Browsing by Issue Date, starting with "2016-01-04"

Now showing 1 - 20 of 18145

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
(2016-01-04)
Chow, Chi-Nga
;
Zheng, Han-Qin
;
Wu, Nai-Yun
;
Chien, Chia-Hung
;
Huang, Hsien-Da
Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of plant promoters. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between similar gene promoters are also identified. The current PlantPANrelease (version 2.0) contains 16 960 TFs and 1143 TF binding site matrices among 76 plant species. In addition to updating of the annotation information, adding experimentally verified TF matrices, and making improvements in the visualization of transcriptional regulatory networks, several new features and functions are incorporated. These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions, (iii) protein-protein interactions among TFs and their co-factors, (iv) TFtarget networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is provided in PlantPAN 2.0. The PlantPAN 2.0 is a systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.
Silicon Nanowires for Solar Thermal Energy Harvesting: an Experimental Evaluation on the Trade-off Effects of the Spectral Optical Properties
(2016-01-04)
Sekone, Abdoul Karim
;
Chen, Yu-Bin
;
Lu, Ming-Chang
;
Chen, Wen-Kai
;
Liu, Chia-An
Silicon nanowire possesses great potential as the material for renewable energy harvesting and conversion. The significantly reduced spectral reflectivity of silicon nanowire to visible light makes it even more attractive in solar energy applications. However, the benefit of its use for solar thermal energy harvesting remains to be investigated and has so far not been clearly reported. The purpose of this study is to provide practical information and insight into the performance of silicon nanowires in solar thermal energy conversion systems. Spectral hemispherical reflectivity and transmissivity of the black silicon nanowire array on silicon wafer substrate were measured. It was observed that the reflectivity is lower in the visible range but higher in the infrared range compared to the plain silicon wafer. A drying experiment and a theoretical calculation were carried out to directly evaluate the effects of the trade-off between scattering properties at different wavelengths. It is clearly seen that silicon nanowires can improve the solar thermal energy harnessing. The results showed that a 17.8 % increase in the harvest and utilization of solar thermal energy could be achieved using a silicon nanowire array on silicon substrate as compared to that obtained with a plain silicon wafer.
CircNet: a database of circular RNAs derived from transcriptome sequencing data
(2016-01-04)
Liu, Yu-Chen
;
Li, Jian-Rong
;
Sun, Chuan-Hu
;
Andrews, Erik
;
Chao, Rou-Fang
Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNAtarget networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e. g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA-miRNA-gene regulatory networks. It not only extends themost up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database
(2016-01-04)
Chou, Chih-Hung
;
Chang, Nai-Wen
;
Shrestha, Sirjana
;
Hsu, Sheng-Da
;
Lin, Yu-Ling
MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.
Complementing Crystallography with Ultralow-Frequency Raman Spectroscopy: Structural Insights into Nitrile-Functionalized Ionic Liquids
(2016-01-04)
Chen, Hong-Kai
;
Srivastava, Nitin
;
Saha, Satyen
;
Shigeto, Shinsuke
;
應用化學系
Functionalized ionic liquids are a subclass of ionic liquids that are tailored for a specific application. Structural characterization in both solid and liquid phases is central to understanding their physical properties. Here, we used ultralow-frequency Raman spectroscopy, which can measure Raman spectra down to approximately 5cm(-1), to study the structures and physical properties of 1-(4-cyanobenzyl)-3-methylimidazolium salts with five different anions. A comparison of the observed low-frequency Raman spectral patterns enabled us to predict the crystal symmetry of one of the synthesized salts for which single-crystal X-ray diffraction data were unobtainable. Real-time tracking of the low-frequency Raman spectral changes during melting revealed peak shifts indicative of different degrees of microscopic heterogeneity in the ionic liquids. The results show that our method provides a facile means that is complementary to X-ray crystallography, for obtaining structural information of ionic liquids.
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins
(2016-01-04)
Huang, Kai-Yao
;
Su, Min-Gang
;
Kao, Hui-Ju
;
Hsieh, Yun-Chung
;
Jhong, Jhih-Hua
Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource.
The corrosion protection study on inner surface from welding of aluminum alloy 7075-T6 hydrogen storage bottle
(2016-01-05)
Wu, Shinn -Dar
;
Cheng, Wei-Yang
;
Yang, Jason H. C.
