VictorJuiz/thesis huggingface dataset:
Unified Framework for Matrix-Variate Linear Discriminant Analysis
Keywords: 2DLDA
face recognition
feature extraction
Kronecker separability
linear discriminant analysis
matrix-variate data

The linear discriminant analysis (LDA) is a feature extractor used in classification of high-dimensional data in a wide range of applications. In the classification of matrix-variate data, LDA can be used on the vectorized representation of the data in the commonly called one-dimensional LDA (1DLDA) approach. However, 1DLDA leads to overwhelming computational complexity and ignores the inherent structure of the data in many applications. A more recent two-dimensional LDA (2DLDA) approach avoids the initial vectorization step, and leads to a computationally efficient matrix-variate feature extractor formulation. Yet, the theoretical foundations and Bayes optimality of the existing 2DLDA formulations are mostly unclear. This work provides a theoretical framework to develop and analyze the 2DLDA methods, and unify the 2DLDA and 1DLDA formulations. This thesis utilizes the general framework of separable transformations underlying common 2D image compression techniques, and provides a similar framework for separable 2D feature extraction. First, the necessary and sufficient conditions for separability of the 1DLDA operator into the row-wise and column-wise operators of 2DLDA are found. It is shown that an additional condition is required to provide the computational advantages of a completely matrix- variate training procedure similar to the existing 2DLDA methods. Based on the resulting data model, a separable matrix-variate LDA formulation is developed which provides both the Bayes optimality of 1DLDA and the computational and structural advantages of 2DLDA methods. Furthermore, it is shown that the block-wise feature selection approach used by the majority of 2DLDA methods generally results in unnecessary restrictions and loss of discriminatory information. In contrast, the feature selection in the proposed framework is based on sorting of the features based on a discriminance score. Finally, a simple criterion is provided to decide the required number of extracted features in most practical problems. Experimental results using face image databases indicate that assuming basic preprocessing steps, the proposed 2DLDA feature extractor provides the best classification performance if there are only moderate pose and expression variations in the face images. Although this thesis mainly focuses on the design of 2DLDA methods for matrix-variate face images, the derived framework is mainly extensible to the design of multi-linear LDA methods for higher-order tensor-variate data in different applications.
Inhibition of Gamma Oscillations as a Neurophysiological Endophenotype of Schizophrenia
Keywords: Cortical Inhibition
Electroencephalography
Endophenotype
Obsessive-Compulsive Disorder
Schizophrenia
Transcranial Magnetic Stimulation

Abstract Background The pathophysiology of schizophrenia (SCZ) has not been fully elucidated. Studies have demonstrated that SCZ patients have impairments in the dorsolateral prefrontal cortex (DLPFC). Two findings have been shown in the DLPFC: deficits in GABAergic inhibitiory neurotransmission and abnormal inhibition of cortical oscillations. Thus, we aimed to assess frontal inhibition as a potential endophenotype of SCZ. Objectives The first objective was to quantitatively assess transcranial magnetic stimulation (TMS) motor cortex measures of inhibition and excitation in obsessive-compulsive disorder (OCD), major depressive disorder (MDD) and SCZ, as a meta-analysis. The second objective was to evaluate the inhibition of overall and gamma oscillations in the DLPFC and motor cortex using TMS and EEG in SCZ and OCD. The final objective was to evaluate the inhibition of overall and gamma oscillations in SCZ patients, OCD patients, and their unaffected first-degree relatives with TMS and EEG. Hypotheses First, we hypothesized that motor cortex inhibitory deficits would be a ubiquitous finding across OCD, MDD and SCZ patients. Second, we hypothesized that patients with SCZ would show deficits in overall and gamma inhibition in the DLPFC compared to healthy subjects and patients with OCD. Lastly, it was hypothesized that frontal inhibition in first-degree relatives of SCZ would be intermediate of healthy subjects and their related probands. Results The first study showed that motor inhibitory deficits were a ubiquitous finding across OCD, MDD, and SCZ. The second paper found that SCZ patients demonstrated inhibitory deficits in the DLPFC (overall and gamma inhibition), not observed in OCD patients. This was found to be independent of illness severity and medication. The final study demonstrated deficits in frontal inhibition in SCZ patients, which were significantly less than their unaffected first-degree relatives. No differences were found between first-degree relatives of SCZ and healthy controls. First-degree relatives were intermediate of their related probands and healthy controls. We did not show inhibition deficits in OCD patients and their first-degree relatives. Conclusions Frontal inhibition (measured via TMS and EEG) may be an essential neurophysiological process that is impaired in SCZ. Multi-site trials are needed to investigate inhibition as a potential endophenotype for SCZ.
Development of an Ultra-high Frequency, Piezoelectric, Aptamer Based Sensor Platform for Small Molecule Detection
Keywords: Aptamers
Biosensors
bulk acoustic wave sensor
cocaine detection
organic monolayer
piexoelectric sensor

