VictorJuiz/thesis huggingface dataset:
Alcohol Withdrawal Syndrome Assessment based on Tremor Time-Frequency Analysis

In this thesis we established signal processing techniques to objectively evaluate the severity of Alcohol Withdrawal (AW) tremors. Many medical protocols were used pre- viously to help the physicians in assessing the severity of alcohol withdrawal, but those techniques were subjective and relied on the experience level of the physicians. The key objective throughout this thesis is investigating the logarithmic nature of the energy emitted from tremor signals. We are able to use the energy from tremor recordings in the frequency range of [5, 15] Hz to train a logarithmic model to estimate the severity of tremors. The next step in validating the effectiveness of the logarithmic model is the validation of the methodology in a clinical setting. The model is being validated in the emergency department for a 10-month period. During this period, each of the AW patients have been evaluated by one nurse and have been videotaped while acquiring the signal. The model provides the severity score in realtime after recording the signal. Our model is validated by comparing the score given by the model and the consensus severity rating from a panel of three expert physicians after viewing the videos. We concluded that there is a reliable agreement (kappa 0.92, 95% CI: 0.86, 0.99) between the score given by the model and the rating from our panel. Further contributions of this thesis include an investigation of the features of AW tremors in classifying factitious vs. real tremors, based on the mean peak frequency and band-limited energy. Additionally we evaluate the differences between AW tremors in both hands and observe that by averaging the tremor ratings of each hand, a more ac- curate result can be obtained compared to taking either of the individual hand ratings. Lastly, to remove the noise from the tremor signal, an Empirical Mode Decomposition (EMD) algorithm was utilized. EMD decomposes the signal into different Intrinsic Mode Functions (IMFs) and IMFs with the peak frequency in the frequency range of the tremor will be a part of the reconstructed signal. Using this technique, we successfully enhanced the accuracy of our logarithmic model.

Keywords: Alcohol Withdrawal
Empirical Mode Decomposition
Regression Model
Signal Processing
Advisor: Aarabi, Parham
Effect of Pore Structure and Chemistry on the Performance of Activated Oil Sands Petroleum Coke Electrodes for use in Electrochemical Double-Layer Capacitors

Electrical energy storage is a limiting barrier to widespread usage and commercialization of sustainable and renewable energy sources, such as wind and solar energy, as well as integration of electric vehicles. Electrochemical double-layer capacitors (EDLCs) are a promising energy storage technology that offers the benefits of high power density, long cycle life, rapid charging rates, and moderate energy density. The energy storage mechanism of EDLCs is physical ion adsorption on the surface of porous carbon electrodes. This thesis is an investigation of three different sections relating to EDLCs: 1) techniques to properly characterize novel porous carbon electrode materials, 2) investigation of activated oil sands petroleum coke (APC) as the electrode material for EDLCs, and 3) a systematic study of the effects of porous carbon structure and chemistry on EDLC performance. In the first section, it was shown that variations in operating conditions and testing techniques can lead to discrepancies in measured and reported capacitance. Therefore, it was concluded that a standardized approach is necessary in order to properly compare different porous carbon electrodes. In the second section, APC was investigated as a novel electrode material for EDLCs. PetCoke is a carbon dense material that can be activated with potassium hydroxide to generate high surface area porous carbon materials. These materials show promising electrochemical performance in EDLCs, with capacitance values up to 400 Fg-1 in 4M potassium hydroxide aqueous electrolytes, depending on the operating conditions. Additionally, the power density of these materials is comparable to that of other carbon nanomaterials, which are more costly and challenging to produce. Finally, the third section investigates the relationship between measured capacitance, and carbon macrostructure, meso-structure, microstructure, and oxygen content. In each of these studies, the desired parameter was varied, while all others (surface area, pore size, chemistry) were maintained constant. Through this systematic approach, this thesis investigates and quantifies the relationship between EDLC performance and important characteristic parameters through isolation of each individual parameter. By understanding the key structural and chemical features that improve EDLC performance, focus can be placed on engineering a sustainable and economic porous carbon material that has these desired features.

