VictorJuiz/thesis huggingface dataset:
Essays on Housing Markets, Housing Market Policies, and Taxation

This thesis collects three papers studying topics related to housing markets, taxation, and macroeconomics. In Chapter 1, I study how capital and housing should be taxed. I formulate a housing model where credit is limited and the ability to invest capital varies across households. I calibrate the model to U.S. data and use it to determine the effect of housing and capital income taxation on the housing market and societal welfare. My main finding is that housing should be taxed at a positive rate and capital income should be subsidized. On the one hand, the housing tax raises housing costs for both renters and home-owners. On the other hand, the capital income subsidy encourages the most productive households to increase their capital investments, and thus, wages paid to labor rise. Since wages rise more rapidly than housing costs, overall welfare rises. In Chapter 2, I examine the misallocation of residential land in Israel and its implications for income taxation and societal welfare. I develop a methodology to calibrate a housing model to a transition path of over 50 years of Israeli data on land sales and show that Israel's government substantially oversold land and could have reduced its income tax rate by 1.8 percentage points. Restricting land sales is optimal because initial retired households own little land, initial housing demand is low and grows faster than interest rates, and because of the need to preserve land for large future generations. In Chapter 3, I explore the effect of wage income expectations on housing prices. I build a housing model, calibrate it to U.S. data, and show that wage income expectations alone can explain about 20% of the 2008 boom-bust in U.S. housing prices. The result is an outcome of households' perception that their expected life-time wage income is going up (down) during a sequence of good (bad) income shocks, which leads to a rapid increase (decrease) in housing demand and thus housing prices. This phenomenon is absent with rational expectations.

Keywords: Housing
Taxation
Wealth Distribution
Advisor: Kuruscu, Burhanettin
Kambourov, Gueorgui
Examining the Sensorimotor Integration Processes Prior to and During Movements to Somatosensory Targets

Previous research on multisensory integration for movement planning and control has focused on movements to targets external to the body. In this dissertation, three experiments were conducted to examine the sensorimotor transformation processes underlying goal-directed actions to targets defined by body positions (i.e., somatosensory targets). The goal of the first experiment was to investigate if the modality of the cue used to indicate the location of a somatosensory target affects the body representation used to encode the target’s position during movement planning. The results showed that auditory cues prompted the use of an exteroceptive body representation for the encoding of movements to a somatosensory target in visual coordinates. The goal of the second experiment was to examine the neural processes associated with the visual remapping of an auditory-cued somatosensory target. It was found that the sensorimotor transformation processes responsible for the conversion of a somatosensory target position into visual coordinates engages visuomotor cortical networks to a greater extent than movements to external visual targets. The goal of the third experiment was to examine the sensorimotor transformation processes employed for the online control of movements to a somatosensory target. The results of this experiment revealed that the remapping of a somatosensory target into visual coordinates may not occur prior to online corrections. Altogether the findings of this thesis reveal that sensory cues can facilitate the remapping of a somatosensory target prior to goal-directed actions. However, these remapping processes may be too costly for use during online control when there is no vision of the reaching limb.

Keywords: Proprioception
Advisor: Tremblay, Luc
Blouin, Jean
Ultrafast Lasers and Amplifiers based on Yb-doped Gain Materials

