To be able to understand characteristics and purpose of biological sequences correctly, it is crucial to have a possibility to sort and compare them. Because of this need and to extend existing knowledge pool, numerous methods were proposed. Especially in field of multiple sequences alignment. Methods for multiple sequences alignment may provide various valuable information about sequences which failed to show enough similarity in pairwise alignment. According to this, several algorithms were implemented in various computer applications which provide a way to analyse huge sets of data. One of those, the progressive alignment algorithm, is implemented as a part of this thesis

The current decision-making processes involved in Environmental Impact Assessments (EIAs) in South Africa suffer from a lack of coherence and do not include evaluation of trade-offs between qualitative and quantitative impacts, as well as environmental, economic, and social dimensions. In addition, insufficient capacity and knowledge among authorities, a lack of objectivity among Environmental Assessment Practitioners (EAPs), and mediocre reports add to the problems associated with effective decision-making. This work presents a framework aimed at improving the effectiveness and objectivity of the decision-making process applied in South Africa’s EIAs in the energy sector. A number of decision-making models and tools are available to researchers and practitioners throughout the world that could potentially be applied in EIAs. Among these are Cost-Benefit Analysis (CBA), Rapid Impact Assessment Matrix (RIAM), and Multi Criteria Analysis (MCA). Each of the tools has its own advantages and disadvantages. With respect to the CBA, its biggest disadvantage is the fact that it requires conversion into monetary terms of all impacts, which is sometimes difficult to achieve. The RIAM, on the other hand, fails to provide a systematic approach to the ranking of alternatives. Both of these issues are addressed by the MCA tools. The MCA framework, furthermore, is universal, transparent, easy to replicate, and does not require a particularly large amount of labour and financial resources to complete. It is, however, subjective, but this shortcoming can be overcome by making the decision process more transparent. The framework proposed in this research paper is based on the Multi Criteria Analysis (MCA) technique that allows the identification of the proposed development's cumulative impact versus the current status of the environment. It then compares possible alternatives, where available, in order to identify the most optimal solution. The proposed solution takes into account the trade-offs between the different impact metrics. The research methodology followed in this paper comprised four steps, namely:<ul><li> Selection of case studies, </li><li> Information collection, </li><li> Framework application and testing and </li><li> Feedback. </li></ul> The development of the framework followed an eight-step approach that is generic for MCA and was tested on two case studies that have already gone through the Environmental Impact Assessment process, i.e. the Open Cycle Gas Turbine (OCGT) plant in the Western Cape and the Concentrating Solar Power (CSP) plant in the Northern Cape. The former was evaluated against the "no-go option", but included a decision tree comprised of impact areas, categories of impacts and dimensions (environmental, social, and economic). The latter included alternatives for four components of the project, but the decision tree comprised only of categories and dimensions. The effectiveness of the framework was verified by testing the results of the case studies against the recommendations proposed in the respective Environmental Impact Reports. In all cases, but one, the results of the framework correlated with the recommendations made by the Environmental Assessment Practitioners in the respective studies. In addition, a workshop with the decision-makers was held to obtain their viewpoints regarding the usefulness of the framework in their decision-making environment. These decision-makers supported the use of the framework in their environment as it offered an integrated and transparent approach to the evaluation of projects and alternatives. They emphasised, however, that the decision-making process was complex and the application of the framework alone would not be able to address all the challenges. The case studies demonstrated that the proposed framework could be successfully applied in the process of undertaking impact assessments in the energy sector. It can be used to determine the trade-offs between impacts and dimensions, while taking into consideration the opinions of specialists and decision-makers when assigning weights. The framework has the ability to clearly illustrate the benefit of introducing mitigation measures and it also indicates an alternative that produces the optimal cumulative impact. In conclusion, the work presented contributes to the new body of knowledge in the field of Environmental Impact Assessment in the energy sector as it will assist authorities in making objective and informed decisions, while ensuring greater transparency in the process. It also opens opportunities for conducting follow-on investigations, such the application of the framework in other sectors of the economy, undertaking a sensitivity analysis to compare the range of scores used in the evaluation of impacts, and investigating the possibility of acquiring input from Interested and Affected Parties (I&APs) and integrating those into the framework. / Dissertation (MSc)--University of Pretoria, 2011. / Graduate School of Technology Management (GSTM) / unrestricted