;
Yang, Chien-Hua
;
Liao, Shao-Yen
This study investigated the resistance effect of Sodium-Silicate solution coated on the welding zone surface on stress corrosion cracking, which was caused by the penetration of storage hydrogen into micro cracks. This phenomenon occasionally occurred while welding the joint with gas tungsten arc welding (GTAW) between the bottle cover and body fabricated using aluminum alloy 7075 (Al-Zn-Mg). The coating effect of Sodium-Silicate was evaluated using four factors, namely, hardening agent, solidification method, coating thickness, and baking temperature. Taguchi analysis was applied to determine the optimal parameters, which were then used to effectively improve the corrosion resistance of the welding zone. The corrosion resistance of the group added with magnesium oxide as a hardening agent increased to 200% compared with the group added with Sodium-Silicate but without hardening agent. The penetration depth of the tested group added with talc as a hardening agent also increased to 20%. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.
Preparation of Cu2ZnSnS4 (CZTS) sputtering target and its application to the fabrication of CZTS thin-film solar cells
(2016-01-05)
Lin, Yu-Pin
;
Chi, Yi-Fang
;
Hsieh, Tsung-Eong
;
Chen, Yen-Chih
;
Huang, Kun-Ping
The CuS, ZnS and SnS2 raw powders were adopted as the starting materials for preparing the 2-inch Cu2ZnSnS4 (CZTS) sputtering target. The powders were mixed at various molar ratios of Cu:Zn:Sn:S = 1.6:1:1:4, 1.8:1:1:4 and 2:1:1:4, pressed into 6-mm pellet forms, and then sintered at different temperatures for 8 h. Accordingly, the influence of powder constitution and heat-treatment conditions on the microstructure, composition and morphology of CZTS pellets were investigated. Microstructure and composition analyses indicated that the sample prepared with the Cu molar ratio of 1.6 and sintered at 600 degrees C for 8 h forms the kesterite CZTS single-phase structure with the Cu-poor/Zn-rich composition. The 2-inch CZTS sputtering target was prepared by utilizing the method established by the study of 6-mm pellets and adopted for depositing the CZTS thin films. The CZTS layer deposited at the working pressure of 1 mtorr followed by the sulfurization at 570 degrees C for 1 h possessed the stoichiometry of Cu24.15Zn14.73Sn10.75S50.37 which is the closest to the ideal stoichiometric ratio of 2:1:1:4. Moreover, it exhibited the bandgap of 1.5 eV, p-type carrier concentration of 2.8 x 1017 cm(-3) and mobility of 8.61 cm(2) V-1 s(-1). Such a CZTS layer was implanted in the thin-film solar cells with the device structure of Mo/CZTS/CdS/i-ZnO/IZO/Al. Under the AM1.5 illumination condition, the CZTS thin-film solar cell sample with the open-circuit voltage of 0.52 V, the short-circuit current density of 19.17 mA/cm(2), the fill factor of 52.7% and the conversion efficiency of 5.2% was achieved. (C) 2015 Published by Elsevier B.V.
Smooth solutions of the one-dimensional compressible Euler equation with gravity
(2016-01-05)
Hsu, Cheng-Hsiung
;
Lin, Song-Sun
;
Yang, Chi-Ru
;
應用數學系
;
Department of Applied Mathematics
We study one-dimensional motions of polytropic gas governed by the compressible Euler equations. The problem on the half space under a constant gravity gives an equilibrium which has free boundary touching the vacuum and the linearized approximation at this equilibrium gives time periodic solutions. But it is difficult to justify the existence of long-time true solutions for which this time periodic solution is the first approximation. The situation is in contrast to the problem of free motions without gravity. The reason is that the usual iteration method for quasilinear hyperbolic problem cannot be used because of the loss of regularities which causes from the touch with the vacuum. Due to this reason, we try to find a family of solutions expanded by a small parameter and apply the Nash-Moser Theorem to justify this expansion. Note that the application of Nash-Moser Theorem is necessary for the sake of conquest of the trouble with loss of regularities, and the justification of the applicability requires a very delicate analysis of the problem. (C) 2015 Elsevier Inc. All rights reserved.
