Browsing by Author "Chang, HY"

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An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species
(2005)
Lin, YC
;
Lu, CL
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Chang, HY
;
Tang, CY
;
生物科技學系
In the study of genome rearrangement, the block-interchanges have been proposed recently as a new kind of global rearrangement events affecting a genome by swapping two nonintersecting segments of any length. The so-called block-interchange distance problem, which is equivalent to the sorting by block-interchange problem, is to find a minimum series of block-interchanges for transforming one chromosome into another. In this paper, we study this problem by considering the circular chromosomes and propose a O(deltan) time algorithm for solving it by making use of permutation groups in algebra, where n is the length of the circular chromosome and 3 is the minimum number of block-interchanges required for the transformation, which can be calculated in O(n) time in advance. Moreover, we obtain analogous results by extending our algorithm to linear chromosomes. Finally, we have implemented our algorithm and applied it to the circular genomic sequences of three human vibrio pathogens for predicting their evolutionary relationships. Consequently, our experimental results coincide with the previous ones obtained by others using a different comparative genomics approach, which implies that the block-interchange events seem to play a significant role in the evolution of vibrio species.
Analysis of human UDP-glucose dehydrogenase gene promoter: Identification of an Sp1 binding site crucial for the expression of the large transcript
(2005-06-01)
Vatsyayan, J
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Peng, HL
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Chang, HY
;
生物科技學系
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Department of Biological Science and Technology
UDP-glucose dehydrogenase (UGDH) catalyzes the conversion of UDP-glucose to UDP-glucuronic acid, which is required in liver for the excretion of toxic compounds, and for the biosynthesis of complex carbohydrates, such as hyaluronan, in many cell types. Analysis of a human EST database, as well as the results of a 5'-RACE experiment, have revealed the presence of two transcription start sites approximately 160 bp apart in the human UGDH gene confirming previous Northern hybridization results. To delineate the regions in the UGDH promoter required for regulating the expression of the gene, in particular the synthesis of the large transcript, serial deletions of the 2.1-kb UGDH promoter region were constructed and their activities determined by the firefly luciferase reporter gene assay. Our results indicate that the region from nucleotide position -486 to -632 relative to the start of the small transcript contains positive regulatory elements that contribute to gene expression. Mithramycin A, an inhibitor of transcription factor Sp1, abrogates the promoter activity, suggesting the involvement of this specific protein in UGDH expression. By using site-directed mutagenesis, we analyzed the functional contribution of three putative Sp1 binding elements within this region. A mutation at position -564 demonstrated that this site serves as an enhancing element in both HepG2 and HeLa cells. The complex formation pattern revealed by an electrophoretic mobility shift assay as well as an anti-Sp1 antibody-mediated supershift; assay confirmed the identity of this GC box as an Sp1 binding motif. Our results thus identify an alternative transcription start site on the UGDH promoter, and locate the cis-element that greatly enhances the basal transcriptional activity of UGDH gene.
Characterization of mdcR, a regulatory gene of the malonate catabolic system in Klebsiella pneumoniae
(1999-04-01)
Peng, HL
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Shiou, SR
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Chang, HY
;
生物科技學系
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Department of Biological Science and Technology
The Klebsiella pneumoniae mdcR gene, which encodes a LysR-type regulator, was overexpressed in Escherichia coli, Purified MdcR was found to bind specifically to the control region of either the malonate decarboxylase (mdc) genes or mdcR, We have also demonstrated that MdcR is an activator of the expression of the mde genes, whereas it represses the transcription of the putative control region of mdcR, P-mder, indicating a negative autoregulatory control.
Design of vocabulary-independent Mandarin keyword spotters
(2000-07-01)
Liu, CM
;
Chiu, CC
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Chang, HY
;
資訊工程學系
;
Department of Computer Science
This paper considers the design of a vocabulary-independent keyword spotter for Mandarin speech according to the framework by Huang et al. [1]. This paper considers three varieties of filler model structures for the framework based on subsyllabic grammar of Mandarin speech. On the basis of the three structures, we infer the problems of this framework through three arguments and presents two methods to modify the spotting vehicle.