The development and advancement of high powered, sub-picosecond laser sources have been crucial to the progression of ultrafast optical studies in the visible and near-infrared spectrum. Highly energetic, broadband pulses can be used to probe the electronic and structural dynamics of some of the fastest possible chemical and biological processes. This work outlines the development of a novel ultrafast laser system operating in the 1μm wavelength regime, using a chirped-pulse amplification scaling scheme. The system, based solely on ytterbium-doped fiber amplifiers, delivers pulses up to 400 μJ and average powers up to 100 W. An extremely stable fiber-based oscillator is presented, delivering 8 nJ pulses at a repetition rate of 38 MHz. Employing a stretched-pulse cavity design, an adjustable dispersive element enables operation in both positive and negative dispersion regimes. Compressed pulses as short as 43 fs were measured from the oscillator. A custom pulse-stretching fiber is used in lieu of a traditional grating compressor, and two single mode preamplifiers complete the front-end of the system, generating 100 mW output at rates ranging from 0.1 MHz to 1 MHz. Two diode-pumped, large-mode-area, ytterbium-doped fibers provide high power amplification. A large-core fiber amplifier delivers single mode output up to 10W average power and a photonic-crystal rod amplifier provides final amplification up to 100 W. The beam quality remains excellent, even at high power operation. At 200 kHz the amplifier produced 400 μJ pulses which can be compressed to 350 fs, which represents among the highest peak power generated from this class of amplifier. In addition to this complete laser system, two other ytterbium-based ultrafast lasers were developed: a Yb:KGW crystal regenerative amplifier, and an all-fiber oscillator. The regenerative amplifier is seeded by the front-end discussed. It operates at lower repetition rates, 1 kHz to 10 kHz, outputting 400 μJ pulses compressible to 250 fs. Further development of this amplifier should enable mJ-level output. The single- diode-pumped, all-fiber oscillator is based on a nonlinear amplifying loop mirror. It outputs 1 nJ pulses at 13 MHz. The oscillator may serve as an extremely stable and compact seed laser for a future high power system.

Advisor: Miller, R.J. Dwayne
The Influence of Ontogeny and Physiological Microbial Exposure on Macrophage Maintenance and Function

Macrophages are highly phagocytic cells found in almost every tissue of the body and are involved in several physiological processes, including pathogen defense and tissue development. The work presented in this thesis sought to determine whether factors such as ontogeny and microbial diversity can affect macrophage maintenance and function in homeostatic conditions and disease. First, we isolated and characterized a unique population of macrophages that exists in the vasculature during steady state. Using lineage-tracing techniques we demonstrated that adult vascular macrophages derive from embryonic and adult origins. We found that survival and maintenance of this population is dependent on the interaction between the fractalkine receptor and its ligand. This study highlights the importance of tracking the ontogenetic source of macrophages in tissues as we see key differences in maintenance and function between resident and recruited subsets in the vasculature. The second chapter in this dissertation focuses on evaluating whether exposure to diverse environmental pathogens can affect macrophage maintenance and function. It was observed that physiological exposure to microbes significantly alters monocyte and macrophage subsets in mice – specifically, we detected an expansion of resident macrophages in the peritoneum; we note that local proliferation, and not monocyte recruitment, accounts for this change. Microbial exposure did not affect phagocytosis, responses to bacterial pathogens and sepsis, and only slightly altered cytokine production in response to toll-like receptors (TLRs) agonists. In a mouse model of atherosclerosis, we found that microbial exposure reduces lesion development exclusively at 8 weeks. In summary, this work examined the influence of ontogeny and microbial exposure on macrophage function in the steady state and in the course of disease.

Keywords: atherosclerosis
inflammation
innate immunity
macrophages
monocytes
ontogeny
Advisor: Robbins, Clinton S
The Development of In vivo Comprehensive Multiphase NMR and Its Potential for the Investigation of Aquatic Toxicity

