Browsing by Issue Date, starting with "2013-04-10"

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GI-POP: A combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects
(2013-04-10)
Lee, Chi-Ching
;
Chen, Yi-Ping Phoebe
;
Yao, Tzu-Jung
;
Ma, Cheng-Yu
;
Lo, Wei-Cheng
Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. (c) 2012 Elsevier B.V. All rights reserved.
A new method for post Genome-Wide Association Study (GWAS) analysis of colorectal cancer in Taiwan
(2013-04-10)
Wang, Hwei-Ming
;
Chang, Tzu-Hao
;
Lin, Feng-Mao
;
Chao, Te-Hsin
;
Huang, Wei-Chih
Recently, single nucleotide polymorphisms (SNPs) located in specific loci or genes have been identified associated with susceptibility to colorectal cancer (CRC) in Genome-Wide Association Studies (GWAS). However, in different ethnicities and regions, the genetic variations and the environmental factors can widely vary. Therefore, here we propose a post-GWAS analysis method to investigate the CRC susceptibility SNPs in Taiwan by conducting a replication analysis and bioinformatics analysis. One hundred and forty-four significant SNPs from published GWAS results were collected by a literature survey, and two hundred and eighteen CRC samples and 385 normal samples were collected for post-GWAS analysis. Finally, twenty-six significant SNPs were identified and reported as associated with susceptibility to colorectal cancer, other cancers, obesity, and celiac disease in a previous GWAS study. Functional analysis results of 26 SNPs indicate that most biological processes identified are involved in regulating immune responses and apoptosis. In addition, an efficient prediction model was constructed by applying Jackknife feature selection and ANOVA testing. As compared to another risk prediction model of CRC for European Caucasians population, which performs 0.616 of AUC by using 54 SNPs, the proposed model shows good performance in predicting CRC risk within the Taiwanese population, i.e., 0.724 AUC by using 16 SNPs. We believe that the proposed risk prediction model is highly promising for predicting CRC risk within the Taiwanese population. In addition, the functional analysis results could be helpful to explore the potential associated regulatory mechanisms that may be involved in CRC development. (c) 2012 Elsevier B.V. All rights reserved.
Deriving correlated motions in proteins from X-ray structure refinement by using TLS parameters
(2013-04-10)
Liu, Yen-Yi
;
Shih, Chien-Hua
;
Hwang, Jenn-Kang
;
Chen, Chih-Chieh
;
生物資訊及系統生物研究所
Dynamic information in proteins may provide valuable information for understanding allosteric regulation of protein complexes or long-range effects of the mutations on enzyme activity. Experimental data such as X-ray B-factors or NMR order parameters provide a convenient estimate of atomic fluctuations (or atomic auto-correlated motions) in proteins. However, it is not as straightforward to obtain atomic cross-correlated motions in proteins - one usually resorts to more sophisticated computational methods such as Molecular Dynamics, normal mode analysis or atomic network models. In this report, we show that atomic cross-correlations can be reliably obtained directly from protein structure using X-ray refinement data. We have derived an analytic form of atomic correlated motions in terms of the original MS parameters used to refine the B-factors of X-ray structures. The correlated maps computed using this equation are well correlated with those of the method based on a mechanical model (the correlation coefficient is 0.75) for a non-homologous dataset comprising 100 structures. We have developed an approach to compute atomic cross-correlations directly from X-ray protein structure. Being in analytic form, it is fast and provides a feasible way to compute correlated motions in proteins in a high throughput way. In addition, avoiding sophisticated computational operations; it provides a quick, reliable way, especially for non-computational biologists, to obtain dynamics information directly from protein structure relevant to its function. (c) 2012 Elsevier B.V. All rights reserved.
