VictorJuiz/thesis huggingface dataset:
Contrast-enhanced Doppler Ultrasound Imaging using Plane Waves
Keywords: Doppler
Microbubble
Perfusion imaging
Plane-wave ultrasound
Vascular morphology

There is a clear advantage in having an imaging method that would be capable of displaying perfusion and vascular imaging simultaneously. In ultrasound, Doppler can visualize veins and arteries, but cannot detect the capillary level perfusion. Conversely, microbubble contrast-enhanced ultrasound imaging enables low velocity perfusion to be detected and separated from the tissue echo, but has a limited ability to depict the vascular morphology within the perfused tissue. To date, it has been challenging to combine these two methods due to realistic imaging time constraints severely limiting the number of pulses available for Doppler estimates. However, recent breakthroughs in plane-wave synthetic ultrasound considerably increased the maximal imaging frame rate, enabling new imaging trade-off previously unavailable. In this thesis, we first implement pulse inversion Doppler using plane-wave ultrasound and demonstrate the ability of the technique in segmenting fast from slow blood flow, which has applications, for example, in the detection, diagnosis and assessment of anti-angiogenic treatment of focal lesions. As the ability to differentiate perfusion from the tissue signal is limited by the contrast-to-tissue ratio achieved by the contrast-enhanced pulsing sequence, independently of the Doppler ensemble length, we develop a new Doppler sequence based on amplitude modulation (AM) which improves bubble detection specificity compared to conventional Pulse Inversion Doppler. We also demonstrate that modifying the pressure of the acoustic pulse (e.g. AM) introduces a characteristic phase delay in the microbubble echo, with no equivalent in tissue. A novel microbubble imaging scheme taking advantage of this behaviour is shown to further improve the contrast-to-tissue ratio. Lastly, while it is known that long Doppler acquisitions enable accurate velocity estimation in blood (hematocytes), microbubbles are only quasi-stable during repeated ultrasound exposure. Short acoustic pulses are helpful in mitigating microbubble destruction, but concurrently introduce a classical error associated to uncertainty limit of waves. Existing contrast agents are also polydispersed in their physical properties, which adds another degree of statistical randomness in the received echoes. In this work, we assess how these factors affect our ability to measure the velocity of flowing microbubbles.
The Vibrochord: Investigating a Virboractile Musical Instrument
Keywords: cross modal
human factors
music
tactile
vibrochord
vibrotactile

A novel device called the Vibrochord is proposed and validated for its use in the composition and production of vibrotactile music. Vibrotactile music is patterns of vibration applied to the skin rather than the ear. In the first of four studies, four audio music composers were recruited to offer suggestions for the design of the Vibrochord and to probe their composition style and process. Several design ideas that will be implemented in future versions of the Vibrochord were elicited. Attitudes about the Vibrochord and vibrotactile music seemed cautiously optimistic. In the second study participants were recruited to compare various aspects of the Vibrochord to the traditional piano keyboard. It seems that for playing short vibrotactile phrases the design of the Vibrochord allowed for an increase in player accuracy. In the third study, three artists composed a happy and sad vibrotactile song using the Vibrochord and Emoti-Chair. All composers were able to complete this task suggesting the Vibrochord is a viable tool for the composition and production of vibrotactile music. It seems that each artist thought similarly about what characteristics of vibrotactile music would convey the desired emotions. In the fourth study an audience rated the emotional content of the vibrotactile songs composed and produced in study three. All artists were successful in composing and producing vibrotactile music that conveyed the basic emotions of either happy or sad. It seems that notes per second, jumps per second, lengths per second, average note length and lengths per jump are primarily responsible for the conveyance of emotion. The fifth study had audiences rating the emotional content of short vibrotactile clips created using the fourth study as a guide. Notes per second, or "tempo", most likely plays a role in the conveyance of basic emotion. Note frequency also plays a role in this conveyance. Faster tempo songs with higher frequency notes were interpreted as conveying more happiness and vice versa. A regression model showing the relationship between emotional rating of a vibrotactile song and the songs notes per second and average note frequency is proposed.
Languages, Cultures and Identities of Newcomer Adolescent Learners: Deconstructing Multicultural Education in South Korea
Keywords: Critical Discourse Analysis
Diversity
Linguistic and Cultural Identity
Newcomer Youth
Policy and News Media Analysis
South Korea

