This thesis is devoted to a component model for Web application and the corresponding tools for its development. The model is described after the review of various existing Web application development methods and models. A case study is also provided to support the analysis. / thesis (PhD)--University of South Australia, 2003.

Web information retrieval is a relatively new research area that has attracted a significant amount of interest from researchers around the world since the emergence of the World Wide Web in the early 1990s. The problems facing successful web information retrieval are a combination of challenges that stem from traditional information retrieval and challenges characterised by the nature of the World Wide Web. The goal of any information retrieval system is to provide an information need fulfilment in response to an information need. In a web setting, this means retrieving as many relevant web documents as possible in response to an inputted query that is typically limited to only containing a few terms expressive of the user's information need. This thesis is primarily concerned with firstly reviewing pertinent literature related to various aspects of web information retrieval research and secondly proposing and investigating a novel concept and context-based approach. The approach consists of techniques that can be used together or independently and aim to provide an improvement in retrieval accuracy over other approaches. A novel concept-based term weighting technique is proposed as a new method of deriving query term significance from ontologies that can be used for the weighting of inputted queries. A technique that dynamically determines the significance of terms occurring in documents based on the matching of contexts is also proposed. Other contributions of this research include techniques for the combination of document and query term weights for the ranking of retrieved documents. All techniques were implemented and tested on benchmark data. This provides a basis for performing comparison with previous top performing web information retrieval systems. High retrieval accuracy is reported as a result of utilising the proposed approach. This is supported through comprehensive experimental evidence and favourable comparisons against previously published results.

<p>Technological advancements in video technology have placed stringent requirements on video analog front ends (AFEs) to deliver high resolutions crisp images while consuming low power to deliver optimal performance.</p><p>One of the vital parts of an AFE is a delay locked loop (DLL). The DLL is a first order system that aligns  a delayed signal with respect to a reference signal while working in a feedback manner. DLLs find their applications in many electronic devices that deal with clocks in their operation. They are used to improve timing margins and clock delays in microprocessors, memory elements and other such applications. The vital function of a DLL is to delay the input clock (one period delay), by passing it through delay line and aligning the input clock and the delayed clock of the DLL through phase detector. Once this is done multiple phases canbe derived from various stages of the delay line with each providing a stable clock signal that is a delayed version of the input clock. Due to the increasing clock speeds this task of deriving multiple phases has become quite cumbersome. The task may become complicated due to noise generated from switching activity in digital circuits thus resulting in jitter at DLL output. As the design of analog circuits becomes quite exigent especially below the 100 nm mark, the goal hereis to design an all digital DLL to take advantage of the 65 nm process and a simplified design cycle.</p><p>The aim of this thesis is to implement an all digital delay locked loop with an input frequency range of 60 MHz to 300 MHz with a worst case jitter of 66 ps.The DLL provides 32 uniformly spaced phases between input and output clocks.The DLL operation is divided in to two stages. In the first step the first delayline quantizes input clock period with the help of a binary time to digital converter.Based on this quantization information second delay line introduces actual delay between input and output clocks with 32 intermediate phases in between.The entire process takes up to 9 clock cycles until a lock state is achieved. These 32 phases provide a greater phase resolution enhancing the sync processing characteristics of the video AFE thus improving the one screen display characteristics.</p>

<p>Phase locked loop (PLLs) are the keystone for the electronic as well as for the communication circuits. Without any exaggeration, PLLs are found almost in every electronic and communication devices. Countless research has been performed, for the modification and enhancement of the PLLs circuit. While, due to the numerous advantage of the digital circuitry, the recent research is focusing on the all digital implementation of the PLLs. Therefore, it was competitive to touch with burning research.</p><p>Low power and wide range all digital phase locked loop (ADPLL), for video applications is presented. ADPLL has an operating input frequency between 10kHz to 150 kHz and output frequency between 10 MHz to 300 MHz. The phase frequency detector (PFD) is based on D-flip flops, having two output error and direction signal. The traditional charge pump (CP) is replaced by time-to-digital converters (TDC) and analog low pass filter (LPF) by digital low pass filter (digital-LPF). For completely digital architecture, voltage controlled oscillator (VCO) is replaced by the digitally controlled oscillator (DCO). In DCO, eleven bits are dedicated for controlling bits, two bits for biasing and one bit for enable the DCO. The designed steps for ADPLL were almost similar to the designed steps of a second order analog PLL. The ADPLL is implemented on a CMOS 65-nm technology.</p>

