VictorJuiz/thesis huggingface dataset:
On the Reflexive Prioritisation of Locations in Visual Space

The efficiency of human visual information processing is supported by numerous attentional resources. These resources ensure that behaviourally relevant information within visual scenes is selected for detailed processing, while behaviourally irrelevant information is ignored. One of these attentional resources—reflexive visuospatial attention—operates by prioritising locations in visual space in response to the appearance of salient stimuli. The purpose of the present dissertation was to examine how this type of attention contributes to the efficiency of visual processing by asking: How is processing altered for information presented at the location of attention? To develop some initial evidence of the stage of processing affected by reflexive visuospatial attention, Chapters 1 to 6 assessed whether this attentional resource is related to four other stimulus-driven effects that are each associated with a specific stage of visual processing: identity processing, object filtering, visual working memory (VWM), and response generation. Based on the observation that only the stimulus-driven effects on VWM are related to reflexive visuospatial attention (i.e., only those effects were contingent on attentional control settings), a VWM model of reflexive visuospatial attention was proposed in Chapter 7, and tested in Chapters 8 to 11. According to this model, reflexive visuospatial attention alters visual processing by triggering VWM to update. Thus, the effect of reflexive visuospatial attention is to speed the encoding of attended information into VWM. As a result, this information is more likely than unattended information to bias our behaviour, in particular those behaviours that depend on VWM. Further, by biasing VWM, reflexive visuospatial attention can interact with other attentional resources that have also been associated with VWM. In this way, these attentional resources can coordinate in optimising the process of selection, thus, contributing to the efficiency of the human visual system.

Keywords: attention
working memory
attention capture
visual working memory
attentional control settings
reflexive visuospatial attention
Advisor: Pratt, Jay
CYP2A6 and CYP2B6: Sources of Variation and their Role in Nicotine Metabolism

Nicotine is the primary substance in tobacco causing addiction. In humans the majority (70-80%) of nicotine is inactivated to cotinine in a reaction predominantly catalyzed by CYP2A6 (80-90%), with a minor possible role for CYP2B6. Substantial interindividual variability is observed in the rate of nicotine’s inactivation to cotinine and this variation contributes to differences in smoking behaviors (e.g. cigarette consumption). Twin studies suggest an important genetic contribution to the variability in nicotine metabolism. However in 2004, genetic variation in CYP2A6 and CYP2B6 accounted for only a small portion of the variability suggesting gaps in our knowledge. Our objective was to identify additional genetic and non-genetic sources of variability in CYP2A6 expression/activity, CYP2B6 expression, and nicotine to cotinine metabolism in vivo and/or in vitro. Participants included individuals from different world populations phenotyped for CYP2A6 activity either following oral nicotine administration or using metabolite ratios derived from baseline smoking. Genotyping and sequencing were utilized to identify and characterize multiple new CYP2A6 alleles. In total 17 novel CYP2A6 alleles were identified, many of which were found predominantly among individuals of black African descent and exhibited lower CYP2A6 activity. In addition, human livers were assessed for CYP2A6 and CYP2B6 expression and nicotine to cotinine metabolism. The mechanisms underlying the lower CYP2A6 activity associated with some of the variant CYP2A6 alleles included either a reduction in hepatic CYP2A6 protein expression, an alteration of CYP2A6’s structural property, or a combination of both. DNA methylation was not associated with altered hepatic CYP2A6 expression/activity. Livers from female donors were associated with higher CYP2A6 and CYP2B6 protein expression compared to male livers, while age did not influence the expression of either CYP. Finally, CYP2B6 and its prevalent altered function genetic variant (CYP2B6*6) did not influence nicotine to cotinine metabolism. Identification of factors that contribute to the variability in CYP2A6 and nicotine metabolism is important to improve future association studies between CYP2A6 genotype, nicotine metabolism, and smoking behaviors. In addition, this information could provide the potential to personalize therapy in order to improve the clinical efficacy of nicotine, particularly as a smoking cessation aid.

Keywords: Nicotine
CYP2A6
Pharmacogenetics
CYP2B6
Advisor: Tyndale, Rachel
Ground Penetrating Radar Imaging of Ancient Clastic Deposits: A Tool for Three-dimensional Outcrop Studies

