VictorJuiz/thesis huggingface dataset:
Relaxing Concurrency Control in Transactional Memory

Transactional memory (TM) systems have gained considerable popularity in the last decade driven by the increased demand for tools that ease parallel programming. TM eliminates the need for user-locks that protect accesses to shared data. It offers performance close to that of fine-grain locking with the programming simplicity of coarse-grain locking. Today’s TM systems implement the two-phase-locking (2PL) algorithm which aborts transactions every time a conflict occurs. 2PL is a simple algorithm that provides fast transactional operations. However, it limits concurrency in applications with high contention because it increases the rate of aborts. We propose the use of a more relaxed concurrency control algorithm to provide better concurrency. This algorithm is based on the conflict-serializability (CS) model. Unlike 2PL, it allows some transactions to commit successfully even when they make conflicting accesses. We implement this algorithm both in a software TM system as well as in a simulator of a hardware TM system. Our evaluation using TM benchmarks shows that the algorithm improves the performance of applications with long transactions and high abort rates. Performance is improved by up to 299% in the software TM, and up to 66% in the hardware simulator. We argue that these improvements come with little additional complexity and require no changes to the transactional programming model. This makes our implementation feasible

Keywords: parallel programming
multi threaded programs
transactional memory
synchronization
serializability
concurrency control
Advisor: Abdelrahman, Tarek S.
Functional Characterization of T-lineage Cells derived in vitro from Human Hematopoietic Stem Cells

T lymphocytes play a critical role in adaptive immunity by eliciting and regulating specific immune responses against viral and bacterial pathogens. The development of T cells occurs within the highly specialized thymus and follows a defined set of stage-specific differentiation steps. However, the molecular and cellular events occurring at early stages of human T-cell development remain to be fully elucidated. This was in part due to the inability to obtain substantial numbers of T-lineage cells from hybrid/human fetal thymic organ culture (FTOC) and the inability to recapitulate human T-lymphopoiesis using other systems. To address the molecular and cellular events occurring during early human T-lymphopoiesis, human umbilical cord-blood (UCB) hematopoietic stem cells (HSCs) were induced to differentiate to the T-lineage utilizing OP9-DL1 stromal cells. A developmental program involving a sequential and temporally discrete expression of key differentiation markers was revealed. In addition, this Thesis demonstrates that in vitro-generated CD34+CD7++ progenitors effectively engrafted the thymus of immunodeficient mice. In addition, two distinct progenitor subsets, CD34+CD45RA+CD7++CD5-CD1a- (proT1) and CD34+CD45RA+CD7++CD5+CD1a- (proT2), were identified with proT2 cells showing a 3-fold enhanced engrafting capacity than the proT1 subset. As proT2 cells exhibit superior engrafting capacity, these cells were tested for their ability to enhance T cell generation following hematopoietic stem cell transplant (HSCT). We observe that when HSCs are coinjected with proT2 cells, a dramatic improvement in HSC-derived T-lymphopoiesis is observed. This Thesis demonstrates that in vitro-derived proT2 cells reorganize the thymus stromal compartment of the host NOD/SCID/γcnull mouse compared to the highly disorganized cortical and medullary compartments in mice not receiving proT cells. This alteration in thymic architecture likely favours the recruitment of BM derived progenitors. Lastly, we address whether functional CD8 T cells can be generated in vitro using hematopoietic stem cells (HSCs) in coculture with OP9-DL1 cells and indeed these cells were capable of proliferating, and secreting effector molecules typical of cytotoxic T cells. Taken together, the ability to generate proT cells and mature T cells from Notch-ligand cultures offers a new tool to study human T cell development.

Keywords: Notch
hematopoietic stem cell
T cell development
immune-reconstitution
progenitors
hematopoiesis
Advisor: Zuniga-Pflucker, Juan Carlos
Martian Boneyards: Sustained Scientific Inquiry in a Social Digital Game

