台灣留學生出席國際會議補助

2010年4月27日星期二

Electrical and Mechanical Properties of Conducting Polymer Blend PEDOT/PVA in Microelectronicmechanical Applications

論文發表人:陳常修 (加州大學爾灣分校材料系博士班)
 
 
高導電度高分子PEDOT:PSS跟強韌合成高分子PVA混合之微機電系統可以形成高結構性的材料,他們在生物微機電領域光電領域有高度的應用並可以增加其拉伸強度,耐用度及柔軟度,詳細的製程將會介紹,利用四點探針的方式可以測量交流電及直流電的特性,在機械強度方面,經由測量元件的共振強度及電容測量可以得知楊氏系數及拉伸強度,此混合性高分子的楊氏系數大約是1-5GPa,這些低楊氏系數的高分子可以將微機電或是其他相關元件微小化並增加其柔軟度,這是矽半導體所做不到的,另外高分子的壓阻特性也被發現,結合這些特殊的機械性質,如低楊氏系數及高應變規,再加上高導電度及柔軟度,將可以加強甚至取代現在應變規的材料多晶矽。

High conductivity polymer Poly(3,4-ethlenedioxythiophene)/poly(styrenesulfonate) (PEDOT:PSS) and strong synthetic polymer polyvinyl Alcohol (PVA) were mixed and prepared to the structure materials of microelectromechanical systems (MEMS). It has tremendous applications in BioMEMS areas and optical electronic fields and leads to increase tensile strength, durability and flexibility. Detailed process of fabrication technique will be presented. The AC and DC electrical properties of the thin films are studied using the four point probe method. For the mechanical properties, such as Young's Modulus and tensile strength of the thin films were measured by resonance frequency and capacitance measurement. Young's Modulus of polymer blends are about 1-5GPa. These lower than metals' Young's Modulus polymers can minimize the dimension of MEMS devices and other applications need flexible devices which silicon semiconductor couldn't perform. In addition, piezoresistive property has also been found in polymer blends of PEDOT/PVA. Combined with low Young's Modulus, high strain gauge factor materials are introduced. It also features high conductive and flexible properties and will extend the applications of the current popular strain gauge material polycrystalline silicon.

A Systolic Array for Linear MIMO Detection Based on an All-Swap Lattice Reduction Algorithm

論文發表人:王迺鈞/加州大學洛杉磯分校/電機系
 
 
多輸入輸出天線通訊系統(MIMO)可提供高速率傳輸以及提高抗雜訊能力,然而相對的在接收端的訊號偵測也有相當高的複雜度。對於有即時處理(real-time)需求的系統而言,無疑的需要相當高的硬體需求。本論文提出以脈動陣列為架構的晶格優化(lattice reduction)訊號偵測方法。在晶格優化訊號偵測法中,每當傳輸通道的特性改變,接收端就必須重新計算新的優化晶格。在高速行動通訊中,通道特性通常非常迅速的改變,因此接收端必須非常快速的計算優化晶格。而脈動陣列是一種簡易的平行處理架構,其特性在於使用多個簡易的運算元同時運作來提高輸出效率,因此在使用高運算能力的硬體下亦能提供高速的運算。本論文亦提出適合平行處理的晶格優化演算法,相較於過去文獻中常用的LLL晶格優化法,本論文的方法運用在脈動陣列上有相當優異的效能表現。
 
A systolic array to implement lattice-reduction-aided linear detection is proposed for a MIMO receiver. The lattice reduction algorithm and the ensuing linear detections are operated in the same array, which can be hardware-efficient. All-swap lattice reduction algorithm (ASLR) is considered for the systolic design. ASLR is a variant of the LLL algorithm, which processes all lattice basis vectors within one iteration. Lattice-reduction-aided linear detection based on ASLR and LLL algorithms have very similar bit-error-rate performance, while ASLR is more time efficient in the systolic array, especially for systems with a large number of antennas.

