VictorJuiz/thesis huggingface dataset:
A Mixed Biosensing Film Composed of Oligonucleotides and Poly (2-hydroxyethyl methacrylate) Brushes to Enhance Selectivity for Detection of Single Nucleotide Polymorphisms

This work has explored the capability of a mixed film composed of oligonucleotides and oligomers to improve the selectivity for the detection of fully complementary oligonucleotide targets in comparison to partially complementary targets which have one and three base-pair mismatched sites. The intention was to introduce a “matrix isolation” effect on oligonucleotide probe molecules by surrounding the probes with oligomers, thereby reducing oligonucleotide-to-oligonucleotide and/or oligonucleotide-to-surface interactions. This resulted in a more homogeneous environment for probes, thereby minimizing the dispersity of energetics associated with formation of double-stranded hybrids. The mixed film was constructed by immobilizing pre-synthesized oligonucleotides onto a mixed aminosilane layer and then growing the oligomer portion by surface-initiated atom transfer radical polymerization (ATRP) of 2-hydroxy methacrylate (PHEMA). The performance of the mixed film was compared to films composed of only oligonucleotides in a series of hybridization and melt curve experiments. Surface characterization techniques were used to confirm the growth of the oligomer portion as well as the presence of both oligonucleotides and oligomer components. Polyatomic bismuth cluster ions as sources for time-of-flight secondary ion mass spectrometry experiments could detect both components of the mixed film at a high sensitivity even though the oligomer portion was at least 200-fold in excess. At the various ionic strengths investigated, the mixed films were found to increase the selectivity for fully complementary targets over mismatched targets by increasing the sharpness of melt curves and melting temperature differences (delta Tm) by 2- to 3-fold, and by reducing non-specific adsorption. This resulted in improved resolution between the melt curves of fully and partially complementary targets. A fluorescence lifetime investigation of the Cy3 emission demonstrated that Cy3-labeled oligonucleotide probes experienced a more rigid microenvironment in the mixed films. These experiments demonstrated that a mixed film composed of oligonucleotides and PHEMA can be prepared on silica-based substrates, and that they can improve the selectivity for SNP discrimination compared to conventional oligonucleotide films.

Keywords: DNA
biosensor
single nucleotide polymorphisms
mixed film
surface characterization
poly(2-hydroxyethyl methacrylate)
Advisor: Krull, Ulrich Jorg
The Plant Transcriptome and Its Response to Envrionmental Stimuli

The relationship between an organism’s genome, developmental stage, and environment is complex. The aim of the research presented herein was to provide experimental evidence to contribute to the annotation of the P. trichocarpa genome and to test two major hypotheses addressing the interaction between drought and time of day in A. thaliana and in two hybrid Populus clones. In order to generate data to address these aims, three separate experiments were undertaken. First, all members of the R2R3-MYB family of transcription factors in the P. trichocarpa genome were characterised by phylogenetic analysis and their transcript accumulation patterns across a range of tissues and organs were assessed using whole genome poplar microarrays. Results of this analysis indicated that expansion and diversification of the R2R3-MYB family may have contributed to phenotypic innovation in the Populus lineage. Second, drought-responsive transcriptome adjustments of two hybrid poplar clones, DN34 (P. deltoides X P. nigra) and NM6 (P. nigra X P. maxiomowiczii) were assessed for time-of-day and genotype dependent patterns. For each genotype, each of four time points was characterised by discrete sets of drought-responsive genes. Furthermore, while a number of genes were identified that were responsive to drought in both genotypes, a much larger number of genotype-dependent, drought-responsive transcriptome changes were detected. Finally, the drought-responsive transcriptome adjustments A. thaliana plants were assessed for time-of-day dependent accumulation patterns. Results of this analysis indicate that time-of-day-dependent differences in the drought response were manifest as changes of different magnitudes for a conserved set of genes across the four time points measured. These results emphasise the complex interplay of a plant’s genome, developmental stage, and environment in shaping the observed transcriptome.

