Browsing by Issue Date, starting with "2015-12-09"

Now showing 1 - 20 of 20145

Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes
(2015-12-09)
Srinivasulu, Yerukala Sathipati
;
Wang, Jyun-Rong
;
Hsu, Kai-Ti
;
Tsai, Ming-Ju
;
Charoenkwan, Phasit
Background: Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been developed for predicting the binding affinity of protein-protein complexes based on structure and functional information. This work aims to predict the binding affinity of heterodimeric protein complexes from sequences only. Results: This work proposes a support vector machine (SVM) based binding affinity classifier, called SVM-BAC, to classify heterodimeric protein complexes based on the prediction of their binding affinity. SVM-BAC identified 14 of 580 sequence descriptors (physicochemical, energetic and conformational properties of the 20 amino acids) to classify 216 heterodimeric protein complexes into low and high binding affinity. SVM-BAC yielded the training accuracy, sensitivity, specificity, AUC and test accuracy of 85.80%, 0.89, 0.83, 0.86 and 83.33%, respectively, better than existing machine learning algorithms. The 14 features and support vector regression were further used to estimate the binding affinities (Pkd) of 200 heterodimeric protein complexes. Prediction performance of a Jackknife test was the correlation coefficient of 0.34 and mean absolute error of 1.4. We further analyze three informative physicochemical properties according to their contribution to prediction performance. Results reveal that the following properties are effective in predicting the binding affinity of heterodimeric protein complexes: apparent partition energy based on buried molar fractions, relations between chemical structure and biological activity in principal component analysis IV, and normalized frequency of beta turn. Conclusions: The proposed sequence-based prediction method SVM-BAC uses an optimal feature selection method to identify 14 informative features to classify and predict binding affinity of heterodimeric protein complexes. The characterization analysis revealed that the average numbers of beta turns and hydrogen bonds at protein-protein interfaces in high binding affinity complexes are more than those in low binding affinity complexes.
Enhanced Magnetocaloric Effect Driven by Interfacial Magnetic Coupling in Self-Assembled Mn3O4-La0.7Sr0.3MnO3 Nanocomposites
(2015-12-09)
Vandrangi, Suresh K.
;
Yang, Jan-Chi
;
Zhu, Yuan-Min
;
Chin, Yi-Ying
;
Lin, Hong-Ji
Magnetic refrigeration, resulting from the magneto caloric effect of a material around the magnetic phase-transition temperature, is a topic of great interest as it is considered to be an alternate energy solution to conventional vapor-compression refrigeration. The viability of a magnetic refrigeration system for magnetic cooling can be tested by exploiting materials in various forms, from bulk to nanostrucutres. In this study, magnetocaloric properties of self-assembled Mn3O4-La0.7Sr0.3MnO3 nanocomposites, with varying doping concentrations of Mn3O4 in the form of nanocrystals embedded in the La0.7Sr0.3MnO3 matrix, are investigated. The temperatures corresponding to the paramagnetic-to-ferromagnetic transitions are higher, and the values of change in magnetic entropy under a magnetic field of 2 T show an enhancement (highest being similar to 130%) for the nanocomposites with low doping concentrations of Mn3O4, compared to that of pure La0.7Sr0.3MnO3 thin films. Relative cooling power remain close to those of La0.7Sr0.3MnO3. The enhanced magnetic phase-transition temperature and magnetocaloric effect are interpreted and evidenced in the framework of interfacial coupling between Mn3O4 and La0.7Sr0.3MnO3. This work demonstrates the potentiality of self-assembled nanostructures for magnetic cooling near room temperature under low magnetic fields.
Acid/Base and H2PO4- Controllable High-Contrast Optical Molecular Switches with a Novel BODIPY Functionalized [2]Rotaxane
(2015-12-09)
Arumugaperumal, Reguram
;
Srinivasadesikan, Venkatesan
;
Raju, Mandapati V. Ramakrishnam
;
Lin, Ming-Chang
;
Shukla, Tarun
A novel multifunctional mechanically interlocked switchable [2]rotaxane R4 containing two molecular stations and rotaxane arms terminated with boron-dipyrromethene (BODIPY) fluorophores and its derivatives were synthesized for the first time by CuAAC click reaction. The shuttling motion of macrocyde between the dibenzylammonium and triazolium recognition sites and the distance dependent photoinduced electron transfer process of R4 is demonstrated by utilizing external chemical stimuli (acid/base). Interestingly, the reversible self-assembly process of R4 was recognized by the acid-base molecular switch strategy. Notably, two symmetrical triazolium groups acted as molecular stations, H2PO4- receptors, and H-bonded donors. Both [2]rotaxane R4 and thread R2 demonstrated excellent optical responses and high selectivity toward H2PO4- ion. The specific motion and guest-host interactions of mechanically interlocked machines (MIMs) were also further explored by quantum mechanical calculations. The thread R2 also demonstrated to enable the detection of H2PO4- in RAW 264.7 cells successfully.
