VictorJuiz/thesis huggingface dataset:
Understanding the Teacher’s Role in a Knowledge Community and Inquiry Curriculum

Knowledge and Community Inquiry (KCI) is an innovative instructional model that integrates a dimension of scaffolded inquiry within a knowledge community approach. While early studies of KCI successfully implemented the model in the form of substantive curricular units, the teacher’s role within those curricula was not clearly explicated, nor is it included formally within current versions of the model. This dissertation seeks to clarify the teacher’s role in the KCI model by examining one KCI curriculum unit in which three high school science teachers coordinated five sections of a ninth grade general science course (n = 106) to collectively study the topic of climate change over a nine-week period. One teacher had been engaged in the development of the curriculum. The study uses open coding and content analysis to examine: (a) the teacher’s role as it was designed or intended in the curriculum design; (b) the three teachers’ prior knowledge and experience, to examine the knowledge disparity among the teachers; (c) the teachers’ enactment of the curriculum, to capture what teachers actually did in their classroom, as contrasted with the designed curriculum; and (d) the teachers’ interaction with students, to identify the interaction patterns and their relationship to the teachers’ prior knowledge and experience. Curriculum design documents, teacher interviews, and video recordings of classroom teaching provided the data sources. The curriculum design analysis identified six categories of teacher’s role: (a) content lecturing, (b) evaluating students, (c) introducing learning activities, (d) making connections, (e) explanation or elaboration, and (f) classroom management. The teacher knowledge analysis identified the differences among the teachers in terms of the knowledge and experience of: (a) scientific content on climate change, (b) inquiry and community learning pedagogy, (c) their role as a teacher, (d) technology’s role in teaching, and (e) in the coherence of their knowledge. The enactment analysis revealed that all teachers performed more roles than the research team had anticipated in the designed curriculum. The interaction analysis indicated that while teachers spent a lot of class time dealing with logistical and pedagogical issues, they also spent considerable time guiding students’ learning activity, setting the learning context, and helping students to elaborate their ideas. The contributions of this study include: (a) a formal description of the teacher’s role in the KCI model, (b) specific guideline for teachers teaching with KCI model, (c) scientific information concerning different forms of teacher knowledge and their correlation with classroom practice, (d) methods of analysing teacher-student interaction and measuring the coherence of teachers’ knowledge.

Keywords: Classroom enactment
Knowledge Community and Inquiry
Teacher knowledge
Teacher's role
Advisor: Slotta, James D
An Investigation of the Regulation of RNA Polymerase II Transcription

The C-terminal domain (CTD) of the largest RNA polymerase II (RNAPII) subunit, POLR2A, is a platform for modifications specifying the recruitment of factors that regulate transcription, messenger RNA (mRNA) processing, and chromatin remodeling. I found that a CTD arginine residue (R1810) is symmetrically dimethylated (me2s), allowing it to recruit the Tudor domain of the SMN protein, which is mutated in spinal muscular atrophy (SMA). SMN can oligomerize and interact with Senataxin (SETX), which is sometimes mutated in ALS4 (Amyotrophic Lateral Sclerosis). I showed that CTD R1810me2s and SMN, like SETX, are required for resolving R-loops created by RNAPII in transcription termination regions. A defect in this process is recapitulated in the SMA disease state. FUS and TDP-43 (TARDBP) are DNA/RNA binding proteins that are involved in numerous aspects of gene regulation, and they are known to interact with each other and with SMN. As well, they are sometimes mutated in neurodegenerative diseases such as ALS and FTD (Frontal Temporal Dementia). I was able to show that FUS and TDP-43 act downstream of the CTD R1810me2s-SMN pathway, and that defects in the recruitment of these proteins can influence RNAPII transcription termination through the accumulation of R-loops and also cause DNA damage. I propose that mis-regulation of RNAPII termination could lead to DNA damage, which may contribute to neurodegenerative disorders like SMA and ALS/FTD.

Advisor: Greenblatt, Jack F
How Does a Virtual Learning Environment Support and Enhance Community Building in Initial Teacher Education Cohorts?

