Browsing by Issue Date, starting with "2017-12-19"

Now showing 1 - 20 of 12444

iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm
(2017-12-19)
Chang, Hui-Yin
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Chen, Ching-Tai
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Ko, Chu-Ling
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Chen, Yi-Ju
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Chen, Yu-Ju
Top-down proteomics using liquid chromatogram coupled with mass spectrometry has been increasingly applied for analyzing intact proteins to study genetic variation, alternative splicing, and post-translational modifications (PTMs) of the proteins (proteoforms). However, only a few tools have been developed for charge state deconvolution, monoisotopic/average molecular weight determination and quantitation of proteoforms from LC-MS1 spectra. Though Decon2LS and MASH Suite Pro have been available to provide intraspectrum charge state deconvolution and quantitation, manual processing is still required to quantify proteoforms across multiple MS1 spectra. An automated tool for interspectrum quantitation is a pressing need. Thus, in this paper, we present a user-friendly tool, called iTop-Q (intelligent Top-down Proteomics Quantitation), that automatically performs large-scale proteoform quantitation based on interspectrum abundance in top-down proteomics. Instead of utilizing single spectrum for proteoform quantitation, iTop-Q constructs extracted ion chromatograms (XICs) of possible proteoform peaks across adjacent MS' spectra to calculate abundances for accurate quantitation. Notably, iTop-Q is implemented with a newly proposed algorithm, called DYAMOND, using dynamic programming for charge state deconvolution. In addition, iTop-Qperforms proteoform alignment to support quantitation analysis across replicates/samples. The performance evaluations on an in-house standard data set and a public large-scale yeast lysate data set show that iTop-Q achieves highly accurate quantitation, more consistent quantitation than using intraspectrum quantitation. Furthermore, the DYAMOND algorithm is suitable for high charge state deconvolution and can distinguish shared peaks in coeluting proteoforms. iTop-Qis publicly available for download at http://ms.iis.sinica.edu.tw/COmics/Software_iTop-Q.
Carbon Fiber Ionization Mass Spectrometry for the Analysis of Analytes in Vapor, Liquid, and Solid Phases
(2017-12-19)
Wu, Min-Li
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Chen, Te-Yu
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Chen, Yen-Chun
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Chen, Yu-Chie
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應用化學系
Various ionization methods in mass spectrometry (MS) are available for the analysis of analytes with different properties. Nonetheless, the use of a single ionization method to analyze mixtures containing analytes with different polarities and volatilities in different phases at atmospheric pressure remains a challenge. Exploring an ionization method that can ionize small organics and large biomolecules with different properties for MS analysis is advantageous. Carbon fiber ionization mass spectrometry (CFI-MS), which uses a carbon fiber bundle as the ion source, is useful for the analysis of small organics with low polarities. Voltage needs to be applied on the carbon fiber bundle to initiate corona discharge for ionization of analytes. In this study, we explore the suitability of using CFI-MS in the analysis of analytes in vapor, liquid, and solid phases using a single carbon fiber (length : similar to 1 cm; diameter: similar to 10 mu m) as the ion source. Furthermore direct electric contact on the carbon fiber is not required. We demonstrate that CFI-MS is useful for analyzing not only small and low-polarity organics but also polar biomolecules, such as peptides and proteins. The limits of detection for analytes with high polarities such as dodecyl trimethylammonium bromide and bradykinin are estimated to be similar to 16 and similar to 53 pM, respectively. Ionization mechanisms, including corona discharge and electrospray, are involved in the ionization of analytes with the polarity from low to high. Furthermore, sesame oil containing aromatic volatiles and compounds with different polarities is used as a model sample to demonstrate the capability of the developed ionization method to provide comprehensive chemical information from a complex sample. In addition, the feasibility of using the developed method for quantitative analysis of nonpolar as well as medium and high polarity analytes is also demonstrated. The sensitivity of the developed method toward analytes with high polarity is higher than those with low polarity. The method precision was estimated to be similar to 7.8%.
ESI MS for Microsized Bioparticles
(2017-12-19)
Ozdemir, Abdil
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Lin, Jung-Lee
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Gulfen, Mustafa
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Lai, Szu-Hsueh
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Hsiao, Chun-Jen
An ESI ion trap mass spectrometer was designed for high-throughput and rapid mass analysis of large bioparticles. Mass calibration of the instrument was performed using commercially available polystyrene (PS) microparticles with a size comparable to cancer cells. Different sites of MCF-7 breast cancer cells (8 to 15 mu m) were used in this study. The masses of different cancer cells were measured. This system allows for the analysis of all types of particles.
Concurrent intersection point of magnetization and magnetoconductivity curves in strongly fluctuating superconductors
(2017-12-20)
Chi, Cheng
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Jiang, Xujiang
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Wang, Jiangfan
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Li, Dingping
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Rosenstein, Baruch
The thermal fluctuations contribution to magnetization and magnetoconductivity of type-II layered superconductors is calculated in the framework of the Lawrence-Doniach model. For numerous high-temperature cuprate superconductors, it was discovered that the magnetization dependence on temperature in a wide range of fields exhibits an intersection point at a temperature slightly below Tc. We notice a similar intersection point of the magnetoconductivity curves at the approximate same temperature. The phenomenon is explained by strong (non-Gaussian) thermal fluctuations with interactions treated using a self-consistent theory. All higher Landau levels should be included. Dimensionality of the fluctuations is defined, and the two- to three-dimensional crossover is the key for the existence of intersection points.
