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- Genre: Masters Thesis
- Creators: Berman, Spring
Description
Random peptide microarrays are a powerful tool for both the treatment and diagnostics of infectious diseases. On the treatment side, selected random peptides on the microarray have either binding or lytic potency against certain pathogens cells, thus they can be synthesized into new antimicrobial agents, denoted as synbodies (synthetic antibodies). On the diagnostic side, serum containing specific infection-related antibodies create unique and distinct "pathogen-immunosignatures" on the random peptide microarray distinct from the healthy control serum, and this different mode of binding can be used as a more precise measurement than traditional ELISA tests. My thesis project is separated into these two parts: the first part falls into the treatment side and the second one focuses on the diagnostic side. My first chapter shows that a substitution amino acid peptide library helps to improve the activity of a recently reported synthetic antimicrobial peptide selected by the random peptide microarray. By substituting one or two amino acids of the original lead peptide, the new substitutes show changed hemolytic effects against mouse red blood cells and changed potency against two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. Two new substitutes are then combined together to form the synbody, which shows a significantly antimicrobial potency against Staphylococcus aureus (<0.5uM). In the second chapter, I explore the possibility of using the 10K Ver.2 random peptide microarray to monitor the humoral immune response of dengue. Over 2.5 billion people (40% of the world's population) live in dengue transmitting areas. However, currently there is no efficient dengue treatment or vaccine. Here, with limited dengue patient serum samples, we show that the immunosignature has the potential to not only distinguish the dengue infection from non-infected people, but also the primary dengue infection from the secondary dengue infections, dengue infection from West Nile Virus (WNV) infection, and even between different dengue serotypes. By further bioinformatic analysis, we demonstrate that the significant peptides selected to distinguish dengue infected and normal samples may indicate the epitopes responsible for the immune response.
ContributorsWang, Xiao (Author) / Johnston, Stephen Albert (Thesis advisor) / Blattman, Joseph (Committee member) / Arntzen, Charles (Committee member) / Arizona State University (Publisher)
Created2013
Description
The object of this study is to charac terize the effect of focused ultrasound stimulation (FUS) on the rat ce rvix which has been observed to speed its ripening during pregnancy. Ce rvical ripening is required for successful fetal delivery. Timed-pregnant Sprague-Dawley rats (n=36) were used. On day 14 of gestation, the FUS system was placed on the body surface of the rat over the cervix and ultrasound energy was applied to cervix for variable times up to 1 hour in the control group, the FUS system was placed on rats but no energy was applied. Daily measurement of cervix light-induced florescence (LIF, photon counts of collagen x-bridge fluorescence) were made on days 16 of gestation and daily until spont-aneous delivery (day22) to estimate changes in cervical ripening. We found that pulses of 680 KHz ultrasound at 25 Hertz, 1 millisecond pulse duration at 1W/cm^2 applied for as little as 30 minutes would immediately afterwards show the cervix to hav e ripened to the degree seen just before delivery on day 22. Delivery times, fetal weights and viability were unaffected in the FUS-treated animals.
ContributorsLuo, Daishen (Author) / Towe, Bruce C (Thesis advisor) / Wang, Xiao (Committee member) / Caplan, Michael (Committee member) / Arizona State University (Publisher)
Created2012
Description
The presented work in this report is about Real time Estimation of wind and analyzing current wind correction algorithm in commercial off the shelf Autopilot board. The open source ArduPilot Mega 2.5 (APM 2.5) board manufactured by 3D Robotics is used. Currently there is lot of development being done in the field of Unmanned Aerial Systems (UAVs), various aerial platforms and corresponding; autonomous systems for them. This technology has advanced to such a stage that UAVs can be used for specific designed missions and deployed with reliability. But in some areas like missions requiring high maneuverability with greater efficiency is still under research area. This would help in increasing reliability and augmenting range of UAVs significantly. One of the problems addressed through this thesis work is, current autopilot systems have algorithm that handles wind by attitude correction with appropriate Crab angle. But the real time wind vector (direction) and its calculated velocity is based on geometrical and algebraic transformation between ground speed and air speed vectors. This method of wind estimation and prediction, many a times leads to inaccuracy in attitude correction. The same has been proved in the following report with simulation and actual field testing. In later part, new ways to tackle while flying windy conditions have been proposed.
