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.

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.

Photograph - Log cutting

A photograph with a male dressed in a shirt and bow-tie cutting a log and two other men in suits standing on either side of the log. They are surrounded by a large crowd.

Certificate for One Share of Capital Stock in Nicola Valley Coal and Coke Company

Certificate for 1 share of capital stock in Nicola Valley Coal and Coke Company to Welland D. Woodruff, May 13, 1905.

Certificate for Twenty-One Shares of Capital Stock in Nicola Valley Coal and Coke Company

Certificate for 21 shares of capital stock in Nicola Valley Coal and Coke Company to Welland D. Woodruff, Oct. 16, 1905.

Certificate for One Thousand Shares of Capital Stock in Lincoln-Nipissing Development Co. Ltd.

Certificate for 1,000 shares of capital stock in Lincoln-Nipissing Development Co. Ltd. to Hamilton K. Woodruff, Feb. 21, 1907.

Certificate for One Share of Capital Stock in St. Catharines Golf Club Ltd.

Certificate for 1 share of capital stock in St. Catharines Golf Club Ltd. to Dr. Thos. Woodruff, April 15, 1911.

Certificate for One Share of Capital Stock in the Lincoln County Greater Production Company

Certificate for 1 share of capital stock in the Lincoln County Greater Production Company to Hamilton K. Woodruff, Jan. 20, 1919.

Certificate for Six Shares of Capital Stock in Gove Motor Car Company, Detroit, Michigcan

Certificate for 6 shares of common capital stock in Gove Motor Car Company, Detroit, Michigan to Hamilton K. Woodruff, June 13, 1921.

Certificate for Two Shares of Preferred Capital Stock in Gove Motor Car Company, Detroit, Michigan

Certificate for 2 shares of preferred capital stock in Gove Motor Car Company, Detroit, Michigan to Hamilton K. Woodruff, June 13, 1921.

Certificate for Two Shares of Capital Stock in The Henley Aquatic Association Limited

Certificate for 2 shares of capital stock in Henley Aquatic Association Limited to Hamilton K. Woodruff, Oct. 15, 1921.

Certificate for Sixty Shares of Capital Stock in High Pressure Oil and Gas Syndicate, Limited

Certificate for 60 shares of capital stock in High Pressure Oil and Gas Syndicate, Limited to Hamilton K. Woodruff, Nov. 1, 1922.

Certificate for Five Shares of Common Stock in Lincoln Manufacturing Company Limited

Certificate for 5 shares of common stock in Lincoln Manufacturing Company Limited to Hamilton K. Woodruff, April 10, 1923.

Certificate for Ten Shares of Accumulative Preference Capital Stock in Lincoln Manufacturing Company Limited

Certificate for 10 shares of accumulative preference capital stock in Lincoln Manufacturing Company Limited to Hamilton K. Woodruff, April 10, 1923.

Certificate for Twenty Shares of Accumulative Preference Capital Stock in Lincoln Manufacturing Company Limited

Certificate for 20 shares of accumulative preference capital stock in Lincoln Manufacturing Company Limited to Hamilton K. Woodruff, April 14, 1923.