VictorJuiz/thesis huggingface dataset:
Peer Effects in the Classroom: Evidence from New Peers

This thesis investigates the role of classmates in the academic achievement of an individual student. I propose a new strategy to identify ability spillovers and combine this strategy with a unique data set to estimate peer effects in education. Using this innovative approach, I quantify the average effect of peers on own academic achievement in middle school and analyze heterogeneity of own response to peers along ability and gender lines. In Chapter 1, I provide a comprehensive empirical analysis of linear-in-means model of peer interactions and estimate the effect of the average quality of peers on academic progress of six-graders in Ontario public schools. I provide convincing evidence of the validity of my identification strategy and show that the average quality of classmates measured by their lagged test scores matters for individual academic achievement. I find positive, large and significant ability spillovers from peers in the same classroom. To reconcile the broad spectrum of peer effect's estimates in the literature, I also investigate the impact of peers in the same school and grade. I show that once a peer group is aggregated to a grade or class level, the effect attenuates towards zero. In Chapter 2, I relax the main assumption of linear-in-means model and compare alternative models of peer interactions with the empirical results from the first chapter. My findings imply that all students unambiguously benefit from the presence of high achieving peers. At the same time, academic progress of high-achievers does not suffer from the presence of low-achieving classmates. This finding provides important policy implications for ability grouping of students in schools. With the help of a policy experiment I demonstrate that spreading out high ability students across classrooms is an efficient strategy to increase the achievement level of every student. In the third chapter, I introduce gender dimension into the analysis of peer effects and investigate the role of class gender composition on individual academic achievement. I employ two different identification strategies and find that large share of girls in a class facilitates academic progress of both boys and girls. While he average quality of girls is one of the determinants of own achievement, peer-to-peer interactions and improved discipline in a classroom, when more girls are present, also play an important role.

Keywords: Education
Peer Effects
Standardized tests
Knowledge spillovers
Endogeneity
Instrumental Variables
Advisor: Benjamin, Dwayne
The Concept of Self-reflexive Intertextuality in the Works of Umberto Eco

Umberto Eco’s novels are complex texts that work, that can be read and thus interpreted on several levels, including but not limited to the literary, semiotic, linguistic, philosophic, and historical. Notwithstanding the postmodern ideology of the irrelevance of the author (in terms of identity and intentionality) to a text’s interpretation, Eco’s novels offer another level of reading and interpreting that includes the author’s own personal reading experiences. In this way, the author arguably becomes an integral part of the text and is directly involved in the interpretive process. This dissertation is a reconsideration of the figure of the postmodern author whose authority in a text’s interpretation has been challenged by theories of structuralism, post-structuralism, and intertextuality. It undertakes this rethinking by considering the role of the author as reader--and thus as writer in the process of rereading and rewriting. This study also investigates the postmodern theory of intertextuality (i.e., the notion that all texts are [re]iterations of other texts) from the point of view of the author’s own reading experiences (since inevitably, consciously or unconsciously, what the author reads becomes an intertext). Thus, through a combination of the author’s own reading and writing experiences, presented and perceived intertextually and intratextually throughout the text itself, and a series of fictionalized versions of personal experiences, not only is the reader able to gain insight into the author’s motives, intentions and personality, but the author is also able to retain or regain some of the authority over the text he or she creates.

Keywords: Comparative Literature
Advisor: Hutcheon, Linda
Poisson Structures and Lie Algebroids in Complex Geometry

