Le transfert d'ADN chez les bactéries est un processus essentiel dans la ségrégation des chromosomes lors de la progression du cycle cellulaire et de nombreuses protéines sont impliquées dans ce processus. Parmi elles, on trouve la famille des protéines SpoIIIE / FtsK, et différentes fonctions leur ont été attribuées. SpoIIIE a été identifiée comme étant essentielle a la sporulation chez Bacillus subtilis. Au cours de la sporulation, un septum de division asymétrique se développe à proximité d'un pôle de la cellule et divise la cellule en deux compartiments : la préspore et la cellule mère. SpoIIIE est responsable de la translocation directionnelle de l'ADN de la cellule mère à la préspore. Ce transport implique l'interaction de SpoIIIE avec des séquences spécifiques qui sont distribuées de forme asymétrique le long des chromosomes (séquences de reconnaissance SpoIIIE ou SRS). Dans cette thèse, je développe des méthodes de molécule unique pour aborder les différents aspects des mécanismes de translocation de SpoIIIE. Cette thèse est divisée en trois sections : (1) les développements et de l'optimisation méthodologiques, (2) la caractérisation de sytox comme un nouveau colorant intercalant l ‘ADN pour les expériences en molécules uniques, et (3) l'utilisation de ces méthodes de molécules uniques pour tester les modèles de translocation d'ADN par SpoIIIE. Pour commencer, j'ai développé deux méthodes de détection et manipulation par molécules uniques: 1) le premier permet la visualisation simultanée de l'ADN et les protéines fluorescentes par microscopie TIRF et à épifluorescence, et (2) l'utilisation de pinces magnétiques dans une configuration transversale qui, couplée à la détection par fluorescence, permet la détection simultanée de l’ extension de l'ADN et la visualisation de la localisation des protéines. Au cours de la thèse, j'ai construit ces configurations optiques, les ai caractérisé, et optimisé. Deuxièmement, j’ai étudié le mécanisme de liaison et des propriétés de fluorescence de sytox, un nouveau colorant d’ADN. Plus précisément, j'ai déterminé que: (1) sytox se lie à l'ADN rapidement dans un processus en deux étapes séquentielles qui implique des interactions électrostatiques; (2) la dynamique rapide de liaison et de dissociation de sytox conduit à un taux extrêmement faible de photoblanchiment , (3) la dégradation de l'ADN par sytox est quatre fois inférieure à celle observée pour d'autres bis-intercalants, tels que YOYO-1, et 4) sytox est un intercalant d'ADN qui augmente la longueur de l'ADN de 43%, et n'affecte pas ses propriétés mécaniques (mesurée par la longueur de persistance). Enfin, pour observer l'interaction entre SpoIIIE et SRS, la protéine SpoIIIE a été chimiquement étiquetée et caractérisée. Substrats d'ADN contenant la séquence SRS ont été préparés et adaptés aux méthodes de molécule unique développées pendant ma thèse. L’observation directe des interactions SpoIIIE-SRS par ces méthodes ont permis de réfuter un des modèles existant. / DNA contains the genetic information of cells. Several cellular processes, including chromosome segregation during cell division and sporulation, and plasmid conjugation require the transport of double-stranded DNA (dsDNA) within and between bacterial cells. SpoIIIE/FtsK/Tra are a family of ring-shaped, membrane-anchored, ATP-fueled, directional motors required to segregate DNA across membranes during sporulation, cell division and conjugation. In particular, SpoIIIE is responsible for packaging the chromosome inside the prespore during the process of sporulation in Bacillus subtilis. This transport is directional and requires that SpoIIIE recognizes highly-skewed octameric sequences (SpoIIIE Recognition Sequences, or SRS) sparsely distributed along the whole chromosome. In this thesis, I developed different single-molecule methods to investigate the molecular mechanism by which SpoIIIE-SRS interactions lead to directional DNA transport. This thesis is divided in three sections: methodological developments and optimization, characterization of sytox as a new intercalating dye for single molecule experiments, and the use of single molecule methods to test the models for directional DNA translocation by SpoIIIE. First, I developed two single molecule methods that involved 1) the simultaneous visualization of DNA and protein by using intercalating dyes and direct protein labels to detect the localization of SpoIIIE on DNA using TIRF and epi-fluorescence microscopy; and (2) the use of a transverse magnetic tweezers setup coupled to fluorescence detection to simultaneously detect DNA extension and visualize protein localization. I built these optical setups, characterized them, and optimized several parameters. Secondly, we investigated the binding mechanism and fluorescence properties of sytox, a new bright, low photo-damage, multi-color DNA labeling agent. Specifically, I determined that: (1) sytox binds DNA rapidly in a two-step sequential process that involves electrostatic interactions; (2) the fast dynamics of binding and unbinding of sytox leads to an extremely low photobleaching rate; (3) DNA degradation by sytox is four-fold lower than that observed for other bis-intercalators, such as YOYO-1; and 4) sytox is a DNA intercalator that increases the DNA length upon binding by 43 %, while not affecting its mechanical properties (measured by the persistence length). Finally, to observe SpoIIIE-SRS interactions, SpoIIIE was chemically labeled and characterized. DNA substrates containing SRS sequence were prepared suitable for the different single molecule approaches undertaken and also characterized. Observation of SpoIIIE-SRS interactions allowed us to conclude that: (1) in the absence of SRS, SpoIIIE can bind DNA non-specifically (2) this first binding event does not require threading through the DNA end or assembly of monomers but rather the binding of a hexamer from an open to a closed conformation, (3) in the presence of ATP, SpoIIIE translocates on DNA and is predominantly located in DNA ends, and (4) can often condense DNA by looping, reconstituting the activity observed in magnetic tweezers assays, (5) when SRS sequences are present, SpoIIIE is redistributed from non-specific sites by a diffusional or 3D looping mechanism and locates SRS sequences where it remains bound with a higher affinity than to non-specific sequences.