Embedding cycles in IEH graphs
(1997-10-14)
Chang, HY
;
Chen, RJ
;
資訊工程學系
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Department of Computer Science
We embed cycles into IEH graphs. First, IEH graphs are proved to be Hamiltonian except when they are of size 2(n) -1 for all n greater than or equal to 2. Next, we show that for an IEH graph of size N, an arbitrary cycle of even length N-e where 3 < N-e < N is found. We also find an arbitrary cycle of odd length N-o where 2 < N-o < N if and only if a node of this graph has at least one forward 2-Inter-Cube (IC) edges. These results help describe the whole cycle structure in IEH graphs. (C) 1997 Elsevier Science B.V.
Embedding cycles in IEH graphs
(1997-10-14)
Chang, HY
;
Chen, RJ
;
資訊工程學系
;
Department of Computer Science
We embed cycles into IEH graphs. First, IEH graphs are proved to be Hamiltonian except when they are of size 2(n) -1 for all n greater than or equal to 2. Next, we show that for an IEH graph of size N, an arbitrary cycle of even length N-e where 3 < N-e < N is found. We also find an arbitrary cycle of odd length N-o where 2 < N-o < N if and only if a node of this graph has at least one forward 2-Inter-Cube (IC) edges. These results help describe the whole cycle structure in IEH graphs. (C) 1997 Elsevier Science B.V.
Evolutionary analysis of the two-component systems in Pseudomonas aeruginosa PAO1
(2004-12-01)
Chen, YT
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Chang, HY
;
Lu, CL
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Peng, HL
;
生物科技學系
Gene organization and functional motif analyses of the 123 two-component system (2CS) genes in Pseudomonas aeruginosa PAO1 were carried out. In addition, NJ and ML trees for the sensor kinases and the response regulators were constructed, and the distances measured and comparatively analyzed. It was apparent that more than half of the sensor-regulator gene pairs, especially the 2CSs with OmpR-like regulators, are derivatives of a common ancestor and have most likely co-evolved through gene pair duplication. Several of the 2CS pairs, especially those with NarL-like regulators, however, appeared to be relatively divergent. This is supportive of the recruitment model, in which a sensor gene and regulator gene with different phylogenetic history are assembled to form a 2CS. Correlation of the classification of sensor kinases and response regulators provides further support for these models. Upon comparison of the phylogenetic trees comprised of sensors and regulators, we have identified six congruent clades, which represent the group of the most recently duplicated 2CS gene pairs. Analyses of the congruent 2CS pairs of each of the clades revealed that certain paralogous 2CS pairs may carry a redundant function even after a gene duplication event. Nevertheless, comparative analysis of the putative promoter regions of the paralogs suggested that functional redundancy could be prevented by a differential control. Both codon usage and G+C content of these 2CS genes were found to be comparable with those of the P. aeruginosa genome, suggesting that they are not newly acquired genes.
Graph embedding aspect of IEH graphs
(2001-01-01)
Chang, HY
;
Chen, RJ
;
資訊工程學系
;
Department of Computer Science
In order to overcome the drawback of the hypercube that the number of nodes is limited to a power of two, the incrementally extensible hypercube (IEH) graph is derived for an arbitrary number of nodes [12]. In this paper, we first prove that the incomplete hypercube (IH) is a spanning subgraph of IEH. Next. we present a new method to construct an IEH From an IH. From the aspect of graph embedding, we determine the minimum size of the IEH that contains a complete binary tree. WI: then embed a torus (with a side length as power of two) into an IEH with dilation 1 and expansion 1.
Hot-electron relaxation via optical phonon emissions in GaAs/AlxGa1-xAs quantum well structures: dependence upon the alloy composition and barrier width
(2000-12-01)
Sun, KW
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Chang, HY
;
Wang, CM
;
Wang, SY
;
Lee, CP
We present a systematic investigation of the dependence of the hot-electron-optical-phonon interactions on Al composition and barrier width in GaAs/AlxGa1-xAs MQW structures. Raman scattering measurements at 15 K are presented for samples with different barrier widths and Al composition. The optical phonon energies emitted by the photoexcited electrons in quantum wells were also determined by using hot-electron-neutral acceptor luminescence techniques. It is shown that the relaxation of hot electrons in the quantum wells is dominated by the GaAs LO phonon emission for small x, but by AlAs-like LO phonons for larger Al composition. For samples with larger barriers, the electrons in the GaAs layer relax mostly through the AlAs-like optical phonon emission. However, in samples with smaller barriers, the relaxation of hot electrons is dominated by the GaAs optical phonon emission.
