VictorJuiz/thesis huggingface dataset:
Approximation Techniques for Large Finite Quantum Many-body Systems
Keywords: Quantum Many-body systems
Approximation Techniques
Algebraic Hamiltonian
Eigenvector

In this thesis, we will show how certain classes of quantum many-body Hamiltonians with [special characters omitted](2)1 ⊕ [special characters omitted](2)2 ⊕...⊕ [special characters omitted](2)k spectrum generating algebras can be approximated by multidimensional shifted harmonic oscillator Hamiltonians. The dimensions of the Hilbert spaces of such Hamiltonians usually depend exponentially on k. This can make obtaining eigenvalues by diagonalization computationally challenging. The Shifted Harmonic Approximation (SHA) developed here gives good predictions of properties such as ground state energies, excitation energies and the most probable states in the lowest eigenstates. This is achieved by solving only a system of k equations and diagonalizing k × k matrices. The SHA gives accurate approximations over wide domains of parameters and in many cases even across phase transitions. The SHA is first illustrated using the Lipkin-Meshkov-Glick (LMG) model and the Canonical Josephson Hamiltonian (CJH) which have [special characters omitted](2) spectrum generating algebras. Next, we extend the technique to the non-compact [special characters omitted](1, 1) algebra, using the five-dimensional quartic oscillator (5DQO) as an example. Finally, the SHA is applied to a k-level Bardeen-Cooper-Shrieffer (BCS) pairing Hamiltonian with fixed particle number. The BCS model has a [special characters omitted](2)1 ⊕ [special characters omitted](2)2 ⊕...⊕ [special characters omitted](2)k spectrum generating algebra. An attractive feature of the SHA is that it also provides information to construct basis states which yield very accurate eigenvalues for low-lying states by diagonalizing Hamiltonians in small subspaces of huge Hilbert spaces. For Hamiltonians that involve a smaller number of operators, accurate eigenvalues can be obtained using another technique developed in this thesis: the generalized Rowe-Rosensteel-Kerman-Klein equations-of-motion method (RRKK). The RRKK is illustrated using the LMG and the 5DQO. In RRKK, solving unknowns in a set of 10 × 10 matrices typically gives estimates of the lowest few eigenvalues to an accuracy of at least eight significant figures. The RRKK involves optimization routines which require initial guesses of the matrix representations of the operators. In many cases, very good initial guesses can be obtained using the SHA. The thesis concludes by exploring possible future developments of the SHA.
Biotic Resistance to Non-indigenous Plants: Are Phylogenetically Novel Invaders More Likely to Escape Enemies?
Keywords: invasion biology
enemy release hypothesis
community phylogenetics
Darwin's naturalization hypothesis
community ecology
plant ecology

The degree to which biotic interactions influence invasion success may partly depend on the evolutionary relationship between invaders and native species. In particular, since host-use by enemies such as invertebrate herbivores and fungal pathogens tends to be phylogenetically conserved, exotic plants that have close native relatives in the invaded range should be more likely to interact with enemies. In this thesis, I explore this idea using a series of experiments and field surveys at nested taxonomic levels. My results indicate that exotics from multiple plant families experience lower damage if their average phylogenetic distance from locally co-occurring native family members is higher. I then demonstrate that within the Asteraceae, foliar and capitular damage are lower on exotic compared to native species. Both damage types had a relatively large phylogenetic component, but did not decline with phylogenetic distance to native or exotic confamilials. Finally, I show that communities with versus without close relatives are unlikely to differ in resistance to the novel invader, Solidago virgaurea: biotic resistance imposed by competitors, generalist vertebrates, and specialist invertebrates resulted in similar patterns of damage and mortality regardless of the presence of congeneric natives. In some cases, effects of biota were positive: growth of S. virgaurea seedlings in soils collected near congeneric natives was enhanced more than in soils from communities where congenerics were absent. Overall, these results suggest that biotic interactions between exotic and native species can be phylogenetically structured, although trends based on distance measures tend to be weak. In some cases, damage does decline with phylogenetic distance to native species; however this trend is unlikely to be a strong force limiting invasion or structuring plant communities. These results have significant implications for current theories of invasion biology including the "Enemy Release Hypothesis" and "Darwin's Naturalization Hypothesis", as well as for community phylogenetics.
Cis-elements Affecting Disease-associated Repeat Sequences
Keywords: trinucleotide
myotonic dystrophy
CTCF
Spinocerebellar ataxia
cis-element