Most realistic financial derivatives models are too complex to allow explicit analytic solutions. The computational techniques used to implement those models fall into two broad categories: finite difference methods for the solution of partial differential equations (PDEs) and Monte Carlo simulation. Accordingly, the course consists of two sections. The first half of the course focuses on finite difference methods. The following topics are discussed; Parabolic PDEs, Black-Scholes PDE for European and American options; binomial and trinomial trees; explicit, implicit and Crank- Nicholson finite difference methods; far boundary conditions, convergence, stability, variance bias; early exercise and free boundary conditions; parabolic PDEs arising from fixed income derivatives; implied trees for exotic derivatives, adapted trees for interest rate derivatives. The second half of the course focuses on Monte Carlo. The following topics are discussed; Random number generation and testing; evaluation of expected payoff by Monte Carlo simulation; variance reduction techniques�antithetic variables, importance sampling, martingale control variables; stratification, low-discrepancy sequences and quasi-Monte Carlo methods; efficient evaluation of sensitivity measures; methods suitable for multifactor and term-structure dependent models. Computational Methods of Financial Mathematics is taught by Marcel Blais, a professor at Worcester Polytechnic Institute.

L'objectif de cette thèse est de proposer une nouvelle formulation variationnelle du problème de diffusion électromagnétique avec des conditions au bord 'impédance approximatives. On étudie un conducteur parfait recouvert d'une couche mince diélectrique. L'operator d'impedance est approximé par un rapport de polynômes d'opérateurs différentiels, de sorte que les conditions sur la bord sont présentées comme une équation des polynômes. Nous appelons cette condition d'ordre supérieur IBC (HOIBC). Nous proposons la formulation de ce problème, la discrétisation et les résultats numériques dans le cas bidimensionnel. Aussi, nous élaborons la formulation et différentes méthodes de discrétisation pour le cas tridimensionnel. / The main subject of this thesis is to propose a new variational formulation of electromagnetic scattering problem with approximate impedance boundary conditions. We consider a perfect conductor coated with a thin dielectric layer. The impedance operator is approximated as a ratio of polynomials of differential operators, so that the boundary conditions are presented as an equation of these polynomials. We call this condition as higher order IBC (HOIBC). We propose the formulation of the problem, the discretization and the numerical results in two dimensional case. Also we elaborate the formulation and some different methods of discretization for three dimensional case.

