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Chloroplast DNA Variation between and within Japonica and Indica Rice Subspecies
No full text高等植物之葉綠體基因體在結構上一般區分為大單一拷貝(LSC)區域、小單一拷貝(SSC)區域與一組倒置重複序列(IRs)，而水稻葉綠體之基因體大小約為134.5-kb，目前已知至少包含4個rRNA基因、30個tRNA基因及超過100個具蛋白質功能的基因。本研究在整理及歸納前人有關限制酵素剪切所造成品種間之DNA長度多型性後，發現秈稉稻之間特定區域的葉綠體DNA序列確實存在長度及單一核苷酸的變異，又考量目前國際有關水稻葉綠體DNA變異之研究只採用三個品種互相比較，且其中兩個屬於稉稻另一為秈稻品種，無法深入探討亞種間或亞種內品種之DNA序列變異。因此，本研究以秈稻及稉稻各九個品種為材料，欲釐清秈稉稻亞種之間及亞種內特有的葉綠體DNA序列變異，並進一步探討這些變異可能影響之葉綠體基因，以及葉綠體DNA與粒線體DNA及核內DNA的演化關係。在總定序長度約576-kb內，共發現97個秈稉稻之間特有的變異，包括27個插入或缺失的片段(InDel)，以及70個單一核苷酸多型性(SNP)。亞種間變異中， LSC區域內發生InDel機率遠高於其他區域，有0.03％；而SNP的變異率則以SSC區域內最高，LSC區域次之。另外，在LSC區域內的76 kb附近也發現稉稻高雄139號獨有的一段35-bp的DNA序列插入；而嘉農秈6號、高雄秈2號、台中在來一號與台中秈17號的葉綠體基因體也存在兩個特有且相鄰的SNPs。因而亞種內的葉綠體DNA序列變異以秈稻品種間(6.6x10-3/kb)較稉稻品種間(8.3x10-4/kb)有較大之變異。由於發現所有秈稻與稉稻亞種間具有逆向互補序列存在，可知DNA序列倒置(Inversion)現象發生在兩個亞種分化之前；另外，僅有秈稻亞種內在葉綠體基因體不同區域發現逆向互補序列，可知DNA序列倒置亦發生在亞種分化後之秈稻品種。根據BLAST搜尋的結果，葉綠體具序列變異之DNA片段轉移至核內各染色體的平均事件約為6.42次，相近於轉移至粒線體基因體的7次，可以得知葉綠體DNA片段併入核內或粒線體基因體甚為頻繁。而葉綠體單一拷貝DNA序列內的變異區域轉移至核內基因體的平均次數為6.05，重複序列內變異區域的平均次數則為14.0，約為前者的兩倍，結果也顯示葉綠體DNA片段轉移至核內基因體的頻度大致上沒有區域性的偏好。本研究結果不但有助於瞭解水稻品種間葉綠體DNA之變異，亦有助於探討葉綠體基因與重要農藝性狀之關係。Chloroplast genomes in higher plants generally contain two large inverted repeats (IRs), separated by a large single copy region (LSC) and a small single copy region (SSC). In rice, the chloroplast genome is about 134.5-kb in length and comprises at least four rRNA genes, 30 tRNA genes, and over 100 genes that encoding proteins. By summarizing previous studies on DNA polymorphisms resulted from restriction sites analysis in Oryza, the inter-subspecific length-polymorphisms and SNPs between the chloroplast genomes of Japonica and Indica rice were verified. The cpDNAs have been sequenced completely only in three varieties (the Japonica type, Nipponbare and PA64S; and the Indica type, 93-11), and the relative variation between/within subspecies is still unclear due to lack of more representive varieties. In this study, nine varieties of each subspecies were used to elucidate inter- or intra-subspecific chloroplast variations, the chloroplast genes related to these variations, and the evolutionary relationships among chloroplast, nuclear and mitochondrial DNA. In a total sequence of 576-kb in length, 97 variations in the rice chloroplast genomes between Japonica and Indica, including 27 InDels and 70 SNPs, were detected. In the inter-subspecific variations, the InDel rate in the LSC region (0.03%) was much higher than the other regions, and the highest SNP rate was in the SSC region, followed by the LSC region. In addition, an I-35 was found around the 76 kb in the LSC region existed in KS139 merely, and two adjacent SNPs specifically emerged in CHS6, KSS2, TCN1, and TCS17. And the frequency of variation among Indica varieties was 6.6x10-3 per kb larger than that among Japonica varieties (8.2x10-4 per kb). Based on the differences in reverse-complementary sequence variations between Indica and Japonica varieties, and within Indica varieties, the timings of inversion incidents could be traced back at pre- or post-differentiation stages of rice subspecies, respectively. According to the results from BLAST queries, the average number of cpDNA fragments integrated into the nuclear chromosomes was 6.42, which was near to the number of seven of cpDNA flux to the mitochondrial genome, and it appeared that the occurrence of cpDNA transferring to the nuclear or mitochondrial genomes was frequently. And the averaged transferring frequency for a single copy cpDNA fragment was 6.05, and the transferred frequency for cpDNA fragments in the inverted repeat regions was twice (14 on average) more than the single copy regions. It also indicated that the cpDNA fragments transferring to the nuclear genome were distributed evenly over the chloroplast genome. Results of this study not only contribute the information on chloroplast DNA variations among varieties, but also facilitate further researches on the relation between chloroplast genes and important agronomic traits of rice.Abstract (Chinese)
