VictorJuiz/thesis huggingface dataset:
Standing By and Doing Nothing about Genocide in Sudan and Canada
Keywords: bystander
colonial
genocide
grounded theory
indigenous research
relational sociology

The purpose of this research is to understand how riverain Sudanese stand by to genocide targeting peoples of Sudan’s peripheries, and how non-Indigenous Canadians stand by to genocide targeting Indigenous peoples in Canada. Influenced by Indigenous relational approaches to research, this study was designed collaboratively with scholars and activists targeted by genocide in both contexts. Employing constructivist grounded theory methods (Charmaz, 2008) I have conducted in-depth interviews with 44 riverain Sudanese and 18 non-Indigenous Canadians complicit in genocide. Genocides such as these destroy social figurations (Elias, 1978), the value-laden networks of relationships that define us. Reflecting this I uncovered two grounded theories of standing by to genocide, one for riverain Sudanese and one for non-Indigenous Canadians, with four relational dimensions in common: 1. relationships with place and their failure to connect across vast distances with those targeted by genocide; 2. relationships within their communities, and the colonial nature of relations between those complicit and those targeted by genocide; 3. a mesh of colonial ideas originating in Britain — capitalism, liberal values, the nation state, “modern” bureaucratized institutions, formal education, and race — that legitimize genocidal relationships in both contexts; and 4. Resulting from these relational networks a habitus (Bourdieu, 1990) that predisposes rather than prevents riverain Sudanese and non-Indigenous Canadians from standing up. Kinship relations in Sudan facilitate the colonizing riverain figuration monopolizing power at the centre, relegating peoples targeted by genocide to the peripheries. Riverain Sudanese both connect with and “other” peoples targeted in ways that facilitate doing nothing about genocide. Non-Indigenous Canadians have instead engineered themselves in a binary relationship, distant from, in contrast, and superior to Indigenous peoples in Canada. Their standing by is facilitated by the few and often poor relationships they have with Indigenous people and their denial of racism and domination. In both contexts the disposition of standing by can be explained along dimensions of (in)action, knowledge, feeling, and motivation. This theory suggests that even modest changes could transform these networks of genocidal relationships in ways that would facilitate riverain Sudanese and non-Indigenous Canadians standing up.
Genetic Modifiers of Caffeine and Endurance Performance in Athletes
Keywords: Athletes
Caffeine
Ergogenic Aids
Genetic Testing
Nutrigenomics
Sport Nutrition

Background: Caffeine is used as an ergogenic aid by athletes to improve performance. However, the effects of caffeine differ between athletes. This may be due to genetic differences affecting caffeine metabolism and caffeine response during exercise. Objective: The aim was to determine whether variation in the CYP1A2 gene, which affects caffeine metabolism, and the HTR2A gene, which encodes serotonin receptors and may affect caffeine response, modify the ergogenic effects of caffeine during a 10-km cycling time trial. Methods: Competitive male athletes (n=101; age: 25 ± 4 years) completed the time trial under three conditions: 0, 2 or 4 mg of caffeine per kg body mass, using a split-plot randomized, double-blinded, placebo-controlled design. DNA was isolated from saliva and genotyped for polymorphisms in CYP1A2 (rs762551) and HTR2A (rs6313). Results: Overall, 4 mg/kg caffeine decreased cycling time by 3% versus placebo. A significant (p
Water Quality and Hydraulic Trade-offs in Drinking Water Distribution Networks
Keywords: Distribution
Fire
Pareto
Water