Keywords: Electrical Doube Layer
Energy Storage
Oil Sands Petroleum Coke
Pore Structure
Porous Carbon
Supercapacitors
Advisor: Jia, Charles Q
Kirk, Donald W
A FRAMEWORK FOR MULTI-PLATFORM ANALYTICAL AND EXPERIMENTAL SIMULATIONS OF REINFORCED CONCRETE STRUCTURES

This study presents a framework for multi-platform analysis and hybrid (experimental-analytical) simulation of reinforced concrete structures. In this approach, each potentially critical member, based on its mechanical characteristics, is modelled using the most suitable finite element analysis tool or is represented with a test specimen, while the rest of the structure is modelled with computationally fast global analysis software. The interaction between substructure modules is fully considered by satisfying compatibility and equilibrium requirements. The framework is based on object-oriented methodology and uses a standardized data exchange format, facilitating addition of new analysis tools or test equipment. The effectiveness of the framework is evaluated by several verification examples including analysis of structures repaired with fibre-reinforced polymer sheets. The multi-platform analysis computes the behaviour of structures with a level of accuracy that was previously difficult to achieve with most single-platform analysis software. In addition, a new interface element, named F2M, is introduced to connect layered beam elements to membrane elements. Compared to existing methods, the F2M element provides more realistic stress distributions and allows for transverse expansion at the connection section between substructures. The accuracy of the proposed element is verified through mixed-dimensional modelling of a series of beam specimens presented in the literature. A small-scale experimental program was conducted using a six degree-of-freedom hydraulic testing equipment to verify the hybrid simulation framework and provide additional data for small-scale testing of shear-critical reinforced concrete frames. The physical models were 1/3.23-scale representations of a beam and two columns. A multi-platform modelling technique was employed to analyze the remainder of the frames. The hybrid simulation results were compared against those obtained from a similar large-scale test and finite element analyses. The study found that, with proper precautions, small-scale hybrid testing can sufficiently well simulate the behaviour of shear-critical frames. However, to draw general conclusions, additional test data are required.

Keywords: Beam-Column Joints
Hybrid Simulation
Multi-Platform Nonlinear Analysis
Reinforced Concrete
Repaired Structures
Shear Behavior
Advisor: Vecchio, Frank
Kwon, Oh-Sung
Snap, Twang, and Blue Note: A Cross-Cultural Examination of Features that Accompany Temporal Deviations in African-American Musics

The present study establishes meaning and linkage among a cluster of specific structural features —the snap, twang, and blue note— and between this cluster and the temporal deviations they can be found accompanying. These features are explored through their perceived sonic, textual, and motional properties, as they have emerged across cultures and historical periods, with distinct ethos. Consideration is taken for the ethnic, social, and spiritual meanings invoked by each feature, their interrelationships as a cluster, and with temporal deviation. Interrelationships include: snap and temporal deviations both emerging from polytempic interactions, yet contrasting in their respective grounded and floating qualities; snap and twang each articulating (i.e.: ‘worrying’) flexible blue note pitch regions; and twang and blue note’s respective articulations of vocal harmonics. I propose an isomorphic continuum may explain the ratios of temporal deviations identified in a number of African-American musics, suggesting deep interrelationships among snap, twang, blue note, and temporal deviations. If the blue note and certain temporal deviations are isomorphic, we can also learn about temporal deviation by studying the ethos of the blue note: I compare the ‘blue third’ with the diatonic minor third. The relationships between these features and temporal deviations suggest they function as co-expressions of, or redundant cues for, the performer’s awareness and commitment. I interpret the consistency of heightened arousal invoked by these features, as embodied understanding across cultural contexts. When embodied, the cue is perceived directly: for example, commitment and intensity is experienced, not merely represented, in the snap. Such cross-cultural consistency of meaning does not preclude the possibility that the features function as code-switching cues to mark transformative moments in music, since consistency of meaning doesn’t indicate consistency of ideology. Connecting the features to their subdivided variations opens the door to understanding the relevance and applicability of this study’s findings across an even wider breadth of musical practices. The spontaneous participant —artist, witness, researcher— kinesthetically channelling the creative spirit, stands to gain appreciation for the compatibility and complexity of different gestures, their consonances and dissonances, across disciplines and traditions.

Keywords: BeyoncĂŠ Knowles
John Coltrane
Judaic Studies
Kendrick Lamar
Linguistics
Western Music
Advisor: Hatzis, Christos
TARGETING THE MITOCHONDRIAL DNA POLYMERASE GAMMA IN ACUTE MYELOID LEUKEMIA