<p>Transcriptional regulation largely determines which proteins and the protein levels that are found in a cell, and this is crucial in development, differentiation and responses to environmental stimuli. The major effectors of transcriptional regulation are a group of proteins known as transcription factors, which importance is supported by their frequent involvement in mendelian and complex diseases.</p><p>In paper I, we attempted to establish the importance of DNA sequence variation in transcriptional control, by analyzing the potential functionality of polymorphic short repetitive elements as cis-regulatory elements. However, the relevance of this study was constrained by the limited number of analyzed sequences and the <i>in vitro</i> nature of the experiments. To overcome these limitations, (paper II) we optimized an <i>in vivo</i> large-scale technology named ChIP-chip, which couples chromatin immunoprecipitation and microarray hybridization. We successfully identified the binding profiles of metabolic-disease associated transcription factors in 1% of the human genome, using a liver cellular model, and inferred the binding sites at base pair resolution.</p><p>Another important characteristic of transcriptional regulation is its plasticity, which allows adjusting the cellular transcriptome to cellular and environmental stimuli. In paper III, we investigated such plasticity by treating HepG2 cells with butyrate, a histone deacetylase inhibitor (HDACi) and interrogating the changes in histone H3 and H4 acetylation levels in 1% of the genome. Observation of frequent deacetylation around transcription start sites and hyperacetylation at the nuclear periphery challenges pre-assumed HDACi mechanisms of action.</p><p>Finally, in paper IV we extended the DNA binding profiles of the medically relevant transcription factors, USF1 and USF2, and H3 acetylation to the whole non-repetitive fraction of the human genome. Using motif finding tools and chromatin profiling, we uncovered the major determinants of USF-DNA interactions. Furthermore, USFs and H3ac were clearly localized around transcription start sites, frequently in the context of bidirectional promoters.</p>

Thesis (Ph.D.)--University of Delaware, 2006. / Principal faculty advisor: Lori L. Pollock, Dept. of Computer & Info Sciences. Includes bibliographical references.

Recent developments in data packets based high speed digital communications have opened the door for new types of applications in power system protection and control. Intelligent Electronic Devices (IEDs) are equipped with various communication capabilities that make their functional integration a natural next step. Existing integration of substation equipment is not capable of clustering with the purpose of pooling hardware resources. <p> Presently, every electric device requiring protection has its dedicated hardware performing the predetermined set of protective functions. A new function-based protection and control philosophy is proposed, based on an open-system solution. In the proposed system, the resources of the protective and control hardware are pooled, and as a clustered system provide each protected unit (line, transformer, breaker, etc) with functions required for complete direct and backup protection. <p> The work presented in this thesis identifies the performance requirements of a digital relaying algorithm for processing samples that are sent across Ethernet-based communication channels. The work shows the shortcomings and unstable performance of widely used protective algorithms in accommodating data samples that are out of step from their proper position due to variable time delays of the communications media. A new digital relaying algorithm was developed that is able to extract the amplitude and phase angle of signals from data samples received across Ethernet networks with variable jitter. <p> The performance of the algorithm was tested by using the recovered phasor amplitude and phase angle information in protective solutions. The results show that there is significant flexibility in the algorithm that can be used to facilitate less performant communication channels, or, to take advantage of faster communications channels by reducing the response time of the protective function. <p> The results show that the algorithm works well with variable length data windows, and variable sampling frequencies. Higher sampling rates make communications problems more visible, but the presented algorithm is able to compensate for wide variations in network performance, effectively maintaining sampled signal phase and amplitude information during network performance fluctuations.

