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Spinal Cord Injury Therapy through Active Learning
Get PDFTherapy employing epidural electrostimulation holds great potential for improving therapy for patients with spinal cord injury (SCI) (Harkema et al., 2011). Further promising results from combined therapies using electrostimulation have also been recently obtained (e.g., van den Brand et al., 2012). The devices being developed to deliver the stimulation are highly flexible, capable of delivering any individual stimulus among a combinatorially large set of stimuli (Gad et al., 2013). While this extreme flexibility is very useful for ensuring that the device can deliver an appropriate stimulus, the challenge of choosing good stimuli is quite substantial, even for expert human experimenters. To develop a fully implantable, autonomous device which can provide useful therapy, it is necessary to design an algorithmic method for choosing the stimulus parameters. Such a method can be used in a clinical setting, by caregivers who are not experts in the neurostimulator's use, and to allow the system to adapt autonomously between visits to the clinic. To create such an algorithm, this dissertation pursues the general class of active learning algorithms that includes Gaussian Process Upper Confidence Bound (GP-UCB, Srinivas et al., 2010), developing the Gaussian Process Batch Upper Confidence Bound (GP-BUCB, Desautels et al., 2012) and Gaussian Process Adaptive Upper Confidence Bound (GP-AUCB) algorithms. This dissertation develops new theoretical bounds for the performance of these and similar algorithms, empirically assesses these algorithms against a number of competitors in simulation, and applies a variant of the GP-BUCB algorithm in closed-loop to control SCI therapy via epidural electrostimulation in four live rats. The algorithm was tasked with maximizing the amplitude of evoked potentials in the rats' left tibialis anterior muscle. These experiments show that the algorithm is capable of directing these experiments sensibly, finding effective stimuli in all four animals. Further, in direct competition with an expert human experimenter, the algorithm produced superior performance in terms of average reward and comparable or superior performance in terms of maximum reward. These results indicate that variants of GP-BUCB may be suitable for autonomously directing SCI therapy
Quantifying Synergistic Information
Get PDFWithin the microcosm of information theory, I explore what it means for a system to be functionally irreducible. This is operationalized as quantifying the extent to which cooperative or "synergistic" effects enable random variables X1, ... , Xn to predict (have mutual information about) a single target random variable Y . In Chapter 1, we introduce the problem with some emblematic examples. In Chapter 2, we show how six different measures from the existing literature fail to quantify this notion of synergistic mutual information. In Chapter 3 we take a step towards a measure of synergy which yields the first nontrivial lowerbound on synergistic mutual information. In Chapter 4, we find that synergy is but the weakest notion of a broader concept of irreducibility. In Chapter 5, we apply our results from Chapters 3 and 4 towards grounding Giulio Tononi’s ambitious φ measure which attempts to quantify the magnitude of consciousness experience.</p
Techniques for Strength Measurement at High Pressures and Strain-Rates using Transverse Waves
Get PDFThe study of the strength of a material is relevant to a variety of applications including automobile collisions, armor penetration and inertial confinement fusion. Although dynamic behavior of materials at high pressures and strain-rates has been studied extensively using plate impact experiments, the results provide measurements in one direction only. Material behavior that is dependent on strength is unaccounted for. The research in this study proposes two novel configurations to mitigate this problem.
The first configuration introduced is the oblique wedge experiment, which is comprised of a driver material, an angled target of interest and a backing material used to measure in-situ velocities. Upon impact, a shock wave is generated in the driver material. As the shock encounters the angled target, it is reflected back into the driver and transmitted into the target. Due to the angle of obliquity of the incident wave, a transverse wave is generated that allows the target to be subjected to shear while being compressed by the initial longitudinal shock such that the material does not slip. Using numerical simulations, this study shows that a variety of oblique wedge configurations can be used to study the shear response of materials and this can be extended to strength measurement as well. Experiments were performed on an oblique wedge setup with a copper impactor, polymethylmethacrylate driver, aluminum 6061-t6 target, and a lithium fluoride window. Particle velocities were measured using laser interferometry and results agree well with the simulations.
