Over the past several years, new DNA sequencing technologies have led to a great in- crease in the quantity of biological sequence data that can be generated. Typically there may be millions or even billions of short reads sequences of a few hundred base pairs that are to some degree redundant: the data fall naturally into clusters of sequences that are highly similar to each other. In order to reduce the time required for analysis of the data, it therefore becomes of interest to compute representatives of these clusters, based on some definition of similarity. In this thesis we examine two clustering software packages, USEARCH and DNACLUST, that seek to perform this clustering task efficiently. We provide an overview of the techniques used by these two packages; we compare and evaluate them both from a methodological and experimental perspective, and draw conclusions about their effectiveness and utility. / Thesis / Master of Science (MSc)

The Canadian Broadcasting Corporation’s Canada Reads program, based on the popular television show Survivor, welcomes five Canadian personalities to defend one Canadian book, per year, that they believe all Canadians should read. The program signifies a common discourse in Canada as a nation-state regarding its own lack of coherent and fixed identity, and can be understood as a nationalist project. I am working with Canada Reads as an existing archive, utilizing materials as both individual and interconnected entities in a larger and ongoing process of cultural production – and it is important to note that it is impossible to separate cultural production from cultural consumption. Each year offers a different set of insights that can be consumed in their own right, which is why this project is written in the present tense. Focusing on the first ten years of the Canada Reads competition, I argue that Canada Reads plays a specific and calculated role in the CBC’s goal of nation-building: one that obfuscates repressive national histories and legacies and instead promotes the transformative powers of literacy as that which can conquer historical and contemporary inequalities of all types. This research lays bare the imagined and idealized ‘communities’ of Canada Reads audiences that the CBC wishes to reflect in its programming, and complicates this construction as one that abdicates contemporary responsibilities of settlers. / Thesis (Master, Gender Studies) -- Queen's University, 2012-08-14 21:44:50.087

This thesis explores, through a neo-Marxist/cultural materialist lens, how discourses of class conflict in three pieces of contemporary Canadian fiction — Megan Gail Coles’ Small Game Hunting at the Local Coward Gun Club (2019), Tracey Lindberg’s Birdie (2015), and André Alexis’s Fifteen Dogs (2015) — are suppressed in broader public discussions of the texts, particularly on the CBC Radio program Canada Reads. Through close-reading the texts and their respective Canada Reads seasons for how class is operating “equiprimordially” (Ashley Bohrer) — an intersectional conceptualization of class that views class and its relations to other systems of oppression such as race, gender, sexuality, and settler-colonialism as co-constitutive, not separate — I argue that Canada Reads serves as a cultural arm of the neoliberal Canadian state’s project of erasing the political saliency of class conflict so that it may continue to reproduce its conditions of existence. To demonstrate this, I first outline the history of Canadian state cultural policy in relation to class, as well my theoretical framework. I then close read the thesis’s three pieces of fiction to determine how they mobilize class in relation to Canadian state narratives of class. Following this, I close read each book’s respective Canada Reads broadcast to see if class is taken up at all in the discussions. I then examine Canada Reads as a “mass reading event” (MRE) [Danielle Fuller and DeNel Rehberg Sedo] and explore alternative modes of shared reading that escape the nationalist logic of Canada Reads and thus have potential for bringing class discourses forward. Ultimately, the thesis demonstrates that Canada Reads as a model of shared reading is too deeply tied to the liberal humanist values of the Canadian state for any radical class discourse to emerge from it. Radical class discourses in literature that could spur collective, transformative action must come from elsewhere. / Thesis / Master of Arts (MA) / This thesis examines how messages of class conflict in three pieces of Canadian fiction — Megan Gail Coles’ Small Game Hunting at the Local Coward Gun Club, Tracey Lindberg’s Birdie, and André Alexis’s Fifteen Dogs — are suppressed in broader public discussions of each piece, particularly on the CBC Radio program Canada Reads. Reading both the books and the Canada Reads seasons each book appeared on through a neo-Marxist lens that places class in relation to other systems of oppression, such as gender, race, sexuality, and settler-colonialism, I argue that Canada Reads serves as a cultural arm of the neoliberal Canadian state’s project of erasing the political saliency of class conflict — something that it requires in order to reproduce itself. Based on this finding, I turn at the end to alternative models of shared reading that could serve as spaces that recognize class messages in literature.

This thesis is an exploration of liminal teen agency in Heather O’Neill’s Lullabies for Little Criminals and Raziel Reid’s When Everything Feels Like the Movies. By focusing on two teen characters from working class families, one female, one queer, I investigate how teens assert their autonomy while still living under the constraints of classism and (hetero)sexism. While these teens are able to retain some form of autonomy, I argue that their agency is often obscured or overwritten by the disgust reactions of other characters in each novel. Drawing on affect theory, particularly Sara Ahmed’s body of work, Jonathan Dollimore, and Sianne Ngai, and drawing on Joan Sangster’s work on the construction of female delinquency, I investigate the significance of the disgust reaction, and how the reaction is a means of reasserting power over the willful, resistant teen body. As the Canada Reads competition reveals, the middle class, cis-hetero readerly discomfort with these novels becomes an avenue through which this literature is deemed “unpalatable,” providing a justification to doubt the testimony of narrators like Baby and Jude. This thesis is ultimately an intervention into doubted testimony, and demonstrates how affective disgust is the source of doubt. Since agency and testimony are tightly intertwined in each novel, doubting testimony becomes a violent form of denying these characters, and the authors, agency. / Thesis / Master of Arts (MA)

