Our ability and capacity to generate, record and store multi-dimensional, apparently unstructured data is increasing rapidly, while the cost of data storage is going down. The data recorded is not perfect, as noise gets introduced in it from different sources. Some of the basic forms of noise are incorrect recording of values and missing values. The formal study of discovering useful hidden information in the data is called Data Mining. Because of the size, and complexity of the problem, practical data mining problems are best attempted using automatic means. Data Mining can be categorized into two types i.e. supervised learning or classification and unsupervised learning or clustering. Clustering only the records in a database (or data matrix) gives a global view of the data and is called one-way clustering. For a detailed analysis or a local view, biclustering or co-clustering or two-way clustering is required involving the simultaneous clustering of the records and the attributes. In this dissertation, a novel fast and white noise tolerant data mining solution is proposed based on the Crossing Minimization (CM) paradigm; the solution works for one-way as well as two-way clustering for discovering overlapping biclusters. For decades the CM paradigm has traditionally been used for graph drawing and VLSI (Very Large Scale Integration) circuit design for reducing wire length and congestion. The utility of the proposed technique is demonstrated by comparing it with other biclustering techniques using simulated noisy, as well as real data from Agriculture, Biology and other domains. Two other interesting and hard problems also addressed in this dissertation are (i) the Minimum Attribute Subset Selection (MASS) problem and (ii) Bandwidth Minimization (BWM) problem of sparse matrices. The proposed CM technique is demonstrated to provide very convincing results while attempting to solve the said problems using real public domain data. Pakistan is the fourth largest supplier of cotton in the world. An apparent anomaly has been observed during 1989-97 between cotton yield and pesticide consumption in Pakistan showing unexpected periods of negative correlation. By applying the indigenous CM technique for one-way clustering to real Agro-Met data (2001-2002), a possible explanation of the anomaly has been presented in this thesis.

The aim of this essay is to explore motherhood in two postcolonial literary works by African American author Toni Morrison and British author Caryl Phillips, who was born in the Caribbean. The essay is based on Morrison’s award winning novel Beloved, which was published in 1987 and was inspired by the escaping African American slave Margareth Garner. It is set just after the American Civil War and the novels deals with the trauma of slavery from the perspective of Sethe, a slave who kills her own daughter to save her from slavery. The second novel on which this essay is based is Caryl Phillips’ novel Crossing the River, which was published 1993 and focused on the African diaspora from different perspectives. Crossing the River is a non-chronological narrative covering four different characters (three African American people and one white slave trader during the eighteenth century). This essay, however, only deals with the last of the four narratives depicting white British Joyce who mothers a child with African American soldier Travis. The hypothesis on which the essay is based is that the institution of American slavery has denied the female protagonists in the two novels, Sethe and Joyce, their maternal selves. The analysis revealed that both women suffer from racial domination, and race, or simply skin color, is what leads to the maternal loss of the two protagonists. Both authors depict the world of the colonizer and the colonized and they address the common pain and guilt shared by black as well as white people.

This thesis consists of four papers that concern error estimates for the Born-Oppenheimer molecular dynamics, and adaptive algorithms for the Car-Parrinello and Ehrenfest molecular dynamics. In Paper I, we study error estimates for the Born-Oppenheimer molecular dynamics with nearly crossing potential surfaces. The paper first proves an error estimate showing that the difference of the values of observables for the time-independent Schrödinger equation, with matrix valued potentials, and the values of observables for the ab initio Born-Oppenheimer molecular dynamics of the ground state depends on the probability to be in the excited states and the nuclei/electron mass ratio. Then we present a numerical method to determine the probability to be in the excited states, based on the Ehrenfest molecular dynamics, and stability analysis of a perturbed eigenvalue problem. In Paper II, we present an approach, motivated by the so called Landau-Zener probability estimation, to systematically choose the artificial electron mass parameters appearing in the Car-Parrinello and Ehrenfest molecular dynamics methods to approximate the Born-Oppenheimer molecular dynamics solutions. In Paper III, we extend the work presented in Paper II for a set of more general problems with more than two electron states. A main conclusion of Paper III is that it is necessary to resolve the near avoided conical intersections between all electron eigenvalue gaps, including gaps between the occupied states. In Paper IV, we numerically compare, using simple model problems, the Ehrenfest molecular dynamics using the adaptive mass algorithm proposed in Paper II and III and the Born-Oppenheimer molecular dynamics based on the so called purification of the density matrix method concluding that the Born-Oppenheimer molecular dynamics based on purification of density matrix method performed better in terms of computational efficiency. / <p>QC 20161102</p>

