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Doctoral thesis recital (piano) chamber
No full textPiano trio in C minor, op. 1 no. 3 / Ludwig van Beethoven -- Piano trio no. 2 in E minor, op. 67 / Dmitri Shostakovich. (Grace Youn, violin ; Cory Blais, cello ; Shih-Ting Wu, piano).Musi
Pr oton MR Spectr oscopy of the Femor al Head - Evaluation of Patients at Risk for Avascular Necr osis
No full textTo measure the lipid / water ratio of the femoral head from normal individuals
and also, the non-diseased femoral head from patients with contralateral avascular
necrosis (AVN) using proton magnetic resonance spectroscopy (MRS). Twenty-four
femoral heads from 12 normal subjects and 15 non-diseased femoral heads from
patients with contralateral AVN were included. Marrow composition was measured
by using single-voxel stimulated-echo acquisition method (STEAM) (TR/TE =
5000/20 msec) with a voxel placed in the femoral head. The area under each
resonance for lipid and water was calculated.
The area of lipid (L) to area of water (W) ratio (L/W ratio) of the femoral head
was significantly different between the patients with AVN on the contralateral side
and normal individuals (P = 0.0048), this ratio revealing a greater value for those at
risk of AVN. This detected difference appears to precede any other morphological
change associated with AVN, such an increase in L/W ratio possibly suggesting the
pathogenic route for AVN
Correlation of MR Lumbar Spine Bone Marrow Perfusion with Bone Mineral Density in Female Subjects
No full textPURPOSE: To prospectively assess lumbar spine bone marrow perfusion at dynamic
magnetic resonance (MR) imaging and correlate perfusion with bone mineral
density (BMD) in female subjects.
MATERIALS AND METHODS: BMD measurement and dynamic MR imaging of
the lumbar spine were performed in 69 female subjects (mean age standard
deviation, 57 years 11). Subjects were stratified into premenopausal (n 19) and
postmenopausal (n 50) groups, with the latter group including both women who
were (n 13) and women who were not (n 37) receiving hormone replacement
therapy. BMD (in grams per square centimeter) was measured with dual energy
absorptiometry in the lumbar spine. Peak enhancement ratio, measured with time–
signal intensity curves calculated from dynamic MR image data, represented bone
marrow perfusion. Peak enhancement ratio was compared with age and BMD by
using linear regression analysis and Pearson correlation.
RESULTS: A significant positive correlation was found for BMD with peak enhancement
ratio of lumbar vertebrae among all subjects (n 69, r 0.63, P .001), all
postmenopausal women (n 50, r 0.50, P .001), and postmenopausal women
without hormone replacement therapy (n 37, r 0.61, P .001). However, the
correlation between BMD and peak enhancement ratio was not significant (P .05)
in premenopausal women (n 19) or postmenopausal women receiving hormone
therapy (n 13). Both BMD and peak enhancement ratio were inversely correlated
with age (P .001, Pearson correlation). Pearson partial correlation coefficient for
peak enhancement ratio and mean in all subjects, with control for inverse correlation
with age, was significant (r 0.63, P .001).