The expansion of repetitive sequences leads to more than 40 neurological, neurodegenerative and neuromuscular diseases. These diseases are frequently characterized by ongoing DNA repeat instability upon transmission, worsening of disease severity and decreasing age of onset with each successive generation. The mechanism of repeat instability and contribution of repeat instability to disease pathogenesis are unknown. My thesis examines the contribution of cis-elements – sequences around and within repeats as well as surrounding epigenetic environments – to repeat instability, and discusses their possible contribution to repeat diseases. Here I identify the first cis-element regulating repeat instability, a DNA binding site for a trans factor protein, CTCF. Loss of CTCF binding at the spinocerebellar ataxia type 7 disease locus induces somatic and germline instability in an age- and tissue-specific manner in mice. CTCF protects against instability in an epigenetic manner, and may function at other disease loci also possessing CTCF binding sites near the repeat. Given that CTCF flanks many repeat loci and is often situated between a replication origin and disease-associated repeat, I assess the role of CTCF on replication and instability at the myotonic dystrophy repeat locus. Templates with CTCF binding sites reduce overall replication efficiency in primate cells that may be partly due to replication fork stalling. Mutating CTCF binding sites can alter the stability of the repeat depending on the distance from the origin of replication to the repeat. Finally I examine chromatinization of (ATTCT)n repeats from the spinocerebellar ataxia type 10 locus. These repeats induce very strong nucleosome formation, and at physiological conditions form even more strongly on (ATTCT)n repeats with interruptions that are also found in some patients. These data contribute to the understanding of repeat instability in the causation of many diseases, and suggest that the presence of cis-elements at repeat-associated disease loci alter the behaviour of repeats.
Is Evidence-based Psychiatric Practice, Ethical Practice?: A Conceptual and Qualitative Study
Keywords: evidence-based medicine
psychiatry
ethics

Since its addition to the medical lexicon in 1992, the concept of ‘evidence-based medicine’ (EBM) has captured the imagination of the medical world, attracting both passionate advocates and ardent opponents. EBM is defined clinically as “the conscientious, explicit, and judicious use of current best evidence in making decisions about the care of individual patients.” Yet, its boldest claim is an ethical one: that EBM, rather than any other method, is the most effective way to fulfill our moral duty to help patients achieve better health. Academic debate on this point has been deeply polarized, from those who assert that ethical practice is evidence-based practice to those who argue that evidence-based practice impoverishes practice and robs it of ethical substance. Mainstream psychiatrists have endorsed EBM which holds out the promise of greater ethical legitimacy for psychiatric disorders and treatments through improved scientific substantiation. Evidence-based psychiatry arises through the straightforward application of EBM to the practice of psychiatry and thus shares the same ethical goal of EBM, to improve patients’ health. Given the ethical debates that have framed psychiatry since its inception as a medical specialty, and the particular nature of mental disorders and their treatments, it is unclear if EBM can be applied to psychiatry, and therefore, whether it can deliver on its ethical promises. This thesis project involved two phases. The first, a conceptual phase, included an analysis of EBM’s ethical commitments as they are represented in its two authoritative textbooks (‘literal’ EBM). This provisional analysis was then extended by a qualitative analysis of the views of three groups of participants concerning the ethics of EBM: 1) EBM developers; 2) mental health practitioners; and 3) philosophers or bioethicists. Combining the analyses from both phases, a more complete depiction of the ethics of EBM was developed in order to address the main thesis question. Evidence-based psychiatric practice cannot be ethical practice by itself. Instead, it can play a small ethical role in clinical practice, only if it is situated within the larger value structure of contemporary medicine and psychiatry.
The Functional Characterization of Two Regulators of G-protein Signaling Proteins Abundantly Expressed in Vascular Smooth Muscle Cells
Keywords: Regulators of G-protein Signaling
Cell physiology

