquer, incluindo corrugações nos tubos internos e externos. Pelo método de Galerkin-Budnov deduz-se um operador integral bilinear, aplicado ao campo magnético, expandido em todo o domínio da estrutura, coaxial-descontinuidade-coaxial. As portas de entrada e saída da estrutura são posicionadas distantes da descontinuidade, de forma que nelas só haja o modo Transversal Eletromagnético (TEM). O campo magnético procurado e obtido pelo MEF. Os resultados encontrados; perdas de retorno, comportamento do campo magnético e as equi-fases nas portas de entrada e saída da estrutura, foram calculados e confrontados com as do Método de Casamento de Modos (MCM), com um alto grau de concordância.

SPEECH RECOGNITION IN VODIS II.

VODIS II, a research system in which recognition is based on the conventional one-pass connected-word algorithm extended in two ways, is described. Syntactic constraints can now be applied directly via context-free-grammar rules, and the algorithm generates a lattice of candidate word matches rather than a single globally optimal sequence. This lattice is then processed by a chart parser and an intelligent dialogue controller to obtain the most plausible interpretations of the input. A key feature of the VODIS II architecture is that the concept of an abstract word model allows the system to be used with different pattern-matching technologies and hardware. The current system implements the word models on a real-time dynamic-time-warping recognizer.

The modified Kanerva model for automatic speech recognition

A parallel processing network derived from Kanerva's associative memory theory Kanerva 1984 is shown to be able to train rapidly on connected speech data and recognize further speech data with a label error rate of 0·68%. This modified Kanerva model can be trained substantially faster than other networks with comparable pattern discrimination properties. Kanerva presented his theory of a self-propagating search in 1984, and showed theoretically that large-scale versions of his model would have powerful pattern matching properties. This paper describes how the design for the modified Kanerva model is derived from Kanerva's original theory. Several designs are tested to discover which form may be implemented fastest while still maintaining versatile recognition performance. A method is developed to deal with the time varying nature of the speech signal by recognizing static patterns together with a fixed quantity of contextual information. In order to recognize speech features in different contexts it is necessary for a network to be able to model disjoint pattern classes. This type of modelling cannot be performed by a single layer of links. Network research was once held back by the inability of single-layer networks to solve this sort of problem, and the lack of a training algorithm for multi-layer networks. Rumelhart, Hinton & Williams 1985 provided one solution by demonstrating the "back propagation" training algorithm for multi-layer networks. A second alternative is used in the modified Kanerva model. A non-linear fixed transformation maps the pattern space into a space of higher dimensionality in which the speech features are linearly separable. A single-layer network may then be used to perform the recognition. The advantage of this solution over the other using multi-layer networks lies in the greater power and speed of the single-layer network training algorithm. © 1989.

Innovative Stereo Vision-Based Approach to Generate Dense Depth Map of Transportation Infrastructure

Three-dimensional (3-D) spatial data of a transportation infrastructure contain useful information for civil engineering applications, including as-built documentation, on-site safety enhancements, and progress monitoring. Several techniques have been developed for acquiring 3-D point coordinates of infrastructure, such as laser scanning. Although the method yields accurate results, the high device costs and human effort required render the process infeasible for generic applications in the construction industry. A quick and reliable approach, which is based on the principles of stereo vision, is proposed for generating a depth map of an infrastructure. Initially, two images are captured by two similar stereo cameras at the scene of the infrastructure. A Harris feature detector is used to extract feature points from the first view, and an innovative adaptive window-matching technique is used to compute feature point correspondences in the second view. A robust algorithm computes the nonfeature point correspondences. Thus, the correspondences of all the points in the scene are obtained. After all correspondences have been obtained, the geometric principles of stereo vision are used to generate a dense depth map of the scene. The proposed algorithm has been tested on several data sets, and results illustrate its potential for stereo correspondence and depth map generation.

