Browsing by Issue Date, starting with "2008-07-15"

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Computational identification of ubiquitylation sites from protein sequences
(2008-07-15)
Tung, Chun-Wei
;
Ho, Shinn-Ying
;
生物科技學系
;
生物資訊及系統生物研究所
;
Department of Biological Science and Technology
Background: Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undiscovered ubiquitylation sites, this study aims to develop an accurate sequence-based prediction method to identify promising ubiquitylation sites. Results: We established an ubiquitylation dataset consisting of 157 ubiquitylation sites and 3676 putative non-ubiquitylation sites extracted from 105 proteins in the UbiProt database. This study first evaluates promising sequence-based features and classifiers for the prediction of ubiquitylation sites by assessing three kinds of features (amino acid identity, evolutionary information, and physicochemical property) and three classifiers (support vector machine, k-nearest neighbor, and NaiveBayes). Results show that the set of used 531 physicochemical properties and support vector machine (SVM) are the best kind of features and classifier respectively that their combination has a prediction accuracy of 72.19% using leave-one-out cross-validation. Consequently, an informative physicochemical property mining algorithm (IPMA) is proposed to select an informative subset of 531 physicochemical properties. A prediction system UbiPred was implemented by using an SVM with the feature set of 31 informative physicochemical properties selected by IPMA, which can improve the accuracy from 72.19% to 84.44%. To further analyze the informative physicochemical properties, a decision tree method C5.0 was used to acquire if-then rule-based knowledge of predicting ubiquitylation sites. UbiPred can screen promising ubiquitylation sites from putative non-ubiquitylation sites using prediction scores. By applying UbiPred, 23 promising ubiquitylation sites were identified from an independent dataset of 3424 putative non-ubiquitylation sites, which were also validated by using the obtained prediction rules. Conclusion: We have proposed an algorithm IPMA for mining informative physicochemical properties from protein sequences to build an SVM-based prediction system UbiPred. UbiPred can predict ubiquitylation sites accompanied with a prediction score each to help biologists in identifying promising sites for experimental verification. UbiPred has been implemented as a web server and is available at http://iclab.life.nctu.edu.tw/ubipred.
Effect of antimony incorporation on the density, shape, and luminescence of InAs quantum dots
(2008-07-15)
Chen, J. F.
;
Chiang, C. H.
;
Wu, Y. H.
;
Chang, L.
;
Chi, J. Y.
This work investigates the surfactant effect on exposed and buried InAs quantum dots (QDs) by incorporating Sb into the QD layers with various Sb beam equivalent pressures (BEPs). Secondary ion mass spectroscopy shows the presence of Sb in the exposed and buried QD layers with the Sb intensity in the exposed layer substantially exceeding that in the buried layer. Incorporating Sb can reduce the density of the exposed QDs by more than two orders of magnitude. However, a high Sb BEP yields a surface morphology with a regular periodic structure of ellipsoid terraces. A good room-temperature photoluminescence (PL) at similar to 1600 nm from the exposed QDs is observed, suggesting that the Sb incorporation probably improves the emission efficiency by reducing the surface recombination velocity at the surface of the exposed QDs. Increasing Sb BEP causes a blueshift of the emission from the exposed QDs due to a reduction in the dot height as suggested by atomic force microscopy. Increasing Sb BEP can also blueshift the similar to 1300 nm emission from the buried QDs by decreasing the dot height. However, a high Sb BEP yields a quantum well-like PL feature formed by the clustering of the buried QDs into an undulated planar layer. These results indicate a marked Sb surfactant effect that can be used to control the density, shape, and luminescence of the exposed and buried QDs. (C) 2008 American Institute of Physics.
Saturated flow boiling heat transfer of R-407C and associated bubble characteristics in a narrow annular duct
(2008-07-15)
Hsieh, F. C.
;
Li, K. W.
;
Lie, Y. M.
;
Chen, C. A.
;
Lin, T. F.
