VictorJuiz/thesis huggingface dataset:
Development of Polymer-based Gels for Multimodal Medical Imaging Phantoms
Keywords: CT
Medical Imaging
MRI
Phantom
Polymer
US

Development of Polymer-based Gels for Multimodal Medical Imaging Phantom By Eunji In Doctor of Philosophy Department of Mechanical and Industrial Engineering University of Toronto 2016 Abstract In the field of medical imaging, there have been numerous efforts to combine multiple imaging modalities such as ultrasound (US), Magnetic Resonance Imaging (MRI), x-rays and Computed Tomography (CT), positron emission tomography (PET), ultrasound (US), and single photon emission CT. Multimodal imaging allows the fusion and analysis of various image data to provide morphological and functional information. With the progress in medical imaging technology and increased importance of quality assurance, the research in medical imaging phantom is necessary. Phantom is an anthropomorphic object that mimics the properties of human tissue for calibration, training and surgical planning purposes. This research thesis examines four different types of polymer-based materials for constructing medical phantoms: carrageenan-based polymer gel, polymer cross-linked aerogels, UV-curable silicone and self-healing polymer materials. In the first study, water-based carrageenan gel found to have a good correlation with the imaging properties of human tissue, but its long-term stability issue restricts its applicability as commercial phantoms. Since samples contained high water content, mechanical and imaging properties of carrageenan-based gel fluctuated due to water expulsion and absorption cycles over six-week period. In the second study, silica and cellulose aerogel cross-linked with polymer was also investigated as a phantom material. Contrast agents are cross-linked to fabricate an MRI/CT-compatible material. Results demonstrate that the imaging properties of these aerogels met the values of some human tissue values but due to volume shrinkage and complex fabrication process restricts its production in large scale. Furthermore, in the third study UV-curable silicone material was considered as a 3D printable phantom material. The addition of hydrophilic silicone and water is shown to improve the curing time and imaging properties of silicone. With suitable properties of UV-curable silicone, it will assist to produce real-size liver phantom using 3D printing technique for a patient-specific phantoms. There is an increased demand for phantom application in clinician training and surgical planning with needle-insertion or dissection is necessary. In the final chapter, self-healing silicone with microcapsule healing mechanism was investigated as proof-of-concept for surgical planning tool. Throughout four different studies, different polymer-based materials are examined subsequently with novelty in each study.
Unsupervised Indoor Localization for Smartphones
Keywords: Localization
Smartphones
Tracking
Wi-Fi
Wireless communications
Wireless sensor networks

In this work, the problem of indoor localization for smartphones is investigated. An indoor localization system is designed, that relies on two general techniques: received signal strength based localization and dead reckoning. The system is designed to be trained by the collected data via crowdsourcing, with no need for active human intervention. Sensor fusion techniques are used to resolve different issues of the localization problem. The combination of accelerometer and gyroscope are used as a dead reckoning system to measure the user's displacement. Graph matching algorithms are used to merge crowdsourced data to make a unified data structure, in a fully unsupervised fashion. We investigate the problem of translating topological indoor localization to geographical localization, by modeling the building map and the semantic maps as graphs. Two matching algorithms are proposed along with a node similarity measure based on finding the minimum distance between all sets of permutations of two vectors. We provide an efficient algorithm to calculate the similarity measure, and prove its correctness via a theorem. The proposed systems are implemented and shown to perform well, both in simulations and on real data. A novel magnetic sensor based localization system is also introduced and implemented that does not require any available infrastructure in the indoor area. Sensor fusion techniques are used to improve the system's accuracy.
Applied Plasmonics for the Cultivation and Study of Photosynthetic Microorganisms
Keywords: biofuels
cyanobacteria
microalgae
photobioreactor
plasmonics
solar energy