NMR based metabolomics has been extensively used to provide a molecular-level understanding of underlying biological processes due to environmental stimuli. Previously reported in vivo NMR studies were limited to detecting dynamic and soluble entities, resulting in the need for an approach to detect all bonds (solids, gels and liquids in vivo) and thus provide a comprehensive overview as to all components inside a living organism. CMP-NMR integrates all the electronics from HR-MAS (gel-phase NMR), with high power RF handling to study rigid solids, into a single probe. Therefore, in vivo CMP-NMR holds potential to correlate rapid stress responses (metabolite fluxes) to slower structural changes (thinning of shells). In this regard, the focus of this dissertation was the development of CMP-NMR for the study of living systems. In Chapter 2, CMP-NMR combined with spectral editing isolates the signals arising from the rigid solids (chitin), to gel (lipid membranes) and liquids (amino acids) in Hyalella azteca into discrete spectra for each sub-component. Additionally, 13C isotopic enrichment and 2D NMR enabled the assignment of nearly 40 metabolites. However, the stress exerted on the organisms due to the fast spinning (2.5 KHz) remained a major challenge of the approach. To address this, Chapter 3 introduces a slow spinning technique by concatenating PURGE and TOSS.243, which leads to high resolution in vivo 1D 1H NMR profiles down to 300 Hz. In Chapter 4 hetero-nuclear (31P, 19F 2H, 15N, NMR) experiments are introduced to follow the fate of the contaminants inside the living organism and 2D correlations (1H-13C, 2H-13C) monitor the biomolecular responses of the organism to the nutritional substrates. In Chapter 5 2H/13C isotopic enrichment of the organisms, is combined with 2D 2H-13C NMR leading to the first high resolution sideband free spectra at 50 Hz and extending the experimental time up to 48 h. Combined in vivo CMP NMR techniques show great potential for future application in environmental toxicity risk assessments.

Advisor: Simpson, Andre J
The Impacts of Climate and Climate Change on Aviation in the Canadian North

Aviation is inherently linked to meteorology as severe weather is often responsible for flight delays, cancellations and sometimes accidents. Climate change is expected to change the Arctic environment and the warming rate in this region is greater than most locations on Earth. With a changing climate, the risks of flying will also be changing. In Canada, many Arctic communities in Hudson Bay, Nunavik in northern Quebec and western Labrador rely heavily on aviation to transport passengers, mail and groceries because they lack road networks or railway to access larger settlements and shipping is limited to brief periods in summer. Using historical hourly and daily climate data, this thesis examines four topics related to flying: 1) wind pattern changes (1971 to 2010) at seven locations around Hudson Bay, northern Quebec and western Labrador; 2) fog and visibility trends at 16 Hudson Bay communities (1953-2014); 3) historic long-term soil temperature trends at 5 to 150 cm depths and future projections under three greenhouse gas concentration trajectories at Kuujjuaq, Quebec; 4) appearance and climate conditions for frostquakes. The results of these topics are: 1) an increase in hourly average and daily maximum wind speed around Hudson Bay region and declining trends in western Labrador, plus prevailing wind direction changed at two communities; 2) fog and ice fog frequencies declined but reduced and low visibility trends varied spatially within the Hudson Bay region; 3) soil warming at approximately 1oC per decade from 1967 to 1995 and future soil temperature will be above 0oC under all projected trajectories at Kuujjuaq; 4) identified that water-saturated soil, minimal snow cover and rapid temperature drop to below freezing causes frostquakes and that observations were somewhat dependent on the density of the observational network. Passengers travelling to and from Hudson Bay will benefit from the results of this research to better understand the risks associated with flying to these communities. Pilots, airport operators and airlines will improve their awareness of this issue and increase their understandings of the risks caused by climate change in this area. Improved safety will be achieved by anticipating, adapting to and mitigating these changes.

Keywords: aviation
climate change
fog
soil temperature
visibility
wind
Advisor: Gough, William A
Development of a Multifluid Magnetohydrodynamic Model for Anisotropic, Partially Ionized Plasmas

