VictorJuiz/thesis huggingface dataset:
Design and Practical Implementation of Digital Auto-tuning and Fast-response Controllers for Low-power Switch-mode Power Supplies

In switched-mode power supplies (SMPS), a Controller is required for output voltage or current regulation. In low-power SMPS, processing power from a fraction of watt to several hundred watts, digital implementations of the controller, i.e. digital controllers have recently emerged as alternatives to the predominately used analog systems. This is mostly due to the better design portability, power management capability, and the potential for implementing advanced control techniques, which are not easy to realize with analog hardware. However, the existing digital implementations are barely functional replicas of analog designs, having comparable dynamic performance if not poorer. Due to stringent constraints on hardware requirements, the digital systems have not been able to demonstrate some of their most attractive features, such as parameter estimation, controller auto-tuning, and nonlinear time-optimal control for improved transient response. This thesis presents two novel digital controllers and systems. The first is an auto-tuning controller that can be implemented with simple hardware and is suitable for IC integration. The controller estimates power stage parameters, such as output capacitance, load resistance, corner frequency and damping factor by examining the amplitude and frequency of intentionally introduced limit cycle oscillations. Accordingly, a digital PID compensator is automatically redesigned and the power stage is adapted to provide good dynamic response and high power processing efficiency. Compared to state of the art analog solutions, the controller has similar bandwidth and improves overall efficiency. To break the control bandwidth limitation associated with the sampling effects of PWM controllers, the second part of the thesis develops a nonlinear dual-mode controller. In steady state, the controller behaves as a conventional PWM controller, and during transients it utilizes a continuous-time digital signal processor (CT-DSP) to achieve time-optimal response. The processor performs a capacitor charge balance based algorithm to achieve voltage recovery through a single on-off sequence of the power switches. Load transient response with minimal achievable voltage deviation and a recovery time approaching physical limitations of a given power stage is obtained experimentally.

Keywords: digital control
SMPS
Advisor: Prodic, Aleksandar
Understanding Defloccation of Activated Sludge Under Transients of Short-term Low Dissolved Oxygen

Deflocculation is a common upset event in biological wastewater treatment plants and causes significant problems in biosolids discharge and environmental management. However, fundamental understanding of deflocculation is limited. The overall objective of this work was to explore the fundamentals for deflocculation under transients of short-term low dissolved oxygen (DO). The investigation was carried out in a sequence of batch and continuous experiments on activated sludge, followed by batch experiments on E. coli suspensions. Both batch and continuous experiments on activated sludge demonstrated deflocculation of bioflocs under the transients of low DO (< 0.5 mg/L). Under the short-term low DO (in hours), turbidity increased by 20 times in the batch system and by 1-2 times in the continuous system, concentrations of suspended solids increased by 1-2 times, number of small particles (< 12.5 mm) increased by 2 times, more soluble EPS (proteins and humic substances) were released into supernatant or treated effluents, the removal efficiency of organic compounds was reduced by 50-70%. A 40% of increase in bulk K+ but a 30% of decrease in bulk Ca2+ under the DO limitation were observed in the batch experiments. There were significant increases in bulk K+ and decreases in bulk Ca2+ in the continuous experiments. Reversible changes were observed within 24 hours once the DO stress was removed. Floc strength of the remaining bioflocs after deflocculation increased. Deflocculation under the short-term low DO was consistent with an erosion process. The addition of selected chemicals (i.e., Ca2+, tetraethylammonium chloride, glibenclamide, and valinomycin) did not prevent deflocculation under the short-term low DO. It is proposed that a DO stress causes an efflux of cellular K+ but an influx of extracellular Ca2+, resulting in a decreasing ratio of Ca2+/K+ in extracellular solution and thereby causing deflocculation. The E. coli tests supported that increasing bulk K+ under the DO limit was due to the release of cellular K+ and was a stress response to the DO limitation.

