Much research has been directed toward understanding the roles of essential components in the cell, such as proteins, microRNAs, and genes. This dissertation focuses on two interesting problems in bioinformatics research: microRNA-target prediction and the identification of conserved protein complexes across species. We define the two problems and develop novel approaches for solving them. MicroRNAs are short non-coding RNAs that mediate gene expression. The goal is to predict microRNA targets. Existing methods rely on sequence features to predict targets. These features are neither sufficient nor necessary to identify functional target sites and ignore the cellular conditions in which microRNA and mRNA interact. We developed MicroTarget to predict microRNA-mRNA interactions using heterogeneous data sources. MicroTarget uses expression data to learn candidate target set for each microRNA. Then, sequence data is used to provide evidence of direct interactions and ranking the predicted targets. The predicted targets overlap with many of the experimentally validated ones. The results indicate that using expression data helps in predicting microRNA targets accurately. Protein complexes conserved across species specify processes that are core to cell machinery. Methods that have been devised to identify conserved complexes are severely limited by noise in PPI data. Behind PPIs, there are domains interacting physically to perform the necessary functions. Therefore, employing domains and domain interactions gives a better view of the protein interactions and functions. We developed novel strategy for local network alignment, DONA. DONA maps proteins into their domains and uses DDIs to improve the network alignment. We developed novel strategy for constructing an alignment graph and then uses this graph to discover the conserved sub-networks. DONA shows better performance in terms of the overlap with known protein complexes with higher precision and recall rates than existing methods. The result shows better semantic similarity computed with respect to both the biological process and the molecular function of the aligned sub-networks. / Ph. D. / Much research has been directed toward understanding the roles of essential components in the cell, such as proteins, microRNAs, and genes. The processes within the cell include a mixture of small molecules. It is of great interest to utilize different information sources to discover the interactions among these molecules. This dissertation focuses on two interesting problems: microRNA-target prediction and the identification of conserved protein complexes across species. We define the two problems and develop novel approaches for solving them. MicroRNAs are a recently discovered class of non-coding RNAs. They play key roles in the regulation of gene expression of as much as 30% of all mammalian protein encoding genes. MicroRNAs regulation activity has been implicated in a number of diseases including cancer, heart disease and neurological diseases. We developed MicroTarget to predict microRNAgene interactions using heterogeneous data sources. The predicted target genes overlap with many of the experimentally validated ones. Proteins carry out their tasks in the cell by interacting with each other. Protein complexes conserved among species specify the cell core processes. We identify conserved complexes by constructing an alignment graph leveraging on the conservation of PPIs between species through domain conservation and domain-domain interactions (DDI) in addition to PPI networks. Better integration of domain conservation and interactions in our developed conserved protein complexes identification system helps biologists benefit from verified data to predict more reliable similarity relationships among species. All the test data sets and source code for this dissertation are available at: https://bioinformatics.cs.vt.edu/∼htorkey/Software.

Yes / Guided by academic literature, industry practice and policy recommendations, we analyze a wide range of option and restricted stock plans with exercise and vesting conditions that may be contingent on stock price performance. To assess the effectiveness of these plans at attracting and providing incentives to executives, we create compensation plans with fixed firm cost and executive valuation and calculate their expected total lifetime incentives. We show that performance vesting targets provide the least cost effective incentives, performance exercise targets provide the largest risk incentives, option plans are generally superior to restricted stock plans, and calendar vesting is only efficient up to a maximum of three years. Performance exercise targets can increase the expected total lifetime incentives provided by compensation plans, but in general, standard options with short vesting periods provide the most cost effective pay-for-performance incentives.

The objective of this study is to evaluate the costs of reducing pesticide, nitrogen, phosphorus, and sediment losses of a representative risk-neutral and risk-averse peanut-cotton farmer in Southeast Virginia. Five currently popular rotations and eight alternative conservation rotations are evaluated for the representative farm. The Erosion-Productivity Impact Calculator (EPIC) model is used to simulate pesticide, nitrogen, phosphorus, and soil loss from each rotation using actual rainfall and temperature data from the study area. A Target-MOTAD mathematical programming model, REPVAFARM, is developed and solved with GAMS. The objective of the farmer is to maximize expected net return, while meeting a target income with certain allowable expected shortfall from the income target. The farmer is also constrained by land, labor, peanut quota, and levels of pesticide, nitrogen, phosphorus, and soil losses. Major findings of this study are: reducing pesticide, nitrogen, phosphorus, and soil losses imposes costs to the farmer regardless of his risk attitude, with costs ranking from high to low in the order of reducing all pollutant losses, reducing nitrogen losses, reducing phosphorus losses, reducing soil losses, and reducing pesticide losses. Costs of reducing pollutant losses are higher for more risk-averse farmers than for less risk-averse and risk-neutral farmers implying that risk-aversion is an obstacle to the adoption of alternative conservation practices. Reducing pesticide losses has little impact on other pollutants. Reducing pesticide and nitrogen losses simultaneously achieves similar reductions in soil loss and phosphorus loss. / Master of Science

