Now showing items 18317-18336 of 20306

    • Synthetic Peptide Ligand Mimetics and Tumor Cell Motility

      Cress, Anne E; Sroka, Thomas Charles; Cress, Anne E; Miesfeld, Roger L.; Klewer, Scott E. (The University of Arizona., 2005)
      Human tumor cell progression and metastasis is partially dependent on the ability of tumor cells to adhere to the proteins of the extracellular matrix and migrate to distant locations. Using a combinatorial screening approach, six novel D-amino acid containing peptides were identified and analyzed for their ability to adhere to human prostate tumor cells, support tumor cell adhesion and inhibit tumor cell adhesion to ECM proteins. Two peptides, RZ-3 (kmviywkag) and HYD1 (kikmviswkg) bound to tumor cell surfaces. A scrambled peptide derivative of HYD1, HYDS (wiksmkivkg) is not active. As immobilized ligands, RZ-3 and HYD1 can support prostate tumor cell adhesion. Prostate tumor cell adhesion to immobilized RZ-3 and HYD1 is integrin dependent. Soluble RZ-3 and HYD1 inhibits tumor cell adhesion to extracellular matrix proteins in a concentration dependent manner. These results indicate that RZ-3 and HYD1 are biologically active D-amino acid containing peptides that can support tumor cell adhesion and can inhibit tumor cell adhesion to immobilized extracellular matrix proteins.Cell migration is dependent on adhesive interactions with the extracelluar matrix. These interactions induce signaling and cytoskeletal responses necessary for migration. HYD1 completely blocks random haptotactic migration and inhibits invasion of prostate carcinoma cells on laminin-5. This effect is adhesion independent and reversible. The inhibition of migration by HYD1 involves a dramatic remodeling of the actin cytoskeleton resulting in increased stress fiber formation and actin colocalization with cortactin at the cell membrane. HYD1 interacts with a6 and a3 integrin subunits and elevates laminin-5 dependent intracellular signals including focal adhesion kinase, mitogen activated protein kinase kinase, and extracellular signal-regulated kinase. The scrambled derivative of HYD1, HYDS, does not interact with the a6 or a3 integrin subunits and is not biologically active. The minimal element for bioactivity of HYD1 was determined using alanine-substituted analogs of HYD1 and N- and C-terminal deletion mutants of HYD1. The minimal element necessary to block cell migration on laminin-5 and activate cell signaling through ERK is xikmviswxx. Taken together, these results indicate that HYD1 is a biologically active integrin-targeting peptide that reversibly inhibits tumor cell migration on laminin-5 and uncouples phosphotyrosine signaling from cytoskeletal dependent migration.
    • Synthetic, structural, spectroscopic and computational studies of metal-dithiolates as models for pyranopterindithiolate molybdenum and tungsten enzymes: Dithiolate folding effect

      Enemark, John H.; Joshi, Hemant K. (The University of Arizona., 2003)
      Coordination by an axial oxo and an equatorial ene-dithiolate group is a salient feature of the active sites of the mononuclear pyranopterin Mo/W enzymes. Discrete mononuclear model complexes encompassing these features are important in understanding the metal-ligand interactions in these active sites. The compounds (Tp*)ME(S-S) (M = Mo, W; E = O, NO) and Cp₂M(S-S) (M = Ti, Mo, W) (where Tp* is hydrotris(3,5-dimethyl-1-pyrazolyl)borate, Cp is η⁵-cyclopentadienyl, S-S represents a generic ene-1,2-dithiolate ligand for example 1,2-benzenedithiolate and 3,6-dichloro-1,2-benzenedithiolate) provide access to three different electronic configurations of the metal, formally d¹, d² and d⁰, respectively. These compounds also allow the study of two metal, two axial ligand and two equatorial ene-dithiolate perturbations. X-ray crystallography, density functional theory and photoelectron spectroscopy are utilized to understand the metal-sulfur interaction in the above complexes. Subtle differences in the geometry of these compounds are observed, including the metal-dithiolate fold angle which is sensitive to the electronic occupation of the metal in-plane orbital. This orbital is presumably the "host" orbital to the electrons during catalysis. The work in this area has resulted in the development of a dithiolate-folding-effect. This effect relates to the experimental verification of the Lauher and Hoffmann bonding model for the metal-dithiolate interaction in these complexes. This "dithiolate-folding-effect" is proposed to account for the electronic buffering at the metal center. This effect may provide a regulatory mechanism for the metal-sulfur interactions and could be a factor in the electron transfer reactions that regenerate the active sites of molybdenum and tungsten enzymes. The structure and properties of these compounds are correlated with those of the enzyme active sites.
    • Synthetically Diverse Triazabutadienes and Their Applications Towards Biological Systems

