VictorJuiz/thesis huggingface dataset:
Ergodicity of Adaptive MCMC and its Applications

Markov chain Monte Carlo algorithms (MCMC) and Adaptive Markov chain Monte Carlo algorithms (AMCMC) are most important methods of approximately sampling from complicated probability distributions and are widely used in statistics, computer science, chemistry, physics, etc. The core problem to use these algorithms is to build up asymptotic theories for them. In this thesis, we show the Central Limit Theorem (CLT) for the uniformly ergodic Markov chain using the regeneration method. We exploit the weakest uniform drift conditions to ensure the ergodicity and WLLN of AMCMC. Further we answer the open problem 21 in Roberts and Rosenthal [48] through constructing a counter example and finding out some stronger condition which indicates the ergodic property of AMCMC. We find that the conditions (a) and (b) in [46] are not sufficient for WLLN holds when the functional is unbounded. We also prove the WLLN for unbounded functions with some stronger conditions. Finally we consider the practical aspects of adaptive MCMC (AMCMC). We try some toy examples to explain that the general adaptive random walk Metropolis is not efficient for sampling from multi-model targets. Therefore we discuss the mixed regional adaptation (MRAPT) on the compact state space and the modified mixed regional adaptation on the general state space in which the regional proposal distributions are optimal and the switches between different models are very efficient. The theoretical proof is to show that the algorithms proposed here fall within the scope of general theorems that are used to validate AMCMC. As an application of our theoretical results, we analyze the real data about the ``Loss of Heterozygosity" (LOH) using MRAPT.

Keywords: Adaptive
MCMC
Advisor: Rosenthal, Jeffrey S.
Craiu, Radu V.
A Middle Kingdom Pottery Assemblage from North Abydos

This dissertation is the first detailed description and in-depth analysis of the Middle Kingdom (2055-1650 B.C.) ceramic assemblage from the archaeological site of North Abydos, Egypt. It focuses on the pottery from an area just outside the main temple of the god Osiris, which was called the “Terrace of the Great God” during this period, where many private individuals built mud-brick chapels for their commemoration. Chapter 1 provides the background information, such as the history of previous investigations of the site and the design of the present research project. Chapter 2 describes the archaeological contexts of the pottery assemblage, including the types, distribution, and chronological sequence of the memorial chapels, as well as the stratigraphic information gleaned from new archaeological excavations. Chapter 3 lays out the pottery fabric types that are attested at the site and presents the results of the quantitative analyses of various fabrics. Chapter 4 discusses the form classification system. Each morphological type is defined, illustrated, and provided with comparanda from other sites and notes on their chronological significance. This chapter also presents the results of the quantitative analyses of various forms. In Chapter 5, more specific dates are assigned to the stratigraphic phases discussed in Chapter 2 based on the ceramic evidence. Chapter 6 examines the ceramic industry at North Abydos during the Middle Kingdom and compares and contrasts it with the modes of pottery production and distribution that were practiced in the rest of Egypt during the same period. The assemblage analyzed in this study is catalogued in an appendix and illustrated in the figures. General index is provided.

Keywords: Abydos, Egypt
Ancient pottery
Advisor: Wegner, Mary-Ann
Efficient Location Constraint Processing for Location-aware Computing

For many applications of location-based services, such as friend finding, buddy tracking,information sharing and cooperative caching in ad hoc networks, it is often important to be able to identify whether the positions of a given set of moving objects are within close proximity. To compute these kinds of proximity relations among large populations of moving objects, continuously available location position information of these objects must be correlated against each other to identify whether a given set of objects are in the specified proximity relation. In this dissertation, we state this problem, referring to it as the location constraint matching problem, both in the Euclidean space and the road network space. In the Euclidean space, we present an adaptive solution to this problem for various environments. We also study the position uncertainty associated with the constraint matching. For the road network space, where the object can only move along the edges of the road network, we propose an efficient algorithm based on graph partitioning, which dramatically restricts the search space and enhances performance. Our approaches reduce the constraint processing time by 80% for Euclidean space and by 90% for road network space respectively. The logical combination of individual constraints with conjunction, disjunction and negation results in more expressive constraint expressions than are possible based on single constraints. We model constraint expressions with Binary Decision Diagrams (BDD). Furthermore, we exploit the shared execution of constraint combinations based on the BDD modeling. All the algorithms for various aspects of the constraint processing are integrated in the research prototype L-ToPSS (Location-based Toronto Publish/Subscribe System). Through experimental study and the development of an analytical model, we show that the proposed solution scales to large numbers of constraints and large numbers of moving objects.