Investigation of Optical Absorption and Thermal Transport in Suspended Carbon Nanotube Bundles

論文發表人: 許易凱 (南加州大學材料所博士班)
 
 
在本實驗中, 我們結和拉曼光譜與架在奈米碳管兩側微米制程的電阻溫度探測器來測量奈米碳管對於雷射光加熱吸收的能力.  根據熱傳導的路徑, 碳管從雷射加熱點所吸收的熱會等於熱從加熱點到左右兩端的總量也會相等於電阻溫度探測器所偵測到的總熱能量. 實驗所用的碳管直徑從 7.1-8.2奈米, 長度從11.7-14.3微米而我們用單一波長532nm 雷射在碳管中間點加熱. 實驗結果顯示出 0.03%-0.44% 的雷射能量可以被碳管所吸收.  藉著測量加熱點與碳管兩側的溫度, 碳管的熱導系數也可以得到. 在此碳管在雷射加熱點的溫度則是由觀察拉曼光譜位移所得到. 
 
The optical absorption in suspended carbon nanotube (CNT) bundles is measured using Raman spectroscopy and two platinum resistance thermometers (PRTs), located at both ends of the suspended CNTs. The power absorbed from an incident focused laser is determined from the thermal power flowing through both ends of the CNT, detected by resistance changes in the PRTs. The results show 0.03 to 0.44% absorption of a focused 532nm laser with a 0.4 mm diameter spot size incident on CNT bundles with diameters and lengths varying from 7.1-8.2nm and 11.7-14.3 mm, respectively. The thermal conductance of the suspended CNT bundles can also be obtained by measuring the temperature difference between the incident laser spot and both ends of the suspended CNT. Here, temperatures in the center of the nanotube are extracted from the temperature-induced downshifts of the G band Raman mode.

Matrix Updates for Perceptron Training of Continuous Density Hidden Markov Models

論文發表人: 程芝潔 (加州大學聖地牙哥分校資訊科學系博士班)
 
http://www.cs.mcgill.ca/~icml2009/index.html
 
在這篇論文中,我們研究一種簡易快速,並以錯誤驅動的學習方法以應用於鑑別式(discriminative training)的連續空間馬可夫模型(continuous density hidden Markov models)的訓練。大部分使用於自動語音辨識(automatic speech recognition)的馬可夫模型皆使用高斯分佈(Gaussian emission densities)來模型化,通常使用的參數為平均數(mean)及協方差距陣(covariance matrix)。為了利用鑑別式方法來訓練馬可夫模型,我們重新參數化高斯分佈,以單一半正定矩陣(positive semidefinite matrix)涵括所有所需之參數。我們在內文中將闡述如何利用以錯誤驅動的方式更新參數矩陣,並達到最小化錯誤率的目的。我們也實驗了不同型式的更新所產生的效果,以及比較數種不同的矩陣分解、初始化及平均化對錯誤率的影響。我們實驗此訓練架構在自動語音辨識的資料庫上,且實驗結果顯示此錯誤驅動的學習方法可以顯著及快速地使語音辨識錯誤率下降。
 
In this paper, we investigate a simple, mistake-driven learning algorithm for discriminative training of continuous density hidden Markov models (CD-HMMs). Most CD-HMMs for automatic speech recognition use multivariate Gaussian emission densities (or mixtures thereof) parameterized in terms of their means and covariance matrices. For discriminative training of CD-HMMs, we reparameterize these Gaussian distributions in terms of positive semidefinite matrices that jointly encode their mean and covariance statistics. We show how to explore the resulting parameter space in CD-HMMs with perceptron-style updates that minimize the distance between Viterbi decodings and target transcriptions. We experiment with several forms of updates, systematically comparing the effects of different matrix factorizations, initializations, and averaging schemes on phone accuracies and convergence rates. We present experimental results for context-independent CD-HMMs trained in this way on the TIMIT speech corpus. Our results show that certain types of perceptron training yield consistently significant and rapid reductions in phone error rates.