Through the critical discourse analysis of Anglophone Caribbean literature as a polyrhythmic performance, this research sets out to examine the claim that, in a world in a state of constant flux, emerging Caribbean voices are offering a challenging perspective on how to negotiate identity away from the binary constructs of centre and margin. It argues that the Caribbean writer, as a self-conscious producer of alternative discourses, offers an innovative and transcultural vision of the self. This research consists of three stages which integrate critical discourse and literary analysis with colonial/postcolonial and socio-cultural theories. Firstly, it investigates the power of language as an operation of discourse through which to apprehend reality within a binary system of representation. It then examines how the concept of discourse, as a site of contestation and meaning, enables the elaboration of a Caribbean counter-discourse. Finally, it explores the role, within the Caribbean text, of literary techniques such as narrative fragmentation, irony, dialogism, intertextuality, ambivalence and the carnivalesque to challenge, disrupt the established order and offer new perspectives of being. My study of Anglophone Caribbean texts highlights the power of language and the authority of the ‘book’ as subtle, insidious tools of domination and colonisation. It also demonstrates how, by allowing hitherto marginalised voices to write themselves into being, Caribbean writers enable linear narratives and monolithic visions of reality to be contested and other perspectives of understanding and of meaning to be uncovered. It exposes the plurality and the interweaving of discourses in the Caribbean text as a liberating, dynamic force which enables new subject positions and realities to emerge along the lines of similarity and difference. At a time when the issue of identity is one of the central problems in the world today, the research argues that this celebration of the plural, the fluid and the ambivalent offers new ways of being away from the stultifying perspective of essentialist forms.

<p>Mitotic genome instability can occur during the repair of double-strand breaks (DSBs) in DNA, which arise from endogenous and exogenous sources. Studying the mechanisms of DNA repair in the budding yeast, Saccharomyces cerevisiae has shown that Homologous Recombination (HR) is a vital repair mechanism for DSBs. HR can result in a crossover event, in which the broken molecule reciprocally exchanges information with a homologous repair template. The current model of double-strand break repair (DSBR) also allows for a tract of information to non-reciprocally transfer from the template molecule to the broken molecule. These “gene conversion” events can vary in size and can occur in conjunction with a crossover event or in isolation. The frequency and size of gene conversions in isolation and gene conversions associated with crossing over has been a source of debate due to the variation in systems used to detect gene conversions and the context in which the gene conversions are measured. </p><p>In Chapter 2, I use an unbiased system that measures the frequency and size of gene conversion events, as well as the association of gene conversion events with crossing over between homologs in diploid yeast. We show mitotic gene conversions occur at a rate of 1.3x10-6 per cell division, are either large (median 54.0kb) or small (median 6.4kb), and are associated with crossing over 43% of the time. </p><p>DSBs can arise from endogenous cellular processes such as replication and transcription. Two important RNA/DNA hybrids are involved in replication and transcription: R-loops, which form when an RNA transcript base pairs with the DNA template and displaces the non-template DNA strand, and ribonucleotides embedded into DNA (rNMPs), which arise when replicative polymerase errors insert ribonucleotide instead of deoxyribonucleotide triphosphates. RNaseH1 (encoded by RNH1) and RNaseH2 (whose catalytic subunit is encoded by RNH201) both recognize and degrade the RNA in within R-loops while RNaseH2 alone recognizes, nicks, and initiates removal of rNMPs embedded into DNA. Due to their redundant abilities to act on RNA:DNA hybrids, aberrant removal of rNMPs from DNA has been thought to lead to genome instability in an rnh201Δ background. </p><p> In Chapter 3, I characterize (1) non-selective genome-wide homologous recombination events and (2) crossing over on chromosome IV in mutants defective in RNaseH1, RNaseH2, or RNaseH1 and RNaseH2. Using a mutant DNA polymerase that incorporates 4-fold fewer rNMPs than wild type, I demonstrate that the primary recombinogenic lesion in the RNaseH2-defective genome is not rNMPs, but rather R-loops. This work suggests different in-vivo roles for RNaseH1 and RNaseH2 in resolving R-loops in yeast and is consistent with R-loops, not rNMPs, being the the likely source of pathology in Aicardi-Goutières Syndrome patients defective in RNaseH2.</p> / Dissertation

In this thesis, we consider the trajectory planning of an autonomous vehicle to cross an intersection within a given time interval. The vehicle communicates its sensordata to a central coordinator which then computes the trajectory for the given time horizon and sends it back to the vehicle. We consider a realistic scenario in which the communication links are unreliable, the evolution of the state has noise (e.g., due to the model simplification and environmental disturbances), and the observationis noisy (e.g., due to noisy sensing and/or delayed information). The intersection crossing is modeled as a chance constraint problem and the stochastic noise evolution is restricted by a terminal constraint. The communication impairments are modeled as packet drop probabilities and Kalman estimation techniques are used for predicting the states in the presence of state and observation noises. A robust sub-optimalsolution is obtained using convex optimization methods which ensures that the intersection is crossed by the vehicle in the given time interval with very low chance of failure.