<p>När Fröbel var verksam gick han metodiskt tillväga genom att tillhandahålla barnen varsin griffeltavla. Fröbels metod kan idag anses, som mycket lärarstyrd. Under 1950- talet fick Herbert Reads tankar sitt genombrott. Barnen fick då ett fritt sätt att arbeta på. Det var alltså ett fritt skapande som förelåg. Mot bakgrund av våra erfarenheter och intresse av bildskapande aktiviteter var vi nyfikna på att undersöka hur olika pedagogers förhållningssätt ser ut i samband med barns bildskapande.Vi har i vår undersökning i första hand fokus på pedagogerna. Syftet med undersökningen är att belysa och finna likheter och skillnader i lärarnas interaktion med och förhållningssätt till barnen i samband med barnens bildskapande aktiviteter. Därigenom bidrar studien till att öka förståelsen för hur pedagogen agerar och förhåller sig till barnens bildskapande.Eftersom vårt syfte med undersökningen är att finna likheter och skillnader i förskolepedagogers förhållningssätt i samband med barns bildskapande, valde vi att använda oss av den kvalitativa metoden observation.Vi dokumenterade fyra pedagoger med hjälp av videokamera för att kunna gå tillbaka till bildaktiviteterna. Vid vår bearbetning och tolkning av resultatet har vi fokuserat på en del av pedagogers förhållningssätt. Den del vi har fokuserat på är hur pedagogerna värderar, bemöter, uppmuntrar, utmanar barnen, samt vilka förväntningar pedagogen har på barnen.Vårt resultat visar att pedagogernas intresse för barnens bildskapande varierar.De flesta pedagogerna samtalar med barnen om vad deras målningar föreställer och om hur barnen går tillväga i sitt skapande Resultatet visar också att vissa av pedagogerna inte uppmärksammar vissa barn. De visar dessutom ett bristfälligt intresse för deras målningar. De medverkande pedagogerna låter barnen skapa fritt med det framtagna materialet.</p>

När Fröbel var verksam gick han metodiskt tillväga genom att tillhandahålla barnen varsin griffeltavla. Fröbels metod kan idag anses, som mycket lärarstyrd. Under 1950- talet fick Herbert Reads tankar sitt genombrott. Barnen fick då ett fritt sätt att arbeta på. Det var alltså ett fritt skapande som förelåg. Mot bakgrund av våra erfarenheter och intresse av bildskapande aktiviteter var vi nyfikna på att undersöka hur olika pedagogers förhållningssätt ser ut i samband med barns bildskapande.Vi har i vår undersökning i första hand fokus på pedagogerna. Syftet med undersökningen är att belysa och finna likheter och skillnader i lärarnas interaktion med och förhållningssätt till barnen i samband med barnens bildskapande aktiviteter. Därigenom bidrar studien till att öka förståelsen för hur pedagogen agerar och förhåller sig till barnens bildskapande.Eftersom vårt syfte med undersökningen är att finna likheter och skillnader i förskolepedagogers förhållningssätt i samband med barns bildskapande, valde vi att använda oss av den kvalitativa metoden observation.Vi dokumenterade fyra pedagoger med hjälp av videokamera för att kunna gå tillbaka till bildaktiviteterna. Vid vår bearbetning och tolkning av resultatet har vi fokuserat på en del av pedagogers förhållningssätt. Den del vi har fokuserat på är hur pedagogerna värderar, bemöter, uppmuntrar, utmanar barnen, samt vilka förväntningar pedagogen har på barnen.Vårt resultat visar att pedagogernas intresse för barnens bildskapande varierar.De flesta pedagogerna samtalar med barnen om vad deras målningar föreställer och om hur barnen går tillväga i sitt skapande Resultatet visar också att vissa av pedagogerna inte uppmärksammar vissa barn. De visar dessutom ett bristfälligt intresse för deras målningar. De medverkande pedagogerna låter barnen skapa fritt med det framtagna materialet.

This thesis looks at three seasons of the Canadian Broadcasting Corporation’s (CBC) radio show Canada Reads – 2014, 2015, and 2016. I examine how each year’s debates over reconciliation (2014), inclusive multiculturalism (2015), and Canada’s role as a global refuge (2016) commonly presume a national mythology that Indigenous peoples have either disappeared or become “Canadian.” I argue that despite the show’s desire to build a better society through encouraging Canadians to read Canadian books, the debates featured on Canada Reads reflect the way assumed Canadian control of Indigenous lands is embedded in the language of Canadian literature and culture to both limit the political disruptiveness of Indigenous presence and reproduce ongoing colonial domination. Central to my argument is the sad truth that, even as the show invites diverse critiques of Canadian society, it nonetheless favours stereotypical narratives of Canadian multiculturalism, benevolence, and civility, and by doing so buttresses Canada’s unchanged status as a settler colonial state. I track and evaluate ruptures in the show's civil language and decorum by reading moments of debate when the logical foundations of these stereotypical national narratives are challenged. Thus, this thesis examines not only what panelists say to each other, but also what their dialogue says to other Canadians. I argue that panelists’ critiques of the nation drawn from their readings of the books - readings that are not so much holistic interpretations of books but strategies for winning the Survivor-style game - are welcomed by the show’s annual social justice themes which then use them to purvey the nation’s virtuous liberalism. Ultimately, my analysis traces how the civil protocols of the program through these three seasons reproduce conflicts between Indigenous peoples and Canadians by reinforcing the inequity of the arrangements of the existing nation-state. / Thesis / Doctor of Philosophy (PhD)

