VictorJuiz/thesis huggingface dataset:
Searching for Dark Matter with the ATLAS Detector in Events with an Energetic Jet and Large Missing Transverse Momentum

Hadron colliders, such as the Large Hadron Collider (LHC), principally produce events involving hadronic activity. Such activity is typically modelled by jets, which provide a useful representation of the underlying physics. Given the ubiquity of jets in LHC events, it becomes important to ensure that their properties and performance are well understood. The full approach to jet reconstruction and calibration, as used by the ATLAS Experiment, is detailed with a focus on recent improvements. The systematic uncertainties associated with jets are quantified, with the procedures and resulting reductions in uncertainties thoroughly detailed. Extra attention is placed on the treatment of high energy jets, and particularly the impact of inactive calorimeter regions and calorimeter non-containment (punch-through). The mono-jet topology is presented as an analysis where high energy jets are particularly relevant. This search makes use of very high missing transverse momentum balanced purely by jets, enabling measurements of the production cross-section of new physics processes producing weakly interacting particles. The full Standard Model background determination is shown, and the data are seen to be consistent with the Standard Model expectations. Limits are set on the visible cross-section for new physics processes. The results are interpreted as a search for the pair-production of Dark Matter (DM), both through Effective Field Theories (EFTs) and simplified models. Scenarios where the DM is either a scalar or fermionic particle are both considered. The validity of the EFT approach is thoroughly investigated, providing the first complete collider study into all relevant interaction types. Limits are then set on the EFT suppression scale, the WIMP-nucleon scattering cross-section, and the WIMP annihilation cross-section in order to compare with other types of DM experiments. The simplified model is used to conduct a full parameter-space scan of the mono-jet sensitivity to a wide range of conditions. First projections for the mono-jet analysis at an upgraded LHC are presented, demonstrating the significant gain in both discovery potential and limit sensitivity that accompanies higher collision energies. The analysis is projected to double in sensitivity in the coming year, hinting at the exciting times to come.

Keywords: ATLAS
Dark Matter
Jets
Mono-jet
WIMP
Advisor: Savard, Pierre
Integrated Microsimulation Modelling of Crowd and Subway Network Dynamics For Disruption Management Support

In many large cities around the world, public transit networks have been carrying an ever-increasing burden of commuters. This has resulted in large movements of crowds in major transit hubs, and high levels of congestion in systems running near or at capacity. In such situations, service disruptions can negatively impact service and transit users well after they are resolved. Currently, transit agencies handle these disruption situations in an ad-hoc fashion. This is due to the lack of a tool capable of analyzing the network-level impacts of response strategies, especially with performance sufficient to handle large-scale systems. Existing tools are limited in their ability to accurately simulate all dynamic facets of the transit network, or model the behaviour of passengers following disruption events. As a result, they do not adequately capture the two-way interaction between crowds and mass transit service, or the complexities of train operation. This dissertation presents Nexus, an innovative crowd dynamics and transit network simulation platform, that enables full simulation of all actors in the transit system and integrated dynamic transit assignment, while being both flexible and scalable to handle large-scale networks. Instead of developing new simulators for surface transit, trains and stations, Nexus enables interfacing of existing simulators together to form a network. An agent-based framework was overlaid to allow for responsive agents, while a virtual communication system permitted on-the-fly modifications to transit service operation. With crowd behaviour in stations key to network performance, new models were constructed to better explain passenger behaviour at two critical locations. First, discrete choice models were developed of passenger choice of stairs versus escalators. Second, a simulation-based model of passenger behaviour on train platforms was developed using a diffusion-inspired approach and accounting for preferred waiting locations. Field data collected across several Toronto subway stations informed both models. Finally, a proof-of-concept case study was conducted on the Toronto transit network. The impact of disruptions of various lengths at a key platform in the network was examined, and an illustrative example was conducted to show how the system could be used to test strategies to reduce impact on transit passengers.

Keywords: crowd dynamics
disruption management
microsimulation
public transit
subway networks
Advisor: Shalaby, Amer
The Politics of Metropolitan Development: Institutions, Interests, and Ideas in the Making of Urban Governance in the United States and Canada, 1800-2000