      Jewett, John; Wondrak, Georg; Shepard, Abigail J.; Hulme, Christopher; Sun, Daekyu (The University of Arizona., 2021)
      Small molecule tools for interrogating biological systems are important for studying the inner workings of the cell, from protein-protein interactions to understanding protein fluctuations and dynamics in different disease states. Aryl diazonium ions have been found to be a useful tool for studying proteins, capable of labeling tyrosine residues on a proteins surface. To prevent this electrophile from labeling everything in sight affording nonspecific reactions, a protecting group can be invoked. Once such example is the triazabutadiene, a nitrogen rich structural motif capable of falling apart upon protonation or in the presence of light. Previous studies have focused on characterizing deprotection kinetics at a physiological pH, and aryl diazonium ion adducts have been characterized on single proteins using a fluorophore conjugate. To further the understanding of the triazabutadiene system for both synthetic and biological applications, more complex probes must be designed, synthesized, and characterized to move towards in cellulo experiments. A triazabutadiene was designed bearing an alkyne handle on the sacrificial imidazole ring, which can be functionalized using copper-click chemistry to add on cell targeting moieties such as vitamins for active transport or small molecule signals for a specific organelle of interest. The development of such probes adds layers of synthetic complexity to the system as an acid and base sensitive functional group have been installed. Difficulties associated with methyl ester deprotection led to the explorative synthesis of less stable alkyl and silyl functional groups. While informative on general reactivity, all efforts were futile, either due to azide instability, triazabutadiene instability, or unsuccessful ester deprotection. Synthetic efforts for triazabutadiene functionalization have traditionally stayed away from the use of heat, due to the possibility of thermal intramolecular rearrangements, and metal catalysts, due to the chelating potential of the nitrogen rich scaffold. Previous findings have shown the triazabutadiene scaffold is compatible with copper-click chemistry conditions. These findings inspired the work of optimizing a Suzuki-coupling method for facile attachment of aryl rings to the triazabutadiene scaffold. Although there is a lack of support from literature, it was determined the scaffold is compatible with palladium-ferrocene complexes and can withstand temperatures of 95 °C for up to one hour. The biphenyl triazabutadienes, a novel synthetic class of compounds, are capable of deprotecting at physiological pH and labeling proteins, as determined using native mass spectrometry. An interesting nitrobenzoxadiazole triazabutadiene probe was discovered which displays a turn-on fluorescence profile upon protein labeling, with the intact triazabutadiene being non-fluorogenic. The aryl diazonium ion released upon deprotection was synthesized by an alternate route and tested on proteins to confirm these findings. A triazabutadiene containing a mitochondria targeting small molecule, a triphenylphosphonium ion, and a bromobenzene ring for mass spectrometry identification was synthesized and evaluated on proteins. The bromobenzene azo-adduct was found to label proteins, as confirmed using native mass spectrometry, and the adduct also remained intact during tandem mass spectrometry/mass spectrometry allowing for easy identification of labeled protein residues. The triazabutadiene was found to fall apart at pH 7 with the help of ultraviolet light, giving support for moving this system into a cellular setting for protein identification. In conclusion, this dissertation highlights the synthetic explorations of functionalizing triazabutadienes using novel synthetic plans, and the development of more complex probes with unexpected characteristics which will certainly find a use in the field of biological chemistry.
    • SYSTEM ANALYSIS THROUGH BOND GRAPH MODELING

      Cellier, Francois E; McBride, Robert Thomas; Cellier, Francois E; Sundareshan, Malur K.; Tharp, Hal S.; Nikravesh, Parviz E.; Chan, Cho Lik (The University of Arizona., 2005)
      Modeling and simulation form an integral role in the engineering design process. An accurate mathematical description of a system provides the design engineer the flexibility to perform trade studies quickly and accurately to expedite the design process. Most often, the mathematical model of the system contains components of different engineering disciplines. A modeling methodology that can handle these types of systems might be used in an indirect fashion to extract added information from the model.This research examines the ability of a modeling methodology to provide added insight into system analysis and design. The modeling methodology used is bond graph modeling. An investigation into the creation of a bond graph model using the Lagrangian of the system is provided. Upon creation of the bond graph, system analysis is performed. To aid in the system analysis, an object-oriented approach to bond graph modeling is introduced. A framework is provided to simulate the bond graph directly. Through object-oriented simulation of a bond graph, the information contained within the bond graph can be exploited to create a measurement of system efficiency. A definition of system efficiency is given. This measurement of efficiency is used in the design of different controllers of varying architectures. Optimal control of a missile autopilot is discussed within the framework of the calculated system efficiency.
    • System And Algorithm Design For Varve Image Analysis System