This thesis is devoted to the study of holomorphic Poisson structures and Lie algebroids, and their relationship with differential equations, singularity theory and noncommutative algebra. After reviewing and developing the basic theory of Lie algebroids in the framework of complex analytic and algebraic geometry, we focus on Lie algebroids over complex curves and their application to the study of meromorphic connections. We give concrete constructions of the corresponding Lie groupoids, using blowups and the uniformization theorem. These groupoids are complex surfaces that serve as the natural domains of definition for the fundamental solutions of ordinary differential equations with singularities. We explore the relationship between the convergent Taylor expansions of these fundamental solutions and the divergent asymptotic series that arise when one attempts to solve an ordinary differential equation at an irregular singular point. We then turn our attention to Poisson geometry. After discussing the basic structure of Poisson brackets and Poisson modules on analytic spaces, we study the geometry of the degeneracy loci---where the dimension of the symplectic leaves drops. We explain that Poisson structures have natural residues along their degeneracy loci, analogous to the Poincar\'e residue of a meromorphic volume form. We discuss the local structure of degeneracy loci that have small codimensions, and place strong constraints on the singularities of the degeneracy hypersurfaces of log symplectic manifolds. We use these results to give new evidence for a conjecture of Bondal. Finally, we discuss the problem of quantization in noncommutative projective geometry. Using Cerveau and Lins Neto's classification of degree-two foliations of projective space, we give normal forms for unimodular quadratic Poisson structures in four dimensions, and describe the quantizations of these Poisson structures to noncommutative graded algebras. As a result, we obtain a (conjecturally complete) list of families of quantum deformations of projective three-space. Among these algebras is an ``exceptional'' one, associated with a twisted cubic curve. This algebra has a number of remarkable properties: for example, it supports a family of bimodules that serve as quantum analogues of the classical Schwarzenberger bundles.

Keywords: algebraic geometry
Poisson geometry
Lie algebroids
meromorphic connections
degeneracy loci
Advisor: Gualtieri, Marco
Measuring the 21cm Power Spectrum from the Epoch of Reionization with the Giant Metrewave Radio Telescope

The Epoch of Reionization (EoR) is the transitional period in the universe's evolution which starts when the first luminous sources begin to ionize the intergalactic medium for the first time since recombination, and ends when the most of the hydrogen is ionized by about a redshift of 6. Observations of the 21cm emission from hyperfine splitting of the hydrogen atom can carry a wealth of cosmological information from this epoch since the redshifted line can probe the entire volume. The GMRT-EoR experiment is an ongoing effort to make a statistical detection of the power spectrum of 21cm neutral hydrogen emission due to the patchwork of neutral and ionized regions present during the transition. In this work we detail approximately five years of observations at the GMRT, comprising over 900 hours, and an in-depth analysis of about 50 hours which have lead to the first upper limits on the 21cm power spectrum in the range z=8.1 to 9.2. This includes a concentrated radio frequency interference (RFI) mitigation campaign around the GMRT area, a novel method for removing broadband RFI with a singular value decomposition, and calibration with a pulsar as both a phase and polarization calibrator. Preliminary results from 2011 showed a 2-sigma upper limit to the power spectrum of (70 mK)^2. However, we find that foreground removal strategies tend to reduce the cosmological signal significantly, and modeling this signal loss is crucial for interpretation of power spectrum measurements. Using a simulated signal to estimate the transfer function of the real 21cm signal through the foreground removal procedure, we are able to find the optimal level of foreground removal and correct for the signal loss. Using this correction, we report a 2-sigma upper limit of (248 mK)^2 at k=0.5 h/Mpc.

Keywords: reionization
hydrogen
radio astronomy
interferometry
Advisor: Pen, Ue-Li
Comparisons of spherical shell and plane-layer mantle convection models

Plane-layer geometry convection models remain useful for modelling planetary mantle dynamics however they yield significantly warmer mean temperatures than spherical shell models. For example, in a uniform property spherical shell with the same radius ratio, f, as the Earth's mantle; a bottom heating Rayleigh number, Ra, of 10^7 and a nondimensional internal heating rate, H, of 23 (arguably Earth-like values) are insufficient to heat the mean temperature, θ, above the mean of the non-dimensional boundary value temperatures (0.5), the temperature in a plane-layer model with no internal heating. This study investigates the impact of this geometrical effect in convection models featuring uniform and stratified viscosity. To address the effect of geometry, heat sinks are implemented to lower the mean temperature in 3D plane-layer isoviscous convection models. Over 100 models are analyzed, and their mean temperatures are used to derive a single equation for predicting θ, as a function of Ra, H and f in spherical and plane-layer systems featuring free-slip surfaces. The inclusion of first-order terrestrial characteristics is introduced to quantitatively assess the influence of system geometry on planetary scale simulations. Again, over 100 models are analyzed featuring a uniform upper mantle viscosity and a lower mantle viscosity that increases by a factor of 30 or 100. An effective Rayleigh number, Raη, is defined based on the average viscosity of the mantle. Equations for the relationship between θ, Raη, and H are derived for convection in a spherical shell with f = 0.547 and plane-layer geometries. These equations can be used to determine the appropriate heating rate for a plane-layer convection model to emulate spherical shell convection mean temperatures for effective Rayleigh numbers comparable to the Earth’s value and greater. Comparing cases with the same H and Raη, the increased lower mantle viscosity amplifies the mismatch in mean temperatures between spherical shell and plane-layer models. These findings emphasize the importance of adjusting heating rates in plane-layer geometry models and have important implications for studying convection with temperature-dependent parameters in plane-layer systems. The findings are particularly relevant to the study of convection in super-Earths where full spherical shell calculations remain intractable.