Yang, Kar Lai Alice. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

二代cDNA测序技术，又名“RNA-Seq“，为转录组(transcriptome)的研究提供了新的手段。作为革命性的技术方法，RNA-Seq 不仅可以帮助准确测量转录体(transcript)的表达水平，更可以发现新的转录体和揭示转录调控的机理。同时，整合多个不同水平的测序数据，例如基因组(genome)测序，甲基化组(methylome)测序等，可以为深入挖掘生物学意义提供一个强有力的的工具。 / 我的博士研究主要集中在二代测序(next-generation sequencing，NGS)，特别是RNA-Seq数据的分析。它主要包含三部分：分析工具开发，数据分析和机理研究。 / 大量测序数据的分析对于二代测序技术来说是一个重大的挑战。目前，相对于剪接比对工具(splice-aware aligner)，普通比对工具可以极速(ultrafast)的将数以千万记的短序列(Reads)比对到基因组，但是他们很难处理那些跨过剪接位点(splice junction)的短序列(spliced reads)或者匹配多个基因组位置的短序列(multireads)。我们开发了一个利用two-seed策略的全新的序列比对工具-ABMapper。基准测试(Benchmark test) 结果显示ABMapper比其他的同类工具：TopHat和SpliceMap有更高的accuracy和recall。另一方面，spliced reads和multireads在基因组上会有多个匹配的位置，选择最可能的位置也成为一个大问题。在计算基因表达值时，multireads和spliced reads常会被随机的选定其中之一，或者直接被排除。这种处理方式会引入偏差而直接影响下游(downstream)分析的准确性。为了解决multireads和spliced reads位置选择问题，我们提出了一个利用内含子(intron)长度的Geometric-tail (GT) 经验分布的最大似然估计 (maximum likelihood estimation) 的方法。这个概率模型可以适用于剪接位点位于短序列上或者位于成对短序列(Pair-ended, PE) 之间的情况。基于这个模型，我们可以更好的确定那些在基因组上存在多个匹配的成对短序列（pair-ended, PE reads）的最可能位置。 / 测序数据的积累为深入研究生物学意义提供了丰富的资源。利用RNA-Seq数据和甲基化测序数据，我们建立了一个基于DNA甲基化模式 (pattern) 的基因表达水平的预测模型。根据这个模型，我们发现DNA甲基化可以相当准确的预测基因表达水平，准确率达到78%。我们还发现基因主体上的DNA甲基化比启动子 (promoter) 附近的更重要。最后我们还从整合所有甲基化模式和CpG模式的组合数据集中，利用特征筛选(feature selection)选择了一个最优化子集。我们基于最优子集建立了特征重叠作用网络，进一步揭示了DNA甲基化模式对于基因表达的协作调控机理。 / 除了开发RNA-Seq数据分析的工具和数据挖掘，我们还分析斑马鱼(zebrafish)的转录组(transcriptome)。RNA-Seq数据分析结合荧光成像，定量PCR等生物学实验，揭示了Calycosin处理之后的相关作用通路(pathway)和差异表达基因，分析结果还证明了Calycosin在体内的血管生成活性。 / 综上所述，本论文将会详细阐述我在二代测序数据分析，基于数据挖掘的生物学意义的发现和转录组分析方面的工作。 / The recent development of next generation RNA-sequencing, termed ‘RNA-Seq’, has offered an opportunity to explore the RNA transcripts from the whole transcriptome. As a revolutionary method, RNA-Seq not only could precisely measure the abundances of transcripts, but discover the novel transcribed contents and uncover the unknown regulatory mechanisms. Meanwhile, the combination of different levels of next-generation sequencing, such as genome sequencing and methylome sequencing has provided a powerful tool for novel discovery in the biological context. / My PhD study focuses on the analysis of next-generation sequencing data, especially on RNA-Seq data. It mainly includes three parts: pipeline development analysis, data analysis and mechanistic study. / As the next-generation sequencing (NGS) technology, the analysis of massive NGS data is a great challenge. Many existing general aligners (as contrast to splicing-aware alignment tools) are capable of mapping millions of sequencing reads onto a reference genome. However, they are neither designed for reads that span across splice junctions (spliced reads) nor for reads that could match multiple locations along the reference genome (multireads). Hence, we have developed an ab initio mapping method - ABMapper, using two-seed strategy. The benchmark results show that ABMapper can get higher accuracy and recall compared with the same kind of tools: TopHat and SpliceMap. On the other hand, the selection of the most probable location for spliced reads and multireads becomes a big problem. These reads are randomly assigned to one of the possible locations or discarded completely when calculating the expression level, which would bias the downstream analysis, such as the differentiated expression analysis and alternative splicing analysis. To rationally determine the location of spliced reads and multireads, we have proposed a maximum likelihood estimation method based on a geometric-tail (GT) distribution of intron length. This probabilistic model deals with splice junctions between reads, or those encompassed in one or both of a pair-ended (PE) reads. Based on this model, multiple alignments of reads within a PE pair can be properly resolved. / The accumulation of NGS data has provided rich resources for deep discovery of biological significance. We have integrated RNA-Seq data and methylation sequencing data to build a predictive model for the regulation of gene expression based on DNA methylation patterns. We found that DNA methylation could predict gene expression fairly accurately and the accuracy can reach up to 78%. We have also found DNA methylation at gene body is the most important region in these models, even more useful than promoter. Finally, feature overlap network based on an optimum subset of combination of all methylation patterns and CpG patterns has indicated the collaborative regulation of gene expression by DNA methylation patterns. / Not only new algorithms were developed to facilitate the RNA-Seq data analysis, but the transcriptome analysis was performed on zebrafish. The analysis of differentially-expressed genes and pathways involved after calycosin treatment, combined with other experimental evidence such as fluorescence microscopy and quantitative real-time polymerase chain reaction (qPCR), has well demonstrated the proangiogenic effects of calycosin in vivo. / In summary, this thesis detailed my work on NGS data analysis, discovery of biological significance using data-mining algorithms and transcriptome analysis. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Lou, Shaoke. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 135-146). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / 摘要 --- p.iii / Acknowledgement --- p.v / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Bioinformatics --- p.1 / Chapter 1.2 --- Bioinformatics application --- p.1 / Chapter 1.3 --- Motivation --- p.2 / Chapter 1.4 --- Objectives --- p.3 / Chapter 1.5 --- Thesis outline --- p.3 / Chapter Chapter 2 --- Background --- p.4 / Chapter 2.1 --- Biological and biotechnology background --- p.4 / Chapter 2.1.1 --- Central dogma and biology ABC --- p.4 / Chapter 2.1.2 --- Transcription --- p.5 / Chapter 2.1.3 --- Splicing and Alternative Splicing --- p.6 / Chapter 2.1.4 --- Next-generation Sequencing --- p.10 / Chapter 2.1.5 --- RNA-Seq --- p.18 / Chapter 2.2 --- Computational background --- p.20 / Chapter 2.2.1 --- Approximate string matching and read mapping --- p.21 / Chapter 2.2.2 --- Read mapping algorithms and tools --- p.22 / Chapter 2.2.3 --- Spliced alignment tools --- p.27 / Chapter Chapter 3 --- ABMapper: a two-seed based spliced alignment tool --- p.29 / Chapter 3.1 --- Introduction --- p.29 / Chapter 3.2 --- State-of-the-art --- p.30 / Chapter 3.3 --- Problem formulation --- p.31 / Chapter 3.4 --- Methods --- p.33 / Chapter 3.5 --- Results --- p.35 / Chapter 3.5.1 --- Benchmark test --- p.35 / Chapter 3.5.2 --- Complexity analysis --- p.39 / Chapter 3.5.3 --- Comparison with other tools --- p.39 / Chapter 3.6 --- Discussion and conclusion --- p.41 / Chapter Chapter 4 --- Geometric-tail (GT) model for rational selection of RNA-Seq read location --- p.42 / Chapter 4.1 --- Introduction --- p.42 / Chapter 4.2 --- State-of-the-art --- p.44 / Chapter 4.3 --- Problem formulation --- p.44 / Chapter 4.4 --- Algorithms --- p.45 / Chapter 4.5 --- Results --- p.49 / Chapter 4.5.1 --- Workflow of GT MLE method --- p.49 / Chapter 4.5.2 --- GT distribution and insert-size distribution --- p.50 / Chapter 4.5.3 --- Multiread analysis --- p.51 / Chapter 4.5.4 --- Splice-site comparison --- p.52 / Chapter 4.6 --- Discussion and conclusion --- p.55 / Chapter Chapter 5 --- Explore relationship between methylation patterns and gene expression --- p.56 / Chapter 5.1 --- Introduction --- p.56 / Chapter 5.2 --- State-of-the-art --- p.58 / Chapter 5.3 --- Problem formulation --- p.62 / Chapter 5.4 --- Methods --- p.62 / Chapter 5.4.1 --- NGS sequencing and analysis --- p.62 / Chapter 5.4.2 --- Data preparation and transformation --- p.64 / Chapter 5.4.3 --- Random forest (RF) classification and regression --- p.65 / Chapter 5.5 --- Results --- p.68 / Chapter 5.5.1 --- Genome wide profiling of methylation --- p.68 / Chapter 5.5.2. --- Aggregation plot of methylation levels at different regions --- p.72 / Chapter 5.5.3. --- Scatterplot between methylation and gene expression --- p.75 / Chapter 5.5.4 --- Predictive model of gene expression using DNA methylation features --- p.76 / Chapter 5.5.5 --- Comb-model based on the full dataset --- p.87 / Chapter 5.6 --- Discussion and conclusion --- p.98 / Chapter Chapter 6 --- RNA-Seq data analysis and applications --- p.99 / Chapter 6.1 --- Transcriptional Profiling of Angiogenesis Activities of Calycosin in Zebrafish --- p.99 / Chapter 6.1.1 --- Introduction --- p.99 / Chapter 6.1.2 --- Background --- p.100 / Chapter 6.1.3 --- Materials and methods and ethics statement --- p.101 / Chapter 6.1.4 --- Results --- p.104 / Chapter 6.1.5 --- Conclusion --- p.108 / Chapter 6.2 --- An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database). --- p.110 / Chapter 6.2.1 --- Introduction --- p.110 / Chapter 6.2.2 --- Background --- p.110 / Chapter 6.2.3 --- Construction and content --- p.113 / Chapter 6.2.4 --- Utility and discussion --- p.116 / Chapter 6.2.5 --- Conclusion and future development --- p.119 / Chapter Chapter 7 --- Conclusion --- p.121 / Chapter 7.1 --- Conclusion --- p.121 / Chapter 7.2 --- Future work --- p.123 / Appendix --- p.124 / Chapter A1. --- Descriptive analysis of trio data --- p.124 / Chapter A2. --- Whole genome methylation level profiling --- p.125 / Chapter A3. --- Global sliding window correlation between individuals --- p.128 / Chapter A4. --- Features selected after second-run filtering --- p.133 / Bibliography --- p.135 / Chapter A. --- Publications --- p.135 / Reference --- p.135

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Thesis. 1979. M.Arch.--Massachusetts Institute of Technology. Dept. of Architecture. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND ROTCH. / Bibliography: leaves 148-151. / M.Arch.

