VictorJuiz/thesis huggingface dataset:
Multimode Spectroscopy for Self-referenced Plasmonic Biosensing

Surface plasmon resonance (SPR) is an efficient mechanism for biosensing due to its high field intensity and subwavelength confinement. However, the information obtained from these sensors is limited as they only rely on a single measurement at TM polarization. This limitation results in cross sensitivity of the surface plasmon (SP) wave to several parameters such as variations in bulk solution concentration or temperature fluctuations, in addition to the analyte to be measured. In this dissertation the possibility to decouple the aforementioned parameters from the analyte by spectroscopy with more than one mode is investigated. A hybrid plasmonic waveguide (HPWG) and a plasmon waveguide resonance (PWR) sensor are considered for exciting two resonance modes using dual-polarization spectroscopy. These sensors are based on different combinations of a dielectric waveguide and a plasmonic guiding layer. Depending on the overlap of each mode (TE or TM) with the sensing region, each mode exhibits different sensitivity to the measurand. The structural properties of these sensors have been optimized using a genetic algorithm (GA) to ensure optimum performance. Moreover, a method to decouple the interfering surface and bulk effects is presented. The applications of the PWR sensor for refractive index sensing, thin film measurement, and kinetic analysis of protein-nanoparticle interactions are experimentally demonstrated and compared with the conventional SPR sensor. It is demonstrated that for refractive index sensing the TM mode of the PWR sensor has six times smaller refractive index resolution than that of the SPR sensor. To further enhance the functionality of the plasmonic sensors, two grating based designs are proposed which can perform three-mode spectroscopy. The first design contains a one dimensional dielectric grating based SPR sensor (DGSPR) and the second grating sensor contains a one dimensional metallic grating loaded on an SPR sensor (MGSPR). Both designs are optimized with a GA to obtain three resonance modes. A detailed analysis of these designs using numerical and analytical methods is presented. The performance of each mode is compared with that of the conventional SPR sensor. Finally, a method to differentiate three interfering effects is provided.

Keywords: Multimode
Optic
Plasmonic
Sensing
Spectroscopy
Waveguide
Advisor: Aitchison, James Stewart
Mojahedi, Mohammad
Estimating Endogenous Dopamine at D2 and D3 Receptors in the Human Brain using the Agonist Radiotracer [11C]-(+)-PHNO: Clinical, Cognitive, and Metabolic Correlates

Using positron emission tomography (PET), and reversibly binding radiotracers which label the dopamine (DA) D2/3 receptors (D2/3R), it is possible to estimate endogenous DA levels in the brain of humans in vivo. This thesis has four themes. The first theme is validating the use of an agonist radiotracer for D2/3R to estimate endogenous DA levels. The second theme is applying this method to better understand differences in DA levels between healthy persons and persons with schizophrenia. The third theme is determining other biologically relevant factors which may affect endogenous DA levels in the human brain in vivo, in particular, factors related to metabolic health. The final theme combines those previous – attempting to extend the basic metabolic correlates relating to endogenous DA to better understand how abnormalities in DA levels may arise in persons with schizophrenia. For the first time, an agonist radiotracer for the DA D2/3R was used to provide in vivo estimates of endogenous DA in the brains of healthy humans. Furthermore, it was determined that this radiotracer could be used to estimate endogenous DA in the brains of persons with schizophrenia who were currently taking antipsychotics. Elucidating relevant cognitive and biological factors which may relate to differences in endogenous DA levels is pertinent for better understanding how abnormalities in DA tone may arise in neuropsychiatric diseases. Thus, for the first time it is demonstrated that differences in insulin sensitivity among healthy persons is related to differences in endogenous DA in the ventral striatum. Given that insulin resistance can be comorbid or concurrent in persons with schizophrenia, future studies are proposed.