This thesis explores nano-scaled plasmonic solutions to the problem of light capture and distribution in microalgae cultivation schemes. An evaluation of the effect of light quality on productivity under different photobioreactor geometries shows a 2x increase in productivity under 630-nm red light for low density cultures under low light intensity, compared to 534-nm green light. The opposite was true however when high density cultures are exposed to high intensity light â 534-nm performed 4x better than strongly ab-sorbed 630-nm red light. These results highlight the coupled influence of light quality and conventional photobioreactor design parameters. Wavelength specific, near-field plasmonic phenomena are then used as a means to couple light into cyanobacteria biofilms showing that plasmonic fields can be used to drive photosynthesis in living cells. 10-Âľm thick biofilms with maximum cell volume density of 20% vol/vol (2% more total accumulation than control experiments with direct light) were cultivated over three days. Far-field plasmonic phenomena were also applied to bulk cyanobacteria cultures to demonstrate a 6.5% enhancement in productivity. Resonant light is scattered back towards the culture increasing total ab-sorption while off-resonance light is transmitted. Supporting technology that enables patterning of plas-monic nano-features with a commercial CO2 laser system is also presented. Patterning speeds of 30 mm2/min and patterning costs of $0.10/mm2 are demonstrated which are ~30 fold faster and ~400 fold less expensive than e-beam lithography. Finally, crude oil characterization based on surface plasmon reso-nance is demonstrated, with applicability to both conventional and alternative energy industries. Bitumen-toluene mixture tests show a measurement sensitivity of 74o RIU-1, and a limit of detection below 1% toluene. Seven crude oils from around the world are differentiated with refractive indices spanning 1.44 to 1.56, with a sensor limit of detection of 0.0006 RIU.
Adaptive Decision Feedback Equalization With Continuous-time Infinite Impulse Response Filters
Keywords: Clock and data Recovery
Decision Feedback Equalization
Equalization
Infinite Impulse Response DFE
Wireline

In high-speed (10+Gb/s) chip-to-chip links, the primary impairments to signal integrity are noise, crosstalk, and a smooth tail in the pulse response resulting in inter-symbol interference (ISI) sometimes spanning more than 10 unit intervals (UIs). Although often simple in their implementation, continuous time linear equalizers amplify high-frequency noise and crosstalk and consume extra power. A conventional discrete-time (DT) decision feedback equalizer (DFE) is well-suited and power efficient for channels with a few dominant post-cursor ISI terms, however, the power can become prohibitive for channels with many post-cursor ISI terms. Infinite impulse response (IIR) DFEs can equalize post-cursor ISI persisting 10 or more UIs while consuming low-power comparable to just one DT tap. DFE architectures with varying numbers of DT and IIR taps are compared for use in typical wireline channels, and it is found that 2 IIR taps can offer an excellent compromise between power consumption and performance. However, an IIR DFEâ s performance degrades significantly as the feedback loop delay increases. Fortunately, adding a single DT tap can eliminate the degradation. The first ever hybrid DFE combining 1 DT and multiple (2) IIR taps is presented equalizing 24dB loss at half the bitrate while consuming 4.1mW at 10Gb/s. A novel edge based adaptation algorithm is also presented for DT DFEs which converges faster than previous algorithms while using the same high-speed circuitry and signals required for clock recovery. The edge based algorithm is extended to work for a 1 DT + 1 IIR DFE. The 1 DT + 1 IIR DFE along with integrated clock recovery and adaptation is demonstrated in 28nm FD-SOI CMOS. At 16Gb/s with a 30dB-loss channel, a BER below 10â 12 is measured over a 0.3UI timing window. The novel edge-based algorithm adapts both IIR and discrete-tap equalizer coefficients using the same high-speed circuitry and signals required for clock recovery. The adaptive DFE converges within 5us and is robust in the presence of poorly-conditioned data.
Revealing Retention Mechanisms of Duplicated Genes and Surveying Triple Mutant Genetic Interaction Space in Yeast
Keywords: complex genetic interactions
genetic interactions
genetics
genomics
higher-order genetic interactions
yeast

