Journal of Computers 

About: Journal of Computers is an academic journal. The journal publishes majorly in the area(s): Cluster analysis & Artificial neural network. It has an ISSN identifier of 1796-203X. It is also open access. Over the lifetime, 5807 publications have been published receiving 37846 citations.

Are there pathways for protein folding

Abstract: Denatured proteins, which have had essentially all of their native three-dimensional structure disrupted, can refold from their random disorderd state into a well-defined unique structure, in which the biological activity is virtually completely restored. This experimental result has lead to the suggestion that a native protein exists in some kind of thermodynamic configurational equilibrium, with the biologically active state being the one of lowest configurational energy. An alternative view is that the native protein is in a uniquely selected metastable state, in which the configurational energy is at a local minimum but not necessarily at an absolute minimum. In this latter model, the protein is not assumed to be in an equilibrium state, and one must postulate some sequence of events which takes place for each molecule so that the protein reaches the correct metastable state.One possible sequential process which might lead a protein to land in a particular state, is the growth of the peptide chain on the ribosome, starting with the amino terminal end and preceding to the carboxyl terminus. Although one could imagine a protein folding as it grows, and thus attaining a particular metastable state, this is clearly not a necessary condition for correct folding, at least for those proteins which have been shown to be reversibly denaturable. However, the fact that folding on the ribosomes is not necessary for the establishment of structure, does not imply that any theory invoking a pathway of folding can be eliminated. Such a pathway only requires some local initiations or condensations of segments of the polypeptide chain whenever the denatured protein is put into the appropriate renaturing medium. These segments would form unique three-dimensional structures which make further condensation more likely. Thus, a pathway of folding means that there exist a well- defined sequence of events which follow one another so as to carry the protein from the unfolded random coil to a uniquely folded metastable state. If the final folded state turned out to be the one of lowest configurational energy, it would be a consequence of biological evolution not of physical chemistry.Three approaches have been used in investigating this problem. First, the refolding and dimerzation of the enzyme alkaline phosphatase obtained from the bacterium E. Coli has been studied under varying conditions and from a variety of mutant strains. Mutants have been selected which fail to make active enzyme at 44 °C. About half of these mutants have activity when the cells are grown at 25 °C, and the enzyme produced at the low temperature has been found to be stable even at temperatures much higher than that used in the selection. Thus, these mutants have a temperature-sensitive step in one of the events which normally leads to the formation of active enzyme, but the enzyme produced is not temperature sensitive.A second approach involved the use of computer- aided molecular model building in attempts to deduce plausible pathways which proteins can follow as they are folding. Starting with an amino acid sequence we can describe the configuration of the protein i.e., the position of each of its atoms in space if we know the dihedral angles for the backbone and, in addition, the rotation angles about the appropriate bonds of the amino acid residues. Using a computer controlled display system, the molecule thus generated can be displayed in such a way that the observer can see the three-dimensional relationships in the structure. Computer programs have been written in such a way that any configuration can be altered to minimize the Van der Vaals energy and to insure close packing of the structure. However, this energy minimization can only be expected to alter the structure to the bottom of the local minimum; it is not intended to search through all possible configurations for a true minimum energy. In addition, the investigator can alter the computer generated structure as if he were dealing with physical models in which one part could be pushed or pulled relative to another. Thus, the computer- aided model building is not designed to find the configuration of minimum energy rather, it is designed as an aid to the investigator as various sequentially folding steps are tried.This system has been used in an attempt to obtain such a pathway of folding for the protein cytochrome C. A plausible structure has been obtained in this way which satisfies all of the known chemical interactions of the molecule. However, the uniqueness of the proposed folding process has not been determined.Finally, the computer system has been used in attempts to deduce plausible folding pathways for myoglobin and lysozyme. Three-dimensional pictures of the structures and some of the folding sequences will be shown.

Neighborhood Component Feature Selection for High-Dimensional Data

Abstract: Feature selection is of considerable importance in data mining and machine learning, especially for high dimensional data. In this paper, we propose a novel nearest neighbor-based feature weighting algorithm, which learns a feature weighting vector by maximizing the expected leave-one-out classification accuracy with a regularization term. The algorithm makes no parametric assumptions about the distribution of the data and scales naturally to multiclass problems. Experiments conducted on artificial and real data sets demonstrate that the proposed algorithm is largely insensitive to the increase in the number of irrelevant features and performs better than the state-of-the-art methods in most cases.

Biometric Gait Authentication Using Accelerometer Sensor

Abstract: This paper presents a biometric user authentication based on a person’s gait. Unlike most previous gait recognition approaches, which are based on machine vision techniques, in our approach gait patterns are extracted from a physical device attached to the lower leg. From the output of the device accelerations in three directions: vertical, forward-backward, and sideways motion of the lower leg are obtained. A combination of these accelerations is used for authentication. Applying two different methods, histogram similarity and cycle length, equal error rates (EER) of 5% and 9% were achieved, respectively.

A Multi-focus Image Fusion Method Based on Laplacian Pyramid

Abstract: This paper presented a simple and efficient algorithm for multi-focus image fusion, which used a multi-resolution signal decomposition scheme called Laplacian pyramid method. The principle of Laplacian pyramid transform is introduced, and based on it the fusion strategy is described in detail. The method mainly composed of three steps. Firstly, the Laplacian pyramids of each source image are deconstructed separately, and then each level of new Laplacian pyramid is fused by adopting different fusion rules. To the top level, it adopts the maximum region information rule; and to the rest levels, it adopts the maximum region energy rule. Finally, the fused image is obtained by inverse Laplacian pyramid transform. Two sets of images are applied to verify the fusion approach proposed and compared it with other fusion approaches. By analyzing the experimental results, it showed that this method has good performance, and the quality of the fused image is better than the results of other methods.

Mobile Agent Based Wireless Sensor Networks

Abstract: Recently, mobile agents have been proposed for efficient data dissemination in sensor networks. In the traditional client/server-based computing architecture, data at multiple sources are transferred to a destination; whereas in the mobile-agent based computing paradigm, a task specific executable code traverses the relevant sources to gather data. Mobile agents can be used to greatly reduce the communication cost, especially over low bandwidth links, by moving the processing function to the data rather than bringing the data to a central processor. This paper proposes to use the mobile agent paradigm for reducing and aggregating data in a planar sensor network architecture. The proposed architecture is called mobile agent based wireless sensor network (MAWSN). Extensive simulation shows that MAWSN exhibits better performance than client/server communications in terms of energy consumption and the packet delivery ratio. However, MAWSN has a longer end-to-end latency than client/server communications in certain conditions.