VictorJuiz/thesis huggingface dataset:
Quantifying Vascular Markers in Cancer Using Targeted Microbubbles

The growing demand for a personalized approach to treatment of disease has accentuated the importance of molecular imaging. As the characterization and measurement of key biomolecules in vivo, molecular imaging has the potential to dramatically impact all facets of patient care, from early disease detection to diagnosis, staging, treatment monitoring and follow-up. In ultrasound, functional and molecular imaging is possible through the use of microbubbles, a contrast agent that can be transformed into targeting agents that bind to vascular biomarkers of interest. This strategy has been employed by a number of groups to demonstrate the ability of targeted ultrasound contrast imaging to monitor molecular expression in a variety of tumour models and it is suggested that a positive correlation between specific biomarker expression levels and the detected acoustic signal of the bubbles exists. The limitations of traditional tumour models, however, have hindered any concrete demonstrations of quantitative measures of vascular biomarkers using microbubbles. This thesis demonstrates that targeted ultrasound contrast enhanced imaging can provide a quantitative measure of angiogenic biomarker expression on endothelial cells, both in vitro and in a mouse embryo model. New methodologies were first developed to introduce microbubbles into the vasculature of living, isolated, late gestational stage embryos. Non-linear microultrasound imaging was employed to collect basic perfusion parameters in these animals and molecular imaging of endogenously expressed endothelial cell surface markers in the developing mouse was successfully achieved. An endoglin loss of function model was subsequently used to examine the relationship of receptor densities to quantifiable molecular ultrasound levels. This design enabled direct modulation of surface target protein densities. Parallel plate perfusion chambers were used to assess the adhesion of targeted microbubble binding to cultured embryonic mouse endothelial cells, while binding in vivo was evaluated in living transgenic embryos. In both cases, molecular ultrasound was capable of reliably differentiating between molecular genotypes. This work represents the first demonstration of quantitative molecular imaging with ultrasound, a critical first step in establishing the abilities of molecular ultrasound to deliver accurate and specific noninvasive information in patients.

Keywords: Angiogenesis
High Frequency
Microbubbles
Molecular Imaging
Mouse Embryos
Ultrasound
Advisor: Foster, Stuart
PRECARIOUS LIVES: A CRITICAL EXAMINATION OF HOMELESS YOUTH TRANSITIONS TO INDEPENDENT HOUSING

Precarious Lives: A Critical Examination of Homeless Youth Transitions to Independent Housing Naomi S. Thulien Graduate Department of Nursing Science University of Toronto 2017 ABSTRACT Homelessness has reached epidemic proportions in Canada, with youth comprising a significant segment of this population. While we know a great deal about the risk factors associated with young people entering street life, we know much less about how to facilitate and sustain homeless youth transitions off the streets. To date, there have been only a handful of longitudinal studies designed to examine the trajectories of youth who exit homelessness. Moreover, none of these longitudinal studies were designed to exclusively examine the experiences of youth transitioning to independent housing, where youth pay market rent and are required to be more self-sufficient. The goal of the study was to address this knowledge gap by producing an emic (insider) perspective on the experiences of formerly homeless youth as they transitioned into independent housing and attempted to achieve meaningful social integration. To achieve a more nuanced understanding of the subjective and objective aspects of meaningful social integration, the study was guided by a Postcolonial Feminist theoretical framework alongside the World Health Organization Commission on Social Determinants of Health conceptual framework. A critical ethnography was utilized to reveal socioeconomic and political factors that shape the transition to independent housing and to meaningful social integration. During ten months of fieldwork, I met every other week with nine formerly homeless youth who had recently moved into independent housing. The majority of youth were individually interviewed 13 to 19 times. In total, I conducted 119 hour-long informal interviews. Three key findings emerged: 1) youth appeared “successfully” housed but lived in chronic precarity; 2) youth experienced a shift in identity and employed this as a self-preservation strategy; and 3) the process of independently maintaining housing undermined the youths’ sense of mastery and control. Despite their remarkable agency, participants’ lack of tangible and intangible resources meant they were housed in poverty and remained marginalized. I propose a new conceptual framework, highlighting the tangible and intangible resources needed by youth attempting the daunting task of transitioning off the streets.