Precise regulation of heterotrimeric G-protein signaling is important for maintaining proper cardiovascular system function. Indeed, G-protein signaling is frequently upregulated during cardiovascular disease suggesting that identifying mechanisms for inhibiting G-protein signaling may be an effective therapeutic strategy for the treatment and prevention of disease. The work presented in this thesis is directed at two RGS proteins, RGS2 and RGS5, the two highest expressing RGS proteins in VSMCs. Despite the large number of studies published on them, there is still much to be learned about the specific G-protein pathways that each RGS protein controls. Using genetic and molecular models, we set out to identify novel regulatory pathways controlling RGS2 and RGS5 function. We hypothesize that characterizing the determinants and regulation of RGS protein function will provide a better understanding of the signaling that occurs within VSMCs under both physiologic and pathophysiologic conditions. Our work presented in the first three studies of this thesis, describes novel regulatory pathways that are involved in regulating RGS2 protein function. We describe the production of RGS2 protein isoforms that are the result of alternative translational start site usage. Interestingly, the expression pattern of these proteins is controlled by the signaling status of the cell. In the second two studies, we identify a functional consequence of RGS2-interaction with the plasma membrane. We show that this is dependent on the interaction between the amphipathic α-helix and anionic phospholipids present in the plasma membrane. We further show that disruptions in this interaction, as occurs in the human population, can lead to reduced RGS2 function and thus potentially hypertension. Finally, our last study focuses on the function and regulation of RGS5, the single highest expressing RGS protein in VSMCs. We show that the regulation of RGS5 is dependent, similar to other VSMC-specific genes, on the activity of SRF and myocardin. However, interestingly, RGS5 expression is further controlled by the extent of DNA methylation that occurs in its proximal promoter. We show that this is an important regulator of RGS5 expression both in development as well as during disease, specifically in-stent restenosis.
The Study of Inhomogeneous Cosmologies Through Spacetime Matchings
Keywords: Cosmology

Our universe is inherently inhomogeneous yet it is common in the study of cosmology to model our universe after the homogeneous and isotropic Friedmann-Lemaıtre-Roberson-Walker (FLRW) model. In this thesis spacetime matchings are applied to investigate more general inhomogeneous cosmologies. The Cheese Slice universe, constructed from matching together FLRW and Kasner regions satisfying the Darmois matching conditions, is used as a prime example of an inhomogeneous cosmology. Some observational consequences of this model are presented. The lookback time verses redshift relation is calculated using a numerical algorithm and it is shown that the relative thickness of the Kasner regions have the greatest impact on anisotropies an observer would see. The number of layers and distribution of layers play a smaller role in this regard. The relative thickness of the Kasner slice should be on the order of one ten thousandth the thickness of the FLRW regions to have the anisotropies fall within the observed CMB limit. The approach to the singularity of a spacetime matching is examined. A criterion is presented for a matched spacetime to be considered Asymptotically Velocity Term Dominated (AVTD). Both sides of the matching must be AVTD and each leaf of the respective foliations mush match as well. It is demonstrated that the open and flat Cheese Slice universe are both AVTD and the singularity is also of AVTD type. The Cheese Slice model is then examined as a braneworld construction. The possibility of a Cheese Slice brane satisfying all the energy conditions is shown. However, the embedding of such a brane into a symmetric bulk is non-trivial. The general embedding of a matched spacetime into a bulk is investigated using a Taylor series approximation of the bulk. It is found that the energy-momentum tensor of such a brane cannot have discrete jumps if the embedding does not have a corner. A 3+1+1 decomposition of the bulk spacetime is then carried out. With the spacetime being deconstructed along two preferred timelike hypersurfaces, this becomes a natural environment to discuss the matching of branes. We find that there are conditions on the matter content of the branes to be matched if an observer on the brane is to see the matching surface as a boundary surface with no additional stress energy. Matching more than two bulks is also examined and shown to allow for more general brane configurations.
Sri Lankan Tamil Diaspora: Contextualizing Pre-migration and Post- migration Traumatic Events and Psychological Distress
Keywords: 0452
0347