Experiments are conducted here to investigate how the channel size affects the R-407C saturated flow boiling heat transfer and associated bubble characteristics in a horizontal narrow annular duct. The gap of the duct is fixed at 1.0 and 2.0 mm in this study. The measured data indicate that the saturated flow boiling heat transfer coefficient increases with a decrease in the duct gap. Besides, raising the imposed heat flux can cause a significant increase in the boiling heat transfer coefficients. However, the effects of the refrigerant mass flux and saturated temperature on the boiling heat transfer coefficient are milder. The results from the flow visualization show that the mean diameter of the bubbles departing from the heating surface decreases noticeably at increasing R-407C mass flux. Moreover, the bubble departure frequency increases at reducing duct size and at a high imposed heat flux many bubbles generated from the cavities in the heating surface tend to merge together to form big bubbles. Meanwhile comparison of the present heat transfer data for R-407C with R-134a in the same duct and with some existing correlations is conducted. Furthermore, correlation for the present R-407C saturated flow boiling heat transfer data is proposed. Additionally, the present data for some quantitative bubble characteristics such as the mean bubble departure diameter and frequency and the active nucleation site density are also correlated. (C) 2008 Elsevier Ltd. All rights reserved.
Affinity capture of uropathogenic Escherichia coli using pigeon ovalbumin-bound Fe(3)O(4)@Al(2)O(3) magnetic nanoparticles
(2008-07-15)
Liu, Jr-Chi
;
Tsai, Pei-Jane
;
Lee, Yuan C.
;
Chen, Yu-Chie
;
應用化學系
Escherichia coli and Staphylococcus saprophyticus are the most common causes of urinary tract infections, with 80% of these infections caused by uropathogenic E. coli. Because the P fimbriae of E. coli have specificity toward Gal(alpha 1-4)Gal beta units, pigeon ovalbumin (POA), whose structure contains terminal Gal(alpha 1-4)Gal beta moieties, was used as a probe for interaction with P fimbriated E. coli. The functional affinity probes for these bacteria by immobilizing POA-a phosphoprotein-onto the surface of magnetic iron oxide nanoparticles (NPs) coated with alumina (Fe(3)O(4)@Al(2)O(3)), using the phosphate units of POA as linking groups for the formation of phosphate-alumina complexes. The immobilization process occurred within 30 s when performing the reaction under microwave heating. The magnetic POA-Fe(3)O(4)@Al(2)O(3) NPs generated using this facile approach exhibited specificity toward P fimbriated E. coli. The bacteria targeted by the affinity probes were characterized by matrix-assisted laser desorption/ionization mass spectrometry. The detection limit toward uropathogenic bacteria when using this approach was similar to 9.60 x 10(4) cfu/mL (0.5 mL).
Numerical study of phonon radiative transfer in porous nanostructures
(2008-07-15)
Li, Sheng-Yen
;
Chu, Hsin-Sen
;
Yan, Wei-Mon
;
機械工程學系
;
Department of Mechanical Engineering
This study analyzes the phonon radiative transfer in two-dimensional porous silicon nanostructures with a phonon transport model based on the Boltzmann transportation equation. We focus on the inter-scattering between pores. The numerical results show that when the aspect ratio is less than 1.22, the scale factor dominates the thermal conductivity, and the thermal conductivity of nanostructures with in-line arrangement pores is determined by the dependent phonon scattering effect. In nanostructures with staggered arrangement pores, the phonons are prevented from transporting through the material. In general, the results show that the larger the pore size, the lower the thermal conductivity of the nanostructure. The results presented in this study provide a useful reference for the development of high-efficiency thermoelectric structures. (C) 2008 Elsevier Ltd. All rights reserved.
A possibility of detection of the non-charge based analytes using ultra-thin body field-effect transistors
(2008-07-15)
Sheu, J. -T.
;
Chen, C. C.
;
Chang, K. S.
;
Li, Y. -K.