Recent genome sequencing efforts have revealed astounding genetic diversity between individuals in the human population. The current challenge is to assign functions to the thousands of genes in our genomes and to understand how individual differences in genes contribute to disease. Much progress has been made in identifying causal loci of single gene disorders for both common and rare genetic diseases. However, many phenotypes are influenced by more complex genetic interactions involving larger sets of genes and genetic variants. Thus, deciphering the genotype-phenotype relationship requires that we expand our focus beyond pair- wise genetic interactions to include complex, higher-order genetic interactions involving more than two genes. In this thesis I used the simple model organism, the budding yeast, and a method for automated yeast genetics called Synthetic Genetic Array (SGA) analysis, to construct double and triple mutants, and to measure the resulting genetic interactions by using colony size as a proxy for cell fitness. I first applied this methodology to dissect and characterize the mechanisms of functional divergence of duplicated genes. I also applied it more generally to estimate the prevalence of complex genetic interactions in a eukaryotic cell. My results suggest that triple mutant genetic interactions occur frequently in the yeast genome and are therefore expected to have a major impact on our understanding of the relationship between genotype and phenotype. This map of complex genetic interactions provides a unique dataset for studying how the content of our genomes is shaped and how this relates to complex disease.
Acceptability and Feasibility of Behavioural and Sweet-tasting Solution Interventions for Procedural Pain Treatment in Neonatal Units in Kenya
Keywords: Acceptability
Behavioural
Feasibility
Neonatal units
Procedural pain
Sweet-tasting

Acceptability and Feasibility of Behavioural and Sweet-tasting Solution Interventions for Procedural Pain Treatment in Neonatal Units in Kenya Oâ Brien Munyao Kyololo Doctor of Philosophy Graduate Department of Nursing Science University of Toronto 2016 Abstract Background Although, over the last decade, the frequency of procedures has decreased and pain treatment practices have improved in high-income countries, in most low- and middle-income countries (LMICs), the burden of pain remains very high and procedural pain is severely undertreated. The nature and frequency of procedures and pain treatment practices has not been comprehensively examined in Kenya. Additionally, acceptability and feasibility of behavioural and sweet-tasting solution interventions has not been comprehensively examined. Objectives To determine the: (a) nature and frequency of painful procedures, (b) use of behavioural and sweet-tasting solution pain treatment interventions and (c) acceptability and feasibility of behavioural and sweet-tasting solution interventions and factors influencing their acceptability and feasibility in Kenya. Methods A three-phase sequential mixed-methods study involving (a) review of medical charts, (b) prospective observations and (c) photo-elicitation semi-structured interviews was conducted in two neonatal units in Kenya. Descriptive analysis, t-tests, Mann-Whitney U test, chi-square tests, multiple regression and ecological comparative analysis were used to describe the frequency of procedures, use of pain treatment interventions and factors predicting frequency of procedures and use of interventions. Inductive content analysis was conducted for qualitative data. Results Neonates experienced 1.6 (SD = 1.1, range 1-12) painful procedures per day; more tissue-damaging (1.2Âą1.7) than non tissue-damaging procedures (0.3Âą0.6) were performed (p = .03). Term neonates were less likely to undergo procedures (RR 0.85, 95% CI [0.76, 0.95], p = .003) while neonates were 1.8 times and 1.6 times more likely to undergo procedures during the 3rd - 7th day of life and if admitted in the Level II unit respectively (p
Linking Laboratory Engine Studies to Real-world Observations: Assessing the Air Quality Implications of Gasoline Direct Injection Engines
Keywords: air quality
black carbon
emission factors
engine emissions
gasoline direct injection
ultrafine particles