The growing need for better definition of flow units and depositional heterogeneities in petroleum reservoirs and aquifers has stimulated a renewed interest in outcrop studies as reservoir analogues in the last two decades. Despite this surge in interest, outcrop studies remain largely two-dimensional; a major limitation to direct application of outcrop knowledge to the three dimensional heterogeneous world of subsurface reservoirs. Behind-outcrop Ground Penetrating Radar (GPR) imaging provides high-resolution geophysical data, which when combined with two dimensional architectural outcrop observation, becomes a powerful interpretation tool. Due to the high resolution, non-destructive and non-invasive nature of the GPR signal, as well as its reflection-amplitude sensitivity to shaly lithologies, three-dimensional outcrop studies combining two dimensional architectural element data and behind-outcrop GPR imaging hold significant promise with the potential to revolutionize outcrop studies the way seismic imaging changed basin analysis. Earlier attempts at GPR imaging on ancient clastic deposits were fraught with difficulties resulting from inappropriate field techniques and subsequent poorly-informed data processing steps. This project documents advances in GPR field methodology, recommends appropriate data collection and processing procedures and validates the value of integrating outcrop-based architectural-element mapping with GPR imaging to obtain three dimensional architectural data from outcrops. Case studies from a variety of clastic deposits: Whirlpool Formation (Niagara Escarpment), Navajo Sandstone (Moab, Utah), Dunvegan Formation (Pink Mountain, British Columbia), Chinle Formation (Southern Utah) and St. Mary River Formation (Alberta) demonstrate the usefulness of this approach for better interpretation of outcrop scale ancient depositional processes and ultimately as a tool for refining existing facies models, as well as a predictive tool for subsurface reservoir modelling. While this approach is quite promising for detailed three-dimensional outcrop studies, it is not an all-purpose panacea; thick overburden, poor antenna-ground coupling in rough terrains typical of outcrops, low penetration and rapid signal attenuation in mudstone and diagenetic clay- rich deposits often limit the prospects of this novel technique.

Keywords: Ground Penetrating Radar
GPR
Advisor: Miall, Andrew
The Effect of Temperature Primes on Impulsivity

Temperature-related words such as “hot” and “cold” are often used to describe impulsive and calculated behaviors, respectively. These metaphoric connotations of thermal concepts raise the question as to whether temperature, psychological states and decision making are related to each other, and if so, how. The current research examines these questions and finds support for a relationship. Across four laboratory experiments and two field studies, I demonstrate that both hot temperature primes (e.g., pictures, words, therapeutic packs) and hot ambient temperature trigger decision outcomes in line with the metaphoric association between hot temperature and impulsivity. I suggest that the theory of embodied cognition provides an explanation for these findings.

Keywords: Impulsivity
Temperature Primes
Embodied Cognition
Metaphor
Advisor: Soman, Dilip
Mazar, Nina
Nonparametric Estimation and Inference for the Copula Parameter in Conditional Copulas

The primary aim of this thesis is the elucidation of covariate effects on the dependence structure of random variables in bivariate or multivariate models. We develop a unified approach via a conditional copula model in which the copula is parametric and its parameter varies as the covariate. We propose a nonparametric procedure based on local likelihood to estimate the functional relationship between the copula parameter and the covariate, derive the asymptotic properties of the proposed estimator and outline the construction of pointwise confidence intervals. We also contribute a novel conditional copula selection method based on cross-validated prediction errors and a generalized likelihood ratio-type test to determine if the copula parameter varies significantly. We derive the asymptotic null distribution of the formal test. Using subsets of the Matched Multiple Birth and Framingham Heart Study datasets, we demonstrate the performance of these procedures via analyses of gestational age-specific twin birth weights and the impact of change in body mass index on the dependence between two consequent pulse pressures taken from the same subject.

Keywords: Dependence
Conditional Copula
Copula Parameter
Covariate Adjustment
Local Likelihood
Advisor: Craiu, Radu V.
Yao, Fang
Designing Randomized Clinical Trials for Rare Diseases

Objectives: 1) To evaluate the quality of randomized clinical trials (RCTs) in rare diseases using Juvenile Idiopathic Arthritis (JIA) as an example, 2) to evaluate the time to treatment response in patients with rheumatic diseases, 3) to evaluate the power of the Randomized Placebo-Phase Design (RPPD) under various response time distributions, and 4) to examine the use of Value of Information (VOI) methodology in the optimal design of clinical trials for rare disease using hemophilia prophylaxis with factor VIII as an example. Methods. The methods include a systematic review, a secondary analysis of data from an RCT and from a patient registry, a computer simulation study, and an evaluation of hypothetical RCT scenarios with VOI methodology. Results. The quality of RCTs in JIA based on selected quality indicators was poor with some positive changes over time. In the data sets used for the assessment of hazard distributions, the response times followed mostly generalized gamma or lognormal distributions. The impact of time-to-event distribution on the power of RCTs was assessed in computer simulations. Based on the simulation results, the highest sample sizes were observed for response times following the exponential distribution. In most scenarios, the parallel groups RCT design had higher power than the RPPD. The conclusion of the VOI analyses indicated that at threshold values lower than 400,000 the current evidence supported the use of on-demand therapy. Threshold values higher than 1,000,000 supported the use of tailored or alternate day prophylaxis. At threshold values between 400,000 - 1,000,000 the optimal decision varied from on-demand to prophylaxis therapies. Conclusions. New, more powerful and acceptable designs should be developed for rare diseases. When time-to-event outcomes are used, investigators should use various sources of information to evaluate response time distributions before the new trial is designed, and consider this information in sample size calculation and analysis. VOI methodology should be used in the planning stage of studies to determine the relevant costs and benefits of future research, and to determine the optimal trial parameters that maximize the cost-benefit trade-off.

