Browsing by Author "Huang, SL"

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Computing motif correlations in proteins
(2003-12-01)
Horng, JT
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Huang, HD
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Wang, SH
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Chen, MY
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Huang, SL
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/. (C) 2003 Wiley Periodicals, Inc.
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures
(2006-04-30)
Wu, LC
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Horng, JT
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Huang, SL
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Huang, HD
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Liu, BJ
Recent investigations on the stability of proteins have demonstrated various structural factors, but few have considered sequence factors such as protein motifs. These motifs represent highly conserved regions and describe critical regions that may only exist on proteins that remain functional at high temperatures. This investigation presents a method for identifying and comparing corresponding mesophilic and thermophilic sequence motifs between protein families. Discriminative motifs that are conserved only in the mesophilic or thermophilic subfamily are identified. Analysis of the results shows that, although the subfamilies of most protein families share similar motifs, some discriminative motifs are present in particular thermophilic/mesophilic subfamilies. The thermophilic discriminative motifs are conserved only in thermophilic organisms, revealing that physiochemical principles support thermostability. (c) 2006 Wiley Periodicals, Inc.
Identifying the combination of genetic factors that determine susceptibility to cervical cancer
(2004-03-01)
Horng, JT
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Hu, KC
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Wu, LC
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Huang, HD
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Lin, FM
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 population-based 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.
Identifying transcriptional regulatory sites in the human genome using an integrated computation
(2004)
Huang, HD
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Horng, JT
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Sun, YM
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Tsou, AP
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Huang, SL
Recently, biological databases and analytical methods have become available for analyzing gene expression and transcriptional regulatory sequences. However, users must make the complicated analyses to query the data in various databases, and to analyze the gene upstreams using various predictive tools. Beyond methods for predicting transcriptional regulatory sites, new automated and integrated methods for analyzing gene upstream sequences on a higher level are urgently required. We present an integrated system to predict transcriptional regulatory sites and detect co-occurrence of these regulatory sites after a set of genes are input. The system comprises a biological data warehousing system, patient discovery programs, pattern occurrence association detectors and user interfaces. User profiles and history pages enable users to trace the sequence analyses for transcriptional regulatory sites.
Identifying transcriptional regulatory sites in the human genome using an integrated system
(2004-03-01)
Huang, HD
;
Horng, JT
;
Sun, YM
;
Tsou, AP
;
Huang, SL
This work develops an integrated system which, after a set of genes are inputted, is able to predict transcriptional regulatory sites and to detect the co-occurrence of these regulatory sites. The system integrates several site detection methods such as known site matching, over-presented oligonucleotide detection and DNA motif discovery programs. User profiles and history pages enable users to trace the sequence analyses of these transcriptional regulatory sites. Two groups of co-regulated genes were used to test the proposed system. The results predicted by the proposed system consist of known site homologs and putative regulatory sites. By comparing these sites with previously published results, the proposed system is able to help biologists identify possible candidates for the regulatory sites from groups of co-regulated genes. The integrated system is now available at http://rgsminer. csie.ncu.edu.tw/.
On-wafer electrooptic probing using rotational deformation modulation
(2000-09-01)
Chen, WH
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Kuo, WK
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Huang, SL
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Huang, YT
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電子工程學系及電子研究所
On-wafer electrooptic probing of two-dimensional electric-field vector (E-vector) is demonstrated by using one laser beam and one electrooptic prober. This technique utilizes both compressed-stretched deformation and rotational deformation on the index ellipsoid of the electrooptic crystal. Both experiment and simulation were performed to map the E-vector on a circuit hoard, and the measurement error is within 2.2%.