CONCLUSION: Significant correlation was found between the peak enhancement
ratio of vertebral bone marrow and BMD in postmenopausal female subjects. This
result may suggest a vascular component in the pathogenesis of osteoporosis
Transcriptional and translational analysis of shrimp white spot syndrome virus structural protein gene wssv396
No full text由蝦類白點症病毒 (white spot syndrome virus, WSSV) 引起之白點症為目前嚴重威脅全世界養蝦產業之病毒性疾病。基於白點症病毒蛋白質體學及基因體序列分析之研究，在其532個預測之開放譯讀區中，有部分功能已知之非結構性蛋白質及結構性蛋白質基因，在其轉譯終點前後不具有聚腺嘌呤訊號 (AATAAA)，推測可能與其下游之開放譯讀區共用加聚腺嘌呤位置 (poly A addition site) 有關。白點症病毒結構性蛋白質基因wssv396、wssv395及wssv394為同向轉錄基因群 (cluster)，三者之加聚腺嘌呤位置皆位於wssv394基因下游之聚腺嘌呤訊號後第17個核苷酸處，符合真核細胞聚腺嘌呤訊號規則。根據北方雜合法分析結果，此基因群利用wssv396之5’端啟動子 (promoter) 轉錄出包含wssv396、wssv395及wssv394之三基因mRNA (3.4 kb)；wssv394基因之riboprobe尚可偵測到利用其5’端啟動子轉錄之單基因mRNA (1.6 kb)。實驗結果證明wssv396及wssv394基因主要利用帽依賴型轉譯作用 (cap-dependent translation) 合成蛋白質，而位於第二個基因之wssv395係以非帽依賴型轉譯作用即內部核醣體進入位置 (Internal Ribosome Entry Site, IRES)合成蛋白質，推測IRES序列可能位於wssv396基因轉錄區內 (coding region)，關於其確切位置猶待進一步之實驗分析以確認之。WSSV396, WSSV395 and WSSV394 are identified in pervious research as the three of thirty-nine structural proteins of shrimp white spot syndrome virus (WSSV). This study focuses on the transcriptional and translational analysis of wssv396, wssv395 and wssv394. The 3’RACE results reveal that wssv396, wssv395, and wssv394 share the same polyA tail. A common ~3.4-kb transcript, which is consistent with the predicted size of a polycistronic transcript encoding these three genes, was detected by using gene-specific probes respectively in northern blot analysis. Two primer sets were designed to generate two overlapping RT-PCR products to confirm the existence of the ~3.4-kb transcript, and the sequence data also indicated that the ~3.4-kb transcript is entire and intron-less. It reveals that wssv396, wssv395 and wssv394 are transcribed from the same promoter of wssv396. In the northern blot analysis, another ~1.6-kb transcript was recognized by wssv394-specific probe. According to the in vitro transcription and translation data, it could be concluded that WSSV396 and WSSV394 are translated from the ~3.4-kb and ~1.6-kb transcript by cap-dependent translation mechanism; the wssv395 is translated from the ~3.4-kb transcript by cap-independent translational mechanism. Based on the in vitro transcription and translation analysis of bicistronic constructs encoding wssv396 and wssv395, it suggests that the translational mechanism of wssv395 from the polycistronic transcript might occur by a mechanism using the internal ribosome entry site (IRES) on the upstream of the wssv396 ORF.前言...............................................1
材料與方法................................................................................................................14
1. 白點症病毒液之製備及人工注射感染試驗..................................................14
2. 純化及製備白點症病毒顆粒..........................................................................15
3. 蝦體組織全蛋白之萃取..................................................................................16
4. 檢體RNA之萃取...........................................................................................16
5. 反轉錄酶-聚合酶鏈反應................................................................................16
6. 快速增殖cDNA末端.....................................................................................18
7. 北方轉印雜合法..............................................................................................20
8. 大腸桿菌基因表現..........................................................................................24
9. 大腸桿菌之轉型作用......................................................................................26
10. 西方轉印法......................................................................................................26
11. 以RT-PCR分析wssv396/wssv395/wssv394三基因mRNA.........................27
12. 構築wssv396/wssv395/wssv394三基因質體.................................................28
13. 構築wssv396/wssv395雙基因質體................................................................29
14. 試管內轉錄和轉譯反應..................................................................................31
結果............................................................................................................................33
1. 白點症病毒基因wssv396.................................................................................33
2. 白點症病毒wssv396基因轉錄表現................................................................34
3. 結構性蛋白質WSSV396於白點症病毒顆粒上之位置................................34
