VictorJuiz/thesis huggingface dataset:
FPGA Micro-Architecture-Code Co-Design For Low-Density Parity-Check Codes For Flash Memories
Keywords: Decoder
Error Correcting Code
Flash Memory
FPGA
Low-Density Parity-Check Codes
Micro-Architecture-Code Co-Design

The exponential growth of digital data has led to the proliferation of cloud storage systems as well as high-capacity, low-latency storage devices such as flash memory based solid-state drives (SSDs). These advances, along with the technology shrink, have increased the error rate both at system and device level. Storage device manufacturers and service providers often promise data reliability through error control coding. This dissertation is centered around the implementation of error correcting code (ECC) in data storage. In particular, we target low-density parity-check (LDPC) codes used for device-level and erasure codes used for system-level data reliability. Due to the ever-changing ECC requirements in the storage industry, we focus on field programmable gate arrays (FPGAs), given their short design cycles. Many studies on FPGA implementation of ECC focus on improving the hardware efficiency for a certain code of interest. This thesis extends this theme by considering hardware and code performance simultaneously. With the focus on ECCs used in data storage, we demonstrate a study of hardware-code co-design through an efficient FPGA micro-architecture that strikes a trade off between hardware efficiency and code performance. To this end, we leverage the FPGA’s inherent physical architecture to propose an efficient reconfigurable micro-architecture for LDPC decoders. Then, we address the limitations of ECC in flash memories and define a finite decoder design space. Finally, we propose an end-to-end solution in which we leverage machine learning techniques to design a finite alphabet iterative decoder which strikes a trade off between hardware efficiency and code performance. In a separate effort, we perform a quantitative study of erasure coding design on FPGAs. We demonstrate, through probabilistic analysis, that an efficient implementation ought to allocate more resources to the common-case, while reducing the performance target for less probable cases.
Synthetic Strategies for Enhancing Metal-ligand Cooperation and Enantioselective Polar Bond Hydrogenation with Base Metal Catalysts
Keywords: Base metal
Catalysis
Enantioselective
Hydrogenation
Phosphine
Polar bond

Chiral alcohols and amines are widely used in pharmaceutical, agricultural and fine chemical industries as synthetic building blocks and asymmetric polar bond hydrogenation offers an efficient method for their preparation. However, 2nd and 3rd row transition metals are still predominantly used for asymmetric hydrogenation of the substrates owing to their high activity and stability, and there has been a push towards replacing them with cheap, non-toxic and environmentally friendly base metals. Our group has extensively studied metal-ligand cooperation in the effort to enhance the activity of the base metals. Particularly, we have developed unsymmetrical pincer complexes synthesized with phosphonium dimers, where the amine exhibits the “N-H effect” bifunctional activity. The focus of this research was to explore the capability of base metal pincer complexes and to develop synthetic methods to expand the ligand synthesis.An unsymmetrical P-NH-P’ ((S,S)-Ph2PCHPhCHPhNHCH2CH2PiPr2) ligand was used to synthesize iron and manganese precatalysts and these were applied to hydrogenation of N-phosphinoyl and N-sulfonyl imines, and aryl-alkyl ketones, respectively. With iron P-NH-P’ catalyst, 3 mol% of catalyst and 10 mol% of base loading was optimal and high enantioselectivity was observed. We identified the enantiodetermining step as outer-sphere hydride transfer with N-H moiety of the ligand pre-organizing the substrate by forming a hydrogen bond with a P=O or S=O group on the substrate. A manganese amido P-N-P’ complex was used in base-free ketone hydrogenation and was found to be a viable precatalyst in terms of activity and stability. A comparison was made between the isoelectric base metal complexes and the manganese complex has the higher overall energy barrier for hydride transfer, but also the larger ΔΔG‡ between pro-R and S transition states, as supported by the experimental results. Dichloro(N,N-diethylamino)phosphine was used as a precursor to secondary phosphine in order to expand the ligand library. Dicyclopentylphosphine was targeted as novel alkyl phosphine and its respective phosphonium dimer and PNP ligand were synthesized. Manganese bis(2-dicyclopentylphosphinoethyl)amine complex was synthesized and tested for benzonitrile and methyl benzoate hydrogenation by the Beller group at Leibniz Institute for Catalysis. It showed low activity towards the ester hydrogenation and moderate selectivity for the nitrile reduction.
Mutations of the Predicted Mpp Cleavage Sites in the Intracellular Domain of Ft Affect PCP and Hippo Signalling
Keywords: Hippo
Mitochondria
PCP