Keywords: deflocculation
activated sludge
low oxygen
transient
Advisor: Allen, D. Grant
YETI: a GraduallY Extensible Trace Interpreter

The implementation of new programming languages benefits from interpretation because it is simple, flexible and portable. The only downside is speed of execution, as there remains a large performance gap between even efficient interpreters and systems that include a just-in-time (JIT) compiler. Augmenting an interpreter with a JIT, however, is not a small task. Today, Java JITs are typically method-based. To compile whole methods, the JIT must re-implement much functionality already provided by the interpreter, leading to a ``big bang'' development effort before the JIT can be deployed. Adding a JIT to an interpreter would be easier if we could more gradually shift from dispatching virtual instructions bodies implemented for the interpreter to running instructions compiled into native code by the JIT. We show that virtual instructions implemented as lightweight callable routines can form the basis for a very efficient interpreter. Our new technique, interpreted traces, identifies hot paths, or traces, as a virtual program is interpreted. By exploiting the way traces predict branch destinations our technique markedly reduces branch mispredictions caused by dispatch. Interpreted traces are a high-performance technique, running about 25% faster than direct threading. We show that interpreted traces are a good starting point for a trace-based JIT. We extend our interpreter so traces may contain a mixture of compiled code for some virtual instructions and calls to virtual instruction bodies for others. By compiling about 50 integer and object virtual instructions to machine code we improve performance by about 30% over interpreted traces, running about twice as fast as the direct threaded system with which we started.

Keywords: dynamic optimization interpretation
branch prediction
Advisor: Brown, Angela Demke
Gene Association Studies of Schizophrenia and Tardive Dyskinesia

Schizophrenia (SCZ) is a severe neuropsychiatric disorder with a genetic component. Most candidate gene association studies have given mixed results. We investigated the GABAA receptor gamma2 subunit gene GABRG2, the dopamine receptor gene DRD3, and the Brain-derived neurotrophic factor gene BDNF that is required for D3 expression by genotyping polymorphisms spanning and surrounding these genes for association with SCZ, as well as suicidal behaviour. We also examined the BDNF, DRD3, as well as the dopamine receptor gene DRD2 and Protein Kinase B gene AKT1 for association with Tardive Dyskinesia (TD), a potentially irreversible motor side effect of long-term antipsychotic medication. Our analysis included single-marker tests, haplotype tests, and gene-gene interactions. We found a haplotype in the 5’ region of GABRG2 to be associated with SCZ in both families and matched case-control samples. We also found two synonymous DRD2 polymorphisms, rs6275 (C939T) and rs6277 (C957T), and their haplotypes, as well as a polymorphism 5’ of DRD3, rs905568, to be associated with TD. Further, we reviewed two putative functional DRD2 polymorphisms, -141C Ins/Del and TaqIA, in TD and found TaqIA 3’ of the gene to be associated with TD in a meta-analysis. Lastly, we found a significant interaction between AKT1 rs3730358 and DRD2 C939T in TD. Though replication studies are required, these results contribute to the future development of genetic tests to assess for the risks of SCZ and TD, leading to better outcome for patients suffering from these debilitating conditions.

Keywords: Schizophrenia Genetics
Pharmacogenetics
Tardive Dyskinesia
Dopamine
GABA
Advisor: Kennedy, James
Multivariate Bayesian Process Control

