1,199 research outputs found
Single ICCII Sinusoidal Oscillators Employing Grounded Capacitors
Two inverting second-generation current conveyors (ICCII) based sinusoidal oscillators are presented. The first sinusoidal oscillator is composed of one ICCII, two grounded capacitors and two resistors. The oscillation condition and oscillation frequency can be orthogonally controllable. The second sinusoidal oscillator is composed of one ICCII, two grounded capacitors and three resistors. The oscillation condition and oscillation frequency can be independently controllable through different resistors
Bending-wave Instability of a Vortex Ring in a Trapped Bose-Einstein Condensate
Based on a velocity formula derived by matched asymptotic expansion, we
investigate the dynamics of a circular vortex ring in an axisymmetric
Bose-Einstein condensate in the Thomas-Fermi limit. The trajectory for an
axisymmetrically placed and oriented vortex ring is entirely determined,
revealing that the vortex ring generally precesses in condensate. The linear
instability due to bending waves is investigated both numerically and
analytically. General stability boundaries for various perturbed wavenumbers
are computed. In particular, the excitation spectrum and the absolutely stable
region for the static ring are analytically determined.Comment: 4 pages, 4 figure
Performance Evaluation of a Database of Repetitive Elements in Complete Genomes
[[abstract]]The analysis of repetitive elements reveals repetitive elements in our genome may have been very important in the evolutionary genomics. In this work, we propose approaches to improve the performance of the repetitive elements in a database, namely Repetitive Sequence Database (RSDB). There are hundreds of millions of repetitive elements in RSDB. Performance evaluation and tuning are critical for us to manage such a large database. Not only does this study have a lot of performance improvements on centralized RSDB, but also this study provides a comparison of performance between centralized RSDB and distributed RSDB. From the experimental results, we find the improvements proposed speed up our RSDB very much
Computing motif correlations in proteins
[[abstract]]Protein motifs, which are specific regions and conserved regions, are found by comparing multiple protein sequences. These conserved regions in general play an important role in protein functions and protein folds, for example, for their binding properties or enzymatic activities. The aim here is to find the existence correlations of protein motifs. The knowledge of protein motif/domain sharing should be important in shedding new light on the biologic functions of proteins and offering a basis in analyzing the evolution in the human genome or other genomes. The protein sequences used here are obtained from the PIR-NREF database and the protein motifs are retrieved from the PROSITE database. We apply data mining approach to discover the occurrence correlations of motif in protein sequences. The correlation of motifs mined can be used in evolution analyses and protein structure prediction. We discuss the latter, i.e., protein structure prediction in this study. The correlations mined are stored and maintained in a database system. The database is now available at http://bioinfo.csie.ncu.edu.tw/ProMotif/. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2032-2043, 200
Mining putative Regulatory Elements in promoter Regions of Saccharomyces cerevisiae
[[abstract]]The availability of genome-wide gene expression data provides a unique set of genes from which
we can decipher the mechanisms underlying the common transcriptional response. Transcription factors, which
can bind to specific DNA sites, cooperatively regulate the transcription of genes. This study attempts to mine
putative binding sites to investigate how combinations of the sites predicted from known sites and overrepresented
repetitive elements are distributed in the promoter regions of groups of functionally related genes.