2010年4月14日星期三

Generalized Triangular Transform Coding

論文發表人:翁竟智( 加州理工學院電機系博士班)

 

http://www.asilomarssc.org/

 

在這篇文章中我們運用了廣義三角矩陣分解提出了廣義三角編碼器. 這類編碼器包括了KLT以及PLT為特殊的例子. 在這一類編碼器中, 編碼增益可以被證明是最佳的. 而且我們可以提出更多新的編碼器, 符合不同的應用. 譬如果 BID編碼器以及GMD編碼器. GMD編碼器特別有一個好的特性, 就是他不需要位元分配就可達到最佳化的編碼增益.  這篇文章最大的貢獻是, 整合了所有已知的最佳化編碼器理論.

 

This paper introduces a new family of optimal transform coders (TC) based on the generalized triangular decomposition (GTD) developed by Jiang, et al. The new class contains the Karhunen-Loeve transform (KLT), and the prediction-based lower triangular transform (PLT) introduced by Phoong and Lin, as special cases. The coding gain of the entire family, with optimal bit allocation, is equal to that of the KLT (equivalently the PLT). Even though the original PLT was only applicable for blocked versions of scalar wide sense stationary (WSS) processes, the GTD based family includes members which are natural extensions of the PLT. These extensions enjoy the MINLAB structure of the PLT which has the unit noise-gain property. The paper also discusses special cases of the GTD-TC such as the GMD (geometric mean decomposition) and the BID (bidiagonal transform). A very important property shown here is that optimum bit allocation for GMD is a uniform allocation; the dynamic ranges of the coefficients to be quantized are therefore identical in this special case.

 

Evaluation of Tortuosity Models for Predicting Solute Diffusion in Unsaturated Soils

 

論文發表人;周心儀 (加州大學河濱分校環境科學研究所土壤與水資源科學組 博士班)

 

https://www.acsmeetings.org/

 

http://a-c-s.confex.com/crops/2009am/s1/papers/index.cgi?invited=&sessionid=6031&username=52240&password=166079

 

對於溶質在土壤中的傳輸,擴散(Diffusion)是一種重要的機制。溶質在土壤中的擴散率會比在純液相中的擴散率低;因其擴散是經由土壤孔隙中不連續分布的液體。在非飽和的土壤中,溶質擴散率會隨著土壤含水量降低而減少;因其造成溶質擴散傳輸路徑的增長和液體媒介斷面積的減少。Fick's擴散傳輸方程式便是描述溶質在非飽和土壤中的擴散率,而其中曲折係數 (tortuosity factor)便是用以量化溶質在土壤液相中之擴散率隨液體分布變化的情形。

直接測量溶質於土壤中的有效擴散係數(Effective diffusion coefficients)來求得曲折係數是耗時耗工的方法,所以曲折係數通常會藉由曲折係數模型來預估。這些模型可分為四類:(1)含水量為基礎,(2)含水量、孔隙度及總體密度為基礎,(3)含水量、總體密度和土壤水分特性曲線為基礎,及(4)概念化模型。本研究的目的為評估上列模型的預測度及應用性。

本研究使用離子交換試膜(ion exchange membrane) 方法測量溶質於砂土、黏土和砂質黏壤土之三種不同質地土壤中,不同含水量之下的有效擴散係數,進而求得曲折係數,並用以評估上列之曲折係數模型。

結果顯示第一類和第二類模型的可應用性相對地較低,因提高其預測度需要針對不同的土壤質地和不同的總體密度輸入不同的參數。而第三類模型有較高的預測度和可應用性,因為這類模型在輸入溶質於三種實驗土壤中的飽和有效擴散係數和其土壤水分特性曲線於對數座標上的斜率後,便可以提供較高準確度的預測。第四類模型對於曲折係數的預測度很低,但其比前三類模型更能夠描述曲折係數隨含水量變化的趨勢,可用以解釋溶質於非飽和土壤中的擴散動力機制。