In 2012-2013, a new virtual learning environment called Pepper was introduced to six face-to-face student cohort groups in an Initial Teacher Education (ITE) program at a large Ontario university. Cohort instructors reported a high level of student engagement and felt that Pepper was more successful at supporting community than the previous commercial course management system. These findings inspired the current case study. What specific features and functionality of Pepper seemed to promote a deeper sense of community within these cohort-based environments, and why? The research questions were answered by collecting data from a variety of sources. First, in order to comprehend student/instructor online behaviours, automatically generated Pepper log files were examined. A survey was conducted to gather student opinions about different aspects of Pepper’s functionality. Finally, students, instructors and the developer were interviewed to gather in-depth perspectives and experiences. Data analysis revealed that, contrary to expectations, Pepper was not used to conduct community-wide discussions, since most conversations took place daily during face-to-face classes. Instead, Pepper’s perceived value was associated with its ease of use and its ability to i) share documents; ii) send and receive private messages; iii) make announcements; and iv) integrate calendars. Thus it complemented face-to-face community activities rather than replacing them. The research documented unconventional and innovative instructor uses of Pepper, including the hosting of multiple cohort groups in one shared environment and the use of a shared folder feature to foster overlapping cohort memberships. These behaviours mark a change from other course management systems where courses exist in separate online silos with no opportunity for interaction or collaboration. Logfiles revealed that private messaging was used more often than public postings, despite the environment’s open format, raising questions about the possible importance of private discourse in communities. Finally, there was a perceived need for Pepper to be more accessible through smartphones to better support students’ moment-by-moment need for information between and during classes. Recommendations are made relating to instructor and student training, full open access courses, additional tools and graphic representations. The concept of participatory presence is introduced as a new online cohort community framework.

Keywords: cohorts
community
education
environment
teacher
virtual
Advisor: Hewitt, James
Operations Research Methodologies to Improve the Quality, Accessibilty and Equity of Primary Care

A growing body of evidence reveals the importance of primary care to the overall health of populations, resulting in an increasing interest in efficient, effective, timely and equitable delivery of primary care services. This research focuses on two perspectives of delivering primary care. First, the work focuses on the quality of primary care delivery, represented by distribution of facilities that provide primary care on different quality levels and incur varying costs on the regulator. The proposed model optimizes the geographic distribution of facilities (locations and types) and provides tradeoffs between two objectives - the quality of provided care and the annual operating cost. The Pampalon deprivation index is incorporated directly as a proxy of varying needs, as it was correlated with complex health-care problems, more frequent visits and barriers to obtain care. Results are showcased on the area of Kingston, Ontario. Second, the distribution of general practitioners is addressed, measured in terms of general practitioners (GPs) per population. Many countries are experiencing inequitable distribution of GPs, such that does not match the distribution of the population. It usually results from the fact that health professionals are choosing practice locations according to their own preferences and considerations. To address this issue, human choice is incorporated into the modeling approach explicitly, using Huff’s spatial interactions approach. The utilities of the professionals when choosing communities are modeled, affecting in turn the probabilities of location choice. The presented model explores the option of modifying policies so that the resulting distribution of general practitioners in the studied geographic area will be more equitable. As an example, educational policies are explored, devising the optimal locations of residency training of family physicians and their background combinations (at each training location) for Ontario. The developed methodologies showcased for the province of Ontario, Canada, however they are general enough to be used in any jurisdiction with similar characteristics.

Keywords: Healthcare
Optimization
Primary Care
Advisor: Carter, Michael W
Verter, Vedat
Sexual and Viability Selection on a Wild Population of Tree Crickets Experiencing Female-biased Predation

Sex-biased predation can have important evolutionary consequences for prey, however female-biased predation is uncommon in nature and understudied in science. Understanding female-biased predation is necessary to create a complete picture of the costs of sex-specific behaviours and phenotypes. In this thesis, I used a system of tree crickets, Oecanthus nigricornis, which suffer female-biased predation by wasp predators, Isodontia mexicana, to 1) test hypotheses about the causes of female-biased predation; 2) quantify how viability selection caused by such predation may affect male and female traits differently; and 3) test if sexual selection opposes or reinforces viability selection among each sex. To address the first objective, I compared tree cricket prey taken from I. mexicana nests to surviving tree crickets, and found that wasps took significantly more adult females only when females were larger than males. I also found that females with more ovarian eggs were more likely to be caught by wasps, and laboratory experiments showed that female jumping ability is negatively affected by egg load. To address the second objective, I compared viability selection (from wasp predation) on males and females over several years. Within single study seasons, male and female phenotypes were affected differently by viability selection, but temporal variation in selection across years resulted in overall weak nonlinear selection on both sexes, and no significant effect on sexual dimorphism. To address the third objective, I compared the direction and form of sexual selection (calculated using estimates of mating success) in males and females to those of viability selection, and found that sexually selected traits had viability costs in males but not in females. Thus, in this predator-prey system, I found that females pay a viability cost for investing in fecundity traits, and males pay a viability cost for investing in sexual traits.

