VictorJuiz/thesis huggingface dataset:
Streaming of Markov Sources over Burst Erasure Channels

Real-time streaming communication systems require both the sequential encoding of information sources and playback under strict latency constraints. The central focus of this thesis is on the fundamental limits of such communication systems in the presence of packet losses. In practice packet losses are unavoidable due to fading in wireless channels or congestion in wired networks. While several ad hoc approaches are used to deal with packet losses in streaming systems, in this thesis we examine these approaches using an information theoretic framework.In our setup, the source process is a sequence of vectors sampled from a spatially i.i.d. and temporally a first-order stationary Markov distribution. The encoder sequentially compresses these source vectors into channel packets. The channel may introduce a burst erasure of length up to B in an unknown location during the transmission period, and perfectly reveals the rest of the packets to the destination. The decoder is interested in reconstructing the source vectors with zero delay, except those at the time of erasure and a window of length W following it. The minimum attainable compression rate for this setup R(B,W), termed the rate-recovery function, is investigated for discrete source with lossless recovery, and Gauss-Markov sources with a quadratic distortion measure. The above setup introduces a new problem in network information theory. Our key contributions include: (1) Upper and lower bounds on the rate-recovery function for discrete memoryless sources and lossless recovery, which coincide in some special cases. (2) A new coding scheme for the Gauss-Markov sources and a quadratic distortion measure. This scheme can be interpreted as a hybrid between predictive coding and memoryless quantization-and-binning. (3) Extensions of our zero-delay setup to incorporate non-zero decoding delays. We further show that our proposed hybrid coding scheme yields significant performance gains over baseline schemes such as predictive coding, memoryless quantization-and-binning and interleaving, over statistical channels such as the i.i.d. erasure channel and the Gilbert Elliott channel, and performs close to optimally, over a wide range of channel parameters. While our information theoretic framework involves coding theorems for burst-erasure channels our resulting schemes are applicable for much broader class of erasure channels and can yield significant performance gains in practice.

Keywords: Multimedia Streaming
Multi-terminal Source Coding
Netweork Information Theory
Rate-Distortion Theory
Advisor: Khisti, Ashish
Flat, Electronically Steered λ/2-Spaced Phased Arrays for Focused Ultrasound Surgery

One of the promising applications of non-invasive focused ultrasound surgery is the treatment of women with uterine fibroids. Without any incision, fibroids can be thermally ablated in an outpatient procedure allowing patients to return to normal activity within two days.Despite its benefits and potential, the adoption of focused ultrasound surgery has been slow. Current applications of the technique are slow, exclude many women for physiological reasons, and rely on expensive MR-guidance. This thesis describes the development of a new type of focused ultrasound therapy array designed to reduce treatment time consisting of elements with half-wavelength spacing arranged in a flat array. Using simulations, this thesis will discuss the benefits and consequences of sparse phased arrays (a common technique to reduce complexity), and explore the ability of a flat, half-wavelength-spaced phased array to ablate fibroids efficiently and safely. Finally, preliminary feasibility results with a device prototype will be presented in vitro and in vivo.The first simulation study presented here compares flat phased arrays with half-wavelength inter-element spacing with randomly-spaced sparse arrays with element populations of 75%, 50%, and 25%. Though even the very sparse (and least complex) arrays were able to perform comparable ablations, it was found that they required much more power, which was preferentially deposited in the near-field of the transducer which could extend treatment time. The second simulation study claims that a half-wavelength-spaced array at 500 kHz could perform a realistic fibroid ablation as close as 40 mm from the spine without the need for any mechanical translation. Five simulated treatments were performed at an average treatment rate of 90 +/- 20 mL/hr.Finally, this thesis reports preliminary evidence that it is feasible to construct an array of over 1000 individually-controlled elements, arranged in 64-element blocks with half-wavelength element spacing, producing acoustic powers of over 100 W. In vitro, this array was shown to be capable of steering to its edge losing only 24% to 25% of its peak pressure. Extrapolating, this prototype suggests that it is feasible to construct a 6000+ element array suitable for efficient uterine fibroid ablation.