The urban form and local government organization of Canadian and American cities differ in consequential ways. These differences are typically explained by political cultural or economic and social structures. On the basis of archival and interview research, and supported by descriptive statistics and mapping, this dissertation argues that the long-term development of different national urban forms is the product of how Canadian and American subnational political institutions structured contention among societal interests and processed policy ideas within a changing normative context. During long-term periods of single-party dominance during the early postwar period (1945-70), Westminster institutions in Canadian provinces were highly autonomous from societal influence, which enabled them to establish land-use planning systems administered by metropolitan governments as recommended by American reformers. Fragmented authority and permeability to societal interests kept American state governments from doing the same. As a result, metropolitan land-use and infrastructure policies guided a greater proportion of urban development in Canadian cities than in their American counterparts. In some American states, highly organized bipartisan civic elite networks briefly overcame state governments' centrifugal nature to install metropolitan institutions. On both sides of the border, institutions and policies were enabled by a normative context of faith in government and deference to elites and expert knowledge. In the later postwar period (1970-2000), however, they were delegitimized by a new normative context that rejected narrow technical rationality in favour of livability concerns, participatory policymaking, and the protection of the natural environment and urban place qualities. At the same time, political contention became increasingly polarized, especially in the United States. It became more difficult to create new metropolitan institutions and policies, however the historical analysis shows that earlier, technocratic institutions may be brought into alignment with the new normative context if policies are framed in relation to new concerns and institutions cultivate new support coalitions. The analysis challenges the narrowly municipal, present-oriented, and single-case focus of urban political research, instead arguing for a multi-level, long-term historical, and comparative perspective. To this end, the argument is made through a comparative analysis of two Canadian-American pairs of cities (Toronto and Minneapolis-St. Paul, and Vancouver and Portland, OR) over the course of their development in the nineteenth and twentieth centuries.

Keywords: Comparative politics
Institutional change
Local government
North America
Planning history
Urban politics
Advisor: Wolfe, David
An Automated Pipeline for Phenotyping Embryonic Lethal Mice using 3D Imaging

With the completion of the Human Genome Project, the chemical sequence and location of every gene is now known. However, little is known about the function of each of the protein-coding genes in the human genome. The International Mouse Phenotyping Consortium (IMPC) is phenotyping single gene knockout mouse lines in an attempt to elucidate gene function and gain insight into genetic diseases. The goal of the IMPC is to provide phenotype information for knockout mouse lines for each of the 20,000+ genes in the mouse genome by 2021. A primary screen needed to be developed for phenotyping mouse embryos because approximately thirty percent of these knockout lines are predicted to be embryonic or perinatal lethal. This thesis describes the implementation of three-dimensional imaging as a method to identify morphological phenotypes in the developing mouse embryo. The IMPC has incorporated imaging as the primary screen for phenotyping embryonic lethals, but the classical method of qualitative annotation of individual two-dimensional sections is low-throughput and prone to observer bias. This thesis presents computer automated image analyses to identify statistically significant morphological phenotypes from knockout mouse embryo images. The generation of a 3D segmented atlas of wild-type anatomy provides baseline volume measurements of 48 mouse embryo organs and a template for automatic volume calculation of these structures for a given embryo image. Image registration methods combined with intensity, deformation, and atlas-based analyses are described, which automatically flag statistical abnormalities in anatomical volume and shape. A novel staging system is described that uses a computed four-dimensional developmental atlas to evaluate the stage of development of any mouse embryo at the global, structural, or voxel level. The described methods will be incorporated into the IMPC embryonic phenotyping pipeline to provide standardized image analyses that report mutant phenotypes in an automated and unbiased fashion.

Keywords: Developmental Biology
Image Registration
Imaging
Micro-CT
Mouse Embryo
Optical Projection Tomography
Advisor: Henkelman, R. Mark
Nation and Class Subjectivity in International Law and its Institutions in the Middle East (1919-1939)

This dissertation makes visible the neglected economic dimensions of the interventions by interwar international institutions in three cases: the League of Nations' intervention in the dispute between Turkey and the French Mandate for Syria and the Lebanon over the province of Alexandretta (1936), the dispute between Turkey and the British Mandate of Iraq over the province of Mosul (1925), and the technical assistance missions of the International Labour Organization (ILO) to Egypt (1931). To different degrees, international legal institutions were involved in nation-building projects in the interwar Middle East, over-determining "the problem of nationalities" at the expense of other factors. These three episodes problematize the absence of "class" as an analytical category in both critical international legal scholarship and the actual politics of international institutions, and similarly the inattention to the struggle over capital that operated beneath the legal mechanisms used by the League and the ILO. They show the specificities of the Arab semi-periphery that reflected the nationalist anger and revolutionary anti-colonialism of the periphery and yet served, at the same time, as ideal places for capital accumulation and foreign investments from the core countries. Therefore, the episodes presented in this dissertation illuminate the ways in which class society and capital accumulation together with national self-determination were constitutive of the new interwar global order imagined for the semi-periphery by international legal institutions.