;
材料科學與工程學系奈米科技碩博班
Ultra-thin body of p-type field-effect transistors were developed as transducer for biosensors. Changes of conductance resulted from the changes of the surface potentials of ultra-thin body field-effect transistors (UTB-FETs) due to surface chemical modifications were demonstrated. The channel surface of UTB-FETs were modified with N-[3-(trimethoxysilyl)propyl]ethylenediamine (AEAPTMS) and then gold nanoparticles (AuNPs) to immobilize the bio-component, the genetically engineered Delta(5)-3-ketosteroid isomerase (Art_KSI) or the Art_KSI conjugated with charged reporter (Art_KSI_mA51). The binding of charge-based molecules or nanoparticles has been demonstrated to strongly affect the conductivity of UTB-FETs: the increase or decrease of the conductance depends on the polarity of the immobilized molecules or nanoparticles. A new protocol involving the detection of a non-charged analyte relied on the competitive binding of analyte (19-norandrostendione) and a charged reporter (mA51) with KSL When exposed to a 19-norandrostendione solution (10 mu M), the conductance of Art_KSI_mA51-modified UTB-FET increased by 265 nS (similar to 12%). On the other hand, conductance of Art_KSI_modified UTB-FET showed no distinct change under the same detection conditions. (c) 2008 Elsevier B.V. All rights reserved
Affinity capture of uropathogenic Escherichia coli using pigeon ovalbumin-bound Fe3O4@Al2O3 magnetic nanoparticles
(2008-07-15)
Liu, Jr-Chi
;
Tsai, Pei-Jane
;
Lee, Yuan C.
;
Chen, Yu-Chie
;
應用化學系
Escherichia coli and Staphylococcus saprophyticus are the most common causes of urinary tract infections, with 80% of these infections caused by uropathogenic E. coli. Because the P fimbriae of E. coli have specificity toward Gal(alpha 1-4)Gal beta units, pigeon ovalbumin (POA), whose structure contains terminal Gal(alpha 1-4)Gal beta moieties, was used as a probe for interaction with P fimbriated E. coli. The functional affinity probes for these bacteria by immobilizing POA-a phosphoprotein-onto the surface of magnetic iron oxide nanoparticles (NPs) coated with alumina (Fe3O4@Al2O3), using the phosphate units of POA as linking groups for the formation of phosphate-alumina complexes. The immobilization process occurred within 30 s when performing the reaction under microwave heating. The magnetic POA-Fe3O4@Al2O3 NPs generated using this facile approach exhibited specificity toward P fimbriated E. coli. The bacteria targeted by the affinity probes were characterized by matrix-assisted laser desorption/ionization mass spectrometry. The detection limit toward uropathogenic bacteria when using this approach was similar to 9.60 x 10(4) cfu/mL (0.5 mL).
Disposable amperometric immunosensing strips fabricated by Au nanoparticles-modified screen-printed carbon electrodes for the detection of foodborne pathogen Escherichia coli O157 : H7
(2008-07-15)
Lin, Yueh-Hui
;
Chen, Sz-Hau
;
Chuang, Yao-Chen
;
Lu, Yi-Chen
;
Shen, Thomas Y.
A disposable amperometric immunosensing strip was fabricated for rapid detection of Escherichia coli O157:H7. The method uses an indirect sandwich enzyme-linked immunoassay with double antibodies. Screen-printed carbon electrodes (SPCEs) were framed by commercial silver and carbon inks. For electrochemical characterization the carbon electrodes were coupled with the first E. coli O157:H7-specific antibody, E. coli O157:H7 intact cells and the second E. coli O157:H7-specific antibody conjugated with horseradish peroxidase (HRP). Hydrogen peroxide and ferrocenedicarboxylic acid (FeDC) were used as the substrate for HRP and mediator, respectively, at a potential +300 mV vs. counter/reference electrode. The response current (RC) of the immunosensing strips could be amplified significantly by 13-nm diameter Au nanoparticles (AuNPs) attached to the working electrode. The results show that the combined effects of AuNPs and FeDC enhanced RC by 13.1-fold. The SPCE immunosensing strips were used to detect E. coli O157:H7 specifically. Concentrations of E. coli O157:H7 from 10(2) to 10(7) CFU/ml could be detected. The detection limit was approximately 6 CFU/strip in PBS buffer and 50 CFU/strip in milk. The SPCE modified with AuNPs and FeDC has the potential for further applications and provides the basis for incorporating the method into an integrated system for rapid pathogen detection. (c) 2008 Elsevier B.V. All rights reserved.
Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations
(2008-07-15)
Chiu, Yi-Yuan
;
Hwang, Jenn-Kang
;
Yang, Jinn-Moon
;
生物科技學系
;
生物資訊及系統生物研究所
We have developed a soft energy function, termed GEMSCORE, for the protein structure prediction, which is one of emergent issues in the computational biology. The GEMSORE consists of the van der Waals, the hydrogen-bonding potential and the solvent potential with 12 parameters which are optimized by using a generic evolutionary method. The GEMSCORE is able to successfully identify 86 native proteins among 96 target proteins on six decoy sets from more 70,000 near-native structures. For these six benchmark datasets, the predictive performance of the GEMSCORE, based on native structure ranking and Z-scores, was superior to eight other energy functions. Our method is based solely on a simple and linear function and thus is considerably faster than other methods that rely on the additional complex calculations. In addition, the GEMSCORE recognized 17 and 2 native structures as the first and the second rank, respectively, among 21 targets in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction). These results suggest that the GEMSCORE is fast and performs well to discriminate between native and normative structures from thousands of protein structure candidates. We believe that GEMSCORE is robust and should be a useful energy function for the protein structure prediction. (C) 2008 Wiley Periodicals, Inc.
空時編碼／正交分頻多工系統中合併通道估計與資料偵測方法
(2008-07-16)
古孟霖
;
黃家齊
本發明係以最佳化方法合併通道估計及資料偵測,利用資料子載波與稀疏領航子載波追蹤通道變化;其特徵在於使用牛頓法及資料子載波達到合併通道估計及資料偵測之最佳化,並利用稀疏領航子載波所形成之最大相似函數之一階部分微分方向向量做為通道估計器追蹤通道變化之初始參考方向以得到更好的通道估計。本發明在高車行速度及大通道延遲環境下具有良好系統效能表現。
揚聲機構及應用其之電子裝置
(2008-07-16)
游文鼎
;
白明憲
;
陳榮亮
一種揚聲機構及應用其之電子裝置。揚聲機構包括一音箱、一揚聲元件及一聲音補償元件。揚聲元件係設置於音箱表面。揚聲元件用以發出一聲音訊號。聲音補償元件係設置於音箱表面。聲音補償元件包括一共振薄膜及一增重元件。共振薄膜係可與聲音訊號共振於一共振頻率範圍,以補償聲音訊號於共振頻率範圍之聲音强度。增重元件係貼附於共振薄膜之表面。增重元件之重量係與共振頻率範圍相關。
Effect of an organically modified nanoclay on low-surface-energy materials of polybenzoxazine
(2008-07-16)
Fu, Huei-Kuan
;
Huang, Chih-Feng
;
Kuo, Shiao-Wei
;
Lin, Han-Ching
;
Yei, Ding-Ru
Novel low surface free energy materials of polybenzoxazine/organically modified silicate nanocomposites have been prepared and characterized. The CPC (cetylpyridinium chloride)/ claylo%/poly(3-phenyl-3,4-dihydro-2H-1,3-benzoxazine) (PP-a) material possesses an extremely low surface free energy (12.7 Mj. M-2) after 4 h curing at 200'C, which is even lower than that of poly(tetrafluoroethylene) (22.0 Mj. M-2) calculated on the basis of the threeliquid geometric method. X-Ray photoelectron spectroscopy (XPS) shows a higher silicon content on the surface of the nanocomposites than for an average composition, which implies that the clay is more preferentially enriched on the outermost layer. In addition, the glass transition temperature (Tg) of the polybenzoxazine (PP-a) in the nanocomposite is 22.6'C higher and its thermal decomposition temperature is also 31.5'C higher than the pure PP-a. This finding provides a simple way to prepare low surface energy and high thermal stability materials.
