VictorJuiz/thesis huggingface dataset:
Electrical Rhythms of the Brain Under Impaired Consciousness Conditions: Epilepsy and Anesthesia

This dissertation explores the neural coding and mechanisms associated with consciousness by analyzing electrical rhythms of the brain under altered states of consciousness, namely epilepsy and anesthesia. First, transformation of neural coding under epileptogenic conditions is examined by computing the Volterra kernels in a rodent epilepsy model, where the epileptogenic condition is induced by altering the concentrations of Mg2+ and K+ of the perfusate for different levels of excitability. Principal dynamic modes (PDMs) are further deduced from the Volterra kernels to compare the changes in neural dynamics under epileptogenic conditions. The integrating PDMs are shown to dominate at all levels of excitability in terms of their relative contributions to the overall response, whereas the dominant frequency responses of the differentiating PDMs shift to higher ranges under epileptogenic conditions, from ripple activities (75 - 200 Hz) to fast ripple activities (200 - 500 Hz). Second, markers of anesthetic states are explored by analyzing amplitude and phase of brain rhythms as well as their interaction and modulation, utilizing electroencephalogram (EEG) recorded from patients undergoing anesthesia. Anesthesia shifts the power to low frequency rhythms, especially alpha rhythms. Additionally anesthesia increases the coupling between alpha rhythms and gamma rhythms while disrupting the coupling between alpha rhythms and ripples (70 - 200 Hz). The results also indicate that the dose responses (i.e. depth of anesthesia) are not necessarily monophasic or linear. The commonality and differences of the changes in brain rhythms associated with these conditions are discussed to elucidate on the possible underlying mechanisms involved in producing consciousness.

Keywords: EEG
Consciousness
Neuronal modes
Electrophysiology
Coherence
System kernels
Advisor: Bardakjian, Berj
Carlen, Peter Louis
An Optimal Transport Approach to Nonlinear Evolution Equations

Gradient flows of energy functionals on the space of probability measures with Wasserstein metric has proved to be a strong tool in studying certain mass conserving evolution equations. Such gradient flows provide an alternate formulation for the solutions of the corresponding evolution equations. An important condition, which is known to guarantees existence, uniqueness, and continuous dependence on initial data is that the corresponding energy functional be displacement convex. We introduce a relaxed notion of displacement convexity and we show that it still guarantees short time existence and uniqueness of Wasserstein gradient flows for higher order energy functionals which are not displacement convex in the standard sense. This extends the applicability of the gradient flow approach to larger family of energies. As an application, local and global well-posedness of different higher order non-linear evolution equations are derived. Examples include the thin-film equation and the quantum drift diffusion equation in one spatial variable.

Keywords: Nonlinear Evolution Equations
Optimal Transport
Wasserstein Gradient Flows
Well-posedness
Advisor: Burchard, Almut
The Role of Semaphorin-Neuropilin-1 Signalling in Pulmonary Vascular Development

Increasing evidence suggests that normal pulmonary vascular morphogenesis is critical for the formation and maintenance of the lung parenchyma, both pre- and postnatally. Indeed, the disruption of angiogenic pathways, whether through inherent genetic predisposition or as a consequence of life-saving interventions, may underlie many pulmonary diseases of infancy, including alveolar capillary dysplasia (ACD) and bronchopulmonary dysplasia (BPD). To understand the etiology of – and advance treatments for – such diseases, we must first identify the fundamental genetic regulators that orchestrate normal parenchymal development. Neuropilin-1 (NRP1) is a transmembrane receptor that plays essential roles in normal and pathological vascular development, and binds two distinct ligand families: Vascular endothelial growth factor (VEGF) and Class 3 Semaphorins (SEMA3). Although VEGF-NRP1 interactions in systemic vascular development have been described, the importance of SEMA3-NRP1 signalling in systemic or pulmonary vascular morphogenesis is uncertain. We hypothesized that SEMA3-NRP1 and VEGF-NRP1 interactions are fundamental pathways in the orchestration of pulmonary vascular development in both the embryo and neonate. Disruption of these pathways would therefore lead to significant interruption of normal angiogenic and vascular maturation processes that are relevant to the pathogenesis of pulmonary diseases. Using extensive histopathological analyses of NRP1 loss-of-function mice, we show evidence of a significant role for SEMA3-NRP1 signalling in fetal microvascular development: congenital loss of SEMA3-NRP1 signalling resulted in severely attenuated development of the distal vasculature and alveolar-capillary interface, leading to fatal respiratory distress at birth that is reminiscent of clinical ACD. By contrast, VEGF-NRP1 and SEMA3-NRP1 signalling appear unessential for normal alveolar and vascular development in the postnatal period, per se, despite increased mortality. Our results demonstrate the critical involvement of SEMA3-NRP1 signalling in endothelial development and substantiate the idea that NRP1 mediates opposing and cooperative functions between SEMA3 and VEGF ligands.