Keywords: [11C]-(+)-PHNO
D2R
D3R
Dopamine
PET
Schizophrenia
Advisor: Graff-Guerrero, Ariel
Transfusion, Iron, and Leukemogenesis: Implications for Myelodysplastic Syndrome

Patients with myelodysplastic syndrome (MDS) require chronic red blood cell (RBC) transfusion due to anemia. Multiple RBC transfusions cause secondary iron overload and subsequent excessive generation of reactive oxygen species (ROS), which leads to mutations, cell death, organ failure, and inferior disease outcomes. The goal of this project is to assess the roles of anemia, secondary iron overload, and iron chelation in several aspects related to MDS including transfusion requirements, oxidative stress, and leukemogenesis. Using the RBC transfusion history from MDS patients, we discovered that patients who have high initial transfusion intensity (ITI) had higher long-term transfusion requirement and reduced overall survival. Our results suggest that the underlying pathology of patients with high ITI may be more severe. We next analyzed early bone marrow hematopoietic cells from MDS patients and revealed that the ROS level of these cells is correlated with serum ferritin, a clinical marker of iron burden, in patients with high blast count. Conversely, iron chelation therapy (ICT) decreased serum ferritin and ROS level in these cells. Our findings established the relationship between iron and ROS in early hematopoietic cells. To elucidate the effect of iron overload and iron chelation on leukemogenesis, we utilized a radiation-induced acute myeloid leukemia (AML) animal model. Iron loading in irradiated B6D2F1 mice accelerated AML development. However, there was a progressive decrease in AML risk for irradiated mice with increase in iron burden from 7.5 to 15 to 30 mg. In addition, ICT decreased AML incidence in the 7.5 mg iron-loaded irradiated mice, while AML onset was earlier for the 30 mg iron-loaded irradiated mice that received ICT. We concluded that iron is a promoter of mutation and leukemogenesis in vivo up to a peak iron dose, but further iron loading decreases AML risk by increasing cell death. Taken together, these studies support the possibility that iron toxicity as a result of chronic RBC transfusion leads to poor outcome in MDS by impairing primitive hematopoietic cells via oxidative stress. ICT can partially mitigate the adverse effects of iron overload, and to maximize its benefit this intervention should be undertaken prior to the development of extreme iron overload.

Keywords: Acute Myeloid Leukemia
Animal Model
Iron Chelation
Iron Overload
Myelodysplastic Syndrome
Transfusion
Advisor: Wells, Richard A
High-order Implicit Time-marching Methods for Unsteady Fluid Flow Simulation

Unsteady computational fluid dynamics (CFD) is increasingly becoming a critical tool in the development of emerging technologies and modern aircraft. In spite of rapid mathematical and technological advancement, these simulations remain computationally intensive and time consuming. More efficient temporal integration will promote a wider use of unsteady analysis and extend its range of applicability. This thesis presents an investigation of efficient high-order implicit time-marching methods for application in unsteady compressible CFD. A generalisation of time-marching methods based on summation-by-parts (SBP) operators is described which reduces the number of stages required to obtain a prescribed order of accuracy, thus improving their efficiency. The classical accuracy and stability theory is formally extended for these generalised SBP (GSBP) methods, including superconvergence and nonlinear stability. Dual-consistent SBP and GSBP time-marching methods are shown to form a subclass of implicit Runge-Kutta methods, which enables extensions of nonlinear accuracy and stability results. A novel family of fully-implicit GSBP Runge-Kutta schemes based on Gauss quadrature are derived which are both algebraically stable and L-stable with order 2s-1, where s is the number of stages. In addition, a numerical tool is developed for the construction and optimisation of general linear time-marching methods. The tool is applied to the development of several low-stage-order L-stable diagonally-implicit methods, including a diagonally-implicit GSBP Runge-Kutta scheme. The most notable and efficient method developed is a six-stage fifth-order L-stable stiffly-accurate explicit-first-stage singly-diagonally-implicit Runge-Kutta (ESDIRK5) method with stage order two. The theoretical results developed in this thesis are supported by numerical simulations, and the predicted relative efficiency of the schemes is realised.