4. 結構性蛋白質WSSV396轉譯時序點之分析.................................................35
5. 白點症病毒wssv396基因5’端起始點及wssv396、wssv395基因3’端加聚腺
嘌呤位置分析.........................................................................................................36
6. 白點症病毒wssv396基因轉錄本分析............................................................36
7. 白點症病毒wssv395基因轉錄本分析............................................................37
8.白點症病毒wssv394基因轉錄本分析..............................................................37
9. 分析wssv396/wssv395/wssv394三基因mRNA之剪接作用........................38
10. 探討wssv396、wssv395及wssv394基因轉錄及轉譯作用之相關性........38
討論.............................................................................................................................42
結論.............................................................................................................................51
未來研究方向.............................................................................................................52
參考文獻........................................................................ ............................................53
圖表及附錄.................................................................................................................6
A Study on the Multivariate Permutation Test to Detect the Minimal Fold Changes of Gene Expression Levels
No full text傳統的假設檢定法利用檢定兩組樣本差異是否等於零來鑑定基因是否有顯著表現，但卻沒有考慮到具有生物意義的倍數變化量，然而在生物領域中基因表現的倍數變化超過某些定值即認定該基因是有表現的。相較於傳統的假設檢定法，2006年由戴家彥碩士論文提出一個區間假設的雙單尾檢定法，此方法不僅能考慮到生物意義亦能更準確地鑑別出有顯著表現的基因。在此我們將進一步將區間假設的雙單尾檢定法推展到無母數領域，以區間假設為基礎，應用多變量排列作出可以偵測基因表現值最小變化量的非介量檢定方法，探討其決策程序、整體型一錯誤、平均檢定力以及型一誤差。
模擬結果顯示在足夠的陣列重複數之下，區間假設檢定方法相較於其它傳統假設檢定方法，不僅整體與平均型一錯誤較低，檢定力亦比傳統的單尾檢定方法來得好，而非介量的多元排列檢定法能進ㄧ步改善這種區間假設檢定。The traditional hypothesis for identification of differentially expressed genes fails to take the biological meaning fold changes into consideration. However, a gene is differentially expressed if its fold change exceeds a threshold value in biological field. Compared with the traditional hypothesis of equality, the two one-sided tests procedure based on interval hypothesis（Liu, et al, 2007）not only consider the minimal biologically meaningful expression but truly identify the differentially expressed genes. To continue the research, we will apply multivariate permutation test to the interval hypothesis. Based on this proposed method, we conduct a simulation study to investigate its power, overall type I error and average type I error when the normal assumption of expression levels is in doubt.
The simulation results indicate that because of lower overall type I error and average type I error and higher average power, the interval hypothesis works better than the traditional hypothesis of equality when there are enough replicates in array. And the multivariate permutation test which is a non-parametric approach could improve the ability of identifying gene expression with interval hypothesis.論文口試委員審定書 I
謝辭 II
摘要 III
ABSTRACT IV
CONTENTS V
LIST OF FIGURES VII
LIST OF TABLES VIII
CHAPTER 1 INTRODUCTION 1
CHAPTER 2 CURRENT METHODS 3
2.1 THE TRADITIONAL AND THE INTERVAL HYPOTHESIS 3
2.1.1 The Traditional Hypothesis of Equality 3
2.1.2 The Interval Hypothesis 4
2.2 THE CURRENT PROCEDURES WITH THE TRADITIONAL HYPOTHESIS 5
2.2.1 Unpaired Two-sample t-test 5
2.2.2 Unpaired Two-sample t-test with Bonferroni Adjustment 6
2.2.3 The Fixed Fold-change Rule 6
2.2.4 Combination of the Unpaired Two-sample t-test and Fold-changes Rule 7
2.3 THE TWO ONE-SIDED TESTS PROCEDURE BASED ON INTERVAL HYPOTHESIS 7
CHAPTER 3 MULTIVARIATE PERMUTATION METHOD 9
3.1 PERMUTATION TEST 9
3.1.1 Permutation t-test 9
3.1.2 Multivariate Permutation Test 10
3.2 INTERVAL HYPOTHESIS BASED ON MULTIVARIATE PERMUTATION TEST 12
CHAPTER 4 SIMULATION 15
4.1 STATISTICAL MODELS TO GENERATING MICROARRAY EXPERIMENT DATA 15
4.1.1 Statistical Models for Generating Background-subtracted Raw Intensity Data 15
4.1.2 Statistical Models for Normalized Log-transformed Data 17
4.2 THE EMPIRICAL OVERALL AND AVERAGE TYPE I ERROR AND AVERAGE POWER 18
4.3 SIMULATION PROCEDURE 22
4.3.1 Multivariate Permutation Process 23
4.3.2 Parameter Combinations 25
4.4 SIMULATION RESULTS 26
4.4.1 Comparison between Different Size of Arrays 26
4.4.2 Results by Different Methods 27
4.4.3 Result from Different Settings of Multiplicative and Additive Error 28
4.4.4 Compare the Result from Four Different Models 28
CHAPTER 5 EXAMPLE 31
CHAPTER 6 DISCUSSION AND CONCLUSION 3
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