The purpose of this research study was to examine the effectiveness of training for college work study students who participated in an America Reads program, which was designed to help at-risk children struggling with reading. Two groups participated in this research study. One group of college tutors had minimal training in reading strategies at the beginning of the study and the other group of college tutors had continuous training and feedback throughout the study. The research study sought to answer the following questions: 1) Will training for college student tutors in the area of reading, more specifically in the strategies and skills, help improve their comprehension and vocabulary? And 2) Will training for college student tutors in the area of reading, more specifically in strategies and skills, significantly improve the comprehension and vocabulary scores of the children being tutored? This was a quasi-experimental research design, used to examine the effectiveness of training college students participating in the America Reads program. The tutors were pre-and post-tested, measuring both their vocabulary and comprehension knowledge at the beginning and the end of the study. The children being tutored were also pre- and post-tested, measuring both their vocabulary and comprehension knowledge at the beginning and the end of the study. The statistical analysis for this design was the analysis of covariance (ANCOVA). The ANCOVA was used to handle the main threat to the internal validity of this research design, due to the fact that the tutors for the control and experimental group were not selected randomly. The tutors and the children were randomly assigned to two groups. The control group of tutors received minimal training (11 hours) and the experimental group received the same minimal training with extra (21 hours) weekly training added. The study began in October 1999 and ended in December 1999. The tutoring sessions were 1 ½ hours long, three days a week. The training for the experimental group was for 1 ½ to 2 hours weekly. The results from this study found no significant difference between the control and experimental groups on comprehension, as measured by the assessment instruments. The results from this study did find, however, a significant difference between the control and the experimental groups on vocabulary, as measured by the assessment instruments.

This thesis is devoted to designing and applying advanced algorithmical and statistical tools for analysis of NGS data related to cancer and infection diseases. NGS data under investigation are obtained either from host samples or viral variants. Recently, random peptide phage display libraries (RPPDL) were applied to studies of host's antibody response to different diseases. We study human antibody response to breast cancer and mouse antibody response to Lyme disease by sequencing of the whole antibody repertoire profiles which are represented by RPPDL. Alternatively, instead of sequencing immune response NGS can be applied directly to a viral population within an infected host. Specifically, we analyze the following RNA viruses: the human immunodeficiency virus (HIV) and the infectious bronchitis virus (IBV). Sequencing of RNA viruses is challenging because there are many variants inside population due to high mutation rate. Our results show that NGS helps to understand RNA viruses and explore their interaction with infected hosts. NGS also helps to analyze immune response to different diseases, trace changing of immune response at different disease stages.

Next-Generation Sequencing (NGS) technologies have been evolving at an unparalleled pace. The ability to generate millions of base pairs of data in a short time and at lower cost than previously has led to a dramatic expansion of technologies within the field. This dissertation discusses the development and validation of new methods for assessing genomic variation, dynamic changes in gene expression, high-accuracy sequencing, and analysis of recombination events. By reducing the cost of analyzing many samples for genetic divergence by genotyping the same region of the genome in multiple samples, researchers can pursue investigations on a larger scale. Next-RAD (Nextera fragmentation with Restriction-Associated Digestion) allows analysis of a uniform subset of loci between organisms for comparison of populations by genetic differences with reduced burdens of cost and data analysis. This method was applied to the Anopheles darlingi mosquito to identify three distinct species that were thought to be a uniform population. The lowering cost of large-scale sequencing investigations allows for massively parallel analysis of genomic function in a single assay. Regulation of gene expression in response to stress is a complex process which can only be understood by analyzing many pathways in tandem. A novel method is described which quantifies on a genome-wide scale the expression of millions of randomer tags driven by associated transcriptional enhancers. This method provides novel data in the form of high-resolution analysis of gene regulation. Aside from generating novel data types, another force behind development of new technologies is to improve data quality. One limitation of NGS is the inherent error rate. PELE-Seq (Paired End Low Error Sequencing) was developed to address this problem, by employing completely overlapping paired-end reads as well as a dual barcoding strategy to eliminate incorrect sequences resulting from final library amplification. This new tool improves data quality dramatically. Finally, the rapid expansion of tools necessitates the identification of new applications for these technologies. To this end, 10x Genomics Linked-Read sequencing was employed to identify recombination events in multiple species. The haplotype-resolved nature of the data generated from such assays has many promising applications.