Despite the South Korean government’s recent policy interventions to accommodate the emerging social and classroom reality that has increasingly become multicultural, few guidelines have been provided for multicultural education practice at the local and municipal levels in South Korea (Henceforth, Korea). In particular, investigations focusing on newcomer adolescents’ linguistic and cultural identities are scarce. In this light, this doctoral inquiry investigates how multicultural students, their languages and cultures are reflected in Korean society and schools and especially, how newcomer adolescents’ linguistic and cultural identities are negotiated in terms of their own success in Korea. 8 multicultural education policies and 27 news media publications as well as the narratives of 7 students and 6 educators from two high schools are analyzed through Fairclough’s (1992, 2003) critical discourse analysis. Based on the analysis, the discourses of diversity embedded in the nation-state texts and popular media as well as in the institutional contexts are discussed in relation to five orientations to diversity, which are derived from Ruiz’s (1984) theoretical framework of three orientations to language planning and Cummins’(2001) empowerment framework. The study reveals that an ideology of Korean ethnocentrism is reflected throughout the policy and news media articles as well as school administrators’ conceptualizations of diversity and multicultural education. Despite the emergent progressive orientations of viewing diversity as a right and resource, the predominant discourses of viewing diversity are that diversity is a problem/threat to society and is a problem/impediment to multicultural students’ social integration. It is evident that diversity is only appreciated once multicultural students are fully assimilated into Korean society. Thus, the notion of multicultural identity is absent or at best hidden in the Korean context. The study highlights that schools and policy makers need to make a shift in their orientations to diversity toward diversity as a right, resource and a form of empowerment through critical multicultural education in order to instill just and equitable worldviews in students. Educators’ negligence in considering these possibilities contributes to reproducing unequal power relations that disadvantage linguistic and cultural minorities and perpetuate the hegemonic status quo in Korean society.
Contrastive Representations in Non-segmental Phonology
Keywords: contrast
length
phonology
prosody
stress
tone

This thesis develops and tests a unified model of word-level prosodic contrasts. Traditionally, word prosody has been analyzed within disparate models (such as autosegmental theory for tone, metrical theory for stress, and CV, X-slot, or moraic theory for length), meaning that it has not been possible to make clear predictions about how many different prosodic features can be employed in a single language. I present a minimal architecture for word prosodic representations based on a single set of formal elements. A tier of segmental root nodes, or X-slots, bears the binary contrastive features that divide the segmental inventory and represents quantity contrasts through two-to-one linking, while a tier of prosodic root nodes, or "pi-nodes", bears the binary features dividing the autosegmental inventory. Features on pi-nodes are used in tone languages with more than one tonal autosegment, but in privative tone languages, the pi-node itself reflects the phonetic realization of the marked member of the tone opposition. The same featureless pi-node is used as an autosegmental marker of accented positions in lexical stress systems, where its language-specific phonetic realization is that of stress: some combination of increased pitch, duration, and intensity. The predictive power of this model is that it restricts systems to a maximum of two independent word prosodic contrasts, since each requires its own tier of root nodes. The pi-tier can represent either tone or accent separately from length on the X-tier, but this leaves no means to represent a third contrast. In certain systems, surface stress may be represented covertly as length on the X-tier with tone represented on the pi-tier, but no mechanism is available to host a third contrast, since the X-tier is already used for stress.
Controlled Delivery of Therapeutic Proteins to the Injured Spinal Cord
Keywords: drug delivery
hydrogel
nanoparticle
PLGA
protein
spinal cord injury