Social digital gaming is an explosive phenomenon where youth and adults are engaged in inquiry for the sake of fun. The complexity of learning evidenced in social digital games is attracting the attention of educators. Martian Boneyards is a proof-of-concept game designed to study how a community of voluntary gamers can be enticed to engage in sustained, high-quality scientific inquiry. Science educators and game designers worked together to create an educational game with the polish and intrigue of a professional-level game, striving to attract a new audience to scientific inquiry. Martian Boneyards took place in the high-definition, massively multiplayer online environment, Blue Mars, where players spent an average of 30 hours in the game over the 4-month implementation period, with some exceeding 200 hours. Most of the players’ time was spent in scientific inquiry activities and about 30% of the players’ in-game interactions were in the analysis and theory-building phases of inquiry. Female players conducted most of the inquiry, in particular analysis and theory building. The quality of scientific inquiry processes, which included extensive information gathering by players, and the resulting content were judged to be very good by a team of independent scientists. This research suggests that a compelling storyline, a highly aesthetic environment, and the emergent social bonds among players and between players and the characters played by designers were all responsible for sustaining high quality inquiry among gamers in this free-choice experience. The gaming environment developed for Martian Boneyards is seen as an evolving ecosystem with interactions among design, players’ activity, and players’ progress.

Keywords: virtual learning environments
game-based learning
scientific inquiry
MMO games
Advisor: Hewitt, James
Leadership in Times of Change: An Examination of a Merger Experience

Mergers continue to increase globally. Leaders have a critical role in the success of those mergers based on the practices that they employ during this change phenomenon. This study examines leadership practices within a financial organization during a merger and explores how these practices influence the merger. This study also identifies challenges faced by organizations during the merger process. During this qualitative study, interviews were conducted with 17 leaders to understand what leaders do in times of mergers. Through their stories, they identified leadership practices and described how these practices influenced the merger process. Seven leadership themes emerged from the data including: (a) Providing Strategic Vision, (b) Utilizing Effective Communication, (c) Creating a Positive Organizational Culture, (d) Commitment to Fairness, (e) Effective Negotiation and Conflict Resolution, (f) Problem Solving and Decision Making, and (g) Managing Change and the Unknown. The interviews also provided insights into some of the challenges faced by organizations before, during, and after a merger. A conceptual model grounded in theory helped guide the study. Although the body of literature regarding mergers continues to grow, there has been limited examination about the influence of leadership practices before, during, and after a merger. This study adds to the research literature in two ways. First, it has made a new contribution as academic research dealing with financial institutions and specifically the co-operative movement. Secondly, this study also builds on some of the scholarly work related to the leadership practices as they relate to creating a vision, creating a positive culture, effective communication, commitment to fairness, problem solving and decision making, effective negotiation, and managing change.

Keywords: Leadership
Change
Mergers
Advisor: Ryan, James
Investigations Related to Dietary Sodium in Chronic Heart Failure

Sodium restriction is the primary dietary therapy for individuals with heart failure (HF); however, there is little information available to support or refute the use of sodium restriction to manage HF. The overall goal of this work was to generate data related to dietary sodium in patients with chronic HF that would contribute to the development of evidence-based guidelines. The specific objectives were to investigate the optimal methods for measuring sodium intake in HF, to describe the habitual consumption of sodium and other nutrients in HF, and to evaluate the relationship between sodium intake and clinical outcomes in HF. We studied stable ambulatory HF patients who were optimally medicated and participating in multidisciplinary HF programs. We determined that: (1) a strong relationship exists between 24-hour urine collections and food records for sodium intake assessment in non-HF cardiac patients and HF patients not taking loop diuretics. However, the relationship between urinary sodium excretion and sodium intake in HF patients taking loop diuretics was disturbed, suggesting that food records may be a better method for estimating sodium intake in this group. (2) Mean sodium intake in HF and non-HF cardiac patients was similar, and approximately half of patients in each group had sodium intake levels that exceeded the Dietary Reference Intakes tolerable upper level of 2300 mg/d. We also found that both groups had inadequate intakes of several nutrients, including potassium, calcium, magnesium, folate, and vitamin D and E. (3) Finally, we showed that a high sodium diet (>2800 mg/day) in HF was associated with risk of acute decompensated HF, all-cause hospitalization, and all-cause mortality over a median 3 year follow-up period. This is the first published study that prospectively related sodium intake to clinical outcomes in HF. In summary, these data provide novel contributions related to the measurement of sodium intake that can be used in clinical or academic settings. We also describe inadequacies in intake of several vitamins and minerals, which could be addressed through dietary counselling. Finally, we importantly offer insight into a threshold of sodium intake (>2800 mg/day) that could contribute to adverse clinical outcomes in HF.