Keywords: Drought
R2R3-MYB
Diurnal
Arabidopsis
Hybrid poplar
Populus
Genomics
Microarray
Advisor: Campbell, Malcolm M.
Structural Metaphor: An Exploration of the Subjective Experience of Psycho-analytic Essence

In this study the subjective experience of psycho-analytic essence is approached through an examination of conscious and unconscious representations of self-in-work (Dreyfus, 1991). The study begins with an heuristic identified as the psycho-analytic moment, a transitory self-state arising in the course of conducting a psycho-analysis and felt to correspond to occasions of right, expert, good or exemplary therapeutic practice. The study advances to an examination of the lived experience of clinical psycho-analysis through a set of structured and unstructured interviews with two psycho-analysts. The study’s general approach incorporates a revised version of Goethe’s delicate empiricism as adapted by Hoffman (1989). The methods for interviewing participants and for analyzing transcripts were designed to access unconscious communications regarding subjective experience. Interview procedures combined phenomenological and free-associative narrative techniques: Procedures for transcript analysis were developed from literary studies, psycholinguistics, psycho-analysis and grounded theory. The analysis of participants’ utterance led to the hypothesis that an unconscious configuration of inference and memory gives shape to the subjective experience of composite elements of psycho- analytic practice. This hypothesized coherence of unconscious memory and process structures is identified as a structural metaphor. The structural metaphor is posited to underwrite the verisimilitude of lived experience, personal idiom and aesthetic within the clinical encounter. Thus, the structural metaphor is hypothesized to shape not only the psycho-analyst’s representations of his or her way of being-in-work and linguistic deportment within the interview setting, but to also shape the subjective experience of psycho-analytic practice. Thus reconsidered, the psycho-analytic moment is viewed as an existential moment in the ongoing phenomenology of lived experience, occasioned by a convergence of unconscious identity and experience within the clinical field. This existential moment is taken to be indicative of the presence of something essential about self, work or self-in-work, as a result of a set of psychological, affective and visceral factors that arise in this moment of convergence. However, the psycho-analytic moment is assigned little epistemic value in identifying properties of psycho-analysis as a discipline or a practice, instead reflecting the structural metaphor that underlies the experience of that practice.

Keywords: Psychoanalysis
Subjectivity
Structural Metaphor
Delicate Empiricism
Clinical Practice
Qualitative Research
Phenomenology
Interviews
Advisor: Miezites, Solvegia
Political Learning and the Pathways to Political Engagement

This thesis addresses two central questions: How in the long run do Canadian citizens learn about politics? And how does long term experience with politics influence democratic political engagement? The theoretical framework employed in this study makes four basic assumptions about citizens: they are intendedly rational, they use cognitive shortcuts, they are adaptive, and they often face deep uncertainty about the political world. These core assumptions generate a broad set of expectations about how long term experience with politics systematically affects citizen behaviour. This evidence indicates that years of accumulated experience with Canadian politics fundamentally shapes the political outlooks and behaviours of Canadian citizens. Political experience affects whether citizens vote, whether they get the requisite political information that helps them to make reasoned political judgments, and how different considerations enter into their vote choices. Moreover, and despite their different backgrounds, long term experience with Canadian politics influences democratic political engagement among Canadian born citizens and immigrant Canadians in strikingly similar ways.

Keywords: Canadian politics
political behaviour
Advisor: Nevitte, Neil
A Scattering-based Approach to the Design, Analysis, and Experimental Verification of Magnetic Metamaterials Made from Dielectrics

The design, modeling, fabrication, and validation of an optical magnetic response in dielectric-based metamaterials are studied. These metamaterials consist of either periodic or random arrays of dielectric particle inclusions, which may be spheres, coated spheres, or completely randomly shaped. It is demonstrated that because of the simple particle shapes and dielectric materials, these metamaterials are quite easy and feasible to implement in a bulk, three-dimensional sample, and the response is isotropic. This in is contrast to other predominant designs of optical metamaterials, which are planar and anisotropic arrays of complicated metallic fishnet or split-ring resonator structures, which require stringent tolerances and sophisticated assembly. It is shown that SiC is one of many materials from which such infrared magnetic metamaterials can be constructed. A simple SiC powder is used to verify these claims. The milled micropowder of crystalline SiC is comprised of particles of random shapes and sizes. A model of the electromagnetic response of such powders is developed, whereby the induced magnetic dipole response is modeled by equivalently-sized spheres of SiC, whereas the electric dipole response is modeled by a continuous distribution of ellipsoidal particles. Infrared spectroscopic measurements and numerical calculations are performed, verifying both the magnetic and electric response of the powder. A alternate approach is also described, where uniform SiC microspheres are fabricated using more sophisticated nanochemical techniques. In the final portion of the dissertation, the mutual near-field coupling between ideal magnetic dipoles induced in dielectric spheres is studied. This is implemented for microwave frequencies using large permittivity ceramic spheres. An approximate coupled dipole model of the multiple scattering among the spheres is developed, and a transition matrix method is implemented to calculate the exact scattering by the clusters. Experimental measurements are performed, confirming the two models. The results for pairs, chains, and rings of spheres indicates that the magnetic dipole modes hybridize in analogy to atomic bonding. A notable result is that certain hybridized magnetic dipole modes may have a net electric dipole moment. The similarity to atomic and molecular bonding should prove useful in conceptualizing and designing more sophisticated metamaterials.