Keywords: Computational fluid dynamics
Generalized summation by parts
Implicit time marching
Stiff initial value problems
Superconvergence
Advisor: Zingg, David W
Integrated Circuits for Rapid Sample Processing and Electrochemical Detection of Biomarkers

The trade-off between speed and sensitivity of detection is a fundamental challenge in the design of point-of-care diagnostics. As the relevant molecules in many diseases exist natively at extremely low levels, many gold-standard diagnostic tests are designed with high sensitivity at the expense of long incubations needed to amplify the target analytes. The central aim of this thesis is to design new strategies to detect biologically relevant analytes with both high speed and sensitivity. The response time of a biosensor is limited by the ability of the target analyte to accumulate to detectable levels at the sensor surface. We overcome this limitation by designing a range of integrated devices to optimize the flux of the analyte to the sensor by increasing the effective analyte concentration, shortening the required diffusion distance, and confining the analyte in close proximity to the sensor. We couple these devices with novel ultrasensitive electrochemical transduction strategies to convert rare analytes into a detectable signal. We showcase the clinical utility of these approaches with several applications including cancer diagnosis, bacterial identification, and antibiotic susceptibility profiling. We design and optimize a device to isolate rare cancer cells from the bloodstream with near 100% efficiency and 10 000-fold specificity. We analyse pathogen specific nucleic acids by lysing bacteria in close proximity to an electrochemical sensor and find that this approach has 10-fold higher sensitivity than standard lysis in bulk solution. We design an electronic chip to readout the antibiotic susceptibility profile with an hour-long incubation by concentrating bacteria into nanoliter chambers with integrated electrodes. Finally, we report a strategy for ultrasensitive visual readout of nucleic acids as low as 100 fM within 10 minutes using an amplification cascade. The strategies presented could guide the development of fast, sensitive and low-cost diagnostics for diseases not previously detectable at the point-of-care.

Keywords: Biosensors
Diagnostics
Electrochemical Sensors
Electrochemistry
Lab-on-a-chip
Nanotechnology
Advisor: Kelley, Shana O
Analyzing an Emerging Field of Public Health Practice in Ontario, Canada: The Case of Climate Change Adaptation

This dissertation uses the case of public health adaptation to climate change in Ontario, Canada to develop an understanding of how new fields of public health practice emerge, and how practices become legitimated by practitioners. Since climate change became an identified public health issue by way of the Ontario Public Health Standards, 2008 (OPHS), and given that health equity is a normative dimension of practice and climate change holds the potential to exacerbate existing health inequalities, this work makes three primary contributions. First, I utilize Bourdieu’s theory of practice to describe how social change occurs within the professional field of public health. Second, I share practitioner interpretations of the OPHS to develop an understanding of how policy on climate change adaptation is translated into practice. Third, I highlight the role of health equity in climate change work, as practiced by Ontario public health practitioners. The dissertation draws on data from a web-scan of the thirty-six Ontario public health unit web pages and twenty in-depth interviews with public health practitioners from twenty health units. By identifying specific practices and interpretations of public health policy related to climate change, I show how specific practices are imbued with discursive meaning that shape how public health action on climate change is framed and understood as ‘legitimate’. Findings illustrate that climate change is very much an emerging field of practice, with a variety of approaches taken by practitioners including inaction, the repackaging of existing environmental health activities, and championing innovative practices. I demonstrate how practitioners selectively utilize policy to both enable and constrain public health action on climate change, and to document how health equity is employed as a discursive strategy by the champions of this work to try and legitimate climate change adaptation as a unique sub-field of public health practice.