The expression of CCR7 was evaluated in different cancer cell lines by using flow cytometry, western blot, Immunofluorescence and immunohistochemistry. We showed for the selected cell lines that the expression is maintained in cells grown as spheroids, and xenoplanted in mice. Furthermore, we showed the expression of CCR7 correlates with stage of the disease in patient derived head and neck cancer tissue. We also showed that expression of CCR7 in cancer cell lines correlates with migratory aptitude towards CCL21 in a scratch assay, Boyden chamber assay and spheroid invasion assay. We then showed that the expression of CCR7 is elevated under serum starvation and under hypoxia in cancer cell lines grown as monolayers and as spheroids; and that there is a correlation between hypoxia and CCR7 expression in spheroids, xenografted cells and clinical cancer tissue. However, we found that in cell line OSC-19, the increase in the expression of CCR7 did not correlate to increased migration. Our investigations following this observation showed that whilst hypoxia increases the expression of CCR7, it concurrently causes a decrease in reactive oxygen species (ROS) which strongly abrogates migratory aptitude in OSC-19, resulting in an overall loss of migration in OSC-19 cells. In addition, we characterised OSC-19 as a suitable model to evaluate small molecule CCR7 antagonists using a number of different assays. In particular, we showed that ICT13069 antagonised response of this cell line across a number of drivers of malignancy such as migration, invasion in 2D and 3D models. / Zarqa University / The full text was made available at the end of the embargo, 3rd December 2019

Although growth in the Hispanic population and its buying power has outpaced by far non-Hispanic U.S. growth in the last decade, only a limited amount of attention has been given to study consumer acculturation among Hispanic subcultures. That lack of research represents one of the biggest gaps in the ethnic marketing literature. Previous research has shown that leveln of acculturation is one of the best ways to segment markets, yet key concepts in the acculturation literature have been used interchangeably (Wallendorf & Reilly, 1983 ; Metha & Belk, 1991 ; Hui, Laroche and Kim, 1998 ; Webster, 1994 ; Penaloza, 1994 ; Laroche, Kim, Hui, and Tomiuk, 1998 ; Ogden, Ogden & Schau, 2004). This research clarifies such concepts and studies the effects of level of acculturation on attitudes toward money among Mexican Americans. Findings suggest that one of the sub-processes of acculturation, integration, can be effectively used to predict Mexican American attitudes toward money. Results address the need of a better understanding of consumption among Hispanic Americans. The importance of research in this area is underlined for public administrators, marketing managers and scholars alike. / by Luis Eduardo Torres. / Thesis (Ph.D.)--Florida Atlantic University, 2012. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

Le sujet de cette thèse est le développement d'une cible liquide haute puissance capable de gérer les contraintes liées a un impact de faisceau de protons de haute puissance (de l'ordre du GW en quelques ms) tout en optimisant la production d'isotopes a court temps de demi-vie (ici, l'intérêt se porte sur du Mercure, de temps de demi vie 130 ms). L'objectif est d'améliorer l'extraction des particules élémentaires d'intérêt pour les physiciens une fois celles-ci créées. La thèse a été principalement préparée au CERN (Genève, Suisse). De plus en plus, la puissance des faisceaux primaires envoyés sur les cibles augmente jusqu'à atteindre plusieurs centaines de kiloWatt, créant ainsi de nouvelles problématiques et de nouveaux défis. De nouveaux concepts de cibles ont ainsi vu le jour. Parmi eux, une boucle liquide utilisant du Plomb Bismuth Eutectic (LBE) comme matériau de cible, et dans lequel un échangeur de chaleur et une pompe sont intégrés, a été proposée durant la phase de développement du projet EURISOL. Ce concept prévoit de plus de transformer le liquide irradié sous forme degouttes de manière à faciliter l'extraction des isotopes créés et ainsi d'augmenter la production d'isotopes à court temps de demi-vie. Cette thèse présente le développement de ce design. Un prototype a été développé et sera testé sous faisceau de protons à ISOLDE au CERN. Plusieurs outils analytiques pour l'étude et la conception de cible haute puissance sont proposés, prenant en considération divers paramètres de design. Ces outils peuvent être utilisés pour d'autres cibles haute puissance et permettent un dimensionnement simple de ce genre de cible. De plus, un design innovant d'échangeur de chaleur est présenté, permettant d'extraire une puissance constante pour différentes températures de LBE. Le design proposé est validé grâce à divers outils numériques et analytiques. De plus, des tests expérimentaux ont été réalisés pour valider la faisabilité de douche. Des gouttes de 400 um ont été obtenues. La cible proposée est la première combinant l'utilisation d'une chambre de diffusion où la douche est créée, avec une pompe et un échangeur de chaleur. Les concepts avancés peuvent être utilisés pour ledéveloppement de cibles similaires dans d'autres instituts. / The subject of this thesis is to design a liquid target able to account for the stress induced by the impact of a highpower proton beam (of the order of GW in few ms) and to optimize the isotopes production of species with short half-life (here, the isotope of interest is a Mercury one, with a half-life of 130 ms). The objective is to improve the extraction of elementary particles of interest for physicists. The thesis was mainly conducted at the CERN (Geneva, Switzerland).More and more, the power of primary beam sent onto targets increases until reaching several kiloWatts of magnitude, inducing new problematic and challenges. Consequently, the need of new target design arises and leads to new conceptual design proposal. Amongst them, a concept of Lead Bismuth Eutectic (LBE) loop target making use of an heat exchanger (HEX) and a pump has been proposed during the European project EURISOL Design Study. This concept proposed an improvement in terms of release efficiency of short-lived species by transforming the irradiated liquid into droplets shape. This thesis presents the development of this target design proposal. A prototype target has been developed and will be tested under proton beam at ISOLDE at CERN. Several analytical tools for the study of this kind of targets are proposed, taking into account different design parameters. These tools can be applied for other high power target concept and allow an easy dimensioning of this kind of targets. As well, an innovative heat exchanger is developed, allowing to extract constant power out of the target for different LBE temperature. The proposed target design is validated thanks to different numerical and analytical tools while experimental tests have been conducted in order to assess the droplet formation feasibility. These tests prove that a shower of droplets of 400 ¿m is possible. The developed target is the first one combining a diffusion chamber where a shower is created combined with a pump and a HEX. The concepts of this design could be applied for similar targets that could be developed in other facilities.