Identification and characterization of KvgAS, a two-component system in Klebsiella pneumoniae CG43
(2003-01-21)
Lai, YC
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Lin, GT
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Yang, SL
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Chang, HY
;
Peng, HL
A two-component system encoding gene cluster kvgAS that is present only in virulent Klebsiella pneumoniae CG43 was isolated and its sequence determined. RT-PCR and Southern analysis demonstrated that kvgAS is organized as an operon. No apparent effect of a kvgS deletion on bacterial virulence was observed in a mouse peritonitis model. In the presence of paraquat or 2,2-dipyridyl, the activity of kvgAS promoter in the kvgS mutant was found to be reduced to half of the level in the wild-type strain. The data suggest that the KvgAS system is autoregulated and plays a role in countering free radical stresses and sensing iron-limiting conditions. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Identification of genes induced in vivo during Klebsiella pneumoniae CG43 infection
(2001-11-01)
Lai, YC
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Peng, HL
;
Chang, HY
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生物科技學系
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Department of Biological Science and Technology
A novel in vivo expression technology (IVET) was performed to identify Klebsiella pneumoniae CG43 genes that are specifically expressed during infection of BALB/c mice. The IVET employed a UDP glucose pyrophosphorylase (galU) -deficient mutant of K. pneumoniae which is incapable of utilizing galactose and synthesizing capsular polysaccharide, as demonstrated by its low virulence to BALB/c mice and a white nonmucoid colony morphology on MacConkey-galactose agar. By using a functional galU gene as the reporter, an RT, promoter could render the galU mutant virulent while maintaining the white nonmucoid colony phenotype. A total of 20 distinct sequences were obtained through the in vivo selection. Five of them have been identified previously as virulence-associated genes in other pathogens, while another five with characterized functions are involved in regulation and transportation of nutrient uptake, biosynthesis of isoprenoids, and protein folding. No known functions have been attributed to the other 10 sequences. We have also demonstrated that 2 of the 20 IVE genes turn on under iron deprivation, whereas the expression of another five genes was found to be activated in the presence of paraquat, a superoxide generator.
Identification of genes present specifically in a virulent strain of Klebsiella pneumoniae
(2000-12-01)
Lai, YC
;
Yang, SL
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Peng, HL
;
Chang, HY
;
生物科技學系
Klebsiella pneumoniae is a common cause of septicemia and urinary tract infections. The PCR-supported genomic subtractive hybridization was employed to identify genes specifically present in a virulent strain of K. pneumoniae. Analysis of 25 subtracted DNA clones has revealed 19 distinct nucleotide sequences. Two of the sequences were found to be the genes encoding the transposase of Tn3926 and a capsule polysaccharide exporting enzyme. Three sequences displayed moderate homology with bvgAS, which encodes a two-component signal transduction system in Bordetella pertussis. The rest of the sequences did not exhibit homology with any known genes. The distribution of these novel sequences varied greatly in K. pneumoniae clinical isolates, reflecting the heterogeneous nature of the K. pneumoniae population.
Incrementally extensible folded hypercube graphs
(2000-03-01)
Chang, HY
;
Chen, RJ
;
資訊工程學系
;
Department of Computer Science
In this paper, we propose the incrementally extensible folded hypercube (IEFH) graph as a new class of interconnection networks for an arbitrary number of nodes. We show that this system is optimal fault tolerant and almost regular (i.e., the difference between the maximum and the minimum degree of nodes is at most one). The diameter of this topology is half of that of the incomplete hypercube (IH), the supercube, or the IEH graph. We also devise a simple routing algorithm for the IEFH graph. Finally, we embed cycles and complete binary trees into this graph optimally.