In response to stringent regulations on fleet-average fuel economy, vehicle manufacturers have increasingly replaced port fuel injection (PFI) engines with gasoline direct injection (GDI) engines. These engines emit substantial quantities of ultrafine particulate matter (PM) and black carbon (BC) which is of concern due to their associated health and climate effects, respectively. This thesis investigated GDI emissions, with a focus on the particle phase, in both laboratory and real-world environments to help understand the air quality impacts of this engine technology. As part of the study, advanced PM measurement techniques were assessed, and a correction protocol for a popular high-time resolution particle sizing instrument needed to accurately measure vehicle exhaust size distributions was developed. A laboratory study to quantify phase-partitioned polycyclic aromatic hydrocarbon (PAH) concentrations was also conducted. Compared to PFI engines, GDI engines emitted elevated concentrations of heavy molecular weight PAHs, including benzo(a)pyrene, a PAH with established associations to negative health outcomes. The GDI engine exhaust also had elevated concentrations of the PAHs pyrene and fluoranthene; these PAHs also exhibited the greatest extent of particle-gas partitioning. A study of real-world GDI emissions in an urban environment showed that GDI particle number and BC emissions were in the upper end of the fleet distribution, and that exhaust plumes exhibited dynamic behaviour in the near-road region, with increasing particle number emission factors with increasing distance from the roadway. This behaviour was unique to GDI vehicles, the same effects were not observed for heavy-duty garbage trucks or a PFI-equipped vehicle. Comparing size distributions at different distances from the roadway, rapid particle growth of sub-5 nm soot cores due to condensation of low volatility organic gases, such as pyrene and fluoranthene, was proposed to be the dominant growth mechanism in GDI vehicle exhaust. Comparing laboratory and real-world emission factors, BC emission factors were in good agreement, while real-world particle number emission factors were up to an order of magnitude higher. An estimate of the climate impacts of increased BC relative to fuel savings from GDI also showed that fuel economy gains of up to 12% may be needed to offset the radiative forcing of BC.
Perceptions, Experiences and Management of Knee Symptoms in Adults Age 35-65 Years - A Qualitative Study
Keywords: Disease management
Focus groups
Illness perceptions
Interviews
Osteoarthritis
Qualitative Research

Background: Osteoarthritis (OA) is a highly prevalent and costly chronic condition which can begin as early as the third or fourth decade of life. To date, interventions have focused on older adults. There is an urgent need to focus on younger adults with OA symptoms to improve management and potentially limit progression of OA. However, there is an inadequate understanding of the perceptions, experiences and management of younger adults to begin to develop interventions which address peoples’ needs earlier in life. Objectives: To explore, in adults aged 35-65 years with knees symptoms: 1) the meaning of knee symptoms to people; 2) how people manage knee symptoms; and 3) the consequences of knee symptoms on peoples’ lives. Methods: Six focus groups and 10 one-on-one interviews were conducted with 51 participants (median age 49; 61% female) who self-reported knee OA or reported knee symptoms (i.e. pain, aching or stiffness) on most days of the past month. Constructivist grounded theory guided sampling, data collection and analysis. Data were analyzed using a constant comparative method, in which comparisons constituted each stage of analysis. Results: Central to participants’ understanding of their knee symptoms was a perception that symptoms were preventable, meaning there was the potential to prevent the onset of symptoms and to alter the course of symptoms. Their approach to management was not linear, but rather, a process that moved back and forth between searching for “solutions” and active management (ongoing use of strategies). During the process, participants consulted health care providers but often perceived that medical care offered limited options and guidance. Participants experienced a range of disruptions and changes in their lives due to knee symptoms. They described the consequences of symptoms on their physical activity, social life and emotions. Participants reported a new awareness of their knee, a lack of trust in their knee and that their sense of self was altered. Conclusions: This study provides new insights into the perceptions and experiences of adults age 35-65 years with knee symptoms. Findings have implications for the development of health policies and interventions to support primary and secondary prevention of knee symptoms.
Josephs of the Country: James Jones's Thirty-year Men and the Image of the WWII Soldier in American Culture
Keywords: American war fiction
WWII American novels

This dissertation analyzes the war trilogy written by James Jones and argues that Jones’s GI characters are foundational sources of the American World War II soldier’s popular culture image in their own time and in the decades that followed. Not only do From Here to Eternity, The Thin Red Line, and Whistle demonstrate the influences of factors both historic and contemporary across the thirty years of their publication span, but they also serve as a generative medium in which the American soldier’s representative capacity, fluidity, and adaptability are highlighted. While a central goal of this thesis is to encourage new understandings of Jones’s characters as interstitial figures capable of expressing dissent within the channels of regulated society, the study also offers a critique of the ways that these same soldiers perpetuate certain values associated with a traditional American character. The dissertation begins by showing how Jones’s secondary soldiers rework the figure of the colonial yeoman in contemporary contexts, proceeds by explaining the characters’ reflection of Weberian influences in the organization of post-war American life, and finishes by examining their response to America in Vietnam. At stake in the study is a deeper understanding of the soldier’s image in American life and the ways that this malleable image both shapes and reflects the cultural imagination. By seeking to restore balance to the discourse currently surrounding the soldier, the study engages current scholarship in the fields of Jones scholarship, studies of the war novel, and veteran studies.
Development of an automated and scalable lab-on-a-chip platform with on-chip characterization
Keywords: digital micrfluidics
electrowetting
feedback
inkjet printing
microfluidics
resistive forces