Keywords: rare diseases
randomized clinical trials
Advisor: Feldman, Brian M.
Chronic Hepatitis C Viral Infection: Natural History and Treatment Outcomes in Substance Abusers

Hepatitis C is the most common blood-borne viral illness in the North America. Chronic hepatitis C infection may lead to cirrhosis of the liver, liver failure and liver cancer. In North America, injection drug use is the most important risk factor for infection and substance abusing populations are disproportionately affected by the disease. Antiviral therapy exists and approximately 50% of infected individuals can be cured. The aim of this thesis was to provide information to help clinicians and policy-makers minimize the impact of hepatitis C in substance abusers. The thesis is comprised of three studies. The first assessed the rate of progression to cirrhosis for those acquiring infection through injection drug use, using a meta-analysis of 44 studies from the published literature. We estimated that fibrosis progression occurs at a rate of 8.1 per 1000 person-years (95% Credible Region (CR), 3.9 to 14.7) corresponding to a 20-year cirrhosis prevalence of 14.8% (95% CR, 7.5 to 25.5). The second study measured the association between successful antiviral therapy and quality of life. We demonstrated that sustained responders to therapy had higher scores on the hepatitis-specific Medical Outcomes Survey Short-Form-36 (SF-36), Health Utilities Index Mark 2/3 (HUI2/3), and time-tradeoff (TTO) than treatment failures, an average of 3.7 years following antiviral therapy. The third study assessed rates of adherence to antiviral therapy and rates of sustained response in current or former iii substance abusers on methadone maintenance. We demonstrated that while use of illicit substances prior to therapy negatively affected adherence, rates of sustained response were comparable to non-substance abusing populations. Our work indicates the future burden of disease in current and former substance abusers, demonstrates that antiviral therapy can be successful in this population, and indicates that the benefits of successful therapy may extend beyond decreased disease burden to improved quality of life.

Keywords: hepatitis C
substance abuse
Advisor: Krahn, Murray
Radical Intimacies: Affective Potential and the Politics of Love in the Transatlantic Sex Reform Movement, 1900-1930

This dissertation explores the transatlantic shaping of the early twentieth century sex reform movement as a pivotal moment in the history of affect. I focus on a set of influential white middle class British and American radical intellectuals who emphasized emotions, instincts, and energies as transformative forces that could politically, socially, and materially alter the world. Crucially, this dissertation shifts historical attention on this period as a watershed in sexual practices toward the lens of a politics of love that informed sex reformers' construction of discourses and practices. I argue that sex reformers' politics of love amounted to the emergence of new registers of organizing bodies along the lines of gender, race, class, and sexuality by differentiating these bodies in terms of what I call their affective potential to achieve love. By examining the sex reform movement through this lens of a politics of love, I highlight the multiple ways that sex reformers radicalized the domain of intimacy as an arena of intense concern in matters of both social and political organization as well as ontological questions of spiritually and ecologically relating to the world. Each of this dissertation's chapters aims to take the reader on a journey thorugh the multiple worlds that took shape as sex reformers looked to develop scientific, spiritual, social, political, and economic strategies to engineer relationships defined by love. This journey spatially and temporally situates sex refomers' bodies as affective compasses that moved through and constructed historically specific worlds out of Darwinian maps of cities and nations, bohemian living arrangements, 'modern' schools and playgrounds, Edenic gardens, plant breeding and animal sex research laboratories, and imagined eugenic utopias of future species and races.

Keywords: gender
sexuality
Advisor: Murphy, Michelle
Examining the Impact of a Human-Tech Framework for Understanding Technology Integration in Teacher Education

This research examines on the importance of considering context as design criteria for technology integration and technology design, and in particular, what that means for teacher education. While others (Fishman, Marx, Blumenfeld, Krajcik, & Soloway, 2004) have broadly considered context as a factor in supporting technology integration, this current research uses a Human-Tech framework (Vicente, 2003) to identify and examine the implications of individual contextual constraints for the design of technology-enhanced learning; therefore, the researcher begins to answer the important - and arguably unexplored - question of how the complexities of varying contexts ought to be used to inform design. Broadly, this design research study explores the impact of using a Human-Tech framework for understanding technology integration in education and specifically, to inform the design of technology-enhanced learning practices in the context of teacher education. Further, the research reports on the impact of an open online research support forum - designed using a Human-Tech framework - on the experiences of teacher candidates while carrying out classroom-based research as part of their initial teacher education program. Overall, results of the research study suggest that using a Human-Tech framework for understanding technology integration was helpful in supporting a broader and more systematic approach to designing for more effective use of technology in the context of teacher education. In terms of the design of the open online research support forum, findings suggest that there were key Organizational constraints that likely continued to have a limiting impact on the innovations across the two-year design study. Therefore, this research also points to future technology-specific and non technology-specific design strategies which may have implications for technology integration, and fulfilling the functional purposes of the program more broadly.