Följande arbete utgör en fallstudie där en hybridanalys bestående av de två analysverktygen SWOT och AHP tillämpats. Syftet med arbetet har varit att identifiera vad den studerade verksamheten bör prioritera för att bli mer effektiv. Med hjälp av SWOT-modellen har styrkor, svagheter, möjligheter och hot kunnat identifieras. SWOT visar dock inte relevansen av de olika faktorerna och därför har modellen kompletterats med hjälp av AHP. Vid tillämpningen av AHP har en numerisk metod införts, vilket gör det möjligt att kvantifiera faktorerna inom SWOT och således kan de relativa viktfaktorerna härledas. Detta skapar ett tillförlitligare underlag för de strategiska beslut som verksamheten bör vidta, jämfört med om SWOT-analysen utförs självständigt. Studien har med signifikans identifierat att byråkratin ligger bakom en del av ineffektiviteten, vilket medför utdragna inköpsprocesser och planeringsprocesser. Studien utvärderar två olika skalor som en del av den numeriska metoden, en linjär och en kvadratisk. Den kvadratiska kräver normalt mer tid, men medför också högre tillförlitlighet. Däremot kan den medföra nackdelar om man inkluderar allokerandet av resurser, såsom tid, pengar eller personal som en tredje dimension inom AHP. Slutligen föreslår denna studie ett upplägg av hybridmodellen där man utnyttjar signifikansmåttet för att undersöka samstämigheten mellan exempelvis två individer kring vad som bör prioriteras. / This thesis presents a case study where a hybrid analysis containing the two frameworks SWOT and AHP has been made. The purpose has been to identify what the studied support business should prioritize in order to be more efficient. Using SWOT, one has been able to identify strengths, weaknesses, opportunities and threats for the function. However, SWOT fails to show their relevance and therefor it has been supplemented with an AHP analysis. When applying AHP, a numerical method has been introduced that makes it possible to quantify the factors. Thus, the relative weight of the factors can be derived. This will create a more reliable basis for the strategic decisions that the support business should implement. The study shows, with significance that the biggest issue of the support function lies in bureaucracy, causing the purchase and planning processes to be inefficient. The study also evaluates two different scales as a part of the numerical method, one linear and one quadratic. The quadratic usually requires more time but provides a more reliable result. However, it can bring some disadvantages if one includes allocations of resources, such as time, money or labor as a third dimension within AHP. Finally, the thesis proposes a way of using the hybrid model and the significance measurement to find out how two people agrees regarding what should be prioritized.

Soil microbial communities are affected extensively by addition of amendments to their environment. Of particular concern is the addition of poultry litter, which contains a substantial C, energy, and nutrient supply, but also antibiotic resistance genes (ARG), antimicrobials, and a multitude of microbial species. This project seeks to primarily assess if there is a change in bacterial community structure in response to poultry litter amendments to pasture land across geographically independent land across northern Georgia. It may be that changes in the relative abundance of bacterial communities also result in alteration in ARGs, and the community resistance to antibiotics (“resistome”) which in turn increases the potential threat of antibiotic resistance genes. While another part of this study will determine changes in integrons and specific ARGs, this project will focus on changes in bacterial communities and the potential functional changes in the community, which in turn have consequences for ARG levels and its horizontal transfer to various members of the soil community. Addition of waste from livestock is a historical method for increasing nutrients needed in the soil for the cultivation of crops, and in turn causes pronounced shifts in soil microbial communities due to the addition of large amounts of carbon, nutrients, foreign microbes, and other material. This study is unique because it utilizes a novel and relatively large landscape-scale to determine if there are discernable and repeatable patterns of bacterial community structure change in response to amendment regardless of exact soil type or source of chicken litter amendment. In the future, these data can also provide insight into the changes in the relative abundance antibiotic related genes associated with community change. / M.S. / Soil is complicated, both in terms of its physical makeup and the organisms that live inside of it. Predicting changes in soil based on the addition of foreign material such as chemicals or biological waste is not an easy process, and whether or not it is even possible to reliably predict those changes is a matter of some dispute. This study is designed to illustrate that such changes can in fact be reliably and consistently predicted even with regard to the addition of complicated materials to the soil. In this study, specifically, the material in question is chicken litter. A mix of the bedding and waste produced by chickens, litter is commonly handled by composting and is added to soil in farms as a fertilizer rich in organic matter. It is possible to point at specific elements of the soil such as the chemistry and bacteria and see how it is changed with the addition of chicken litter, which allows us to determine the nature and extent of the change that chicken litter has on soil. This study is conducted on a larger scale than similar experiments conducted in the past, making it apparent that these relationships exist on a repeated basis. It is the object of this study to pave the way and make it easier for scientists in the future to determine these relationships in other unique contexts.