      Schowengerdt, Robert A.; He, Zhijun; Schowengerdt, Robert A.; Marcellin, Michael W.; Strickland, Robin N.; Thome, Kurtis J. (The University of Arizona., 2007)
      This dissertation describes the design and implementation of a computer vision based varve image analysis system. The primary issues covered are software engineering design, varve image calibrations, varve image enhancement, varve Dynamic Spatial Warping (DSW) profile generation, varve core image registration, varve identification, boundary identification and varve thickness measurement. A varve DSW matching algorithm is described to generate DSW profile and register two core images. Wavelet Multiple Resolution Analysis (MRA) is also used to do the core image registrations. By allowing an analyst to concentrate on other research work while the VARVES software analyzes a sample, much of the tedious varve analysis work is reduced, and potentially increasing the productivity. Additionally, by using new computer vision techniques, VARVES system is able to do some varve analysis which was impossible handled manually.
    • System and material aspects of volumetric bit-wise optical data storage

      Milster, Tom D.; Zhang, Yan (The University of Arizona., 2004)
      There are several primary factors that limit the data capacity of a volumetric bit-wise optical data storage system. Firstly, the data density in each layer is limited by the spot size formed at the focus of the objective lens. The spherical aberration induced by the medium also limits the maximum depth that an optical system can reach with diffraction limited focus. A second primary factor is the undesired detection of data from layers other than the layer at the laser focus, which is an effect called inter-layer crosstalk. In the last, the transmission and the reflection rate of the medium sets the limit of the number of the data layers for a given laser diode. In the modeling, the inter-layer crosstalk of volumetric bit-wise storage systems is simulated by using three methods. Several far-field and near-field systems with spherical aberration compensators are presented. In addition, the maximum surface densities of these systems are discussed. A dynamic test stand equipped with a tracking servo is built for testing the fluorescent material performance in a simulated space environment. Coupon samples made of Super-Rens material are tested in another dynamic test stand equipped with a focus servo. Controls of writing conditions for Super-Rens material are investigated with respect to the focus spot speed and data rate. Overall, this dissertation provides a description of volumetric bit-wise optical data storage technology, in terms of the system and material aspects, through simulation and experiments.
    • System Calibration and Image Reconstruction for a New Small-Animal SPECT System

      Barrett, Harrison H; Chen, Yi-Chun; Barrett, Harrison H; Furenlid, Lars R.; Kupinski, Matthew A. (The University of Arizona., 2006)
      A novel small-animal SPECT imager, FastSPECT II, was recently developed at the Center for Gamma-Ray Imaging. FastSPECT II consists of two rings of eight modular scintillation cameras and list-mode data-acquisition electronics that enable stationary and dynamic imaging studies. The instrument is equipped with exchangeable aperture assemblies and adjustable camera positions for selections of magnifications, pinhole sizes, and fields of view (FOVs). The purpose of SPECT imaging is to recover the radiotracer distribution in the object from the measured image data. Accurate knowledge of the imaging system matrix (referred to as H) is essential for image reconstruction. To assure that all of the system physics is contained in the matrix, experimental calibration methods for the individual cameras and the whole imaging system were developed and carefully performed. The average spatial resolution over the FOV of FastSPECT II in its lowmagnification (2.4X) configuration is around 2.4 mm, computed from the Fourier crosstalk matrix. The system sensitivity measured with a ⁹⁹ᵐTc point source at the center of the FOV is about 267 cps/MBq. The system detectability was evaluated by computing the ideal-observer performance on SKE/BKE (signal-known-exactly/background-known-exactly) detection tasks. To reduce the system-calibration time and achieve finer reconstruction grids, two schemes for interpolating H were implemented and compared: these are centroid interpolation with Gaussian fitting and Fourier interpolation. Reconstructed phantom and mouse-cardiac images demonstrated the effectiveness of the H-matrix interpolation.
    • System design and demonstration of a CCD-based solar spectroradiometer