The human genome contains slightly more than 20 000 genes that are expressed in a tissue specific manner. Transcription factors play a key role in gene regulation. By mapping the transcription factor binding sites genome-wide we can understand their role in different biological processes. In this thesis we have mapped transcription factors and histone marks along with nucleosome positions and RNA levels. In papers I and II, we used ChIP-seq to map five liver specific transcription factors that are crucial for liver development and function. We showed that the mapped transcription factors are involved in metabolism and other cellular processes. We showed that ChIP-seq can also be used to detect protein-protein interactions and functional SNPs. Finally, we showed that the epigenetic histone mark studied in paper I is associated with transcriptional activity at promoters. In paper III, we mapped nucleosome positions before and after treatment with transforming growth factor  β (TGFβ) and found that many nucleosomes changed positions when expression changed. After treatment with TGFβ, the transcription factor HNF4α was replaced by a nucleosome in some regions. In paper IV, we mapped USF1 transcription factor and three active chromatin marks in normal liver tissue and in liver tissue of patients diagnosed with alcoholic steatohepatitis. Using gene ontology, we as expected identified many metabolism related genes as active in normal samples whereas genes in cancer pathways were active in steatohepatitis tissue. Cancer is a common complication to the disease and early signs of this were found. We also found many novel and GWAS catalogue SNPs that are candidates to be functional. In conclusion, our results have provided information on location and structure of regulatory elements which will lead to better knowledge on liver function and disease.

Depuis son apparition, le logiciel T-Rex (tree and reticulogram recontruction) est un outil puissant pour la reconstruction et la visualisation d'arbres phylogénétiques et de réticulogrammes. Un réticulogramme est un réseau phylogénétique permettant de représenter les phénomènes d'évolution réticulée tels que l'hybridation, la recombinaison génétique et le transfert latéral de gènes. La reconstruction peut être faite à partir des matrices de distances complètes, des matrices de distances incomplètes et des séquences moléculaires. Dans le but de permettre aux biologistes et aux bioinformaticiens de bénéficier des différentes options, modes de calcul, ainsi que des diverses nouveautés de T-Rex, nous avons développé la version Web de ce logiciel. Dans ce mémoire, nous décrivons les différentes fonctions, méthodes et outils inclus dans T-Rex Web. Nous décrivons aussi les nouveaux programmes ajoutés à T-Rex Web, tels que ClustalW, Calcul de la distance topologique de Robinson et Foulds, et Species Taxonomy. La dernière option permet de générer une matrice de distances d'arbre et de reconstruire des arbres phylogénétiques à partir des listes des lignées des espèces données. La version Web du logiciel T-Rex est disponible à l'adresse URL suivante: www.trex.uqam.ca. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : T-Rex, arbre phylogénétique, matrice de distance, réticulogramme, interface Web, taxonomie d'espèces.

Transcriptional regulation largely determines which proteins and the protein levels that are found in a cell, and this is crucial in development, differentiation and responses to environmental stimuli. The major effectors of transcriptional regulation are a group of proteins known as transcription factors, which importance is supported by their frequent involvement in mendelian and complex diseases. In paper I, we attempted to establish the importance of DNA sequence variation in transcriptional control, by analyzing the potential functionality of polymorphic short repetitive elements as cis-regulatory elements. However, the relevance of this study was constrained by the limited number of analyzed sequences and the in vitro nature of the experiments. To overcome these limitations, (paper II) we optimized an in vivo large-scale technology named ChIP-chip, which couples chromatin immunoprecipitation and microarray hybridization. We successfully identified the binding profiles of metabolic-disease associated transcription factors in 1% of the human genome, using a liver cellular model, and inferred the binding sites at base pair resolution. Another important characteristic of transcriptional regulation is its plasticity, which allows adjusting the cellular transcriptome to cellular and environmental stimuli. In paper III, we investigated such plasticity by treating HepG2 cells with butyrate, a histone deacetylase inhibitor (HDACi) and interrogating the changes in histone H3 and H4 acetylation levels in 1% of the genome. Observation of frequent deacetylation around transcription start sites and hyperacetylation at the nuclear periphery challenges pre-assumed HDACi mechanisms of action. Finally, in paper IV we extended the DNA binding profiles of the medically relevant transcription factors, USF1 and USF2, and H3 acetylation to the whole non-repetitive fraction of the human genome. Using motif finding tools and chromatin profiling, we uncovered the major determinants of USF-DNA interactions. Furthermore, USFs and H3ac were clearly localized around transcription start sites, frequently in the context of bidirectional promoters.