Historically, water distribution network design focused on providing water at the appropriate flow and pressure, particularly during high-demand and firefighting conditions. More recently, it was discovered that 18% of waterborne disease outbreaks in the U.S. could be linked to deficiencies in the distribution network (DN), shifting the distribution network research focus towards water quality. This thesis uses genetic algorithms to assess some of the tensions between providing high flows for firefighting and water quality in drinking water distribution networks. It is shown that relaxing the traditional design restrictions on minimum pipe diameters (i.e., that they be greater than 150 mm) can provide an improved balance of fire flow, water quality, and cost. Using genetic algorithms to generate a series of Pareto Fronts, it is shown that there are significant trade-offs between fire flow and achieving high flow velocities associated with establishing self-flushing pipes. Self-flushing pipes are believed to reduce high-turbidity water events, a major source of consumer complaints. A Monte Carlo simulation suggests that a velocity of 0.10 to 0.25 m/s is self-flushing. An additional benefit of high velocity networks may include better disinfectant mass transfer to the pipe wall, where opportunistic pathogens are likely to be found. To achieve these higher velocities, this work suggests a need to relax minimum pipe diameters, reduce redundant network loops, and reduce available fire flows. This approach is now used in several European countries but has yet to be adopted in North America. Finally, it is shown that health risks associated with intrusion remain relatively constant over time, even as the number of defects in the pipe and intrusion volume increase. It is suggested that health risks are a weak function of intrusion volume. Important risk factors for intrusion likely include the number of low-pressure events and the average pipe residence time.
Systematic Analysis of Alternative Polyadenylation from High-throughput RNA Sequencing Data
Keywords: alternative polyadenylation
high-throughput RNA sequencing
post-transcriptional regulation

Alternative polyadenylation (APA) of pre-messenger RNA (pre-mRNA) results in the formation of multiple mature mRNA transcripts from a single gene with distinct 3′ untranslated regions (3′ UTRs). It has been estimated that as many as 80% of mammalian protein-coding genes contain multiple polyadenylation (poly[A]) sites, thus contributing extensively to eukaryotic transcriptome diversity and complexity. In this thesis, I describe a new computational method, ‘Quantification of APA’ (QAPA), for profiling APA using conventional bulk RNA-seq data that accurately infers changes in APA by estimating differential 3′ UTR isoform expression. To demonstrate QAPA’s utility, I analyzed a longitudinal RNA-seq study of differentiation of mouse embryonic stem cells (ESCs) into glutamatergic neurons. By characterizing global changes of APA during this developmental process, I found a large number of genes with lengthening 3′ UTRs. These genes do not significantly overlap with those with steady-state gene expression or alternative splicing (AS) changes, indicating that APA represents a largely distinct regulatory layer. Modelling of poly(A) site usage using machine learning techniques further revealed cis-elements that are predictive of this process. I next used QAPA along with additional RNA-seq analysis tools that I helped develop to characterize the transcriptomes of different neuronal cell subtypes of the mouse hippocampus. This study revealed transcriptomic variation between different subtypes involving distinct programs of co-ordinated regulation between gene expression, AS, and APA. Among these programs, in comparing hippocampal neurons from the proximal and distal axis versus other regions, I identified a program of genes displaying differential expression of a subset of ribosomal proteins that are co-regulated with 3′ UTR lengthening of genes known to localize to the synapse. This observation suggests an important role for the coordination of local translation and mRNA localization in neurons. This also highlights the importance of profiling different post-transcriptional regulatory layers to begin to understand their contributions to cell type diversity. My thesis thus contributes new methods for profiling transcriptomes using RNA-seq data and demonstrates the utility of these methods in defining multilayered regulatory networks that underlie the development and specification of neuronal subtypes.
Voter-buying, Electoral Reform, and Public Good Provision in Brazil
Keywords: Clientelism
Regression Discontinuity
Voter-Buying