      Reagan, John A.; Zielinskie, David Alphonse (The University of Arizona., 2001)
      The Atmospheric Remote Sensing Lab at the University of Arizona's Electrical and Computer Engineering Department has been involved with the study and measurement of atmospheric gases and aerosols for many years. The research has been conducted using instruments designed and constructed by the lab. This dissertation presents a system design for the next step in the evolution of spectroradiometers designed by the Atmospheric Remote Sensing Lab. The design draws upon the lessons learned from previous generations of radiometers and from the requirements of ongoing research. The proposed spectroradiometer uses an inexpensive CCD as the detector and takes advantage of modern processors and re-programmable CPLDs. The new design employs an embedded DSP in a novel way; it provides high level control over the CCD detector, receives serial ADC data and communicates with a Host computer. Through the use of one of the serial channels, the DSP identifies when to accumulate charge in the CCD and when to dump it. This controlled sampling allows charge to accumulate from adjacent cells internal to the CCD, improving the SNR in regions of poor spectral transmission. Since the charge accumulate/reset is controlled by the DSP through software, the sequence is programmable using the host computer interface and can be dynamically re-programmed to accommodate changing atmospheric conditions. A re-programmable CPLD isolates the DSP from the detector hardware and provides low level control of the detector assembly. The CPLD accepts high level commands from the DSP and generates the low level clocks and control signals used by the CCD and ADC. This capability permits the CPLD to be re-programmed to accommodate various CCDs and ADCs available today and in the future without altering the Host communication, control or analysis software. The capabilities of the instrument can be altered by downloading new software to the embedded DSP. Provisions have been made to download software or configuration data to the instrument and execute from RAM. Once correct operation of the software has been verified, it can copied to non-voltile memory.
    • The system design process is intractable, but robust.

      Chapman, William Luther.; Bahill, A. Terry; Wymore, A. Wayne; Duckstein, Lucien; Pierce, Edwin; Rozenblit, Jerzy (The University of Arizona., 1994)
      The system design process is intractable, but robust. The process is intractable because it is proven to be NP-complete. It is robust, because the tools used to do the system design are robust and allow for very good, but not optimal, solutions. The system design process is proven to be NP-complete by reduction of the Knapsack problem. The solutions used to solve the NP-complete problem called the Traveling Salesman Problem, will be examined with respect to how real designs are done. The design methodology is analyzed by a series of seventeen actual case studies. The tools evaluated are Quality Function Deployment and Design of Experiments. A sensitivity analysis of Quality Function Deployment is performed. It is proven to be insensitive to changes in weights and relationships. The needs and uses of modeling and prototypes in the system design process are examined. An actual prototype is analyzed using Design of Experiments. The Design of Experiments technique is shown to be very useful during the test and integration activity of the system design process.
    • A system for constructing configurable high-level protocols

      Schlichting, Richard D.; Bhatti, Nina Trappe (The University of Arizona., 1996)
      Distributed applications often require sophisticated communication services such as multicast, membership, group RPC (GRPC), transactions, or support for mobility. These services form a large portion of the supporting software for distributed applications, yet the specific requirements of the service vary from application to application. Constructing communication services that are useful for multiple diverse applications while still being manageable and efficient is a major challenge. This dissertation focuses on improving the construction of complex communication services. The contributions of the dissertation are a new model for the construction of such services and the design and implementation of a supporting network subsystem. In this model, a communication service is decomposed into distinct micro-protocols, each implementing a specific semantic property. Micro-protocols have well-defined interfaces that use events to coordinate actions and communicate state changes, which results in a highly modular and configurable implementation. This model augments, rather than replaces, the conventional hierarchical protocol model. In this implementation, a conventional x-kernel protocol is replaced with a composite protocol in which micro-protocol objects are linked with a standard runtime system that externally presents the standard x-kernel interface. Internally, the runtime system provides common message services, enforces a uniform inter-face between micro-protocols, detects and generates events, and synchronously or asynchronously executes event handlers. The viability of the approach is demonstrated by performance tests for several different configurations of a suite of micro-protocols for a group RPC service. The micro-protocols in this suite implement multiple semantic properties of procedure call termination, message ordering, reliability, collation of responses, call semantics, membership, and failure. The tests were conducted while running within the x-kernel as a user level task on the Mach operating system. Additional micro-protocols for mobile computing applications validate the generality of the model. We designed micro-protocols for quality of service (QoS), transmitting and renegotiating QoS parameters during handoffs, as well as for mobility management, covering cell detection, handoff, and disconnection. This suite of micro-protocols can be configured to accommodate a range of different service requirements or even to mimic existing mobile architectures such as those found in the Crosspoint, PARC TAB, InfoPad, or DataMan projects.
    • A system for three-dimensional SPECT without motion.