Diffusion is an important mechanism of solute transport in porous media. It is often described by Fick's Law. In unsaturated porous media, the rate of solute diffusion decreases with decreasing soil water content due to the reduced cross-sectional area of the liquid phase and the more tortuous diffusive pathway. This reduction is accounted by the 'tortuosity' factor, the fraction of diffusion coefficients of solute in soil and liquid phase. Direct measurement of effective diffusion coefficient to obtain tortuosity is time and labor consuming, thus many models have been proposed to predict the tortuosity for unsaturated porous media. These models can be categorized into four groups: (1) water content based, (2) water content-porosity/bulk density based, (3) water content-bulk density-soil water characteristic based, and (4) conceptual models. In this study, effective diffusion coefficients of packed soil cores of a sand, a sandy clay loam, and a clay were measured to evaluate the aforementioned tortuosity models. Soil cores were equilibrating with 0.01M KBr solution to a range of desired water contents obtained by applying 1.53 x 105 cm-H2O to 10 cm-H2O matric potential. The effective diffusion coefficients of bromide were measured by ion exchange membrane method. Results show that the water content based and water content-porosity/bulk density based models have very limited prediction capability, as they require individual empirical constants to model soils in different textures and bulk densities. Water content-bulk density-soil water characteristic based models give better prediction if the measured effective diffusion coefficient at saturation and the soil water characteristic data are available. The conceptual models have limited prediction capability, but they serve to explain the dynamics of the diffusion process and can predict the trend of the effective diffusion coefficient change as water content changes.

Self and Knowledge: A Primary Investigation of Confucian Epistemic Subjectivity

論文發表人:陳寬鴻(夏威夷大學哲學系博士班)

  

http://ph.ourpower.com.tw/cubekm02/ezcatfiles/cust/download/attach/2/ISCP-program.pdf

 

http://ph.ourpower.com.tw/cubekm02/front/bin/cglist.phtml?Category=68

 

It is a common belief that there is no epistemology in the Confucian philosophical tradition. Even though it may be true that the Confucian wisdom has little to do with epistemology "proper"—that is, a theory of knowledge in general—it certainly does not entail that there are no distinct epistemic stances in Confucianism. In this project, I would like to construct the idea of epistemic subjectivity in Confucianism. Such a construction will inevitably call the premises of the conventional epistemology into question because the Confucian philosophical narratives provide a much different set of assumptions about the contents and practices of self and knowledge. In this project, the investigations of the problematic of the notion of epistemic subjectivity will be the continuous strand that penetrates these assumptions. Through the investigations, I shall revisit the issue of how knowledge is recognized in classical Confucianism with special attention on the Analects and the Xunzi. I would like to argue that knowledge in Confucian tradition is irreducibly social via articulating the following theses: that knowing how is prior to knowing that, that knowing a way is prior to knowing the truth and that knowing people is prior to knowing objects.

 

 

對於絕大多數的哲學家來說,儒家傳統並沒有所謂「知識論」的存在。儘管以西方嚴格意義的系統知識論為基準,儒學確實與其不甚相關;然而這並不表示儒學傳統中沒有自成一格的知識立場。

本文將重新建構儒學傳統中「知識主體性」的概念做深入分析。在建構的過程當中無可避免的將會對西方現代系統知識論的基本假設提出質疑,因為儒學傳統中對於知識的規範與認定是奠基於另一套迥然不同的預設之上。以「知識主體性」的概念為核心,筆者將側重於對《論語》和《荀子》兩部文獻的考察,論證儒學傳統中知識的社會性以及以下子題:(一)技能性知識較言說性知識重要;(二)「通道」概念比「真理」概念重要;(三)人際知識比物件知識重要

Kinetic control of negative feedback regulators of NF-kB/RelA determines their pathogen- and cytokine-receptor signaling specificity

論文發表人:史逢聖 (加州大學聖地牙哥分校 生化所博士班)

 

http://www.keystonesymposia.org/

 