Advisor: Hynynen, Kullervo
The Stages of Building Public-private Partnerships in Public Health: Factors Influencing the Engagement Process in the Context of Healthy Eating in Restaurants in Ontario

Public-private partnerships (PPPs) in public health are powerful tools to promote collaboration among organizations that cannot achieve their specific goals alone. Although there are frameworks that explain important aspects of multisectoral partnerships, they lack detailed descriptions of the stages and related factors to enable organizations progress along the path of PPP development, particularly in relation to obesity prevention or diet-related chronic diseases.This dissertation focuses on advancing the knowledge and understanding of factors that influence the process of building PPPs in public health, using healthy eating in restaurants in Ontario as the context for the study. A sequential explanatory mixed-methods research design was used to survey high-level representatives of organizations from the public and private sectors, non-governmental organizations and academia. Follow-up interviews were conducted to complement and expand the findings of previous survey, as well as to discover new perspectives from research participants.The integration of the findings, complemented by relevant literature, yielded the first theory-driven, empirically-based framework, which highlights 8 stages of building PPPs in public health: Awareness, Recognition, Contemplation, Dialogue, Negotiation, Deliberation, Engagement Decision, and Preparation. The Framework is a transparent tool that details the expected stages involved in PPP development, and uncovers associated factors that could enable or hinder collaboration, while enabling organizations to discuss, negotiate, and eventually deliberate and prepare openly for the successful creation of PPPs in public health, and possibly beyond.

Keywords: Framework development
Government
Healthy eating
Mixed-methods research
Public-private partnerships
Restaurants
Advisor: Jadad, Alex
Development of Biosensors to Monitor the Interaction of Small Molecules with Amyloidogenic Proteins using Optical and Electrochemical Methods

Amyloidogenic protein fibrils are well known pathological hallmark of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). The Amyloid Cascade Hypothesis attributes the onset and progression of AD to an imbalance in amyloid-beta (Abeta). In PD, a definitive diagnosis of Parkinson's disease can be confirmed only by post mortem examination of the patient's substantia nigra for the presence of Lewy bodies, mainly comprised of alpha-synuclein (a-S). As the toxicity in these neurodegenerative diseases is highly correlated with the formation of soluble oligomers from their corresponding proteins, a strategy to inhibit the aggregation of Abeta and a-S may help to ameliorate AD and PD respectively (Chapter 1). Herein, we review the fundamentals of electrochemistry (Chapter 2) before demonstrating the use of electrochemical techniques, acoustic wave sensor and BiacoreX surface plasmon resonance (SPR) to characterize the aggregation of Abeta (Chapter 3). We have shown that amyloid aggregation could be monitored through these label-free methods and clioquinol (CQ) inhibits the progression of aggregation. We further increased the throughput of monitored small molecules and Abeta interactions through the use of SPR imaging (SPRi) (Chapter 4) and LED-interferometric reflective imaging sensor (LED-IRIS) (Chapter 5). These studies showed that epigallocatechin gallate (EGCG) modulates the Abeta aggregation pathway to form beta-sheet absent aggregates while certain metal ions generally accelerate the Abeta aggregation process to form thick mature fibrils. These results are supported by Thioflavin T (ThT) and transmission electron microscopy (TEM) studies.We then studied the effects of CQ on a-S (Chapter 6) using electrochemical techniques and spectroscopic dyes such as ThT and Congo Red. Both electrochemical and spectroscopic studies showed that Cu(II) accelerated the fibril formation of a-S, while CQ inhibited such activity. This electrochemical analysis was further modified to include an optical screening test on the same transduction platform by utilizing nanosphere lithography (NSL) (Chapter 7). Complemented by Localized-SPR, SPRi, TEM and ThT studies, it was found that dense and unstructured amorphous a-S aggregates were induced by EGCG, while beta-sheet-rich and compact a-S mesh-networks were promoted by Cu(II) ions, in agreement with previous results.

Keywords: aggregation
amyloid
biosensor
electrochemistry
optical
small molecules
Advisor: Kerman, Kagan
Porphyrin-based Nanostructure-dependent Photodynamic and Photothermal Therapies

This thesis presents the investigation of nanostructure-dependent phototherapy. We reviewed the liposomal structures for delivery of photosensitizers, and introduced a novel class of phototransducing liposomes called "porphysomes". Porphysomes are self-assembled from high packing density of pyropheophorbide -conjugated phospholipids, resulting in extreme self-quenching of porphyrin fluorescence and comparable optical absorption to gold nanoparticles for high photothermal efficiency. We demonstrated this self-assembly of porphyrin-lipid conjugates converts a singlet oxygen generating mechanism (photodynamic therapy PDT activity) of porphyrin to photothermal mechanism (photothermal therapy PTT activity). The efficacy of porphysome-enhanced PTT was then evaluated on two pre-clinical animal models. We validated porphysome-enabled focal PTT to treat orthotopic prostate cancer using MRI-guided focal laser placement to closely mimic the current clinic procedure. Furthermore, porphysome-enabled fluorescence-guided transbronchial PTT of lung cancer was demonstrated in rabbit orthotopic lung cancer models, which led to the development of an ultra-minimally invasive therapy for early-stage peripheral lung cancer. On the other hand, the nanostructure-mediated conversion of PDT to PTT can be switched back by nanoparticle dissociation. By incorporating folate-conjugated phospholipids into the formulation, porphysomes were internalized into cells rapidly via folate receptor-mediated endocytosis and resulted in efficient disruption of nanostructures, which turned back on the photodynamic activity of densely packed porphyrins, making a closed loop of conversion between PDT and PTT. The multimodal imaging and therapeutic features of porphysome make it ideal for future personalized cancer treatments.