Keywords: climate change adaptation
environmental health
Ontario
Pierre Bourdieu
public health
social change
Advisor: Poland, Blake
The Role of CEP120 and SPICE1 in Human Centriole Duplication

The centrosome is a collection of proteins scaffolded upon microtubule based structures called centrioles. Centrosomes play critical roles as the primary microtubule organizing centers in interphase and mitotic cells, and template the formation of cilia and flagella. A mitotic cell contains two centrosomes, each with two centrioles, and following mitosis daughter cells inherit one centrosome. Before the next mitotic division, centrioles are duplicated in a process where one procentriole forms adjacent to each existing centriole. Mutations in proteins required for centriole duplication and/or centrosome function cause developmental defects such as primordial dwarfism, microcephaly and ciliopathies. Additionally many tumor cells contain excess centrosomes, and extra centrosomes are a driver of cancer progression. Thus, the correct number and function of centrosomes is critical for human health, and understanding the proteins involved in centriole assembly will offer insights into important diseases. Here, I describe the functions of CEP120 and SPICE1 as proteins required for centriole assembly. I show that CEP120 and SPICE1 cooperate with CPAP in the assembly of centrioles. Within the centriole duplication pathway, CEP120 and SPICE1 are dependent upon the presence of SASS6, STIL, CPAP and CEP135, and are in turn required for CEP135, CP110, CEP97 and Centrin recruitment. Further, CEP120 interacts with CPAP, and they cooperate with SPICE1 in centriole microtubule assembly and elongation. Following up on this work, I identify a group of proteins with previously undescribed roles in centriole duplication, including the human nucleosome assembly protein NAP1L1. These proteins were identified by screening for proteins in the proximity of CEP120 and SPICE1, and several of them are important for centriole elongation, suggesting a functional link to CEP120 and SPICE1 in centriole assembly. The results herein represent important advances in our understanding of how CEP120 and SPICE1 function, and in our understanding of centriole assembly and elongation.

Keywords: Centrioles
Centrosomes
CEP120
CPAP
Duplication
SPICE1
Advisor: Pelletier, Laurence
Overcoming the Cancer Experience: Narrative Identity in Young Adult Survivors of Childhood Cancer

Although young adult survivors of childhood cancer (YAs) face a series of significant physical and psychosocial challenges, only a portion of these survivors will actually develop mental health difficulties. Research on narrative identity and posttraumatic growth suggests that developing a coherent life-story narrative, making meaning, and finding benefits from negative life events, can contribute to better psychosocial adjustment. The aim of the present study was twofold: understanding the mechanisms that link young adults’ cancer experience with positive psychosocial adjustment outcomes (i.e., empathy, attributional style, and coping), and investigating maternal distress-related communication and young adult attachment style as predictors of narrative identity and psychosocial adjustment. One hundred and eighteen YAs completed an adapted version of McAdams’ life-story interview (2001), which was coded for meaning making and coherence. YAs could choose to talk about cancer or non-cancer-related turning points. YAs completed online questionnaires assessing posttraumatic growth, attachment style, and three measures of psychosocial adjustment. Ninety-five mothers of YAs wrote a narrative of a past experience with their child’s cancer, and completed measures of distress-related disclosure, cancer-talk, and dispositional optimism. Results revealed that meaning making was higher for cancer-related than for non-cancer related turning points. Posttraumatic growth mediated the associations between cancer meaning making and both coping and empathy. Mothers’ cancer-talk frequency was related to YA cancer meaning making, and mothers’ distress-related disclosure was associated with YA posttraumatic growth. Mothers’ narrative coherence about a memory of their child’s cancer was unrelated to YA narrative coherence, but was positively related to YA negative attribution style, but only for mothers who scored low on optimism. Finally, secure attachment style was associated with YA narrative coherence about their cancer experience, and YA overall narrative coherence (cancer and non-cancer) mediated between YA secure attachment and YA empathy. These findings indicate that YA’s successful incorporation of the cancer experience into their narrative identities through meaning making and posttraumatic growth processes is linked to positive psychosocial adjustment outcomes. Also, mothers who engage in distress-related conversations with their children contribute to YA’s capacity to overcome their cancer experience. Implications for research on narrative identity development and clinical practice are discussed.