細胞中的訊息傳遞網絡包含了許多參與負回饋機制的分子, 這些分子可能擁有重複的功能或者具有專一性。在 NF-kB 的傳遞單元裡 , 不僅 IkBa 參與負回饋機的反應,  新發現的抑制分子 IkBd 的蛋白質表現也受免疫反應激發因子而增加。為了檢驗 IkBd 在免疫反應訊息傳遞中的功能, 我門利用數學方程式模擬了包含四個 IkB 抑制分子的 NF-kB 傳導單元, 並且發展出以電腦程式分析基因表現型的方法。我們發現 IkBd 相同於 IkBa , 參與負回饋機制反應, 但兩者對於不同的免疫反應激發因子具有專一性。IkBd 減緩經由病原體接觸受器 (TLR) 所引起的持續反應 , 而具有快速反應特性的 IkBa , 其主要功能則為決定細胞激素引起 NF-kB 活性的時間曲線。除此之外 , 當活化 NF-kB 功能的細胞激素腫瘤壞死因子 (TNF) 從實驗鼠中被移除 , 過去因缺伐抑制分子 IkBa 導致過度免疫反應而致死的突變老鼠 , 在此實驗中可維持其生命力。最後 , 我們發現 IkBd 因具有較長的蛋白質降解週期 , 可統整細胞的免疫反應記憶 , 並減弱 NF-kB的反應。

 

Mammalian signaling networks contain an abundance of negative feedback regulators that may have overlapping ("fail-safe") or specific functions.  Within the NF-kB signaling module, IkBa is known as a negative feedback regulator, but the newly characterized inhibitor IkBd is also inducibly expressed in response to inflammatory stimuli.  To examine IkBd's roles in inflammatory signaling, we mathematically modeled the four-IkB-containing NF-kB signaling module and developed a computational phenotyping methodology of general applicability. We found that IkBd, like IkBa, can provide negative feedback, but each functions stimulus-specifically.  Whereas IkBd attenuates persistent, pathogen-triggered signals mediated by TLRs, the more prominent IkBa does not.  Instead, IkBa, which functions more rapidly, is primarily involved in determining the temporal profile of NF-kB signaling in response to cytokines that serve intercellular communication.  Indeed, when removing the inducing cytokine stimulus by compound deficiency of the tnf gene, we found that the lethality of ikba-/- mouse was rescued.  Finally, we found that IkBd provides signaling memory owing to its long half-life; it integrates the inflammatory history of the cell to dampen NF-kB responsiveness during sequential stimulation events.

Relationships between Psychosocial, Behavioral, and Familial Factors and Sleep Duration in Chinese Adolescents

論文發表人:許雅雯 (南加州大學預防醫學所博士班)

http://www.journalsleep.org/PDF/AbstractBook2009.pdf

大部分青少年睡眠研究以針對西方國家居多, 對華裔族群的了解甚少. 然而近期研究指出比起美國青少年, 華裔青少年有較多不良的睡眠習慣. 因此, 探討影響華裔青少年睡眠的因素的重要性相對提高. 本研究主旨為探討華裔青少年的睡眠時間與社會心理(憂鬱,一般壓力,學校壓力,生活品質),健康行為(運動,看電視及上網等久坐生活方式,飲食),及家庭因素(父母管教方式和父母監督程度)之關係. 本研究對象包含9023位華裔青少年 (平均年齡15, 53%女生, 平均睡眠8小時). 我們發現較高的運動量,較高的一般壓力和學校壓力和華裔青少年有較短的睡眠時間有關. 長期久坐, 常吃零食, 和父母監督越嚴格的華裔青少年有較長的睡眠. 此外, 身為女性, 體重過重, 較高年級,和已過青春期的的華裔青少年擁有較短的睡眠時間. 本研究結論為肥胖和不佳的心理健康(較高一般壓力和學校壓力)會導致華裔學生有較短睡眠時間. 然而本研究也發現高運動量和較短的久坐時間與較短睡眠時間有關. 可能的解釋為運動量較高的華裔青年, 他們相對感到擁有較多活力, 不易感到疲累. 因此和那些運動量低的華裔青少年相比, 運動量高的青少年不需要那麼久的睡眠時間就能獲得充分休息來維持基本生活運作.

Recent research suggests that Chinese youth have shorter sleep duration, later bedtime, and earlier wake time when compared to American youths. However, little is known about the correlates of sleep duration in Chinese adolescents. Therefore, it is important to identify potential determinants for sleep duration in Chinese adolescents.

