VictorJuiz/thesis huggingface dataset:
Systematic Analysis of Cell Size Control in the Budding Yeast Saccharomyces cerevisiae
Keywords: yeast
cell size
microarray
parallel analysis
growth control
DNA damage response

The budding yeast Saccharomyces cerevisiae exhibits exquisite control of cellular size in response to the nutritional composition of its environment. Size control is mediated at the G1/S phase transition, termed Start: passage through Start represents an irreversible commitment to cell division and is contingent on achieving a critical size. When nutrients are plentiful, yeast increase their critical size set-point resulting in larger cells; in contrast, in poor nutrients, yeast pass Start at a smaller size. The genetic basis for nutrient-dependent size control and the means by which yeast sense their size remain elusive. One measure of growth potential is ribosome biogenesis, the rate of which correlates with cell size. I characterized a G-patch domain containing protein, Pfa1, which has been shown to activate the helicase activity of the pre-rRNA processing factor Prp43. Intriguingly, Pfa1 is multiply phosphorylated in response to inhibition of the TOR kinase, the central player in growth regulation. This phosphorylation occurs in a region required for Pfa1 function in ribosome biogenesis, independent of its role as a helicase activator. Consistently, phosphorylation correlates with loss of physical interactions with ribosome biogenesis and altered interactions with the ribosome. Mutation of these phosphorylation sites eliminates TOR-dependent phospho-regulation, and confers sensitivity to TOR inhibition. I propose a model wherein Pfa1 is phosphorylated in response to nutrient stress, leading to relocalization of essential processing factors, and inhibition of both ribosome biogenesis and tRNA maturation. Further, I constructed and verified a non-covalent short oligonucleotide barcode microarray platform, and applied it to genome-scale parallel analyses of both the DNA damage response and cell size control in S. cerevisiae. Through these studies, I uncovered novel connections between size control and numerous cellular processes including: the large subunit of the ribosome; the mitochondrial pH gradient; and proteins involved in oxidant-induced cell cycle arrest.
Shadows of Futurity: Yeats, Auden, and the Poetics of Utopia
Keywords: Poetry
Utopia

This dissertation works to illuminate modern poetry’s ambivalent stance toward the concept of utopia through the work of two of its most politically engaged practitioners. One of the most quoted literary maxims of the twentieth century is W.H. Auden’s assertion, in his 1939 elegy “In Memory of W.B. Yeats,” that “poetry makes nothing happen.” For Yeats, poets serve as harbingers of new worlds, imaging more ideal societal orders while working to actualize these private speculations in the public realm – a viewpoint which Auden, always concerned to define poetry’s social niche, finds both ludicrous and naggingly attractive. This dissertation examines this ambivalence, tracing the two poets’ modulating views on poetry’s world-building capacities, and their shifting stances toward the Shelleyan analogy between poetic forms and social formations. Spanning a period from the 1880s of early Yeats to Auden’s death in 1973, and devoting two chapters to each poet, I take up the following questions: Why is their work so often concerned with the future? What images of better worlds does it present? And more expansively, how can lyric poetry – so often predicated upon solitude – work to embody social aspirations? Given the sheer prevalence of an affirmative future-orientation in the two poets’ work, I see them as embodying (albeit in various ways at different stages in their careers) a poetics of utopia, whereby both poetry itself and the vocation of writing it stand as crucial manifestations of the impulse to strive after better ways of life in more ideal futures. Engaging with theorists of utopia from Lewis Mumford and his contemporary Ernst Bloch to, more recently, Fredric Jameson and Ruth Levitas, I work to mediate among the various senses of “utopia” with which the two poets engage in their work. Writing in dialogue with recent efforts to recuperate the drive for social change at the root of the utopian impulse, I highlight the centrality of this impulse not just to the work of Yeats and Auden, but to twentieth-century poetry more generally, as it strives to underscore its indispensability to our search for better futures.
Fallahin on Trial in Colonial Egypt: Apprehending the Peasantry through Orality, Writing, and Performance
Keywords: colonial justice
Egyptian peasantry
Nile Delta
archives
performance
agency

