VictorJuiz/thesis huggingface dataset:
The Role of Consumer Interactions in the Consequences and Causes of Community Phylogenetic Structure
Keywords: Community Ecology
Phylogenetic Ecology

Phylogenetic structure measures patterns of evolutionary history within communities – are some communities composed of species more distantly or closely related than expected by chance? Due to common descent, closely related species are more ecologically similar, and so degrees of relatedness in a community may be good predictors of its ecology, more so than the number of species. Whether we are speaking of how phylogenetic structure arises as a consequence of ecological processes, or how phylogenetic structure affects the functioning of communities, the role of consumer organisms has received less attention than the role of resources. In this thesis, I ask what are the consequences and causes of phylogenetic structure of a potentially multi-level community, focusing on the underappreciated effects of consumer-resource interactions. In Chapter 2, I show how phylogenetic diversity of plant communities predicts the diversity and abundance of arthropods captured in a long-running biodiversity experiment better than species richness alone. In Chapter 3, I show how phylogenetic diversity and species richness interact to explain herbivore damage at a whole community level. In Chapter 4, I explore how phylogenetic structure of old field plant communities differs in plots of contrasting disturbance history, and speculate as to what factors – such as herbivory – may have contributed to these differences. In Chapter 5, I present a model which incorporates competition – through both resources and consumers of a focal trophic level – and environmental filtering, two factors which are thought to impact phylogenetic structure through their influence on ecological similarity. I show that environmental filtering interacts with competition to determine the coexistence of similar species, and that consumers may have different effects than do resources. My dissertation provides new insight into the importance of consumers in ecological communities, both through their effect on, and through their response to, patterns of evolutionary history in their prey.
The Role of GSK-3 in Mammary Gland Development and Oncogenesis
Keywords: Breast Cancer
Signal Transduction
Mouse Model
Mammary Gland
Stem Cell
Tumorigenesis

Glycogen synthase kinase-3 (GSK-3) alpha and beta are central regulators of key developmental pathways, including Wnt, Hedgehog and Notch, which control stem cell activities and cellular differentiation. Both forms of GSK-3 are also regulated by receptor tyrosine kinases via the PI3K/Akt growth-promoting pathway and are involved in feedback mechanisms that maintain signaling homeostasis. These signaling systems have critical functions in mammary gland development and aberrations in them have been implicated in breast cancer. However, the role of GSK-3 in breast oncogenesis is unclear. Here, I provide evidence that maintenance of appropriate GSK-3 activity is necessary for normal acinar morphogenesis of mammary cells in the ductal/alveolar epithelium. Inadequate GSK-3 levels result in enlarged structures that often lack hollow lumens and resemble early premalignant breast cancer lesions. A potential contribution for PI3K signaling to this phenotype was identified as a PI3K inhibitor partially reversed the observed morphological defects. Mammary epithelial cell (MEC) identity also requires modulation of signals through the Wnt/beta-catenin pathway. GSK-3-depleted mammary glands not only transdifferentiate into squamous epithelium but also develop highly proliferative adenosquamous carcinomas characterized by activated beta-catenin. Furthermore, beta-catenin appears to be required for both cell fate changes and tumorigenesis in the absence of GSK-3 function. Mammary tissues engineered to enable conditional deletion of beta-catenin in a GSK-3-null background also assumed an epidermoid cell fate with ensuing tumor formation albeit with a significantly longer latency and different histopathology. The metaplastic nature of tumors observed is similar to a rare yet aggressive form of human breast disease, metaplastic breast carcinomas (MBCs). Mammospheres (MS) generated from GSK-3 depleted MECs exhibited a less compact morphology compared to those with activated beta-catenin, which also exhibited an expansion of the CD24:CD49f double positive progenitor population and enhanced self-renewal. No MS were formed by MECs lacking GSK-3 and beta-catenin. ErbB2/Neu-mediated mammary tumor progression has been associated with Wnt/beta-catenin pathway activation. Loss of beta-catenin delayed tumor onset in a constitutively active ErbB2 mouse model but did not alter either the luminal characteristics of the ensuing tumors nor their metastatic potential. Collectively these studies indicate GSK-3 plays important roles in mammary gland function thereby suppressing mammary tumor formation.
Locating Critical Care Nurses in Mouth Care: An Institutional Ethnography
Keywords: oral hygiene
mouth care
ventilator-associated pneumonia
institutional ethnography
critical care
intensive care
nursing