Keywords: critical ethnography
homeless youth
housing
postcolonial feminist
social determinants of health
transitions
Advisor: Gastaldo, Denise
The Role of the Development in Felix Mendelssohn's Sonata Forms

This dissertation presents a theory of development sections based on their roles in Felix Mendelssohn’s instrumental sonata forms. Given its contextual perspective on developments, my theory critiques established approaches in Schenkerian studies and recent formal treatises by Caplin (1998) and Hepokoski and Darcy (2006), which focus mainly on the inner workings of formal areas rather than their inter-relationships. My theory for classifying an extensive body of developments holds the potential to further sonata-form study across works by other nineteenth-century composers. I apply what I call an “inner-outer perspective” to offer local and global delineations of developmental space. My "inner perspective" enables detailed discussions of developments by contributing concepts like the “developmental gap (DG)”, “retransition (RT)-prep zone”, “retransitional sequence”, “retransitional caesura (RTC)”, and “retransition (RT)-connect”, and it expands on what I call “development-recapitulation (D-R) overlap”. The "outer perspective" of my theory proposes that all developments are classifiable according to two criteria: (1) developments achieve a tonic- or a non-tonic-articulated “development-recapitulation (D-R) border”, and (2) developments have either a minimal or a strong tie to the rest of the form. I combine these criteria to produce four “development classes”—I, II, III, and IV—but focus on those fifty Class-I and -II developments that exhibit a strong tie to the rest of the form. My analyses identify five DRTs, or “developmental relationship types”, by which to classify all fifty of Mendelssohn’s developments selected for detailed study. In DRT1, the development forwards material to the coda (“development-coda pairings”); in DRT2, the development forwards material which helps to defer the essential structural close (ESC); in DRT3, the retransition calls for “compensation” towards the movement’s end; in DRT4, the development furthers an aspect from the exposition or introduction into the recapitulation and/or coda; and in DRT5, the underplayed D-R border channels motion and contributes to the movement’s single-sweep design. DRTs offer important insights on developments, large-scale form, and Mendelssohn’s music. The pathways that arise from considering the confluence of various musical parameters within developments and beyond suggest transformation narratives through the form. DRTs therefore highlight the development’s importance to Mendelssohn’s aesthetic and early-nineteenth-century sonata form.

Keywords: Development section
Felix Mendelssohn-Bartholdy
Musical narrative
nineteenth-century music
Sonata form and sonata theory
Transformation
Advisor: McClelland, Ryan
Improved Phase Detection for Digital Phase-locked Loops

Digital PLLs (DPLLs) have emerged as reliable alternatives to analog PLLs since they are more robust in the presence of process variations and mismatch and do not need a large on-chip capacitor to realize a loop ﬁlter. However, a DPLL employs a time to-digital converter (TDC) to resolve the phase error in quantized steps which shows up as deterministic jitter in the output clock. Similarly, a DPLL tunes a digitally controlled-oscillator (DCO) in discrete frequency steps which adds an extra source of jitter. Furthermore, the quantized response of the DPLL may cause chaotic limit cycles in some conﬁgurations. This thesis presents innovations to make DPLLs suitable for a wide range of applications. First, a novel low-power TDC with 4 ps resolution, approximately an order of magnitude better than an inverter delay in the 0.13 µm CMOS technology, is enabled by employing a highly digital coarse-ﬁne TDC with a calibrated coarse stage followed by a ﬁne stochastic stage. On power-up, on-chip calibration algorithm based on a balanced mean code density test is used to minimize nonlinearities in the coarse TDC, reducing worst-case spurs from -54.4 dBc to -70.55 dBc at 1.995 GHz operation. The thesis also investigates dead-zone behavior in DPLLs caused by the quantization eﬀect of the TDC. It results in chaotic limit cycle behavior; producing higher than expected in-band phase noise and strong spurious tones. To alleviate this problem, a noise-shaped oﬀset is added to the phase error to keep the TDC active and away from the dead-zone. The proposed solution is demonstrated in a 0.13 µm CMOS prototype achieving consistent low in-band noise. A binary bang-bang phase detector (BBPD) is a commonly used alternative to the power hungry TDC. However, BBPD based DPLLs have limited frequency pull-in and capture range that are traded oﬀ for steady-state jitter performance. The thesis proposes an alternative to BBPD by using a multi-phase bang-bang detector (MPBBD). Also, the thesis presents a rigorous mathematical analysis of the cycle slipping behavior to quantify the pull-in and capture range as well as the locking time for DPLL with either BBPD or MPBBD. The ﬁnal formula gives a useful insight into the eﬀect of various loop parameters on the cycle slipping behavior. A DPLL architecture with a MPBBD is presented and implemented in 28 nm CMOS technology to improve the pull-in and capture range while not aﬀecting the steady-state jitter performance.