O melhor entendimento sobre como o milho responde ao suprimento de N é requerido por motivos econômicos e ambientais. Genótipos contrastantes são indispensáveis para estudos genéticos e fisiológicos e a identificação da resposta ao N de linhas de milho e seus híbridos foi o objetivo deste trabalho. Foram usadas sete linhas S5 e uma S4, originadas de dois híbridos comerciais. No primeiro experimento de campo, com duas doses de N e as linhas 2, 3, 4, 5, 6, 10 e 13, a dose alta de N apresentou efeito de excesso, aumentando a produtividade de grãos somente da linha 2, diminuindo a produtividade na linha 13 e aumentando o teor de clorofila em todas as linhas exceto na 3. No segundo experimento de campo, com as linhas 2, 3, 4, 5, 6, e 10, existiu severa deficiência de N reduzindo a produtividade de grãos nas linhas 2, 3, 5 e 10, a prolificidade nas linhas 2, 3, 4 e 5, o teor de N nos grãos em todas as linhas exceto a 10, o N total nas linhas 2, 3, e 5 e a sincronia no florescimento nas linhas 3 e 5. Esta deficiência provocou o aumento na massa de cem grãos na linha 2. O comportamento interativo das linhas indica que estas variáveis possuem controle genético distinto em cada nível de N. Estes resultados também indicam independência na resposta desta variáveis ao N, pois não existiu consistência destas respostas entre as linhas. A análise dialélica, com os 15 híbridos provenientes das seis linhas do experimento anterior, indicou interação da capacidade geral de combinação (CGC) com os níveis de N para as variáveis produtividade de grãos, número de grãos por planta e teor de clorofila. Não houve associação entre as produtividades de grãos das linhas e dos seus efeitos de CGC para esta variável, nos níveis alto e baixo de N. Existiu associação da sensibilidade da produtividade de grãos ao N das linhas com os seus efeitos de CGC para esta variável nos níveis alto e baixo de N, uma vez que as linhas que sofreram os maiores efeitos das doses de N foram as de maior efeito de CGC, enquanto as linhas que sofreram os menores efeitos das doses de N apresentaram os menores efeitos de CGC. Esta associação indica que a resposta das linhas ao N deve ser considerada nos programas de melhoramento para EUN. As plantas do dialelo entre as linhas 2, 4 e 6, avaliadas em casa de vegetação com 32 dias após a germinação, apresentaram heterose média para absorção e utilização de N, indicando a possibilidade de seleção precoce para estas variáveis, as quais também apresentaram significância para os efeitos não aditivos no experimento de campo. Foi detectada heterose média para a razão Fv/Fm mas não para a fotossíntese indicando uma maior eficiência das medidas associadas à fluorescência da clorofila em relação àquelas associadas com a fixação de carbono. A deficiência de N reduziu o número de isoenzimas da glutationa redutase nas raízes de milho, cevada e Arabidopsis thaliana, e são discutidas possíveis explicações para este fenômeno, relacionadas à síntese de amido ou à proteção contra radicais livres. / A better understanding as to how maize responds to N supply is required for both economic and environmental purposes. Contrasting genotypes are indispensable for genetic and physiological studies of any trait. The investigation of the response to N supply for a range of maize lines, was the aim of this work. Seven S5 and one S4 lines, originating from two commercial hybrids, were studied for agronomic traits related to nitrogen use efficiency (NUE). Two field experiments with two levels of nitrogen were carried out. In the first experiment, in which the lines 2, 3, 4, 5, 6, 10, 13 and 17 were tested, the N supplied appeared to be in excess and only increased the grain yield in line 2, decreased the grain yield in line 13 and increased the chlorophyll content in all lines except line 3. In the second experiment, in which the lines 2, 3, 4, 5, 6, and 10 were tested, there was a severe N deficiency that caused a reduction in grain yield in lines 2, 3, 5 and 10, prolificacy in lines 2, 3, 4 and 5, grain N content in all lines except line 10 and total plant N in lines 2, 3, and 5. On the other hand, a severe N deficiency caused an increase in hundred kernel weight in line 2 and anthesis-silking in lines 3 and 5. The interactive behaviour of these traits indicates that they have different genetic controls at each N level. These results also demonstrate that the response to N of these traits are under separate controls from each other, since they did not exhibit consistency in all the lines tested. The diallel analysis with 15 hybrids of the six lines from the previous experiment, indicated an interaction of the general combining ability (GCA) with the levels of N for the traits; grain yield, grain number per plant and chlorophyll content. There was no association between the grain yield of the lines and the effects of GCA for this variable, at either level of N. Productivity responses of grains to the N levels for the different lines was associated with GCA effects for this trait. The lines that suffered the largest dosage effects of N were the ones with the larger effect of GCA while the lines that suffered the smallest dosage effects of N presented the smallest effects of GCA. This association indicates that the response of the lines to N must to be considered in the genetics programs for improvement of NUE. The plants of the crosses between the lines 2, 4 and 6, evaluated in the glass house, 32 days after the germination, presented average heterosis for the absorption and utilization of N. This indicates the possibility of precocious selection for these traits, which also presented significance non additive effects during the field experiment. Average heterosis was detected for Fv/Fm but not for photosynthesis, which indicates a greater efficiency of the measurements associated to the chlorophyll fluorescence in relation to those associated with carbon fixation. The deficiency of N reduced the number of glutathione reductase isoforms in corn, barley and Arabidopsis thaliana roots, and possible explanations are discussed for this phenomenon, related to starch synthesis and the protection against free radicals.