Abstract (English)
Introduction………………………………………………………01
Materials and methods.…………………………………………07
Results
Chloroplast genomic variations between Japonica and Indica subspecies…………………………………………………………12
Inter-subspecific nucleotide length-polymorphisms………13
Inter-subspecific single nucleotide polymorphisms………19
Intra-subspecific variations…………………………………25
DNA transfer from chloroplasts to nucleus and mitochondria ………………………………………………………………………27
Discussion
Inter-subspecific variations…………………………………30
Major and minor chloroplast genotypes within Japonica and Indica rice subspecies…………………………………………34
Occurrence of InDels and inversions…………………………35
Genes related to cpDNA sequence variations………………36
Intra-subspecific variations…………………………………38
cpDNA transfer……………………………………………………39
Conclusion…………………………………………………………40
Reference……………………………………………………………4
Measuring Brand Equity by Hierarchical Bayes Conjoint Analysis-An Example of Notebook Computer Industry
No full text一般研究消費者偏好結構時，聯合分析為行銷研究領域中常被使用的方法，聯合分析法是一種衡量產品屬性間的抵換關係之方法，透過將品牌與價格納入考量的屬性中，以聯合分析迴歸方法，得到品牌間轉換之願付價格差異。 本研究運用以選擇為基礎之聯合分析法，並使用層級貝氏模型進行資料分析，衡量筆記型電腦之品牌權益。層級貝氏模型兩階段的後驗修正有助於在消費者異質性的情況下，更準確地衡量區隔內消費者的偏好結構；同時配合理想點分析及知覺品質調查結果進行解釋，以利廠商釐清本身與競爭對手之差異及改進方向。 基於上述，本研究擬採用層級貝氏聯合分析模式，來達成以下目的： 1. 針對筆記型電腦使用者在選購筆電產品時的實際購買偏好，衡量不同的產品屬性水準為消費者帶來的效用，評估不同屬性對消費者的相對重要性，並找出不同特性的消費族群對各產品屬性的偏好情形。 2. 以Aaker的理論為基礎，建構筆記型電腦品牌所具有的相對價值衡量模式，解釋其中的行銷與管理意涵，做為廠商在銷售時的訂價參考。Conjoint analysis is one of the most widely-used methodology in the field of marketing research when studying general structure of consumer preferences. Conjoint analysis requires research participants to make a series of trade-off, analysis of these trade-off can reveal the relative importance of component attributes. Take Brand and Price as two of attributes into consideration in the research, we can use regression analysis to measure consumer’s willingness to pay when they switch from one brand to another. This study uses choice-based conjoint analysis, and adopts hierarchical Bayes conjoint analysis to analyze the data. Hierarchical Bayes model can improve the predictive ability given that consumers are heterogeneous. Besides, the study uses an ideal point method and positioning map to find out the different features among companies. Consequently, this study uses hierarchical Bayes conjoint analysis to draw some conclusions. The first thing is to measure the relative importance of different attributes to consumers and find out the preference of different consumer groups. Secondly, based on Aaker’s thesis, the study results the meaning of marketing and management; also, it explains the limiting factor this institute faces and recommends future research directions
Smart Color Image Recognition for Steel Bridge Rust Inspection
No full text影像處理已廣泛用於學術研究及產業，於公共工程維護檢測之應用，包括鋼橋塗漆檢測及下水道管壁檢測等。雖然相關文獻顯示，K-Means聚類法是最有效的鋼橋生鏽偵測法，但此法仍無法穩定地辨識光度不均之影像，以及輕微生鏽部分；且在過去應用影像處理的鋼橋檢測研究中，尚無有效的模型可解決照片中光度不均之問題，亦未發展出自動化的彩色辨識系統。因此，本研究以鋼橋塗漆生鏽檢測為例，處理此二問題，並以發展自動化模型為目標。為選取抵抗光度不均能力較佳之彩色座標，本研究首先從現今十四個常見的彩色座標系統中，選取相對最佳的生鏽辨識之彩色座標。經由實驗決定a*b*座標為最具抵抗光度不均能力之座標，本研究並以此座標發展以下兩個模型：Adaptive ellipse approach (AEA) 及 Box and ellipse-based neural fuzzy approach (BENFA)。第一個模型Adaptive ellipse approach (AEA)中，一張生鏽影像被分為三個區域，生鏽、背景(即塗漆顏色)及輕微生鏽到背景顏色之漸變色區域。此模型可適當處理漸變色區域，排除光度不均之影響，以達到輕微生鏽辨識的目的。透過自動偵測背景，可決定基本的背景色；由收集的生鏽照片，作者以基本橢圓形定義生鏽顏色。本模型藉由擴大基本橢圓形加強偵測輕微生鏽顏色之成效，其擴大百分比取決於生鏽顏色與塗漆顏色之關係。與K-Means聚類法之處理結果比較後，顯示此模型可更適當地辨識輕微生鏽區域。