This dissertation explores the experiences of Egyptian peasants from the Delta province of Minufiyya who were tried for murder by newly created "native" or "national" courts between 1884 and 1914. Through the study of 2,000 pages of criminal files, I deconstruct how the colonial state used the modern techniques of judicial orality, writing, and performance, both to justify a series of reforms that turned the entire legal process into a parody of justice, and to develop a grand narrative that essentialized peasants as revengeful, greedy, and passionate and ultimately linked their alleged immorality to their illiteracy. Furthermore, my work sheds light on how peasants reacted to this process of moralization of the law by promoting the "honor of the brigand" through violence and poetry. Finally, by focusing on the many petitions contained in the judicial files, my dissertation provides new insight into the development of a "vernacular" culture of the law that betrays the peasants' awareness of the highly political nature of the legal process. By presenting and analyzing an untapped wealth of Egyptian archives produced by the native courts, this research not only sheds invaluable light on the workings and hence the very nature of British colonial justice in Egypt, but also represents a significant advance in the knowledge of the origins of Egypt's current legal system. On a more theoretical level, this study also constitutes an important contribution to the reflection on the subaltern subject initiated by Rosalind O'Hanlon and Talal Asad, by showing how the peasants' agency paradoxically lies in their "disempowerment."
Race, Ethnicity and Cardiovascular Risk: A Population-based Study in Ontario, Canada
Keywords: ethnicity
cardiovascular
risk factors

Background: Ethnic and immigrant groups represent a large and growing segment of the Canadian population, however, little is known about how these groups differ in their cardiovascular risk factor profiles when compared to the White population. This thesis describes three large, population-based studies examining cardiovascular risk among people of White, South Asian, Chinese and Black ethnicity living in Ontario. It was hypothesized that ethnic groups would differ significantly in their cardiovascular risk factor profiles. Methods: The study population included 154 653 White, 3364 South Asian, 3038 Chinese, and 2742 Black subjects derived from Statistics Canada’s National Population Health Survey and Canadian Community Health Surveys. In Project 1, the age- and sex-standardized prevalence of cardiovascular risk factors, heart disease, and stroke were compared across the four ethnic groups. In Project 2, the degree to which cardiovascular risk factor profiles differed between recent immigrants and long-term residents was compared across ethnic groups. In Project 3, a subsample of the study population was used to compare the ethnic-specific incidence and age at diagnosis of diabetes. We also derived ethnically appropriate body-mass index (BMI) cutoff values for obesity for assessing diabetes risk. Results: Ethnic groups living in Ontario differ strikingly in their cardiovascular risk profiles. The Chinese group had the most favourable cardiovascular risk factor profile, with 4.3% of the population reporting ≥2 major cardiovascular risk factors (i.e., smoking, obesity, diabetes, hypertension), followed by the South Asian (7.9%), White (10.1%) and Black (11.1%) groups. For all ethnic groups, cardiovascular risk factor profiles were worse among those with longer duration of residency in Canada. Nonwhite subjects developed diabetes at a higher rate, at an earlier age, and at lower ranges of BMI than White subjects. For the equivalent incidence rate of diabetes at a BMI of 30 in White subjects, the BMI cutoff value was 24, 25, and 26 in South Asian, Chinese, and Black subjects, respectively. Interpretation: These findings highlight the need for designing ethnically tailored cardiovascular disease prevention strategies and for lowering current targets for ideal body weight for nonwhite populations.
Nothingness, Being, and Dao: Ontology and Cosmology in the Zhuangzi
Keywords: Daoism
Zhuangzi
Cosmology

The following dissertation is a philosophical exploration of the cosmology of the Zhuangzi, arguing it is meontological due to the prominence afforded the Chinese word wu 無, rendered as both nothingness and nonbeing. It puts forth the argument that the Zhuangzi’s cosmology creates a relationship whereby nonbeing and being are intertwined under the purview of Dao 道. As a result, the text’s axiology is unique in that it states cosmological freedom is attainable via uniting with primal nothingness. Chapter one seeks to disprove the notion that nonbeing cannot be anything but a transcendental other by arguing that Dao is a negatively creative source that simultaneously gives birth to nonbeing and being, making it impossible for nonbeing to be nihilistic or seen as an absolute void. Chapter two delves into the manifestation of things and how the sage, as an epitome of the naturalness of Dao, follows the becoming and returning of things to the One, darkening himself in nothingness in order to cultivate his life. Chapter three poses the question of whether or not the ontological movement of things is temporal and how temporality can even be possible considering the meontological nature of the universe. The next two chapters focus on the arts of useful uselessness and forgetting, the two principal means by which the sage achieves harmony with the oneness of things. Chapter six concludes by arguing that freedom attained by perfecting the arts of uselessness and forgetfulness is not rooted in ethical virtue but is the pinnacle of one’s cosmological relationship with Dao and is embodied in the act of carefree wandering. Zhuangzi’s cosmology is thus rooted in the life force of nothingness and doing away with ontic distinctions so as to return to natural equanimity and stillness of spirit.
Improvisation and the Politics of Error
Keywords: Music
Improvisation
Jazz