Electoral fraud is often a problem for new democracies. I study the consequences of voter-buying, defined as the act of inducing outsiders to fraudulently transfer their voter registration across jurisdictions in exchange for private benefits. Specifically, I explore the effects of Brazil's 2007 voter re-registration reform which was intended to curb voter-buying. Exploiting a fuzzy regression discontinuity design in the targeting of municipalities assigned to the reform, I examine the response of mayoral elections, public expenditures and socioeconomic outcomes to the imposition of exogenous barriers to voter-buying. The reform led to an increase in political competition and a rise in healthcare expenditures, a programmatic public good salient to poor voters. The increased investments in health are reflected in greater utilization of health services and better health outcomes: a 6.6 % increase in prenatal visits, a 15 % decrease in the incidence of low birth-weight, and 5.3 % reduction in the infant mortality rate. Consistent with imported voters being more pivotal in less populous municipalities, I find the impacts are larger in targeted municipalities that are small, and provide additional evidence that restrictions on voter-buying are the main driver of my results. I also provide evidence for more positive selection of politicians, and show that unintended disenfranchisement and incumbent reputation effects are not driving my results.
Natural Enemies of Wood-boring Beetles in Northeastern Temperate Forests and Implications for Biological Control of the Emerald Ash Borer (Coleoptera: Buprestidae) in North America
Keywords: Agrilus planipennis
Atanycolus spp.
Augmentative biological control
Conservation biological control
Invasive species
Phasgonophora sulcata

The emerald ash borer (hereafter EAB), Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), is a wood-boring beetle accidentally introduced into North America during the 1990s, and has since been killing millions of ash trees, Fraxinus spp. L. (Lamiales: Oleaceae), as it spreads across Canada and the USA. Native North American natural enemies, especially parasitoid wasps, are important mortality factors of EAB, but little information is available on their arrival and detection in EAB-infested regions, and their feasibility for augmentative biological control against EAB is uncertain. Two important native parasitoid groups, Phasgonophora sulcata Westwood (Hymenoptera: Chalcididae) and Atanycolus spp. Foerster (Hymenoptera: Braconidae), were investigated to determine (1) factors influencing their capacity to disperse, (2) vegetation and habitat characteristics influencing their local abundance and role in EAB mortality, (3) whether their populations can be augmented to increase parasitism of EAB, and (4) how best to detect and monitor their populations as EAB continues to spread. The weak dispersal capacity of P. sulcata suggests it should be released as pupae close to EAB if used in an augmentative biological control program. Forest vegetation and habitat structure determine local abundance of P. sulcata and Atanycolus spp., and tree biomass, tree condition, and floral resource availability are important predictors of high parasitism on EAB. Relocating parasitoid-infested ash logs to EAB-infested sites can significantly augment populations of native parasitoids to increase EAB parasitism by 64.8 ± 18.1 % three years after introduction. Purple prism traps can be used to detect and monitor changes in populations of relocated P. sulcata and Atanycolus spp. These findings improve our understanding of the role of native natural enemies in suppressing EAB population growth and slowing ash tree mortality in North America.
Engrams, Neurogenesis, and Forgetting
Keywords: Engram
Forgetting
Infantile amnesia
Memory
Memory trace
Neurogenesis

In this thesis, three projects are described that add to our understanding of how forgetting is represented in the brain. In project 1, age-dependent changes in forgetting of spatial information is characterized in mice. Infant mice displayed significant forgetting when tested one month following training (i.e., infantile amnesia). Overtraining infant mice did not overcome the forgetting phenotype, indicating that the observed forgetting is not due to a deficit in memory encoding. Presentation of an environmental reminder one month following training led to memory recovery, suggesting that infantile forgetting is caused, at least in part, by a deficit in memory retrieval. Given the evidence that infantile amnesia is a deficit in memory retrieval, project 2 asked whether infantile forgetting can be overcome via a dentate gyrus engram ‘tag-and-activate’ strategy. Optogenetic stimulation of dentate gyrus encoding neural ensembles recovered ‘lost’ infant memories even 90 days following the initial learning event. In a process akin to pattern completion, memory recovery was associated with reinstatement of both hippocampal and cortical engram neurons. Recent work from our lab has shown that hippocampal neurogenesis promotes forgetting in both infants and adults. In project 3, the mechanism underlying neurogenesis-mediated forgetting was explored. Multiple transgenic mouse lines were used that granted bidirectionally control over the extent to which adult-generated dentate gyrus neurons remodel surrounding neural circuitry. Using this strategy, we found evidence that newborn neurons promote forgetting by reconfiguring the circuitry within which hippocampal memories are embedded. Importantly, neurogenesis-induced forgetting was negatively correlated with engram reinstatement in the hippocampus. Together, this thesis adds to the growing literature on the neural basis of forgetting.
Imaging Lactate Metabolism in Breast Cancer with Hyperpolarized 13C Magnetic Resonance Imaging
Keywords: breast cancer
compressed sensing
hyperpolarized MRI
lactate
metabolism
MRI