Keywords: mantle convection
geodynamics
geophysical fluid dynamics
Rayleigh number
heat flux
super-Earths
evolution of the Earth
numerical modelling
Advisor: Lowman, Julian
Cardiovascular Consequences of Estrogen Deficiency: Studies in Premenopausal Women

The influence of estrogen deficiency in physically active women with functional hypothalamic amenorrhea (ExFHA) on cardiovascular regulation is unknown. Three mechanistic studies compared cardiovascular responses to exercise and orthostatic stress in ExFHA women with responses in physically active (ExOv) and sedentary (SedOv) eumenorrheic ovulatory women. Measures included calf blood flow (BF), brachial artery (BA) endothelial dependent and independent function, shear rate (SR), vascular resistance (VR), blood pressure (BP), heart rate (HR), HR variability (HRV), muscle sympathetic nervous activity (MSNA), and serum renin-angiotensin-aldosterone system (RAAS) components. Study one examined the effects of a single bout of dynamic exercise on vascular function in ExFHA (n=12), ExOv (n=14), and SedOv (n=15) women. Pre-exercise, calf BF and BA endothelium-dependent flow-mediated vasodilation (FMD%) were lower (p<0.05) in ExFHA versus ovulatory women in association with higher (p<0.05) calf VR and lower (p<0.05) SR, respectively. Endothelium-independent vasodilation, assessed at baseline only, was also lower (p<0.05) in ExFHA. Post-exercise, calf BF was increased and VR decreased (p<0.05) in ExFHA women, similar (p>0.05) to that observed in ovulatory women. FMD% and SR were augmented (p<0.05) post-exercise, but both remained lower (p<0.05) in ExFHA versus ovulatory women (p<0.05). Study two investigated neurohumoral (MSNA and RAAS) BP regulation during orthostatic stress in ExFHA (n=12) and ExOv (n=17) women. Baseline systolic BP was lower (p<0.05) in ExFHA versus ExOv. Neurohumoral measures did not differ (p>0.05) between the groups at baseline. However, during hypotensive stimuli, MSNA increased to a greater extent (p<0.05), yet angiotensin II and renin were not activated in ExFHA women. Study three examined autonomic control of HR during orthostatic stress in ExFHA (n=11), ExOv (n=17), and SedOv (n=17) women. Lower HR (p<0.05) at rest and during orthostatic stress in ExFHA was associated with markedly elevated (p<0.05) HRV due to higher (p<0.05) parasympathetic modulation. Sympathetic modulation did not differ (p>0.05) between the groups. These studies indicate altered cardiovascular regulation in otherwise healthy ExFHA women. The influence of estrogen deficiency per se in these alterations are not clear, but in light of the etiology of amenorrhea, it is likely that complex interactions between estrogen and energy deficiency and exercise training are involved.