This paper investigates the relationship between error and choice in jazz improvisation. In the first of four complementary chapters, key terms (e.g. error, jazz, improvisation) are defined within the context of this dissertation. Next, a series of original interchangeable exercises for musical improvisation are annotated. These exercises are discussed within a jazz-specific framework, however they are easily adaptable to a wide range of improvisational settings. Chapter Three details the effectiveness of these exercises in several case studies. Issues surrounding listening, interaction, error, and choice are examined. Finally, avenues for future study are considered, in particular a reframing of error within the process of jazz improvisation.
Child and Adolescent Emergency Department Presentations for Self-harm: Population-based Data from Ontario, Canada
Keywords: Self-Injurious Behavior
Suicide, Attempted
Child
Adolescent
Health Services

Objective: Describe emergency department (ED) presentations for self-harm by youth (12-17 yearolds), including the mental health follow-up they receive after their first-ever presentation, and analyze the association between this mental health follow-up and repeat presentation(s). Methods: Population-based health services data from Ontario, Canada, covering April 2002 to March 2009, were used to ascertain ED presentations for self-harm by youth (n=16,835). These data were used to create a retrospective cohort (n=3,497) of those making their first-ever presentation, and individually-linked to inpatient admission and ambulatory physician contact data. Mental health follow-up within 30-days of discharge, either from a psychiatrist or from any physician specialty, was assessed. The associations between follow-up and repeat self-harm presentation(s) within the following year were then analyzed. Results: Conservatively, the overall incidence rate for ED presentations for self-harm by Ontario youth was 239.0 per 100,000 person-years. Rates were higher in girls, increased with age and inversely related to neighbourhood income and community size (population). Self-harm made up a small but severe proportion of ED use by youth. Over half (57.2%) making their first-ever self-harm presentation had no mental health contact with a physician within 30 days of discharge (and several demographic, clinical and health service variables were associated with follow-up). However, mental health follow-up was not associated with reduced odds of repetition or fewer repeat presentations. Conclusions: ED presentations for self-harm by youth in Ontario are remarkably consistent with those reported from other Western countries. Self-harm is an important public health issue in Canada and requires a comprehensive prevention strategy. These data suggested follow-up youth received after their first-ever ED presentation for self-harm may be inadequate and strategies to improve follow-up may be needed. Still, more research is needed to establish the effect of follow-up on relevant outcomes.
Development of Continuous Bio-composite Fibres
Keywords: Bio-composite fibres, wood pulp, lignin, polypropylene, polyethylene oxide, electrospinning, extrusion

The purpose of this research work was to develop novel continuous bio-composite fibres with a combination of wood pulp or lignin and synthetic polymers, using continuous electrospinning and extrusion processes. The electrospun composite fibres have potential application in filtration, wound dressing, non-woven fabrics and support of thin polymeric separation membranes. Lignin fibres could be used for the development of carbon fibres. Two types of polyethylene oxide electronspun composite fibres (300-600 nm in diameter) were formulated using treated and untreated wood fibre. The optimum polymer solution concentration (7 wt.%) and addition of 5 wt.% wood pulp were found to produce uniform composite fibres. Superior dispersion and orientation were obtained with acetylated wood pulp as compared to untreated fibres. Similarly, wood pulp and nylon 6,6 based bio-composite fibres were generated successfully by electrospinning process. In this study solution concentration was found to be a critical parameter in regulating the diameter of fibres. Bio-composite fibres were developed from wood pulp and polypropylene (PP) by an extrusion process and subsequently characterized by various techniques. Tensile properties of composite fibres were improved by addition of maleated polypropylene (MAPP) and wood pulp. Fourier transform infrared spectroscopy provided the nature of chemical interaction between wood pulp reinforcement and PP matrix. Scanning electron microscopy results revealed that MAPP treatment was effective in increasing reinforcing fibre-matrix compatibility. X-ray computed tomography showed that the fibre becomes more aligned along the length axis possibly due to compression and die geometry of the extruder. Finally, blended lignin fibres (hardwood lignin/polyethylene oxide) were successfully developed by an extrusion process. Softening temperature and glass transition temperature of lignin were measured by differential scanning calorimetry which was helpful in selecting an optimal temperature profile for the extrusion process. Rheological studies provided information about the viscosity of hardwood lignin which was useful in producing lignin fibres.
The Search for Meaning: What Do the Narratives of Grieving Individuals Reveal?
Keywords: Grief
bereavement
meaning-making
narrative
meaning-reconstruction
grief and culture