Embedded systems hold immense potential, but their integration into advanced devices comes with significant costs. Malfunctions in these systems can result inequipment failures, posing serious risks and potential accidents. To ensure theirproper functionality, embedded system components undergo rigorous testing phases,which can be time-consuming, especially for components with numerous connections. Therefore, it is crucial to reduce test time while maintaining high-qualitytesting to detect and address failures early in the development cycle, resulting in improved and safer products. This report delves into various techniques and algorithms aimed at expediting testingprocesses, such as machine learning, risk analysis, test parallelization, and combinatorial testing. It examines the practicality of mathematical models and automatedapproaches in real-world companies through experimentation and implementation.In essence, the report tackles the challenges involved in testing embedded systems,explores different approaches to reduce test time, and presents a suitable model formaintaining test quality. The ultimate goal is to present and implement a methodthat effectively reduces test time while upholding an acceptable level of test quality.The obtained results provide valuable insights for future test groups and researchersseeking to optimize their testing processes and deliver safer products

This PhD thesis is comprised of 3 results in computational geometry and graph theory. In the first paper, I demonstrate that the piercing number of a set S of pairwise intersecting convex shapes in the plane is bounded by O(\alpha(S)), where \alpha(S) is the fatness of the set S, improving upon the previous upper-bound of O(\alpha(S)^2). In the second article, I show that anagram-free vertex colouring of a 2\times n square grid requires a number of colours that increases with n. This answers an open question in Wilson's thesis and shows that even graphs of pathwidth 2 do not have anagram-free colouring with a bounded number of colours. The third article is a study on the geodesic anagram-free chromatic number of chordal and interval graphs. \emph{Geodesic anagram-free chromatic number} is defined as the minimum number of colours required to colour a graph such that all shortest paths between any pair of vertices are coloured anagram-free. In particular, I prove that the geodesic anagram-free chromatic number of a chordal graph G is 32p'w, where p' is the pathwidth of the subtree intersection representation graph (tree) of G, and w is the clique number of G. Additionally, I prove that the geodesic anagram-free chromatic number of an interval graph is bounded by 32p, where p is the pathwidth of the interval graph. This PhD thesis is comprised of 3 results in computational geometry and graph theory.

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Structural algorithms incorporate the interdependence of outputs into the prediction, the loss, or both. Frank-Wolfe optimizations of pairwise losses and Gaussian conditional random fields for multivariate output regression are two such structural algorithms. Pairwise losses are standard 0-1 classification surrogate losses applied to pairs of features and outputs, resulting in improved ranking performance (area under the ROC curve, average precision, and F-1 score) at the cost of increased learning complexity. In this dissertation, it is proven that the balanced loss 0-1 SVM and the pairwise SVM have the same dual loss and the pairwise dual coefficient domain is a subdomain of the balanced loss 0-1 SVM with bias dual coefficient domain. This provides a theoretical advancement in the understanding of pairwise loss, which we exploit for the development of a novel ranking algorithm that is fast and memory efficient method with state the art ranking metric performance across eight benchmark data sets. Various practical advancements are also made in multivariate output regression. The learning time for Gaussian conditional random fields is greatly reduced and the parameter domain is expanded to enable repulsion between outputs. Last, a novel multivariate regression is presented that keeps the desirable elements of GCRF and infuses them into a local regression model that improves mean squared error and reduces learning complexity. / Computer and Information Science