ContributorsBiradar, Anandrao Shesherao (Author) / Saripalli, Srikanth (Thesis advisor) / Berman, Spring (Thesis advisor) / Thanga, Jekan (Committee member) / Arizona State University (Publisher)
Created2014
Description
Single cell phenotypic heterogeneity studies reveal more information about the pathogenesis process than conventional bulk methods. Furthermore, investigation of the individual cellular response mechanism during rapid environmental changes can only be achieved at single cell level. By enabling the study of cellular morphology, a single cell three-dimensional (3D) imaging system can be used to diagnose fatal diseases, such as cancer, at an early stage. One proven method, CellCT, accomplishes 3D imaging by rotating a single cell around a fixed axis. However, some existing cell rotating mechanisms require either intricate microfabrication, and some fail to provide a suitable environment for living cells. This thesis develops a microvorterx chamber that allows living cells to be rotated by hydrodynamic alone while facilitating imaging access. In this thesis work, 1) the new chamber design was developed through numerical simulation. Simulations revealed that in order to form a microvortex in the side chamber, the ratio of the chamber opening to the channel width must be smaller than one. After comparing different chamber designs, the trapezoidal side chamber was selected because it demonstrated controllable circulation and met the imaging requirements. Microvortex properties were not sensitive to the chambers with interface angles ranging from 0.32 to 0.64. A similar trend was observed when chamber heights were larger than chamber opening. 2) Micro-particle image velocimetry was used to characterize microvortices and validate simulation results. Agreement between experimentation and simulation confirmed that numerical simulation was an effective method for chamber design. 3) Finally, cell rotation experiments were performed in the trapezoidal side chamber. The experimental results demonstrated cell rotational rates ranging from 12 to 29 rpm for regular cells. With a volumetric flow rate of 0.5 µL/s, an irregular cell rotated at a mean rate of 97 ± 3 rpm. Rotational rates can be changed by altering inlet flow rates.
ContributorsZhang, Wenjie (Author) / Frakes, David (Thesis advisor) / Meldrum, Deirdre (Thesis advisor) / Chao, Shih-hui (Committee member) / Wang, Xiao (Committee member) / Arizona State University (Publisher)
Created2011
Description
Recombinases are powerful tools for genome engineering and synthetic biology, however recombinases are limited by a lack of user-programmability and often require complex directed-evolution experiments to retarget specificity. Conversely, CRISPR systems have extreme versatility yet can induce off-target mutations and karyotypic destabilization. To address these constraints we developed an RNA-guided recombinase protein by fusing a hyperactive mutant resolvase from transposon TN3 to catalytically inactive Cas9. We validated recombinase-Cas9 (rCas9) function in model eukaryote Saccharomyces cerevisiae using a chromosomally integrated fluorescent reporter. Moreover, we demonstrated cooperative targeting by CRISPR RNAs at spacings of 22 or 40bps is necessary for directing recombination. Using PCR and Sanger sequencing, we confirmed rCas9 targets DNA recombination. With further development we envision rCas9 becoming useful in the development of RNA-programmed genetic circuitry as well as high-specificity genome engineering.
ContributorsStandage-Beier, Kylie S (Author) / Wang, Xiao (Thesis advisor) / Brafman, David A (Committee member) / Tian, Xiao-jun (Committee member) / Arizona State University (Publisher)
Created2018
Description
Research literature was reviewed to find recommended tools and technologies for operating Unmanned Aerial Systems (UAS) fleets in an urban environment. However, restrictive legislation prohibits fully autonomous flight without an operator. Existing literature covers considerations for operating UAS fleets in a controlled environment, with an emphasis on the effect different networking approaches have on the topology of the UAS network. The primary network topology used to implement UAS communications is 802.11 protocols, which can transmit telemetry and a video stream using off the shelf hardware. Other implementations use low-frequency radios for long distance communication, or higher latency 4G LTE modems to access existing network infrastructure. However, a gap remains testing different network topologies outside of a controlled environment.
With the correct permits in place, further research can explore how different UAS network topologies behave in an urban environment when implemented with off the shelf UAS hardware. In addition to testing different network topologies, this thesis covers the implementation of building a secure, scalable system using modern cloud computation tools and services capable of supporting a variable number of UAS. The system also supports the end-to-end simulation of the system considering factors such as battery life and realistic UAS kinematics. The implementation of the system leads to new findings needed to deploy UAS fleets in urban environments.
With the correct permits in place, further research can explore how different UAS network topologies behave in an urban environment when implemented with off the shelf UAS hardware. In addition to testing different network topologies, this thesis covers the implementation of building a secure, scalable system using modern cloud computation tools and services capable of supporting a variable number of UAS. The system also supports the end-to-end simulation of the system considering factors such as battery life and realistic UAS kinematics. The implementation of the system leads to new findings needed to deploy UAS fleets in urban environments.