Innovative Stereo Vision-Based Approach to Generate Dense Depth Map of Transportation Infrastructure

Three-dimensional (3-D) spatial data of a transportation infrastructure contain useful information for civil engineering applications, including as-built documentation, on-site safety enhancements, and progress monitoring. Several techniques have been developed for acquiring 3-D point coordinates of infrastructure, such as laser scanning. Although the method yields accurate results, the high device costs and human effort required render the process infeasible for generic applications in the construction industry. A quick and reliable approach, which is based on the principles of stereo vision, is proposed for generating a depth map of an infrastructure. Initially, two images are captured by two similar stereo cameras at the scene of the infrastructure. A Harris feature detector is used to extract feature points from the first view, and an innovative adaptive window-matching technique is used to compute feature point correspondences in the second view. A robust algorithm computes the nonfeature point correspondences. Thus, the correspondences of all the points in the scene are obtained. After all correspondences have been obtained, the geometric principles of stereo vision are used to generate a dense depth map of the scene. The proposed algorithm has been tested on several data sets, and results illustrate its potential for stereo correspondence and depth map generation.

Single-mode condition for silicon rib waveguides with large cross sections

The single-mode condition for silicon rib waveguides with large cross sections is obtained using a numerical method based on the finite-difference beam propagation method (FD-BPM). An ultrawide computation window is used to contain the wide mode profile near cutoff. Comparison with previous results shows that the formula predicted by the mode-matching technique is in a better agreement with our results. (C) 2004 Society of Photo-Optical Instrumentation Engineers.

一种改进的BMH模式匹配算法

分析了目前网络上最流行的BM算法及其改进算法BMH,在此基础上提出了BMH算法的改进算法BMH2。考虑了模式串自身的特征,在原有移动距离数组的基础上增加一个新的移动数组,从而充分利用模式串特征进行更大距离的移动,使算法获得更高的效率。实验证明,改进后的算法能够增加"坏字符"方法的右移量,有效地提高匹配速率。

function definition language fdl and its implementation

A Function Definition Language (FDL) is presented. Though designed for describing specifications, FDL is also a general-purpose functional programming language. It uses context-free language as data type, supports pattern matching definition of functions, offers several function definition forms, and is executable. It is shown that FDL has strong expressiveness, is easy to use and describes algorithms concisely and naturally. An interpreter of FDL is introduced. Experiments and discussion are included.

Quantum coherent networks: A theoretical study

Electron transport in quantum coherent networks (interacting quantum waveguide arrays) is investigated theoretically with use of the scattering-matrix method. The scattering matrix for the basic unit of networks, the cross junction with Square or rounded corners, is derived using the mode-matching technique, The overall scattering matrix for the network is obtained by the composition of the scattering matrices associated with each unit of the network, For a uniform network, the transmission spectra are calculated in the single-mode regime and an found notably dependent on the junction geometry. Small reflection for the input terminal and uniform output for some output ports are obtained, which means that the quantum coherent network can be used as a distributing net for the electron waves. Cross junctions with rounded corners of large radii are found to play a negative role in the device application of quantum coherent networks. (C) 1997 American Institute of Physics.

An application of a multiple agent system for flexible assemble tasks

C.H. Orgill, N.W. Hardy, M.H. Lee, and K.A.I. Sharpe. An application of a multiple agent system for flexible assemble tasks. In Knowledge based envirnments for industrial applications including cooperating expert systems in control. IEE London, 1989.

Model-based detection of spiculated lesions in mammograms

R. Zwiggelaar, T.C. Parr, J.E. Schumm. I.W. Hutt, S.M. Astley, C.J. Taylor and C.R.M. Boggis, 'Model-based detection of spiculated lesions in mammograms', Medical Image Analysis 3 (1), 39-62 (1999)

Debugging: the good, the bad, and the quirky -- a qualitative analysis of novices' strategies

Murphy, L., Lewandowski, G., McCauley, R., Simon, B., Thomas, L., and Zander, C. 2008. Debugging: the good, the bad, and the quirky -- a qualitative analysis of novices' strategies. SIGCSE Bull. 40, 1 (Feb. 2008), 163-167