Advisor: Knop, Karen
Capsaicin as a Novel Chemopreventive and Therapeutic Option for Prostate Cancer

Capsaicin, the active compound in chilli peppers, has been reported to have anti-carcinogenic properties. In the following thesis, the chemopreventive and therapeutic potential of capsaicin on prostate cancer has been investigated. To examine the chemopreventive properties of capsaicin, in vitro studies were carried out using a panel of prostate cancer cell lines. Here, it was deduced that capsaicin alone and in combination with the antioxidant lycopene significantly reduced the proliferation and induced apoptosis in a dose-dependent manner. Detailed mechanistic studies revealed that these effects were predominately mediated though intrinsic apoptosis. Based on these studies, the effect of capsaicin was assessed using a transgenic chemoprevention model of prostate cancer. Long-term oral administration of capsaicin reduced the tumour grade and metastatic burden in the transgenic adenocarcinoma of the mouse prostate (TRAMP) model, compared to control mice. To understand the therapeutic value of capsaicin, prostate cancer radio-sensitivity studies were carried out using various pre-clinical models. A dose-dependent growth inhibition in colony survival was demonstrated in prostate cancer cell lines following exposure to capsaicin with radiotherapy. Using the LNCaP xenograft mouse model, capsaicin and radiation therapy reduced the growth of prostate cancer tumours over time, greater than either monotherapy. A number of mechanisms were involved in mediating these effects, including the suppression of the NFκB pathway. Interestingly, the TRP-V1 capsaicin receptors were present on prostate cancer cells; however, they were not found to predominately mediate the anti-cancer effects of capsaicin. Evidence from this thesis has formed the basis for a clinical trial that is currently examining the effect of capsaicin supplementation on prostate cancer patients. If this trial proves to show benefit of capsaicin supplementation on prostate cancer, it may be integrated into the management and treatment strategies for prostate cancer, thus reducing the morbidity and mortality of the disease.

Keywords: Cancer
Capsaicin
Chemoprevention
Prostate
Therapeutic
Advisor: Venkateswaran, Vasundara
Klotz, Laurence
Application of the UV/Chlorine Advanced Oxidation Process for Drinking Water Treatment

This research investigated the feasibility of a novel advanced oxidation process (AOP) using ultraviolet light combined with free chlorine (UV/chlorine) in drinking water treatment. A bench-scale study using a medium pressure UV collimated beam apparatus showed that the UV/chlorine process was more efficient than the UV combined with hydrogen peroxide (UV/H2O2) AOP for the destruction of trichloroethylene (TCE) at pH 5 in a laboratory prepared water, but was less efficient than the latter at pH 7.5 and 10. A Matlab® mathematical model made accurate predictions of the observed experimental rates of TCE decay. The model predicted that increasing concentrations of hydroxyl radical scavengers in the treated water would tend to raise the pH at which UV/chlorine would remain competitive relative to UV/H2O2. Full-scale experiments at the City of Cornwall Water Purification Plant (Ontario, Canada) and pilot-scale tests in a Rayox® batch UV reactor using water from the Keswick Water Treatment Plant (Ontario, Canada) demonstrated comparable performance of UV/chlorine AOP to UV/H2O2 for geosmin, 2-methylisoborneol (MIB), and caffeine destruction. Organic and inorganic disinfection by-products (DBPs) were also monitored in the full- and pilot-scale tests. Minimal trihalomethane and haloacetic acid formation was observed across the UV reactor, while dichloroacetonitrile and bromochloroacetonitrile were produced rapidly, although overall concentrations were below 6 g L-1. Adsorbable organic halide was formed rapidly (up to 70 g Cl L-1) in water that had not been prechlorinated, while little formation was observed in previously chlorinated water. Chlorate and bromate were formed, equivalent to approximately 2-17% and 0.01-0.05% of the photolyzed chlorine, respectively, while no perchlorate or chlorite formation was observed. In addition, the 24 h organic DBP formation potential was increased by UV/chlorine pretreatment to an extent that was similar to that observed when the water was pretreated with UV/H2O2.

Advisor: Hofmann, Ron
Markers of Circadian Disruption and Reproductive Risk Factors for Breast Cancer

