New Contig Creation Algorithm for the de novo DNA Assembly Problem

DNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.

Parents of the Gifted in Ontario: An Investigation of Parental Satisfaction with the Education of their Gifted Children

The opinions of parents in relation to the education of their gifted child were examined, with particular attention paid to their satisfaction and the type and amount of programming their child is receiving. This study employed a mixed methods research design that focused on parents’ experiences with gifted education programming and their perceptions and level of satisfaction with these programs. A survey was used to gather the perceptions and opinions of parents of gifted children in Ontario. The data were quantified and used to make observations in relation to differences in parental satisfaction and to provide a more thorough understanding of the experiences of parents in Ontario in regards to the education of gifted children. Information was also gathered regarding the recommendations that parents have for the improvement of education for their gifted child. The results of the study found that parents of gifted children were satisfied with the connections their child made within a gifted placement with like-minded peers and with opportunities for their children to learn in a more individualized and in-depth manner. However, parents expressed dissatisfaction with the timing of the initial gifted identification and the lack of knowledge that teachers, in both regular and specialized classrooms, have about gifted children and the types of programming best suited to these children. The results of the study also showed parental dissatisfaction with the lack of funding allocated to gifted education programs by district school boards and the lack of involvement they were allowed with respect to the education of their child.

Perceived Deservingness and the Toleration of Human Rights Violations: The Problem and a Possible Solution

Despite general endorsement of universal human rights, people continue to tolerate specific human rights violations. I conducted a two-part study to investigate this issue. For Part I, I examined whether people tolerated torture (a human rights violation) based on the morality and deservingness of the target. Participants tolerated torture more when the target had committed a highly morally reprehensible transgression. This effect was mediated by the target’s perceived deservingness for harsh treatment, and held over and above participants’ abstract support for the right to humane treatment. For Part II, hypocrisy induction was used in an attempt to reduce participants’ toleration of the torture. Participants were assigned to either the hypocrisy induction or control condition. Unexpectedly, participants who tolerated the torture more in Part I reduced their toleration the most in the control condition, possibly because of consistency and floor effects. Limitations and implications of the findings are discussed.

Informing the structure of subjective well-being through examining changes in life satisfaction, positive affect, and negative affect

Subjective well-being (SWB) refers to how individuals evaluate and experience their lives in positive ways, and encompasses global judgments of life satisfaction (LS), as well as the frequency of positive and negative affect (PA and NA, respectively) in one’s life. To inform the current ambiguity concerning the structure of SWB, the aim of this Masters thesis was to evaluate the structure of SWB based on whether the three components of SWB change together or independently naturally, over time and following experimental manipulation. In Study 1, associations among changes in LS, PA, and NA were evaluated using a longitudinal approach tracking natural changes in the components over periods of three months and three years. Results indicated that change in one component was related to change in the other two components. In Study 2, an experimental design was used to manipulate each SWB component individually, and evaluate changes in all three components following each manipulation. Manipulation materials designed to target LS only were effective (i.e., led to heightened focus on LS, and not PA or NA) and created an increase in both LS and PA. Manipulation materials designed to target PA and NA only were not effective (i.e., led to heightened focus on the target component, as well as on LS). Furthermore, in both studies the strength of an individual’s SWB (assessed in terms of structural consistency and structural ambivalence in Study 1 and Study 2, along with subjective ambivalence in Study 2) did not consistently moderate the degree to which changes in the components were associated with one another. Together, these findings indicate that the structure of SWB may be complex and dynamic, rather than static. Alternatively, the components of SWB may not be easily manipulated in isolation of one another. Implications for existing structural models of SWB are discussed.

Properties and Algorithms of the KCube Interconnection Networks

The KCube interconnection network was first introduced in 2010 in order to exploit the good characteristics of two well-known interconnection networks, the hypercube and the Kautz graph. KCube links up multiple processors in a communication network with high density for a fixed degree. Since the KCube network is newly proposed, much study is required to demonstrate its potential properties and algorithms that can be designed to solve parallel computation problems. In this thesis we introduce a new methodology to construct the KCube graph. Also, with regard to this new approach, we will prove its Hamiltonicity in the general KC(m; k). Moreover, we will find its connectivity followed by an optimal broadcasting scheme in which a source node containing a message is to communicate it with all other processors. In addition to KCube networks, we have studied a version of the routing problem in the traditional hypercube, investigating this problem: whether there exists a shortest path in a Qn between two nodes 0n and 1n, when the network is experiencing failed components. We first conditionally discuss this problem when there is a constraint on the number of faulty nodes, and subsequently introduce an algorithm to tackle the problem without restrictions on the number of nodes.

Bureaucratic Corruption As a Constraint on Voter Choice

It Has Often Been Assumed That a Country's Tax Level, Tax Structure Progressivity and After-Tax Income Distribution Are Chosen by Voters Subject Only to Their Budget Constraints. This Paper Argues That At Certain Income Levels Voters' Decisions May Be Constrained by Bureaucratic Corruption. the Theoretical Arguments Are Developed in Asymmetry Limits the Capacity of the Fiscal System to Generate Revenues by Means of Direct Taxes. This Hypothesis Is Tested Witha Sample of International Data by Means of a Simultaneous Equation Model. the Distortions Resulting From Corruption Ar Captured Through Their Effects on a Latent Variable Defined As the Overall Fiscal Structure. Evidence Is Found of Causality Running From This Latent Variable to the Level of Taxes and the Degree of After Tax Inequality.

Investment Under Demand Uncertainty: the Newsboy Problem Revisited.

In this article we study the effect of uncertainty on an entrepreneur who must choose the capacity of his business before knowing the demand for his product. The unit profit of operation is known with certainty but there is no flexibility in our one-period framework. We show how the introduction of global uncertainty reduces the investment of the risk neutral entrepreneur and, even more, that the risk averse one. We also show how marginal increases in risk reduce the optimal capacity of both the risk neutral and the risk averse entrepreneur, without any restriction on the concave utility function and with limited restrictions on the definition of a mean preserving spread. These general results are explained by the fact that the newsboy has a piecewise-linear, and concave, monetary payoff witha kink endogenously determined at the level of optimal capacity. Our results are compared with those in the two literatures on price uncertainty and demand uncertainty, and particularly, with the recent contributions of Eeckhoudt, Gollier and Schlesinger (1991, 1995).

The Wage Rate and the Profit Rate in the Price of Production Equation: a New Solution to an Old Problem

The aim of this paper is to demonstrate that, even if Marx's solution to the transformation problem can be modified, his basic concusions remain valid.

Reported Job Satisfaction : What Does It Mean?

By reporting his satisfaction with his job or any other experience, an individual does not communicate the number of utils that he feels. Instead, he expresses his posterior preference over available alternatives conditional on acquired knowledge of the past. This new interpretation of reported job satisfaction restores the power of microeconomic theory without denying the essential role of discrepancies between one’s situation and available opportunities. Posterior human wealth discrepancies are found to be the best predictor of reported job satisfaction. Static models of relative utility and other subjective well-being assumptions are all unambiguously rejected by the data, as well as an \"economic\" model in which job satisfaction is a measure of posterior human wealth. The \"posterior choice\" model readily explains why so many people usually report themselves as happy or satisfied, why both younger and older age groups are insensitive to current earning discrepancies, and why the past weighs more heavily than the present and the future.

A maximum likelihood framework for protein design

Affiliation: Claudia Kleinman, Nicolas Rodrigue & Hervé Philippe : Département de biochimie, Faculté de médecine, Université de Montréal

Aspects de la satisfaction au travail.

Rapport de recherche