VictorJuiz/thesis huggingface dataset:
Neocortical Inhibitory Interneuron Subtypes Display Distinct Responses to Synchrony, Rate and Layer-specific Inputs

Almost a hundred years after the recording of the first voltage “spikes”, the question of how neurons use spikes to convey information about the outside world remains elusive. The standard model of how neurons encode information is through their different frequencies of spiking. High fidelity rate coding requires high spiking rates, but many regions of the brain, such as the supragranular layers 2/3 (L2/3) of the neocortex exhibit sparse, low firing activity. Evidence from L2/3 of the cortex supports the idea that the timing and synchrony of spikes may also encode relevant stimulus information. There is increasing evidence to suggest that high-frequency, nonlinear bursting may be another distinct form of coding within L2/3, particularly when integrating feedback inputs from higher order regions arriving in Layer 1 (L1). How such different coding regimes could exist within the neocortex may be due to the diversity of neuronal cell types that reside in this region. To understand how different neurons in L2/3 encode different types of information, I used ex vivo whole cell patch clamping to examine the responses of PV+ and SST+ inhibitory interneurons in the somatosensory cortex of mice when inputs were driven either optogenetically or electrically. First, I sought to determine whether different interneuron types were sensitive to information conveyed through the rates or synchrony of inputs. To do this, I developed a novel setup that would encode a random 1-bit signal controlling either the synchrony or rates of optical inputs. I then examined the amount of information encoded by PV+, SST+ and pyramidal neurons about this 1-bit signal. I found that these two inhibitory classes of cells were differentially sensitive to each input type. I also examined whether these different classes of cells responded differently to inputs from L1 of the neocortex. Similar to my optogenetic experiments, these two classes showed different bursting responses to increasing stimulation of inputs from Layer 1. These results demonstrate that the interneuron subtypes studied here have distinct sensitivities to different types of coding regimes utilized by L2/3 and strongly suggests potential divisions of labour for information encoding within the neocortical circuit.

Advisor: Richards, Blake A
Entanglement and Non-locality in Games and Graphs

Quantum graph theory, also known as non-commutative graph theory, is an operator space generalization of graph theory. The independence number, and Lovasz theta function were generalized to this setting by Duan, Severini, and Winter [DSW13] and two different version of the chromatic number were introduced by Stahlke [Sta16] and Paulsen [HPP16]. We introduce two new generalizations of the chromatic number to non-commutative graphs and provide an upper bound on the parameter of Stahlke. We provide a generalization of the graph complement and show the chromatic number of the orthogonal complement of a non-commutative graph is bounded below by its theta number. We also provide a generalization of both Sabidussi's Theorem and Hedetniemi's conjecture to non-commutative graphs. The study of non-local games considers scenarios in which separated players collaborate to provide satisfying responses to questions given by a referee. The condition of separating players makes non-local games an excellent setting to gain insight into quantum phenomena such as entanglement and non-locality. Non-local games can also provide protocols known as self-tests. Self-testing allows an experimenter to interact classically with a black box quantum system and certify that a specific entangled state was present and a specific set of measurements were performed. The most studied self-test is the CHSH game which certifies the presence of a single EPR entangled state and the use of anti-commuting Pauli measurements. We introduce an algebraic generalization of CHSH and obtain a self-test for non-Pauli operators resolving an open question posed by Coladangelo and Stark (QIP 2017). Our games also provide a self-test for states other than the maximally entangled state, and hence resolves the open question posed by Cleve and Mittal (ICALP 2012). This thesis is primarily based on two collaborative works written by the author and several coauthors [CMMN20], [KM19].

Keywords: quantum information
Advisor: Yuen, Henry
“Freaked out” by Pediatric Concussion: An Exploration of Drawing and Interview Data Produced by Children ‘at risk’ of and Living with Concussion

This dissertation provides a critical examination of how children experienced concussion as a social phenomenon. Oriented by the post-structuralist theory of Michel Foucault (1926-1984), namely concepts of discourse, power/knowledge, and the subject, I explored how children responded to what I have identified as the Pediatric Concussion Discourse (PCD), a convergence of discourses of risk, childhood vulnerability, and responsibility that construct children as especially ‘at risk’ of concussion, and as responsible (at least in part) for protecting themselves from risk. I conducted a critical qualitative arts-based research study, using drawing and semi-structured interviewing methods. My analysis draws on data produced with 43 participants, with and without a history of concussion, between nine and 16 years of age. My findings suggest that children responded to the PCD as neoliberal citizens-to-be, on their way to becoming the responsible and self-reliant citizens that are valued in contemporary Western society. Notably, there were differences in how children at the younger and older end of the age range in this study responded to the PCD. While older children re/produced normative assumptions of citizenship that expect ‘good’ citizens-to-be to assume responsibility for their health as they age, younger children drew on notions of childhood vulnerability, representing themselves as ‘just’ naïve children who required adult protection and could not be solely responsible for their own health. In a field of study and practice dominated by developmentalism, these findings might appear self-evident, as differences of ‘age and stage’. However, by re/framing these findings through a critical social lens, I came to see that children, ‘younger’ and ‘older,’ acquired specific social competencies in relation to concussion. Findings suggest that children were forced into this social competence through an absence of adults in protective roles, an absence that was consequential for children regardless of age or stage. Children were “freaked out” by concussion, the risk it posed, and the responsibilities and competencies it demanded, particularly in the absence of adult protectors. This research suggests a need to re/consider how the PCD and child/adult relations shape how children experience concussion. Suggestions are made for clinical and research practice.

