VictorJuiz/thesis huggingface dataset:
International University Partnerships in Contemporary Cambodian Higher Education
Keywords: Cambodia
cosmopolitanism
international university partnerships
mutuality
power relationships

This thesis explores the issue of power relationships in international partnership programs between Cambodian universities and universities in France, the United States, Japan and South Korea, two decades after Cambodia began to be reintegrated into the regional and international communities in the early 1990s. In particular, it examines how far each of the four cases is characterized by mutuality. The cosmopolitan concept of mutuality - made up of equity, autonomy, solidarity and participation - is adopted as the theoretical framework. The study follows a qualitative case study research design, with interviews as the primary method of data collection. The findings have revealed that although in decline in recent years, French-Cambodian university partnerships over the last two decades have been supported by the French government, whose primary purpose is to promote French culture and language in Cambodia. American-Cambodian university partnerships have taken place on a relatively small scale, with modest support from American aid agencies. Clearly, the US has shown limited interest in Cambodia, other than spreading such concepts as liberal democracy and neo-liberalism in the country. Cambodian university partnerships with Japanese and Korean universities have recently expanded and have been seen to be tied to the increased economic activities of both countries in Cambodia. Most international partnerships between Cambodian universities and their French, American and Japanese counterparts manifested each aspect of mutuality to some degree. In those programs, academicians from both sides had already built close relationships with each other before moving to establish a formal institutional agreement. By comparison, the degree of mutuality varied among Cambodian-Korean university partnerships, mostly newly established with few prior people-initiated connections. The findings suggest not only the greater maturity in the international experience of French, American and Japanese universities, as opposed to South Korean universities, but also the significant role of human agency and culture in international academic activities.
Prospective Evaluation of Cognitive Functioning following Allogeneic Hematopoietic Stem Cell Transplantation
Keywords: cognitive functioning
medication management
neuropsychological performance
nursing
self-reported cognitive problems
stem cell transplantation

Cognitive functioning may be affected by cancer and its treatment, including allogeneic hematopoietic stem cell transplantation (HCT). However, clinicians are poorly suited to counsel patients in this regard, given the lack of prospective evidence to describe how cognitive functioning may change over time, which patients may be most vulnerable to these effects, and what the consequences of these effects may be. The objectives of this study were to: (1) evaluate cognitive functioning among patients treated with allogeneic HCT over the first six months following transplant; (2) identify demographic, physiological and psychological factors that predict cognitive functioning in the six months following transplant; (3) evaluate the relationship between neuropsychological performance and self-reported cognitive problems; and (4) explore the relationship between cognitive functioning with functional performance, specifically medication management ability. To this end, 58 patients treated with allogeneic HCT completed measures of cognitive functioning prior to transplant, and at Day 100 and six months post-transplant. Measures of cognitive functioning included a standardized battery of neuropsychological tests and questionnaires of self-reported cognitive problems. Medication management ability at each time point was assessed using a standardized task in which they were asked to dispense and make inferences about a simulated medication regimen. Finally, demographic, physiological and psychological characteristics were collected through chart abstraction and self-administered questionnaires. Linear multilevel models and correlational analyses formed the basis of the analytic procedure. Prior to transplant, 46% of participants met the criteria for neuropsychological impairment. On average, cognitive functioning at six months after transplant was stable in comparison to pre-transplant levels. This was shown for measures of both neuropsychological performance and self-reported cognitive problems. Pre-transplant characteristics, such as age, sex, IQ, education, and pre-transplant co-morbidities were significant predictors of neuropsychological performance at all time points. However, post-transplant outcomes, such as lower functional status at six months, and higher peak severity of acute graft-versus-host disease were also significant predictors of worse neuropsychological performance after allogeneic HCT. Self-reported cognitive problems were predictive of poorer neuropsychological performance, even when controlling for depression. Poorer cognitive functioning, particularly in the domain of executive functioning and working memory was associated with impaired medication management ability.
Melodic Jazz Drumming
Keywords: Drummers
Drumming
Drums
Drum Set
Jazz
Melody