Many current aptasensor signal transduction methodologies are designed around the binding mechanism of the aptameric probe. Furthermore, many sensor designs are dependent on a label or signal amplification techniques, adding assay complexity to achieve the sensitivity levels required. The matter is further complicated when small molecule targets are considered. The work presented in this PhD thesis outlines the development of an acoustic wave aptasensing platform that provides more universality in terms of compatible aptamer binding mechanisms. A cocaine aptamer was employed as the aptamer-ligand model system and two aptamer constructs were studied; the rigid MN4 construct that only undergoes tertiary folding upon ligand binding and the MN6 variant that undergoes secondary structure ordering and tertiary structure folding in the presence of cocaine. Aptameric probes were anchored to the surface through an organic adlayer. Several surface configurations were evaluated until an optimized configuration was attained. The first sensor constructed was based on the MN4 construct, whose solution affinity for cocaine that is 7 fold higher than MN6 and exhibited an apparent Kd of 45 ± 12 µM, and a limit of detection of 0.9 µM. The MN6 (structure-switching aptamer) based sensor achieved an apparent Kd of 27 ± 6 µM, and a limit of detection of 0.3 µM, comparable to cocaine aptasensors that implement a signal amplification step. Repeated regenerability of both sensors and the ability to operate in multi-component matrices with multiple interferences was also demonstrated. The work presented within this thesis reveals a sensor platform that functions with both rigid and structure-switching aptamers in the same format while maintaining a facile one step assay without the use of a label or additive and a simple two-step surface preparation. This work constitutes the first piezoelectric aptasensor featuring the probe immobilized to an organic adlayer coated surface to directly detect the binding of a small molecule.
The HLA Complex Group 9 Gene Modification Study in Major Psychosis
Keywords: bipolar disorder
bisulfite sequencing
DNA modification
epigenetics
micorarray
schizophrenia

Epigenetic mechanisms can offer new insights into the non-Mendelian features of complex psychiatric disorders. The first epigenome-wide scan in major psychosis, conducted by our group, identified DNA modification differences at HLA complex group 9 (non-protein coding) gene (HCG9) in the post-mortem brain samples of individuals affected with schizophrenia (SCZ) and bipolar disorder (BPD). In this thesis we present results from bisulfite pyrosequencing based fine mapping of a ~700 bp region of HCG9 in 1,402 DNA samples from post-mortem brain, germline (sperm), and peripheral white blood cells (WBC) of SCZ and BPD patients as well as unaffected controls. We observed significant differences in CpG modification between BPD samples and controls across all tissues and demonstrated the utility of WBC DNA modification density as an epigenetic marker for BPD. We further extended our analysis to full length HCG9 with bisulfite padlock probe-based deep sequencing in SCZ, BPD and control post-mortem brain samples. We identified significant differences in CpH modification between sense and anti-sense DNA strands and between major psychosis patients and controls. Next, we characterized genome-wide distribution of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in neural and non-neural tissue from mice and humans. 5-hmC has been recently found to be abundant in brain but its function is poorly understood. We assayed 5-hmC by using glucosylation coupled with restriction enzyme digestion and microarray analysis. We detected enrichment of 5-hmC in genes with synapse-related functions and tissue-specific differential distribution of 5-mC and 5-hmC at the exon-intron boundary. This boundary change was mainly due to 5-hmC in the brain but due to 5-mC in non-neural tissue. Our study suggests a new role for 5-hmC in RNA splicing and synaptic function in the brain. Finally, we determined 5-mC and 5-hmC modification density at HCG9 CpG6 in post-mortem brain tissue and WBCs of SCZ, BPD and control samples. Consistent with our previous report, we identified significant differences between the major psychosis group and controls, which were due to 5-hmC but not 5-mC as it was previously assumed.
Feedback Regulation of Human Hematopoietic Stem Cell Fate
Keywords: computational biology
feedback regulation
hematopoietic stem cell
systems biology