In this thesis, a new real-time multi-agent moving target pursuit algorithm and a moving target algorithm are developed and implemented. The environment is a grid world, in which a coordinated team of agents cooperatively blocks the possible escape routes of an intelligent target in real-time. Most of the moving target search algorithms presume that the agents are faster than the targets, so the pursuit is sure to end in favor of the agents. In this work, we relax this assumption and assume that all the moving objects have the same speed. This means that the agents must find a new approach for success in the pursuit, other than just chasing the targets. When the search agents and the moving targets are moving with the same speed, we need more than one search agent which can coordinate with the other agents to capture the target. Agents are allowed to communicate with each other. We propose a multi-agent search algorithm for this problem. To our best knowledge, there is no alternative algorithm designed based on these assumptions. The proposed algorithm is compared to the modified versions of its counterparts (A*, MTS and its derivatives) experimentally.

The trajectories of ballistic targets are determined significantly by the characteristics that are specific to them. In this thesis, these characteristics are presented and a set of algorithms in order to track short-range ballistic targets are given. Firstly, motion and measurement models for the ballistic targets are formed and then four different filtering techniques are built on these models which are the extended Kalman filter, the unscented Kalman filter, the particle filter and the marginalized particle filter. The performances of these filters are evaluated by making Monte Carlo simulation. The simulations are run using target scenarios obtained according to six degrees-of-freedom trajectory for ballistic targets. Apart from the tracking errors of the filters, drag parameter estimations and the effect of drift calculation on the filter performances are investigated. The estimation results obtained by each filter are discussed in detail by making various simulations.

Ground based radars often experience difficulties in target detection and direction finding (DF) applications due to the interference between the direct and surface reflected signals when the targets fly at low altitudes. In this thesis, the phenomena governing the low angle propagation are overviewed and a multipath signal model including the effects of refraction, specular reflection, diffuse reflection, curvature of the earth and antenna polarization is presented. Then, the model is utilized to develop detection and DF algorithms for the targets at low altitudes. The target detection algorithm aims to increase signal-to-noise ratio (SNR) to overcome the effects of signal fading caused by surface reflections. The algorithm is based on diversity combining and the combining weight vector is calculated by maximizing average value of SNR. The technique is compared with Maximum Ratio Combining (MRC) algorithm which is optimal in terms of SNR. In direction finding, it is the height of the target that is explored since the target range information is obtained from the time delay. The target height is estimated by utilizing Maximum Likelihood Estimation (MLE). The performance of our algorithm is compared with that of the technique that is known in the literature as Refined Maximum Likelihood (RML).

Nearly 80 years earlier, Henry Ford advised during the 1930 depression that: "A man who stops advertising to save money is like a man who stops a clock to save time". The purposes of this case study was to determine whether legal firms have taken cognisance of these wise words and have refrained from cutting back on expenses, and more particularly its promotional budget expenses during a down turning economy. It was discovered that, like nearly 80 years ago, costs today is still an important issue when considering and exploreing promotional opportunities. Small legal organisations have in general indicated that cost effectiveness is an important factor to take into consideration when deciding which type of promotion to explore. A further prerequisite was that the promotion should be target market orientated and effective. Interestingly enough, more than 60% of the sample organisations have failed to analyse their target market before commencing with any type of promotion. This immediately raised the question whether costs have not been wasted on wrong promotional efforts, rather than costs being an issue when considering promotion? It was concluded that small legal organisations have failed to properly analyse their target market and hence was unaware of their client?s needs. Various types of promotion were undertaken by the organisation, but in many instances were ineffective and costly. Should organisations have properly analysed their target markets they would have been in a better position to select an effective and less costly type of promotion. Limited recommendations were made in an attempt to assist small legal organisations to firstly analyse their target market which will result in more cost effective marketing and will enable them to address the needs of their target market directly. / Thesis (M.B.A.)--North-West University, Potchefstroom Campus, 2011.