Intubated and mechanically ventilated patients are vulnerable to respiratory tract infections. In response, the Ontario government has recently mandated surveillance and reporting of ventilator-associated pneumonia (VAP). Serious respiratory infections, and the related costs of additional care can be reduced in part, through oral hygiene. However, the literature asserts that oral care is neglected in busy, high-tech settings. Despite these concerns, little research has examined how mouth care happens in the critical care unit. The purpose of this institutional ethnography (IE) was to explore the social organization of mouth care in one critical care unit in Ontario, Canada. As a reflexive and critical method of inquiry, IE focuses on features of everyday life that often go unnoticed. In paying special attention to texts, the ethnographer traces how institutional forces that arrive from outside the practice setting coordinate experiences and activities. Inquiry began in the field with day/night participant observation to better understand the particularities of nursing care for orally intubated patients. Other data sources included reflexive fieldnotes, stakeholder interviews, and transcripts as well as work documents and artifacts. Over time, the analysis shifted from the critical care unit to the larger social context of Ontario’s Critical Care Transformation Strategy. Analysis traced the discursive and translocal social relations that permeate nursing work. Findings revealed a disjuncture between the ideals of VAP prevention and the actualities of mouth care. Tensions and contradictions emerged as nurses described their location within an expansive accountability network: nursing duties now extend beyond oral care to a controversial project of epidemiological surveillance. Patient comfort and safety now rest upon a hidden nursing agenda to overcome limited time, training and tools in oral care. Nurses worried that the effectiveness of preventative oral care was inhibited by technical problems of application that remain uninvestigated and unresolved. As a counterpoint to assertions that oral care is neglected, this study demonstrates how nursing knowledge and agency is obscured. Because international infection-prevention guidelines increasingly endorse oral care, novel research investigating the practice problems nurses encounter is warranted.
Mining the Medulloblastoma Genome and Transcriptome
Keywords: medulloblastoma
cancer
brain tumor
epigenetics
genomics

Medulloblastoma is a devastating disease of the cerebellum, and the most common solid pediatric malignancy of the central nervous system. Recently, transcriptome-wide profiling has dissected medulloblastoma from one single disease into four disparate molecular subgroups – namely WNT, SHH, Group3 and Group4. Distinct genomic, cytogenetic, mutational and clinical spectra associated with these subgroups highlight the pressing need for targeted therapies, of which encouraging preliminary results have been generated. While the promise of personalized medicine is within our reach, improved understanding of the molecular mechanisms driving pathogenesis is critical to this process. The intent of my PhD thesis research was to characterize the molecular mechanisms contributing to medulloblastoma pathogenesis, and the clinical impact of these aberrations. Through a combinatorial use of genetic and epigenetic profiling, next-generation sequencing and bioinformatics analyses we have identified subsets of tumors with transcriptional signatures that influence their clinical properties. Furthermore, our results have shed light on the establishment of the normal cerebellar cytoarchitecture, identifying a physiological glutamate gradient with critical implications to both cerebellar development and disease. This thesis stresses the importance of interrogating medulloblastoma in a subgroup-specific manner. Our findings demonstrate the utility of pursuing an integrated (copy number, mutational, transcriptional and epigenetic) molecular approach, to further our understanding of the pathobiology of medulloblastoma. Finally, we propose rationale therapeutic targets that may improve the treatment of aggressive variants of this disease.
Understanding Genome Structure and Response to Perturbation
Keywords: Genomics
Chemical Genomics
Chromatin
Drug resistance
Archaea

The past few decades have witnessed an array of advances in DNA science including the introduction of genomics and bioinformatics. The quest for complete genome sequences has driven the development of microarray and massively parallel sequencing technologies at a rapid pace, yielding numerous scientific discoveries. My thesis applies several of these genome-scale technologies to understand genomic response to perturbation as well as chromatin structure, and it is divided into three major studies. The first study describes a method I developed to identify drug targets by overexpressing human genes in yeast. This chemical genomic assay makes use of the human ORFeome collection and oligonucleotide microarrays to identify potential novel human drug targets. My second study applies genome resequencing of yeast that have evolved resistance to antifungal drug combinations. Using massively parallel genomic sequencing, I identified novel genomic variations that were responsible for this resistance and it was confirmed in vivo. Lastly, I report the characterization of chromatin structure in a non-eukaryotic species, an archaeon. The conservation of the nucleosomal landscape in archaea suggests that chromatin is not solely a hallmark of eukaryotes, and that its role in transcriptional regulation is ancient. Together, these 3 studies illustrate how maturation of genomic technology for research applications has great utility for the identification of potential human and antifungal drug targets and offers an encompassing glance at the structure of genomes.
Bridging Understandings of Differences, Learning and Inclusion: Voices of Minoritized Students
Keywords: disabilities/autism
ethnicity
race
language
intersecting differences
social science research
diversity
inclusion
narratives
critical discourse analysis
critical theory
new sociology of childhood
children as co-researchers
mosaic/multi-method research
social model lens of disability
middle years