Electromigration Mechanism of Failure in Flip-Chip Solder Joints Based on Discrete Void Formation
(2017-12-20)
Chang, Yuan-Wei
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Cheng, Yin
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Helfen, Lukas
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Xu, Feng
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Tian, Tian
In this investigation, SnAgCu and SN100C solders were electromigration (EM) tested, and the 3D laminography imaging technique was employed for in-situ observation of the microstructure evolution during testing. We found that discrete voids nucleate, grow and coalesce along the intermetallic compound/solder interface during EM testing. A systematic analysis yields quantitative information on the number, volume, and growth rate of voids, and the EM parameter of DZ*. We observe that fast intrinsic diffusion in SnAgCu solder causes void growth and coalescence, while in the SN100C solder this coalescence was not significant. To deduce the current density distribution, finite-element models were constructed on the basis of the laminography images. The discrete voids do not change the global current density distribution, but they induce the local current crowding around the voids: this local current crowding enhances the lateral void growth and coalescence. The correlation between the current density and the probability of void formation indicates that a threshold current density exists for the activation of void formation. There is a significant increase in the probability of void formation when the current density exceeds half of the maximum value.
Controlling bottom-up rapid growth of single crystalline gallium nitride nanowires on silicon
(2017-12-20)
Wu, Ko-Li
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Chou, Yi
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Su, Chang-Chou
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Yang, Chih-Chaing
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Lee, Wei-I.
We report single crystalline gallium nitride nanowire growth from Ni and Ni-Au catalysts on silicon using hydride vapor phase epitaxy. The growth takes place rapidly; efficiency in time is higher than the conventional nanowire growth in metal-organic chemical vapor deposition and thin film growth in molecular beam epitaxy. The effects of V/III ratio and carrier gas flow on growth are discussed regarding surface polarity and sticking coefficient of molecules. The nanowires of gallium nitride exhibit excellent crystallinity with smooth and straight morphology and uniform orientation. The growth mechanism follows self-assembly from both catalysts, where Au acts as a protection from etching during growth enabling the growth of ultra-long nanowires. The photoluminescence of such nanowires are adjustable by tuning the growth parameters to achieve blue emission. The practical range of parameters for mass production of such high crystal quality and uniformity of nanowires is suggested.
Bispentafluorophenyl-Containing Additive: Enhancing Efficiency and Morphological Stability of Polymer Solar Cells via Hand-Grabbing-Like Supramolecular Pentafluorophenyl-Fullerene Interactions
(2017-12-20)
Hung, Kai-En
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Tsai, Che-En
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Chang, Shao-Ling
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Lai, Yu-Ying
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Jeng, U-Ser
A new class of additive materials bis(pentafluorophenyl) diesters (BFEs) where the two pentafluorophenyl (C6F5) moieties are attached at the both ends of a linear aliphatic chain with tunable tether lengths (BFS, BF7, and BF13) were designed and synthesized. In the presence of BF7 to restrict the migration of fullerehe by hand-grabbing-like supramolecular interactions induced between the C6F5 groups and the surface of fullerene, the P3HT:PC61BM:BF7 device showed stable device characteristiCs after thermal heating at 150 degrees C for 25, 'IL The morphologies Of the active layers were systematically investigated by optical microscopy, grazing-incidence small-angle X-ray scattering (GISAXS), and atomic force microscopy. The tether length between the two C6F5 groups plays a pivotal role in controlling the intermolecular attractions. BF13 with a long and flexible tether might form a BF13-fullerene sandwich complex that fails to prevent fullerene's movement and aggregation, while BF5 with too short tether length decreases the possibility of interactions between the C6F5 groups and the fullerenes. BF7 with the optimal tether length has the best ability to stabilize the morphology. In sharp contrast, the nonfluorinated BP7 analogue without C6F5-C-60 physical interactions does not have the capability of morphological stabilization, unambiguously revealing the necessity of the C6F5 group. Most importantly, the function of BF7 can be also applied to the high-performance PffBT4BT-20D:PC71BM system, which exhibited an original PCE of 8.80%. After thermal heating at 85 degrees C for 200 h, the efficiency of the Pffi3T4BT-20D:PC71BM:BF7 device only decreased slightly to 7.73%, maintaining 88% of its original efficiency. To the best of our knowledge, this is the first time that the thermabdriven morphological evolution of the high-performance PffBT4BT-20D polymer has been investigated, and its morphological stability in the inverted device can be successfully preserved by the incorporation of BF7. This research also demonstrates that BF7 is not only effective with PC61BM but also to PC71BM.
交大e-News第246期-國士無雙！張懋中校長、賴明治教授榮膺教育部國家講座
(2017-12-20)
國立交通大學秘書室
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Secretariat
Modeling the CH Stretch/Torsion/Rotation Couplings in Methyl Peroxy (CH3OO)
(2017-12-21)
Huang, Meng
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Miller, Terry A.