Keywords: arts-based research
children's rehabilitation
critical social theory
discourse
pediatric concussion
Advisor: Reed, Nick
FPGA Micro-Architecture-Code Co-Design For Low-Density Parity-Check Codes For Flash Memories

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.

Keywords: Decoder
Error Correcting Code
Flash Memory
FPGA
Low-Density Parity-Check Codes
Micro-Architecture-Code Co-Design
Advisor: Zhu, Jianwen
Synthetic Strategies for Enhancing Metal-ligand Cooperation and Enantioselective Polar Bond Hydrogenation with Base Metal Catalysts

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.

Keywords: Base metal
Catalysis
Enantioselective
Hydrogenation
Phosphine
Polar bond
Advisor: Morris, Robert RHM
Replication and Workload Management for In-Memory OLTP Databases

Online transaction processing (OLTP) databases are a critical component of modern computing infrastructure services. As a result, they must be highly available, and they must process requests efficiently for a wide range of workloads. Databases provide high availability by using replication so that when a database replica fails, a backup can take over. They use workload management mechanisms for efficiently supporting different types of workloads with varying levels of skew and contention. This thesis revisits the challenges of database replication and workload management for in-memory databases. Unlike traditional disk-based databases, in-memory databases are designed for workloads whose entire dataset fits in DRAM memory. These databases are highly scalable, raising challenges for replication and workload management. For example, traditional database replication schemes suffer from the network, instead of storage, bottlenecks because in-memory databases have much higher throughput, and traditional workload management solutions significantly limit the performance of in-memory databases. In this thesis, we propose using deterministic concurrency control as the basis for replication and workload management. Deterministic concurrency control allows transactions to execute concurrently while guaranteeing equivalence to a predetermined serial ordering of transactions. For data replication, we propose a replay-based scheme that executes transactions concurrently and scalably on the backup database in the serial order predetermined by the primary database. Our solution reduces network bandwidth requirements to 10-15% of traditional database replication schemes. For workload management, we propose two optimizations to deterministic concurrency control that help parallelize internal database operations. These optimizations enable handling contention and skewed workloads efficiently and provide 30% to 6x performance improvements.

Advisor: Goel, Ashvin
Demke Brown, Angela
Mutations of the Predicted Mpp Cleavage Sites in the Intracellular Domain of Ft Affect PCP and Hippo Signalling

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.

Keywords: Hippo
Mitochondria
PCP
Advisor: McNeill, Helen
Influence of Climate on Open Earth-air Heat Exchanger Potential

Space heating and cooling constitute significant energy demands in buildings. The interdependence between climate and heating and cooling energy usage makes this sector a prominent candidate for climate change mitigation as well as making it susceptible to climate change impacts. Earth-air heat exchangers (EAHE) have the potential to provide heated or cooled air to buildings by allowing for heat exchange between the subsurface and supplied ambient air, hypothetically reducing energy demands for space heating and cooling. However, the system is naturally tied to the climate as it relies on both air and subsurface ground temperatures. Therefore, to ¬recognize the feasibility of these systems and their capacity for becoming tools for climate change mitigation, the influence of climate on these systems require further understanding. The influence of seasonal variations in air and subsurface temperatures were gauged for Canadian climates to understand the impacts of assuming temporal homogenous ground or typical weather conditions. Heating potential was less dependent on the timing of seasonal variations when compared to cooling potential, with ground temperature changes exhibiting a heightened effect. This emphasized the importance of parameterizing temporally heterogenous ground surface conditions for estimates of EAHE potential. The importance of daily air temperature behavior was investigated through the temporal decomposition of surveyed air and ground temperatures from an EAHE system employed in Aichi, Japan. The reliance of cooling on the diurnal variations in air temperature implied EAHE cooling may be susceptible to increases in overnight/morning temperatures when system cooling is least favorable. Finally, ‘future’ EAHE potential was estimated by pairing a climate driven approach with climate change scenarios. Projections of geo-climatic suitability showed EAHE systems can continue to be useful in temperate climates, with a more balanced heating and cooling demand, despite an evolving heating and cooling regime. Further work should endeavor to incorporate the climate influences highlighted in this work to create a comprehensive climate-based approach for estimating EAHE. Ultimately, stakeholders looking to harness the benefits of EAHE systems should consider climate effects, avoiding oversimplifications, when estimating EAHE feasibility for present and future conditions.

Advisor: Gough, William A
The Role of the Discoidin Domain Receptor-1 (DDR1) in Vascular Smooth Muscle Cell (VSMC) Mechanosensing

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.

Keywords: Actomyosin Contractility
Discoidin Domain Receptor-1
Mechanosensing
Vascular Calcification
Vascular Smooth Muscle Cells
YAP/TAZ
Advisor: Bendeck, Michelle P
Addressing Math Content Knowledge and Math Anxiety in a Teacher Education Program

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.

Keywords: elementary teacher candidates
math anxiety
math confidence
math content knowledge
mixed methods
program evaluation
Advisor: McDougall, Douglas