Keywords: Location Constraint Processing
Location-based Services
Spatio-temporal Databases
Proximity Relations
Advisor: Hans-Arno, Jacobsen
The Influence of Axial Load and Prestress on The Shear Strength of Web-shear Critical Reinforced Concrete Elements

Experimental research was conducted to investigate the influence of axial load and prestress on the shear strength of web-shear critical reinforced concrete elements. The ability of two design codes, the ACI code and the CSA code, to accurately predict the shear strength of web-shear critical reinforced concrete elements was investigated through two sets of experiments performed for this thesis, the panel tests and the beam tests. The experimental results indicated that the CSA code provided better predictions for the shear strength of web-shear critical reinforced concrete members subjected to combined axial force and shear force than the ACI code. A total of six panels, reinforced almost identically, were tested under different combinations of uni-axial stress and shear stress. In addition to the panel tests, a total of eleven I-shaped beams, with the same web thickness, were tested under different combinations of axial force and shear force. The parameters for these beams were the amount of longitudinal reinforcement, the amount of transverse reinforcement, and the thickness of the flanges. The beams were simply supported, but the loading geometry was specially designed to simulate the loading conditions in continuous beams near points of inflection. The experimental results from the panel tests and the beam tests followed a similar trend of variations. Both the inclined cracking strength and the ultimate shear strength were increased by compression and were reduced by tension. The specimens subjected to very high compression failed explosively without developing many cracks. The inclined cracking strength could be predicted with good accuracy if the influence of the co-existing compression on the cracking strength of the concrete and the non-uniform distribution of the stresses over the depth of the cross-section were considered. The strength predictions using the ACI code for these tests were neither accurate nor consistent. The ACI code was unconservative for members subjected to compression and was excessively conservative for members subjected to tension. In contrast, the strength predictions using the CSA code for these tests were generally conservative and consistent. The CSA code accurately predicted the response of specimens subjected to compression and was somewhat conservative in predicting the shear strength of specimens subjected to tension.

Keywords: Reinforced Concrete
Web-Shear Critical
Axial Load
Prestress
Advisor: Collins, Michael P.
Bentz, Evan
Regulation in Switched Bimodal Linear Systems

In the past few decades, significant progress has been made in addressing control problems for a variety of engineering systems having smooth dynamics. In practice, one often encounters also non-smooth systems in various branches of science and engineering, such as for example mechanical systems subject to impact. Motivated by the read/write head flying height regulation problem in hard disk drives, where the close proximity of the read/write head to the disk surface results in intermittent contact between the two and a bimodal system behavior, this thesis studies the output regulation problem in switched bimodal linear systems against known and unknown exogenous input signals. The regulation problems in bimodal systems presented in this thesis are solved within sets of Q-parameterized controllers, in which the Q parameters are designed to yield internal stability and exact output regulation in the closed loop switched system. The proposed parameterized controllers are constructed mainly in two steps. The first step is based on constructing a switched observer-based state feedback central controller for the switched linear system. The second step involves augmenting the switched central controller with additional dynamics (i.e. Q parameter) to construct a parameterized set of switched controllers. Based on the proposed sets of Q-parameterized controllers, four main regulation problems are addressed and corresponding regulator synthesis algorithms are proposed. The first problem concerns regulation against known deterministic exogenous inputs, where no stability or structural constraints are imposed on the Q parameter. The second problem is similar to the first, except that the Q parameter is constrained to be a linear combination of basis functions. This structure of the Q parameter is considered in the rest of the thesis. The third problem involves regulation against exogenous inputs involving known deterministic components and unknown random components, and where the regulator is designed subject to an H2 performance constraint. The last problem involves the development of adaptive regulators against unknown sinusoidal exogenous inputs. The different regulator synthesis algorithms are developed based on solving sets of linear matrix inequalities or bilinear matrix inequalities. The last two proposed regulation methods are successfully evaluated on an experimental setup motivated by the flying height regulation problem in hard disk drives, and involving a mechanical system with switched dynamics.

Keywords: Switched Bimodal Systems
Regulation
Advisor: Amara, Foued Ben
Public Forests, Private Governance: The Role of Provincial Governments in FSC Forest Certification

This dissertation examines changes that companies made in order to obtain Forest Stewardship Council (FSC) certification in the Canadian provinces of British Columbia, Alberta, Ontario and Quebec, and the role that provincial governments have played in the implementation of this emerging market-based form of governance. It analyzes the indirect roles that governments have played in either encouraging or inhibiting the adoption of certification through their policies, as well as the direct roles played in response to particular certification attempts that occurred on public land. Through the use of case studies of individual operations in each province, the interaction between state and non-state authority is explored, as well as the role that forest tenure played in each operation’s ability to obtain certification. The results reveal that the changes required to obtain certification were substantial but associated with only a small subset of the FSC’s Principles and Criteria, heavily weighted towards environmental issues. While corrective action requests are issued to the company pursuing certification, the results show that non-exclusive tenure limits a company’s ability to respond to these requests without the cooperation of the provincial government and resource users with overlapping tenure rights. However, limited duration of forest tenure does not preclude certification, and for the most part, provincial governments are found to play important facilitative roles in certification, both through their policies and regulations, and as providers of information and technical support. Further, the majority of the corrective actions were not required to be implemented prior to certification being awarded, but within the five year term of the certificate. This appears to have acted as a flexibility mechanism, allowing the certification system to secure the participation of companies in the short term, with the hope of leveraging greater change in the long term from the company, the government in question, and other resource users with overlapping tenure rights.