Keywords: bang bang phase locked loop
dead zone of phase detector
Digital phase locked loop
frequency synthesizer
modulator dithering
time to digital converter
Advisor: Chan Carusone, Anthony
Towards Self-Pumped Difference Frequency Generation in Bragg Reflection Waveguide Lasers

Bragg reflection waveguide lasers are demonstrated in the GaAs/AlGaAs material system for phase-matched frequency conversion through second order nonlinearities. Bragg waveguide design considerations such as modal propagation loss and far-field are studied. Effect of etch depth on propagation loss of 2D ridge Bragg lasers is assessed both theoretically and experimentally, and the underlying physics is examined. The results allow for design of functional Bragg lasers with minimal propagation loss. Far-field properties of Bragg lasers are also systematically investigated providing an analytical framework for the design of single-lobed far-field operation of devices for improved in- and out- coupling to integrated devices. An ebeam lithography process is developed for the fabrication of various laser configurations including ring and DFB lasers in a single-sided Bragg laser structure. This is the first time that the full fabrication of diode lasers based on ebeam lithography is developed in the TNFC cleanroom in University of Toronto. The fabricated lasers are tested for various characteristics such as laser performance, modal analysis, and nonlinear conversion. The mode selection mechanism in the single-sided structure is studied and based on the results an improved double-sided Bragg laser wafer design structure is proposed. The new wafer design is confirmed to emit only at the Bragg mode, which shows the efficacy of the applied methodology. A comprehensive study of difference frequency generation (DFG) is presented in double-sided ridge Bragg lasers. We report internal normalized nonlinear conversion efficiency of 1.84/W/cm2 in the structure, as a first time demonstration of DFG in active semiconductor devices. Tuning of phase-matching wavelength through thermal effects as well as current injection is documented. This study provides a clear roadmap to inform future device designs to realize self-pumped DFG, and to predict their performance when electrically injected. When fully optimized, milliwatt level output powers can be generated through nonlinear conversion using this platform, which is useful for various applications such as on-chip sensing. % Specifically, a surface Bragg grating was integrated with the Bragg lasers for light emission at the phase-matching wavelength and self-pumped DFG. Lastly, given that the current platform can allow for self-pumped nonlinear generation, an analysis of modulation properties of such semiconductor optical parametric oscillators was carried out and presented. To facilitate the analysis of dynamic properties, a novel model based on diode laser rate equations and nonlinear conversion is developed.

Advisor: Helmy, Amr S
Biogeographic Patterns of Lemur Species Richness and Occurrence in a Fragmented Landscape