This dissertation examines and explores how jazz drummers consider the concept of "melodic drumming" and how it relates to their own personal performance practice. The drum set, in the context of jazz music, can easily be considered a primarily rhythmic instrument by its very nature. It is, nevertheless, worthwhile and necessary to discuss the significance of how jazz drummers consider other musical elements in their own personal style. An overall musical approach to the drum set is recognized and encouraged, but the term and concept of playing "melodically" is also important. However, an exact definition of this idea is difficult to absolutely define. The definition and application of a melodic approach to jazz drumming is often as unique as the individual who chooses to either define or apply it. For the purpose of this research, the question of how jazz drummers incorporate and consider melody in their own playing was determined through a series of extensive interviews with contemporary jazz drummers. The interviews also explore how melody is viewed in the larger scope of jazz drumming. The findings from these interviews, combined with various other available sources, were then compared with the findings further organized, compared and discussed. In addition to the importance of playing the drums with an overall musical agenda, jazz drummers also describe using melody on the drum set in the context of being both an accompanist and a soloist. This includes very literal expressions of melodic structures on the drum set to more conceptual (and perhaps less obvious) applications. Many drummers also explored how melody can be an effective tool in pedagogical applications. Furthermore, many jazz drummers also discussed their sources of melodic influence. Jazz drummer Max Roach figured quite prominently in many of these interviews and his contributions and stylistic relationship to melodic drumming are also discussed.
Computational Methods of Inferring Context-specific MicroRNA Regulatory Networks
Keywords: Cancer
Gene regulation
Machine Learning
MicroRNA
Network analysis
Probabilistic models

MicroRNA (miRNA) is a class of small endogenous non-coding RNA species, which regulate gene expression post-transcriptionally by forming imperfect basepair with the target sites primarily at the 3 prime untranslated regions of the messenger RNAs. Since the 1993 discovery of the first miRNA let-7 in worms, a vast number of studies have been dedicated to functionally characterizing miRNAs with a special emphasis on their roles in cancer. A single miRNA can potentially target ~400 distinct genes, and there are thousands of distinct endogenous miRNAs in the human genome. Thus, miRNAs are likely involved in virtually all biological processes and pathways including carcinogenesis. However, functionally characterizing miRNAs hinges on the accurate identification of their mRNA targets, which has been a challenging problem due to imperfect base-pairing and condition-specific miRNA regulatory dynamics. In this thesis, I developed several novel computational methods to elucidate the functional implications of miRNAs by inferring their context-specific regulatory roles in human transcriptional programs. Each method is established through an effective and integrative design by exploiting the static sequence-based information pertinent to existing knowledge of miRNA targeting and the dynamic information of miRNA activities using the recently available large data compendia, which interrogate genome-wide expression profiles of miRNAs and/or mRNAs across various cell conditions.
Quantum Measurement on a Budget
Keywords: Measurement

Quantum computation - the use of quantum systems as bits, or qubits, to perform computation - has been proven to be exponentially faster than what is thought possible with classical computation for several tasks. Quantum computers have the unique ability to store an amount of information that is exponential in the number of constituent particles used to encode that information. This property, which is arguably where quantum computers derive their power, makes it very difficult to characterize quantum systems. In order to fully characterize an unknown quantum state, a series of measurements must be performed on it and the state deduced from the results of those measurements. This process, called quantum tomography, is known to require exponential resources in the number of qubits. Both the number of measurements - the measurement complexity - and the number of times each measurement must be repeated - the sample complexity - present serious challenges when performing tomography. In addition, the measurement apparatus itself, which is usually a quantum system, must be characterized leading to even more experimental complexity. Here, I present three experiments which aim to reduce the experimental complexity of quantum tomography. The first aims to reduce the number of measurements needed to locate the decoherence-free subspaces of a noisy quantum channel. The process of locating these subspaces, which would normally require full process tomography, is performed with quadratically fewer measurement settings. The second experiment aims to characterize both an uncalibrated measurement apparatus and an unknown quantum state at the same time. With a specific model of measurement, it is found that an uncalibrated parameter of the measurement can be directly extracted using a single measurement. In the third experiment, I perform an experiment in which the optimal sample complexity for quantum state tomography is obtained using adaptivity: the ability to change measurement settings part way through an experiment. All three experiments were performed using the polarization degree of freedom of photons generated by spontaneous parametric downconversion. The source of photon pairs and the measurement techniques used are described in detail, along with the theory of quantum distinguishability and its relevance to tomography.
Generalized Inverse Optimization with Application to Cancer Therapy
Keywords: Cancer therapy
Inverse optimization
Multicriteria optimization
Operations research
Optimization
Radiation therapy treatment planning