To investigate the associations between psychosocial (depression, perceived stress, school stress, and quality of life), behavioral (physical activity, sedentary behavior, and diet intake), familial (parenting style and parental monitoring), and demographic factors (school grade, gender, puberty status, weekly allowance, parental education, parental income, and self-perceived health status) with sleep duration among Chinese adolescents. This study includes complete baseline data from a longitudinal smoking prevention and health promotion study conducted in 7 cities in China (N=9023, 52.71% girls, mean age 15, mean sleep duration 7.97 hours). Higher frequency of participation in vigorous physical activity, higher levels of perceived stress, and school stress were related to shorter sleep duration. Time spent on sedentary behavior, frequency of snack intake, and parental monitoring were positively associated with sleep duration. Adolescents who were overweight, female, in higher school grade, and in post-puberty status reported shorter sleep duration. Overweight status and poor mental health (higher level of perceived stress/school stress) were associated with shorter sleep duration. Greater participation in vigorous physical activity and less time in sedentary behavior were related to shorter sleep duration. Perhaps, youths who engage in vigorous physical activity more frequently generally might feel more energetic and they thus might not need as much as sleep as physically inactive youth need in order to maintain normal daily function. Future longitudinal studies are needed to clarify theses associations in Chinese youths.

Harmonic Holographic Microscopy Using Nanoparticles as Probes for Three-Dimensional Cell Imaging

論文發表人:謝佳龍 (加州理工學院電機系博士班)

 

CLEO 2009 Conference Link: http://www.cleoconference.org/

 

OpticsInfoBase Link: http://www.opticsinfobase.org/abstract.cfm?uri=CLEO-2009-CFA6

 

本篇論文報導使用鈦氧化鋇奈米粒子作為三度空間影像標記。鈦氧化鋇奈米粒子具有很高的二倍頻轉換效率,因此在細胞影像中能產生很好的對比。利用奈米粒子產生的二倍頻作為影像訊號有幾個特點:二倍頻訊號非常穩定,不會受限於光漂白,且能自由的選擇激發波長。另外,利用二倍頻的同調性質,奈米粒子所產生的二倍頻光波可以用干涉技術(例如本篇論文中使用全像術)來記錄量測。利用全像數來量測這些奈米粒子的好處是,二倍頻光波的振幅和相位可同時被紀錄,因此利用數位還原技術,三度空間的奈米粒子分佈可以從一張二維影像中被完全解析,此技術不須掃描,所以三度空間記錄的速度不受限於機械掃描。本篇論文報導了在細胞中分佈的奈米粒子可以成功的利用倍頻全像顯微術來量測。

 

We demonstrate the three-dimensional imaging capability of harmonic holographic microscopy by using the second harmonic generation from BaTiO3 nanoparticles as the signal. Three-dimensional distributions of the BaTiO3 nanoparticles in biological cells are recorded without scanning.

2010年1月5日星期二

Integration of Tunable Capacitors and Bonded-Wires for Contactless RF Switch and Tunable Filter

論文發表人:陳世叡 (南加州大學電機所博士班)

 

http://www.transducers09.org/

 

本文提出由表面微機電加工可調式電容及黏合線所組成的非接觸式微機電射頻開關。這個微機電射頻開關在2.4GHz的窄頻範圍可以達到10dB的能量隔離及41的電容變化。採用黏合線的方法可以大幅的減少可調式電容中移動平板的變形需求。更可以進一步允許氧化鋅壓電薄膜被用於改變電容的空氣間隙。如此形成一個非接觸式微機電射頻開關。

 

This paper describes a contactless RF MEMS switch, composed of two surface-micromachined tunable capacitors and two bonded-wire inductors, which can achieve a power isolation ratio of 10 dB with a capacitance variation of mere 4:1 over a narrow bandwidth near 2.4 GHz.  This novel approach of using inductors eases the deflection requirement for the deformable bridge for the variable capacitor, and allows piezoelectric ZnO film to be used to deflect the capacitor bridge to vary the air gap, thus yielding a contactless RF switch.