The objective of this study was to generate a deeper understanding of the influence of pre- and post-migration traumatic experiences on refugees’ psychological distress, including historical, political and social factors. This dissertation used a multi-method design to examine the impact of trauma on the psychological well-being of refugees. Further, the design included a qualitative component to provide a contextual framework for understanding refugee psychological distress that is not limited to an analysis of a disease model alone but by also making connections to important historical, social and political events. Post-Colonial, Refugee, Trauma and Feminist theories are used as analytic lenses to explain the social structures and events contributing to refugees’ pre- and post-migration traumatic events, and psychological distress. This was an international study that spanned two continents. Sampling included 50 Sri Lankan Tamil refugee participants who lived in Chennai, India and 50 Sri Lankan refugees in Toronto, Canada. Inclusion criteria included a residency period of the last 12 months in either of the sampling sites, and participants 18 years of age or older. Participants from Toronto were recruited through social service agencies and associations, and participants from Chennai were recruited from refugee camps, and the Organization for Elam Refugee Rehabilitation. Tamil versions of the Harvard Trauma Questionnaire, the Post-Migration Living Difficulties Questionnaire, and the Symptoms Check List – 90R were utilized to measure participants’ pre- and post-migration traumatic events and psychological distress. The Harvard Trauma Questionnaire contained qualitative open-ended questions to triangulate the quantitative data in identifying and exploring the impact of contextual influences. Results showed that post-migration traumatic event scores positively predicted psychological distress, and refugee claimants living in Canada had the highest scores on pre-migration and post-migration scores. The qualitative analysis revealed themes related to civil war and resettlement as significant issues. Implications of these findings support the development of a multi-level approach within social work practice which emphasizes contextual issues, focuses on individuals, and promotes social advocacy. Recommendations for future research point to conducting longitudinal studies to assess the cumulative effects of historical, social and political factors on refugees and identify resiliencies that mobilize their capacity to survive.
OH-initiated Heterogeneous Oxidation of Atmospheric Organic Aerosols
Keywords: atmospheric chemistry
hydroxyl radicals

The chemical aging of organic aerosols by OH-initiated heterogeneous oxidation was investigated using both model organic and ambient aerosol particles. Organic aerosol particles were exposed to OH radicals in an aerosol flow tube and the modification of their chemical composition and particle properties was studied. Overall, this work has shown that OH-initiated heterogeneous oxidation enhanced the degree of oxidation and the Cloud Condensation Nucleus (CCN) activity of organic aerosol particles for equivalent OH exposure timescales of a few days to a week. Aerosol Mass Spectrometer (AMS) measurements showed that the heterogeneous uptake kinetics of OH radicals onto model primary organic aerosols was efficient. The heterogeneous reaction of organic aerosols with OH led to the production of high molecular weight particle-phase species with the addition of multiple oxygenated functional groups. These results were consistent with the observed increase in particle density with OH exposure. With the exception of solid organic aerosols, the particle volume and mass of organic particles were reduced by less than 20% from OH oxidation at high OH exposures due to volatilization of particle-phase reaction products. The degree of oxidation of the organic fraction of urban ambient aerosols was significantly enhanced for an equivalent atmospheric OH exposure time of 4 days for a daily average atmospheric OH concentration of 2×106 cm-3. Ambient aerosol particles sampled from a sparsely populated, forested region were initially more oxygenated than the urban aerosol particles and did not become more oxidized from reaction with OH radicals. The modification of the hygroscopicity of model primary and secondary organic aerosols from chemical aging was investigated by measuring the CCN activity of organic aerosols exposed to OH radicals. Primary organic aerosols, initially CCN inactive, became as CCN active as secondary organic aerosols due to heterogeneous reaction, where surface tension reduction played a major role. The CCN activity for model secondary organic aerosols was also enhanced due to OH oxidation, but changes were less dramatic than for the model primary organic aerosols.
Categories and Evaluation Bias in Valuation of Technological Innovation
Keywords: valuation
innovation