Digital Microfluidics (DMF) is a fluid-handling technique that enables precise control of drops on an array of electrodes using electrostatic forces. In contrast to most other lab-on-a-chip technologies (e.g., channel-based microfluidics), DMF is highly reconfigurable (i.e., function is defined by software and not by the physical structure of the chips). Thus, DMF offers the possibility for a truly general-purpose lab-on-a-chip platform, where a wide variety of biological and chemical protocols may be implemented at the microscale, under automated control, and on a generic chip. Widespread adoption of this technology has thus far been limited by: (1) lack of access to control hardware/software, (2) the high-cost and specialized equipment required for fabricating DMF chips, (3) an incomplete understanding of DMF device physics, and (4) lack of methods for performing on-chip characterization. This thesis aims to address these limitations. We describe the development of a control instrument and software capable of applying a precise electrostatic force and measuring device capacitance, drop position, and drop velocity on-chip. We also demonstrate a low-cost method for fabricating DMF devices that does not require a cleanroom facility: inkjet printing of silver electrodes on paper. We present new on-chip methods for characterizing the resistive forces that oppose drop movement on DMF and report the results from an initial screen of conditions, establishing the effects of surface tension, conductivity, viscosity, protein content, and driving frequency on resistive forces. Finally, we demonstrate an extension of impedance-based drop sensing techniques (e.g., device capacitance, drop position, and drop velocity) to facilitate measurement across multiple electrodes in parallel. In combination, these advancements represent significant progress toward the goal of establishing a general-purpose lab-on-a-chip platform that is accessible to the wider biomedical and chemical research communities.
Monoamine Oxidase A in Relation to Subtypes and Treatment of Major Depressive Disorder
Keywords: Major Depressive Disorder
Monoamine Oxidase A
Monoamine Oxidase Inhibitors
Positron Emission Tomography

Identification of central biomarkers related to subtypes of major depressive episodes (MDEs) can contribute to a more personalized treatment approach of major depressive disorder (MDD). Monoamine Oxidase-A (MAO-A) is a replicated central biomarker of MDE and may represent a biomarker of MDE subtypes. The current body of research aimed to identify clinical predictors of elevated MAO-A total distribution volume (VT), to evaluate the relationship of MAO-A VT to replicated brain structural changes seen in MDD and to assess the targeting of MAO-A with monoamine oxidase inhibitors (MAOIs). Greater severity and reversed neurovegetative MDE symptoms were associated with elevated MAO-A VT in the prefrontal cortex (PFC) and anterior cingulate cortex (ACC) (Multivariate Analysis of Variance (MANOVA), severity: F(2,38)=5.44, p=0.008; reversed neurovegetative symptoms: F(2,38)=5.13, p=0.01). There was no significant relationship between hippocampal MAO-A VT and hippocampal volume or PFC and ACC MAO-A VT to PFC or ACC cortical thickness in MDD. Mean brain MAO-A occupancies ranged from 74-84% for moclobemide (300-1200mg daily dose) and was 87% for phenelzine (45-60mg daily dose). There was significantly greater MAO-A occupancy by phenelzine (45-60mg) and higher dose moclobemide (900-1200mg) compared to lower moclobemide doses (300-600mg) (F(7,16)=3.94, p=0.01). In conclusion, this research suggests elevated MAO-A VT as a distinct biomarker of MDE compared to structural brain changes that has the greatest elevation in MDEs with the highest severity or reversed neurovegetative MDE symptoms and this research has identified the optimal occupancy and treatment algorithm of MAOIs available to target MAO-A.