Browsing by Issue Date, starting with "2015-01-19"

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A genetic algorithm for the maximum edge-disjoint paths problem
(2015-01-19)
Hsu, Chia-Chun
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Cho, Hsun-Jung
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運輸與物流管理系註：原交通所+運管所
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Department of Transportation and Logistics Management
Optimization problems concerning edge-disjoint paths have attracted considerable attention for decades. These problems have a lot of applications in the areas of call admission control, real-time communication, VLSI (Very-large-scale integration) layout and reconfiguration, packing, etc. The maximum edge-disjoint paths problem (MEDP) seems to lie in the heart of these problems. Given an undirected graph G and a set of I connection requests, each request consists of a pair of nodes, MEDP is an NP-hard problem which determines the maximum number of accepted requests that can be routed by mutually edge-disjoint (s(i),t(i)) paths. We propose a genetic algorithm (GA) to solve the problem. In comparison to the multi-start simple greedy algorithm (MSGA) and the ant colony optimization method (ACO), the proposed GA method performs better in most of the instances in terms of solution quality and time. (C) 2014 Elsevier B.V. All rights reserved.
Control and sensing system for diffusion optical tomography and method for operating the same
(2015-01-20)
Fang Wai-Chi
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Chen Tien-Ho
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Kang Shih
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Wu Shih-Yang
;
Cheng Ching-Ju
A control and sensing system for diffusion optical tomography and a method for operating the same are disclosed. The control and sensing system includes a control unit and a sensing circuit with a plurality of light sources and sensors, each light source being surrounded by a corresponding predetermined number of the sensors. The control unit instructs the light sources to individually emit light to an object, so the object generates a plurality of optical signals, and instructs the predetermined number of the sensors corresponding to each light source to receive the optical signals and transmit them to the control unit, thereby reducing the complexity of the control and sensing system.
System for real traffic replay over wireless networks
(2015-01-20)
Lin Ying-Dar
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Ku Chia-Yu
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Li Pei-Hsuan
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Lai Yuan-Cheng
A real traffic replay over wireless networks with environment emulation and an event-driven automata-synchronized replay method are disclosed. The system includes a first traffic capture module configured to capture packet traces and environment effects in a real environment, a first event transform module configured to transform the packet traces into a sequence of events, and a reproduce module configured to receive the environment effects from the first traffic capture module and the sequence of events from the first event transform module such as to control a replay of the environment effects in the real environment and the sequence of events coordinately by means of automata.
Dissoluble PDMS-modified p(HEMA-MAA) amphiphilic copolymer and method for fabricating the same
(2015-01-20)
Liu Dean-Mo
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Huang Yun-Chun
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Hsu Chung-Yu
The present invention discloses a dissoluble PDMS-modified p(HEMA-MAA) amphiphilic copolymer and the method of fabricating the same. The amphiphilic copolymer of the present invention is fabricated via chemically bonding HEMA, MAA, and poly(dimethylsiloxane), bis(3-aminopropyl) terminated (PDMS) in aqueous solution. The PDMS-modified p(HEMA-MAA) amphiphilic copolymer can be dissolved completely in polar solvents, particularly alcohol solvents, to facilitate subsequent processing. The amphiphilic copolymer features adjustable hydrophobic-hydrophilic properties and exhibits excellent biocompatibility. Thus, it can be utilized in a number of advanced applications, including anti-fouling and drug delivery.