Spinal cord injury (SCI) results in severe disability and currently lacks effective clinical treatments. Pre-clinical and clinical research have demonstrated the potential for both cell and protein therapeutic strategies; however, a critical challenge is the lack of localized, sustained delivery of bioactive therapeutics. A composite drug delivery system (DDS) consisting of poly(lactic-co-glycolic acid) (PLGA) nanoparticles (np) dispersed in a hyaluronan/methyl cellulose (HAMC) hydrogel was previously found to provide sustained protein release in vitro and compatibility in vivo. This np/hydrogel DDS was further developed for the localized, sustained, and bioactive delivery of platelet-derived growth factor-AA (PDGF-AA), neurotrophin-3 (NT-3), and anti-NogoA. The release of PDGF-AA was sustained over 21 d and the PDGF-AA DDS induced the oligodendrocyte differentiation of neural stem/progenitor cells in vitro. The release of PDGF-AA was affected by the excipient poly(ethylene glycol) (PEG400), which had variable effects on protein stability. The delivery of NT-3 was sustained for up to 49 d in vitro and at least 28 d in vivo, and the NT-3 DDS induced axon growth and modest recovery of function in a model of compressive SCI. Surprisingly, electrostatic interactions occurred between soluble NT-3 and the DDS that delayed release. This discovery led to the development of an encapsulation-free np/hydrogel DDS that provides sustained, tunable release of NT-3 as well as stromal cell-derived factor (SDF) and brain-derived neurotrophic factor (BDNF) and is applicable to many other proteins. Finally, the np/hydrogel DDS was adapted for the combined, bioactive delivery of NT-3 and anti-NogoA. Combined delivery of NT-3 and anti-NogoA increased axon density, reduced the inhibitory environment, and promoted functional recovery after delivery to the injured spinal cord. This work demonstrates that the np/hydrogel DDS is effective for the delivery of growth/differentiation factors as well as therapeutic proteins for the treatment of spinal cord injury.
MCMC Methods for Non-linear State Space Models
Keywords: MCMC

This thesis is concerned with developing efficient MCMC (Markov Chain Monte Carlo) techniques for non-linear, non-Gaussian state space models. These models are widely applicable in many fields, such as population ecology and economics. However, Bayesian inference in such models remains challenging, since sampling the latent variables and parameters in them can be difficult. We begin by showing how an efficient MCMC method can be developed for a queueing model, inference for which has previously been done with ABC (Approximate Bayesian Computation). This example is an illustration of how we can do inference with MCMC in a model in which inference is considered difficult and for which ABC was used. We do this by expanding the state to include variables involved in the process used to generate the observed data. We then proceed to the main contributions of the thesis, which are developing general MCMC methods for non-linear, non-Gaussian state space models based on the ensemble MCMC and embedded HMM MCMC frameworks. The embedded HMM and ensemble MCMC methods we introduce provide a unified framework that is sufficiently flexible to often address difficult issues in MCMC sampling for non-linear, non-Gaussian state space models, without having to resort to specialized methods for different cases. We start with the basic embedded HMM method of Neal (2003), and Neal, Beal and Roweis (2004), designed for sampling latent state sequences given known parameter values, and develop an efficient ensemble MCMC method for sampling parameters when the parameters and the latent sequence are strongly dependent. This method is tested on a non-linear model of population dynamics. We then show how ensembles can be used to make parameter sampling more efficient in a stochastic volatility model by making use of a caching technique (Neal (2006)). Finally, we develop an ensemble MCMC method for sampling sequences in non-linear, non-Gaussian state space models when the state space is high-dimensional and test it on two sample models with high-dimensional state spaces, one of which is multimodal, and compare the performance of this method to a particle MCMC method.
Solvation and Conformational Stability of Proteins and DNA
Keywords: Calorimetry (DSC and PPC)
DNA G-Quadruplex
Folded and Unfolded Protein States
Glycine Betaine
Urea
Volume and Compressibility