Keywords: Mating systems
Natural selection
Nuptial gifts
Predator-prey interactions
Sex-biased predation
Sexual selection
Advisor: Gwynne, Darryl T
Interactive Visual Data Exploration: A Multi-focus Approach

Recently, the amount of digital information available in the world has been growing at a tremendous rate. This huge, heterogeneous, and complicated data that we are continuously generating could be an incredible resource for us to seek insights and make informed decisions. For this knowledge extraction to be efficient, visual exploration of data is demanded in addition to fully automatic methods, because visual exploration can integrate the creativity, flexibility, and general experience of the human user into the sense-making process through interaction and visualization techniques. Due to the scale and complexity of data, robust conclusions are usually formed by coordinating many sub-regions in an information space, which leads to the approach of multi-focus visual exploration that allows browsing different data segments with multiple views and perspectives simultaneously. While prior research has proposed a myriad of information visualization techniques, there still lacks comprehensive understanding about how visual exploration can be facilitated by multi-focus interactive visualizations. This dissertation investigates issues and techniques of multi-focus visual exploration through five design studies, touching various types of data in a range of application domains. The first two design studies address the exploration of numerical data values. KronoMiner presents a multi-purpose visual tool for exploring time-series based on a dynamic radial hierarchy; and the ChronoLenses system supports exploratory visual analysis of time-series by allowing users to progressively construct advanced analytical pipelines. The third design study focuses on the exploration of logical data structures, and presents DAViewer that facilitates computational linguistics researchers to explore and compare rhetorical trees. The last two design studies consider the exploration of heterogeneous data attributes (or facets). TimeSlice facilitates the browsing of multi-faceted events timelines by organizing visual queries in a tree structure; and PivotSlice aids the mining of relationships in multi-attributed networks through a dynamic subdivision of data with customized semantics. This dissertation ends with critical reflections and generalizations of the experiences obtained from the case studies. High-level design considerations, conceptual models, and visualization theories are distilled to inform researchers and practitioners in information visualization for devising effective multi-focus visual interfaces.

Keywords: Human-computer interaction
Information visualization
Multi-focus visualization
Visual analytics
Visual data exploration
Advisor: Balakrishnan, Ravin
The Solidarity Encounter between Indigenous Women and White Women in a Contemporary Canadian Context

This dissertation tracks the gendered operation of white settler liberal subjectivity at a specific site of settler colonial relations—the “solidarity encounter” between Indigenous women and white women in Canada. Through in-depth qualitative analysis of interviews and self-reflection (as a white settler woman ally), I examine the encounter’s intersubjective relations, shining the theoretical spotlight on how white women negotiate our tenuous status as settlers. Attentive to the complexity of these relations, including how white women allies grapple with our dominant positionality, I signal the perniciousness of white settler liberal subjectivity and the deep quest for legitimacy/innocence at its core. This quest, I argue, manifests itself as a white desire for proximity to Indigenous women, which in turn takes various forms and is often experienced by Indigenous women as invasive. I dedicate three chapters to mapping the sometimes subtle expressions of this desire (e.g., the need for acceptance, inclusion, forgiveness, healing, empowerment/purpose, friendship) and its role in liberal self-making projects, i.e., how it serves to negate colonial hierarchies and/or white settler women’s colonial complicity therein. Further, I develop the concept of the “impulse to solidarity”—the bundle of desires and discursive practices that propels white settler women in their pursuit of proximity, an impulse related to, but distinct from the “helping imperative” (Heron, 2007). White women allies find it difficult to resist the gendered dictates of liberal subjectivity, which in a settler colonial context demand our reproduction as legitimate national subjects vis-à-vis Indigenous women Others. Despite the inescapability of the “colonial present” (Gregory, 2004), I also note a cautious optimism among participants regarding the possibility of non-colonizing solidarity. I propose a framework for reconfiguring intersubjective relations in the solidarity encounter best encapsulated by the directive “step back, but not out.” Struck by pervasive spatial references in participant narratives, I characterize the problem (colonizing solidarity) and its solution (non-colonizing solidarity) in spatialized terms—white settler women must interrogate and curb our solidarity impulse and related practices of proximity. We must recognize when settler liberal self-interest takes centre stage, compels us to “come too close” and diminishes the collective political work of solidarity.