Reconstructing Genome-Wide Protein-Protein Interaction Networks Using Multiple Strategies with Homologous Mapping
(2015-01-20)
Lo, Yu-Shu
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Huang, Sing-Han
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Luo, Yong-Chun
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Lin, Chun-Yu
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Yang, Jinn-Moon
Background One of the crucial steps toward understanding the biological functions of a cellular system is to investigate protein-protein interaction (PPI) networks. As an increasing number of reliable PPIs become available, there is a growing need for discovering PPIs to reconstruct PPI networks of interesting organisms. Some interolog-based methods and homologous PPI families have been proposed for predicting PPIs from the known PPIs of source organisms. Results Here, we propose a multiple-strategy scoring method to identify reliable PPIs for reconstructing the mouse PPI network from two well-known organisms: human and fly. We firstly identified the PPI candidates of target organisms based on homologous PPIs, sharing significant sequence similarities (joint E-value <= 1 x 10(-40)), from source organisms using generalized interolog mapping. These PPI candidates were evaluated by our multiple-strategy scoring method, combining sequence similarities, normalized ranks, and conservation scores across multiple organisms. According to 106,825 PPI candidates in yeast derived from human and fly, our scoring method can achieve high prediction accuracy and outperform generalized interolog mapping. Experiment results show that our multiple-strategy score can avoid the influence of the protein family size and length to significantly improve PPI prediction accuracy and reflect the biological functions. In addition, the top-ranked and conserved PPIs are often orthologous/ essential interactions and share the functional similarity. Based on these reliable predicted PPIs, we reconstructed a comprehensive mouse PPI network, which is a scale-free network and can reflect the biological functions and high connectivity of 292 KEGG modules, including 216 pathways and 76 structural complexes. Conclusions Experimental results show that our scoring method can improve the predicting accuracy based on the normalized rank and evolutionary conservation from multiple organisms. Our predicted PPIs share similar biological processes and cellular components, and the reconstructed genome-wide PPI network can reflect network topology and modularity. We believe that our method is useful for inferring reliable PPIs and reconstructing a comprehensive PPI network of an interesting organism.
交大e-News第179期-交大與諾貝爾化學獎團隊合作有機會再獲諾貝爾榮耀
(2015-01-20)
Secretariat
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國立交通大學秘書室
影像顯示裝置
(2015-01-21)
黃冠達
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潘瑞文
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吳重雨
一種影像顯示裝置，適於配置於一使用者的單眼之前。影像顯示裝置包括一顯示器、一第一反射鏡以及一第二反射鏡。顯示器輸出一影像光。第一反射鏡位於影像光的傳遞路徑上。第一反射鏡適於反射影像光。第二反射鏡位於被反射之影像光的傳遞路徑上，且位於顯示器與第一反射鏡之間的傳遞路徑以外的區域。第二反射鏡的兩端分別鄰近顯示器與第一反射鏡。第一反射鏡將影像光反射至第二反射鏡，第二反射鏡進一步將被反射之影像光傳遞至使用者的眼中。
Interfacial characterization of nickel-yttria-stabilized zirconia cermet anode/interconnect joints with Ag-Pd-Ga active filler for use in solid-oxide fuel cells
(2015-01-21)
Chao, Chih-Long
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Chu, Chun-Lin
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Fuh, Yiin-Kuen
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Hsu, Ray-Quen
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Lee, Shyong
Nickel yttria-stabilized zirconia cermet anode (Ni-YSZ)/interconnect joints with silver palladium gallium (Ag-9Pd-9Ga) active fillers are prepared by vacuum brazing. The joint structure and microstructure are analyzed by X-ray diffraction (XRD) and scanning electron microscopy coupled with energy dispersive spectroscopy (SEWEDS), and by using an electron probe microanalyzer (EPMA). SEM observations of the joint show no cracks near the interface, confirming the compatibility of the Ag-9Pd-9Ga filler with a different anode and interconnect. The XRD pattern of the joint specimens oxidized at 800 degrees C for 250 h shows Cr2O3 and (Mn,Cr)(3)O-4 surface layers. EPMA analysis of the cell/Ag-9Pd-9Ga/alloys joint at the cross section shows Cr, O, Fe, Zr, Ni, Ag, Pd, Ga, Y, and Mn. Overall, the results indicate that the bonding between metal and cermet is well established and the interface is smooth. By correlating the XRD and EPMA analysis results, we also analyzed the possible stages during joint oxidation. The joint strength was evaluated at 25 and 800 degrees C under shear and tensile loading conditions, respectively, and the brazed Ag-9Pd-9Ga sealant compared favorably with the commercially available glass-ceramic GC-9 counterpart. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.