緬懷張恬君教授紀念特輯
(2008-07-16)
Secretariat
;
國立交通大學秘書室
微探針陣列及其翻印模具之製造方法
(2008-07-16)
洪振鈞
;
張志瑋
;
邱俊誠
本發明提供一種可快速翻印製備微探針陣列及其翻印模具之的製造方法,其係利用微機電所製作出具高深寬比的矽材微探針作為內模具,接續利用內模具來製備出翻印模具,再於翻印模具內填入熱塑性材並經過適當烘烤、壓模、脫模處理,以大量生產可隨用即丟之實心高分子微探針陣列。
A low-temperature specific heat study of giant dielectric constant materials
(2008-07-16)
Sun, C. P.
;
Liu, Jianjun
;
Lin, J-Y
;
Duan, Chun-Gang
;
Mei, W. N.
A low-temperature specific heat study has been performed on the insulating giant dielectric constant material CaCu(3)Ti(4)O(12) and two related compounds, Bi(2/3)Cu(3)Ti(4)O(12) and La(0.5)Na(0.5)Cu(3)Ti(4)O(12), from 0.6 to 10 K. From analyzing the specific heat data in a very low-temperature range, 0.6-1.5 K, and moderately low-temperature range, 1.5-5 K, in addition to the expected Debye terms, we observed significant contributions originating from the linear and Einstein terms, which we attributed as the manifestation of low-lying elementary excitations due to lattice vibrations occurring at the grain boundaries and induced by local defects. Together with the findings on electronic and mechanical properties, a phenomenological model is proposed to explain the high dielectric constant behavior in both low and high frequency regions.
Sound broadcasting mechanism and electronic device using the same
(2008-07-17)
Yu, Wen-Ting
;
Bai, Mingsian R.
;
Chen, Rong-Liang
A sound broadcasting mechanism and an electronic device using the same are provided. The sound broadcasting mechanism includes a sound box, a sound broadcasting element and a sound enhancing element. The sound broadcasting element is disposed at the surface of the sound box to generate a sound signal. The sound enhancing element is disposed at the surface of the sound box. The sound enhancing element includes a resonating film and a weight increasing element. The resonating film can resonate with the sound signal in a resonating frequency range to enhance the sound intensity of the sound signal in the resonating frequency range. The weight increasing element is attached to the surface of the resonating film. The weight of the weight increasing element is related to the resonating frequency range.
Core/single-crystal-shell nanospheres for controlled drug release via a magnetically triggered rupturing mechanism
(2008-07-17)
Hu, Shang-Hsiu
;
Chen, San-Yuan
;
Liu, Dean-Mo
;
Hsiao, Chi-Sheng
;
材料科學與工程學系
Core/single-crystal-shell nanospheres are constructed from a poly-(N-vinyl2-pyrrolidone) (PVP)-modified silica core with an outer layer of single-crystal iron oxide shell. The nanospheres show outstanding release- and-zero-release characteristics via the addition and removal, respectively, of an external high-frequency magnetic field.
Excited-state molecular vibration observed for a probe pulse preceding the pump pulse by real-time optical spectroscopy
(2008-07-18)
Kobayashi, Takayoshi
;
Du, Juan
;
Feng, Wei
;
Yoshino, Katsumi
;
電子物理學系
It is shown experimentally that the absorbance change observed in the "negative" time range, where probe pulse precedes pump pulse in real-time vibrational spectroscopy is induced only by the excited-state wave-packet motion as theoretically expected. Coherent molecular vibration of a polymer in the excited state was observed in the real-time trace without the effect of wave-packet motion in the ground state, which usually makes it difficult to ascribe the signal either to the ground state or to the excited state.