Keywords: cancer survivors
meaning making
narrative coherence
narrative identity
parenting
posttraumatic growth
Advisor: Grusec, Joan E
The Atmospheric Fate of Organic Nitrogen Compounds

Organic nitrogen compounds are present in our atmosphere from biogenic and anthropogenic sources and have impacts on air quality and climate. Due to recent advances in instrumentation, these compounds are being detected in the gas and particle phases, raising questions as to their source, processing and sinks in the environment. With their recently identified role as contributors to aerosol formation and growth, their novel large scale use as solvents in carbon capture and storage (CCS) technology and their emissions from cigarette smoke, it is now important to address the gaps in our understanding of the fate of organic nitrogen. Experimentally and theoretically, I studied the chemical atmospheric fate of specific organic nitrogen compounds in the amine, amide and isocyanate families, yielding information that can be used in chemical transport models to assess the fate of this emerging class of atmospheric molecules. I performed kinetic laboratory studies in a smog chamber to measure the room temperature rate coefficient for reaction with the hydroxyl radical of monoethanolamine, nicotine, and five different amides. I employed online-mass spectrometry techniques to quantify the oxidation products. I found that amines react quickly with OH radicals with lifetimes of a few hours under sunlit conditions, producing amides as oxidation products. My studies on amides revealed that they have much longer lifetimes in the atmosphere, ranging from a few hours to a week. Photo-oxidation of amides produces isocyanates and I investigated these mechanisms in detail using ab initio calculations. Furthermore, I experimentally measured isocyanic acid’s Henry’s Law constant as well as its hydrolysis rate constants to better understand its sinks in the atmosphere. Finally, I re-examined the structure-activity relationship (SAR) of organic nitrogen molecules for improved model parameterizations.

Keywords: atmospheric fate
isocyanic acid
mechanisms
nicotine
organic nitrogen
oxidation
Advisor: Abbatt, Jonathan P. D.
Murphy, Jennifer G.
"Melancholy: Female Identity Conflict in Contemporary Mexican Literature'

“Melancolía: conflicto de identidad femenina en la literatura mexicana contemporánea” es un estudio crítico de la melancolía como característica de la representación literaria femenina mexicana contemporánea. Se analizan tres obras literarias: Nadie me verá llorar de Cristina Rivera Garza, Oficio de tinieblas de Rosario Castellanos y Arráncame la vida de Ángeles Mastretta. A pesar de que estas novelas representan diferentes etapas de la historia de México, como la posrevolución, el período colonial y la modernidad, ponen en relieve el conflicto y la crisis de identidad que no permite que los personajes femeninos asuman su subjetividad. Este estudio sugiere que esta imposibilidad es producto de lo que he denominado castración política, esto es, la invisibilidad política y social que enfrentan las figuras femeninas a causa de su supuesta inferioridad biológica. Esta inferioridad, según Freud, ocurre durante el establecimiento sexual, en el cual la mujer desarrolla la envidia fálica. En la teoría freudiana la melancolía, es una pérdida desconocida que se instala en el individuo. Se utiliza asimismo a Kristeva, en particular su teoría de lo abyecto, para reafirmar la idea de que la mujer es un ser abyecto por estar reducida a su mera capacidad biológica, lo cual no le permite adquirir el lenguaje y por ende asumirse como sujeto. La mujer mexicana es codificada a través de dos figuras mitológicas; la Malinche y la virgen de Guadalupe. Por un lado, la Malinche representa la degradación de la mujer mexicana y por otro, la virgen de Guadalupe es la madre virginal de un pueblo huérfano. La pérdida que enfrentan los personajes femeninos es producto de la imposición de moldes que no les permite establecer su propia identidad. En las novelas analizadas, existe una reflexión en cuanto a lo que constituye el yo femenino. Este estudio ofrece un entendimiento del establecimiento del Yo melancólico. Este Yo está disfrazado de máscaras, las cuales permiten la sobrevivencia de las protagonistas, estas máscaras representadas por: la locura, la internalización y la música, marginalizan a los personajes femeninos y a su vez les otorga libertad. Asimismo, este estudio ofrece alternativas de liberación al proponer una identidad androgina, como también a través de la desmitificación de la materinidad y la falsedad del final feliz propuesto por el patriarcado.

Keywords: Contemporary Literature
Female Representation
Mexican Literature
Psychoanalysis
Women writers
Advisor: Antebi, Susan