Keywords: Cardiovascular
Estrogen
Exercise
Functional Hypothalamic Amenorrhea
Advisor: Goodman, Jack
Harvey, Paula J.
c-MET and KRAS: Signalling and Clinical Implications in Colorectal Cancer

Colorectal cancer (CRC) is the third leading cause of death from cancer in North America. The KRAS gene is mutated in approximately 40-50% of all CRC, and this mutation precludes treatment with promising targeted therapeutics. c-MET is a receptor tyrosine kinase that is overexpressed in ~70% of CRCs, and expression is correlated with disease progression. We hypothesized that high c-MET plus mutant KRAS would result poor survival of CRC patients, by activating unique signalling pathways that may be targeted for therapeutic purposes. To this end, we used phosphoproteomics in a KRAS mutant cell line, and identified proteins phosphorylated on tyrosine in response to HGF stimulation, including a subset of those that contain SRC family kinase consensus motifs. Small molecule inhibitors of either SRC or c-MET reduced tyrosine phosphorylation of both proteins, indicating reciprocal signalling. We chose the c-MET target p190RhoGAP for future study, as it is often ubiquitously bound to p120RasGAP via phosphorylated tyrosine. We found that RasGAP expression is mediated in part by KRAS signalling, and that expression of RasGAP could partly rescue tumourigenicity of a CRC cell line where the mutant KRAS allele has been inactivated, indicating the requirement of both mutant KRAS and RasGAP expression in this model. We then conclude by looking at CRC patient samples to determine the role of KRAS mutation in the progression and survival of CRC. We found that both KRAS and c-MET copy number are correlated to KRAS mutation status, and that c-MET polysomy plus KRAS mutation leads to worse overall survival than KRAS mutation alone. Overall, we identified novel targets of c-MET and KRAS oncogenic signaling, and identify a population which may derive the most benefit from treatments targeting both of these lesions.

Keywords: c-MET
KRAS
Advisor: Tsao, Ming-Sound
Functional DNA Aptamers as Biotherapeutic Molecules

Aptamers are single-stranded oligonucleotides, DNA or RNA, which can bind to a myriad of targets such as ions, peptides, proteins, drugs, organic and inorganic molecules with high affinity and specificity. Aptamers are derived using combinatorial libraries comprised of a variable region flanked by two primer regions used for a process termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The central theme of my thesis was to use this technology to develop aptamers able to bind to validated therapeutic targets, specifically the Tumour Necrosis Factor alpha (TNFα) and Carcinoembryonic Antigen (CEA), and block their biological functions. As well, I investigated the use of CEA and MUC1 binding aptamers as targeting agents to guide and detect the delivery of contrast agent-loaded liposomes in tumour-bearing mice using computed tomography (CT) imaging. Aptamer selections successfully identified a 25-base aptamer (VR11) that can bind with high affinity and specificity to TNFα. VR11 blocked TNFα signaling, prevented apoptosis, reduced nitric oxide (NO) production in cultured cells and was non-immunogenic when injected into C57BL/6 mice. As well, aptamers were derived to the IgV-like N-domain of CEA. Two DNA aptamers were isolated containing a 40-base variable region, N54 and N56, bearing anti- CEA homotypic adhesive properties. These aptamers are not cytotoxic or immunogenic and III are able to prevent CEA-mediated homotypic and heterotypic cell adhesion events. In addition, the pretreatment of murine cancer cells expressing CEA with these aptamers prior to their intraperitoneal injection into C57BL/6 mice resulted in the prevention of tumour foci formation. Finally, the in vivo targeting of nanoparticles such as pegylated liposomes to tumour cells was enhanced by introducing tumour marker-specific DNA aptamers on their surface. The CEA-specific aptamer N54 and a 40-base second generation aptamer MUC1-VR1 that recognizes the tumour-associated mucin MUC1 were incorporated into liposomes containing the CT contrast agent Omnipaque350™ and Cy5 to characterize their binding to CEA and MUC1-expressing cancer cells in vitro. Pharmacokinetic studies also revealed that the incorporation of these aptamers into pegylated liposomes significantly lenghthened their circulation half-lives to values that parrallel that of untargeted pegylated liposomes.