Many Canadian children from minority status groups experience long-term academic complexities, influencing their sense of school belonging and engagement (Willms, 2003; Willms & Flanagan, 2007). Research demonstrates children with intersecting differences of race, ethnicity, language, and disability, and those in their middle years (10-13 years old), undergo heightened academic challenges (Blanchett, Klingner, & Harry, 2009; Cobbold, 2005). Within Toronto, one of the most diverse Canadian cities, this study explores the narratives of 6 middle years children with intersecting differences of race, ethnicity, language, and disabilities. The narratives highlight participants’ understandings of differences, learning, and inclusion. Specifically, what are marginalized children’s personal schooling experiences, and how may these insights support inclusive learning, teaching, and sense of belonging? Underpinned by conceptual lenses of (a) critical theory, from which stems critical pedagogy and critical multicultural education, and (b) the “new sociology of childhood” (Greene & Hogan, 2005), which includes social constructivist and participatory frames, this study employed qualitative narrative and critical discourse analysis research methods throughout 7 research sessions over a 4 month period. Accessing children’s multiple views, data collection included a “mosaic” (Clark & Moss, 2001) multi-method approach, such as semi-structured interviews with open-ended questions, writing activities, imaginative story games, photography, and drawings. The children’s narratives are re-presented as portrait narrative summaries within this paper. Surfacing findings include two predominant themes: (a) Participants’ conceptualizations of differences, race, ethnicity, language, culture, disability, and autism. Participants’ views relate to theories of denying differences, colour blindness, White discourse, and Othering; and (b) Interconnecting factors of inclusive and exclusive elements contributing to participants’ overall sense of school belonging. Additionally this theme highlights matters of meritocracy, individualization, and the “good” student. Underscoring both themes are notions of normalcy, and deficit and deficient-based discourses. Inviting student voice into educational conversations and research processes, this study demonstrates the importance of listening to voices of children with intersecting differences, as they may adeptly advance areas of inclusion and diversity.
Physiological Effects of Barley: Examining the Effects of Cultivar, Processing and Food Form on Glycemia, Glycemic Index, Satiety and the Physico-chemical Properties of β-glucan
Keywords: Carbohydrates
glycemic index
Barley
beta-glucan

Barley has been receiving increased attention as a human food due to the health benefits associated with β-glucan fiber and its potential as a low glycemic index (GI) functional food. Research has shown a relationship between the physico-chemical properties of β-glucan and the physiological effects, which may be altered by processing. However, it is not known if the physiological effects of consuming barley are affected by variations in chemical composition among cultivars or by common processing methods such as pearling or milling. The primary objective of this thesis was to characterize the effects of differences in cultivar starch and fibre content, level of pearling and milling on the GI, satiety and the physico-chemical properties of β-glucan. Nine barley cultivars varying in starch-type and β-glucan content were studied in three experiments in separate groups of ten healthy participants. Blood glucose and satiety ratings were measured and the GI was calculated. Total starch, total fibre, β-glucan, molecular weight (MW), solubility and β-glucan viscosity were determined in vitro. Results showed that GI varied by cultivar (CDC-Fibar, 26 ± 3 vs. AC-Parkhill, 35 ± 4, P < 0.05) and pearling (WG, 26 ± 4 vs. WP 35 ± 3, P < 0.05). When two cultivars were milled and processed to wet pasta the GI increased by 184% (P < 0.05). The pearled wet pasta had a significantly lower GI compared to the whole grain (P < 0.05). Boiled barley kernels tended to elicit greater satiety than white bread, but the difference was not significant. In both the boiled barley kernels and the wet pasta, pearling did not affect the MW, viscosity and solubility. MW did not significantly differ between cultivars but solubility and viscosity did (P < 0.05). The wet pasta had significantly lower MW, solubility, viscosity but not β-glucan content than the boiled barley kernels (P < 0.05). In conclusion, pearling did not have an effect but milling and extruding resulted in significant reduction in MW, solubility and viscosity. The GI of barley is influenced significantly by cultivar, pearling and milling. Further studies are required to determine the effect on satiety.
Eh 440: Tuning into the Effects of Multiculturalism on Publicly Funded Canadian Music
Keywords: Music
Multiculturalism
Canadian Music
Arts Councils
Canada Council for the Arts
Ontario Arts Council
Toronto Arts Council