Keywords: Educational technology
Teacher education
Design research
Human-Tech
Cognitive Work Analysis
Online learning
Advisor: Woodruff, Earl
Effectiveness of Specialized Palliative Care for Patients with Advanced Cancer

Despite the rapid development of palliative care teams, evidence for their effectiveness in oncology care is lacking. This thesis reviews and contributes towards this evidence, focusing on the randomized controlled trial as a research method. We conducted a systematic review of 22 trials reviewed that measured effectiveness of specialized palliative care. Family satisfaction with care improved in seven of 10 studies, but only four of 13 trials assessing quality of life and one of 14 assessing symptoms showed a benefit of the intervention. Conclusions were limited by methodologic problems in all of the trials. We conducted a phase II study of the efficacy of a palliative care team for symptom control and satisfaction of 150 patients with advanced cancer. Symptom severity (Edmonton Symptom Assessment System Distress Score) improved at one week and one month, as did patient satisfaction (all p<0.0001). We investigated factors associated with symptom severity and response for patients enrolled in the phase II study. Symptoms at baseline were worse for women and those with worse performance status (both p<0.005); female gender and worse baseline symptom severity independently predicted symptom improvement (both p<0.05). We planned and initiated an RCT of the effectiveness of an early palliative care intervention for improvement of health-related quality of life (HRQL) and satisfaction with care. Using baseline data from this RCT, we examined factors associated with HRQL in patients with advanced cancer. The strongest determinants of overall HRQL (combined FACT-G total score and FACIT-Sp Meaning and Peace subscore) were increased age (p<0.001), good performance status (p<0.001) and survival time >6 months (p=0.001). Compared to patients receiving cancer treatment, those awaiting new treatment had worse emotional well-being (p<0.001) while those on surveillance or whose treatment had been stopped had worse existential well-being (p=0.03). Male gender predicted better emotional and physical well-being and lower income predicted worse social well-being. Lastly, we developed recommendations for those planning an RCT in a palliative care population, incorporating information from the studies presented. Although such RCTs are challenging to conduct, they are feasible and necessary to improve the evidence base for the treatment of patients with advanced cancer.

Keywords: palliative care
cancer
quality of life
randomized controlled trial
Advisor: Tannock, Ian
Summarizing Spoken Documents Through Utterance Selection

The inherently linear and sequential property of speech raises the need for ways to better navigate through spoken documents. The strategy of navigation I focus on in this thesis is summarization, which aims to identify important excerpts in spoken documents. A basic characteristic that distinguishes speech summarization from traditional text summarization is the availability and utilization of speech-related features. Most previous research, however, has addressed this source from the perspective of descriptive linguistics, in considering only such prosodic features that appear in that literature. The experiments in this dissertation suggest that incorporating prosody does help but its usefulness is very limited—much less than has been suggested in some previous research. We reassess the role of prosodic features vs. features arising from speech recognition transcripts, as well as baseline selection in error-prone and disfluency-filled spontaneous speech. These problems interact with each other, and isolated observations have hampered a comprehensive understanding to date. The effectiveness of these prosodic features is largely confined because of their difficulty in predicting content relevance and redundancy. Nevertheless, untranscribed audio does contain more information than just prosody. This dissertation shows that collecting statistics from far more complex acoustic patterns does allow for estimating state-of-the-art summarization models directly. To this end, we propose an acoustics-based summarization model that is estimated directly on acoustic patterns. We empirically determine the extent to which this acoustics-based model can effectively replace ASR-based models. The extent to which written sources can benefit speech summarization has also been limited, namely to noisy speech recognition transcripts. Predicting the salience of utterances can indeed benefit from more sources than raw audio only. Since speaking and writing are two basic ways of communication and are by nature closely related to each other, in many situations, speech is accompanied with relevant written text. Richer semantics conveyed in the relevant written text provides additional information over speech by itself. This thesis utilizes such information in content selection to help identify salient utterances in the corresponding speech documents. We also employ such richer content to find the structure of spoken documents—i.e., subtopic boundaries—which may in turn help summarization.

Keywords: speech
summarization
Advisor: Penn, Gerald