The work performed in this dissertation is devoted to understanding and quantifying solute-solvent interactions in the folded and unfolded states of proteins and DNA G-quadruplexes using volumetric techniques. We characterized the interactions of the protein stabilizer, glycine betaine (GB), with proteins and their functional groups through a combination of partial molar volume and adiabatic compressibility measurements of N-acetyl amino acid amides, oligoglycines, cytochrome c, ribonuclease A, lysozyme, and ovalbumin at GB concentrations ranging from 0 to 4 M. We evaluated the equilibrium (binding) constant, k, for the reaction in which a GB molecule binds each of the functionalities under study replacing four water molecules. We found that GB forms direct interactions with all protein groups studied here. In addition, the differential free energy of solute-solvent interactions in a concentrated GB solution and water, ΔΔGI, is negative for all the proteins studied and ΔΔGI becomes more favourable as the concentration of GB increases. We also employed volumetric measurements of lysozyme, apocytochrome c, ribonuclease A, and α-chymotrypsinogen A in the solutions at 0 to 8 M urea to quantify the urea-induced solvation changes in the native and unfolded states of proteins. An increase in the concentration of urea to 8 M leads to a ~20% increase in the solvent accessible surface area of apocytochrome c. The urea-induced unfolding of ribonuclease A and α-chymotrypsinogen A is accompanied by increases in solvent accessible surface area of 1.9 ± 0.4 and 2.0 ± 0.6 times that of the native states, respectively. Furthermore, we characterized the volumetric properties of the folded and unfolded states of the Na+-stabilized antiparallel G-quadruplex conformation of Tel22, d[A(GGGTTA)3GGG], and the K+-stabilized hybrid-1 conformation of Tel26, d[AAAGGG(TTAGGG)3AA]. The coil-to-G-quadruplex transition of Tel26 accompanies a release of 434 ± 19 water molecules from its hydration shell to the bulk, which is more than four times the number of waters released compared to Tel22 (103 ± 44). We proposed that this extensive DNA dehydration originates from both the waters in direct contact with the domains that become buried in G-quadruplex formation and a general decrease in solute-solvent interactions all over the surface of the folded structure.
Assisting Converter Based Topologies for Low-volume High-efficiency Battery Management Systems
Keywords: Battery management architectures
Battery management systems
Cells balancing
Dc-dc converters
Dual active bridge converter
Flyback converter

Conventional battery management systems (BMSs) for applications that require voltage stepping-up, such as automotive and portable systems, usually consist of a battery pack, a battery charger, and a step-up dc-dc converter. In those applications, a balancing circuit which compensates for different states of charge (SOC) of individual cells is a highly desirable feature. The SOC difference occurs due to aging and differences in the manufacturing process. Through cell balancing the effective capacity and lifetime of the battery pack can be significantly increased. Even though the benefits of cell balancing circuits have been recognized, their use is relatively sparse in the targeted applications, due to overly large extra cost, weight, and volume they add to the system. In this work, a novel battery management architecture (BMA) that integrates voltage stepping-up and cells balancing functionalities in a single converter topology is introduced, offering a solution for a cost-effective implementation of the balancing feature. Moreover, the new architecture has a smaller overall size and better power processing efficiency than the conventional solutions not incorporating the balancing feature. In the new BMA, named the assisting converter architecture, the output of the converter is placed on top of the battery pack and is therefore processing only a portion of the output power. Two assisting converters utilizing the new BMA are introduced in this dissertation namely, the assisting dual active bridge (DAB) converter and the assisting flyback converter. The assisting DAB converter represents the battery power management system for automotive applications and the assisting flyback converter is designed for portable electronics applications.
Prevalence of and Risk Factors for Anxiety, Depression, and Post-traumatic Stress in Substitute Decision-makers of Patients in the Intensive Care Unit
Keywords: Anxiety
Critical care
Decision-makers
Depression
Intensive care unit
Post-traumatic stress