Complex Columnar Hexagonal Polymorphism in Supramolecular Assemblies of a Semifluorinated Electron-Accepting Naphthalene Bisimide
(2015-01-21)
Wu, Yu-Chun
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Leowanawat, Pawaret
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Sun, Hao-Jan
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Partridge, Benjamin E.
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Peterca, Mihai
Simple synthetic methods for a strongly electron-accepting naphthalene bisimide (NBI) derivative functionalized with a new environmentally friendly chiral racemic semifluorinated alkyl group and with AB(3) minidendrons containing the same semifluorinated group are reported. The semifluorinated dendron was attached to the imide groups of the NBI via one, two, and three (m = 1, 2, 3) methylenic units. The NBI-containing semifluorinated groups and the dendronized NBI with m = 1 and 2 self-organize into lamellar crystals. The dendronized NBI with m = 3 self-assembles into an unprecedentedly complex and ordered column that self-organizes in a columnar hexagonal periodic array. This array undergoes a continuous transition to a columnar hexagonal superlattice that does not display a first-order phase transition during analysis by differential scanning calorimetry at heating and cooling rates of 10 and 1 degrees C/min. These complex columnar hexagonal periodic arrays with intramolecular order could be elucidated only by a combination of powder and fiber X-ray diffraction studies and solid-state NMR experiments. The lamellar crystals self-organized from m = 1 and the two highly ordered columnar hexagonal periodic arrays of m = 3 are assembled via thermodynamically controlled processes. Since strongly electron-accepting derivatives are of great interest to replace fullerene acceptors in organic photovoltaics and for other supramolecular electronic materials, the multitechnique structural analysis methodology elaborated here must be taken into consideration in all related studies.
考慮耗時與耗電的卸載運算量的決策方法與運算系統
(2015-01-21)
林盈達
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黃霆鈞
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賴源正
;
朱宗賢
一種考慮耗時與耗電的卸載運算量的決策方法。此方法包括：取得運算任務；從影響因子表中取得多個靜態影響因子；蒐集多個動態影響因子。此方法還包括：根據動態影響因子與靜態影響因子，產生各個運算單元與伺服器執行運算任務所需的耗電量與運算時間；根據耗電量與運算時間來計算出執行運算任務的成本數值；根據成本數值，判斷由一目標單元來執行運算任務，此目標單元是一運算單元或一伺服器；由目標單元執行運算任務。藉此，可同時考慮耗電與運算時間，適當地將運算量分配至運算單元與伺服器的其中之一。
Highly Efficient Flexible Hybrid Nanocrystal-Cu(In,Ga)Se-2 (CIGS) Solar Cells
(2015-01-21)
Liao, Yu-Kuang
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Brossard, Mael
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Hsieh, Dan-Hua
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Lin, Tzu-Neng
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Charlton, Martin D. B.
A novel scheme for hybridizing inkjet-printed thin film Cu(In,Ga)Se-2 (CIGS) solar cells with self-assembled clusters of nanocrystal quantum dots (NQDs), which provides a 10.9% relative enhancement of the photon conversion efficiency (PCE), is demonstrated. A non-uniform layer of NQD aggregates is deposited between the transparent conductive oxide and a CdS/CIGS p-n junction using low cost pulsed-spray deposition. Hybridization significantly improves the external quantum efficiency of the hybrid devices in the absorption range of the NQDs and in the red to near-IR parts of the spectrum. The low wavelength response enhancement is found to be induced by luminescent down-shifting (LDS) from the NQD layer, while the increase at longer wavelengths is attributed to internal scattering from NQD aggregates. LDS is demonstrated using time-resolved spectroscopy, and the morphology of the NQD layer is investigated in fluorescence microscopy and cross-sectional transmission electron microscopy. The influence of the NQD dose on the PCE of the hybrid devices is investigated and an optimum value is obtained. The low costs and limited material consumptions associated with pulsed-spray deposition make these flexible hybrid devices promising candidates to help push thin-film photovoltaic technology towards grid parity.