Hematopoietic stem cell (HSC) fate decisions at least in part determine cellular composition of the hematopoietic system. It is known that differentiated blood cells produce ligands that act on HSCs to influence HSC fate. However, fundamentals underlying the feedback regulation of HSC fate are poorly understood. Here, we explored the fundamentals of the feedback regulation of HSC fate at the microenvironmental, intercellular (between cells), and intracellular (inside a cell) levels. First, we developed a machine learning algorithm to decompose heterogeneous blood cell samples isolated from cell culture. The results suggest the microenvironmental condition in which HSCs reside affects their transcriptional program. Further, we explicitly mapped feedback signals from 11 differentiated blood cells to HSCs by integrating microarray data, bioinformatics databases, and high content in vitro screening data. The results demonstrate the existence of blood cell type-specific feedback effect on HSC fate decisions. Intriguingly, we found that HSC self-renewal inducing ligands and proliferation inducing ligands were enriched in the NF-κB pathway and the STAT3 pathway, respectively. We constructed a kinetic model of the NF-κB – STAT3 pathway. The model serves a foundation for future development and optimization, and the final model could generate hypotheses of extracellular and intracellular intervention for controlling in vitro HSC expansion. Overall, this work has laid a conceptual and technical foundation for investigating cell-cell communication in other multicellular dynamic systems; one important application is in the use of cell-cell communication as a therapeutic avenue to treat various diseases.
Financial Health Incentives in Cardiac Rehabilitation
Keywords: Cardiac Rehabilitation
Exercise
Health behaviour change
Incentive
Reward

Financial health incentives, such as paying people to exercise, are being widely implemented despite limited evidence of their effectiveness. Accordingly, the objectives of this work were to (1) examine the efficacy of incentives-for-exercise in adults, (2) determine the potential for incentives to promote long-term exercise adherence (> 6 mo.) and (3) to explore incentive ‘acceptability’ and efficacy in cardiac rehabilitation (CR). A comprehensive CR outpatient program designed to help individuals recover from and manage their cardiovascular disease (CVD) was a suitable initial target for incentives in Canadian health care since many CVD risk factors are under behavioural control (e.g., physical inactivity). To determine the impact of incentives on exercise adherence in adults a systematic review and meta-analysis of randomized trials was conducted. In this review incentives increased exercise adherence 80% of the time, by about 12% on average (SD 5.61%, 17.50%; test for overall effect z=3.81, p
Conspicuous Peripheries: Black Identity, Memory, and Community in Chatham, ON, 1860-1980
Keywords: Black Canadians
Black history
Census
Chatham
Masons