An immersed boundary method for interfacial flows with insoluble surfactant
(2008-07-20)
Lai, Ming-Chih
;
Tseng, Yu-Hau
;
Huang, Huaxiong
;
應用數學系
;
Department of Applied Mathematics
In this paper, an immersed boundary method is proposed for the simulation of two-dimensional fluid interfaces with insoluble surfactant. The governing equations are written in a usual immersed boundary formulation where a mixture of Eulerian flow and Lagrangian interfacial variables are used and the linkage between these two set of variables is provided by the Dirac delta function. The immersed boundary force comes from the surface tension which is affected by the distribution of surfactant along the interface. By tracking the interface in a Lagrangian manner, a simplified surfactant transport equation is derived. The numerical method involves solving the Navier-Stokes equations on a staggered grid by a semi-implicit pressure increment projection method where the immersed interfacial forces are calculated at the beginning of each time step. Once the velocity value and interfacial configurations are obtained, surfactant concentration is updated using the transport equation. In this paper, a new symmetric discretization for the surfactant concentration equation is proposed that ensures the surfactant mass conservation numerically. The effect of surfactant on drop deformation in a shear flow is investigated in detail. (c) 2008 Elsevier Inc. All rights reserved.
第十七屆全國高中青年現代醫學研習營圓滿結束
(國立陽明大學, 2008-07-21)
張智堯
;
秘書室
由本校勵青社所舉辦的「第十七屆全國高中青年現代醫學研習營」於7/29到8/4熱鬧進行。本次營期以未來世界作為包裝，期待能帶領120名高中生一窺醫學領域及大學生活的面貌，並解答他們對於未來的許多問題。風趣且教學生動的中醫吳大鵬老師上課時邀請學員在他頭上扎針晚上精彩活動結束時的小隊合照大家雖然很累卻也都相當開心為了能讓學員們能滿載而歸，營期間精心安排了豐富的課程，風趣且教學生動的中醫吳大鵬老師上課時邀請學員在他頭上扎針，讓學員們印象深刻。另外也邀請連加恩學長以及罕病基金會前來分享，連加恩學長以自身經歷期勉學員們趁學生時代多方嘗試、體驗，走出自己不一樣的路。罕見疾病基金會歐玲君媽媽，則是分享了永強燦爛而不平凡的生命故事，深深感動學員們與隊輔們。而科系介紹也邀請到本校七個系優秀學長姐，將各系特色介紹給即將選擇人生道路的學員們。展現青春活力的舞會，熱情延續了整個晚上最後在眾人的歡呼聲中選出了今晚的舞王舞后血液學實驗時學員認真觀察血液推片的情況實驗課程也是醫學相關科系一大特色。本次營期安排了解剖、有機、藥理、貼紮、血液學等精彩實驗，很多學員克服了恐懼成功採血，也頭一次從顯微鏡中觀察到自己的血球。隊輔帶領著學員們由實驗中學習各項操作技巧及新知識。另外也和榮總合作，安排學員們前往榮總參觀，瞭解醫療的工作環境及醫病關係的真實情況。參觀醫院行程中，學員在復健中心很好奇地試用著復健儀器邀請到七個系優秀學長姐前來的科系介紹圖為醫學系劉俊彥學長在開幕式之後的營歌操，為營期熱鬧地揭開了序幕七天六夜的營期中，也穿插安排許多隊輔辛苦準備的活動。除了讓學員們學習團體合作與感受大學生的創意熱情之外，也帶著他們認識陽明、領略陽明校園之美。充滿知性及趣味的營期，最後在營歌一同舞動青春後劃下完美的句點。不論是學員或是隊輔們，都依依不捨地將這個夏天的收穫與笑聲珍藏在回憶當中。醫學營營長張智堯 / 秘書室整理報導