This dissertation examines the perceptual bias of investors and securities analysts (the “audience” in the stock market) in their valuation of public firms’ innovative activities. I suggest that such bias occurs because the audience views a firm’s innovation through the prism of the firm’s categorization in product markets – its industry category – which may only loosely conform to the technological interrelationship among firms in knowledge space. I explore theoretically the conditions under which evaluation bias is most likely to occur – notably, due to innovations that defy the existing categorical structure used by the audience. Based on this theoretical framework, I develop hypotheses for empirical tests. I first argue that both technological opportunities and technological threats residing outside a firm’s industry are more likely to be underestimated by the stock market than those residing within the industry. In a sample of large U.S. manufacturing firms covering the years 1980 through 2000, I collected patent data to reflect innovative activities of firms. I compare the effect of a firm’s innovative activities on its current market valuation and its future cash flows. Consistent with my predictions, I find that firms capitalizing on cross-industry opportunities are more likely to be undervalued, while firms facing cross-industry technological competition are more likely to be overvalued. I further argue that reliance on categorical identity for information cues may reduce the audience’s ability to adequately assess the value-relevance of innovations that deviate from the technological norm in an industry. By analyzing the absolute forecast errors in security analysts’ reports, I find confirming evidence that deviant innovations increase the forecast bias. I further argue and demonstrate that such bias is less prevalent for diversified firms and in industries with less stable categorical “norms,” two conditions in which the audience is less likely to rely on categorical information and more likely to employ firm-specific information. Finally, I discuss the contribution and implication of the findings to studies of categorization and value-relevance of technological innovations.
Vascular and Metabolic Risk Factors, Carotid Atherosclerosis and Vascular Cognitive Impairment in a First Nations Population
Keywords: Epidemiology

The objectives of the thesis were to examine the associations between vascular and metabolic risk factors, carotid atherosclerosis and cognitive function in a Canadian First Nations population. Eligible individuals were ≥18 years and with First Nations status who had undergone cognitive function assessment by the Clock Drawing Test (CDT) and the Trail Making Test Parts A and B. Parts A and B were combined into an executive function score (TMT-exec). Anthropometric, vascular and metabolic risk factors were assessed by interview, clinical examinations and blood tests. Doppler ultrasonography assessed carotid atherosclerosis (carotid stenosis, plaque volume). For the 190 individuals with TMT-exec scores, obese individuals were at a 4-fold increased risk for lowered cognitive performance compared to those who were not obese (odds ratio [OR]: 3.77, 95% confidence interval [CI]: 1.46-9.72). Those having an increased waist circumference also had 5 times the risk compared to those without an increased waist circumference (OR: 5.41, 95% CI: 1.83-15.99). Individuals having the metabolic syndrome were at a 4-fold increased risk compared to those without the metabolic syndrome (OR: 3.67, 95% CI: 1.34-10.07). No other cardiovascular risk factors were associated and no associations were shown for the CDT. For TMT-exec only, individuals with elevated levels of left (LCS) and total carotid stenosis (TCS) were less likely to demonstrate lowered cognitive performance (LCS, OR: 0.47, 95% CI: 0.24-0.96; TCS, OR: 0.40, 95% CI: 0.20-0.80). In structural equation modeling, for every 1-unit change in the anthropometric factor in kg/m2, there was a 0.86-fold decrease in the percent of TCS (p<0.05). The etiology of VCI is vascular and is affected by non-traditional risk factors such as obesity. The health effects of obesity beyond traditional disease endpoints warrants further study. Mild-moderate levels of carotid stenosis are not detrimental to cognitive functioning and may additionally include acting as a mediator.