Keywords: Pulmonary
vascular development
mouse model
Advisor: Post, Martin
Three Essays in Bayesian Financial Econometrics

This thesis consists of three chapters in Bayesian financial econometrics. The first chapter proposes new dynamic component models of returns and realized covariance (RCOV) matrices based on timevarying Wishart distributions. Bayesian estimation and model comparison is conducted with a range of multivariate GARCH models and existing RCOV models from the literature. The main method of model comparison consists of a term-structure of density forecasts of returns for multiple forecast horizons. The new joint return-RCOV models provide superior density forecasts for returns from forecast horizons of 1 day to 3 months ahead as well as improved point forecasts for realized covariances. Global minimum variance portfolio selection is improved for forecast horizons up to 3 weeks out. The second chapter proposes a full Bayesian nonparametric procedure to investigate the predictive power of exchange rates on commodity prices for 3 commodity-exporting countries: Canada, Australia and New Zealand. I examine the predictive effect of exchange rates on the entire distribution of commodity prices and how this effect changes over time. A time-dependent infinite mixture of normal linear regression model is proposed for the conditional distribution of the commodity price index. The mixing weights of the mixture follow a Probit stick-breaking prior and are hence time-varying. As a result, I allow the conditional distribution of the commodity price index given exchange rates to change over time nonparametrically. The empirical study shows some new results on the predictive power of exchange rates on commodity prices. The third chapter proposes a flexible way of modeling heterogeneous breakdowns in the volatility dynamics of multivariate financial time series within the framework of MGARCH models. During periods of normal market activities, volatility dynamics are modeled by a MGARCH specification. I refer to any significant temporary deviation of the conditional covariance matrix from its implied GARCH dynamics as a covariance breakdown, which is captured through a stochastic component that allows for changes in the whole conditional covariance matrix. Bayesian inference is used and I propose an efficient posterior sampling procedure. Empirical studies show the model can capture complex and erratic temporary structural change in the volatility dynamics.

Keywords: Bayesian Econometrics
Advisor: Maheu, John
Indigenous Maya Knowledge and the Possibility of Decolonizing Education in Guatemala

Maya peoples in Guatemala continue to practice their Indigenous knowledge in spite of the violence experienced since the Spanish invasion in 1524. From 1991 until 1996, the state and civil society signed a series of Peace Accords that promised to better meet the needs of the Maya, Xinka, Garífuna and non-Indigenous groups living there. In this context, how does the current educational system meet the varied needs of these groups? My research investigates the philosophy and praxis of Maya Indigenous knowledge (MIK) in broadly defined educational contexts through the stories of 17 diverse Maya professional women and men involved in educational reform that currently live and work in Guatemala City. How do they reclaim and apply their ancestral knowledge daily? What possible applications of MIK can transform society? The findings reveal that MIK promotes social change and healing within and outside institutionalized educational spaces and argues that academia needs to make room for Indigenous theorizing mainly in areas of education, gender, knowledge production, and nation building. I analyze these areas from anticolonial and critical Indigenous standpoints from which gender and Indigenous identities weave through the text. Thus, I rely on Maya concepts and units of analyses (Jun Winaq’) guided by an Indigenous research methodology (Tree of Life) to conduct informal and in-depth interviews that lasted 2 to 4 hours. In addition, I held a talking circle with half of the participants. My analysis is founded on my own experience as an Indigenous person, my observations and participation in two Maya organizations in 2007 and a review of secondary literature in situ. The study contributes to a general understanding of contemporary Maya peoples and knowledge, and describes the theoretical validity of the Maya concept of Jun Winaq’. I argue that this concept seeks to heal individuals and a society to strengthen the Maya and all peoples. Throughout the dissertation I highlight the value of Indigenous knowledge and voices as parts of a political process that has the potential to decolonize mainstream education. I end with a graphic illustration of the elements in Maya Indigenous education and discuss future research for building a political agenda based on self-determination and healing relevant to Indigenous struggles globally.