Keywords: forest
certification
governance
environment
soft law
voluntary
market
tenure
Advisor: Balsillie, David
Pain During Dressing Change: How does Attachment Style Affect Pain in the Older Adults?

Wound-related pain is complex, integrating the experience of noncyclic acute wound pain, cyclic acute wound pain, and chronic wound pain (Krasner 1995). More than 80% of chronic wound patients report pain during wound dressing change. A constellation of physical and psychological factors may be involved in the mediation of pain during wound dressing change. A burgeoning body of evidence suggests the intricate relationship between anxiety and pain. In this study, the attachment framework was examined to determine how personal views of self (attachment anxiety) and others (attachment avoidance) may affect pain during dressing change. Attachment styles are systematic patterns of expectations, emotional reactivity, strategies for distress management and social behaviour that are based on an individual’s belief about the self and others. Internal working models are cognitive-affective schemas that guide the attachment patterns. Purpose: The purpose of this study was to explore the relationship of attachment style and pain during dressing change in an older population. In particular the study focussed on the role that anxiety, anticipatory self reported pain, and behavioural expression of pain play in this relationships. Method: A questionnaire was used in this cross-sectional study to classify 96 older subjects into four different categories of attachment styles. Subjects were asked to rate their levels of anticipatory pain and actual pain levels at different times during wound care using a numerical rating scale. Results: The results indicated that subjects experienced more pain during dressing change than at baseline. Secure subjects reported less pain and anxiety than subjects with other attachment styles. Results of regression analysis indicated that anxiety mediated the relationship between attachment and pain. Conclusion: The results of this study also support the role that attachment plays in the experience of pain in older adults. Clinicians must be cognizant of the impact of personality, anxiety, and anticipation of pain on the actual pain experience.

Keywords: Pain
Attachment theory
Geriatrics
Chronic wound
Advisor: Sadavoy, Joel
Hemodynamic Regulation of Endothelial Cell Gene Expression: Effects of p65 Expression Level on Constitutive and TNFα Induced NF-κB Signalling

Atherosclerosis is a chronic inflammatory disease of arterial blood vessels, characterized by deposition of lipoproteins in the arterial wall. Atherosclerotic plaques form preferentially in distinct regions of the vasculature such as branch points, curvatures and bifurcations, suggesting that local hemodynamic forces may contribute to disease susceptibility. Shear stress imparted on endothelial cells (ECs) by the flowing blood has been shown to modulate gene expression and remodelling of the artery. In this thesis, an in vitro model was established to recreate the contrasting environments found in atherosclerosis-prone and atherosclerosis-resistant regions of the vasculature to demonstrate a direct causal-relationship between shear stress and expression of endothelial nitric oxide synthase (eNOS) and p65 in ECs. In vitro assessment of cell shape and expression patterns of these anti- and atherogenic genes demonstrated that shear stress can induce cell morphology and gene expression patterns that are similar to ECs in atherosclerosis-prone and atherosclerosis-resistant regions of the mouse vasculature. Regulation of eNOS transcription by shear stress was demonstrated using a transgenic mouse model and in vitro heterogeneous nuclear RNA (hnRNA) quantification. Similar to ECs in atherosclerosis-prone regions, epithelial cells lining the small intestine lumen express high levels of p65. To investigate the effects of p65 expression levels on constitutive and tumour necrosis factor α (TNFα)-induced nuclear factor-κB (NF-κB) signalling, p65 expression was suppressed in HeLa cells by RNA interference. Lower p65 expression resulted in reduced TNFα-induced expression of NF-κB target genes, including many subunits of inhibitor of nuclear factor κB (IκB), demonstrating modulation of NF-κB priming by p65 expression levels. Suppression of p65 also affected constitutive expression levels of IκB, and resulted in re-setting of the NF-κB/IκB equilibrium. Experiments using inhibitors of canonical NF-κB signalling found that basal expression of NF-κB components is independent of nuclear factor κB kinase β (IKKβ) activity and proteasome-mediated degradation of IκBα. Together, these studies elucidate the mechanism of flow-mediated gene regulation and the effect of resulting changes in p65 expression on NF-κB signalling.