This qualitative research project is a narrative inquiry into the loss experiences of four bereaved individuals who have lost an immediate family member; one of them is myself. In particular, the meanings assigned to the losses and how those meanings impacted the grieving process were explored by listening to in-depth narratives of the participants’ experiences of loss and grief. A narrative methodology was used, based on a constructivist epistemology that describes a human tendency to put events in narrative forms in order to give them a sense of continuity and meaning. Four narratives, along with their respective analysis, were presented in separate chapters, with my own narrative presented as the last narrative chapter. Of the four of us, two are males: one from Jewish-American and the other from German-Romanian descent, and two are females: both from Persian descent. The four participants ranged from 39 to 71 years of age at the time of the interviews, with the losses occurring 3 to 25 years before the interviews. Findings of this research reveal the unique and complex grieving processes of the participants. A variety of meanings were assigned to the losses with each meaning having its own possible impact on the course of bereavement. Each participant expressed her/his own personal assumptions about the nature of life, love, suffering, human vulnerabilities, and death stemming from their life experiences and culture. We all expressed in our own unique way that the loss of a special person, a loving bond, and a significant relationship will always remain painful, but their memories, legacies, and love will continue beyond their deaths, which can help us in finding meaningful, productive, and hopeful paths. Hopefully this research project will provide some validation and inspiration for other grieving individuals and contribute to the current understanding of bereavement and grief.
The Effect of Whey Protein on Short-term Food Intake and Post-meal Glycemic Regulation in Young Adults
Keywords: Whey Protein
Glycemia
Short-Term Food Intake
Satiety

The hypothesis that consumption of whey protein (WP) prior to a meal suppresses short-term food intake and reduces post-meal glycemia by insulin-dependent and -independent mechanisms in healthy young adults was explored in three studies. Study one investigated the effect of solid vs. liquid forms of WP (50 g) and sucrose (75 g) on food intake at 1 h. Whey protein, whether in solid or liquid form, suppressed food intake more than sucrose. Study two examined the effect of WP (10-40 g) consumed 30 min prior to a meal on food intake, and pre- and post-meal blood concentrations of glucose and insulin. Whey protein reduced food intake and post-meal glycemia in a dose-dependent manner without increased blood insulin concentrations. In the third study, glycemic control after WP was compared with glucose, at doses of 10 and 20 g. Both pre-meal WP and glucose consumption reduced post-meal glycemia similarly. However, WP resulted in lower pre-meal blood glucose and delayed gastric emptying, lower pre-and post-meal and overall insulin secretion and concentrations and higher GLP-1 and PYY concentrations compared with glucose. Thus, the results of this research support the hypothesis that consumption of WP prior to a meal suppresses short-term food intake and reduces post-meal glycemia by insulin-dependent and -independent mechanisms in healthy young adults.
Physics and Computational Methods for X-ray Scatter Estimation and Correction in Cone-beam Computed Tomography
Keywords: Computed Tomography
Cone-beam Computed Tomography
Monte Carlo
Scatter
Fourier Analysis
X-ray
simulation
compensator

X-ray scatter in cone-beam computed tomography (CBCT) is known to reduce image quality by introducing image artifacts, reducing contrast, and limiting computed tomography (CT) number accuracy. The extent of the effect of x-ray scatter on CBCT image quality is determined by the shape and magnitude of the scatter distribution in the projections. A method to allay the effects of scatter is imperative to enable application of CBCT to solve a wider domain of clinical problems. The work contained herein proposes such a method. A characterization of the scatter distribution through the use of a validated Monte Carlo (MC) model is carried out. The effects of imaging parameters and compensators on the scatter distribution are investigated. The spectral frequency components of the scatter distribution in CBCT projection sets are analyzed using Fourier analysis and found to reside predominately in the low frequency domain. The exact frequency extents of the scatter distribution are explored for different imaging configurations and patient geometries. Based on the Fourier analysis it is hypothesized the scatter distribution can be represented by a finite sum of sine and cosine functions. The fitting of MC scatter distribution estimates enables the reduction of the MC computation time by diminishing the number of photon tracks required by over three orders of magnitude. The fitting method is incorporated into a novel scatter correction method using an algorithm that simultaneously combines multiple MC scatter simulations. Running concurrent MC simulations while simultaneously fitting the results allows for the physical accuracy and flexibility of MC methods to be maintained while enhancing the overall efficiency. CBCT projection set scatter estimates, using the algorithm, are computed on the order of 1-2 minutes instead of hours or days. Resulting scatter corrected reconstructions show a reduction in artifacts and improvement in tissue contrast and voxel value accuracy.