秋風裡的風旗：談馮至的《十四行集》
(2013-04-10)
蔡明諺
;
開放教育推動中心
;
Open Education Office
課程首頁本課程是由交通大學新文藝復興閱讀計畫提供。 96 年 8 月當各大學紛紛摩拳擦掌準備迎接新生的同時，交通大學校長吳重雨則因為一則來自於七月份泰晤士報，有關於英國首相布朗公布其夏日讀書清單的新聞中，看到了他對知識的尊重。在這同時，吳重雨校長也思考著，要如何為學生準備追求知識的環境和激發他們對知識的尊重與喜愛。台積電張忠謀董事長曾陳述他 18 歲進入哈佛那一年，博覽文史哲理工經典群籍，至此奠定了他求知的基礎，並借海明威名言，將其改為「哈佛這一年為人生可帶走的盛宴。」吳重雨校長以張董事長的學習為借鏡，認為學生固然能藉由自我閱讀的方式學習到豐沛的知識，但透過名人、大師親臨現場地介紹經典書籍，更能加深學子們對於書籍的認識與興趣，這也是「新文藝復興閱讀計劃」 ( 以下簡稱 : 「經典名著選讀」 ) 活動展開籌劃的緣由。於是，吳重雨校長便積極敦請「交大通識教育委員會」，接手籌備本計劃的相關活動，而該中心也成為實際施行本計畫的策動、開課以及認證單位。至此，期許交大學子藉由閱讀、聽講來提昇人文素養、開拓視野的「新文藝復興閱讀計劃」，就此展開。
The evolutionary landscape of the Mycobacterium tuberculosis genome
(2013-04-10)
Wang, Tai-Chun
;
Chen, Feng-Chi
;
生物科技學系
;
Department of Biological Science and Technology
Mycobacterium tuberculosis is one of the most deadly human pathogens. The major mechanism for the adaptations of M. tuberculosis is nucleotide substitution. Previous studies have relied on the nonsynonymous-to-synonymous substitution rate (d(N)/d(S)) ratio as a measurement of selective constraint based on the assumed selective neutrality of synonymous substitutions. However, this assumption has been shown to be untrue in many cases. In this study, we used the substitution rate in intergenic regions (d(i)) of the M. tuberculosis genome as the neutral reference, and conducted a genome-wide profiling for d(i), d(s), and the rate of insertions/deletions (indel rate) as compared with the genome of M. canettii using a 50 kb sliding window. We demonstrate significant variations in all of the three evolutionary measurements across the M. tuberculosis genome, even for regions in close vicinity. Furthermore, we identified a total of 233 genes with their d(s) deviating significantly from d(i) within the same window. Interestingly, d(s) also varies significantly in some of the windows, indicating drastic changes in mutation rate and/or selection pressure within relatively short distances in the M. tuberculosis genome. Importantly, our results indicate that selection on synonymous substitutions is common in the M. tuberculosis genome. Therefore, the d(N)/d(S) ratio test must be applied carefully for measuring selection pressure on M. tuberculosis genes. (c) 2012 Elsevier B.V. All rights reserved.
腹式呼吸訓練裝置、腹式呼吸訓練系統及其方法
(2013-04-11)
蕭子健
;
徐如欣
;
謝岱凌
本發明提出一種腹式呼吸訓練裝置、腹式呼吸訓練系統及其方法。所述之腹式呼吸訓練裝置適用於訓練使用者以進行腹式呼吸，並包括訓練單元、感測單元、資訊擷取與轉換單元及顯示單元，而訓練單元產生訓練波形及指示。感測單元鄰接於使用者的腹部，並量測使用者的腹部呼吸訊號。資訊擷取與轉換單元電性耦接至感測單元及訓練單元，並根據所量測的腹部呼吸訊號而產生使用者腹部呼吸波形。顯示單元電性耦接至訓練單元，並顯示訓練波形及指示給使用者，而使用者跟著顯示單元上的訓練波形以進行腹式呼吸。
在無線寬頻基地台的延遲與調變感知動態頻寬分配之方法
(2013-04-11)
林盈達
;
林義能
;
吳哲文
;
賴源正
新一代的無線寬頻系統在高速行動無線網路下可支援高速率且長距離的傳輸。然而連線品質受到長距離及空氣干擾而不穩定，使得及時應用程式面臨嚴峻的考驗。因此，需要一個適當的頻寬分配演算法及設備同時滿足及時應用程式延遲要求且充分利用可用的頻寬來提供差異式服務和公平性。在本發明中提出一個在基地台藉由考慮調適調變及編碼比率與需求急迫性的最高急迫優先演算法來克服上述的問題。在上下行頻寬的動態調節中，分別優先保留其最急迫請求的頻寬，接著根據其餘上下行不急迫請求的需求量比例地分配剩餘頻寬。在上下行獨自分配頻寬給行動裝置階段，則利用一新穎的係數來決定每個需求的急迫性，以最急迫優先的分配方式來反映出延遲保證與公平性。
CONTROLLABLE OPTICAL DEVICE AND THE FORMING METHOD THEREOF
(2013-04-11)
LIU Li-Wei
;
CHEN Chih-Wei
;
SU Yong-Ren
;
HUANG Yi-Pai
A controllable optical device comprises a first substrate, a first conductive layer, a liquid crystal layer, a semiconductor conductive layer, a second conductive layer, and a second substrate. The first conductive layer is formed on the first substrate, the liquid crystal layer is formed on the first conductive layer, the semiconductor conductive layer is formed on the liquid crystal layer, the second conductive layer is formed on the semiconductor layer, and the second substrate is formed on the second conductive layer.
