Gardner's deformations of the Boussinesq equations

Using the algebraic method of Gardner's deformations for completely integrable systems, we construct the recurrence relations for densities of the Hamiltonians for the Boussinesq and the Kaup-Boussinesq equations. By extending the Magri schemes for these systems, we obtain new integrable equations adjoint with respect to the initial ones and describe their Hamiltonian structures and symmetry properties.Comment: Proc. Workshop `Quantizaion, Dualities, and Integrable Systems,' 23-27 January 2006, Pamukkale University, Turkey; 7 pages. MSC 35Q53, 37K05, 37K10, 37K3

On Construction of Recursion Operators From Lax Representation

In this work we develop a general procedure for constructing the recursion operators fro non-linear integrable equations admitting Lax representation. Svereal new examples are given. In particular we find the recursion operators for some KdV-type of integrable equations.Comment: Latex File (AMS format), 23 pages, to be published in Journal of Mathematical Physic

Identification of Novel Reference Genes Based on MeSH Categories

Cataloged from PDF version of article.Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds. © 2014 Ersahin et al

Implicit motif distribution based hybrid computational kernel for sequence classification

Motivation: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive. Results: A system named P2SL that infer protein subcellular targeting was developed through this computational kernel. Targeting-signal was modeled by the distribution of subsequence occurrences (implicit motifs) using self-organizing maps. The boundaries among the classes were then determined with a set of support vector machines. P2SL hybrid computational system achieved ∼81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes. P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol. © The Author 2004. Published by Oxford University Press. All rights reserved

Prediction of protein subcellular localization based on primary sequence data

This paper describes a system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order. Our approach for prediction is to find the most frequent motifs for each protein (class) based on clustering and then to use these most frequent motifs as features for classification. This approach allows a classification independent of the length of the sequence. Another important property of the approach is to provide a means to perform reverse analysis and analysis to extract rules. In addition to these and more importantly, we describe the use of a new encoding scheme for the amino acids that conserves biological function based on point of accepted mutations (PAM) substitution matrix. We present preliminary results of our system on a two class (dichotomy) classifier. However, it can be extended to multiple classes with some modifications. © Springer-Verlag Berlin Heidelberg 2003

A new integrable generalization of the Korteweg - de Vries equation

A new integrable sixth-order nonlinear wave equation is discovered by means of the Painleve analysis, which is equivalent to the Korteweg - de Vries equation with a source. A Lax representation and a Backlund self-transformation are found of the new equation, and its travelling wave solutions and generalized symmetries are studied.Comment: 13 pages, 2 figure

HandVR: a hand-gesture-based interface to a video retrieval system

Cataloged from PDF version of article.Using one's hands in human-computer interaction increases both the effectiveness of computer usage and the speed of interaction. One way of accomplishing this goal is to utilize computer vision techniques to develop hand-gesture-based interfaces. A video database system is one application where a hand-gesture-based interface is useful, because it provides a way to specify certain queries more easily. We present a hand-gesture-based interface for a video database system to specify motion and spatiotemporal object queries. We use a regular, low-cost camera to monitor the movements and configurations of the user's hands and translate them to video queries. We conducted a user study to compare our gesture-based interface with a mouse-based interface on various types of video queries. The users evaluated the two interfaces in terms of different usability parameters, including the ease of learning, ease of use, ease of remembering (memory), naturalness, comfortable use, satisfaction, and enjoyment. The user study showed that querying video databases is a promising application area for hand-gesture-based interfaces, especially for queries involving motion and spatiotemporal relations. © 2014 Springer-Verlag London

Subband domain coding of binary textual images for document archiving

Cataloged from PDF version of article.In this work, a subband domain textual image compression method is developed. The document image is first decomposed into subimages using binary subband decompositions. Next, the character locations in the subbands and the symbol library consisting of the character images are encoded. The method is suitable for keyword search in the compressed data. It is observed that very high compression ratios are obtained with this method. Simulation studies are presented

Data and model driven hybrid approach to activity scoring of cyclic pathways

Analysis of large scale -omics data based on a single tool remains inefficient to reveal molecular basis of cellular events. Therefore, data integration from multiple heterogeneous sources is highly desirable and required. In this study, we developed a data- and model-driven hybrid approach to evaluate biological activity of cellular processes. Biological pathway models were taken as graphs and gene scores were transferred through neighbouring nodes of these graphs. An activity score describes the behaviour of a specific biological process was computed by owing of converged gene scores until reaching a target process. Biological pathway model based approach that we describe in this study is a novel approach in which converged scores are calculated for the cellular processes of a cyclic pathway. The convergence of the activity scores for cyclic graphs were demonstrated on the KEGG pathways. © 2011 Springer Science+Business Media B.V

Which shape representation is the best for real-time hand interface system?

Hand is a very convenient interface for immersive human-computer interaction. Users can give commands to a computer by hand signs (hand postures, hand shapes) or hand movements (hand gestures). Such a hand interface system can be realized by using cameras as input devices, and software for analyzing the images. In this hand interface system, commands are recognized by analyzing the hand shapes and its trajectories in the images. Therefore, success of the recognition of hand shape is vital and depends on the discriminative power of the hand shape representation. There are many shape representation techniques in the literature. However, none of them are working properly for all shapes. While a representation leads to a good result for a set of shapes, it may fail in another one. Therefore, our aim is to find the most appropriate shape representation technique for hand shapes to be used in hand interfaces. Our candidate representations are Fourier Descriptors, Hu Moment Invariant, Shape Descriptors and Orientation Histogram. Based on widely-used hand shapes for an interface, we compared the representations in terms of their discriminative power and speed. © 2009 Springer-Verlag