Breast cancer is a heterogeneous disease. Some patients attain prolonged control with first-line therapies, while others present with highly aggressive, treatment resistant malignancies. Second- and third-line treatments often carry the risk of severe, potentially life threatening side effects and only a minority patients ultimately live longer because of them. The difficulty of identifying which patients would be likely to benefit from which combination of drugs, as well as separating those whose disease is responding to their treatment from those whose is not, contributes to the provision of ineffective care. Hyperpolarized 13C magnetic resonance imaging is an emerging modality that can detect lactate production associated with reprogrammed metabolism in cancer. Changes in 13C lactate signal following treatment may be a valuable early indication of disease response and may help guide treatment decisions. While clinical translation of hyperpolarized 13C MRI has been steadily progressing, there are currently no published studies assessing the value of imaging lactate with hyperpolarized 13C MRI for better understanding and treating patients with breast cancer. In this dissertation, three technical works are presented to address the needs of robust 13C imaging for clinical translation. 13C MRI requires separate radio frequency transmit and receive hardware called RF coils that have been designed to operate at the 13C rather than 1H resonant frequency. RF coils must also conform to the anatomy under investigation. In order to perform 13C imaging in breast, a 13C breast coil system was devised and constructed. While the speed afforded by echo-planar imaging makes it an attractive technique for meeting the strict constraints of 13C MRI, off-resonance magnetization can lead to geometric distortion and spatial misregistration of imaging data. A dual-echo technique is proposed as an approach to account for sources of distortion. Volumetric encoding is highly desirable in order to allow comparison of 13C lactate signals from diseased and normal tissues, but larger regions require more time to encode and this can limit the temporal resolution of dynamic acquisitions. A pseudo-random undersampling scheme is proposed in order to reduce encoding time requirements and improve coverage.
Thermal and Electrical Properties of Graphene-based Polymer Nanocomposite Foams
Keywords: Electrical Conductivity
Graphene
Graphene-Polymer Nanocomposites
Microcellular Foam Processing
Polymer Processing
Thermal Conductivity

Recently, multifunctional polymer-graphene nanoplatelet (GnP) composites have demonstrated great promise as next-generation materials for energy management and storage, electromagnetic interference (EMI) shielding and heat dissipation components in electronic industries. However, the practical underpinning needed to economically manufacture graphene-based polymer composites is missing. Therefore, this dissertation aims to demonstrate how some of the challenges for efficient manufacturing of functional polymer composites, can be strategically tackled by using supercritical fluid (SCF)-treatment and physical foaming technologies. In this PhD research, an industrial-scale technique for in situ exfoliation and dispersion of GnP in polymer matrices was developed and invented. This thesis also developed an in-depth understanding of the effects of cellular structures, GnPs’ orientation, arrangement, and exfoliation on the thermal/electrical conductivity, percolation threshold, dielectric performance, and EMI shielding effectiveness of the graphene-based polymer composites. In particular, it was demonstrated how SCF−treatment and physical foaming can significantly enhance thermal conductivity of polymer-GnP composites. The SCF-treatment and physical foaming exfoliated the GnPs in situ and microscopically tailored the nanocomposites’ structure to enhance the thermal conductivity. The research findings in this thesis have also demonstrated that the introduction of foaming and microcellular structure can substantially increase the electrical conductivity, EMI shielding effectiveness and can decrease the percolation threshold of the polymer-GnP composites. This research also presented a facile technique for manufacturing a new class of ultralight polymer-GnP composite foams with excellent dielectric performance. The generation of a microcellular structure provided a unique parallel-plate arrangement of GnPs around the cell walls. This significantly increased the real permittivity and decreased the dielectric loss. This dissertation developed a fundamental understanding of structure-property relationships and new routes to microscopically engineer the structures and properties of graphene-based polymer composites for various application such as heat management (heat sink materials), EMI shielding, energy storage and capacitors (dielectric materials).
Polarimetry for Breast Cancer Imaging
Keywords: Breast Cancer
Collagen
Polarimetry
Polarized Light
Tumour Margins