      Barnett, H.H.; Rowe, Robert Kjell.; Shoemaker, R.L. (The University of Arizona., 1991)
      This dissertation presents the results of an investigation into the performance characteristics of a unique hemispherical SPECT (single-photon emission computed tomography) imaging system capable of producing three-dimensional (3D) tomographic images of the human brain. The system is completely stationary and collects all necessary views of the patient simultaneously, with no system motion. The imager consists of twenty small (10cm x 10cm crystal area), digital gamma cameras arranged in a hemispherical pattern around the patient's head and a hemispherical lead aperture. The hemispherical aperture is positioned between the cameras and the head and contains a large number of pinholes; in this way each camera sees a number of overlapping pinhole projections of the radioactive distribution within the patient's brain. The initial investigation of the performance characteristics of a 3D SPECT system of this design were carried out using a computer simulation in which effects due to radiometry, finite pinhole size, finite detector resolution, photon noise, and object attenuation were included. We used a digital 3D brain phantom as the test object and an iterative search algorithm to perform the reconstructions. The simulations were used to compare the performance of a variety of system configurations. Based upon the results of the simulation study, we constructed a laboratory prototype of the 3D SPECT system, which we used to further characterize the expected performance of a clinical imaging system of the same design. Prior to collecting SPECT data we calibrated the imaging system, which required that we efficiently measure and store the spatially variant system response function. These calibration data were then included in the reconstructions of the SPECT phantoms that we imaged. A number of different SPECT phantoms were imaged to demonstrate the system performance. We measured a reconstructed spatial resolution of 4.8mm full-width at half-maximum and a full-system sensitivity of 36cps/μCi, where both values were measured for a point source in air located at the center of the field of view. We also describe an analysis that we performed to determine the equivalent, non-multiplexed system sensitivity; using this method, we found that the equivalent sensitivity was 79% of the measured value for the system configuration and the particular task that we investigated.
    • System Identification and Optimal Control of Complex Brain Networks

      Allen, John J.B.; Curham, Kyle John; Chou, Ying-hui; Roveda, Janet; Wilson, Robert (The University of Arizona., 2021)
      The communicability between topologically associated brain regions may provide a globally connected architecture to support communication through coherence. In chapter 1 of the dissertation, connectivity statistics are discovered by inverting a generative model of dynamic functional connectivity (FC) based on the dynamic communicability between brain regions. Dynamic FC and communicability are related by a set of affine transformations that preserve the group structure of Hermitian positive-definite (HPD) matrices. Infinitesimal transformations are integrated over time on a manifold of HPD matrices, describing parametric geodesic curves that represent dynamic changes in communicability. A hierarchical geodesic regression model is fit to a dataset involving 30 participants who performed a modified Eriksen Flanker task, to learn within- and between- subject connectivity statistics. Differences in dynamic FC are highly predictive of trial characteristics, as a linear classifier can predict whether participants respond with left/right hand and whether the response is correct or incorrect. The remaining chapters of the dissertation present new methods that enable causal investigations of functional networks using non-invasive brain stimulation. Chapter 2 simulates a transcranial electrical stimulation (TES) experiment, using a closed-loop feedback controller to drive the system into a priori target states (i.e., activating or deactivating a set of target ROIs) by identifying an optimal stimulation policy that balances difference performance criteria, such as stimulation dose and state error. The optimal control algorithm minimizes an expected future cost function to reduce stimulation dose for participants while achieving the desired effect - driving the system into different functional networks such as the Default Mode Network (DMN) and Cognitive Control Network (CCN). A projected gradient method is used to model variations in controllability due to individual differences (e.g., skull thickness, cortical morphometry, electrode placement and orientation), and an input sensitivity matrix is systematically varied to monotonically increase the controllability of the system. The effect of controllability is assessed under different levels of noise (measurement noise + input noise + system disturbances) for each transition, demonstrating the feasibility of the work under realistic conditions. In chapter 3, a data-driven systems identification is employed to learn dynamic causal models for TES based on simulations of white noise stimulation on a realistic head model. The algorithms learn low-rank realizations of the system that capture the dominant dynamical features of the data with a small number of modal parameters, using only the input-output timeseries data. An interpretable model is derived by constructing a linear mapping between the low-rank realization and the source level model, describing fluctuations in current source density (CSD). This approach relies on a three-step process: 1. Learn the impulse response function consisting of a Markov parameter sequence using the input-output data timeseries; 2. Estimate a reduced-order model from the singular value decomposition of a circulant matrix of repeated Markov parameter sequences; 3. Project the reduced-order model onto source space using the linear map constructed from a realistic finite-element head model. This approach simultaneously removes stimulation artifacts, source localizes scalp EEG, and predicts the dynamics of the system in response to TES.
    • A SYSTEM OF DATA GATHERING TO DESCRIBE TEACHER BEHAVIOR IN THE CLASSROOM