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McCoy, Anne B.
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Hsu, Kuo-Hsiang
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Huang, Yu-Hsuan
The manifestations of CH stretch/torsion/ rotation coupling in the region of the CH stretch fundamentals are explored in the CH3OO radical. Following our earlier study of the fundamental in the totally symmetric CH stretch (the fundamental), this work focuses on the other two CH stretch fundamentals, nu(1) and nu(9), which would be degenerate in the absence of a barrier in the potential along the methyl torsion coordinate. The simplest model, which assumes a decoupling of the CH stretch vibrations from the torsion, fails to reproduce several important features of the spectrum. Specifically, the absence of a strong peak around the origin of the nu(1), fundamental and broadening of the strong peak near the origin in the observed spectrum of the nu(9) fundamental are not captured by this model. The origins of these features are explored through two more sophisticated treatments of the torsion/CH stretch couplings. In the first, a four-dimensional potential based on the three CH stretches and the torsion is developed and shown to reproduce both of these features. On the basis of the results of these calculations, the calculated parameters are adjusted to simulate the recorded spectrum. To further explore the torsion/CH stretch couplings in CH3OO, a 9-state model Hamiltonian is developed and discussed. The implications of various types of couplings on the observed energy level patterns are also discussed.
New phenazine based AIE probes for selective detection of aluminium(III) ions in presence of other trivalent metal ions in living cells
(2017-12-21)
Balamurugan, Gopal
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Velmathi, Sivan
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Thirumalaivasan, Natesan
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Wu, Shu Pao
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應用化學系
Phenazine fluorophore based imidazole derivatives (S1 and S2) were synthesized and sensor studies were carried out with various cations. Aggregation induced emission (AIE) was observed selectively for Al3+ among other cations under study in case of both sensors. H-1 NMR titration supported the aggregation induced emission of S2 with Al3+. ESI mass spectra successfully confirmed the aggregate formation. SEM images clearly showed the aggregation of receptor induced by Al3+ in a flower-like fashion. AIE probe was successfully applied for bio-imaging of RAW264.7 cells.
老爹不老　張政漢一生征寒
(2017-12-24)
范晨星
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Department of Communication and Technology
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傳播與科技學系
童軍老頑童張政漢，退休之後的「淘金」生活。
投筆從農闢花間　郭雅聰
(2017-12-24)
蕭巧昱
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Department of Communication and Technology
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傳播與科技學系
有著咖啡公路美名的東山175號縣道也曾是一片荒土，直到文人農夫郭雅聰開創第一座咖啡廳「大鋤花間」，散發公路上的第一抹咖啡香。
二手玩具物流與新生
(2017-12-24)
楊巧柔
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Department of Communication and Technology
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傳播與科技學系
玩具是每個人童年不可或缺的重要角色，但孩子長大了或是那些玩膩的玩具是否只有被丟掉的命運？二手玩具物流，給舊玩具新生的機會。
CP　我們為何而站
(2017-12-24)
簡文怡
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Department of Communication and Technology
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傳播與科技學系
粉絲與官方對於CP的看法如何？站CP又有什麼魅力使粉絲無法自拔？
Takeshi　為娛樂而活的日本人
(2017-12-24)
巫尹文
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Department of Communication and Technology
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傳播與科技學系
11歲，進入演藝學校。20歲，從日本沖繩來到臺灣。Takeshi經歷了Dance Flow、A4F兩個唱跳團體，現在以個人身份在臺灣娛樂圈打拼，持續地帶給大家歡樂。
第三天然氣接收站　藻礁悲歌
(2017-12-24)
徐仟妤
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Department of Communication and Technology
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傳播與科技學系
配合2025非核家園，中油計畫在大潭建造的第三天然氣接收站恐危及當地藻礁生態。
單側聽損　該納入身障資格嗎？
(2017-12-24)
吳佩芸
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Department of Communication and Technology
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傳播與科技學系
台灣有一群人，外表看似與一般人無異，卻有著不為人知的缺陷與痛苦，他們是「單側聽損者」。
過敏基因檢測現曙光
(2017-12-24)
王毓楷
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Department of Communication and Technology
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傳播與科技學系
研究指出對塵蟎過敏可能來自基因的突變，最新的基因序列檢測技術結合精準醫學的應用，能即時發現基因缺陷並及時治療。
從音樂到閱讀　邱君豪的文化之路
(2017-12-24)
關子茵
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Department of Communication and Technology
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傳播與科技學系
從喜愛搖滾音樂到撰寫樂評，再到獨立書店，之間看似相關但又不太相同，是什麼經歷，令邱君豪產生這樣的念頭？
台灣單車新希望　College bike紀翔
(2017-12-24)
蔡翔宇
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Department of Communication and Technology
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傳播與科技學系
紀翔是College bike的創辦人，他敏銳的眼光看見了學生平價單車的缺口，翻轉舊有的單車產業模式，打造出平價及質量兼具的單車，成為台灣單車新希望。