Incrementally extensible folded hypercube graphs
(1998)
Chang, HY
;
Chen, RJ
;
資訊工程學系
;
Department of Computer Science
In this paper,ce propose the incrementally extensible folded hypercube (IEFH) graph as a new class of interconnection networks. for arbitrary number of nodes. We show this system is optimal fault tolerant and almost regular (i.e., the difference between the maximum and the minimum degree of nodes is at most one). The diameter of this topology is half of that of the incomplete hypercube (IH), the supercube, or the IEH graph. also devise a simple routing algorithm for the IEFH graph. Further we embed cycles and complete binary, trees into this graph optimally.
Optical phonon emission in GaAs/AlAs and GaAs/Al0.7Ga0.3As multiple quantum well structures
(2000-12-01)
Sun, KW
;
Wang, CM
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Chang, HY
;
Wang, SY
;
Lee, CP
We have performed Raman scattering measurements and hot electron-neutral acceptor (hot(e, Angstrom)) luminescence experiments on Be-doped GaAs/AlAs and GaAs/Al0.7Ga0.3As multiple quantum well structures, with fixed well width of 50 Angstrom and barrier thickness of 5, 25, 50,120 Angstrom, to determine the optical phonon energy emitted by the hot electrons excited in the quantum wells. It was shown that the relaxation of electrons in the GaAs layer is dominated by the AlAs-like optical phonon emission for samples with larger barriers, but by GaAs optical phonons for smaller barriers. (C) 2001 Elsevier Science B.V. All rights reserved.
Raman and hot electron-neutral acceptor luminescence studies of electron-optical phonon interactions in GaAs/AlxGa1-xAs quantum wells
(2000)
Sun, KW
;
Chang, HY
;
Wang, CM
;
Song, TS
;
Wang, SY
Using two optical techniques, we have studied the hot electron-optical phonon interactions in GaAs/AlxGa1-xAs multiple-quantum wells. Raman scattering measurements at 15 K are presented for the Al composition of x = 0.3, 0.5, 0.7 and 1.0. The GaAs-like and AlAs-like phonon frequencies of the first-order modes are also measured as a function of Al composition. The optical phonon energies emitted by the photoexcited electrons in quantum wells are determined by using hot electron-neutral acceptor luminescence techniques. It is shown that the relaxation of hot electrons in the quantum wells is dominated by the GaAs LO phonon emission for small x, but by AlAs-like LO phonons for larger Al composition. (C) 2000 Elsevier Science Ltd. All rights reserved.
RmpA2, an activator of capsule biosynthesis in Klebsiella pneumoniae CG43, regulates K2 cps gene expression at the transcriptional level
(2003-02-01)
Lai, YC
;
Peng, HL
;
Chang, HY
;
生物科技學系
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Department of Biological Science and Technology
The rmpA2 gene, which encodes an activator for capsular polysaccharide (CPS) synthesis, was isolated from a 200-kb virulence plasmid of Klebsiella pneumoniae CG43. Based on the sequence homology with LuxR at the carboxyl-terminal DNA-binding motif, we hypothesized that RmpA2 exerts its effect by activating the expression of cps genes that are responsible for CPS biosynthesis. Two luxAB transcriptional fusions, each containing a putative promoter region of the K. pneumoniae K2 cps genes, were constructed and were found to be activated in the presence of multicopy rmpA2. The activation is likely due to direct binding of RmpA2 to the cps gene promoter through its C-terminal DNA binding motif. Moreover, the loss of colony mucoidy in a K. pneumoniae strain deficient in RcsB, a regulator for cps gene expression, could be recovered by complementing the strain with a multicopy plasmid carrying rmpA2. The CPS production in Lon protease-deficient K. pneumoniae significantly increased, and the effect was accompanied by an increase of RmpA2 stability. The expression of the rmpA2 gene was negatively autoregulated and could be activated when the organism was grown in M9 minimal medium. An IS3 element located upstream of the rmpA2 was required for the full activation of the rmpA2 promoter. In summary, our results suggest that the enhancement of K2 CPS synthesis in K. pneumoniae CG43 by RmpA2 can be attributed to its transcriptional activation of K2 cps genes, and the expression level of rmpA2 is autoregulated and under the control of Lon protease.
Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43
(2004-08-04)
Chen, YT
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Chang, HY
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Lai, YC
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Pan, CC
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Tsai, SF
We have determined the entire DNA sequence of pLVPK, which is a 219-kb virulence plasmid harbored in a bacteremic isolate of Klebsiella pneumoniae. A total of 251 open reading frames (ORFs) were annotated, of which 37% have homologous genes of known function, 31% match the hypothetical genes in the GenBank database, and the remaining 32% are novel sequences. The obvious virulence-associated genes carried by the plasmid are the capsular polysaccharide synthesis regulator rmpA and its homolog rmpA2, and multiple iron-acquisition systems, including iucABCDiutA and iroBCDN siderophore gene clusters, Mesorhizobium loti fepBC ABC-type transporter, and Escherichia coli fecIRA, which encodes a Fur-dependent regulatory system for iron uptake. In addition, several gene clusters homologous with copper, silver, lead, and tellurite resistance genes of other bacteria were also identified. Identification of a replication origin consisting of a repA gene lying in between two sets of iterons suggests that the replication of pLVPK is iteron-controlled and the iterons are the binding sites for the repA to initiate replication and maintain copy number of the plasmid. Genes homologous with E. coli sopA/sopB and parA/parB with nearby direct DNA repeats were also identified indicating the presence of an F plasmid-like partitioning system. Finally, the presence of 13 insertion sequences located mostly at the boundaries of the aforementioned gene clusters suggests that pLVPK was derived from a sequential assembly of various horizontally acquired DNA fragments. (C) 2004 Elsevier B.V. All rights reserved.
Speaker-independent Mandarin polysyllabic word recognition
(1996)
Chang, HY
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Chen, B
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Chou, CS
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Liu, CM
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交大名義發表
In this paper we consider the design of speaker-independent Mandarin polysyllabic word recognition system from two viewpoints: the phonetical modeling and the recognition speeds. For phonetical modeling, we consider the accurate acoustic models that can increase the recognition rate. This paper experiments three phonetical models: context-independent INITIALs, right-context-dependent null-INITIALs models, and right-context-dependent INITIALs and null-INITIALs models. The recognition results show respectively on average recognition rate 99.1%, 93.7% and 83.6% for 500-words, 5000-words, and 25000-words tasks. While for top 3 words, the average rates 99.8%, 98.5% and 95.2% are achieved. On the basis of the recognition results, we consider the fast computing algorithms to increase computing speeds. Since that the tree-trellis search algorithm can retain the recognition rate of system and has the potential to greatly reduce the search time, this paper adopts the search algorithm as the basic framework and investigates some implementation techniques. The results show that the tree-trellis algorithm can provide a search time slightly dependent with word size.
User adaptive handwriting recognition by self-growing probabilistic decision-based neural networks
(2000-11-01)
Fu, HC
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Chang, HY
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Xu, YY
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Pao, HT
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資訊工程學系
It is generally agreed that, for a given handwriting recognition task, a user dependent system usually outperforms a user independent system, as long as a sufficient amount of training data is available. When the amount of user training data is limited, however, such a performance gain is not guaranteed. One way to improve the performance is to make use of existing knowledge, contained in a rich multiuser data base, so that a minimum amount of training data is sufficient to initialize a model for the new user, We mainly address the user adaption issues for a handwriting recognition system, Based on self-growing probabilistic decision-based neural networks (SPDNNs), user adaptation of the parameters of SPDNN is formulated as incremental reinforced and antireinforced learning procedures, which are easily integrated into the batched training procedures of the SPDNN, In this study, me developed 1) an SPDNN based handwriting recognition system; 2) a two-stage recognition structure; and 3) a three-phase training methodology for a) a global coarse classifier (stage 1); b) a user independent hand written character recognizer (stage 2); and c) a user adaptation module on a personal computer. With training and testing on a 600-word commonly used Chinese character set, the recognition results indicate that the user adaptation module significantly improved the recognition accuracy The average recognition rate increased from 44.2% to 82.4% in five adapting cycles, and the performance could finally increase up to 90.2% in ten adapting cycles.