Complex Oxide-Noble Metal Conjugated Nanoparticles
(2013-04-11)
Guo, Jun-Ling
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Chiou, Yao-De
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Liang, Wen-I
;
Liu, Heng-Jui
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Chen, Ying-Jiun
Hybrid nanoparticles (NPs) composed of multiple components offer new opportunities for next-generation materials. In this study, a paradigm for the noble metal/ternary complex oxide hybrid NPs is reported by adopting pulsed laser ablation in liquids. As model hybrids, gold-spinel heterodimer (Au-CoFe2O4) and gold-pervoskite heterodimer (Au-SrTiO3) NPs are investigated. This work has demonstrated the diverse playgroup of NP conjugation enlarged by complex oxides.
有機光電元件
(2013-04-11)
孟心飛
;
洪勝富
;
曾信榮
;
李冠成
一種有機光電元件，包括第一電極；形成於該第一電極上之主動層；形成於該主動層上之第二中間層；以及形成於該第二中間層上之第二電極；其中，該第二中間層包括含有第二聚合物和第二有機小分子的第二混合物，且該第二有機小分子係選自作為電洞傳輸材料、電子傳輸材料、電子阻擋材料或電洞阻擋材料的化合物。本發明之有機光電元件係以溶液製程製備而得，具有製程簡便、改善薄膜成膜性和提升元件效率之優點。
用於生理訊號量測感測器之乾式電極
(2013-04-11)
林進燈
;
廖倫德
本發明係揭露一種用於生理訊號量測感測器之乾式電極，其包含導電海綿、導電布及金屬薄片。導電布包覆導電海綿，且金屬薄片設置於導電布相對於導電海綿之ㄧ面。使用本發明之乾式電極時，可不需塗抹導電膠於待測部位上，故本發明之乾式電極具有長效並即時量測生理訊號之特性，使用上更為簡便。
Infrared Absorption Spectrum of the Simplest Criegee Intermediate CH2OO
(2013-04-12)
Su, Yu-Te
;
Huang, Yu-Hsuan
;
Witek, Henryk A.
;
Lee, Yuan-Pern
;
應用化學系
The Criegee intermediates are carbonyl oxides postulated to play key roles in the reactions of ozone with unsaturated hydrocarbons; these reactions constitute an important mechanism for the removal of unsaturated hydrocarbons and for the production of OH in the atmosphere. Here, we report the transient infrared (IR) absorption spectrum of the simplest Criegee intermediate CH2OO, produced from CH2I + O-2 in a flow reactor, using a step-scan Fourier-transform spectrometer. The five observed bands provide definitive identification of this intermediate. The observed vibrational frequencies are more consistent with a zwitterion rather than a diradical structure of CH2OO. The direct IR detection of CH2OO should prove useful for kinetic and mechanistic investigations of the Criegee mechanism.