Keywords: Indigenous Knowledge
Indigenous feminism
Gender
Education
Decolonization
Guatemala
Advisor: Iseke, Judy
Immigration and Minority Nationalism: The Basque Country in Comparative Perspective

Conventional wisdom suggests that ‘nations without states’ are seeking to preserve cultural and linguistic homogeneity within their homeland by advocating for independence or political autonomy. Accordingly, large-scale immigration has typically been seen as a threat to national minorities because newcomers tend to integrate into the culture of the majority group. In addition, even if immigrants learn the minority’s language, they are unlikely to sympathize with the nationalist movement or vote for nationalist parties. This dissertation seeks to explain why Basque nationalism, despite its historical grounding in racism and exclusivity, developed a group-based multicultural approach in response to foreign immigration. To account for this unexpected outcome, I develop two interrelated causal arguments that integrate the role of ideas and the imperative of nation building for nationalist elites. Nations are forged by a rich legacy of memories and nationalist history requires both an act of collective remembering and collective amnesia. The ideas that stem from the memories of repression constrained the choices of Basque nationalists, preventing the rise of ideas of racial purity and exclusion in favour of multiculturalism and openness. A second argument that I advance is that changing contexts are motivating nationalist elites to find new policy areas with which to distinguish the values of the majority and minority nation. The emergence of a stricter immigration framework in Spain and a backlash against multiculturalism in Europe provided Basque nationalists with an opportunity to link open citizenship and multiculturalism to the distinctiveness of the Basque nation. I apply the arguments developed through an in-depth study of the Basque case to the nationalist movements in Scotland, Quebec, and Flanders and conclude that diversity is an effective, but risky, new value that minority nationalists are employing to further their case for independence.

Keywords: immigration
nationalism
Basque Country
Spain
Advisor: Bertrand, Jacques
Factors affecting Girls' Education in Tajikistan: What Difference did the Girls' Education Project Make?

Since Tajikistan’s independence in 1991 the number of rural girls leaving school after grade 9 has been increasing at an alarming rate. In order to improve rural girls’ secondary school attendance and retention, in 2006 Save the Children, local non-governmental organization (NGO) partners, and the Ministry of Education implemented a two-year UNICEF-funded Girls’ Education Project (GEP). This mixed-method study compares rural girls’ secondary school experiences and opportunities at six schools (three GEP schools and three non-GEP schools) in two districts located in regions with the lowest levels of female secondary school participation nationwide. Two research questions guided this study: 1) What factors serve as obstacles or enablers to girls’ secondary school experiences and opportunities in rural Tajikistan? and 2) How did the GEP attempt to overcome factors limiting rural girls’ secondary school experiences and opportunities and which aspects of the project were perceived to be most effective? The study’s theoretical framework contains concepts from two sets of theories: 1) social reproduction (schooling as a means of maintaining and reproducing the status quo) and 2) empowerment (schooling as a means of changing the status quo). Data collected reveals two groups’ perspectives: 1) adult participants (Ministry of Education officials, NGO staff, school administrators and teachers) and 2) rural female upper secondary school students. A multi-level data analysis process was used to compare findings within and across districts. Factors that serve as either an obstacle or an enabler of girls’ educational experiences and opportunities include those relating to the community/society, family, school, and self. Factors related to community/society include the dominant belief that a girl is “grown-up” by 15 and should no longer go to school which intersects with family poverty to create a major barrier to girls’ non-compulsory secondary schooling. Factors affecting girls’ schooling related to the family were the most significant determinant of a girl’s schooling. Of all the GEP activities, participants consistently considered the girls’ overnight camp to be the “best” activity. Findings show how enabling just a few girls to return to school significantly increases the likelihood of other girls being allowed to attend school in these rural communities.

Keywords: Girls' education
education
Tajikistan
Empowerment
International development
rural Tajikistan
Secondary education
NGO development project
Save the Children
UNICEF
Advisor: Mundy, Karen
Development and Application of a Technique for Three-dimensional Sialography using Cone Beam Computed Tomography

Introduction: Salivary gland obstructive conditions are common and may necessitate imaging of the glands for diagnosis and management purposes. Many imaging options are available but all have limitations. Sialography is considered the gold standard for examining obstructive conditions of the parotid and submandibular glands but it is largely influenced by the imaging technique to which it is coupled. Cone beam computed tomography (cbCT) is a relatively new and very promising imaging modality that has overcome many of the inherent limitations of other imaging modalities used in the past for sialography. Materials and methods: A RANDO®Man imaging phantom was used to determine the effective radiation doses from the series of plain film images that represent the current standard of practice for sialography. Similar experiments were then undertaken to determine the effective radiation doses from cbCT when varying the field-of-view (FOV) size and center, x-ray tube peak kilovoltage (kVp) and milliamperage (mA). Next, cbCT image quality, measured using the signal-difference-to-noise-ratio (SDNR) was used to determine those technical factors that optimized image quality. Finally, using the optimized image acquisition parameters, a prospective clinical study was conducted to test the diagnostic efficacy of cbCT sialography compared to plain film sialography. Results: Effective radiation doses were comparable between the plain film image series and cbCT examinations of the parotid and submandibular glands when a 6” FOV was chosen, and when the x-ray tube was operating at 80 kVp and 10 mA. We also found that these exposure settings optimized the image SDNR. Finally, we demonstrated that the diagnostic capabilities of cbCT sialography were superior to plain film sialography with regards to detecting sialoliths and strictures, and when differentiating normal salivary glands from those with changes secondary to inflammation. Conclusion: We have successfully developed a three dimensional (3D) sialography technique for imaging the parotid and submandibular salivary glands using cbCT that balances radiation effective dose with image quality. We also demonstrated the superior diagnostic capabilities of the new technique in a clinical setting.