Determining the factors that affect species richness and occurrence is vital to the study of primate biogeography. In this study, I investigate the biogeographic patterns of a lemur community within a fragmented landscape in Ankarafantsika National Park, Madagascar. The landscape consists of 42 deciduous dry forest fragments ranging in size from 0.23 to 117.7 ha. I conducted a total of 1218 surveys for lemurs between June and November 2011 in the 42 fragments. I recorded a total of 1023 individual or group sightings of six species. I conducted vegetation sampling in 38 of 42 forest fragments. I measured human disturbance within each fragment and determined fragment isolation and proximity to human settlements. I explored biogeographic patterns of lemur species richness and occurrence using the species-area relationship, metapopulation dynamics, and landscape ecology. I found that lemurs in a fragmented landscape show a species-area relationship in the form of a convex power model. I did not find a sigmoidal pattern for the species-area relationship and I found no evidence of a â small island effect.â Human disturbance and tree height also influence species richness, but it is unclear how. Lemur species form different metapopulations within the same landscape. Metapopulation dynamics suggest that area was a stronger factor determining individual lemur species occurrence than fragment isolation. However, for Microcebus species, area seems to have less influence than for other species (Cheirogaleus medius and Eulemur fulvus). I investigated the landscape ecology of lemur species occurrence and found species-specific scale responses to habitat amount. Area predicted species occurrence for C. medius and M. murinus, but not for M. ravelobensis. M. ravelobensis occurrence may be mediated by factors other than area, such as dispersal ability and edge tolerance. My study shows the importance of a multi-scale approach to lemur biogeography and how it is critical for understanding how lemur species respond to high amounts of forest loss and fragmentation.

Keywords: Biogeography
Landscape Ecology
Lemur Richness and Occurrence
Madagascar
Metapopulation
Species-Area Relations
Advisor: Lehman, Shawn M
The Experiences of Women Entrepreneurs in the English Language Education Sector: Understanding Cross-Cultural and Cross-Linguistic Implications Through a Multiple Narrative Case Study

This research investigates the cross-cultural and cross-linguistic experiences of women entrepreneurs operating businesses in the English language education sector. The study is a multi-narrative case study with qualitative data collected through self-assessment tools, narrative interviewing, critical incident responses, cultural artefact stories, and an asynchronous focus group in response to a mini-lecture on culture and its relationship to language. There are six participants, operating businesses in Algeria, China, Colombia, Egypt, and Canada. The methodology yielded rich, multi-layered data and revealed unexpected significant variation in the participants’ cross-cultural and cross-linguistic experiences. It also yielded unexpected and equally varied data on their experiences as entrepreneurs, as women entrepreneurs, and as entrepreneurs in the English language education sector. The conceptual framework of multiple conceptualizations of culture and its relationship to language proved useful in interpreting the data on the participants’ cross-cultural and cross-linguistic experiences; however, given the unexpected data on the participants’ entrepreneurial experiences, it did not prove adequate for the interpretation of the entire data set. As an exploratory study, the research yielded multiple areas for possible future research. Prime among these is the use of the conceptualization of complex dynamic systems as a way to understand the variation seen in the participants’ experiences as entrepreneurs, women entrepreneurs, and entrepreneurs in the English language education sector as well as their cross-cultural and cross-linguistic experiences.

Keywords: Cross-cultural
Cross-linguistic
English as a second language
English language education
Entrepreneurship
Women entrepreneurs
Advisor: GagnĂŠ, Antoinette
Life-History Traits and Temperature-Dependent Performance of Tranosema rostrale (Hym.: Ichneumonidae), a Parasitoid of Low-Density Spruce Budworm (Lep.: Tortricidae) Populations