A multifluid magnetohydrodynamic (MHD) model based on an extended fluid dynamics description for each plasma species is proposed for the prediction of the flow and behaviour of fully and partially ionized non-equilibrium anisotropic plasmas. Two-(electrons and ions) and three-fluid (ions, electrons and neutrals) plasma models are described that both make use of a 10-moment or Gaussian anisotropic moment closure of the Boltzmann equation. The moment equations for each plasma species are fully coupled to the Maxwell's equations which govern electromagnetic wave propagation within the plasma and a Bhatnagar-Gross-Krook (BGK) relaxation time approximation is used to model non-equilibrium collisional processes between the plasma species. Chemical kinetic models are included to represent the partially ionized plasma processes. Unlike conventional MHD models, the proposed multi-species MHD model is capable of taking into account large temperature anisotropies and temperature differences between the electrons and ions, both of which can occur for low-density, high-temperature plasmas and/or strongly magnetized plasmas. A second-order Godunov-type finite-volume method is developed for the solution of the one- and two-dimensional forms of the multifluid plasma models, which includes temporal limiting in one-dimension and a parallel scheme utilizing a Newton-Krylov-Schwarz (NKS) implicit algorithm for the two-dimensional solution procedure. The numerical fluxes in the Godunov-type scheme are solved using HLLE and Godunov numerical flux functions. The two-dimensional solution procedure includes Generalized Lagrange Multiplier (GLM) and diffusive error correction schemes for the treatment of divergence errors associated with the electromagnetic field. An accuracy assessment is performed for the two-dimensional numerical solution procedure, demonstrating good convergence of solutions for a range of problems. The validated two-dimensional solution procedure for the multifluid MHD model is then applied to the solution of the well-known Geospace Environmental Modelling (GEM) challenge problem involving magnetic field reconnection and numerical results are compared to established solutions in the literature. Results of grid refinement and parametric studies for the GEM case are also described. The proposed multifluid MHD model is shown to recover known published results with relatively small computational effort and the potential of the proposed treatment for describing a range of non-equilibrium anisotropic plasma flows is demonstrated.

Keywords: computational fluid dynamics
geospace magnetic reconnection
magnetohydrodynamics
MHD
plasmadynamics
plasma modelling
Advisor: Groth, Clinton P. T.
Mechanisms Controlling Cell Size in Animal Cells

Although questions on cell size have been investigated for more than half a century, molecular mechanisms that ‘program’ the size of animal cells are only starting to be revealed. My Ph.D. research focuses on the molecular mechanisms that promote cell size uniformity in proliferating mammalian cells. By relying on a high-content small chemical screen, I identified candidate proteins and signaling molecules that may function as cell size specifiers. Intriguingly, analysis of the screen hits suggested a role for the p38 MAPK in the long-sought mammalian cell size checkpoint. In follow-up experiments, I showed that p38 MAPK signaling is activated in small, but not large cells, which selectively inhibits the progression of small cells into S phase. Consistent with this model, chemical and genetic perturbations of p38 resulted in the loss of the compensatory G1 length extension in small cells; cells lacking p38 activity proliferated faster, were smaller in size and displayed increased size heterogeneity. Altogether, my work suggests that the p38 MAPK pathway responds to changes in cell size and regulates G1 exit accordingly, to increase cell size uniformity. In this thesis, I first present an in-depth review of the animal cell size research. Reflecting on literature, I summarize in Chapter 1.1 a convergence of historical and recent evidence that support size sensing as a cell-autonomous function of individual animal cells. I also discuss the historical debates on animal cell size sensing and offer my understanding of how these “conflicting” literature may be resolved through new interpretations. In Chapter 1.2, I discuss in detail how cell size affects cellular, tissue and organismal level functions. I hope this inspires more functional and mechanistic research on cell size in the future. In the last Chapter, I further discuss the implications of the p38 signaling and cell size control and introduce in brief the branches of follow-up research that emerged from my thesis work.

Keywords: cell cycle
cell size
G1/S transition
mTOR pathway
p38 MAPK pathway
Advisor: Kafri, Ran
Entries to Intimacy: Shared Solitude in Garth Greenwell's What Belongs to You, Anne Carson's Nox, and Roni Horn's Another Water (The River Thames, for Example)

This dissertation studies three books that unfold as inquiries into the possibility of being in relation. I argue that Garth Greenwell’s What Belongs to You, Anne Carson’s Nox, and Roni Horn’s Another Water (The River Thames, for Example) attest to a form of togetherness that rests not on recognition or perception, but rather on the sense of a space that remains without relation. Readings these books in light of Michel Foucault’s description of the archive, and Giorgio Agamben’s theorization of thought, I show that this space marks the very place where relations emerge, a place, therefore, that exceeds both sight and thought. The books not only present modes of seeing, knowing, or thinking that turn towards this place, but also stage a sensuous engagement with the unseen, unsaid, or unthought. In each chapter, accordingly, I read scenes that both trace an experience that eludes the seeing or knowing subject, and bring the reader in touch with a space beyond relation. Drawing, in turn, on William Haver’s notion of an erotics of thought, Roland Barthes’ theory of photography, and Maurice Blanchot’s theorization of the essential solitude, I delineate the ways in which these exemplary scenes affirm the impossibility of resolving the question of how to be with others. To engage this impossibility, the books suggest, is to open up relations to possibilities unforeseen.