      Munroe, Mary Jeanne Murphy (The University of Arizona., 1978)
    • A system of deception and fraud detection using reliable linguistic cues including hedging, disfluencies, and repeated phrases

      Nunamaker, Jay F.; Burgoon, Judee K.; Humpherys, Sean L.; Nunamaker, Jay F.; Burgoon, Judee K.; Goes, Paulo B.; Chan, Erwin (The University of Arizona., 2010)
      Given the increasing problem of fraud, crime, and national security threats, assessing credibility is a recurring research topic in Information Systems and in other disciplines. Decision support systems can help. But the success of the system depends on reliable cues that can distinguish deceptive/truthful behavior and on a proven classification algorithm. This investigation aims to identify linguistic cues that distinguish deceivers from truthtellers; and it aims to demonstrate how the cues can successfully classify deception and truth.Three new datasets were gathered: 202 fraudulent and nonfraudulent financial disclosures (10-Ks), a laboratory experiment that asked twelve questions of participants who answered deceptively to some questions and truthfully to others (Cultural Interviews), and a mock crime experiment where some participants stole a ring from an office and where all participants were interviewed as to their guilt or innocence (Mock Crime). Transcribed participant responses were investigated for distinguishing cues and used for classification testing.Disfluencies (e.g., um, uh, repeated phrases, etc.), hedging words (e.g., perhaps, may, etc.), and interjections (e.g., okay, like, etc.) are theoretically developed as potential cues to deception. Past research provides conflicting evidence regarding disfluency use and deception. Some researchers opine that deception increases cognitive load, which lowers attentional resources, which increases speech errors, and thereby increases disfluency use (i.e., Cognitive-Load Disfluency theory). Other researchers argue against the causal link between disfluencies and speech errors, positing that disfluencies are controllable and that deceivers strategically avoid disfluencies to avoid appearing hesitant or untruthful (i.e., Suppression-Disfluency theory). A series of t-tests, repeated measures GLMs, and nested-model design regressions disconfirm the Suppression-Disfluency theory. Um, uh, and interjections are used at an increased rate by deceivers in spontaneous speech. Reverse order questioning did not increase disfluency use. Fraudulent 10-Ks have a higher mean count of hedging words.Statistical classifiers and machine learning algorithms are demonstrated on the three datasets. A feature reduction by backward Wald stepwise with logistic regression had the highest classification accuracies (69%-87%). Accuracies are compared to professional interviewers and to previously researched classification models. In many cases the new models demonstrated improvements. 10-Ks are classified with 69% overall accuracy.
    • System-Level Observation Framework for Non-Intrusive Runtime Monitoring of Embedded Systems

      Lysecky, Roman; Lee, Jong Chul; Lysecky, Roman; Akoghu, Ali; Wang, Meiling (The University of Arizona., 2014)
      As system complexity continues to increase, the integration of software and hardware subsystems within system-on-a-chip (SOC) presents significant challenges in post-silicon validation, testing, and in-situ debugging across hardware and software layers. The deep integration of software and hardware components within SOCs often prevents the use of traditional analysis methods to observe and monitor the internal state of these components. This situation is further exacerbated for in-situ debugging and testing in which physical access to traditional debug and trace interfaces is unavailable, infeasible, or cost prohibitive. In this dissertation, we present a system-level observation framework (SOF) that provides minimally intrusive methods for dynamically monitoring and analyzing deeply integrated hardware and software components within embedded systems. The SOF monitors hardware and software events by inserting additional logic within hardware cores and by listening to processor trace ports. The SOF provides visibility for monitoring complex execution behavior of software applications without affecting the system execution. The SOF utilizes a dedicated event-streaming interface that allows efficient observation and analysis of rapidly occurring events at runtime. The event-streaming interface supports three alternatives: (1) an in-order priority-based event stream controller, (2) a round-robin priority-based event stream controller, and (3) a priority-level based event stream controller. The in-order priority-based event stream controller, which uses efficient pipelined hardware architecture, ensures that events are reported in-order based on the time of the event occurrence. While the in-order priority-based event stream controller provides high throughput for reporting events, significant area requirement can be incurred. The round-robin priority-based event stream controller is an area-efficient event stream ordering technique with acceptable tradeoffs in event stream throughput. To further reduce area requirement, the SOF supports a priority-level based event stream controller that provides an in-ordering method with smaller area requirements than the round-robin priority-based event stream controller. Comprehensive experimental results using a complete prototype system implementation are presented to quantify the tradeoffs in area, throughput, and latency for the various event streaming interfaces considering several execution scenarios.
    • Systematic Analysis and Integrated Optimization of Traffic Signal Control Systems in a Connected Vehicle Environment