Multivariate control charts are valuable tools for multivariate statistical process control (MSPC) used to monitor industrial processes and to detect abnormal process behavior. It has been shown in the literature that Bayesian control charts are optimal tools to control the process compared with the non-Bayesian charts. To use any control chart, three control chart parameters must be specified, namely the sample size, the sampling interval and the control limit. Traditionally, control chart design is based on its statistical performance. Recently, industrial practitioners and academic researchers have increasingly recognized the cost benefits obtained by applying the economically designed control charts to quality control, equipment condition monitoring, and maintenance decision-making. The primary objective of this research is to design multivariate Bayesian control charts (MVBCH) both for quality control and conditional-based maintenance (CBM) applications. Although considerable research has been done to develop MSPC tools under the assumption that the observations are independent, little attention has been given to the development of MSPC tools for monitoring multivariate autocorrelated processes. In this research, we compare the performance of the squared predication error (SPE) chart using a vector autoregressive moving average with exogenous variables (VARMAX) model and a partial least squares (PLS) model for a multivariate autocorrelated process. The study shows that the use of SPE control charts based on the VARMAX model allows rapid detection of process disturbances while reducing false alarms. Next, the economic and economic-statistical design of a MVBCH for quality control considering the control limit policy proved to be optimal by Makis(2007) is developed. The computational results illustrate that the MVBCH performs considerably better than the MEWMA chart, especially for smaller mean shifts. Sensitivity analyses further explore the impact of the misspecified out-of-control mean on the actual average cost. Finally, design of a MVBCH for CBM applications is considered using the same control limit policy structure and including an observable failure state. Optimization models for the economic and economic statistical design of the MVBCH for a 3 state CBM model are developed and comparison results show that the MVBCH performs better than recently developed CBM Chi-square chart.

Keywords: multivariate process control
Bayesian control chart
Advisor: Makis, Viliam
Adaptive Image Quality Improvement with Bayesian Classification for In-line Monitoring

Development of an automated method for classifying digital images using a combination of image quality modification and Bayesian classification is the subject of this thesis. The specific example is classification of images obtained by monitoring molten plastic in an extruder. These images were to be classified into two groups: the “with particle” (WP) group which showed contaminant particles and the “without particle” (WO) group which did not. Previous work effected the classification using only an adaptive Bayesian model. This work combines adaptive image quality modification with the adaptive Bayesian model. The first objective was to develop an off-line automated method for determining how to modify each individual raw image to obtain the quality required for improved classification results. This was done in a very novel way by defining image quality in terms of probability using a Bayesian classification model. The Nelder Mead Simplex method was then used to optimize the quality. The result was a “Reference Image Database” which was used as a basis for accomplishing the second objective. The second objective was to develop an in-line method for modifying the quality of new images to improve classification over that which could be obtained previously. Case Based Reasoning used the Reference Image Database to locate reference images similar to each new image. The database supplied instructions on how to modify the new image to obtain a better quality image. Experimental verification of the method used a variety of images from the extruder monitor including images purposefully produced to be of wide diversity. Image quality modification was made adaptive by adding new images to the Reference Image Database. When combined with adaptive classification previously employed, error rates decreased from about 10% to less than 1% for most images. For one unusually difficult set of images that exhibited very low local contrast of particles in the image against their background it was necessary to split the Reference Image Database into two parts on the basis of a critical value for local contrast. The end result of this work is a very powerful, flexible and general method for improving classification of digital images that utilizes both image quality modification and classification modeling.

Keywords: adaptive image quality improvement
bayesian classification
in-line monitoring
case-based reasoning
automated image processing
0984
0800
Advisor: Balke, Stephen Thomas
Sayad, Saed
Role of the Cell Adhesion Molecule L1 during Early Neural Development in Zebrafish

