VictorJuiz/thesis huggingface dataset:
Bounded Arithmetic and Formalizing Probabilistic Proofs

The first theme of this thesis investigates the complexity class CC and its associated bounded-arithmetic theory. Subramanian defined CC as the class of problems log-space reducible to the comparator circuit value problem (CCV). Using the Cook-Nguyen method we define the two-sorted theory VCC whose provably-total functions are exactly the CC functions. To apply this method, we show CC is the same as the class of problems computed by uniform AC^0 circuits with unbounded CCV oracle gates. We prove that VCC lies between VNL and VP, where VNL and VP are theories for the classes NL and P respectively. We strengthen Subramanian's work by showing that the problems in his paper are indeed complete for CC under many-one AC^0 reductions. We then prove the correctness of these reductions in VCC. The second theme of this thesis is formalizing probabilistic proofs in bounded arithmetic. In a series of papers, Jerábek argued that the universal polynomial-time theory VPV augmented with the surjective weak pigeonhole principle WPHP(LFP) for all VPV functions is the 'right' theory for randomized polynomial-time reasoning in bounded arithmetic. Motivated from the fact that no one had used Jerábek's framework for feasible reasoning about specific interesting randomized algorithms in classes such as RP and RNC^2, we formalize in VPV the correctness of two fundamental RNC^2 algorithms for testing if a bipartite graph has a perfect matching and for finding a bipartite perfect matching. Using Moser's recent constructive proof technique for the Lovász Local Lemma, we show that VPV + WPHP(LFP) proves the existence of a satisfying assignment for every instance of k-SAT in which every clause shares a variable with up to 2^{k-3} other clauses. This result implies the existence of a randomized polynomial-time algorithm for find satisfying assignments such k-SAT instances. The remainder of this thesis was motivated by the lack of fundamental probability concepts like random variables, expectation and variance in Jerábek's work, which means basic yet useful theorems like Markov's inequality, Chebyshev's inequality, linearity of expectation, etc were not available in his work. By choosing suitable definitions of random variables, approximate probability and approximate expectation, we are able prove these theorems and utilize them to prove the Goldreich-Levin theorem within the conservative extension HARD^A of VPV + WPHP(LFP).

Advisor: Cook, Stephen A
Planar Section Representations of 3D Shape

Planes are fundamental geometric primitives. Evidence in art and science shows that planar sections are useful -- structures composed purely of planar primitives are employed in architecture, design and manufacturing, where one can with relative ease physically create a model from planar parts. In medical visualization, patient-aligned planes may suffice to represent important features within a volumetric dataset. Many different applications involving 3D shape can geometrically benefit from a contextually-appropriate piecewise planar representation. This thesis systematically studies planar section representations of 3D shape. We show that humans are consistent in abstracting existing 3D shapes using a minimal number of planar 3D sections. We provide geometric insights that allow us to replicate human planar abstraction of 3D shapes algorithmically, and evaluate the algorithm's performance with a shape recognition study. We study how humans create planar shape representations interactively from scratch. Observations of their interaction patterns are used to develop a streamlined interactive drawing system. The system is further augmented to facilitate procedural creation, incorporate existing geometry and aid fabrication. A physical simulation approach identifies structurally weak models before they are fabricated, and allows interactive refinement. We then study the perceptual efficacy of a range of planar representations of 3D shape in a large-scale user study. The analysis of results reveals geometric sources responsible for error, and we use these sources to create predictive linear models of error. With this knowledge, we demonstrate we are able to improve the quality of algorithmically-created representations. Finally we present a number of applications of planar section representations. Some applications are artistic in nature, such as paper statues, puppets, detailed compositions and scanimations. Other applications are more scientific, including surface reconstruction and compression, 3D annotation, volumetric data visualization, 3D navigation, and poly-postors. Overall, the dissertation provides a comprehensive treatment of various aspects of planar section representations of 3D shape and their applications. We provide both qualitative and quantitative perceptual validation that planar section representations are indeed effective proxies of 3D shape, useful in both artistic and scientific settings.