The over-represented repetitive elements appearing in the associations are possible transcription factor binding
sites. The deduced association rules would facilitate to predict putative regulatory elements and to identify genes
which are potentially co-regulated by the putative regulatory elements. Our proposed approach is applied to
Saccharomyces cerevisiae and the promoter regions of yeast ORFs
Identifying the combination of genetic factors that determine susceptibility to cervical cancer
[[abstract]]Cervical cancer is common among women all over the world. Although infection with high-risk types of human papillomavirus (HPV) has been identified as the primary cause of cervical cancer, only some of those infected go on to develop cervical cancer. Obviously, the progression from HPV infection to cancer involves other environmental and host factors. Recent populationbased twin and family studies have demonstrated the importance of the hereditary component of cervical cancer, associated with genetic susceptibility. Consequently, single-nucleotide polymorphism
(SNP) markers and microsatellites should be considered genetic factors for determining what combinations of genetic factors are involved in precancerous changes to cervical cancer. This study employs a Bayesian network and four different decision tree algorithms, and compares the performance of these learning algorithms. The results of this study raise the possibility of investigations that could identify combinations of genetic factors, such as SNPs and microsatellites, that influence the risk associated with common complex multifactorial diseases, such as cervical cancer. The web site associated with this study is http://140.115.155.8/FactorAnalysis/
Transcritical flow of a stratified fluid over topography: analysis of the forced Gardner equation
Transcritical flow of a stratified fluid past a broad localised topographic
obstacle is studied analytically in the framework of the forced extended
Korteweg--de Vries (eKdV), or Gardner, equation. We consider both possible
signs for the cubic nonlinear term in the Gardner equation corresponding to
different fluid density stratification profiles. We identify the range of the
input parameters: the oncoming flow speed (the Froude number) and the
topographic amplitude, for which the obstacle supports a stationary localised
hydraulic transition from the subcritical flow upstream to the supercritical
flow downstream. Such a localised transcritical flow is resolved back into the
equilibrium flow state away from the obstacle with the aid of unsteady coherent
nonlinear wave structures propagating upstream and downstream. Along with the
regular, cnoidal undular bores occurring in the analogous problem for the
single-layer flow modeled by the forced KdV equation, the transcritical
internal wave flows support a diverse family of upstream and downstream wave
structures, including solibores, rarefaction waves, reversed and trigonometric
undular bores, which we describe using the recent development of the nonlinear
modulation theory for the (unforced) Gardner equation. The predictions of the
developed analytic construction are confirmed by direct numerical simulations
of the forced Gardner equation for a broad range of input parameters.Comment: 34 pages, 24 figure
Mining correlations of human gene expression from digital gene expression profiles
[[abstract]]The study addressed here aimed to analyze a large number of human genome transcripts
from diverse tissues and to discover genes that with similar expression profiles in
different human tissues. These genes may be of potential biological or pharmaceutical
relevance. We propose an approach to discover the correlations of tissue gene expression
by analyzing digital gene expression profiles of different human tissues. A simple statistical
test was used to correlate genes having similar expression profiles. We used the information
of tissue gene expression to discover the correlations of expressed genes. The
correlations of gene expression revealed that such genes were specifically expressed in
particular tissues with similar expression profiles and could be used to identify the relationships
of the genes that be co-regulated, involved in the same biochemical pathway
and signal transduction process
A computational approach to discover differential cooperation of regulatory sites in functionally related genes in yeast genome
[[abstract]]The availability of genome-wide gene expression data provides a unique set of genes from which to decipher the mechanisms underlying the common transcriptional response. A set of transcription factors which bind to targetsites regulate the gene transcription cooperatively. This motivates us to discover the site associations of known transcription factor binding sites and certain repetitive elements. Those over-represented repetitive elements in the promoter regions of functionally related genes are predicted as putative regulatory elements. The study is to analyze how the differential site associations of the known regulatory sites and putative regulatory elements are distributed in the promoter regions of groups of functionally related genes. The functional-specific site associations are discovered by a statistical approach and the over-represented repetitive elements involving in the site associations are possible to be transcription factor binding sites. The site associations facilitate to predict functional-specific putative regulatory elements and to identify genes potentially co-regulated by the putative regulatory elements. Our proposed approach is applied to Saccharomyces cerevisiae and the promoter regions of yeast ORFs
Database of repetitive elements in complete genomes and data mining using transcription factor binding sites
[[abstract]]Approximately 43% of the human genome is occupied by repetitive elements. Even more, around 51% of the rice genome is occupied by repetitive elements. The analysis presented here indicates that repetitive elements in complete genomes may have been very important in the evolutionary genomics. In this study, a database, called the Repeat Sequence Database, is first designed and implemented to store complete and comprehensive repetitive sequences. See http://rsdb.csie.ncu.edu.tw for more information. The database contains direct, inverted and palindromic
repetitive sequences, and each repetitive sequence has a variable length ranging from seven to many hundred nucleotides. The repetitive sequences in the database are explored using a mathematical algorithm to mine rules on how combinations of individual binding sites are distributed among repetitive sequences in the database. Combinations of transcription factor binding sites in the repetitive sequences are obtained and then data mining techniques are applied to mine association rules from these combinations. The discovered associations are further pruned to
remove insignificant associations and obtain a set of associations. The mined association rules facilitate efforts to identify gene classes regulated by similar mechanisms and accurately predict regulatory elements. Experiments are performed on several genomes including C. elegans, human chromosome 22, and yeast
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