追日裝置
(2015-01-21)
謝侑龍
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張翼
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鄭時龍
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成維華
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呂秉翰
一種追日裝置，包括基座、設於該基座上之第一傳動器、第二傳動器與支柱、樞接於該支柱以承載太陽能發電模組之承載座、樞接該第一傳動器與該承載座之第一支撐桿以及樞接該第二傳動器與該承載座之第二支撐桿。本發明具有高結構剛性及高承載能力，除可抗強風外，尚具有高追蹤精度及較大的旋轉角度，使太陽能板能準確且長時間地對準太陽，因此可大幅提升太陽能發電模組之效能。
Integrated analyses to reconstruct microRNA-mediated regulatory networks in mouse liver using high-throughput profiling
(2015-01-21)
Hsu, Sheng-Da
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Huang, Hsi-Yuan
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Chou, Chih-Hung
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Sun, Yi-Ming
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Hsu, Ming-Ta
Background: MicroRNAs (miRNAs) simultaneously target many transcripts through partial complementarity binding, and have emerged as a key type of post-transcriptional regulator for gene expression. How miRNA accomplishes its pleiotropic effects largely depends on its expression and its target repertoire. Previous studies discovered thousands of miRNAs and numerous miRNA target genes mainly through computation and prediction methods which produced high rates of false positive prediction. The development of Argonaute cross-linked immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) provides a system to effectively determine miRNA target genes. Likewise, the accuracy of dissecting the transcriptional regulation of miRNA genes has been greatly improved by chromatin immunoprecipitation of the transcription factors coupled with sequencing (ChIP-Seq). Elucidation of the miRNA target repertoire will provide an in-depth understanding of the functional roles of microRNA pathways. To reliably reconstruct a miRNA-mediated regulatory network, we established a computational framework using publicly available, sequence-based transcription factor-miRNA databases, including ChIPBase and TransmiR for the TF-miRNA interactions, along with miRNA-target databases, including miRTarBase, TarBase and starBase, for the miRNA-target interactions. We applied the computational framework to elucidate the miRNA-mediated regulatory network in the Mir122a(-/-) mouse model, which has an altered transcriptome and progressive liver disease. Results: We applied our computational framework to the expression profiles of miRNA/mRNA of Mir122a(-/-) mutant mice and wild-type mice. The miRNA-mediated network involves 40 curated TFs contributing to the aberrant expression of 65 miRNAs and 723 curated miRNA target genes, of which 56% was found in the differentially-expressed genes of Mir122a(-) mice. Hence, the regulatory network disclosed previously-known and also many previously-unidentified miRNA-mediated regulations in mutant mice. Moreover, we demonstrate that loss of imprinting at the chromosome 12qF1 region is associated with miRNA overexpression in human hepatocellular carcinoma and stem cells, suggesting initiation of precancerous changes in young mice deficient in miR-122. A group of 9 miRNAs was found to share miR-122 target genes, indicating synergy between miRNAs and target genes by way of multiplicity and cooperativity. Conclusions: The study provides significant insight into miRNA-mediated regulatory networks. Based on experimentally verified data, this network is highly reliable and effective in revealing previously-undetermined disease-associated molecular mechanisms. This computational framework can be applied to explore the significant TF-miRNA-miRNA target interactions in any complex biological systems with high degrees of confidence.
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
(2015-01-21)
Li, Yun-Lung
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Weng, Jui-Cheng
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Hsiao, Chiung-Chih
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Chou, Min-Te
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Tseng, Chin-Wen
Background: In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the reads, which are not competent in some applications. Results: Here, we propose a fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for paired-end sequencing. PEAT requires no a priori adaptor sequence, which is convenient for large-scale meta-analyses. We assessed the performance of PEAT with many adapter trimmers in both simulated and real life paired-end sequencing libraries. The importance of adapter trimming was exemplified by the influence of the downstream analyses on RNA-seq, ChIP-seq and MNase-seq. Several useful guidelines of applying adapter trimmers with aligners were suggested. Conclusions: PEAT can be easily included in the routine paired-end sequencing pipeline. The executable binaries and the standalone C++ source code package of PEAT are freely available online.