Keywords: abstraction
geometry processing
perception
planar sections
shape representation
Advisor: Singh, Karan
Exploring a Role for Sleep in Regulating Skeletal Muscle Physiology

Skeletal muscles are remarkably adaptive tissues, with the ability to both modify their phenotypic properties in response to altered functional demands and to recover from serious injury. One mechanism through which changes in physiological and environmental conditions are signaled to muscles is via neural input from motoneurons. During sleep, neural input to the musculature is generally reduced; however, the association between the contractile phenotype of a muscle and its motor activity in sleep is unclear. Moreover, it is unknown whether sleep motor control has a functional influence on muscle physiology. I used an array of electrophysiological, molecular, histological and functional techniques in both naturally-behaving and anaesthetized rats to test the hypothesis that sleep influences skeletal muscle physiology, both under normal conditions and in response to muscle injury. The key findings of my thesis project are the following: 1. The contractile phenotype of a muscle can, in part, predict the degree of muscle tone suppression in non-rapid eye movement (NREM) sleep and phasic activity in REM sleep. Muscle activity of a fast-twitch muscle is potently suppressed in NREM sleep and its phasic activity is enhanced in REM sleep compared to waking, whereas a slow-twitch muscle experiences a low degree of suppression in NREM sleep and less phasic activity in REM sleep compared to waking. 2. Acute sleep restriction does not reverse the sleep-related suppression of fast-twitch muscle activity, ostensibly since enforced waking is characterized by motor behaviour that is distinct from that of spontaneous waking. Moreover, sleep loss does not affect the immediate expression of metabolic and phenotypic molecular markers in either muscle phenotype. 3. Both acute and chronic sleep loss cause impairments in functional muscle recovery following myotoxic injury; specifically, sleep loss is associated with reduced early and medium-term expression of molecular repair markers and contractile function deficits during recovery in a fast-twitch, but not slow-twitch, muscle, although the incidence of newly regenerating muscle fibres in damaged tissue is unaffected by sleep loss. Together, these results suggest that motor regulation in sleep may play a functional role in influencing skeletal muscle physiology, especially during recovery from a severe homeostatic challenge like muscle injury.

Keywords: motoneurons
muscle injury
sleep
Advisor: Peever, John H
Application of Independent Component Analysis (ICA) in Pharmacokinetic Modeling of Tumors Using Dynamic Contrast Enhanced (DCE)-MRI

Dynamic contrast enhanced (DCE)-MRI combined with Pharmacokinetic (PK) modeling of a tumor tissue provides information about its perfusion and vascular permeability. These tumor characteristics have been shown to be related to prognostic factors and thus, their role as cancer biomarkers in assessing anti-angiogenic therapies is increasing. However, the quantitative parameters derived from PK analyses vary significantly between studies and need improvement. Most PK models require the intravascular contrast agent concentration as an input. This vascular input function (VIF) is inseparable from the signal of extravascular extracellular space due to heterogeneity of tumor vasculature, partial volume effect, and low resolution of DCE-MRI. Thus, it is approximated with an arterial input function (AIF) measured outside of the tissue of interest (TOI). Variations and error in calculation of AIF is one of the major sources of discrepancy between PK parameters reported in different studies. The objective of this thesis is developing image processing techniques to identify and separate the VIF at the TOI, which has the potential to improve PK analysis. Such VIF could also be used in cases no artery is available or in animal studies where finding an artery is difficult. The thesis investigates feasibility of using independent component analysis for VIF calculation (using tissue-mimicking phantoms and animal models), and develops an adaptive complex independent component analysis (AC-ICA) algorithm to calculate the VIF and evaluates it using tissue-mimicking phantoms. The AC-ICA algorithm is applied to DCE-MRI of prostate cancer and its performance in PK analysis is compared to AIF-based analyses. Results show the AC-ICA provides more consistent PK parameters and better separation of normal and tumor tissues. Moreover, the proposed VIF is less sensitive (compared to AIF) to decreasing temporal resolution which enables imaging with high spatial resolution that will further improve performance of both PK analysis and AC-ICA algorithm.