      Head, K. Larry; Beak, Byungho; Head, K. Larry; Son, Young-Jun; Valerdi, Ricardo; Wu, Yao-Jan (The University of Arizona., 2017)
      Traffic signal control systems have been tremendously improved since the first colored traffic signal light was installed in London in December 1868. There are many different types of traffic signal control systems that can be categorized into three major control types: fixed-time, actuated, and adaptive. Choosing a proper traffic signal system is very important since there exists no perfect signal control strategy that fits every traffic network. One example is traffic signal coordination, which is the most widely used traffic signal control system. It is believed that performance measures, such as travel times, vehicle delay, and number of stops, can be enhanced by synchronizing traffic signals over a corridor. However, it is not always true that the coordination will have the same benefits for all the traffic in the network. Most of the research on coordination has focused only on strengthening the major movement along the coordinated routes without considering system-wide impacts on other traffic. Therefore, before implementing a signal control system to a specific traffic network, a thorough investigation should be conducted to see how the control strategy may impact the entire network in terms of the objectives of each type of traffic control system. This dissertation first considers two different kinds of systematic performance analyses for traffic signal control systems. Then, it presents two types of signal control strategies that account for current issues in coordination and priority control systems, respectively. First, quantitative analysis of smooth progression for traffic flow is investigated using connected vehicle technology. Many studies have been conducted to measure the quality of progression, but none has directly considered smooth progression as the significant factor of coordination, despite the fact that the definition of coordination states that the goal is to have smooth traffic flow. None of the existing studies concentrated on measuring a continuous smooth driving pattern for each vehicle in terms of speed. In order to quantify the smoothness, this dissertation conducts an analysis of the speed variation of vehicles traveling along a corridor. A new measure is introduced and evaluated for different kinds of traffic control systems. The measure can be used to evaluate how smoothly vehicles flow along a corridor based on the frequency content of vehicle speed. To better understand the impact of vehicle mode, a multi-modal analysis is conducted using the new measure. Second, a multi-modal system-wide evaluation of traffic signal systems is conducted. This analysis is performed for traffic signal coordination, which is compared with fully actuated control in terms of a systematic assessment. Many optimization models for coordination focus mainly on the objective of the coordinated route and do not account for the impacts on side street movements or other system-wide impacts. In addition, multi-modality is not considered in most optimized coordination plans. Thus, a systematic investigation of traffic signal coordination is conducted to analyze the benefits and impacts on the entire system. The vehicle time spent in the system is measured as the basis of the analysis. The first analysis evaluates the effect of coordination on each route based on a single vehicle mode (regular passenger vehicles). The second analysis reveals that how multi-modality affects the performance of the entire system. Third, in order to address traffic demand fluctuation and traffic pattern changes during coordination periods, this dissertation presents an adaptive optimization algorithm that integrates coordination with adaptive signal control using data from connected vehicles. Through the algorithm, the coordination plan can be updated to accommodate the traffic demand variation and remain optimal over the coordination period. The optimization framework consists of two levels: intersection and corridor. The intersection level handles phase allocation in real time based on connected vehicle trajectory data, while the corridor level deals with the offsets optimization. The corridor level optimization focuses on the performance of the vehicle movement along the coordinated phase, while at the intersection level, all movements are considered to create the optimal signal plan. The two levels of optimizations apply different objective functions and modeling methodologies. The objective function at the intersection level is to minimize individual vehicle delay for both coordinated and non-coordinated phases using dynamic programming (DP). At the corridor level, a mixed integer linear programming (MILP) is formulated to minimize platoon delay for the coordinated phase. Lastly, a peer priority control strategy, which is a methodology that enhances the multi modal intelligent traffic signal system (MMITSS) priority control model, is presented based on peer-to-peer (P2P) and dedicated short range communication (DSRC) in a connected vehicle environment. The peer priority control strategy makes it possible for a signal controller to have a flexible long-term plan for prioritized vehicles. They can benefit from the long-term plan within a secured flexible region and it can prevent the near-term priority actions from having a negative impact on other traffic by providing more flexibility for phase actuation. The strategy can be applied to all different modes of vehicles such as transit, freight, and emergency vehicles. Consideration for far side bus stops is included for transit vehicles. The research that is presented in this dissertation is constructed based on Standard DSRC messages from connected vehicles such as Basic Safety Messages (BSMs), Signal Phasing and Timing Messages (SPaTs), Signal Request Messages (SRMs), and MAP Messages, defined by Society of Automotive Engineers (SAE) (SAE International 2016).
    • SYSTEMATIC COMPUTER-AIDED THREE-DIMENSIONAL MODELING OF INTEGRATED BIPOLAR DEVICES