Neste trabalho são investigados alguns aspectos relacionados com a programação de tempos de semáforos isolados. A seguir são comentados os principais resultados obtidos. Os valores obtidos na cidade de São Carlos são os seguintes: tempo médio total (no início e no final) perdido no verde mais amarelo por fase veicular nos semáforos igual a 3,12 s (interseção em nível e fluxo sem conversão); velocidade média dos pedestres na travessia em semáforos igual a 1,28 m/s e velocidade correspondente ao 85 percentil igual a 1,00 m/s. Com exceção de alguns casos especiais, os valores do atraso fornecidos pelos métodos: Webster, HCM-2000, Simulador Integration e Simulador Corsim são da mesma magnitude e, portanto, perfeitamente viáveis de serem utilizados nos estudos práticos. Na determinação dos tempos que compõem a fase destinada à travessia de pedestres em semáforos, os métodos Ferraz e MUTCD são mais indicados que os métodos Webster/Denatran e CET-SP, uma vez que proporcionam adequada segurança sem \"assustar\" os pedestres e com o mínimo de prejuízo à capacidade do fluxo veicular. O emprego de fase exclusiva para pedestres em semáforos com duas fases veiculares leva aos seguintes acréscimos aproximados nos valores do atraso médio dos veículos: 40% para fluxos veiculares até 1000 v/h, 25% para fluxos veiculares da ordem de 1100 v/h e 20% para fluxos veiculares da ordem de 1200 v/h. / In this research some aspects related to time programming of single traffic lights are investigated. The main results are commented as follows. The values obtained in the city of São Carlos are: total average lost time (in the beginning and in the end) in the green and yellow phases in each vehicular signal phase equal to 3.12 s (level intersection and flow without conversion), pedestrians average speed on the traffic lights crossing equal to 1.28 m/s and speed corresponding to the 85º percentile equal to 1.00 m/s. Except for some special cases, the values of the delay provided by the Webster, HCM-2000, Simulator Integration and Simulator Corsim methods are of the same magnitude and, therefore, they are perfectly feasible to use in practical studies. In determining the periods of the pedestrian crossing stage for the traffic signals, the Ferraz and MUTCD methods are more indicated than the Webster/Denatran and CET-SP methods, since they provide appropriate safety without \"scaring\" the pedestrians and with minimal damage to the vehicular flow capacity. The use of exclusive pedestrian phase at two vehicular stage signals leads to the following approximate increases in the values of the vehicles average delay: 40% to vehicle flow up to 1000 v/h, 25% for vehicle flow about 1100 v/h, and 20% for vehicle flow about 1200 v/h. In this research some aspects related to time programming of single traffic lights are investigated.