Keywords: Indigenous/non-Indigenous relations
liberal subject
settler colonialism
solidarity
subjectivity
whiteness
Advisor: Razack, Sherene
Programmed Cell Death is Intrinsic to Yeast Gametogenesis

Studies of the yeast Saccharomyces cerevisiae have provided many critical insights into fundamental eukaryotic cell biology. Programmed cell death (PCD) is integral to animal and plant development, contributing to tissue homeostasis and morphogenesis by removing unneeded cells. Although PCD is of widespread importance to many organisms, studies of yeast have provided relatively limited insight into the mechanisms and physiological roles of PCD. Investigations of yeast cell death pathways have almost exclusively been restricted to cells undergoing vegetative growth, leaving no exploration of their potential functions during developmental transitions in the yeast life cycle. Here, I characterize a novel PCD intrinsic to yeast gametogenesis, or sporulation. Upon sporulation induction under severe carbon limitation, yeast cells subject only a fraction of their potential gametes to spore differentiation. Meiotic products which are not subject to spore development are shown to adopt an alternative fate of programmed destruction. I characterize the elimination of aborted gametes as programmed nuclear destruction (PND), a phenomenon which exhibits hallmarks of animal and plant PCD. Cells executing PND display fragmentation of genomic DNA by endonuclease G, a hallmark of animal apoptosis. The destruction of nuclear protein during PND is mediated by vacuolar proteases which undergo programmed release from the vacuole during sporulation. To understand the mechanisms underlying PND, I consider PND as part of a broader cell death program executing the demise of the meiotic mother cell. Accordingly, I find that the mother cell adopts characteristics of a dying cell following meiosis, including mitochondrial depolarization, vacuolar swelling and the loss of plasma membrane integrity. The timely execution of the mother cell depends on the development of its daughter spores, as cells lacking regulators of spore morphogenesis are unable to execute mother cell demise normally. As an extension of my studies of PCD, I also present preliminary, unanticipated evidence that Nuc1 contributes to mitochondrial genome metabolism. Overall, I propose that PCD of the meiotic mother cell is an intrinsic aspect of yeast gametogenesis which shares common genetic regulation with spore morphogenesis.

Keywords: autophagy
cell death
meiosis
mitochondria
sporulation
vacuole
Advisor: Meneghini, Marc D
Nonparametric Methods for Interpretable Copula Calibration and Sparse Functional Classification

Nonparametric estimation is a novelty statistical method which relaxes the distribution assumption about the relationship between response and covariate, in contrast to parametric estimation. This method has been applied in many field of interest, including density function, regression model and derivative function. One of the important application of nonparametric estimation is modelling dependence among random variables via copula approaches has attracted considerable research attention. With advances in data collection, the strength of dependence often varies according to some covariate, which motivates the dependence calibration using conditional copulas. We propose a penalized estimation framework for the copula parameter function that inherits the flexibility of a nonparametric method and, at the same time, yields a parsimonious and interpretable dependence structure. The theoretical analysis guarantees that the penalized estimators enjoy the oracle properties and behave asymptotically as well as their nonparametric counterparts, while numerical experiments demonstrate the improved empirical performance. We then apply the proposed method to a twin birth weights data. Another important application of nonparametric estimation is classifying the functional data. We consider the classification of sparse functional data that are often encountered in longitudinal studies and other scientific experiments. To utilize the information from not only the functional trajectories but also the observed class labels, we propose a probability enhanced method achieved by weighted support vector machine based on its Fisher consistency property to estimate the effective dimension reduction space. Since only a few measurements are available for some, even all, individuals, a cumulative slicing approach is suggested to borrow information across individuals. We provide justification for validity of the probability-based effective dimension reduction space, and a straightforward implementation that yields a low-dimensional projection space ready for applying standard classifiers. The empirical performance is illustrated through simulated and real examples, particularly in contrast to classication results based on the prominent functional principal component analysis.

Advisor: Yao, Fang