The neural cell adhesion molecule L1 is a member of the immunoglobulin superfamily and it mediates many adhesive interactions during brain development. Mutations in the L1 gene are associated with a spectrum of X-linked neurological disorders known as CRASH or L1 syndrome. The objective of this thesis was to use the zebrafish model to investigate the molecular mechanisms of L1 functions and the pathological effects of its mutations. Zebrafish has two L1 homologs, L1.1 and L1.2. Inhibition of L1.1 expression by antisense morpholino oligonucleotides resulted in phenotypes that showed resemblances to L1 patients. However, knockdown of L1.2 expression did not result in notable neural defects. Furthermore, analysis of the expression pattern of L1.1 has led to the discovery of a novel soluble L1.1 isoform, L1.1s. L1.1s is an alternatively spliced form of L1.1, consisting of the first four Ig-like domains and thus a soluble secreted protein. L1.1 morphants exhibited disorganized brain structures with many having an enlarged fourth/hindbrain ventricle. Further characterization revealed aberrations in ventricular polarity, cell patterning and proliferation and helped differentiate the functions of L1.1 and L1.1s. While L1.1 plays a pivotal role in axonal outgrowth and guidance, L1.1s is crucial to brain ventricle formation. Significantly, L1.1s mRNA rescued many anomalies in the morphant brain, but not the trunk phenotypes. Receptor analysis confirmed that L1.1 undergoes heterophilic interactions with neuropilin-1a (Nrp1a). Peptide inhibition studies demonstrated further the involvement of L1.1s in neuroepithelial cell migration during ventricle formation. In the spinal cord, spinal primary motoneurons expressed exclusively the full-length L1.1, and abnormalities in axonal projections of morphants could be rescued only by L1.1 mRNA. Further studies showed that a novel interaction between the Ig3 domain of L1.1 and Unplugged, the zebrafish muscle specific kinase (MuSK), is crucial to motor axonal growth. Together, these results demonstrate that the different parts of L1.1 contribute to the diverse functions of L1.1 in neural development.

Keywords: zebrafish
neural development
cell adhesion molecule L1
brain ventricle formation
polarity
axonal pathfinding
Advisor: Siu, Chi-Hung
Novel PMOs: Studies in Periodic Mesoporous Organosilicas

The field of mesoporous materials has been expanding rapidly in recent years, and has come to include a wide variety of different types of materials from organic to inorganic, as well as hybrid materials that encompass both worlds. The following account explores one type of mesoporous materials, specifically those consisting of silica with an attached organic group that have come to be known as periodic mesoporous organosilicas (PMOs). Much of the work here involves incorporating new types of organic groups into a mesoporous framework for the purpose of adding a useful functionality, either chemical or physical, to the material. Firstly it is shown that a borazine moiety can be successfully incorporated into a mesoporous material with a very high loading. It was further shown that once incorporated into the material many of the borazine moieties are available for further chemical reactions with acids and transition metals. Next, a new class of materials termed hybrid periodic mesoporous organosilicas (HPMOs) was developed that was able to circumvent many of the problems associated with PMO self-assembly. Now, using very simple techniques, virtually any type of silsesquioxane can be incorporated into a PMO, and the organic group can be specifically at the surface of the pores, thereby maximizing its accessibility. And finally, a PMO is made that incorporates buckyballs, and it is shown that, given the right synthetic conditions, the buckyballs are homogeneously distributed throughout the material.

Keywords: mesoporous
silica
organosilica
PMO
Advisor: Ozin, Geoffrey Alan
Characterization of Shadoo and DPPX: Two Proteins of Potential Relevance to Prion Biology

Prion diseases are fatal neurodegenerative disorders of humans and animals. The prion hypothesis states that PrPSc, a misfolded conformational isoform of the cellular prion protein (PrPC), is the sole component of the infectious particle. Many open questions exist in prion biology including the cellular role of PrPC, the potential involvement of auxiliary factors in prion replication, and the mechanism of PrPSc-induced toxicity in prion disease. The identification of novel prion-like proteins and authentic in vivo prion protein-interacting proteins would certainly assist the process of demystifying these unsolved mysteries. Accordingly, two newly-identified proteins with potential relevance to prion protein biology, Shadoo and DPPX, were selected for biochemical and functional characterization. Shadoo, a hypothetical prion-like protein, is revealed as being a glycoprotein which possesses many overlapping properties with PrPC including neuronal expression, C1-like endoproteolytic processing, and the ability to protect against apoptotic stimuli in cerebellar neurons. Shadoo loosely resembles the disordered N-terminal domain of PrPC and consistent with this notion, Shadoo appears to lack a well-defined structure. Remarkably, Shadoo levels in the brains of mice with clinical prion disease are significantly decreased suggesting that Shadoo may be inherently linked to prion replication or prion disease pathogenesis. These experiments define Shadoo as the third member of the prion protein family and, because of its functional similarities to PrPC, Shadoo may be a useful tool for deciphering the in vivo function of PrPC. DPPX, a neuronal type II transmembrane protein, is demonstrated to be the first protein capable of interacting with all three members of the prion protein family (PrPC, Doppel, and Shadoo) in vivo. Complex formation between prion proteins and DPPX appears to be mediated by multiple binding sites. When coupled with high levels of DPPX expression in cerebellar granular neurons, DPPX is a strong candidate for mediating phenotypic interactions between prion proteins in cerebellar cells. Thus, Shadoo and DPPX comprise two new entry points for studying prion proteins. Further investigation of the roles of Shadoo and DPPX in both the cell biology of prion proteins and prion disease may yield important clues to these enigmatic topics.