ContributorsD'Souza, Daniel (Author) / Panchanathan, Sethuraman (Thesis advisor) / Berman, Spring (Committee member) / Zhang, Yu (Committee member) / Arizona State University (Publisher)
Created2018
Description
The Autonomous Vehicle (AV), also known as self-driving car, promises to be a game changer for the transportation industry. This technology is predicted to drastically reduce the number of traffic fatalities due to human error [21].
However, road driving at any reasonable speed involves some risks. Therefore, even with high-tech AV algorithms and sophisticated sensors, there may be unavoidable crashes due to imperfection of the AV systems, or unexpected encounters with wildlife, children and pedestrians. Whenever there is a risk involved, there is the need for an ethical decision to be made [33].
While ethical and moral decision-making in humans has long been studied by experts, the advent of artificial intelligence (AI) also calls for machine ethics. To study the different moral and ethical decisions made by humans, experts may use the Trolley Problem [34], which is a scenario where one must pull a switch near a trolley track to redirect the trolley to kill one person on the track or do nothing, which will result in the deaths of five people. While it is important to take into account the input of members of a society and perform studies to understand how humans crash during unavoidable accidents to help program moral and ethical decision-making into self-driving cars, using the classical trolley problem is not ideal, as it is unrealistic and does not represent moral situations that people face in the real world.
This work seeks to increase the realism of the classical trolley problem for use in studies on moral and ethical decision-making by simulating realistic driving conditions in an immersive virtual environment with unavoidable crash scenarios, to investigate how drivers crash during these scenarios. Chapter 1 gives an in-depth background into autonomous vehicles and relevant ethical and moral problems; Chapter 2 describes current state-of-the-art online tools and simulators that were developed to study moral decision-making during unavoidable crashes. Chapters 3 focuses on building the simulator and the design of the crash scenarios. Chapter 4 describes human subjects experiments that were conducted with the simulator and their results, and Chapter 5 provides conclusions and avenues for future work.
However, road driving at any reasonable speed involves some risks. Therefore, even with high-tech AV algorithms and sophisticated sensors, there may be unavoidable crashes due to imperfection of the AV systems, or unexpected encounters with wildlife, children and pedestrians. Whenever there is a risk involved, there is the need for an ethical decision to be made [33].
While ethical and moral decision-making in humans has long been studied by experts, the advent of artificial intelligence (AI) also calls for machine ethics. To study the different moral and ethical decisions made by humans, experts may use the Trolley Problem [34], which is a scenario where one must pull a switch near a trolley track to redirect the trolley to kill one person on the track or do nothing, which will result in the deaths of five people. While it is important to take into account the input of members of a society and perform studies to understand how humans crash during unavoidable accidents to help program moral and ethical decision-making into self-driving cars, using the classical trolley problem is not ideal, as it is unrealistic and does not represent moral situations that people face in the real world.
This work seeks to increase the realism of the classical trolley problem for use in studies on moral and ethical decision-making by simulating realistic driving conditions in an immersive virtual environment with unavoidable crash scenarios, to investigate how drivers crash during these scenarios. Chapter 1 gives an in-depth background into autonomous vehicles and relevant ethical and moral problems; Chapter 2 describes current state-of-the-art online tools and simulators that were developed to study moral decision-making during unavoidable crashes. Chapters 3 focuses on building the simulator and the design of the crash scenarios. Chapter 4 describes human subjects experiments that were conducted with the simulator and their results, and Chapter 5 provides conclusions and avenues for future work.
ContributorsKankam, Immanuella (Author) / Berman, Spring (Thesis advisor) / Johnson, Kathryn (Committee member) / Yong, Sze Zheng (Committee member) / Arizona State University (Publisher)
Created2019
Description
The construction industry is very mundane and tiring for workers without the assistance of machines. This challenge has changed the trend of construction industry tremendously by motivating the development of robots that can replace human workers. This thesis presents a computed torque controller that is designed to produce movements by a small-scale, 5 degree-of-freedom (DOF) robotic arm that are useful for construction operations, specifically bricklaying. A software framework for the robotic arm with motion and path planning features and different control capabilities has also been developed using the Robot Operating System (ROS).
First, a literature review of bricklaying construction activity and existing robots’ performance is discussed. After describing an overview of the required robot structure, a mathematical model is presented for the 5-DOF robotic arm. A model-based computed torque controller is designed for the nonlinear dynamic robotic arm, taking into consideration the dynamic and kinematic properties of the arm. For sustainable growth of this technology so that it is affordable to the masses, it is important that the energy consumption by the robot is optimized. In this thesis, the trajectory of the robotic arm is optimized using sequential quadratic programming. The results of the energy optimization procedure are also analyzed for different possible trajectories.