The atypical cadherin Fat plays key roles in regulating tissue development and cell growth. Loss of Ft has been implicated in neurological diseases such as van Maldergem’s syndrome, Hennekam’s syndrome, polycystic kidney disease, and several different cancers. Ft has been previously implicated as an upstream regulator of the Hippo growth signalling and planar cell polarity (PCP) pathways, and in regulating mitochondrial functions. Our lab has previously identified a role for the intracellular domain of Ft in oxidative phosphorylation through the regulation of Complex I and V activity or stability. Two high confidence mitochondrial targeting sequences (MTS) have been predicted in the intracellular domain of Ft by MitoProtII. In this thesis, I have identified two six amino acid sequences at the C-terminal ends of MTS1 and MTS2 that are important for Ft function. I observed that a loss of these two regions affects viability, Hippo signalling and mitochondrial function, and suggests a novel role for these regions in regulating PCP. I have also examined the fully assembled Complex I holoenzyme to understand how the proteome changes in ft null mutants. I have begun to delineate the different functions of Ft comparing the phenotypes from mutants with a loss of these two six amino acid regions. My results suggest a larger role for the MTS sites in the regulation of Ft signalling through the coordination of novel and previously characterized roles in mitochondria, PCP, and Hippo signalling.
The Role of the Discoidin Domain Receptor-1 (DDR1) in Vascular Smooth Muscle Cell (VSMC) Mechanosensing
Keywords: Actomyosin Contractility
Discoidin Domain Receptor-1
Mechanosensing
Vascular Calcification
Vascular Smooth Muscle Cells
YAP/TAZ

Mechanotransduction is the process by which extracellular physical cues are converted into intracellular biochemical responses. The stiffness of the matrix influences numerous processes such as cell differentiation, cell migration, fibrosis, and tumorigenesis. Stiffness is sensed by matrix-binding receptors and transmitted through the cytoskeleton by actomyosin contractility. The work presented in this thesis identifies how Discoidin Domain Receptor-1 (DDR1) mediates stiffness sensing and how this influences vascular smooth muscle cell (VSMC) calcification. In the first study, experiments in primary murine Ddr1+/+ or Ddr1-/- VSMCs revealed that DDR1 promotes VSMC calcification in a stiffness-dependent manner by a positive feedback loop between DDR1 and actomyosin contractility. Increased matrix stiffness promoted increased nuclear RUNX2 levels, increased DDR1 activation and expression, increased Vav2-RhoA activity, and increased stress fibre formation in Ddr1+/+ but not Ddr1-/- VSMCs. RhoA activation increased DDR1 expression and activity independent of ligand, whereas inhibition of RhoA and actomyosin contractility were inhibitory. RUNX2 activity and expression, and VSMC calcification were increased by actomyosin contractility. The second study shows that regulation of stiffness-sensitive genes is mediated by a DDR1-YAP/TAZ nuclear complex. Ddr1-/- VSMCs had reduced nuclear YAP/TAZ, and loss of YAP/TAZ resulted in decreased DDR1 expression. DDR1 activation and increased substrate stiffness promoted DDR1 and YAP/TAZ nuclear localization. DDR1 and YAP/TAZ nuclear translocation were dependent on actomyosin contractility and caveolae. Increased stiffness, collagen stimulation, and RhoA activation all promoted DDR1 and YAP/TAZ localization to the chromatin. Collagen stimulation and RhoA activation stimulated the formation of a DDR1-YAP/TAZ-RNA polymerase II nuclear complex. Finally, DDR1 was found to localize to the promoters of Ddr1 and the canonical YAP/TAZ target gene Ctgf. In summary, these studies show a key role for DDR1 as a stiffness sensor in vascular smooth muscle cells to influence vascular pathologies like vascular calcification. DDR1 can mediate mechanosignaling via a positive feedback loop between DDR1 and actomyosin contractility, and through direct regulation of mechanosensitive genes like Ddr1 itself by a nuclear DDR1-YAP/TAZ complex. This research highlights the role of matrix stiffness in promoting vascular calcification, but also uncovers novel downstream pathways by which DDR1 mechanosignaling occurs at the membrane and in the nucleus.
Addressing Math Content Knowledge and Math Anxiety in a Teacher Education Program
Keywords: elementary teacher candidates
math anxiety
math confidence
math content knowledge
mixed methods
program evaluation

