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Search Results: 1 - 10 of 29172 matches for " Ting-Ying Chien "
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Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures
Chien-Yu Chen,Ting-Ying Chien,Chih-Kang Lin,Chih-Wei Lin,Yi-Zhong Weng,Darby Tien-Hao Chang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030446
Abstract: DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions. Accurate prediction of such target sequences, often represented by position weight matrices (PWMs), is an important step to understand many biological processes. Recent studies have shown that knowledge-based potential functions can be applied on protein-DNA co-crystallized structures to generate PWMs that are considerably consistent with experimental data. However, this success has not been extended to DNA-binding proteins lacking co-crystallized structures. This study aims at investigating the possibility of predicting the DNA sequences bound by DNA-binding proteins from the proteins' unbound structures (structures of the unbound state). Given an unbound query protein and a template complex, the proposed method first employs structure alignment to generate synthetic protein-DNA complexes for the query protein. Once a complex is available, an atomic-level knowledge-based potential function is employed to predict PWMs characterizing the sequences to which the query protein can bind. The evaluation of the proposed method is based on seven DNA-binding proteins, which have structures of both DNA-bound and unbound forms for prediction as well as annotated PWMs for validation. Since this work is the first attempt to predict target sequences of DNA-binding proteins from their unbound structures, three types of structural variations that presumably influence the prediction accuracy were examined and discussed. Based on the analyses conducted in this study, the conformational change of proteins upon binding DNA was shown to be the key factor. This study sheds light on the challenge of predicting the target DNA sequences of a protein lacking co-crystallized structures, which encourages more efforts on the structure alignment-based approaches in addition to docking- and homology modeling-based approaches for generating synthetic complexes.
Discovery of Genes Related to Insecticide Resistance in Bactrocera dorsalis by Functional Genomic Analysis of a De Novo Assembled Transcriptome
Ju-Chun Hsu, Ting-Ying Chien, Chia-Cheng Hu, Mei-Ju May Chen, Wen-Jer Wu, Hai-Tung Feng, David S. Haymer, Chien-Yu Chen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040950
Abstract: Insecticide resistance has recently become a critical concern for control of many insect pest species. Genome sequencing and global quantization of gene expression through analysis of the transcriptome can provide useful information relevant to this challenging problem. The oriental fruit fly, Bactrocera dorsalis, is one of the world's most destructive agricultural pests, and recently it has been used as a target for studies of genetic mechanisms related to insecticide resistance. However, prior to this study, the molecular data available for this species was largely limited to genes identified through homology. To provide a broader pool of gene sequences of potential interest with regard to insecticide resistance, this study uses whole transcriptome analysis developed through de novo assembly of short reads generated by next-generation sequencing (NGS). The transcriptome of B. dorsalis was initially constructed using Illumina's Solexa sequencing technology. Qualified reads were assembled into contigs and potential splicing variants (isotigs). A total of 29,067 isotigs have putative homologues in the non-redundant (nr) protein database from NCBI, and 11,073 of these correspond to distinct D. melanogaster proteins in the RefSeq database. Approximately 5,546 isotigs contain coding sequences that are at least 80% complete and appear to represent B. dorsalis genes. We observed a strong correlation between the completeness of the assembled sequences and the expression intensity of the transcripts. The assembled sequences were also used to identify large numbers of genes potentially belonging to families related to insecticide resistance. A total of 90 P450-, 42 GST-and 37 COE-related genes, representing three major enzyme families involved in insecticide metabolism and resistance, were identified. In addition, 36 isotigs were discovered to contain target site sequences related to four classes of resistance genes. Identified sequence motifs were also analyzed to characterize putative polypeptide translational products and associate them with specific genes and protein functions.
043Expert system-based geocoding method for national economic census application

YU Bin,CHENG Chang-xiu,ZUO Ting-ying,

计算机应用研究 , 2010,
Abstract: After analyzing those domestic and international geocoding methods, this paper proposed an expert system-based geocoding method for national economic census application. This method mined some address characters of every spatial feature based on their corresponding relationships, which had been existed in national economic census spatial database. To a certain vague address to be geocoding, this method would separate it into several address elements, and then located it by analyzing the comparability between those elements of the vague address and the address characters of every spatial feature. This method could promote the locating rate of the vague addresses.
Hydrophilic Aromatic Residue and in silico Structure for Carbohydrate Binding Module
Wei-Yao Chou, Tun-Wen Pai, Ting-Ying Jiang, Wei-I Chou, Chuan-Yi Tang, Margaret Dah-Tsyr Chang
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024814
Abstract: Carbohydrate binding modules (CBMs) are found in polysaccharide-targeting enzymes and increase catalytic efficiency. Because only a relatively small number of CBM structures have been solved, computational modeling represents an alternative approach in conjunction with experimental assessment of CBM functionality and ligand-binding properties. An accurate target-template sequence alignment is the crucial step during homology modeling. However, low sequence identities between target/template sequences can be a major bottleneck. We therefore incorporated the predicted hydrophilic aromatic residues (HARs) and secondary structure elements into our feature-incorporated alignment (FIA) algorithm to increase CBM alignment accuracy. An alignment performance comparison for FIA and six others was made, and the greatest average sequence identities and similarities were achieved by FIA. In addition, structure models were built for 817 representative CBMs. Our models possessed the smallest average surface-potential z scores. Besides, a large true positive value for liagnd-binding aromatic residue prediction was obtained by HAR identification. Finally, the pre-simulated CBM structures have been deposited in the Database of Simulated CBM structures (DS-CBMs). The web service is publicly available at http://dscbm.life.nthu.edu.tw/ and http://dscbm.cs.ntou.edu.tw/.
Exact Timing of Returned Molecular Wavepacket
ZHANG Zhe,WANG Ting-Ying,ZHANG Gui-Zhong,WT Hill III,