      Fossum, Jerry George, 1943- (The University of Arizona., 1971)
    • A Systematic Literature Review of Healing Environments in the Inpatient Healthcare Setting

      Koithan, Mary S.; Linebaugh, Kelly Bartlett; Brewer, Barbara B.; Lamb, Gerri S.; Koithan, Mary S. (The University of Arizona., 2013)
      Background: Health care settings are generally regarded as stress inducing environments. Stress can alter the immune response, impair wound healing and create a greater risk for asthma, diabetes, gastrointestinal disorder and myocardial infarction. Beginning in the 1980s and 1990s, there has been increasing interest in healing environments and evidence-based design concepts. Yet, there has been little progress developing healing environments and using evidence-based design for psychiatric inpatient units, a uniquely stressful environment. Psychiatric units today continue to use designs such as caged in outdoor patio areas that resemble facilities that incarcerate rather than facilities which reduce stress and facilitate healing. The purpose of this systematic literature review was to identify design features that are evidence-based which can be used to create an optimal inpatient psychiatric patient room by: (1) analyzing the research literature for evidence of architectural and design elements that could be used in the inpatient psychiatric care setting to reduce stress and improve the well-being; (2) identifying design elements that are consistent with accreditation and licensing standards for inpatient psychiatric units; and (3) designing a psychiatric inpatient room that has evidence-based elements to reduce stress and improve well-being. Methods: A systematic literature review was conducted to identify factors in the inpatient healthcare environment that support an optimal healing environment. The PICO question for this review was what design factors in the inpatient healthcare environment support an optimal healing environment? A search of five databases and a hand search of reference lists were conducted. The search included studies from 1980 to the present, original research conducted on inpatient units with adult patients that investigated an intervention with an outcome that promotes a healing environment. Experimental, quasi-experimental, non-experimental, systematic literature reviews and expert opinions were sought and evaluated using a scale to analyze scientific rigor and research quality. Results: A total of 6,874 articles were identified in the search. Seventy-six articles were eligible for full text screening. After review of the full text, 38 articles were determined to be eligible for evidence analysis. After removing 11 inadmissible articles due to poor quality, 27 articles were included in the final synthesis. The search found research on eight hospital design features which may support optimal healing environments: artwork (n = 7), building configuration (n = 2), finish materials (n = 7), interior details (n = 6), lighting (n = 11), nature and view (n = 8), noise (n = 10), room configuration (n = 6). More than 50% of the research on optimal healing environments used quasi-experimental and non-experimental designs with rare use of experimental research designs. Overall, the quality of the research on optimal healing environments is not high, but results were reasonably consistent across studies. Conclusions: Evidence suggests seven design features for healing inpatient psychiatric environments, including: (a) single rooms, (b) calm, naturalistic and domestic artwork or photographs, (c) east facing windows, (d) plants, (e) acoustic ceiling tiles, (f) patient rooms removed from noise producing unit areas and (g) a window view of nature. These seven recommendations were examined for consistency with existing Arizona statutes and industry standards for behavioral health care environments. Recommendations found to be inconsistent with these statutes and standards were modified to reach congruency with the statutes and guidelines, and then an evidence-based design of a psychiatric inpatient room design was formulated and is illustrated. Future research on interventions to create healing environments at the greatest scientific rigor is needed along with measurement techniques to quantify stress responses to the environment.
    • SYSTEMATIC MODELING OF SEVERAL SOLID STATE DEVICES

      Lindholm, F. A., 1936- (The University of Arizona., 1963)