by Henry Yurianto. / "18 September 1998." / Thesis (Ph.D.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (p. 138-149). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web.

Asymmetric beams can create significant bias in estimates of the power spectra from cosmic microwave background (CMB) experiments. With the temperature power spectrum many orders of magnitude stronger than the B-mode power spectrum any systematic error that couples the two must be carefully controlled and/or removed. In this thesis, I derive unbiased estimators for the CMB temperature and polarisation power spectra taking into account general beams and scan strategies. I test my correction algorithm on simulations of two temperature-only experiments and demonstrate that it is unbiased. I also develop a map-making algorithm that removes beam asymmetry bias at the map level. I demonstrate its implementation using simulations. I present two new map-making algorithms that create polarisation maps clean of temperature-to-polarisation leakage systematics due to differential gain and pointing between a detector pair. Where a half wave plate is used, I show that the spin-2 systematic due to differential ellipticity can also be removed using my algorithms. The first algorithm is designed to work with scan strategies that have a good range of crossing angles for each map pixel and the second for scan strategies that have a limited range of crossing angles. I demonstrate both algorithms by using simulations of time ordered data with realistic scan strategies and instrumental noise. I investigate the role that a scan strategy can have in mitigating certain common systematics by averaging systematic errors down with many crossing angles. I present approximate analytic forms for the error on the recovered B-mode power spectrum that would result from these systematic errors. I use these analytic predictions to search the parameter space of common satellite scan strategies to identify the features of a scan strategy that have most impact in mitigating systematic effects.

by Bai Tao. / Thesis (Ph.D.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 1-21). / PART I : A new approach to identification by infrared spectrometry / Chapter Chapter 1: --- Introduction --- p.1 / Chapter Chapter 2 : --- Coding system of IR spectra --- p.13 / Chapter Chapter 3 : --- Library search system of IR spectra --- p.46 / Chapter Chapter 4 : --- Identification of pharmaceuticals by the IR database of pharmaceuticals --- p.64 / Chapter Chapter 5 : --- Identification of Chinese mineral drugs by the IR database of Chinese mineral drugs --- p.85 / Chapter Chapter 6 : --- Identification of Chinese herbal drugs by the IR database of Chinese herbal drugs --- p.114 / Chapter Chapter 7 : --- Coding and library search system for IR spectra of some Chinese mineral drugs with no apparent absorption peaks --- p.133 / Chapter Chapter 8: --- Conclusion to Part I --- p.150 / PART II : A new approach to quantification of solid samples by infrared spectrometry / Chapter Chapter 1: --- Introduction --- p.152 / Chapter Chapter 2: --- Derivative method for the IR spectrometric determination of solid samples using polyethylene film as internal standard(DISPE method) --- p.163 / Chapter Chapter 3: --- The IRQA software for quantitative analysis using IR spectrometry --- p.178 / Chapter Chapter 4: --- IR for the quantitative analysis of some Chinese mineral drugs based on the proposed DISPE method --- p.190 / Chapter Chapter 5: --- Determination of iron-containing species in inorganic mixtures using the proposed DISPE method --- p.204 / Chapter Chapter 6: --- Conclusion to Part II --- p.217 / References for Part I / References for Part II / Appendix I for Part I / Appendix II for Part II