Keywords: diet
sodium
nutrition
heart failure
Advisor: Allard, Johane
The Role of Differential Experience in Facial Age Processing

The present study investigated the role of differential experience in one’s processing of facial age information. Study 1 examined how differential experience with own- and other-race individuals, as well as differential experience with own- and other-age individuals, influences children’s and adults’ abilities to process facial age information. Study 2 examined how differential sociocultural experiences influence adults’ abilities to process facial age information. The results suggest that the influence of differential experience with own- and other-race faces is most evident when individuals have extremely limited to no experience with other-race faces. There was also a clear other-age effect in young adults’ facial age judgments, presumably due to their extensive experience with own-age peers. However 9- to 10-year-olds and 13- to 14-year-olds also showed an advantage in processing facial age information for young adult faces relative to child and middle-age adult faces. Thus, the 9- to 10-year-olds and 13- to 14-year-olds may have also had the most extensive experience with young adult individuals relative to individuals from other age groups. In addition, results suggest that the efficiency with which individuals process facial age information is influenced by differential sociocultural emphases on the need to differentiate between the facial ages of social partners.

Keywords: facial age processing
Advisor: Lee, Kang
Impact of Diabetes on Drug Disposition Mechanisms in Pregnancy

Over 220 million people worldwide are diagnosed with diabetes and rising prevalence is reported in nearly all surveyed populations. Accordingly, the percentage of pregnancies affected by pre-existing type 1 or 2 diabetes or by diabetes that develops during pregnancy, called gestational diabetes mellitus (GDM), is also on the rise. Today, approximately 8% of all pregnancies are complicated by diabetes. Diabetes alters drug disposition mechanisms in non-pregnant subjects but the impact of diabetes on drug disposition in pregnancy has not been properly evaluated. Atypical drug disposition in pregnancy has implications for maternal and fetal health. Because liver tissue from pregnant women is not readily available, this thesis investigated drug disposition mechanisms primarily in a rat model of experimental GDM. This model consisted of administering streptozotocin, a diabetogenic toxin, to pregnant rats on gestational day 6. One key finding was that elevated circulating lipids in GDM rats competed with drugs (e.g., glyburide and saquinavir) for plasma protein binding so as to increase free drug concentrations. Another key finding was that important hepatic drug efflux transporters (e.g., Mdr1a/b) and metabolic enzymes (e.g., Cyp3a2 and Ugt1a1) were upregulated in GDM as a consequence of, most likely, enhanced nuclear receptor activity (e.g., pregnane X receptor upregulation). Upregulation of hepatic drug efflux transporters and metabolic enzymes, coupled with larger unbound drug fractions, would be expected to increase the hepatic clearance of many drugs. Consistent with this, in GDM, maternal and fetal exposure to the Mdr1 and Cyp3a2 substrate lopinavir was substantially lower than controls post-administration and data supporting enhanced lopinavir metabolite formation were obtained. Placental drug efflux transporters were also examined in this lopinavir study. Elevated placental Mdr1b and Bcrp expression was observed in GDM, which was associated with decreased fetal exposure to lopinavir (even after correcting for maternal unbound concentrations). Taken together, this thesis demonstrates that experimental GDM can significantly impact drug disposition by altering key drug disposition mechanisms. If confirmed in humans, this drug-disease interaction would need to be considered when atypical therapeutic outcomes occur in diabetic pregnancies. Data from experiments with human placentas, obtained from pregnancies complicated by insulin-managed diabetes, is included/discussed.

Keywords: Gestational diabetes
Drugs
Advisor: Piquette-Miller, Micheline
The Evolution of Necrotrophic Parasitism in the Sclerotiniaceae

Given a shared toolbox of pathogenicity-related genes among a set of species, why is one species a biotroph and specialist while another is a necrotroph and generalist? Is it the result of selection on primary sequence, or on proteins, or alternatively, differences in the timing and magnitude of gene expression? The Sclerotiniaceae (Ascomycota, Leotiomycetes, Helotiales) is a relatively recently evolved family of fungi whose members include host generalists and host specialists, and the spectrum of trophic types. Based on a phylogeny inferred from three, presumably evolutionarily conserved housekeeping genes, the common ancestor of the Sclerotiniaceae was necrotrophic, with at least two shifts from necrotrophy to biotrophy. Phylogenies inferred from eight pathogenicity-related genes, involved in cell wall degradation and the oxalic acid pathway, were incongruent with the presumably neutral phylogeny. Site-specific likelihood analyses, which estimate the rate of nonsynonymous to synonymous substitutions (dN/dS), showed evidence for purifying selection acting on all pathogenicity-related genes, and positive selection on sites within five of eight genes. Rate-specific likelihood analyses showed no differences in dN/dS rates between necrotrophs and biotrophs, and between host generalists and host specialists, indicating that selection acting on the genes does not drive divergence toward changes in trophic type or host association. In vitro screens for oxalic acid production demonstrated that all necrotrophic generalists produce oxalic acid by 72 hours, while production was either absent or delayed among biotrophs and host specialists. This pattern was also observed during the course of Arabidopsis thaliana infection, in which large spikes of expression were seen in the oxalic acid pathway-related gene, oah, within eight hours of inoculation among necrotrophic generalists only. Results suggest that necrotrophic generalists can be distinguished from biotrophs and host specialists in the Sclerotiniaceae by the ability to produce abundant amounts of oxalic acid early in infection and to cause large proliferating lesions on A. thaliana.