 

A 2.89mW 50GOPS 16x16 16-Core MIMO Sphere Decoder in 90nm CMOS

論文發表人:  楊家驤 (加州大學洛杉磯分校電機所博士班)

 

http://www.esscirc2009.org/

 

在這篇論文中,我們以90奈米製程實作了一顆具有16核心適用於多重輸入多重輸出通道的球狀解碼器。這顆球狀解碼器晶片擁有高度彈性,能支援多種格規格:從2x2天線陣列到8x8天線陣列,BPSK64-QAM的調變方式,並且支援16-128載波。操作在16MHz的工作頻率、16x16天線陣列、64QAM模式時,它能提供高達50GOPS的運算量。操作於321mV電壓時,其功率消耗僅2.89mW,產生高達17.3GOPS/mW的功率效率。而操作在256MHz頻率時,使用16MHz的頻率通道,它的最高資料輸出為1.5Gbps

 

A 16-core multi-input multi-output (MIMO) decoder for agile communication systems is implemented in a low-VT 90nm CMOS technology. This chip implements the sphere decoding algorithm and is highly flexible to support multiple configurations: antenna arrays from 2×2 to 16×16, modulations from BPSK to 64QAM, and up to 128 data streams. Operating at 16MHz, the chip provides 50GOPS (12-bit add equivalent) in the 16×16, 64QAM mode. It consumes 2.89mW of power with a 321mV supply voltage, resulting in a power efficiency of 17.3GOPS/mW. At 256MHz, the peak data rate exceeds 1.5Gbps over a 16MHz channel.

 

A Software Tool to Process HIV Ultra-deep Sequencing Nucleotide Data

論文發表人: 羅健記 (新墨西哥大學 電腦科學所 碩士班)

 

http://cnls.lanl.gov/q-bio/index.html

 

454生命科學公司所開發的焦磷酸測序技術是一種超高通量的DNA測序方式,其所產生大量的序列資訊內容可被用於不同的基因組研究。然而如此大量的數據是需要一個適當的處理方式,才能做後續的分析使用。因此,我們開發出一個工具來處理這樣的數據內容,使用者輸入超深度測序序列和參考序列的FASTA檔案,程式將會輸出精簡、壓縮,具有排序統計量和根據密碼子排列好的序列。此工具已成功地應用於最近的一份研究報告並投稿於PLoS One期刊(PLoS ONE 4(5): e5683),該研究報告揭示HIV 1病毒的動態基因序列及可能造成藥物治療失敗的可能機轉。

 

Massive sequence reads generated by 454 Life Sciences pyrosequencing technology enable a variety of applications on genome research. A method for processing the huge amount of datasets for subsequent analysis is necessary. We have developed a software tool for this purpose. Given input with ultra-deep sequencing sequences and a reference sequence in FASTA format, the program will output with compressed, identity-tallied and codon-aligned sequence alignment. This tool has been successfully applied on a recent study to reveal dynamic HIV-1 escape and large population shifts during drug treatment.

2009年12月30日星期三

Imperial Terrains: Decolonization, Nationalisms and Diasporic Interventions in Diaoyutai Movement

王穎(加州大學聖地牙哥校區文學系)

 

http://www.cultural-typhoon.org/

 

透過重訪1969-72年席捲北美台灣留學生與台灣本島學生的保釣運動,本論文試圖論證兩點:其一,美國在冷戰時期對東亞無孔不入的干預,迄今猶有諸多空白等待結構性與歷史性的釐清;其二,戰後台灣在戒嚴前後由官方授意的國族史論述,實際上在對立與互補之間產生了許多問題,需要嚴肅細心地面對。本文藉由閱讀整理太平洋兩岸台灣學生保釣運動當時與事後的出版品、文學創作、自傳與回憶錄、座談發言等文獻,比較了北美和台灣兩地運動在背景和策略上的分歧,而正是在此一脈絡下,本文分析美國在冷戰時期所扮演的多重角色(尤其是帝國霸權的角色),如何顯著影響了太平洋兩岸與海峽兩岸對於「中國」的形塑與表述。進一步,本文指出,當今史論對於二戰之後渡海移植的中華民國與中共所建的中華人民共和國,或者對論戒嚴前與後的台灣,往往襲用既成二元框架,失之粗糙簡化,其中許多癥結顯見於當今台灣對於釣運同時並存的無感失憶與片面追憶之中。對此,如何有效介入權力與知識的循環使力,顯然是知識分子沈重而久遠的責任。