The history of the black population in Chatham, Ontario is incomplete by virtue of partiality and distortion. This partiality and distortion has had real, if difficult to quantify costs for Chatham's local black population. While it is a worthwhile and necessary project to recuperate lost local histories for their own sake in order to encourage and inform the reframing of larger national and historically more influential histories, this study also focuses on the history of black people who lived in Chatham in the nineteenth and twentieth centuries in order to explore situated black lives that were actively constructed and performed. This deliberate attempt to expand the historiography of blacks in Canada from that of black-as-object to black-as-subject required an investigation into the local history of blacks in Chatham, their socio-philosophical and socio-economic heritages and the construction of particular identities shaped by race, class, and gendered interests forged within a shared experience of ongoing white racism. Informed by census data, primary fraternal order documents, and oral testimony, this study also holds that dislocations occurred at the turn of the twentieth century that concretized class membership, exacerbated class distinctions all while complicating the tenability of a coherent and cohesive black community.
Legacies: Kinship and Change in Kumasi, Ghana
Keywords: Asante
Ghana
Inheritance
Kinship
Social change

This study situates current kinship and inheritance practices among the matrilineal Asante within an analysis of cultural and legal change. Based on 18 months of fieldwork in Kumasi, Ghana, I analyze matrilineal kinship and marriage by considering the ways in which ongoing kin relations influence inheritance decision-making in conjunction with broadly shared notions of custom or law. I critically examine a supposed schism between “traditional” and “modern” inheritance to show various points of convergence between past and present notions of inheritance and kinship. I show that people incorporate the principles of both state inheritance law and local custom in multiple ways, not just to distribute property during decision-making about inheritance, but to assign responsibility for the care of the sick or of children and to distribute the funeral debts. In contemporary Ghana, the period of inheritance decision-making is a time when profound ethical ambiguities in kinship and social relations become apparent. To understand how inheritance is changing, I argue that analysts need to discard assumptions that matrilineal kinship and marriage is inherently harmful to women as well as assumptions about the progressive nature of social change. Instead, I argue that inheritance is an emergent process that combines both general cultural knowledge and the particular knowledge of a deceased individual’s life and relationships to produce decisions that assign responsibility and reform relations that have been disrupted by death. From this perspective, both the significant social changes to and ongoing vitality of matrilineal kinship and marriage become apparent.
Multi-Winner Social Choice: Algorithmic and Game-theoretic Approaches
Keywords: Algorithms
Game theory
Social Choice
Social Networks

Decision-making problems in multi-agent settings are commonly characterized by the requirement to choose which items to assign to which agents, or choose which items to offer them for sale, given their preferences. We take an algorithmic approach to problems that commonly face agents in these domains, such as online retail websites (where the agents are vendors) or voting settings (where the agents are the voters). We study problems that are known to be computationally hard, and focus on approaches that deal with these tractability issues using techniques for approximating the optimal solutions. Our work has two recurring themes. First, we introduce competition among selfish agents (e.g., vendors or advertisers) as an additional factor in many of our problems. Second, we introduce an additional component of uncertainty (which comes in various forms), and which plays a key role in our models. This added uncertainty comes in two forms: online (sequential) arrival of the agents (e.g., as in physical stores), and distributional models, in which the decision-maker’s actions are based on probabilistic beliefs about the agents’ preferences. We develop algorithms for selecting the best sets of items in settings where such factors as uncertainty and competition introduce added complications. We also provide game theoretic analyses of settings where competition and uncertainty about the preferences induce best response dynamics in which the vendors iteratively update their strategies in response to each other.
Physiological, Pharmacological and Clinical Factors Associated with Thrombosis in Pediatric Patients Undergoing Cardiac Surgery with Cardiopulmonary Bypass
Keywords: Epidemiology
Heart disease
Imaging
Pediatrics
Physiology
Thrombosis

Postoperative thrombosis in children undergoing cardiac surgery with cardiopulmonary bypass (CPB) is a frequent, under-diagnosed and clinically detrimental complication. The majority of known risk factors for thrombosis in this context are non-modifiable clinical correlates (notably younger age at surgery and cyanosis). We sought to identify modifiable physiological risk factors for post-operative thrombosis after pediatric cardiac surgery to inform the development of thromboprophylaxis strategies. Pediatric patients were prospectively enrolled before cardiac surgery with CPB in an observational cohort study. Children
Dynamical Signatures of Dark Matter Substructures on Tidal Streams
Keywords: dark matter
dynamics
galaxies
streams
structures
subhalos