中国物理快报 , 2006,
Abstract: An ionizing wavepacket of electron will re-visit its parent molecular ion during photoionization by strong laser field. This scenario is associated with physical concepts such as molecular re-scattering/collision, interference, diffraction, molecular clock, and generation of XUV light via high-order harmonic generation. On the workbench of a reduced dimensionality model of molecular hydrogen ions irradiated by laser pulse of 0.01-10.0 a.u. intensities, one-cycle pulsewidth, and 800nm wavelength, by deploying a momentum operator on the time-dependent wavefunction of an ionizing wavepacket, we can determine, in a precise manner, the exact time instant for the re-visiting electron to come back to the cation position. The time value is 57.6% of an optical cycle of the exciting laser pulse. This result may be useful in attosecond pump-probe experiments or molecular clock applications.
Two Unique Ligand-Binding Clamps of Rhizopus oryzae Starch Binding Domain for Helical Structure Disruption of Amylose
Ting-Ying Jiang, Yuan-Pei Ci, Wei-I Chou, Yuan-Chuan Lee, Yuh-Ju Sun, Wei-Yao Chou, Kun-Mou Li, Margaret Dah-Tsyr Chang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0041131
Abstract: The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD) has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21) members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs.
Double-Exponentially Decayed Photoionization in CREI Effect: Numerical Experiment on 3D H2+
Double-Exponentially Decayed Photoionization in CREI Effect: Numerical Experiment on 3D H2^+

LI Feng,WANG Ting-Ying,ZHANG Gui-Zhong,XIANG Wang-Hua,W T Hill III,

中国物理快报 , 2008,
Abstract: On the platform of the 3D H2+ system, we perform a numerical simulation of its photoionization rate under excitation of weak to intense laser intensities with varying pulse durations and wavelengths. A novel method is proposed for calculating the photoionization rate: a double exponential decay of ionization probability is best suited for fitting this rate. Confirmation of the well-documented charge-resonance-enhanced ionization (CREI) effect at medium laser intensity and finding of ionization saturation at high light intensity corroborate the robustness of the suggested double-exponential decay process. Surveying the spatial and temporal variations of electronwavefunctions uncovers a mechanism for the double-exponentially decayed photoionization probability as onset of electron ionization along extra degree of freedom. Henceforth, the new method makes clear the origins of peak features in photoionization rate versus internuclear separation. It is believed that this multi-exponentially decayed ionization mechanism is applicable to systems with more degrees of motion.
Exploring Solutions for the Negative Impact of US Quantitative Easing on Taiwan  [PDF]
Chien-Jung Ting
Journal of Mathematical Finance (JMF) , 2018, DOI: 10.4236/jmf.2018.81002
Abstract: Because Taiwan is export-oriented and highly connected with the US in terms of trade, Quantitative Easing (QE) of the Federal Reserve System (FED) had significant negative impacts on Taiwan. We examine several possible solutions for these negative impacts via the Delphi technique and the Analytic Hierarchy Process, synthesizing judgements from experts. The empirical results point out that a “negative influence on international trade affairs” is the predominant main criteria, and “improvement of international trade and investment regulations”, “easing the impact of increases in the prices of raw materials obtained internationally”, and “raising the competitiveness of the nation’s export industry” are important sub-criteria. Especially, “improvement of international trade and investment regulations” corresponds with the global imbalance phenomenon. To strengthen the trade environment in Taiwan, experts suggest that an overall improvement in balance of payment is necessary that encompasses investment activities and trade regulations. We look forward our results offering useful suggestions.
Pleurotus tuber-regium Polysaccharides Attenuate Hyperglycemia and Oxidative Stress in Experimental Diabetic Rats
Hui-Yu Huang,Mallikarjuna Korivi,Ying-Ying Chaing,Ting-Yi Chien,Ying-Chieh Tsai
Evidence-Based Complementary and Alternative Medicine , 2012, DOI: 10.1155/2012/856381
Abstract: Pleurotus tuber-regium contains polysaccharides that are responsible for pharmacological actions, and medicinal effects of these polysaccharides have not yet been studied in diabetic rats. We examined the antidiabetic, antihyperlipidemic, and antioxidant properties of P. tuber-regium polysaccharides in experimental diabetic rats. Forty rats were equally assigned as diabetic high-fat (DHF) diet and polysaccharides treated DHF groups (DHF
Analysis of Agreement on Traditional Chinese Medical Diagnostics for Many Practitioners
Lun-Chien Lo,Tsung-Lin Cheng,You-Chieh Huang,Ying-Ling Chen,Jeng-Ting Wang
Evidence-Based Complementary and Alternative Medicine , 2012, DOI: 10.1155/2012/178081
Abstract: In Traditional Chinese Medicine (TCM) diagnostics, it is an important issue to study the degree of agreement among several distinct practitioners. In order to study the reliability of TCM diagnostics, we have to design an experiment to simultaneously deal with both of the cases when the data is ordinal and when there are many TCM practitioners. In this study, we consider a reliability measure called “Krippendorff's alpha” to investigate the agreement of tongue diagnostics in TCM. Besides, since it is not easy to obtain a large data set with patients rated simultaneously by many TCM practitioners, we use the renowned “bootstrapping” to obtain a 95% confidence interval for the Krippendorff's alpha. The estimated Krippendorff's alpha for the agreement among ten physicians that discerned fifteen randomly chosen patients is 0.7343, and the 95% bootstrapping confidence interval for the true alpha coefficient is [0.6570, 0.7349]. The data was collected and analyzed at the Department of Traditional Chinese Medicine, Changhua Christian Hospital (CCH) in Taiwan.
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