Background: Circadian disruption is hypothesized to impact reproductive signaling, which in turn has long been linked to breast cancer. The melatonin hypothesis holds that increased exposure to artificial light at night and resulting inhibition of nocturnal melatonin may account for recent increased breast cancer incidence. Coregulation of melatonin, circulating reproductive hormones and precursor gonadotropins has been well documented in animal models, particularly those of seasonal breeders, yet elucidation of these complex hormonal relationships in humans has proven challenging. This work investigates the link between circadian disruption and female gonadal activity and reproductive-related outcomes in the context of breast cancer risk. Methods: We examined the association between rotating shift work and age at menopause among the Nurses' Health Study II cohort, estimating cause-specific hazards using proportional hazards models with time-dependent covariates. The cross-sectional associations between nocturnal melatonin production, menstrual cycle length and circulating sex steroid hormones and prolactin were examined in two additional populations using ordinary least squares regression and generalized estimating equations. Effect modification of nocturnal melatonin and prolactin by age and diurnal preference was additionally investigated. Results: The hazard of natural menopause was observed to be lower in women who had worked >10 years of rotating shifts since baseline (HR: 0.76; 95% CI: 0.69-0.85), in the direction of our hypothesis. The strength of this effect was not maintained upon inclusion of prior exposure. Nocturnal melatonin levels were not found to be associated with menstrual cycle length, nor with daytime circulating levels of estradiol, progesterone or prolactin. However, we observed effect modification of nocturnal melatonin and circulating daytime prolactin by age. Conclusion: Our findings do not conclusively support or refute an association between circadian disruption and reproductive risk factors for breast cancer. Future work will benefit from more precise measurement and observation of the interplay between endocrine markers of circadian activity and reproductive function over time.

Keywords: breast cancer
circadian disruption
gonadal activity
melatonin
night work
prolactin
Advisor: Knight, Julia A
Rigorous Deductive Argumentation for Socially Relevant Issues

The most important problems for society are describable only in vague terms, dependent on subjective positions, and missing highly relevant data. This thesis is intended to revive and further develop the view that giving non-trivial, rigorous deductive arguments concerning such problems -without eliminating the complications of vagueness, subjectivity, and uncertainty- is, though very difficult, not problematic in principle, does not require the invention of new logics (classical first-order logic will do), and is something that more mathematically-inclined people should be pursuing. The framework of interpreted formal proofs is presented for formalizing and criticizing rigorous deductive arguments about vague, subjective, and uncertain issues, and its adequacy is supported largely by a number of major examples. This thesis also documents progress towards a web system for collaboratively authoring and criticizing such arguments, which is the ultimate goal of this project.

Keywords: argumentation
dialogue systems
formal logic
interpreted formal proofs
policy
Advisor: Cook, Stephen A
Urquhart, Alasdair
Measuring Quantum Effects in Photosynthetic Light-harvesting Complexes with Multipartite Entanglement

This thesis is a compilation of studies on delocalization measures, entanglement, and the role of quantum coherence in electronic energy transfer (EET) in light-harvesting complexes. The first two chapters after the introduction provide foundational knowledge of quantum information and light-harvesting, respectively. Chapter 2 introduces concepts from quantum information such as purity, bipartite entanglement and criteria for its measurement. The peripheral light-harvesting complex LH2, isolated from the anoxygenic purple bacterium Rhodopseudomonas acidophila, is employed as model system of interest. This light-harvesting complex, along with a description of the process of light-harvesting, the presence of quantum coherence, and the different models used to simulate EET, are described in chapter 3. In combination these two chapters lay the foundation for chapter 4, a critical assessment of the current measures of delocalization employed in EET studies, their relationship, and overall effectiveness. The conclusion is that entanglement based measures are most effective at measuring quantum effects, and that they can be related to more conventional delocalization measures such as the inverse participation ratio (IPR) by taking into account the entropy of the system under study. All the measures within this chapter are known as bipartite measures, and only measure the strength of correlation between two sites. The fifth chapter presents the core of this thesis. Following a brief introduction to the concept of multipartite entanglement, the development of multipartite delocalization measures that give high-resolution information on quantum coherence in light-harvesting complexes is detailed. In contrast to other measures, these analytical measures can detect many body correlations in large systems undergoing decoherence. We determine that, much like the bipartite entanglement based measures of chapter 4, these measures are also a function of system entropy, and have a similar hierarchial structure as that of multipartite entanglement measures. The final chapter applies these measures to our model LH2 complex, and draws conclusions on the role of bipartite delocalization and multipartite delocalization in EET.

Keywords: decoherence
delocalization
entanglement
light-harvesting complexes
measurement
photosynthesis
Advisor: Scholes, Gregory D.
Toronto Residents' Exposure to Ultrafine Particles

In urban areas, ultrafine particles (UFP: defined as particulate matter with diameters less than 100nm) are emitted in significant quantities from vehicles and form through a complex series of secondary reactions in the atmosphere. Large uncertainties surrounding the long-term behaviour and spatial distribution of UFP in urban areas have been a significant obstacle for exposure assessment. This research examined one of the longest existing urban UFP data sets, collected at a roadside location in downtown Toronto. Between 2006 and 2011, the concentration of particles with diameters

Keywords: Air Pollution Exposure
K-means Clustering
Land Use Regression
Particle Size Distribution
Ultrafine Particles
Wavelet Decomposition
Advisor: Evans, Greg J