Inverse optimization has recently received a growing amount of attention as a data-driven approach to determining parameter values for an optimization problem. In this thesis, we study new inverse optimization methodologies that generalize the traditional method of solving inverse optimization problems and accommodate data that makes the standard method ill-posed. We apply the proposed methodologies to prostate cancer therapy data and provide novel insights for radiation therapy treatment planning. In the first part of the thesis, we briefly review recent theoretical development of inverse optimization and discuss how this thesis contributes to the literature. In the second part of the thesis, we describe a motivational example in radiation therapy treatment planning and illustrate the problem settings and clinical data. In the third part of the thesis, we develop generalized inverse linear optimization models. We characterize the relationship between the generalized models and the standard model in the literature. By building on the models in general inverse multiobjective optimization problems, we establish a new connection between inverse optimization and existing multiobjective optimization techniques. We show how our methods can be used for determining objective function weights for radiation therapy treatment planning. Next, we present a clinical application of the results from the previous part of the thesis, by proposing a statistical model that relates the objective function weights to a patient's anatomical characteristics. Using the statistical relationship, we propose a prediction model that infers objective function weights from patient anatomy and provide a proof of concept of automated, knowledge-based weight determination for radiation therapy treatment planning. Finally, we extend the theory of the second part of the thesis by developing generalized inverse convex optimization models. In the multiobjective optimization framework, we propose inverse convex optimization models that preserve the preference ordering among different objectives that is encoded by given data, and compare our models to existing inverse optimization models using prostate cancer therapy data. We present a unifying framework that encompasses many of the inverse optimization models in the literature.
A Search for Supernova Type Ia Progenitors in the Magellanic Clouds
Keywords: cataclysmic variables
novae
Small Magellanic Cloud
Symbiotic stars
Type Ia Supernovae
White Dwarfs

While it is generally agreed that type Ia supernovae are thermonuclear explosions of carbon-oxygen white dwarfs, there is still an ongoing debate whether the explosions originate from two white dwarfs merging (the double degenerate or DD scenario) or a white dwarf accreting material off of a normal star companion (the single degenerate or SD scenario). In addition, observed number of suitable progenitor systems is significantly smaller than what is required to match the observed supernova rate. White dwarfs with high mass transfer rates from their companion objects have been suggested as one type of type Ia supernova progenitor. I performed a survey looking for rapidly accreting white dwarfs (RAWD) in the central core of the SMC. I detect no candidate RAWD. The upper limits from this non-detection are 10 - 14 RAWD in the SMC, assuming they resemble the LMC source LHA 120-N 66 or fainter versions of Wolf-Rayet stars. I conducted a second survey of the SMC to identify new Symbiotic stars -- white dwarfs accreting off of a giant star companion, usually via winds. They are another possible type Ia supernova progenitor. All of the stars identified as candidates in the survey are false positives. We conclude that there are about 12 - 18 bright symbiotic stars in the SMC. Even under optimistic assumptions, this is too few objects to make up for the 25 - 130 missing SD progenitors in the SMC. I also briefly discuss LHA 115-S 18, a peculiar B[e] supergiant in the SMC, which was observed in the symbiotic star survey. S18 is both photometrically and spectroscopically variable. The system likely contains an approximately 12 solar mass B supergiant, along with a hot compact object. The identity of the hot object remains unclear since either a neutron star or a white dwarf could be formed through normal stellar evolutionary processes and are consistent with the observed properties of the hot object.
Sox17 Regulates Dynamic Gene Regulatory Networks to Specify Cell Fates in Pluripotent Stem Cells
Keywords: embryonic stem cells
endoderm
extraembryonic
gene regulatory network
Sox17