RgS-Miner: A biological data warehousing, analyzing and mining system for identifying transcriptional regulatory sites in human genome
(2004)
Sun, YM
;
Huang, HD
;
Horng, JT
;
Tsou, AP
;
Huang, SL
Recently, biological databases and. analytical methods have become available for analyzing gene expression and transcriptional regulatory sequences. However, users must make the complicated analyses to query the data in various databases, and then they must analyze the gene upstreams using various predictive tools, before finally converting date among formats. Beyond methods for predicting transcriptional regulatory sites, new automated and integrated methods for analyzing gene upstream sequences on a higher level are urgently required. Efficient and integrated data management methods are essential, too. We present an integrated system, namely RgS-Miner, to predict transcriptional regulatory sites and detect co-occurrence of these regulatory sites. RgS-Miner comprises a biological data,, warehousing system, pattern discovery programs, pattern occurrence association detectors and user interfaces. The system is available at http://rgsminer.csie.ncu.edu.tw/.
Synthesis and characteristics of polyimide/siloxane hybrid films for reliability adhesion
(2006-02-24)
Tsai, MH
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Chiang, PC
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Whang, WT
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Ko, CJ
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Huang, SL
Polyimide/siloxane (PISi) hybrid films from 2,2'-bis[4-(3-aminodiphenoxy)phenyl]sulfone (in-BAPS), 3,3'-oxydiphthatic anhydride (ODPA) and p-aminopropyltrimethoxysilane (APrTS) have been successfully fabricated by an in-situ sol-gel process. The APrTS is used to introduce siloxane structure and to be the end-capped agent to control the polymer block chain length in the range of 5000-20000 g/mol. The network structure of the PISi hybrid film is formed through the hydrolysis and condensation reactions. The PISi hybrid films with various polyimide block chain lengths are characterized with regard to the structure effect, mechanical properties, adhesion strength, adhesive melting flow and thermal stability. The result indicates that the more APrTS is contained, the shorter of the polyimide block chain length is formed and thus the lower inherent viscosity of APrTS-PAA is obtained. It is also suggested that the cross-linked density of the PISi hybrid film increases with the increase in the amount of APrTS. The network structure of the hybrid film reinforces the pure PI and makes the coefficient of thermal expansion (CTE) as well as adhesive melting flow decrease. Based on the dynamic mechanical analyses (DMA), the hybrid film with higher cross-linked density possesses superior mechanical property at elevated temperature. In addition, the introduction of APrTS causes an increase in thermal stability due to the network structure of hybrid film and the filler effect of the siloxane. (c) 2005 Elsevier B.V. All rights reserved.
Three-dimensional electric-field vector measurement with an electro-optic sensing technique
(1999-11-15)
Kuo, WK
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Huang, YT
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Huang, SL
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電子工程學系及電子研究所
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Department of Electronics Engineering and Institute of Electronics
A new technique for three-dimensional (3D) electric-field (e-field) vector measurement is presented. Three laser beams with different propagation paths in an electro-optic (EO) crystal were used to resolve 3D components of e-field vectors. We adopted a special geometric shape of bismuth silicon oxide EO crystal so that the three beams would propagate within it. A sensitivity of 0.6 V/cm root Hz was achieved. A commercial Ansoft Maxwell 3D field simulator was also used to verify our measurements. (C) 1999 Optical Society of America.
Two-dimensional electric-field vector measurement by a LiTaO3 electro-optic probe tip
(2000-09-20)
Kuo, WK
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Chen, WH
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Huang, YT
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Huang, SL
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電子工程學系及電子研究所
An electro-optic probe tip that is made from LiTaO crystal to make tangentially two-dimensional electric-field (E-field) vector measurements is presented. We combine a new electro-optic modulation technique and a conventional one to resolve the two E-tield components. The new modulation effect on the optical probing beam is caused by rotation of the principal axis the electro-optic crystal, which is proportional to the E-field. Inasmuch as there is no free charge involved in the axis rotation, rotation modulation of the axis can be as fast as conventional modulation. The principles are carefully derived, and an experimental system constructed, to measure two-dimensional E-field vectors on a test pattern. The results are in good agreement with those obtained with commercial software for electromagnetic simulation. The sensitivities of two tangential E-field components are 76 (mV/cm)/root Hz and 0.8 (V/cm)root Hz, respectively. The root-mean-square error of an E-field directional measurement is 1.5 degrees. (C) 2000 Optical Society of America OCIS codes: 120.5410, 230.2090, 230.4110, 130.6010.