然而，當生鏽影像顏色分佈近似平行於基本橢圓形長軸時，AEA無法適當地辨識輕微生鏽顏色。有鑑於此，作者發展第二個模型Box and ellipse-based neural fuzzy approach (BENFA)以強化漸變色區域處理。本模型應用調適性網路模糊推論系統(Adaptive-network-based fuzzy inference system)描述漸變色。為達到自動化辨識之目的，此模型引用自動偵測背景、光度調整及基本橢圓形，以決定輕微生鏽和嚴重生鏽的門檻值。研究發現，相較於Fuzzy C-Means聚類法，此模型可更穩定地辨識鋼橋表面的生鏽程度。最後，為修正光度不均之生鏽照片，作者發展第三個模型BEMD-morphology approach (BMA)。此模型應用二維經驗模態分解法(bidimensional empirical mode decomposition)降低陰影之影響，並且應用影像形態學(morphology)重建反光點之顏色。結果顯示，以K-Means聚類法處理經由此模型修正後之影像的結果，比起處理未修正影像時更接近實況。Image processing has been widely utilized in scientific research and prevalently adopted in industries. Application in infrastructure condition assessment includes defect recognition on steel bridge painting and underground sewer systems. Nevertheless, there is still no robust method to overcome the non-uniform illumination problem. Although, the K-Means is recognized as one of the best rust defect recognition methods, it cannot recognize the non-uniform illuminated images and the mild rust color well. Also, there is lack of an automated color image recognition system in this field.his research starts with an investigation of 14 color spaces in order to find out a comparatively proper color configuration for non-uniformly illuminated rust image segmentation. Among the 14 color spaces, the color configuration of a*b*, which has moderate ability to filter light, is utilized to develop the proposed two models, adaptive ellipse approach (AEA) and box and ellipse-based neural fuzzy approach (BENFA).n the adaptive ellipse approach (AEA), a rust image is partitioned into three parts, background, rust, and the gradual change color from mild-rust to background. The main idea is to deal with the gradual color change properly for mild rust color extraction. The background colors can be automatically detected from a rust image. A fundamental ellipse is previously defined by the collection of rust colors. The AEA enlarges the fundamental ellipse to include part of the gradual change in color, and the enlarged size depends on the relationship between the rust color and the color of coating. The AEA is expected to deal with the boundary between background color and rust color properly. In addition, illumination adjustment is adopted in this model in order to overcome the non-uniform illumination problem. Finally, the processing results of the AEA are compared with the K-Means clusters method to show that it can recognize the mild-rust-colors.hen the color distribution is almost parallel to the major axis of the fundamental ellipse, the proposed AEA may not recognize the mild-rust-colors well. Therefore, the box and ellipse-based neural fuzzy approach (BENFA) is proposed to deal with the gradual color change from mild-rust to background. The BENFA applies the adaptive-network-based fuzzy inference system (ANFIS) to describe the gradual change colors. In order to achieve automated detection, the BENFA applies the automated detection of background, illumination adjustment, and the fundamental ellipse to determine the thresholds of serious rust and mild rust. Compared to the Fuzzy C-Means (FCM), the BENFA can stably recognize the rust intensity.he third model which is called BEMD-morphology approach (BMA) aims to adjust the color of a non-uniformly illuminated rust image. The BMA applies the bidimesional empirical mode decomposition (BEMD) to mitigate the shade/shadow effect, and morphology to substitute the highlight points by the neighboring colors. Processing a rust image with the BMA is more reliable than processing without the BMA.inally, conclusions will be drawn and recommendations for future work will be made.