SCMMTP: identifying and characterizing membrane transport proteins using propensity scores of dipeptides
(2015-12-09)
Liou, Yi-Fan
;
Vasylenko, Tamara
;
Yeh, Chia-Lun
;
Lin, Wei-Chun
;
Chiu, Shih-Hsiang
Background: Identifying putative membrane transport proteins (MTPs) and understanding the transport mechanisms involved remain important challenges for the advancement of structural and functional genomics. However, the transporter characters are mainly acquired from MTP crystal structures which are hard to crystalize. Therefore, it is desirable to develop bioinformatics tools for the effective large-scale analysis of available sequences to identify novel transporters and characterize such transporters. Results: This work proposes a novel method (SCMMTP) based on the scoring card method (SCM) using dipeptide composition to identify and characterize MTPs from an existing dataset containing 900 MTPs and 660 non-MTPs which are separated into a training dataset consisting 1,380 proteins and an independent dataset consisting 180 proteins. The SCMMTP produced estimating propensity scores for amino acids and dipeptides as MTPs. The SCMMTP training and test accuracy levels respectively reached 83.81% and 76.11%. The test accuracy of support vector machine (SVM) using a complicated classification method with a low possibility for biological interpretation and position-specific substitution matrix (PSSM) as a protein feature is 80.56%, thus SCMMTP is comparable to SVM-PSSM. To identify MTPs, SCMMTP is applied to three datasets including: 1) human transmembrane proteins, 2) a photosynthetic protein dataset, and 3) a human protein database. MTPs showing a-helix rich structure is agreed with previous studies. The MTPs used residues with low hydration energy. It is hypothesized that, after filtering substrates, the hydrated water molecules need to be released from the pore regions. Conclusions: SCMMTP yields estimating propensity scores for amino acids and dipeptides as MTPs, which can be used to identify novel MTPs and characterize transport mechanisms for use in further experiments. Availability: http://iclab.life.nctu.edu.tw/iclab_webtools/SCMMTP/
Low-power CMOS voltage-controlled oscillator with voltage-controlled inductor for V-band wireless personal area network communication systems
(2015-12-10)
Huang, Zhe-Yang
;
Chen, Chun-Chieh
;
Hung, Chung-Chih
;
電機資訊學士班
;
電子工程學系及電子研究所
A low-power voltage-controlled oscillator (VCO) with voltage-controlled inductor for V-band wireless personal area network communication systems is presented in this study. The proposed VCO with a voltage-controlled inductor provides a centre frequency of 45.62 GHz and was implemented in a 90 nm RF-CMOS process. A tuning range of 1.28 GHz (44.98-46.26 GHz) with maximum control voltage of 1.0 V can be achieved. The phase noise is -92.8 dBc/Hz at 1 MHz offset frequency. The VCO core consumes 5.8 mW through a 1.0 V supply voltage and the active area is 0.13 mm(2). The calculated figure-of-merit is -178.3.
頑童鬧冬　歡慶聖誕
(2015-12-13)
蕭泳
;
黃美恩
;
Department of Communication and Technology
;
傳播與科技學系
又到了一年一度的聖誕節，板橋車站站前廣場的頑童鬧冬遊樂園成為度過假期的好去處。
未完的旅途
(2015-12-13)
黃吏玄
;
Department of Communication and Technology
;
傳播與科技學系
環島之旅未完待續，正如人生一樣，未完待續。
未完的旅途
(2015-12-13)
黃吏玄
;
Department of Communication and Technology
;
傳播與科技學系
環島之旅未完待續，正如人生一樣，未完待續。
流浪在城市的孤兒
(2015-12-13)
許凱智
;
Department of Communication and Technology
;
傳播與科技學系
被棄養的狗無家可歸，這群人幫助他們，為他們尋找一個新的家園。
歷史看人性　不一樣的勵志
(2015-12-13)
梅瑞庭
;
Department of Communication and Technology
;
傳播與科技學系
補教業歷史老師，以幽默生動的歷史故事，教大家成為成功的「魯蛇」。
同志　難以通過的家庭學分
(2015-12-13)
胡浣莊
;
Department of Communication and Technology
;
傳播與科技學系
身為同志，秘密與孤獨如影隨形，而我從來都是獨自面對。
頑童鬧冬　歡慶聖誕
(2015-12-13)
蕭泳
;
黃美恩
;
Department of Communication and Technology
;
傳播與科技學系
又到了一年一度的聖誕節，板橋車站站前廣場的頑童鬧冬遊樂園成為度過假期的好去處。
非典型就業　勞工「薪」酸
(2015-12-13)
修瑞韓
;
Department of Communication and Technology
;
傳播與科技學系
非典型就業成為時代趨勢，勞工的權益與保障成為關注的議題。
萬能青年旅店　傳唱社會
(2015-12-13)
馮鈞鈺
;
Department of Communication and Technology
;
傳播與科技學系
來自中國石家庄的萬能青年旅店，透過歌曲傳唱社會百態。
十二嵐　朝著夢想的獸繪師
(2015-12-13)
王鈞鋒
;
Department of Communication and Technology
;
傳播與科技學系
一名喜歡動物與繪畫，朝著自己夢想中走著的獸繪師。
搖滾鮮師飆熱血　吶喊正義
(2015-12-13)
麻愷晅
;
Department of Communication and Technology
;
傳播與科技學系
熱血的高中英文老師，不僅是一位搖滾樂手，也積極參與社會運動，高唱他的反骨精神。
脫離不了動物的家庭
(2015-12-13)
羅宛君
;
Department of Communication and Technology
;
傳播與科技學系
我家的狗羊鵝雞鴨，我的爸媽，與我。
流浪在城市的孤兒
(2015-12-13)
許凱智
;
Department of Communication and Technology
;
傳播與科技學系
被棄養的狗無家可歸，這群人幫助他們，為他們尋找一個新的家園。
淩式音樂　王者之聲
(2015-12-13)
林儒均
;
Department of Communication and Technology
;
傳播與科技學系
擔任睡帽樂團的主唱，白淩憑藉著無所畏懼的信心，唱出自己的王者之聲。
高教大考驗　一〇五大限
(2015-12-13)
呂安文
;
Department of Communication and Technology
;
傳播與科技學系
高教一〇五大限即將來臨，教育部及校方人士該如何面對少子化對教育帶來的影響。