Part I Mitochondrial DNA (mtDNA) biosynthesis requires replication factors and adequate nucleotide pools from the mitochondria and cytoplasm. We performed gene expression profiling analysis of 542 human AML samples and identified 55% with upregulated mtDNA biosynthesis pathway expression compared to normal hematopoietic cells. Genes that support mitochondrial nucleotide pools, including mitochondrial nucleotide transporters and a subset of cytoplasmic nucleoside kinases, were also increased in AML compared to normal hematopoietic samples. Knockdown of cytoplasmic nucleoside kinases reduced mtDNA levels in AML cells, demonstrating their contribution in maintaining mtDNA. To assess cytoplasmic nucleoside kinase pathway activity, we employed a nucleoside analog 2’3’-dideoxycytidine (ddC), which is phosphorylated to the activated anti-metabolite, 2’3’-dideoxycytidine triphosphate (ddCTP) by cytoplasmic nucleoside kinases. ddC is a selective inhibitor of the mitochondrial DNA polymerase, POLG. ddC was preferentially activated in AML cells compared to normal hematopoietic progenitor cells. ddC treatment inhibited mtDNA replication, oxidative phosphorylation, and induced cytotoxicity in a panel of AML cell lines. Furthermore, ddC preferentially inhibited mtDNA replication in a subset of primary human leukemia cells and selectively targeted leukemia cells while sparing normal progenitors cells. In animal models of human AML, treatment with ddC decreased mtDNA, electron transport chain proteins, and induced tumor regression without toxicity. ddC also targeted leukemic stem cells in secondary AML xenotransplantation assays. Thus, AML cells have increased cytidine nucleoside kinase activity that regulates mtDNA biogenesis and can be leveraged to selectively target oxidative phosphorylation in AML. Part II Human mitochondrial DNA is replicated by the mitochondrial DNA polymerase gamma. Using proximity dependent biotin labelling (BioID), we characterized the POLG interactome and identified new interaction partners involved in mtDNA maintenance, transcription, translation and protein quality control. We also identified interaction with the nuclear AAA+ ATPase Ruvbl2, suggesting mitochondrial localization for this protein. Ruvbl2 was detected in mitochondria-enriched fractions in leukemic cells. Additionally, transgenic overexpression of Ruvbl2 from an alternative translation initiation site resulted in mitochondrial co-localization. Overall, POLG interactome mapping identifies novel proteins which support mitochondrial biogenesis and a potential novel mitochondrial isoform of Ruvbl2.

Keywords: AML
mitochondria
mtDNA
nucleoside kinase
nucleotide salvage
POLG
Advisor: Schimmer, Aaron D.
Medium-Strength Modality in Science

Alethic modality is typically understood in terms of necessity, truth in all possible cases, and possibility, truth in at least one possible case. But a great deal of our scientific knowledge falls in between necessity and contingency. We build models which apply to many, but by no means all, possible cases under consideration. Further, alethic modal (henceforth just â modalâ ) claims have typically been understood as applying to very broad domains, like conceptual, logical, or physical necessity. But many more local domains could likewise be considered modal. This thesis is a contribution towards characterizing this middle ground of medium-strength modality, which is graded and local. To show that such domain-relative and graded modality can be given a precise formulation, I develop a measure theoretic model of generality. This is meant mainly as a possibility proof, that we can at least sometimes make graded and domain-relative modal talk formally precise. Using this formal model as a backdrop, I argue that generality and contingency should be understood as modal concepts. Something is general to the extent that it applies to a large measure of a domain of possibilities, and contingent to the extent that it applies to a small measure. Chapter 3 ties this notion of generality to explanatory depth. This way of understanding modality also helps to clarify the relationship between laws and models (chapter 4). Laws, I claim, define domains of possibilities by drawing their limits. Since generality and contingency are best understood as domain-relative concepts, laws set the standard for what counts as general or contingent in a given context. Models operate to fill in the structure and content of domains of possibilities. Finally, medium-strength modal concepts help to clarify the difference between mechanistic and self-organized systems, which corresponds to the traditional distinction drawn between merely resultant and emergent properties. I argue that a system is mechanistic if its system-level regularities are the result of parts-level regularities (general features of its parts). Conversely, a system is self-organized if it displays system-level regularities, despite the contingent behavior of its parts. This analysis shows how we can be non-reductive physicalists.

Keywords: Contingency
Explanation
Generality
Modality
Models
Science
Advisor: Walsh, Denis M
Efficient Erasure Coding in Distributed Storage Systems