Background: Most intensive care units (ICU) patients are incapable of participating in decision-making. Substitute decision-makers (SDMs) generally assume decision-making responsibility yet may vary in preferred level of involvement. Role incongruence refers to discordance between preferred and actual role in decision-making. Role preferences and incongruence may be associated with psychological symptoms (anxiety, depression, and post-traumatic stress) after ICU. Purpose: The primary objective was to explore prevalence and risk factors for symptoms of psychological distress in SDMs after an ICU experience. Methods: Cross-sectional, multi-centre, interviewer-administered survey of SDMs of critically ill adults requiring mechanical ventilation (MV) for greater than 48 hours. Psychological distress was defined as any symptoms of anxiety, depression, or post-traumatic stress using pre-defined cut-points on the Hospital Anxiety and Depression Scale (HADS) and the Impact of Events Scale (IES). The Control Preferences Scale (CPS) was used to evaluate decision-making role preferences and incongruence. Results: 180 SDMs were recruited; response rate was 64%. Active, shared, or passive roles were preferred by 24% (n=43), 44% (n=79), and 31% (n=56) respectively. Almost half (n=85/174; 49%) reported incongruence. Using high thresholds, symptom prevalence was 50% (n=88/176), 32% (n=57/177), and 16% (n=29/177), for post-traumatic stress, anxiety, and depression respectively. The composite outcome of any psychological distress symptom was associated with patient death [OR 2.95 (CI 1.08-8.02); p=0.03], female sex of the SDM [OR 2.96 (95% CI 1.49-5.89); p = 0.002], and role incongruence [OR 3.26 (95% CI 1.67-6.36); p = 0.0005] when high thresholds were considered. High threshold depressive symptoms were associated with spousal relationships [OR 3.01; 95% CI 2.93-3.09; p=0.01] and high threshold post-traumatic stress symptoms were associated with spousal relationships [OR 2.29 (95% CI 1.18-3.26); p=0.01], female sex [OR 2.56 (95% CI 1.28-5.12); p=0.008], role incongruence [OR 2.57 (95% CI 1.33-4.97); p=0.005], and patient death [OR 3.36 (95% CI 1.27-8.86); p=0.01]. Conclusions: High rates of adverse psychological symptoms in this study highlight the need to identify and implement preventative and management strategies for SDMs. Strategies to prepare proxies to engage in decision-making, to enhance shared decision-making, and to mitigate psychological distress symptoms, should be considered before, during, and after the ICU experience.
Studies of Mitochondrial Dysfunction in Models of Rett Syndrome
Keywords: Antioxidants
MeCP2
Mitochondrial cocktail
Mitochondrial dysfunction
Oxidative stress
Rett syndrome

Rett syndrome (RTT) is a neurodevelopmental disorder affecting primarily females that is predominantly caused by mutations in the MECP2 gene. RTT is characterized by a loss of previously acquired skills, ambulatory deficits, respiratory problems and overall retarded growth. Mitochondrial dysfunction and oxidative stress identified in MeCP2-deficient tissues raised the possibility that mitochondrial impairments may play role in the pathogenesis of RTT. To further investigate the role of mitochondrial dysfunction in the absence of MeCP2, I analyzed mitochondrial function and morphology in Mecp2-deficient mouse adult skin fibroblasts (ASF) and in Mecp2-null mouse ESC derived neurons using an array of fluorescent dyes coupled with flow cytometry and confocal microscopy. The heterogeneity of cellular responses in ASF prevented identification of consistent changes in mitochondrial function, making them an unsuitable model for studying mitochondrial dysfunctions. Mecp2-null mouse ESC were differentiated into enriched population of neurons. Mecp2-null neurons displayed hyperpolarized mitochondria, high levels of ROS, low ATP and impaired mitochondrial trafficking. Resveratrol and mitochondrial cocktail that target expression of mitochondrial genes and mitochondrial metabolism, but not simple ROS scavengers, were successful at ameliorating ROS levels and normalizing mitochondrial membrane potential. Since oxidative stress was reported in RTT mice, I tested whether resveratrol and mitochondrial cocktail could reverse or improve behavioral phenotype in RTT mice. Mitochondrial cocktail but not resveratrol improved exploratory, locomotor and social behavior deficits in RTT mice. Taken together these results suggest that both mitochondrial deficits and oxidative stress are not only the consequences of dysfunctional MeCP2, but are likely the causes of the RTT phenotype. Further, I determined that over-expression of mitochondrial Sirt3, known for its multifaceted effects on mitochondrial metabolism, is sufficient to protect neurons form various cytotoxic insults including oxidative stress. Overall, this study paves the way for potential new therapeutic strategies aimed at improving quality of life in RTT patients.