Keywords: Anne Carson
Garth Greenwell
Language and literature
Queer Theory
Roni Horn
Visual Studies
Advisor: Ricco, John Paul
Machine Learning Methodologies for Uncovering the Mechanisms of Complex Diseases

Identifying the mechanisms associated with complex human diseases is one of the main challenges of human genetics and computational medicine. With every technical advance such as the ability to sequence whole genomes and transcriptomes faster and cheaper, there is the promise of finally discovering the root causes of complex genetic diseases and leading the way for efficient personalized medicine. That promise have not been fulfilled yet despite the technological advances and large datasets gathered. All the variations discovered to be statistically associated with a disease can only account for a small proportion of the genetic component of the disease. Given the complexity of the problem, we need to move beyond the state-of-the-art statistical tools and use advanced machine learning techniques that can better fit the complexity of the problem. In this thesis, we propose machine-learning methods that are designed specifically for the biological problem in order to increase the power of identifying mechanisms of complex diseases. We present approaches that can integrate multiple types of data when each dataset contains only a part of the disease mechanism and we incorporate as much biological knowledge and annotations as possible within our framework. We tackle the problem by simultaneously considering all potential sources of aberrations that can lead to a disease and show that we can find more complex mechanisms explaining the disease in a larger proportion of the patients. Our approaches also provide guidelines to investigate the likely root causes for individual patients opening the way to personalized treatment.

Keywords: Compex disease
Computational biology
Genetics
Healthcare
Machine learning
Advisor: Goldenberg, Anna
Investigation of the Effects of Alterations in the Glutamate Receptor, GRIK2 on Osteosarcoma Tumourigenesis

Over the past two decades, osteosarcoma survival rates have remained stagnant, and the discovery of novel molecular alterations is necessary in clinical research. Osteosarcoma tumours were analyzed for copy number alterations on a SNP array, and recurrent copy number losses were observed in 14% of samples in the 6q16.3, suggesting this region may be important in the disease. Focal deletions were adjacent to the GRIK2 gene which encodes an ionotropic glutamate receptor, and members of other glutamate receptor families have been linked to osteosarcoma through genome wide association studies. The mechanistic relationship between the receptors and the disease is unclear, although glutamate receptors are expressed in bone cells and may disrupt the bone remodelling process, which has been hypothesized to lead to tumour formation. The goal of this study was to investigate the relationship between the focal deletions and the expression, function and regulation of the GRIK2 gene in osteosarcoma. The focal deletions overlapped with non-coding regulatory elements in the 5’ intergenic space of GRIK2, and a similar trend was observed in a larger dataset that acted as a validation tool. Expression levels of GRIK2 varied in tumour samples, and there was a subset of samples with high expression that included four tumours with homozygous deletions suggesting a potential link between the deletions and expression. The functional role of GRIK2 was examined in vitro by gene overexpression experiments, and an anti-tumour phenotype was observed in cells with high GRIK2 that was marked by decreased proliferation and migration, and increased incidences of apoptosis. Additionally, the effect of deletions on GRIK2 expression regulation was examined by gene editing experiments. Targeted deletion of the SETDB1 histone methyltransferase binding sequence increased GRIK2 gene and protein levels. In conjunction with higher GRIK2 expression, levels of the repressive H3K9Me3 were decreased. The focal deletions may be involved in shifting GRIK2 from a repressed to an active state, which was associated with a less aggressive phenotype. This study has also demonstrated the potential utility of regulatory elements as possible therapeutic targets as these sequences could play roles in cancer initiation and growth.

Advisor: Andrulis, Irene