The second novel configuration is the y-cut quartz sandwich design, which uses the anisotropic properties of y-cut quartz to generate a shear wave that is transmitted into a thin sample. By using an anvil material to back the thin sample, particle velocities measured at the rear surface of the backing plate can be implemented to calculate the shear stress in the material and subsequently the strength. Numerical simulations were conducted to show that this configuration has the ability to measure the strength for a variety of materials.</p
Community Sense and Response Systems
Get PDFThe proliferation of smartphones and other internet-enabled, sensor-equipped consumer devices enables us to sense and act upon the physical environment in unprecedented ways. This thesis considers Community Sense-and-Response (CSR) systems, a new class of web application for acting on sensory data gathered from participants' personal smart devices. The thesis describes how rare events can be reliably detected using a decentralized anomaly detection architecture that performs client-side anomaly detection and server-side event detection. After analyzing this decentralized anomaly detection approach, the thesis describes how weak but spatially structured events can be detected, despite significant noise, when the events have a sparse representation in an alternative basis. Finally, the thesis describes how the statistical models needed for client-side anomaly detection may be learned efficiently, using limited space, via coresets.
The Caltech Community Seismic Network (CSN) is a prototypical example of a CSR system that harnesses accelerometers in volunteers' smartphones and consumer electronics. Using CSN, this thesis presents the systems and algorithmic techniques to design, build and evaluate a scalable network for real-time awareness of spatial phenomena such as dangerous earthquakes.</p
Baryon and Lepton Numbers in Particle Physics beyond the Standard Model
Get PDFThe works presented in this thesis explore a variety of extensions of the standard model of particle physics which are motivated by baryon number (B) and lepton number (L), or some combination thereof. In the standard model, both baryon number and lepton number are accidental global symmetries violated only by non-perturbative weak effects, though the combination B-L is exactly conserved. Although there is currently no evidence for considering these symmetries as fundamental, there are strong phenomenological bounds restricting the existence of new physics violating B or L. In particular, there are strict limits on the lifetime of the proton whose decay would violate baryon number by one unit and lepton number by an odd number of units.
The first paper included in this thesis explores some of the simplest possible extensions of the standard model in which baryon number is violated, but the proton does not decay as a result. The second paper extends this analysis to explore models in which baryon number is conserved, but lepton flavor violation is present. Special attention is given to the processes of μ to e conversion and μ → eγ which are bound by existing experimental limits and relevant to future experiments.
The final two papers explore extensions of the minimal supersymmetric standard model (MSSM) in which both baryon number and lepton number, or the combination B-L, are elevated to the status of being spontaneously broken local symmetries. These models have a rich phenomenology including new collider signatures, stable dark matter candidates, and alternatives to the discrete R-parity symmetry usually built into the MSSM in order to protect against baryon and lepton number violating processes.</p
Studies of the Serotonin Type 3A Receptor and the Chemical Preparation of tRNA
Get PDFThis thesis describes studies surrounding a ligand-gated ion channel (LGIC): the serotonin type 3A receptor (5-HT3AR). Structure-function experiments using unnatural amino acid mutagenesis are described, as well as experiments on the methodology of unnatural amino acid mutagenesis. Chapter 1 introduces LGICs, experimental methods, and an overview of the unnatural amino acid mutagenesis.
In Chapter 2, the binding orientation of the clinically available drugs ondansetron and granisetron within 5-HT3A is determined through a combination of unnatural amino acid mutagenesis and an inhibition based assay. A cation-π interaction is found for both ondansetron and granisetron with a specific tryptophan residue (Trp183, TrpB) of the mouse 5-HT3AR, which establishes a binding orientation for these drugs.
In Chapter 3, further studies were performed with ondansetron and granisetron with 5-HT3A. The primary determinant of binding for these drugs was determined to not include interactions with a specific tyrosine residue (Tyr234, TyrC2). In completing these studies, evidence supporting a cation-π interaction of a synthetic agonist, meta-chlorophenylbiguanide, was found with TyrC2.
In Chapter 4, a direct chemical acylation strategy was implemented to prepare full-length suppressor tRNA mediated by lanthanum(III) and amino acid phosphate esters. The derived aminoacyl-tRNA is shown to be translationally competent in Xenopus oocytes.
Appendix A.1 gives details of a pharmacological method for determining the equilibrium dissociation constant, KB, of a competitive antagonist with a receptor, known as Schild analysis. Appendix A.2 describes an examination of the inhibitory activity of new chemical analogs of the 5-HT3A antagonist ondansetron. Appendix A.3 reports an organic synthesis of an intermediate for a new unnatural amino acid. Appendix A.4 covers an additional methodological examination for the preparation of amino-acyl tRNA.</p
A Tale of Two Cobalts
Get PDFThere are important problems to overcome if solar energy or other renewable energy sources are to be used effectively on a global scale. Solar photons must not only be harvested and converted into a usable form, but they must also be efficiently stored so that energy is available for use on cloudy days and at night. In this work, both the energy conversion and energy storage problems are addressed. Specifically, two cobalt complexes were designed and their reactivity probed for applications in energy conversion and storage. The first chapter describes a cobalt complex that is the first example of a dimeric cobalt compound with two singly proton-bridged cobaloxime units linked by a central BO4--bridge. Using electrochemical methods, the redox properties of the dimer were evaluated and it was found to be an electrocatalyst for proton reduction in acetonitrile.