In 1988, Canada enshrined multiculturalism into law, a democratizing manoeuver that allowed practitioners of non-Western and non-classical forms of music to agitate for equitable access to public arts funding. This agitation ultimately forced government-funded Canadian arts councils to re-examine their Eurocentric granting programs and to expand the parameters by which they fund music. Today’s arts council peer assessors must now assess applications covering a broad range of musical genres and differing aesthetic values, and must incorporate into their evaluations the councils' sociopolitical priorities emphasizing diversity and inclusivity. Yet, few assessors understand why and how identity politics informs the contemporary music-making of ethnocultural minorities and how collectively held stereotypes influence Canadians’ expectation for ethnocultural representation. In this thesis, I endeavour to separate the historical, sociopolitical and philosophical threads that have contributed to the current musical environment in Canada. I begin by examining the parallel histories of funding for high culture—which led to public arts funding—and early celebrations of multiculturalism. I then examine liberal democratic philosophy and how it fostered the “politics of difference” that characterizes Canadian multiculturalism. Although liberal democracy holds that each citizen be recognized as equal and have equality of opportunity to nurture his or her individual, authentic self, Canadians have historically treated ethnocultural minorities unequally, resulting in the latter pursuing politics of difference based upon collective characteristics. Collective difference politics, though, are prone to stereotype. In the Canadian music world these stereotypes are manifest in external desires for authentic ethnocultural representation, which can overshadow a minority musician’s ability to cultivate a unique musical voice. I devote the second part of my thesis to examining the effects of equity initiatives on Canadian arts councils. Based upon interviews with music and equity officers from the Canada Council, the Ontario Arts Council and the Toronto Arts Council, I show how the dichotomy between collective and individual authenticities results in unequal modes of assessment that perpetuate both ethnocultural stereotypes and Western classical music’s monopoly over funding, limiting our definitions of Canadian music.
Moduli of Abelian Schemes and Serre's Tensor Construction
Keywords: Arithmetic Geometry
Abelian Schemes

In this thesis we study moduli stacks \calM_\Phi^n, indexed by an integer n>0 and a CM-type (K,\Phi), which parametrize abelian schemes equipped with action by \OK and an \OK-linear principal polarization, such that the representation of \OK on the relative Lie algebra of the abelian scheme consists of n copies of each character in \Phi. We do this by systematically applying Serre's tensor construction, and for that we first establish a general correspondence between polarizations on abelian schemes M\otimes_R A arising from this construction and polarizations on the abelian scheme A, along with positive definite hermitian forms on the module M. Next we describe a tensor product of categories and apply it to the category \Herm_n(\OK) of finite non-degenerate positive-definite \OK-hermitian modules of rank n and the category fibred in groupoids \calM_\Phi^1 of principally polarized CM abelian schemes. Assuming n is prime to the class number of K, we show that Serre's tensor construction provides an identification of this tensor product with a substack of the moduli space \calM_\Phi^n, and that in some cases, such as when the base is finite type over \CC or an algebraically closed field of characteristic zero, this substack is the entire space. We then use this characterization to describe the Galois action on \calM_\Phi^n(\overline{\QQ}), by using the description of the action on \calM_\Phi^1(\overline{\QQ}) supplied by the main theorem of complex multiplication.
Remodeling Planning Domains Using Macro Operators and Machine Learning
Keywords: Classical Planning
Learning
Macro Operators
Remodeling

The thesis of this dissertation is that automating domain remodeling in AI planning using macro operators and making remodeling more flexible and applicable can improve the planning performance and can enrich planning. In this dissertation, we present three novel ideas: (1) we present an instance-specific domain remodeling framework, (2) we recast the planning domain remodeling with macros as a parameter optimization problem, and (3) we combine two domain remodeling approaches in the instance-specific remodeling context. In the instance-specific domain remodeling, we choose the best macro-augmented domain model for every incoming problem instance using a predictor that relies on previously solved problem instances to estimate the macros to be added the domain. Training the predictor is achieved off-line based on the observed relation between the instance features and the planner performance in the macro-augmented domain models. On-line, the predictor is used to find the best remodeling of the domain based on the problem instance features. Our empirical results over a number of standard benchmark planning domains demonstrate that our predictors can speed up the fixed-remodeling method that chooses the best set of macros by up to 2.5 times. The results also show that there is a large room for improving the performance using instance-specific over fixed remodeling approaches. The second idea is recasting the domain remodeling with macros as a parameter optimization. We show that this remodeling approach can outperform standard macro learning tools, and that it can significantly speed up the domain evaluation preprocessing required to train the predictors in instance-specific remodeling, while maintaining similar performance. The final idea applies macro addition and operator removal to the instance-specific domain remodeling. While maintaining an acceptable probability of solubility preservation, we build a predictor that adds macros and removes original operators based on the instance’s features. The results show that this new remodeling significantly outperforms the macro-only fixed remodeling, and that it is better than the fixed domain models in a number of domains.