Despite the success of the LambdaCDM model at describing the universe on large scales, the model’s predictions are at odds with observations on sub-galactic scales. In particular, the model predicts that a Milky-Way-sized dark matter halo should contain substructures in the form of low mass subhalos. However, there has yet to be convincing evidence that these subhalos exist. One promising method to probe the abundance of subhalos is by their dynamical effects on tidal streams, which are elongated remnants of tidally disrupted stellar systems as they orbit around the host galaxy. Previous theoretical studies have shown that subhalos can induce longitudinal density variations (or “gaps”) along streams. Although gaps have indeed been observed in some streams, it remains unclear whether those gaps correspond to those expected from subhalos. Previous simulations used idealized models, which did not account for realistic effects that may also induce gaps along streams. In this thesis we investigate a number of these effects. In the first chapter, we simulate streams with self-gravity, in which we successfully model the gaps caused by epicyclic overdensities, intrinsic to the orbit of a stream, rather than subhalo perturbations. We show that the two kinds of gaps are distinguishable in their length distributions. In the second chapter, we simulate self-gravitating streams inside a realistic halo that is constructed from a high-resolution cosmological simulation. We find that streams with similar orbital apo- and pericenters can have very different morphologies which cannot be modelled in idealized halos. In the third chapter, we simulate a collection of self-gravitating streams inside the same realistic halo in order to quantify the difference between using an idealized halo and a realistic halo. We show that the shape of the halo has a large effect on the dispersal of streams. Nevertheless, we find that many of those streams still remain cold and thin. This suggests that upcoming stellar surveys are likely to discover more streams that are suitable for probing the abundance of subhalos.
The Development of Environmental Comprehensive Multiphase Nuclear Magnetic Resonance Spectroscopy
Keywords: Comprehensive Multiphase
Nuclear Magnetic Resonance
Organic matter
Soil

Soil is the most complex mixture on this planet and is central to the transport of contaminants, carbon cycling and sustainable agriculture. However, our understanding of soil is limited in large part due to the lack of analytical approaches that can provide detail information on molecular structure and interactions in the native state. Current pre-treatment practices remove key synergies between components that are responsible for soil's reactivity, kinetics, interactions and numerous other characteristics. Nuclear magnetic resonance (NMR) spectroscopy has played an integral role in furthering soil research because of its versatility and non-destructive nature, but has not been able to study all phases of matter (solid, liquids, and gels) at once in a whole unaltered soil. Recently, comprehensive multiphase NMR (CMP-NMR) was introduced and combines traditional NMR techniques resulting in an instrument that has capabilities allowing for whole soil analysis. After an introduction of soil and NMR, the rst two research chapters focus on solving two key issues with environmental NMR, sensitivity and water suppression through experimental means. Sensitivity is increased by focusing NMR signals into one single spike and forgoing chemical shift. The result is an experiment that can determine experimental run time in low concentration samples as well as a rapid detection system for use in kinetics or dynamics. In the next chapter, a robust water suppression method is developed and applied to real environmental samples including soil by building on the current standard, SPR-W5-WATERGATE. The latter two research chapters apply CMP-NMR to soil research by rst characterizing the composition and structure of soil in its native state. It is found that aliphatic and carbohydrate components are available at the water interface while proteins from microbes and lignin are buried under the surface with hydrogen bonds and hydrophobicity playing a key role in their protection. Finally, contaminant interactions are probed in all phases where kinetics, sorption orientation, and soil binding domains are characterized in all phases. As a whole, this thesis helps to develop CMP-NMR for use in soil research and positions it as an important novel NMR technology with potential widespread application in a range of elds including materials research, biology, biochemistry and medicine.