Keywords: aptamer
therapeutic
biologic
Advisor: Gariepy, Jean
Role of the V-ATPase a3 Subunit in Osteoclast Maturation and Function

Bone resorption involves osteoclast-mediated acidification via a vacuolar type H+-ATPase (V-ATPase) found in lysosomes and at the ruffled border membrane. V-ATPases are proton pumps that include the a3 subunit, one of four isoforms (a1-a4) in mammals. The a3 isoform is enriched in osteoclasts where it is essential for bone resorption. Over 50% of humans with osteopetrosis have mutations in the a3 subunit and a3 mutations in mouse also result in osteopetrosis. A mouse founder with an osteopetrotic phenotype was identified in an N-ethyl-N-nitrosourea (ENU) mutagenesis screen. This mouse bears a dominant missense mutation in the Tcirg1 gene that encodes the a3 subunit resulting in the replacement of a highly conserved amino acid, arginine 740, with serine (R740S). The heterozygous mice (+/R740S) exhibit high bone density but otherwise have a normal appearance, size and weight. Osteoblast parameters are unaffected whereas osteoclast number and marker expression are increased along with a decreased number of apoptotic osteoclasts. V-ATPases from +/R740S osteoclast membranes have severely reduced proton transport along with wild type levels of ATP hydrolysis, indicating that the R740S mutation uncouples ATP hydrolysis from proton transport. The mutation however has no effect on ruffled border formation or polarization of +/R740S osteoclasts. Mice homozygous for R740S (R740S/R740S) have more severe osteopetrosis than +/R740S mice and die by postnatal day 14. Similarly to the mouse models that lack the a3 subunit (oc/oc and Tcirg1-/-) R740S/R740S osteoclasts do not polarize and lack ruffled border membranes. However R740S/R740S osteoclasts exhibit unique phenotypic traits, including increased apoptosis and defective early stage autophagy. Intracellular and extracellular acidification is absent in R740S/R740S osteoclasts, providing evidence for a requirement for lysosomal acidification for cytoplasmic distribution of key osteoclast enzymes such as TRAP and other important osteoclast phenotypic traits. This work provides evidence that the a3 subunit of V-ATPases and the proton pumping function of a3-containing V-ATPases play a major role in osteoclast survival, maturation and function.

Keywords: Bone
Bone biology
Osteoclast
Vacuolar (H+)-ATPase
Proton transport
ATP hydrolysis
Histomorphometry
Osteopetrosis
Advisor: Manolson, Morris Frank
Aubin, Jane E.
Applications of Optical Spectroscopy in Studies on Energy and Electron Transfer and Solvation Effects in Nanoscale and Molecular Systems

This thesis describes three investigations, ranging in subject matters, all of which relating to systems capable of photoinduced reactions involving energy or electron transfer. The phenomenon and the effects of environment in the various systems are explored using different methodologies of optical spectroscopy. As the chapters progress, different investigations introduce and build on fundamental concepts encountered and in complexity of the methodologies used to explore the systems. The first chapter introduces the preparation of water-soluble CdSe nanocrystal clusters. The clusters, created using a protein, are 3-D close-packed self-assemblies of nanocrystals. Due to this close-packed nature, electronic interactions between the nanocrystals allow for energy migration within the cluster. The structural and optical properties of the clusters were described. Then using steady-state spectroscopy, properties of the original nanocrystals were compared to that of the cluster to determine the consequence of nanocrystal coupling interactions and their potential use toward the development of artificial light-harvesting systems. In the second chapter, CdSe nanocrystals are functionalized with a unique electro-active polymer, and the electron transfer between the nanocrystal and the electro-active polymer adsorbate is investigated. Using fluorescence decay measurements, the electron transfer reaction inherent to the system with respect to a comprehensive range of dielectric solvents was explored. The study illustrates the high complexity of seemingly typical nanocrystal-based systems and provides general awareness of what factors need to be considered when dealing with such systems. The final chapter starts with an informal review of ultrafast nonlinear spectroscopy, focusing on two methods, three-pulse photon echo peak shift (3PEPS) and two-dimensional photon echo (2DPE) electronic spectroscopy, and how they are related. A straightforward approach for extracting 3PEPS data from 2DPE results is presented in a preliminary case study of a dye in two different solvents, one of which is electron-donating.

Keywords: electron and energy transfer
optical spectroscopy
Advisor: Scholes, Gregory D.