Distributed storage systems store a substantial amount of data on many commodity servers. As servers failures are common, it is critical for distributed storage systems to store redundancy to tolerate such failures. Conventionally, a distributed storage system replicates data as the redundancy. Recently, erasure coding has been increasingly replacing replication thanks to its lower storage overhead. However, in many scenarios, erasure coding incurs additional overhead, such as higher network traffic, or lowers the performance of data accesses. In this dissertation, we address some of such challenges in two broad areas. Erasure coding with the optimal network overhead. Traditional erasure codes incur high network overhead when data needs to be reconstructed after a server failure. We study the problem of constructing erasure codes that consume the optimal network traffic to reconstruct data from multiple failures. We start from a new construction of minimum-storage cooperative regenerating (MSCR) codes that reconstruct data from two failures with the optimal network traffic. We show that an existing minimum-storage regenerating (MSR) code is also an MSCR code for two failures, and vice versa. For more general cases, we propose Beehive codes that optimize the volume of network traffic to reconstruct data from more than two failures, with storage overhead only slightly higher than optimum. I/O efficient erasure coding and systems. Traditionally erasure coding incurs higher I/O overhead because of its encoding and decoding operations. In this dissertation, we propose solutions to minimize the overhead of writing and reading erasure-coded data. On the input side, we design and implement Mist, a new mechanism for disseminating erasure-coded data efficiently to multiple receiving servers in data centers. On the output side, we exploit the demand skewness in distributed storage systems and propose Zebra, a framework that encodes data into multiple tiers dynamically by their demand to reduce the overall overhead to read erasure-coded data. We also investigate the data parallelism of erasure coding, which may affect the performance of running parallel data processing jobs on the erasure-coded data, such as MapReduce, and construct Carousel codes that allow data parallelism to be expanded into an arbitrary number.

Keywords: distributed storage system
erasure coding
HDFS
local reconstruction code
MapReduce
regenerating codes
Advisor: Li, Baochun
Analysis of Ecological Communities Using Mixture Models

In this dissertation we develop methodology to analyse the structure of ecological communities. Distributions of species within and between communities are characterized by highly skewed and heavy tailed distributions which often causes sparsity in an observed sample. We develop methodologies to account for these factors, focusing on three problems of interest. The first is estimating total species in a community. This quantity is an important measure of community health and is often used to assess sample quality, but due to sparsity when sampling rare species it is not readily determined. Two approaches are proposed, the first models the underlying rate distribution with a mixture distribution and estimates the expected number of zeros when mixed with a Poisson. The mixture distribution is estimated by minimizing a least squares objective function of observed and expected counts or by sampling a Multinomial-Dirichlet mixture. The second approach estimates total species by modelling the detection rate of new species with a parametric function. Methods of model selection and estimates of variance are presented for both approaches. For the second problem, we look at modelling the distribution of a species across multiple sites. Firstly, we differentiate structural zeros from sparse sampling zeros, an important distinction when modelling the underlying rates or fitting a presence-absence model. We also model the outcome as a mixture distribution to stratify the data, as observations from the low rates and heavy tail cannot be analysed on the same scale. The model is estimated using either the least squares or Multinomial-Dirichlet approach, adjusted for varying numbers of observations between sites. A modification of the expectation-maximization algorithm is also proposed to optimize the fit. For the third part, we focus on identifying factors that significantly affect community composition. We use the mixture distribution approach to estimate site specific distributions, then compute pairwise distances between sites to obtain the test statistic for a permutation test. Each method is tested via simulation, compared against current methods and illustrated with an applied example. The methods are motivated by analysis of microbiome data, but are designed to be generally applicable.

Keywords: microbiome
mixture models
sparsity
species distributions
statistical ecology
total species
Advisor: Escobar, Michael
Xu, Wei
Enacting a pedagogy of multiliteracies: A study of six literacy teacher educators

This study examined the knowledge, dispositions, beliefs, experiences, and educational practices of six literacy teacher educators, from three countries, who enacted a multiliteracies approach to teaching. In this qualitative study three semi-structured interviews were conducted of each participant over a three year period. Four significant findings emerged. First, these literacy teacher educators held a broad, holistic, and evolving conceptualization of literacy that was not limited to a notion of literacy as a set of autonomous skills (e.g., reading and writing). This conceptualization included a range of multimodal communications: print-based literacies, arts-based experiences, and digital practices. Second, all of the literacy teacher educators designed coherent courses that were driven by a single overarching purpose (e.g., developing a broad and inclusive understanding of literacy and literacy practices). The overarching purpose was realized through17 specific goals and purposeful assignments. Third, all of the literacy teacher educators were challenged by government restrictions, particularly the participants from England and Australia. The final finding revealed these literacy teacher educators held a unique set of dispositional qualities: a positive and progressive attitude, persistence, and passion; and their attitudes, skills, and knowledge were developed over time and with assistance. Implications for literacy teacher educators include the need for incorporating multimodal forms of expression and communication; addressing issues of social justice; remaining connected to the local community and the practicum aspect of the program; and, creating coherent courses. Implications for preservice teacher education programs include universities creating opportunities for professional development for teacher educators particularly in multiliteracies practices and providing mentors; developing hiring practices that include a multiliteracies interest; and, developing support against deleterious teacher education reforms.

Keywords: Literacy
Literacy teacher educators
Multiliteracies
Teacher education
Advisor: Kosnik, Clare