This dissertation focuses on studying various network formation games in Economics. We explore a different model in each chapter to capture various aspects of networks. Chapter 1provides an overview of this dissertation. Chapter 2 studies the possible Nash equilibrium configurations in a model of signed network formation as proposed by Hiller (2017). We specify the Nash equilibria in the case of heterogeneous agents. We find 3 possible Nash equilibrium configurations: Utopia network, positive assortative matching, and disassortative matching. We derive the specific conditions under which they arise in a Nash equilibrium. In Chapter 3, we study a generalized model of signed network formation game where the players can choose not only positive and negative links but also neutral links. We check whether the results of the signed network formation model in the literature still hold in our generalized framework using the notion of pairwise Nash equilibrium. Chapter 4 studies inequality in a weighted network formation model using the notion of Nash equilibrium. As a factor of inequality, there are two types of players: Rich players and poor players. We show that both rich and poor players designate other rich players as their best friends. As a result, We present that nested split graphs are drawn from survey data because researchers tend to ask respondents to list only a few friends. / Doctor of Philosophy / This dissertation focuses on studying various network formation games in Economics. We explore a different model in each chapter to capture various aspects of networks. Chapter 1 provides an overview of this dissertation. Chapter 2 studies the possible singed network configurations in equilibrium. In the signed network, players can choose a positive (+) relationship or a negative (-) relationship toward each other player. We study the case that the players are heterogeneous. We find 3 possible categories of networks in equilibrium: Utopia network, positive assortative matching, and disassortative matching. We derive the specific conditions under which they arise in equilibrium. In Chapter 3, we study a generalized model of signed network formation game where the players can choose not only positive and negative links but also neutral links. We check whether the results of the signed network formation model in the literature still hold in our generalized framework. Chapter 4 studies inequality in a weighted network formation model using the notion of Nash equilibrium. In this weighted network model, each player can choose the level of relationship. As a factor of inequality, there are two types of players: rich players and poor players. We show that both rich and poor players choose other rich players as their best friends. As a result, we present that nested split graphs are drawn from survey data because these social network data are censored due to the limit of the number of responses.

This thesis aims to contribute to a fundamental objective of Network Economics: to provide based incentives explanations of real social network topologies. By using game theoretical tools, the three papers of this thesis analyze how real social networks can arise from the strategic interaction of self-interested individuals.In the first paper, we discuss the influence of imperfect information on the process of social network formation and, specifically, on the possibilities of observing racially segregated societies when agents' preferences are not racially biased. The second work attempts to complete the Network Economics' explanation of the puzzle regarding how agents can benefit from structural holes over a long time period. The third paper presents a model that focuses on the mechanisms underlying the formation of scientific collaboration networks. We show how researchers' heterogeneity and limited processing capability explain the basic characteristics of these networks. / Aquesta tesi aspira a contribuir a un objectiu fonamental de l'Economia de Xarxes: oferir explicacions basades en els incentius de les topologies que adopten les xarxes socials. Usant les eines de la Teoria de Jocs, els tres articles de la tesi analitzen com les xarxes socials que observem a la realitat poden esser fruit de la interacció entre individus que responen als seus propis interessos.En primer lloc, estudiem la influència de la informació imperfecte en la formació de xarxes socials i, específicament, en les possibilitats de tenir societats racialment segregades quan les preferències dels agents no estan racialment esbiaixades. El segon treball, intenta completar l'explicació que l'Economia de Xarxes dóna a l'interrogant referent als forats estructurals i a la gent que s'en beneficia de manera continuada. El darrer capítol, se centra en els mecanismes que expliquen la formació de xarxes de col·laboració científica. Es mostra com l'heterogeneïtat i la limitada capacitat de processament dels investigadors expliquen les caractarístiques bàsiques d'aquestes xarxes.