交大e-News第201期-120週年校慶系列─交大挾雙甲馳騁躍竹風
(2016-01-06)
國立交通大學秘書室
;
Secretariat
Higher serum betatrophin level in type 2 diabetes subjects is associated with urinary albumin excretion and renal function
(2016-01-07)
Chen, Chang-Chiang
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Susanto, Hendra
;
Chuang, Wen-Han
;
Liu, Ta-Yu
;
Wang, Chih-Hong
Background: Betatrophin is a newly identified liver-derived hormone that is associated with glucose homeostasis and lipid metabolism. Although dysregulated lipid metabolism results in diabetic nephropathy (DN) development in patients with type 2 diabetes mellitus (T2DM), it is not understood whether betatrophin is associated with urinary albumin excretion and renal function. Methods: Based on albumin/creatinine ratio (ACR), 109 T2DM patients were divided into normoalbuminuria (ACR < 30 mg/g), microalbuminuria (ACR between 30 and 300 mg/g), and macroalbuminuria (ACR > 300 mg/g). Serum betatrophin levels of 109 T2DM patients and 32 healthy subjects were determined by enzyme-linked immunosorbent assay (ELISA). Results: Serum level of betatrophin was significantly increased in T2DM patients with normoalbuminuria, microalbuminuria, and macroalbuminuria as compared with healthy subjects (P < 0.001). Serum betatrophin level was positively correlated with sex, duration of diabetes, systolic blood pressure (SBP), body mass index (BMI), ACR, and triglyceride, whereas it was inversely correlated with estimated glomerular filtration rate (eGFR), total cholesterol, and high-density lipoprotein cholesterol (HDL-C) (P < 0.001). Furthermore, multivariate regression analysis showed the betatrophin was significantly and positively independent with triglyceride and low-density lipoprotein cholesterol (LDL-C) (P < 0.05), whereas it was inversely independent with eGFR, total cholesterol, and low-density lipoprotein cholesterol (HDL-C) (P < 0.05). In addition, the betatrophin had higher odds of having DN [odds ratio (OR) = 5.65, 95 % confidence interval (CI) 2.17-14.57, P < 0.001]. Conclusion: Betatrophin is significantly increased in T2DM patients with different stages of albuminuria. Betatrophin may be a novel endocrine regulator involved in DN development.
Metal-free organic dyes for TiO2 and ZnO dye-sensitized solar cells
(2016-01-07)
Selopal, Gurpreet Singh
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Wu, Hui-Ping
;
Lu, Jianfeng
;
Chang, Yu-Cheng
;
Wang, Mingkui
We report the synthesis and characterization of new metal-free organic dyes (namely B18, BTD-R, and CPTD-R) which designed with D-p-A concept to extending the light absorption region by strong conjugation group of p-linker part and applied as light harvester in dye sensitized solar cells (DSSCs). We compared the photovoltaic performance of these dyes in two different photoanodes: a standard TiO2 mesoporous photoanode and a ZnO photoanode composed of hierarchically assembled nanostructures. The results demonstrated that B18 dye has better photovoltaic properties compared to other two dyes (BTD-R and CPTD-R) and each dye has higher current density (J(sc)) when applied to hierarchical ZnO nanocrystallites than the standard TiO2 mesoporous film. Transient photocurrent and photovoltage decay measurements (TCD/TVD) were applied to systematically study the charge transport and recombination kinetics in these devices, showing the electron life time (T-R) of B18 dye in ZnO and TiO2 based DSSCs is higher than CPTD-R and BTD-R based DSSCs, which is consistent with the photovoltaic performances. The conversion efficiency in ZnO based DSSCs can be further boosted by 35%, when a compact ZnO blocking layer (BL) is applied to inhibit electron back reaction.
Remarkably high mobility ultrathin-film metal-oxide transistor with strongly overlapped orbitals
(2016-01-08)
Shih, Chen Wei
;
Chin, Albert
;
Lu, Chun Fu
;
Su, Wei Fang
;
電子工程學系及電子研究所
High mobility channel thin-film-transistor (TFT) is crucial for both display and future generation integrated circuit. We report a new metal-oxide TFT that has an ultra-thin 4.5 nm SnO2 thickness for both active channel and source-drain regions, very high 147 cm(2)/Vs field-effect mobility, high I-ON/I-OFF of 2.3 x 10(7), small 110 mV/dec sub-threshold slope, and a low V-D of 2.5V for low power operation. This mobility is already better than chemical-vapor-deposition grown multi-layers MoS2 TFT. From first principle quantum-mechanical calculation, the high mobility TFT is due to strongly overlapped orbitals.