Keywords: Cancer Biomarkers
Dynamic Contrast Enhanced (DCE)-MRI
Independent Component Analysis (ICA)
Pharmacokinetic Analysis
Advisor: Martel, Anne L
The Provision of Pharmaceutical Care in Oman: Practice and Perceived Facilitators and Barriers to Implementation

Objectives: The study purpose was to determine the extent of the implementation of pharmaceutical care (PC) in Oman and factors affecting its implementation. Methods: A cross-sectional mail survey of all practicing pharmacists in Oman based on the Theory of Planned Behavior (TPB) was conducted. The survey instrument was informed by a focus group study to identify behavioral, normative, and control beliefs amongst pharmacists in three practice settings. Results: The survey useable response rate was 61.2%. Participants provided PC activities between `sometimes' and `most of the time'; however, provision of advanced PC activities was limited. Provision of PC did not significantly differ across inpatient, outpatient, and community settings. Clinical knowledge, communication skills, pharmacist time, and adequate staffing were common facilitators across practice settings; worry about responsibility and culturally-based gender issues regarding patient care were common barriers. While having a private counseling area, and access to patient records and to drug information databases were facilitators identified in the public sector, their absence was a barrier in community pharmacies. Reimbursement was the main barrier in the private sector. Country of origin was significantly related to pharmacists' beliefs about providing PC; specifically, Omani pharmacists had significantly different behavioral, normative, and control beliefs than their South Asian counterparts. All constructs of the TPB (attitude, subjective norm, and perceived behavioral control) were significant predictors of intention to provide PC, but the added construct--past behavior recency was not. The overall variance explained in intention was 43%. Of the two predictors of behavior in the TPB model, only perceived behavioral control was significant; intention was not. The explained variance in PC behavior was 13.0%. Conclusions: This is the first study to examine the implementation of PC in Oman. The findings of this study will inform the development of strategies for advancing PC practice, a mandate of Ministry of Health and the pharmacy profession in Oman. The TPB was useful for explaining pharmacists' intention to provide PC; however, a longitudinal study is recommended to test its predictive validity for PC behavior.

Keywords: Barriers
Care
Facilitators
Oman
Pharmaceutical
Pharmacy
Advisor: MacKeigan, Linda
Complexity of Antiretroviral Drug-drug Interactions in the Intestine: Role of Membrane-associated Drug Transporters

Complex antiretroviral therapy has introduced new obstacles in the treatment of HIV infection such as management of drug-induced toxicities and drug-drug interactions, which are often attributed to changes in cytochrome P450 (CYP)-mediated metabolism. However, interactions between drugs that do not share the same metabolic pathway, such as HIV protease inhibitors (PIs) and nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), remain unexplained. In addition, some PIs (e.g., atazanavir) have pH dependent oral bioavailability and interact with acid-reducing agents, through an unknown mechanism that may involve increased gastrointestinal pH. Human intestinal epithelium expresses a number of ATP-binding cassette transporters (e.g., P-glycoprotein) and solute carrier transporters (e.g., organic anion transporting polypeptides (OATPs)), which can restrict or facilitate intestinal drug absorption. The goal of this thesis was to examine the role of drug transporters in regulating atazanavir permeability and their contribution to atazanavir drug-drug interactions in the intestine. Atazanavir permeability was examined using Caco-2 monolayers, an

Keywords: antiretroviral drugs
atazanavir
drug-drug interactions
drug transporters
HIV protease inhibitors
intestinal permeability
Advisor: Bendayan, Reina
Trading Privacy for Communication

There is a long history of the study of information-theoretic privacy within the context of communication complexity. Unfortunately, it has been shown that most interesting functions are not privately computable [Kus89, BS08]. The unattainability of perfect privacy for many functions motivates the study of approximate privacy. This thesis explores several notions of approximate privacy. In both worst- and average-case situations, we obtain asymptotically tight bounds on the tradeoff between approximate privacy and communication cost. Further, we interrelate the disparate definitions of privacy, and link them to a standard measure of information cost of protocols. This enables the proof of exponential lower bounds on subjective approximate privacy, independent of communication cost. A new, operationalized definition of approximate privacy based on hints is proposed (more closely resembling cryptographic definitions), which may help answer some outstanding open questions in information theory and compression.