Keywords: cone beam CT
sialography
salivary glands
Advisor: Lam, Ernest W.
Colonoscopy use by Primary Care Physicians and Colorectal Cancer Incidence and Mortality

We first studied factors associated with the rate of colonoscopy by primary care physicians (PCPs) in Ontario between the years 1996 and 2005. Next, we conducted an Instrumental Variable Analysis (IVA) to estimate the effect of colonoscopy on colorectal cancer (CRC) incidence and mortality on average-risk subjects aged 50-74 years. Finally, we explored two study cohorts, one by including subjects who had the outcomes during the exposure period (unselected cohort) and the other cohort by excluding those subjects (restricted cohort). We estimated the absolute risk reduction associated with colonoscopy in preventing CRC incidence and mortality using traditional regression analysis, propensity score analysis and IVA. PCPs who were Canadian medical graduates and with more years of experience were more likely to use colonoscopy. PCPs were more likely to use colonoscopy if their patient populations were predominantly women, older, had more illnesses, and if their patients resided in less marginalized neighborhoods (lower unemployment, fewer immigrants, higher income, higher education, and higher English/French fluency). Using PCP rate of discretionary colonoscopy as an instrumental variable, receipt of colonoscopy was associated with a 0.60% absolute reduction in 7-year CRC incidence and a 0.17% absolute reduction in 5-year risk of death due to CRC. The unselected cohort showed an increase in CRC incidence and mortality associated with colonoscopy, whereas the restricted cohort showed a reduction in CRC incidence and mortality associated with colonoscopy. In the restricted cohort, using different statistical models, the absolute risk reduction varied from 0.52-0.60% for CRC incidence and 0.08-0.17% for CRC mortality. There were social disparities in the use of colonoscopy by PCPs and this disparity increased as the overall use of colonoscopy increased over time. Colonoscopy is effective in reducing incidence and mortality due to CRC. Different methods of subject selection and statistical analysis provided different estimates of colonoscopy effectiveness.

Keywords: Colorectal cancer
colonoscopy
Primary Care Physician
Instrumental Variable Analysis
Advisor: Urbach, David Robert
Male Partner Violence against Women in Northern Ghana: Its Dimensions and Health Policy Implications

The study was conducted in northern Ghana to determine the scope of male partner violence (MPV) against women, identify the factors associated with this problem as well as point out the health implications of MPV. In a sample of 443 married women drawn from outpatient populations across six district health centers we found that nearly 7 out of 10 women have experienced some MPV: 62% have experienced psychological violence; 29% have experienced physical violence; and 34% have experienced sexual violence. A multiple regression analysis showed that male controlling behavior, number of children, presence of concubines, partner appreciation, and very good health significantly predicted Total Violence. The results showed that the more controlling a husband is the more likely his wife is to experience severe violence and that more children in the marriage is associated with more violence for the women. Marriage duration was significantly positively correlated with violence, indicating that the longer the time since a woman got married, the more likely she experiences violence. Husband’s education was significantly negatively correlated with violence, indicating that husband education has a decreased effect on violence. Logistic regression and ANOVA models identified a number of socio-demographic factors as significant correlates of MPV. These include couple’s unemployment, particularly husband unemployment, being young – under 30 years and being younger than the husband, presence of concubines, being Muslim or Traditional, living in a rural setting, husband alcohol use, being a healthy woman, and not being appreciated by the husband. We found that MPV is associated with physical and mental health difficulties among women. Some 47 women reported having sustained multiple injuries, including sprains, broken bones and teeth, cuts, and burns. Mental health difficulties among these women included partner phobia, sleep deprivation, and thoughts of suicide. We make recommendations that call on government and other stakeholders to initiate policy that provides services to women experiencing MPV and that implements education and campaign programs to eventually eliminate MPV in Ghana generally.

Keywords: Male partner violence
Men's controlling behaviors
Patriarchy
Northern Ghana
Partner phobia
Advisor: Neysmith, Sheila