Demonstrating 1 nm-oxide-equivalent-thickness La2O3 and HfO2 multi-layer composite oxides on In0.53Ga0.47As MOS capacitor
(2016-01-08)
Wu, Wen-Hao
;
Lin, Yueh-Chin
;
Hou, Tzu-Ching
;
Lin, Tai-Wei
;
Hsu, Hisang-Hua
The use of a high k composite dielectric composed of La2O3 and HfO2 layers as the gate dielectric for In0.53Ga0.47As MOS application is proposed. Two multi-layer structures of La2O3 (1 nm)/HfO2 (1 nm) and La2O3 (0.5 nm)/HfO2 (0.5 nm) were deposited and annealed at 450 and 500 degrees C for device performance comparison. X-ray photoelectron spectroscopy, TEM and C-V measurements were used for the interface analysis between the oxide and the semiconductor. Finally, a 1 nm equivalent-oxide-thickness dielectric with small hysteresis of 88 mV and D-it of 1.9 x 10(12) cm(-2) eV(-1) was achieved for six layers of an La2O3 (0.5 nm)/HfO2 (0.5 nm) composite oxide structure on an In0.53Ga0.47As MOS capacitor with a post-deposition annealing temperature of 450 degrees C.
就讓影像訴說這個世代的日常吳平海紀錄片導演
(國立交通大學客家文化學院, 2016-01-09)
陳曦
;
黃瓊宇
擺設數台電腦與各式攝影機的工作室，書架上塞滿影像專業書籍，牆壁懸掛紀錄片獎狀、影展海報與白玫瑰社會關懷協會的感謝狀。南努客音像工作室紀錄片導演吳平海，曾以義工身分幫助協會拍攝影片，「我的態度是這樣，有錢沒錢是另外一件事，人家需要你，你就要幫忙服務。」
寫下人生的智慧莊華堂／作家
(國立交通大學客家文化學院, 2016-01-09)
石宓婕
;
陳柏州
興許是老舊社區的關係，都市的光亮沒有照進這裡，莊華堂的住家埋藏在一片幽暗之下。走入莊華堂工作室觸目所及是五花八門的書刊，從事小說創作、拍過紀錄片、玩過劇團，這些豐富的文化產業經驗讓莊華堂寫出了歷史族群系列小說，寫出了一個世代地域的故事。
不羈靈魂狂放當代劇場黎煥雄／劇場導演、作家
(國立交通大學客家文化學院, 2016-01-09)
徐煜婷
;
甯尚瑄
雖然誕生再上演著忠貞愛國戲碼的年代，但黎煥雄一站上劇場舞台就開始書寫對抗時代氛圍、追求自由、突破限制的故事；當台灣劇場遇上最狂放不羈的靈魂時，風起雲湧的小劇場狂潮就此展開。
為幸福留下創造永恆的形式喜恩／攝影師
(國立交通大學客家文化學院, 2016-01-09)
林俞君
;
廖珮羽
每一回按下快門，喜恩相信畫面不單純是呈現「美」而已，攝影為的是傳遞相片的內涵與價值。
以一世守護台灣史料魏德文／南天書局創辦
(國立交通大學客家文化學院, 2016-01-09)
許翔
;
陳志愷
南天書局自1976年成立，以出版學術書籍聞名，是台灣文史資料的典藏寶庫。魏德文是南天書局的創始人也是總經理，他的一生有大半時間都奉獻給書籍志業，為台灣出版許多經典書籍。
演一齣人生精采好戲朱陸豪／演員
(國立交通大學客家文化學院, 2016-01-09)
蔡瑋薇
;
史惠如
卸下傳統京劇的華麗服裝，朱陸豪以一身輕便的裝扮走在台北的巷弄街道，而那輕盈的步伐和如煦陽般的笑容，讓人不經意地受他的活力所感染，也無法相信那年輕的外貌下，蘊含的是超過一甲子的風霜歷練。