Keywords: metamaterials
effective media
multiple scattering
magnetic permeability
silicon carbide
negative permeability
negative index
Mie theory
nanofabrication
nanochemistry
infrared spectroscopy
Advisor: Mojahedi, Mohammad
Aitchison, J. Stewart
The Impact of Adverse Events on Hospital Outcomes and Sensitvity of Cost Estimates to Diagnostic Coding Variation

Previous research has established a consensus that in-hospital adverse events are ubiquitous, cause significant harm to patients, and have important financial consequences. However, information on the extent, consequences and costs of adverse events in Canada is limited. For example, there is, as yet, no published study that has investigated the costs of adverse events in a Canadian context. This dissertation aims to redress this situation by providing Ontario-based estimates of the impact of eleven nursing sensitive adverse events on cost, death, readmission, and ambulatory care use within 90 days after hospitalization. This dissertation also aims to contribute more broadly to the patient safety literature by quantifying the impact of diagnostic coding error in administrative data on estimates of the excess costs attributable to adverse events. Given the increasing importance of these estimates in Canada and elsewhere for hospital payment policy and for assessments of the business case for patient safety, this is an important gap in the literature. Each of the adverse events was associated with positive excess costs, ranging from $29,501 (metabolic derangement) to $66,412 (pressure ulcers). Extrapolation from the study hospitals yielded a provincial estimate of $481 million in annual excess costs attributable to the adverse events, which represents 2.8 percent of Ontario’s total hospital expenditures. Several of the adverse events were also associated with significant excess rates of death, readmission, and ambulatory care use. These results suggest that there are economic as well as ethical reasons to improve patient safety in Ontario hospitals. Estimates of adverse event costs were highly sensitive to coding error. The excess cost of adverse events is likely to be significantly underestimated if the error is ignored. This finding, coupled with the observation that the likelihood of error is ignored in most studies, suggests that previous assessments of the business case for patient safety may have been biased against the cost effectiveness of patient safety improvements. Furthermore, the observed extent of institutional level variation in adverse event coding indicates that administrative data are an inadequate basis for adverse event payment policies or for public reporting of adverse event rates.

Keywords: patient safety
outcomes
adverse events
hospital costs
Advisor: Wodchis, Walter
Work-life Balance Programs in Canadian Workplaces: Factors Affecting Availability and Utilization

The thesis explores the factors affecting the availability and utilization of work-life balance programs in Canadian workplaces and how employee involvement and participation programs can help employees balance their work and life. The introductory chapter provides background information on the importance of balancing work and life. It outlines chapters two, three, and four and reveals the overarching theme that unites them. Chapter Two explores how business strategy affects the availability of work-life balance programs. This chapter uses the 2003 and 2004 Canadian Workplace and Employee Survey to demonstrate that product leadership business strategy is positively related to the likelihood of adopting work-life balance programs (i.e. employee assistance programs, fitness and recreation centers). Cost leadership strategy is shown to be negatively correlated to the adoption of these programs. This study also finds that high performance work systems mediate the relationship between business strategy and employer responsiveness to work-life balance issues. Chapter Three investigates how a company’s family-friendly culture affects the likelihood of an employee’s use of parental leave. Using a national representative and linked employer and employee survey, this study finds that a long-hour organizational culture, which is revealed through managers’ work hours, discourages new parents from taking parental leave. This study also finds that when managers work long hours, it has a greater negative effect on the probability of male employees taking parental leave than female employees. Chapter Four discusses how participation in decision making (PDM) can help employees balance the demands from work and life. Using Karasek’s (1979) job demand-job control model, this study finds that PDM can reduce work-life conflict, but the reduction only works for employees who work long hours. For those employees who work short hours, PDM increases their work-life conflict. Chapter Five summarizes the empirical results. Implications for employers, labour unions, and policy makers are discussed.