Keywords: evolution
Sclerotiniaceae
fungi
necrotrophy
biotrophy
Advisor: Kohn, Linda M.
Mastering the Story/Storying the Master: Philosophy of Education Discourse and Empire

This dissertation is an exploration of the role of Euro-North American Philosophy of Education discourse in the genealogy of race struggle. I examine how the reliable narration of Philosophy of Education functions as a project of racial rule premised on moral/temporal/spatial notions of (White) civility and respectability. Tracing the history of race war from the 17th century to present day, I look at how racism has shifted from sovereign power to disciplinary power to biopower as a mode of population management, operating not only through race but through gender and class distinctions as well. I analyze the racialized narrative conventions of liberal modern Enlightenment philosophy and the role these conventions continue to play in the creation and maintenance of a violent racial state. Drawing upon Critical Race Theory, feminist epistemologies, narrative theory, and the work of Michel Foucault, I look at what reliable narration does for philosophers, educators, and students, examining what we/they might have invested in maintaining a distinction between ‘reliability’ and ‘unreliability.’ I ask: How is reliable narration used as a tool by philosophers, educators, and ultimately, the state to distinguish between the civil and uncivil, between those worthy and unworthy of moral consideration, political engagement, and basic human rights? How do the impartiality, univocality, universality, and dispassion of reliable narratives become tied to race and the management of racialized bodies? My aim is to examine the ways in which race as a method of governance acts on a text, its author(s), and its audience. “How are racialized subjectivities constituted through and constitutive of language and knowledge,” I ask, “and to what effect?” I want to trace the social and civil relations mapped out by particular narrative conventions and examine the consequences of failing to adhere to such conventions. I suggest that by questioning the function of reliable narration in philosophical and pedagogical practice, educators, scholars, and students can intervene in the operation of race as a mode of discipline, creating the possibility of a more equitable society in which all have the opportunity to flourish.

Keywords: critical race theory
Foucault
epistemology
narrative
pedagogy
civility
Advisor: Ford, Maureen
Studies in Classical and Quantum Correlations and their Evolution in Physical Systems

More than a century ago, starting with Michelson, the field of classical coherence has developed rapidly. By studying and uncovering the coherence properties of light, many useful applications were discovered. In modern times, these applications have seen large use in fields like astronomy, where the properties of light can be used to discover stars and determine their radius, for example. Another class of correlations, namely quantum correlations, which were discovered in the beginning of the twentieth century, have gained much attention from the scientific community in the last two decades. In particular, the field of quantum information developed, promising great computational power by using quantum correlations to build computers. Currently, quantum computation is a very active field bringing together physicists, mathematicians, engineers, chemists, and computer scientists to find solutions to the problems encountered in building quantum computers. I consider some classical coherence effects of the degree of cross polarization (DCP) on the Hanbury-Brown Twiss effect, with a specific focus on Gaussian Schell-model beams. I show that the DCP is necessary, in general, to determine the correlations in intensity fluctuations of a beam at two different points. As for quantum correlations, I consider entanglement in realistic systems: one in two-qubit systems, and the other in continuous variable quantum systems. In the former case, when the temperature of the system is finite, entanglement always decays in a finite time. However, in the latter case, entanglement is long-lived, although in the long run it is not of much practical use. Finally, I unravel the relationship between quantum discord and quantum entanglement, as well as quantum discord and entropy for the most general two-qubit systems, and I identify the states that define the boundaries of these relationships.

Keywords: Quantum Optics
Quantum Correlations
Advisor: James, Daniel