Discovering monotonic stemness marker genes from time-series stem cell microarray data
(2015-01-21)
Wang, Hsei-Wei
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Sun, Hsing-Jen
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Chang, Ting-Yu
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Lo, Hung-Hao
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Cheng, Wei-Chung
Background: Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Monotonic Feature Selector (MFSelector) based on a concept of total discriminating error (DEtotal) to identify monotonic genes. MFSelector considers various time stages in stage order (i.e., Stage One vs. other stages, Stages One and Two vs. remaining stages and so on) and computes DEtotal of each gene. MFSelector can successfully identify genes with monotonic characteristics. Results: We have demonstrated the effectiveness of MFSelector on two synthetic data sets and two stem cell differentiation data sets: embryonic stem cell neurogenesis (ESCN) and embryonic stem cell vasculogenesis (ESCV) data sets. We have also performed extensive quantitative comparisons of the three monotonic gene selection approaches. Some of the monotonic marker genes such as OCT4, NANOG, BLBP, discovered from the ESCN dataset exhibit consistent behavior with that reported in other studies. The role of monotonic genes found by MFSelector in either stemness or differentiation is validated using information obtained from Gene Ontology analysis and other literature. We justify and demonstrate that descending genes are involved in the proliferation or self-renewal activity of stem cells, while ascending genes are involved in differentiation of stem cells into variant cell lineages. Conclusions: We have developed a novel system, easy to use even with no pre-existing knowledge, to identify gene sets with monotonic expression patterns in multi-stage as well as in time-series genomics matrices. The case studies on ESCN and ESCV have helped to get a better understanding of stemness and differentiation. The novel monotonic marker genes discovered from a data set are found to exhibit consistent behavior in another independent data set, demonstrating the utility of the proposed method.
互動式提醒方法與系統
(2015-01-21)
吳炳飛
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陳盈翰
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王承濬
本發明為一種互動式提醒方法，包括：一第一使用者將目前該第一使用者的位置與一目的地輸入一第一行動裝置，以讓該第一行動裝置進行一路徑規劃，進而產生一預定導航路徑資訊，並將該預定導航路徑資訊與目前該第一使用者的位置上傳至一遠端伺服器；以及一第二使用者應用一第二行動裝置查看該遠端伺服器所儲存的該預定路徑資訊與目前該第一使用者的位置，進而應用一指定方式，以讓該第一使用者到達該目的地時，該遠端伺服器會產生一提示信號，提醒該第二使用者。
Triplet superconductivity in 3D Dirac semi-metal due to exchange interaction
(2015-01-21)
Rosenstein, Baruch
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Shapiro, B. Ya
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Li, Dingping
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Shapiro, I.
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電子物理學系
Conventional phonon-electron interaction induces either triplet or one of two (degenerate) singlet pairing states in time reversal and inversion invariant 3D Dirac semi-metal. Investigation of the order parameters and energies of these states at zero temperature in a wide range of values of chemical potential mu, the effective electron-electron coupling constant. and Debye energy T-D demonstrates that when the exchange interaction is neglected the singlet always prevails, however, in significant portions of the (mu, lambda, T-D) parameter space the energy difference is very small. This means that interactions that are small, but discriminate between the spin singlet and the spin triplet, are important in order to determine the nature of the superconducting order there. The best candidate for such an interaction in the materials under consideration is the exchange (the Stoner term) characterized by constant lambda(ex). We show that at values of lambda(ex), much smaller than ones creating Stoner instability to ferromagnetism lambda(ex) similar to 1, the triplet pairing becomes energetically favored over the singlet ones. The 3D quantum critical point at mu = 0 is considered in detail. This can be realized experimentally in optically trapped cold atom systems.