Keywords: communication complexity
complexity
information theory
lower bound
privacy
tradeoff
Advisor: Cook, Stephen A
Pitassi, Toniann
Molecular Evolution of Zebrafish (Danio rerio) Visual Pigment Function

Photoreception in vertebrates is mediated by opsins, members of the G protein-coupled receptor (GPCR) superfamily of proteins. In the dark, opsins are covalently bound to a light-sensitive chromophore, 11-cis-retinal, which acts as an inverse agonist to suppress dark state activation. When exposed to light, the chromophore isomerizes to its all-trans conformation, activating opsin and initiating a signaling cascade within the photoreceptor cell. Zebrafish (Danio rerio) has a large complement of visual opsins, and serves as a model for the vertebrate visual system on a developmental, physiological, and behavioural level, making it an ideal candidate for the study of opsin evolution and function. Following a general introduction, chapter 2 of my thesis presents the initial characterization of a novel rhodopsin-like gene that we identified in zebrafish, rh1-2. Chapter 3 further investigates rh1-2, showing rh1-2 expression in photoreceptor cells of the zebrafish retina and using in vitro expression to identify functional characteristics of rh1-2 that are similar to rhodopsin, despite the fact that it is a much less stable pigment. Chapter 4 describes biochemical investigations of zebrafish rhodopsin and, in particular, addresses the question of the key molecular mechanisms mediating retinal release rate differences among vertebrate rhodopsins. Finally, chapter 5 investigates duplicated rh2 cone opsin genes in teleost fish and notes that many with multiple rh2 genes have at least one copy with Q122 and one with E122, a discrepancy that is known to help in establishing the contrasting functional identities of rhodopsins and cone opsins. This thesis contributes significantly to the characterization of visual pigment function in zebrafish. These experiments have also increased the understanding of functional variation within rhodopsins and cone opsins, particularly by investigating the molecular mechanisms of retinal release in rhodopsin, and the role of duplicated cone opsin genes, and will serve as an important non-mammalian reference against which future studies of the vertebrate visual system will be compared and contrasted.

Keywords: gene duplication
rhodopsin
visual pigment
zebrafish
Advisor: Chang, Belinda SW
High-quality Amorphous-crystalline Silicon Heterostructures using the Grid-based Triode Radio-frequency Plasma Enhanced Chemical Vapour Deposition Method

The amorphous - crystalline silicon heterojunction (SHJ) represents a new paradigm in crystalline silicon (c-Si) photovoltaics (PV). To achieve the 27% efficiency target for SHJ PV, defects in the silicon heterointerface must be minimized by growing high-quality hydrogenated amorphous silicon (a-Si:H) onto the c-Si surfaces without deposition-related damage. Typically, a-Si:H is deposited using radio-frequency (RF) plasma enhanced chemical vapour deposition (PECVD), which in its conventional configuration directly exposes the c-Si growth surface to the ignited plasma. In this thesis, silicon heterostructures prepared by the grid-based triode RF PECVD method is investigated for the first time. The triode method allows for high-quality a-Si:H growth with the c-Si surfaces shielded from any potential plasma damage. Using a custom-built configurable PECVD facility, a systematic study was conducted and it was demonstrated that the triode method affords the preparation of a-Si:H with excellent bulk film quality and state-of-the-art passivation for c-Si surfaces. Using the triode method, an effective minority carrier lifetime (

Keywords: Heterojunction
PECVD
Silicon
Solar
Advisor: Kherani, Nazir K
Intracavitary Magnetic Resonance Elastography for Prostate Cancer Imaging