A construction testbed setup is simulated in the ROS platform to validate the designed controllers and optimized robot trajectories on different experimental scenarios. A commercially available 5-DOF robotic arm is modeled in the ROS simulators Gazebo and Rviz. The path and motion planning is performed using the Moveit-ROS interface and also implemented on a physical small-scale robotic arm. A Matlab-ROS framework for execution of different controllers on the physical robot is described. Finally, the results of the controller simulation and experiments are discussed in detail.
First, a literature review of bricklaying construction activity and existing robots’ performance is discussed. After describing an overview of the required robot structure, a mathematical model is presented for the 5-DOF robotic arm. A model-based computed torque controller is designed for the nonlinear dynamic robotic arm, taking into consideration the dynamic and kinematic properties of the arm. For sustainable growth of this technology so that it is affordable to the masses, it is important that the energy consumption by the robot is optimized. In this thesis, the trajectory of the robotic arm is optimized using sequential quadratic programming. The results of the energy optimization procedure are also analyzed for different possible trajectories.
A construction testbed setup is simulated in the ROS platform to validate the designed controllers and optimized robot trajectories on different experimental scenarios. A commercially available 5-DOF robotic arm is modeled in the ROS simulators Gazebo and Rviz. The path and motion planning is performed using the Moveit-ROS interface and also implemented on a physical small-scale robotic arm. A Matlab-ROS framework for execution of different controllers on the physical robot is described. Finally, the results of the controller simulation and experiments are discussed in detail.
ContributorsGandhi, Sushrut (Author) / Berman, Spring (Thesis advisor) / Marvi, Hamidreza (Committee member) / Yong, Sze Zheng (Committee member) / Arizona State University (Publisher)
Created2019
Description
This work considers the design of separating input signals in order to discriminate among a finite number of uncertain nonlinear models. Each nonlinear model corresponds to a system operating mode, unobserved intents of other drivers or robots, or to fault types or attack strategies, etc., and the separating inputs are designed such that the output trajectories of all the nonlinear models are guaranteed to be distinguishable from each other under any realization of uncertainties in the initial condition, model discrepancies or noise. I propose a two-step approach. First, using an optimization-based approach, we over-approximate nonlinear dynamics by uncertain affine models, as abstractions that preserve all its system behaviors such that any discrimination guarantees for the affine abstraction also hold for the original nonlinear system. Then, I propose a novel solution in the form of a mixed-integer linear program (MILP) to the active model discrimination problem for uncertain affine models, which includes the affine abstraction and thus, the nonlinear models. Finally, I demonstrate the effectiveness of our approach for identifying the intention of other vehicles in a highway lane changing scenario. For the abstraction, I explore two approaches. In the first approach, I construct the bounding planes using a Mixed-Integer Nonlinear Problem (MINLP) formulation of the given system with appropriately designed constraints. For the second approach, I solve a linear programming (LP) problem that over-approximates the nonlinear function at only the grid points of a mesh with a given resolution and then accounting for the entire domain via an appropriate correction term. To achieve a desired approximation accuracy, we also iteratively subdivide the domain into subregions. This method applies to nonlinear functions with different degrees of smoothness, including Lipschitz continuous functions, and improves on existing approaches by enabling the use of tighter bounds. Finally, we compare the effectiveness of this approach with the existing optimization-based methods in simulation and illustrate its applicability for estimator design.
ContributorsSingh, Kanishka Raj (Author) / Yong, Sze Zheng (Thesis advisor) / Artemiadis, Panagiotis (Committee member) / Berman, Spring (Committee member) / Arizona State University (Publisher)
Created2018
Description
This thesis presents an autonomous vehicle test bed which can be used to conduct studies on the interaction between human-driven vehicles and autonomous vehicles on the road. The test bed will make use of a fleet of robots which is a microcosm of an autonomous vehicle performing all the vital tasks like lane following, traffic signal obeying and collision avoidance with other vehicles on the road. The robots use real-time image processing and closed-loop control techniques to achieve automation. The testbed also features a manual control mode where a user can choose to control the car with a joystick by viewing a video relayed to the control station. Stochastic rogue vehicle processes will be introduced into the system which will emulate random behaviors in an autonomous vehicle. The test bed was experimented to perform a comparative study of driving capabilities of the miniature self-driving car and a human driver.
ContributorsSubramanyam, Rakshith (Author) / Berman, Spring (Thesis advisor) / Yu, Honbin (Thesis advisor) / Jayasurya, Suren (Committee member) / Arizona State University (Publisher)
Created2018