周波数逓倍器装置及びその動作方法
(2013-04-12)
郭建男
;
顏子超
Semi-analytical solution of groundwater flow in a leaky aquifer system subject to bending effect
(2013-04-12)
Yu, Chia-Chi
;
Yang, Shaw-Yang
;
Yeh, Hund-Der
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環境工程研究所
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Institute of Environmental Engineering
The bending of aquitard like a plate due to aquifer pumping and compression is often encountered in many practical problems of subsurface flow. This reaction will have large influence on the release of the volume of water from the aquifer, which is essential for the planning and management of groundwater resources in aquifers. However, the groundwater flow induced by pumping in a leaky aquifer system is often assumed that the total stress of aquifer maintains constant all the time and the mechanical behavior of the aquitard formation is negligible. Therefore, this paper devotes to the investigation of the effect of aquitard bending on the drawdown distribution in a leaky aquifer system, which is obviously of interest in groundwater hydrology. Based on the work of Wang et al. (2004) this study develops a mathematical model for investigating the impacts of aquitard bending and leakage rate on the drawdown of the confined aquifer due to a constant-rate pumping in the leaky aquifer system. This model contains three equations; two flow equations delineate the transient drawdown distributions in the aquitard and the confined aquifer, while the other describes the vertical displacement in response to the aquitard bending. For the case of no aquitard bending, this new solution can reduce to the Hantush Laplace-domain solution (Hantush, 1960). On the other hand, this solution without the leakage effect can reduce to the time domain solution of Wang et al. (2004). The results show that the aquifer drawdown is influenced by the bending effect at early time and by the leakage effect at late time. The results of sensitivity analysis indicate that the aquifer compaction is sensitive only at early time, causing less amount of water released from the pumped aquifer than that predicted by the traditional groundwater theory. The dimensionless drawdown is rather sensitive to aquitard's hydraulic conductivity at late time. Additionally, both the hydraulic conductivity and thickness of the aquifer are the most sensitive parameters in influencing the predicted dimensionless drawdown. (C) 2013 Elsevier B.V. All rights reserved.
Organic thin film transistors as selective sensing platforms for Hg2+ ions and the amino acid cysteine
(2013-04-15)
Ramesh, Mohan
;
Lin, Hong-Cheu
;
Chu, Chih-Wei
;
材料科學與工程學系
;
光電工程學系
In this short communication we report a sensor for divalent mercuric (Hg2+) ions that we constructed from a perylene bisimide (PBI)-based organic thin film transistor. We improved the performance of the n-channel device by positioning N,N'-dioctyl-3,4,9,10-perylenedicarboximide between the dielectric and the active layer (PSI), increasing the electron mobility (mu) from 0.002 to 0.25 +/- 0.04 cm(2) V-1 s(-1) and enhancing the on/off ratio (I-on/I-off) by two orders of magnitude (from 102 to 104). Based on a "thymine-Hg2+-thymine" mechanism and monitoring the shift in the threshold voltage (V-th), we used this transistor to discriminate Hg2+ ions from mixed ion solutions and it extended to different concentration Hg2+ solutions (from 50 to 350 mu M). By monitoring the shifts in drain current (I-DS) and V-th, we also used this bilayer device as a sensor for cysteine, a thiol-containing amino acid; the selective detection of cysteine was accompanied by a red shift in the fluorescence maximum of PBI, from 532 to 537 nm. (C) 2012 Elsevier B.V. All rights reserved.
Association of poly(N-isopropylacrylamide) containing nucleobase multiple hydrogen bonding of adenine for DNA recognition
(2013-04-15)
Yang, Hsiu-Wen
;
Chen, Jem-Kun
;
Cheng, Chih-Chia
;
Kuo, Shiao-Wei
;
應用化學系
In this study we used the poly(N-isopropylacrylamide) (PNIPAAm) as a medium to generate PNIPAAm-adenine supramolecular complexes. A nucleobase-like hydrogen bonding (NLHB) between PNIPAAm and adenine was found that changed the morphology, crystalline structure, and temperature responsiveness of PNIPAAm microgels relatively to the adenine concentrations. With increasing the adenine concentration, the PNIPAAm-adenine supramolecular complexes gradually altered their morphologies from microgel particles to thin film structures and suppressed the thermodynamical coil-to-globule transition of PNIPAAm because of the NLHB existed between the PNIPAAm amide and ester groups and the adenine amide groups (C=O center dot center dot center dot H-N and N-H center dot center dot center dot N-R), verified by FTIR spectral analysis. NLHB was also diverse and extensive upon increasing the temperature; therefore, the thermoresponsive behavior of the complexes was altered with the NLBH intensity, evaluated by the inter-association equilibrium constant (K-a) above and below their LCST. Therefore, PNIPAAm can be as a medium to recognize adenine in various concentrations, which could potentially be applied in DNA recognition. (C) 2013 Elsevier B.V. All rights reserved.