Prostate cancer is currently the most prevalent cancer and third leading cause of cancer related deaths amongst Canadian men. Highly sensitive, but non-specific, diagnostic techniques have made it challenging for clinicians to balance treatment efficacy with associated side-effects. Prostate imaging techniques are being investigated to assist in diagnosis, staging, monitoring, and localizing prostate cancer within the gland itself. Measuring changes in tissue biomechanics could provide important functional and morphological information about prostate cancer. Magnetic resonance elastography (MRE) is a potential candidate for imaging tissue mechanical properties, in vivo. MRE gives quantitative stiffness measurements by transmitting micrometer amplitude shear waves into tissues. Previous reports of performing MRE in prostate cancer patients have used an external source to generate shear waves inside the prostate, which has imposes limitations on the spatial resolution of the stiffness maps (elastograms). An alternative approach is to use an internal or intra-cavitary actuator to generate shear waves in closer proximity to the prostate in order to produce higher resolution elastograms. Since clinically significant prostate cancers can have diameters on the order of 1 cm, high resolution elastograms are essential in order to evaluate MRE as a potential tool for assisting in disease prognosis. This thesis demonstrates the technical feasibility of intra-cavitary (transurethral, endorectal) MRE for the purposes of evaluating localized regions of stiffness within the prostate gland. First, a combination of gel and canine experiments were performed to help outline the imaging characteristics of intra-cavitary MRE. Secondly, the feasibility of performing endorectal MRE by connecting a piezoceramic actuator to an endorectal radiofrequency receive coil while simultaneously preserving the signal to noise ratio of the acquired images wave demonstrated. Thirdly, the feasibility and tolerability of endorectal MRE in conjunction with current clinical endorectal RF coil designs was successfully demonstrated in human volunteers. This represented the first evaluation of endorectal MRE in humans. Lastly, a compliant mechanical amplifier was designed in order to develop a reliable high amplitude piezoceramic actuator for performing intracavitary MRE. Taken together, this work demonstrates the feasibility of intracavitary MRE and provides a method for locally probing the biomechanical properties of the prostate gland.

Keywords: Endorectal MRE
Intracavitary MRE
MR Elastography
Prosate Biomechanics
Prostate Cancer
Transurethral MRE
Advisor: Chopra, Rajiv
Ontological Intelligence: Consciousness, Mind, Inquiry in Education

This ontological and epistemological study is concerned with investigating the phenomenon of consciousness transformation. The study ultimately demonstrates three actualities: 1) People are almost entirely identified with their thinking/mind and this is extremely limiting, 2) There is an intelligence that exists--indeed, that we are--that is beyond, or outside of, thought, and 3) These facts have tremendous implications for the education paradigm we are now operating under and proliferating. I have situated this paper under the umbrella of holistic education as I am arguing that an understanding of the whole human being is absent in current education structures and also that holism in its most lofty and sacred sense is the antidote to the remarkable lack and imbalance in our current education paradigm. Furthermore, this thesis is concerned with the nature of duality relative to an absolute, or, unity consciousness, and as such, points towards the nature of the whole as Truth. Education, as it exists now in its dominant paradigm, creates imbalance by attending only to the intellect as it presumes that knowledge, or, mental concepts, through thought is the source of the highest order of being or highest intelligence. However, I argue that thought by its very nature is extremely limited in what it can perceive and know; it cannot solve the problems that we set out for it--from personal to complex problems such as global conflict, disease, and starvation, for example. Furthermore, conditioning of the mind through education-as-knowledge-acquisition-and-mental-manipulation cripples people through creating an inability for psychological freedom and true creativity to arise. As humans, we confuse the content of consciousness--which is dominated by identification with thought--with the totality of consciousness, whereas there is consciousness beyond thought. Paradoxically, transcending thought is accomplished by inquiring into thought, which is both the essence of, and results in, a transformation of consciousness.

Keywords: Consciousness
Inquiry
Intelligence
Mind
Ontology
Advisor: Miller, John P.