Because hydrogen gas is difficult to handle and store, the hydrogenation of CO2 and later dehydrogenation of the liquid product, formic acid, has been proposed as a hydrogen storage system. Thus, a second complex, described in chapter two, supported by a triphosphine ligand framework was used as a catalyst precursor for this key dehydrogenation step. The studies here demonstrate the efficacy of the complex as a precatalyst for the desired reaction, with good conversion of starting formic acid to CO2 and H2. In order to better understand the properties of the triphosphine cobalt complex, a synthetic procedure for substituting electron donating groups (e.g., methoxy groups) onto the ligand was investigated, yielding a novel diphosphine cobalt(II) complex. </p
A Cocktail of Thermally Stable, Chemically Synthesized Capture Agents for the Efficient Detection of Anti-gp41 Antibodies from Human Sera and Techniques
Get PDFThis thesis reports on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60°C
On the Behavior of Pliable Plate Dynamics in Wind: Application to Vertical Axis Wind Turbines
Get PDFNumerous studies have shown that flexible materials improve resilience and durability of a structure. Several studies have investigated the behavior of elastic plates under the influence of a free stream, such as studies of the fluttering flag and others of shape reconfiguration, due to a free stream.
The principle engineering contribution of this thesis is the design and development of a vertical axis wind turbine that features pliable blades which undergo various modes of behavior, ultimately leading to rotational propulsion of the turbine. The wind turbine design was tested in a wind tunnel and at the Caltech Laboratory for Optimized Wind Energy. Ultimately, the flexible blade vertical axis wind turbine proved to be an effective way of harnessing the power of the wind.
In addition, this body of work builds on the current knowledge of elastic cantilever plates in a free stream flow by investigating the inverted flag. While previous studies have focused on the fluid structure interaction of a free stream on elastic cantilever plates, none had studied the plate configuration where the trailing edge was clamped, leaving the leading edge free to move. Furthermore, the studies presented in this thesis establish the geometric boundaries of where the large-amplitude flapping occurs.</p
Formal Methods for Control Synthesis in Partially Observed Environments: Application to Autonomous Robotic Manipulation
Get PDFModern robots are increasingly expected to function in uncertain and dynamically challenging environments, often in proximity with humans. In addition, wide scale adoption of robots requires on-the-fly adaptability of software for diverse application. These requirements strongly suggest the need to adopt formal representations of high level goals and safety specifications, especially as temporal logic formulas. This approach allows for the use of formal verification techniques for controller synthesis that can give guarantees for safety and performance. Robots operating in unstructured environments also face limited sensing capability. Correctly inferring a robot's progress toward high level goal can be challenging.
This thesis develops new algorithms for synthesizing discrete controllers in partially known environments under specifications represented as linear temporal logic (LTL) formulas. It is inspired by recent developments in finite abstraction techniques for hybrid systems and motion planning problems. The robot and its environment is assumed to have a finite abstraction as a Partially Observable Markov Decision Process (POMDP), which is a powerful model class capable of representing a wide variety of problems. However, synthesizing controllers that satisfy LTL goals over POMDPs is a challenging problem which has received only limited attention.
This thesis proposes tractable, approximate algorithms for the control synthesis problem using Finite State Controllers (FSCs). The use of FSCs to control finite POMDPs allows for the closed system to be analyzed as finite global Markov chain. The thesis explicitly shows how transient and steady state behavior of the global Markov chains can be related to two different criteria with respect to satisfaction of LTL formulas. First, the maximization of the probability of LTL satisfaction is related to an optimization problem over a parametrization of the FSC. Analytic computation of gradients are derived which allows the use of first order optimization techniques.
The second criterion encourages rapid and frequent visits to a restricted set of states over infinite executions. It is formulated as a constrained optimization problem with a discounted long term reward objective by the novel utilization of a fundamental equation for Markov chains - the Poisson equation. A new constrained policy iteration technique is proposed to solve the resulting dynamic program, which also provides a way to escape local maxima.
The algorithms proposed in the thesis are applied to the task planning and execution challenges faced during the DARPA Autonomous Robotic Manipulation - Software challenge.</p