Keywords: liposome
nanoparticle
photodynamic therapy
photothermal therapy
porphyrin
porphysome
Advisor: Zheng, Gang
An Ethnography of Interprofessional Interactions in Discharge in a Canadian Acute Care Setting

Governments and hospital administrators are concerned with patient discharge from hospital, assessing efficiency and quality through length of stay, readmission rates, and discharge summaries. There is less attention being awarded to how health care workers practice and interact in relation to discharge within the context of professional roles, boundaries, and organizational structures. This thesis reports on an ethnographic study using theories of medical dominance and negotiated order to explore the nature of, and interplay between, meso-structural factors that shape interprofessional interactions in discharge in a general internal medicine unit and micro-level interprofessional interactions. Data collection, conducted from January 2012 to May 2013, involved observations, interviews, and documentary analysis. Approximately 65 hours of observations were undertaken, 23 semi-structured interviews were conducted with health care workers, and government and hospital discharge documents were collected. Data were analyzed using a directed content approach. The findings indicate that the division of healthcare labour and managerialism in the form of discharge policy are affecting health care workers' roles and opportunities for interprofessional interactions. While patterns of medical dominance exist, these occur amongst changing professional roles and interprofessional boundaries, due to the impact of managerialism on the range of healthcare workers. Consequently, there were varying opportunities for interprofessional negotiations to occur around discharge. The impact of meso-structural factors and the nature of interprofessional interactions were analyzed in relation to decision-making about patient readiness for discharge and preparation for discharge, and in the context of interprofessional rounds. A further factor affecting interprofessional interactions in relation to discharge examined in this study is the existence of a medical clinical teaching unit. An understanding of the impact of meso-structural factors on interprofessional interactions and the nature of the micro-level negotiations that occur is important for the development of interprofessional education and practice interventions.

Keywords: ethnography
general internal medicine
interprofessional care
patient discharge
social theory
Advisor: Silver, Ivan
Kitto, Simon
Mapping Long-term Cortical Maturation of the Auditory System in Adolescents who are Deaf and have used a Unilateral Cochlear Implant to Hear

In the present Thesis, we used novel imaging tools to study maturation of the auditory brain in adolescents who are deaf and have use a unilateral cochlear implant (CI) to hear for most of their lives. A CI is a surgically implanted auditory prosthesis that establishes hearing in children who are deaf. The aims of implantation are to halt any effects of deafness on the brain and promote normal auditory development. Unfortunately, CIs do not restore normal hearing as they provide only a crude representation of sounds and eliminate important cochlear processing. It has recently been shown that unilaterally stimulating the auditory system with a CI and leaving the opposite pathways deprived of input for longer than 1.5 years compromises bilateral auditory development. We are now exploring the cortical consequences of missing this sensitive period and driving maturation of the auditory cortex with unilateral implant stimulation. We measured electrically-evoked cortical responses in adolescents who had over a decade of unilateral CI experience before receiving a second implant in the opposite deprived ear. This provided an unparalleled opportunity to assess the effects of long-term unilateral stimulation/deprivation on the auditory pathways in the adolescent brain. We tracked the development of cortical responses with CI experience and localized underlying areas of cortical activity in the brain using our beamformer imaging methods. Neural synchrony of these responses was calculated to assess the co-ordination of activity across brain regions in response to sound. Our results indicate that long-term unilateral implant stimulation promotes normal-like maturation of the auditory cortex with good speech perception outcomes, providing a general impression that some degree of auditory development proceeds normally. However, abnormally strengthened activity from the hearing ear to the contralateral cortex and increased synchrony in networks known to be involved in cognitive processing suggests that cortical abnormalities persist into maturation. In the opposite deprived ear, cortical responses were atypical, had abnormally large dipoles and abnormal neural synchrony, perhaps reflecting cortical un-coupling/dis-connectivity in response to sound. We suggest that unilateral maturation of the auditory cortex drives lasting auditory asymmetries and leaves the deprived pathways unprotected from deafness-induced abnormalities.