Keywords: work-life balance programs
business strategy
family-friendly culture
long-hour organizational culture
managers' work hours
parental leave
participation in decision making
job demand
work-life conflict
Advisor: Verma, Anil
An Exploration of Differences in Response to Music Related to Levels of Psychological Health in Adolescents

Popular music plays a significant role in the lives of most adolescents. The central question explored is whether three groups of adolescents (psychiatrically ill, depressed, and non-clinical adolescents) differed on self-reported data on: (a) the role of popular music in their lives, and (b) in their emotional reactions to music. The next question is whether the developmental issues of gender and personality consolidation, age, and school commitment simultaneously influence how the three groups of adolescents use music in their lives and in their emotional reactions to music. The last question is whether the three groups have significantly different music preferences in the five genres of popular (rap, pop/dance, heavy metal/hard rock, classic rock, and alternative). There were 126 subjects employed in this research. I created the Walker Music Questionnaire (WMQ) to explore the role and importance that music plays in the lives of the adolescents. A factor analysis found five factors (Introspection, Identity-Music, Discerning Music Identity, Fantasy-Rebellion, and Identity-Self). The Adolescent Semantic Differential Scales (ASDS) measured the adolescents’ emotional responses to 10 pieces of popular music representing the five genres described above. These scales are well known measures of emotional response and I added eight adjectives that represented adolescent issues. This measure was also factor analyzed and the three factors of Evaluation, Romance, and Potency emerged. Preference for the five genres was determined from the Adolescent Semantic Differential Scales. MANOVAS were done with both sets of factors derived from the WMQ and ASDS simultaneously using the developmental variables of age group, gender, personality, and school commitment. Psychological health was found to be a significant variable. Specifically, the role of music for the depressed group was significantly different from the other two groups of adolescents. The developmental issues that remained significant were personality and school commitment. Furthermore, the psychiatrically ill group reacted more emotionally to the music than the other two groups and this remained significant even when the developmental variable of personality was considered. The three groups were not differentiated by their preference ratings on the ASDS.

Keywords: adolescents
popular music
development
preference
semantic differential scales
Advisor: Bartel, Lee
Statistical Approximation of Natural Climate Variability

One of the main problems in statistical climatology is to construct a parsimonious model of natural climate variability. Such a model serves for instance as a null hypothesis for detection of human induced climate changes and of periodic climate signals. Fitting thismodel to various climatic time series also helps to infer the origins of underlying temporal variability and to cross validate it between different data sets. We consider the use of a spectral power-law model in this role for the surface temperature, for the free atmospheric air temperature of the troposphere and stratosphere, and for the total ozone. First, we lay down a methodological foundation for our work. We compare two variants of five different power-law fitting methods by means of Monte-Carlo simulations and their application to observed air temperature. Then using the best two methods we fit the power-law model to several observational products and climate model simulations. We make use of specialized atmospheric general circulation model simulations and of the simulations of the Coupled Model Intercomparison Project 3 (CMIP3). The specialized simulations allow us to explain the power-law exponent spatial distribution and to account for discrepancies in scaling behaviour between different observational products. We find that most of the pre-industrial control and 20th century model simulations capture many aspects of the observed horizontal and vertical distribution of the power-law exponents. At the surface, regions with robust power-law exponents—the North Atlantic, the North Pacific, and the Southern Ocean — coincide with regions with strong inter-decadal variability. In the free atmosphere, the large power-law exponents are detected on annual to decadal time scales in the tropical and subtropical troposphere and stratosphere. The spectral steepness in the former is explained by its strong coupling to the surface and in the latter by its sensitivity to volcanic aerosols. However power-law behaviour in the tropics and in the free atmosphere saturates on multi-decadal timescales. We propose a novel diagnostic to evaluate the relative goodness-of-fit of the autoregressive model of the first order (AR1) and the power-law model. The collective behaviour of CMIP3 simulations appears to fall between the two statistical models. Our results suggest that the power-law model should serve as an upper bound and the AR1 model should serve as a lower bound for climate persistence on monthly to decadal time scales. On the applied side we find that the presence of power-law like natural variability increases the uncertainty on the long-term total ozone trend in the Northern Hemisphere high latitudes attributable to anthropogenic chlorine by about a factor of 1.5, and lengthens the expected time to detect ozone recovery by a similar amount.

Keywords: climate persistence
climate temporal spectrum
power-law model
Advisor: Kushner, Paul