Keywords: prion
biochemistry
neurodegenerative disease
protein folding
Shadoo
DPPX
PrP
Doppel
protein-protein interaction
mouse models
DPP6
Sprn
neuroscience
DPP10
Advisor: Westaway, David
Schmitt-Ulms, Gerold
Targeting Inflammation to Reduce Secondary Injury after Hemorrhagic Stroke

Intracerebral hemorrhage (ICH) is a devastating form of stroke that results from rupture of a blood vessel in the brain. Tissue inside the hematoma is irreversibly damaged soon after ICH onset and when this thesis research began, there was a dearth of information regarding pathological changes outside the hematoma. Inflammation is often proposed as a mechanism of injury, but very little information was available to show that inflammatory cells were in the right place at the right time to cause secondary brain injury. Using the collagenase-induced model of ICH, this work sought to better define spatial and temporal relationships between secondary brain injury and the inflammatory response after ICH. To test the hypothesis that reducing inflammation can protect the brain from secondary injury, minocycline, an antibiotic with established anti-inflammatory effects, was administered 6 hours after ICH onset. A small number of neurons die in the parenchyma bordering the hematoma between 6 hours and 3 days after ICH onset. This area was not associated with neutrophil infiltration, and most activated microglia/macrophages did not accumulate until after most neuron death had occurred. Despite a pronounced microglial response and prolonged increase in expression of many inflammatory genes, including complement receptor-3, interleukin-1 beta, interleukin-6, and interleukin-1 converting enzyme, no dying neurons were observed further outside the hematoma at any time. Interestingly, less early neuron death was observed in aged than in young animals, without a concomitant difference in the amount of tissue lost at 28 days. However, aged animals had less early microglial activation and a larger residual lesion, which might have resulted from impaired phagocytosis by activated microglia/macrophages. Minocycline was less effective in reducing microglial activation in aged animals, and did not reduce neuron death in either young or aged animals. Edema and BBB disruption was associated with degradation of the basal lamina protein, collagen type IV, and that damaged vessels are associated with tumor necrosis factor-alpha (TNFα)-positive neutrophils and active matrix metalloprotease-12 (MMP-12), all of which were reduced by delayed minocycline treatment. In contrast to ischemic stroke, there is a limited ‘penumbra’ outside the hematoma. Nevertheless, BBB damage in this region appears to be a potential target for protection. Furthermore, the prominent inflammatory response that continues for days after ICH does not appear to be associated with damage to other areas of the brain. Minocycline appears to protect the BBB by reducing neutrophil infiltration and the MMP-12 mediated basal lamina degradation. Future studies should investigate other targets for protection (i.e., white matter injury), and seek drugs that modulate the inflammatory response in aged animals and promote lesion resolution.

Keywords: intracerebral hemorrhage
stroke
microglia
astrocytes
neutrophils
cytokines
neuroinflammation
aging
Advisor: Schlichter, Lyanne C.