Keywords: Children / Adolescents
Cochlear Implant
Development
Hearing Loss / Deafness
NeuroImaging
Unilateral
Advisor: Gordon, Karen A
Three Essays in Energy Economics and Industrial Organization, with Applications to Electricity and Distribution Networks

Electricity industries are experiencing upward cost pressures in many parts of the world. Chapter 1 of this thesis studies the production technology of electricity distributors. Although production and cost functions are mathematical duals, practitioners typically estimate only one or the other. This chapter proposes an approach for joint estimation of production and costs. Combining such quantity and price data has the effect of adding statistical information without introducing additional parameters into the model. We define a GMM estimator that produces internally consistent parameter estimates for both the production function and the cost function. We consider a multi-output framework, and show how to account for the presence of certain types of simultaneity and measurement error. The methodology is applied to data on 73 Ontario distributors for the period 2002-2012. As expected, the joint model results in a substantial improvement in the precision of parameter estimates.Chapter 2 focuses on productivity trends in electricity distribution. We apply two methodologies for estimating productivity growth - an index based approach, and an econometric cost based approach - to our data on the 73 Ontario distributors for the period 2002 to 2012. The resulting productivity growth estimates are approximately ‐1% per year, suggesting a reversal of the positive estimates that have generally been reported in previous periods. We implement flexible semi-parametric variants to assess the robustness of these conclusions and discuss the use of such statistical analyses for calibrating productivity and relative efficiencies within a price-cap framework. In chapter 3, I turn to the historically important problem of vertical contractual relations. While the existing literature has established that resale price maintenance is sufficient to coordinate the distribution network of a manufacturer, this chapter asks whether such vertical restraints are necessary. Specifically, I study the vertical contracting problem between an upstream manufacturer and its downstream distributors in a setting where spot market contracts fail, but resale price maintenance cannot be appealed to due to legal prohibition. I show that a bonus scheme based on retail revenues is sufficient to provide incentives to decentralized retailers to elicit the correct levels of both price and service.

Keywords: Antitrust Issues and Policies
Distribution Networks
Electricity
Energy
Industrial Organization
Advisor: Yatchew, Adonis
H”lder Continuity of the Integrated Density of States in the One-dimensional Anderson Model

In this paper we consider the one-dimensional Anderson model for Random Schrödinger operators Hω = H0 + σVω and study the continuity properties of the integrated density of states. We prove that for any γ > 0, the IDS is Hölder continuous on (−2 + γ,−γ ) ∪ ( γ,2 − γ ), with exponent 1 − Cσ/γ with the constant C depending on the energy. We make only the weak assumption that the distribution of the noise has bounded support. This improves upon the work of Bourgain giving a non-quantitative bound to show that the exponent of Hölder continuity tends to 1 as σ ↓ 0; it is also more general as Bourgain's work was in the more specific Anderson-Bernoulli model.

Advisor: Virág, Bálint
Investigation of Cyclic Deformation and Fatigue of Polycrystalline Cu under Pure Compression Cyclic Loading Conditions

It is commonly accepted that fatigue crack is initiated under tensile fatigue stresses. However, practical examples demonstrate that cracks may initiate under pure compressive fluctuating loads, e.g. the failures observed in aircraft landing gear frames. As the mechanism of such failures is rarely investigated, there is very limited or non-existent knowledge pool on cyclic deformation response under pure compressive fatigue condition. Our recent work verified that fatigue cracks may nucleate from stress concentration sites under pure compression fatigue, but whether or not a form of stress concentration is always needed to initiate a crack remains uncertain. In this study, compression fatigue tests under different peak stresses were carried out on smooth bars of fully annealed OFHC Copper. The purpose of these tests is to investigate not only the cyclic deformation response but also the possibility of crack nucleation without the stress concentrator. Results showed that overall the cyclic stress-strain response and microstructural evolution of OFHC Copper under pure compression fatigue exhibits rather dissimilar behaviour compared to those under symmetrical fatigue. The specimens hardened rapidly within 10 cycles under pure compression fatigue unlike the gradual cyclic hardening behaviour in symmetrical fatigue with the same peak stress amplitude. Compressive cyclic creep behaviour was also observed. Moreover, TEM observation showed that only moderate slip activity was detectable on the surface instead of typical PSB features. The surface observations revealed that surface slip bands did not increase in number nor height as cycling progressed. In addition, surface roughening by grain boundary extrusion was detected to become more severe with further cycling. Therefore, the plastic strain accommodated within the samples was not mainly related to dislocation activities. Instead, the mechanism of cyclic creep response for pure compression fatigue was correlated and caused primarily by grain boundary extrusions. Such phenomenon was found to eventually lead to crack nucleation. Furthermore, from symmetrical fatigue testing, it was noted that depending on the polarity of the loading spectrum in the first half cycle, i.e. compression or tension, regular or anti-Bauschinger effect was observed, respectively. Such observations further elucidate the role of compression loading spectrum versus tension loading in fatigue.

Keywords: cyclic creep
cyclic deformation response
cyclic stress strain curve
fatigue
polycrystalline Cu
pure compression
Advisor: Wang, Zhirui