摘要 IIBSTRACT IVHAPTER 1 INTRODUCTION 1.1 Background 1.2 Problem Statement 2.3 Research Objectives 3.4 Organization of the Research 4HAPTER 2 LITERATURE REVIEW 6.1 Image Processing and Its Application in Infrastructure Condition Assessment 6.1.1 Underground Pipeline 6.1.2 Steel bridge Surface Inspection 7.2 Color Features 9.2.1 Color Image 9.2.2 Color Space and Color Configuration 10.3 Color Image Segmentation 19.3.1 Feature Extraction 19.3.1.1 Color Similarity 19.3.1.2 Histogram 22.3.1.3 Entropy 22.3.1.4 Principal Component Analysis 23.3.2 Threshold Segmentation 26.3.3 Clustering Segmentation 27.3.3.1 K-Means Algorithm 28.3.3.2 Fuzzy C-Means Algorithm 30.4 Artificial Intelligence 33.4.1 Fuzzy Logic Technique 33.4.1.1 Fuzzy Sets 34.4.1.2 Membership Functions 35.4.1.3 Fuzzy Logical Operations 36.4.1.4 Defuzzification 37.4.1.5 Fuzzy Inference 39.4.2 Artificial Neural Network 40.4.2.1 Artificial Neurons 40.4.2.2 Learning Algorithm 42.4.2.3 Framework 43.4.3 Adaptive Network-Based Fuzzy Inference System (ANFIS) 45.4.3.1 Framework of ANFIS 45.4.3.2 Learning rule 47.4.3.3 Sugeno-type fuzzy inference system 51.5 Hilbert-Huang Transform 52.5.1 Hilbert-Huang Transform 52.5.2 Bidimensional Empirical Mode Decomposition (BEMD) 55.6 Morphological Image Processing 59.6.1 Dilation and Erosion 60.6.2 Opening, Closing, and TopHat Transform 61HAPTER 3 COMPARISON OF COLOR CONFIGURATION USING THE K-MEANS ALGORITHM 64.1 Characteristic of Rust Images 64.1.1 Definition of a rust color 65.1.2 Why not K-Means 67.1.3 Principal Component Features 69.2 Artificial Rust Image 72.3 Evaluation the Best Color Feature for Rust Images 74.3.1 Uniform Illumination 74.3.2 Non-uniform Illumination 76.3.3 Summary 76.4 Test the Power of L*a*b* 77.5 Summary of Chapter 81HAPTER 4 ADAPTIVE ELLIPSE APPROACH (AEA) 82.1 Rust Image Preprocessing 82.1.1 Automated Detection of Background 82.1.2 Illumination Adjustment 84.1.3 Definition of rust color by the fundamental ellipse 86.2 Adaptive Ellipse Approach 87.3 Discussion and Comparison 94.3.1 Comparison of K-Means in grayscale, RGB, and a*b* 94.3.2 Comparison of K-Means with AEA 97.4 Summary of Chapter 100HAPTER 5 BOX-AND-ELLIPSE-BASED NEURO- FUZZY APPROACH (BENFA) FOR BRIDGE COATING ASSESSMENT 101.1 Preparation of Training Data 102.1.1 Input Features 102.1.1. Chrominance of the L*a*b* and its eigenvector 103.1.1.2 Chrominance of the L*a*b* and intensity L* 105.1.2 Output Designation 108.1.2.1 Output Value Setting 108.1.2.2 Designation Strategy 110.1.2.2.1 Entropy of Chrominance lower than four 111.1.2.2.2 Entropy of Chrominance higher than four 112.1.3 Illumination Adjustment of Input Image 113.1.4 Division of Training Sets 116.2 Development of Membership Functions 120.2.1 Shape of Membership Function 120.2.2 Number of Membership Function 122.3 Automation of Rust Recognition by ANFIS 124.3.1 Picking Sub-ANFIS 124.3.2 Automated Determination of Two Thresholds 125.4 Stepwise BENFA model 129.5 Applications of BENFA approach 132.6 Summary of Chapter 135HAPTER 6 Illumination Adjustment for Bridge Coating Images Using BEMD-Morphology Approach (BMA) 136.1 Shade and Shadow Elimination by Empirical Mode Decomposition 136.2 Highlight Substitution by Rust Color 142.2.1 Morphological Reconstruction for Brightness Detection 143.2.2 Seed Points of Highlight 145.2.3 Highlight Detection 146.2.4 Color Substitution 148.2.5 Application of Highlight Substitution by Rust Color 150.3 Illumination Adjustment Strategy -BMA 154.3.1 Development of the BMA 155.3.2 Stepwise the BMA 156.3.3 Evaluation of the BMA using the K-Means 158.4 Summary of Chapter 159HAPTER 7 CONCLUSIONS AND RECOMMENDATIONS 162.1 Conclusions of Research 162.2 Research Contributions 166.3 Limitations 167.4 Recommendations for Future Work 168eferences 17
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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