A forma com que indivíduos de uma população composta são acasalados, inuencia diretamente na produção e na variabilidade da população gerada pelos acasalamentos. Identicar quais composições raciais são mais convenientes para determinadas características e viáveis economicamente, além dos efeitos de cada raça ou grupo racial, é de fundamental importância para estabelecer os rumos da produção e uma melhor estratégia para os produtores. Buscou-se, com este trabalho, identicar os efeitos que os grupos raciais N, A, B e C fornecem sobre o mérito médio de uma população composta por todas as combinações destes quatro grupos raciais, na presença e na ausência da padronização das características do índice Montana, possibilitando assim, informar a proporção racial que fornece mérito médio ótimo. Além disso, foi desenvolvida uma metodologia que calcula, por meio das informações raciais de uma população apta ao acasalamento, a combinação ótima a ser acasalada, tornando possível, desta forma, maximizar os desempenhos e os lucros para a geração seguinte. A metodologia foi implementada computacionalmente e testada para a população Montana apta ao acasalamento em 2011, e a superioridade do método, comparado a outros sistemas de acasalamento, foi comprovada. Um programa que calcula o coeciente de endogamia das possíveis futuras progênies geradas pelos acasalamentos de uma população, foi implementado com objetivo de contribuir na tomada de decisão como restrição em programas de acasalamento. / The way in which individuals of a composite population are mated has directly inuence in the production and in the variability of the population generated by mating. Identify which racial compositions are more convenient for certain traits and economically feasible, and also the eects of each breed or racial group, has a fundamental importance to establish the direction of production and a better strategy for producers. The aim of this work was to identify the eects of racial groups called N, A, B e C to provide on the average merit of a composite population for all combinations of these four racial groups, in the presence and absence of standardization of traits of Montana index, thus enabling, to inform the racial proportion that provides great average merit. Furthermore, it was developed a methodology that calculates on the basis of racial information of a population ready to mate, the optimal combination to be mated, making possible, in this way, to maximize performance and prots for the next generation. The methodology was computationally implemented and tested in the Montana\'s population able to mate in 2011, and the superiority of the method compared to other breeding systems has been proven. A program that calculates the inbreeding coecient of the possible future generations\' progeny by mating of a population was implemented in order to contribute in decision making as a constraint on mating programs.

Neste trabalho são investigados alguns aspectos relacionados com a programação de tempos de semáforos isolados. A seguir são comentados os principais resultados obtidos. Os valores obtidos na cidade de São Carlos são os seguintes: tempo médio total (no início e no final) perdido no verde mais amarelo por fase veicular nos semáforos igual a 3,12 s (interseção em nível e fluxo sem conversão); velocidade média dos pedestres na travessia em semáforos igual a 1,28 m/s e velocidade correspondente ao 85 percentil igual a 1,00 m/s. Com exceção de alguns casos especiais, os valores do atraso fornecidos pelos métodos: Webster, HCM-2000, Simulador Integration e Simulador Corsim são da mesma magnitude e, portanto, perfeitamente viáveis de serem utilizados nos estudos práticos. Na determinação dos tempos que compõem a fase destinada à travessia de pedestres em semáforos, os métodos Ferraz e MUTCD são mais indicados que os métodos Webster/Denatran e CET-SP, uma vez que proporcionam adequada segurança sem \"assustar\" os pedestres e com o mínimo de prejuízo à capacidade do fluxo veicular. O emprego de fase exclusiva para pedestres em semáforos com duas fases veiculares leva aos seguintes acréscimos aproximados nos valores do atraso médio dos veículos: 40% para fluxos veiculares até 1000 v/h, 25% para fluxos veiculares da ordem de 1100 v/h e 20% para fluxos veiculares da ordem de 1200 v/h. / In this research some aspects related to time programming of single traffic lights are investigated. The main results are commented as follows. The values obtained in the city of São Carlos are: total average lost time (in the beginning and in the end) in the green and yellow phases in each vehicular signal phase equal to 3.12 s (level intersection and flow without conversion), pedestrians average speed on the traffic lights crossing equal to 1.28 m/s and speed corresponding to the 85º percentile equal to 1.00 m/s. Except for some special cases, the values of the delay provided by the Webster, HCM-2000, Simulator Integration and Simulator Corsim methods are of the same magnitude and, therefore, they are perfectly feasible to use in practical studies. In determining the periods of the pedestrian crossing stage for the traffic signals, the Ferraz and MUTCD methods are more indicated than the Webster/Denatran and CET-SP methods, since they provide appropriate safety without \"scaring\" the pedestrians and with minimal damage to the vehicular flow capacity. The use of exclusive pedestrian phase at two vehicular stage signals leads to the following approximate increases in the values of the vehicles average delay: 40% to vehicle flow up to 1000 v/h, 25% for vehicle flow about 1100 v/h, and 20% for vehicle flow about 1200 v/h. In this research some aspects related to time programming of single traffic lights are investigated.