This study is an in-depth mixed methods study of a math content knowledge (MCK) course from a large scale, urban university’s faculty of education teacher program. The focus of this research is to describe the effect of this course on the math content knowledge and math anxiety levels of elementary teacher candidates. The participants were the course creators, the instructors and the teacher candidates. Quantitative data, in the form of pre- and post-course diagnostic tests and anxiety scales (collected by the course creators), and qualitative interviews were assessed to answer the research questions. This research found that the course had a significant effect on both improving the math content knowledge and decreasing the math anxiety levels of the teacher candidates enrolled in the course. It also helped the teacher candidates to improve their self-efficacy and confidence with mathematics. From an administrative perspective, the course seems to have met the expectations that teacher candidates improve their scores on the diagnostic tests and the teacher candidates interviewed for this study found a direct benefit from the course. In addition, there were suggestions for improvement in the areas of instructor selection, breadth and depth of topics covered in the course, and the creation of targeted course materials. Implications of this research indicate that this course could be applied to other faculties of education, that it could be improved to more closely align with the newly implemented provincial math proficiency testing, and that there are some suggestions for expanding the effectiveness of the course. Further areas of research are also provided.
Synthesis and Reactivity of Electron-deficient Boron Species
Keywords: Boron
Cations
Frustrated Lewis Pair
Lewis acid
Main group chemistry
Radicals

The reactivity of boron-containing molecules of extreme electrophilicity has been minimally explored in comparison with other aspects of fundamental boron chemistry. This dissertation describes research into the fundamental reactivity and bonding of the electron-deficient boron compounds of different molecular charges (0 or +1) and electronic multiplicities (1 or 2). Depending upon their substitution pattern, highly Lewis acidic boron reagents can participate in unusual reactivity. Borocyclic radicals and diamagnetic heterocyclic boroles were prepared in hydroboration and frustrated Lewis pair hydrogenation reactions of redox-active o-iminoquinone and α-diimine ligands and highly electrophilic boron reagents. Hydride-substituted boranes were found to stoichiometrically react with strong aliphatic carbon–fluorine bonds. The net transformation was found to depend on the natures of both the fluorinated substrate and the hydridoborane. For highly electrophilic boranes, a dehydrofluorination or boryldefluorination reaction was observed, whereas hydrodefluorination was found for less electron-deficient boranes. The use of an auxiliary Lewis acid initiator was also briefly explored in carbon–fluorine bond reduction. The synthesis and reactivity of uncommon, two-coordinate borocations was systematically explored. A rare carbon-substituted borinium cation was prepared or generated as the salt of various anions and used in reactivity studies. The reactivity of organo(amino)borinium cations was found to preferentially involve boron–carbon bond insertion over boron–nitrogen bond insertion. A diorganoborinium cation was investigated in frustrated Lewis pair as well as frustrated radical pair chemistry. The formation of an unprecedented diboranium cation in reactions of the borinium cation with reducing agents was observed. Reactivity of the diboranium cation with small molecules indicated both boronium- and borinium-like reactivity. Extension of the diboranium cation synthesis to other boron reagents furnished an unusual triboron(8) cation. Investigations of boron–boron bonded reagents in diboranium synthesis unexpectedly produced an isolable and highly-substituted pentaborane(9) compound, likely via boron(I) intermediates. Reactions of hydridoborane compounds were generally found to undergo redox chemistry in reactions of tetraaryldiborane(4) reagent. Analysis of related reactions involving dihydrogen show previously undocumented similarities. Collectively, these findings show new modes of reactivity for well-known boron reagents and provide strong motivation for further studies of electron-deficient boron compounds.
Individual and Statistical Characterization of the Giant Exoplanet Population
Keywords: Atmospheres
Exoplanet Characterization
Exoplanets
Observational Astronomy
Population Statistics

The field of observational exoplanet astronomy has seen tremendous progress over the span of only a few decades. Now, we find ourselves at the dawn of a new era: the characterization of distant worlds. Novel observational methods and statistical techniques allow us to explore not only the trends in bulk properties within the exoplanet population, but the atmospheric properties of individual planets as well. In this thesis, we aim to produce a more comprehensive view of the giant exoplanet population across a range of orbital distances, from the chemical inventory, thermal structure, and orbital characteristics of hot Jupiters, to the occurrence rate of cold giants and their correlation with inner planets. We begin by characterizing the orbital parameters of a single hot Jupiter, reporting on the spin-orbit misalignment and precession of the planetary system based on gravity-darkened transit observations. We then investigate the composition and thermal structure of an ultra hot Jupiter atmosphere, searching for water vapor and TiO in its optical transmission and emission spectra. We also provide confirmation of neutral atomic iron in the day-side atmosphere of an ultra hot Jupiter, and introduce a new likelihood mapping technique to constrain a planet's day-night contrast and peak phase offset using high-resolution Doppler spectroscopy alone for the first time. Lastly, we turn out attention to characterizing the population of outer planets. We perform an automated search for and statistical study of transiting cold giant planets orbiting Sun-like stars, discussing their occurrence rate, radius distribution, and correlation with inner planets. These works will have implications for theories of planet formation at both the inner and outer edges of planetary systems, allowing us to develop a clearer understanding of planet formation and evolution. The breadth of these studies is also a testament to the advancing capabilities of observational exoplanet science, and we anticipate that the future of the field lies in the study of Earth-like planets and the statistical trends in atmospheric properties across the exoplanet population.
A Public Matter? : An Ethical Analysis of the Canadian Pharmacare Public Policy Debate, 1997-2019
Keywords: Justice
Pharmaceutical insurance
Public health ethics
Qualitative research
Solidarity
Universal health coverage