Keywords: Atherosclerosis
Hemodynamics
Nuclear factor-kappa B
Advisor: Cybulsky, Myron
A Manufactured Solution? The Transfer of Technology for the Local Production of Affordable Antiretrovirals: Case Studies from Tanzania and South Africa

Statement of the issue: Facing large HIV-infected populations, Sub-Saharan African countries are producing antiretroviral (ARV) drugs under provisions of the World Trade Organization’s Agreement on the Trade-Related Aspects of Intellectual Property (TRIPS). Article 7 states that the protection of intellectual property should increase technology transfer to developing countries. This clause and the debate over domestic manufacturers’ ability to provide low-cost ARVs need examination. Methods: Case studies from ARV manufacturing initiatives in Tanzania and South Africa analyzed conditions affecting two outcomes: the type of technology transfer arrangement entered (voluntary license or imitation) and the affordability of ARVs. Data were collected and analyzed from documents, key-informant interviews, and observation. Chi-squared and phi correlation statistics were then conducted across developing countries to test the association of voluntary ARV licensure with TRIPS-compliant patents and domestic firm ownership (state or private). Results: Tanzania’s weak patent system and poorly-financed, partially state-owned firm dissuaded industry investment, but attracted a non-government organization to transfer technology through imitation. Donor-financed ARV tenders, however, restrict competition to international quality-accredited products not produced by the firm. Without large volumes and manufacturing capacity, it cannot achieve economies of scale to reduce prices below imported ARVs. In South Africa, civil society challenged the strong patent system and poor government commitment that inhibited an ARV rollout. This and a well-financed, publicly-traded firm leveraged voluntary licenses. With international quality approval, the firm increased first-line ARV affordability; however, limited domestic competition keeps treatment prices above those of neighbouring countries. A multi-country analysis found 321 generic ARV manufacturing initiatives in 86 firms across 25 developing countries. Voluntary ARV licenses had a strong positive association with TRIPS-patent compliance (ф=.56, p<.0001) and a weak negative association with state-ownership (ф=.19, p<.0001). Firms in South Africa and India were granted 77% of licenses and accounted for most quality accredited generic ARVs. Conclusion: Despite positive association, technology transfer does not readily result from patent protection, particularly to state-owned firms. Developing countries must enact policies to enable affordable ARVs; yet, they must be cautious using local production to increase ARV access, as most initiatives cannot compete with high-volume generic manufacturers.

Keywords: domestic pharmaceutical production
technology transfer
TRIPS Agreement
HIV/AIDS
Antiretrovirals
developing countries
affordability
pharmaceutical patents
drug access
Advisor: Kohler, Jillian Clare
Bonded-particle Modeling of Thermally Induced Damage in Rock

The objective of the research presented in this thesis is to validate the parallel-bonded modeling method in the context of coupled thermo-mechanical simulations. The simulation results were compared with analytical and experimental data, in the attempt to assess the usability of this particular modeling method. Previous studies of numerical approaches that related to the thermal fracturing of hard rock had used continuum-based models with constitutive relations. The simulations in the thesis were conducted using Particle Flow Code (PFC) which was chosen for the research because of its several benefits. The code has unique features such as spontaneous damage development without imposed conditions, and emergent properties such as material heterogeneity, and dynamic behavior giving possibility to monitor synthetic seismic events. The basic code has been available since 1995 and research using the code has produced hundreds of publications. The thermal option for the code is a recent addition and lacked verification, validation and applications. The thesis is the answer for that. In the course of the research work new particle clustering and grouping routines were developed and tested. Three modeling studies were conducted varying from laboratory to field scales. The 2D modeling study of the heated cylinder experiment yielded similar results both in fracture-behavioral and acoustic emission (AE) magnitude ranges when compared with the laboratory data. The 3D cubic numerical specimens, created with breakable particle clusters, were heated, and the induced damage was observed by P wave velocity measurements. The results showed trends comparable to the laboratory data: P wave velocity decreases with rising temperatures of up to 250°C and cluster-boundary cracking occurs, comparable to grain-boundary cracking in the heated rock samples. The large 2D tunnel models captured the phenomena observed in-situ displaying the difference in the damage to the roof and floor regions, respectively. This damage was due to the filling material confinement of about 100 kPa on the tunnel floor. In general, the results of the thermo-mechanical simulations were in accordance with the experimental data. The modeled temperature evolutions during the heating and cooling periods were also in accordance with the experimental and analytical data.

Keywords: coupled modeling
thermo-mechanical simulation
bonded-particle modeling
damage
brittle rock
Advisor: Young, R. Paul