Medical imaging is vital to the successful management of breast cancer. This thesis investigated polarimetry for breast cancer imaging. Polarimetry is the use of polarized light to study properties of matter. The main contributions of this thesis can be divided into those which expand the capabilities of experimental polarimetry, and those which explore polarimetry as a method for breast cancer imaging. Towards an improved polarimetry platform, work was done to test the importance of appropriately selecting which types of polarized light to use for polarimetry measurements. Specifically, an optimum set of input polarization states was experimentally validated for use with a dual photoelastic modulator (PEM) polarimeter. Further, two new polarimetry imaging systems were developed. The first was designed to enable faster polarimetry imaging. A rapid imaging system based on PEMs and a charge-coupled device (CCD) camera was built, calibrated, and used to image biological phantoms. The second imaging system was designed to enable accessible multiscale polarimetry imaging. A removable polarimetry module was designed and built for use with a commercial microscope. Polarimetry was investigated as an imaging method for two important aspects of breast cancer, specifically, breast cancer margins, and collagen organization. The breast cancer margin work was done in the context of providing image-guidance for mass spectrometry. Mass spectrometry is a technique for sensitively acquiring tissue chemical signatures, but is hindered by long imaging times. Polarimetry was found to rapidly differentiate human breast cancer from healthy tissue in a mouse model of breast cancer. It could also identify necrosis in breast cancer lymph node metastases. These findings are promising for polarimetry-guided mass spectrometry. Finally, polarimetry was investigated for imaging collagen organization in a mouse model of breast cancer. A direct comparison with second harmonic generation (SHG) imaging found that polarimetry detects organizational contrast different from that arising exclusively from collagen. Polarimetry shows potential for breast cancer imaging, whether on its own or paired with other techniques such as mass spectrometry. The hope is that the findings of this thesis will help guide the continued development of polarimetry, both for breast cancer, and biomedicine in general.
Allons Enfants de la Patrie: An Analysis and Defence of Patriotism and the Social Self
Keywords: Flourishing
Loyalty
Patriotism
Social Identity
Virtue

My dissertation is a rehabilitation of patriotism as a virtue. The initial theory building corrects for the often vague or empirically unsupported characterizations of the phenomenon. More precisely, I draw on the field of nationalism studies as well as research in economics and social psychology to produce an empirically grounded account. On my view, patriotism is not analogous to personal loyalty because it depends upon a common identity and an intergenerational entity; it is a collective form of loyalty that engages with collective self-understanding. Moreover, I argue that patriotism is predominantly cultural rather than political as loyalty and identity predate and survive regime changes. My defence of patriotism is two-pronged. First, I demonstrate that Charles Taylor’s argument that patriotism is necessary for a well-functioning democracy is best served by a cultural view of patriotism rather than a political version. The key problem is that a patriotism dependent upon a purely political social identity is unable to reliably sustain collective loyalty. Second, I argue that patriotism can make a distinct contribution to human flourishing through what I call deindividuated flourishing. Building upon insights from social psychology, I argue that human flourishing should be understood in both personal and collective terms. The latter is characterized by collective self-understanding and collectivizing the parameters of success. Patriotism, by allowing us to engage in large-scale and intergenerational projects, allows for deindividuated flourishing.