Background: Canada lacks universal pharmaceutical coverage (pharmacare). Calls for the implementation of national pharmacare date back to the introduction of Canadian Medicare and have recently resurfaced on the federal health policy agenda. Although public policies raise ethical and political questions, to date there has been limited analysis of the normative rationales that underpin arguments in the Canadian pharmacare debate. Accordingly, the objective of this study was to examine how bioethics—as a practically-oriented, normative inquiry—could contribute to understanding and informing the contemporary pharmacare policy debate. Methods: I conducted a qualitative, empirical bioethics case study of the Canadian pharmacare public policy debate from 1997 to 2019. I used an adapted thematic analysis to characterize the main policy arguments in 72 policy documents and transcripts in terms of their underlying normative rationales. To inform my analysis and interpretation of the data, I drew on a theoretical framework of four philosophical accounts of the division of public and private responsibility in the organization, financing, and delivery of health insurance. Findings: The contemporary pharmacare policy debate has shifted from considering whether to determining how universal pharmaceutical coverage ought to be realized; three main forms of universal coverage have been considered: public single-payer, a ‘fill-in-the-gaps,’ multi-payer program that builds on the existing mix of public and private insurance, and catastrophic coverage. The three proposals appeal to distinct normative rationales and accounts of political responsibility vis-à-vis health and health insurance. In turn, they frame and justify the problems of access, costs, and appropriateness and their attendant policy solutions differently. Growing support for public single-payer pharmacare in the contemporary debate is justified in reference to more explicit appeals to its efficiency-promoting features in addition to its equity- and community-promoting ones. Conclusion: This study provides an understanding of how arguments in the Canadian pharmacare policy debate are justified normatively. It suggests that the pharmacare debate is a politically normative debate that will require adjudicating between distinct policy objectives. The analysis illustrates how normative policy analysis can help discern and reframe underlying normative disputes in public policy debates.
Development of Hybrid Fire Simulation Methods and Their Applications to Column Fire Tests
Keywords: Fire performance
Fire simulation
Hybrid simulation
Large-scale fire test
Structural fire design

The design philosophy in structural fire design has been shifting from prescriptive design toward performance-based design. The hybrid fire simulation method, where a physical element and a numerical model are integrated, can be used to combine the benefits of the element-level fire test and system-level fire analysis. Although the development of the hybrid fire simulation method started in the late 1990s, a fully automated robust method for large-scale numerical-experimental hybrid fire simulation has not been developed yet. In this study, two hybrid fire simulation methods are proposed and validated through full-scale column tests. The simulation schemes, substructuring methods, and stability issues are discussed in detail in this thesis. A steel moment frame was selected as a reference structure for the validation tests. The proposed methods were applied for parametric studies of steel columns and reinforced concrete columns to investigate the effect of load ratio and the axial constraint ratio on the performance of columns at elevated temperatures. The proposed method is also applied to a scaled steel braced frame that was subjected to fire following an earthquake. A set of temperature- and constraint-dependent demand-capacity curves was proposed for steel columns. The proposed curves were validated through hybrid fire simulations of steel columns. The results of the fire tests in this study demonstrate the importance of considering a realistic boundary condition for evaluating the fire performance of columns. The proposed methods provide a novel way to investigate structural fire performance through large-scale numerical-experimental hybrid fire simulations.
Extracellular Contractile Injection Systems (eCIS) - Characterization of Conserved Phage Tail-like Structures in Streptomyces
Keywords: phage
programmed cell death
secretion system
Streptomyces
tape measure protein

Extracellular contractile injection systems (eCIS) are bacteriophage tail-like structures produced by bacteria that have been implicated in diverse interactions with eukaryotic cells. Despite their distribution across many bacteria and archaea they have been relatively understudied and are often misclassified as other secretion systems or tailocins. In this work I performed a comprehensive analysis of eCIS across bacterial genomes. I show that all eCIS are comprised of nine core protein families and are closely related to contractile phage tails, a relationship emphasized by the discovery of rare eCIS-like prophages that are the likely evolutionary link between the two. I classify eCIS into six distinct groups and show that group 1 eCIS are ubiquitous in the Streptomyces genus, where their production is linked to the developmental program of these complex filamentous bacteria. The eCIS of Streptomyces coelicolor are natively produced as intracellular phage tail-like structures. Mutations that abrogate eCIS formation cause developmental defects and reduced levels of hyphal cell death at specific times during differentiation that correlate with maximal eCIS production, suggesting a potential role in programmed cell death.