The eastern spruce budworm Choristoneura fumiferana (Clemens) (Lepidoptera: Tortricidae) is one of the most important outbreaking defoliator in conifer forests of eastern North America. In low-density populations, the larval endoparasitoid Tranosema rostrale (Brischke) (Hymenoptera: Ichneumonidae) is known as an important mortality factor, but relatively little information is available about the factors influencing its ability to keep spruce budworm populations low. A series of studies were conducted to investigate T. rostrale’s: 1) reproductive biology and behaviour; 2) seasonal pattern of parasitism and host instar preference; 3) developmental, survival, and reproductive response to temperature; 4) ability to abrogate spruce budworm’s immune response at high temperatures; and 5) spatiotemporal biology in response to changing temperature. Three traits of the parasitoid’s reproductive biology contribute to its successful parasitism: its lack of a pre-mating and preoviposition period, the rapid maturity of its eggs soon after emergence despite being synovigenic, and its efficacy in host searching and oviposition behaviour. As T. rostrale does not prefer to attack any one particular host instar, its seasonal pattern of parasitism is likely influenced by its phenology or competition with the ectoparasitoid Elachertus cacoeciae (Howard) (Hymenoptera: Eulophidae). Overall performance by T. rostrale was severely reduced at high temperatures. The negative correlation between the parasitoid’s survival and rearing temperatures above 20°C was associated with a downregulation of T. rostrale’s polydnavirus gene transcription and an enhancement of the accumulation of host immunity gene transcripts. An individual-based simulation model incorporating the parasitoid’s response to temperature allowed insight into unknown facts about its seasonal biology, such as phenology, voltinism, and overwintering strategy. The findings improve our understanding of the influence of temperature on spruce budworm population dynamics via its parasitoids, and our ability to predict pest outbreaks, which is important to develop more effective pest management strategies under scenarios of changing climate.

Keywords: Choristoneura fumiferana
Parasitoid
Spruce budworm
Temperature
Tranosema rostrale
Advisor: Smith, Sandy M.
An Investigation of Non-Cognitive Approaches to the Creative Writing Process

Abstract Much research suggests that the writing process, as taught in public schools, focuses on essay writing and literacy skills development. Statistics published by the Education Quality and Accountability Office (EQAO) in Ontario suggest this focus on essay writing and literacy skills development is both warranted and effective; students consistently achieve or surpass provincial standards for literacy. However, much extant writing research reinforces this narrow view of writing, which is weighted in favour of outcomes-based skills development. Data collected from the Contextual Information (taken from the Student Questionnaire at the conclusion of the Ontario Secondary School Literacy Test) reveal that students view writing as an assignment-driven, un-creative, and stressful activity. Research into the process of writers writing creatively within the public school system is limited. Therefore, this narrative inquiry explores the creative writing process of accomplished, professional Canadian creative writers, and includes my own creative process as a published writer of narrative fiction. This study contributes to composition process theory and pedagogy by considering the process of creative writing, using a holistic framework. Data are collected from the narratives of three accomplished Canadian writers: Margaret Atwood, Lawrence Hill, and Alice Munro, as well as from my own writing narrative. These writing narratives include (auto) biographies, interviews, podcasts, and workshop notes.

Keywords: Creative Writing
Creativity
Holistic
Writing
Advisor: Cooper, Karyn
Informed Anytime Search for Continuous Planning Problems

Navigating uncontrolled dynamic environments is a major challenge in robotics. Success requires solving many different technical problems and path planning is a key component of most autonomous solutions. Path planning is the task of finding a path through the environment that allows a robot to reach its desired position. This path must avoid obstacles and be executable by the robot while often also reducing a specified cost (e.g., path length). The difficulty of meeting these requirements reliably and quickly in continuous state spaces has made path planning an active area of research in robotics. Two popular path planning approaches are informed graph-based search and anytime sampling-based planning. Informed graph-based searches, such as A*, are efficient but use a priori approximations of the problem domain. If these approximations are chosen incorrectly, then the algorithms may be unable to find a (suitable) solution or take a prohibitively long time to do so. Anytime sampling-based planners, such as RRT*, continuously improve their approximations of the problem domain but perform inefficient searches. These searches simultaneously search the entire problem domain and can become prohibitively expensive in large or high-dimensional planning problems, such as when planning for high-DOF manipulation arms. This thesis demonstrates how planning in continuous planning problems can be improved by unifying the informed graph-based search and anytime sampling-based planning approaches. It investigates various ways to use heuristics to focus and order the search of almost-surely asymptotically optimal sampling-based planners. The theoretical and experimental advantages of this informed anytime sampling-based search are demonstrated through the planning algorithms, Informed RRT*, Batch Informed Trees (BIT*), and Sorted RRT* (SORRT*).

Keywords: Anytime Search
Heuristic Search
Informed Search
Optimal Planning
Path Planning
Sampling-based Planning
Advisor: Barfoot, Timothy D