Effectiveness of organic molecules for spin filtering in an organic spin valve: Reaction-induced spin polarization for Co atop Alq(3)
(2015-01-21)
Tu-Ngoc Lam
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Lai, Yu-Ling
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Chen, Chih-Han
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Chen, Po-Hung
;
Chan, Yuet-Loy
The spin polarization of organic-ferromagnetic interfaces in an organic spin valve critically affects the efficiency of spin injection or detection. We examined the chemical and electronic properties of ferromagnetic Co deposited on organic Alq(3) and the interfacial spin-polarized capability of the electronic states. Our x-ray photoemission spectra and calculations with density-functional theory indicate a sequential and unequal distribution of charge from Co clusters to N and then to O atoms in Alq(3). The preferential orbital hybridization at specific functional sites produces efficient spin polarization of organic molecules. Element-specific measurements of x-ray magnetic circular dichroism demonstrate the preferential spin polarization in the lowest unoccupied molecular orbital state of N atoms at the complex interface for Co atop Alq(3), which agrees satisfactorily with calculation. Our results indicate that an induced interfacial spin polarization on engineering the dominant reaction of Co with mainly N and O atoms in Alq(3) might pave a way for effective spin filtering in organic spintronics.
雙埠次臨界靜態隨機存取記憶體單元
(2015-01-21)
邱議德
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張銘宏
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楊皓義
;
黃威
本發明係提供一種創新的雙埠次臨界靜態隨機存取記憶體(static random access memory，下稱SRAM)單元，適用於次臨界電壓(substhreshold voltage)下操作。本發明之雙埠次臨界SRAM單元在寫入時，會切斷記憶元件之正回授，並應用反短通道效應(reverse short-channel effect，RSCE)增強寫入能力。而本發明單端讀寫的架構更能夠進一步降低長位線(long bit line)所造成的功率消耗，因此更適合應用於長時間工作之先進先出(first-in first-out，FIFO)記憶體設計。據此，本發明之SRAM單元在次臨界電壓下仍然能夠提供穩定的操作，解決習知記憶體單元因降低電壓而造成穩定度下降的問題。
SCMPSP: Prediction and characterization of photosynthetic proteins based on a scoring card method
(2015-01-21)
Vasylenko, Tamara
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Liou, Yi-Fan
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Chen, Hong-An
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Charoenkwan, Phasit
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Huang, Hui-Ling
Background: Photosynthetic proteins (PSPs) greatly differ in their structure and function as they are involved in numerous subprocesses that take place inside an organelle called a chloroplast. Few studies predict PSPs from sequences due to their high variety of sequences and structues. This work aims to predict and characterize PSPs by establishing the datasets of PSP and non-PSP sequences and developing prediction methods. Results: A novel bioinformatics method of predicting and characterizing PSPs based on scoring card method (SCMPSP) was used. First, a dataset consisting of 649 PSPs was established by using a Gene Ontology term GO: 0015979 and 649 non-PSPs from the SwissProt database with sequence identity <= 25%.- Several prediction methods are presented based on support vector machine (SVM), decision tree J48, Bayes, BLAST, and SCM. The SVM method using dipeptide features-performed well and yielded - a test accuracy of 72.31%. The SCMPSP method uses the estimated propensity scores of 400 dipeptides - as PSPs and has a test accuracy of 71.54%, which is comparable to that of the SVM method. The derived propensity scores of 20 amino acids were further used to identify informative physicochemical properties for characterizing PSPs. The analytical results reveal the following four characteristics of PSPs: 1) PSPs favour hydrophobic side chain amino acids; 2) PSPs are composed of the amino acids prone to form helices in membrane environments; 3) PSPs have low interaction with water; and 4) PSPs prefer to be composed of the amino acids of electron-reactive side chains. Conclusions: The SCMPSP method not only estimates the propensity of a sequence to be PSPs, it also discovers characteristics that further improve understanding of PSPs. The SCMPSP source code and the datasets used in this study are available at http://iclab.life.nctu.edu.tw/SCMPSP/.