 

With the case of a phenomenal but ephemeral student movement that mobilized thousands of Taiwanese student in the US and at home to come to defense of Diaoyutai Islands from 1969 to 1972, this paper takes questions of the un(der)recognized powerful American presence in  Cold War East Asia and of interlocking problems constituted by state-endorsed national histories dominating postwar Taiwan. Revisiting how and why the movement erupted in 1969 across several cities and college towns in the US, and comparing differences of agenda and tactics between the transpacific interventions, the paper argues the multiple roles played America have significant impacts on varied formations of "China" across both the Pacific and Taiwan Strait. In reflections of the man-made bifurcations imposed on Chiang Kai-shek's transplanted Republic of China and Chinese Communist Party's establishment of People's Republic of China, Taiwan during and after Martial Law Period (1949-87), the presently coexisting oblivion to as well as partisan remembrance of Diaoyutai movement suggest many efforts are yet to be taken for coping with problems caused by the circular reinforcement of power and knowledge.

 

Vascular Fluid-Structure Interaction: Methodology and Application to Cerebral Aneurysms

論文發表人: 徐銘辰 (加州大學聖地牙哥分校結構力學所博士班)

http://usnccm-10.eng.ohio-state.edu/

近年來隨著影像擷取、模型製作、網格產生、計算方法以及視覺化技術的進步,針對特定病患之血流計算模擬也步入成熟階段。當今學界最先進之血管流計算研究為利用對大範圍人體心血管系統之流固耦合模擬,探索心血管疾病肇因進程與血液動力學之聯繫,預測外力介入之結果,並評估電子輔助醫療器具之影響。以上例子包含腹部及腦部之腫瘤模擬,及血管內硬化斑塊之形成與破裂。

本論文針對特定病患中大腦動脈分枝腫瘤進行計算模擬探討。我們提出一流體與固體結構完全耦合之模擬方法,並呈現支持此分析之網格生成技術。此流固耦合計算架構可預測實驗所無法獲得之血液動力數據並進行評估。我們並將其與純流體計算結果做比較,以分析於心血管計算模擬中考慮管壁彈性之重要性。

結果顯示血液與血管壁之交互作用改變了血液動力對管壁之施力。當心臟收縮血液流進腫瘤並衝撞管壁時,考慮管壁彈性將降低腫瘤內壁面剪應力並改變其分布。此結果彰顯了於針對病患之腦腫瘤計算模擬中,流固耦合之重要性。
In recent years patient-specific modeling of blood flow has matured immensely with the emergence of better imaging, modeling, mesh generation, computation and visualization technologies.
State-of-the-art vascular modelings involve fully coupled fluid-structure simulations of large portions of the human cardiovascular system, in an effort to investigate hemodynamic factors influencing the onset and progression of cardiovascular disease, to predict an outcome of an intervention, or to evaluate the effects of electromechanical assist devices. Examples of the first include
abdominal and cerebral aneurysms and formation and rupture of vulnerable plaque.

This work focuses on computation of several patient-specific aneurysm models at the middle cerebral artery (MCA) bifurcation. A fully coupled simulation approach is reviewed and main aspects of mesh generation in support of the fluid-structure analysis are presented.  Quantities of hemodynamic interest, that are unattainable in  experiments, are studied to assess the relevance of fluid-structure  interaction (FSI) modeling as compared to rigid-arterial-wall simulations.

The results show that the interaction between the blood flow and wall deformation changes the hemodynamic forces acting on the arterial wall. When the blood flows straight into the aneurysm and impinges the wall during the systole, the maximum wall shear stress (WSS) at the dome decreases while the effect of the flexible wall is incorporated in the computation. The resulting WSS patterns are altered both qualitatively and quantitatively. Rigid versus flexible wall simulation results reinforce the importance of FSI in the patient-specific modeling of cerebral aneurysms.