A proteomic approach to study molecular mechanisms of andrographolide-mediated degradation of Src oncoproteins.
(2013-04-15)
Liu, Sheng-Hung
;
Chen, Pei-Fen
;
Lin, Chao-Hsiung
;
Sun, Chung-Ming
;
Chi, Chin-Wen
Wireless near-infrared spectroscopy system for determining brain hemoglobin levels in laboratory animals
(2013-04-15)
Kuo, Jinn-Rung
;
Chang, Ming-Hsien
;
Wang, Che-Chuan
;
Chio, Chung-Ching
;
Wang, Jhi-Joung
Traumatic brain injury (TBI) is usually caused by brain shaking or impact. It can affect normal brain function and may even lead to disability or death. However, there are very few studies on the associated physiologic changes in humans or animals. In this study, a non-invasive, wireless multi-channel near-infrared spectroscopy (NIRS) was developed to continuously monitor the concentration change of oxyhemoglobin (HbO(2)), deoxyhemoglobin (HbR), and total hemoglobin (HbT) to elucidate changes in the physiological state of the brain during and after different strength impaction. The triphenyltetrazolium chloride (TTC) staining was also used to monitor changes of infarction volume after different strength impaction. The results indicated that the concentration changes of HbO(2) and HbT, and the changes of infarction volumes were significantly related to the impact strength. In conclusion, the status of TBI can be clinically evaluated by detecting HbO(2) and HbT changes. The system proposed here is stable, accurate, non-invasive, and mostly important wireless which can easily be used for TBI study. (C) 2013 Elsevier B.V. All rights reserved.
Spectral radius and degree sequence of a graph
(2013-04-15)
Liu, Chia-an
;
Weng, Chih-wen
;
應用數學系
;
Department of Applied Mathematics
Let G be a simple connected graph of order n with degree sequence d(1), d(2), ... , dr, in non-increasing, order. The spectral radius rho(G) of G is the largest eigenvalue of its adjacency matrix. For each positive integer l at most n, we give a sharp upper bound for rho(G) by a function of d(1), d(2), ... ,d(l), which generalizes a series of previous results. (C) 2013 Elsevier Inc. All rights reserved.
Enhanced ductility of the ZA85 magnesium alloy fabricated by equal-channel angular pressing
(2013-04-15)
Lin, Che-Yi
;
Bor, Hui-Yum
;
Chao, Chuen-Guang
;
Liu, Tzeng-Feng
;
材料科學與工程學系
Equal-channel angular pressing (ECAP) was applied to the as-cast Mg-8 wt.% Zn-5 wt.% Al (ZA85) alloy to produce a fine-grained structure with fine and uniformly distributed Mg-32 (Al, Zn)(49) (tau-phase) particles. Experiments showed that the ZA85 alloy had an initial grain size of similar to 150 mu m after casting and was significantly reduced to 4 mu m after six ECAP passes at 180 degrees C. After annealing at 300 degrees C for 1 h, the average grain size merely increased to 7.1 mu m. This thermal stability of the fine-grained structure at temperatures at or below 325 degrees C is attributed to the presence of the fine and well distributed tau-phase. It was demonstrated that ECAP processing greatly enhances ductility of the experimental alloy. By testing over a range of temperatures and strain rates, a maximum elongation to failure of 400% was obtained in the ECAP ZA85 alloy tested at 300 degrees C (0.53 T-m) with the initial strain rate of 1.0 x 10 (4) s (1). The dominant deformation mechanism for the specimens tested at 300 and 350 degrees C with the initial strain rates ranging from 1.0 x 10 (4) s (1) to 1.0 x 10 (3) s (1) is GBS controlled by grain boundary diffusion. At the higher testing temperature of 400 degrees C, the deformation mechanism for the experimental alloy is dislocation creep. (C) 2012 Elsevier B. V. All rights reserved.