The gene regulatory networks (GRNs) driving mammalian extraembryonic endoderm (ExEn) and definitive endoderm (DE) specification are not well understood. To extend our understanding of mammalian endoderm specification, we used high-throughput genomic approaches in combination with in vitro gain of function studies to investigate the regulatory interactions of the endoderm GRN candidate Sox17. In our first study, we overexpressed Sox17 in embryonic stem cells (ESCs), driving cell fate conversion to an ExEn stem (XEN) cell-like state (Sox17-XEN), equivalent to embryo-derived XEN cells. To elucidate the dynamic networks activated by Sox17 during XEN conversion, we overlaid 352 promoter occupancy datasets onto RNA-sequencing (RNA-seq) time-series expression data and identified putative ExEn cell fate regulators. We perturbed the expression of putative ExEn repressor Nr5a2, and confirmed its ability to repress ExEn differentiation in ESCs. Moreover, we predicted and tested the ability of Sox17 to drive XEN cell conversion by activating autoregulatory and feedforward GRN motifs. We found that Sox17 autoregulates its expression by binding its own promoter, and further assembles feedforward loops activating Gata4, Gata6 and Sall4 to drive XEN cell fate. In our second study, we overexpressed Sox17 in epiblast stem cells (EpiSCs), and in contrast to ESCs, induced mesendoderm fate, a precursor of DE. We overlaid Sox17 promoter occupancy data onto RNA-seq time-series data following Sox17 overexpression in ESCs and EpiSCs, and drafted putative Sox17 GRN motifs. In ESCs, Sox17 regulates ExEn genes including Cyp26a1, Lgals2 and Muc13 whereas Sox17 activates primitive streak genes Lhx1, Fgf8 and T in EpiSCs, driving ExEn and mesendoderm fate, respectively. Additionally, we predicted Sox17 GRN motifs conserved in both ExEn and mesendoderm, regulating the expression of pan-endoderm genes including Foxa2, Foxq1, and Spink3. Together these data suggest that Sox17 activates conserved core GRN motifs as well as tissue-specific GRN motifs to drive cell fate.
"With a Vow to Defend": Indigenous Direct Mobilization in Canada
Keywords: Canadian Politics
Conflict
Indigenous
Mobilization

Since 1969, Indigenous contentious mobilization has become a fixed feature of public life in Canada. Demonstrations, marches, blockades and occupations are important repertoires of action for Indigenous peoples pursuing historical redress, contemporary recognition, and redistribution of lands and resources. Moreover, institutionalized action channeled primarily through Indian Act band councils and associated peak advocacy organizations increasingly faces legitimacy challenges in Indigenous communities. Adopting theory from the comparative study of intergroup conflict, this dissertation explains the emergence of Indigenous contentious mobilization over the past forty years, and explores the dynamics of individual protest actions. I argue that Indigenous mobilization is best explained by models that emphasize norms and value rationality over interests and instrumental rationality. Historical change cannot be explained without reference to the changes to the complex of norms and institutions that govern Indigenous-Settler relations. Micro-level protest action follows a "calculus of right", wherein mobilization swells and declines with the perceived righteousness of contentious action, rather than material cost-benefit analysis.
Cholinergic and Anatomical Dissociation of the Engagement and Disengagement of Spatial Attention in Rats
Keywords: 192 IgG-saporin
Acetylcholine
Attention
Local field potentials
Orienting
Rat

The spatial allocation of attention is a fundamental process that allows us to detect relevant behavioural stimuli, and involves both the engagement and disengagement of attention. The prefrontal (PFC) and posterior parietal (PPC) cortical regions have been identified as central nodes in a network for allocation of spatial attention. Additionally, these regions are modulated by the neurochemical acetylcholine. In this thesis, I investigated the neural underpinnings of engaging and disengaging spatial attention in rats, with a focus on the role of cholinergic input into the neocortex, including the PFC and the PPC. In the first experiment (Chapter 3), local field potentials in both the PFC and PPC, during the 5-choice serial reaction time task (5-CSRTT), were modulated by cholinergic cortical deafferentation. Specifically, successful target detection was associated with increased PFC-PPC coherence in the beta frequency during the preparatory pre-target period and with the increase in the PPC beta power. Both of these neural responses were attenuated after cholinergic deafferentation of the neocortex, which was also accompanied by a performance decrement. However, the 5CSRTT does not allow an independent examination of the attentional engagement and disengagement. Therefore, I created a cross-modal cued target detection (CTD) task to assess both the overt (Chapter 4) and covert (Chapter 5) orienting of attention. There was a decrement in the PPC beta power during the disengagement of attention and an associated attentional impairment in rats with cholinergic cortical deafferentation. Conversely, there was increased PFC beta power in both groups during the successful engagement of attention. Thus, the CTD experiments demonstrated that cholinergic innervation of the PFC was not critical for the engagement of attention, but was critical in the PPC for the attentional disengagement. In sum, I used behavioural, electrophysiological, and pharmacological methods to dissociate the neural underpinnings for the engagement and disengagement of attention.