VictorJuiz/thesis huggingface dataset:
Robot telemanipulation in unstructured environments [electronic resource] : sensors, algorithms, interfaces

This dissertation presents methods for robot teleoperation, or equivalently, human-in-the- loop robotics. Human-in-the loop systems have the potential to handle complex tasks by combining the cognitive skills of a human operator with autonomous tools and behaviors. Along these lines, we present novel methods in grasp planning, haptic (force-feedback) rendering, and robot control which allow synergy in interaction between a human operator and a robot. We describe the interfaces that employ these algorithms, and validate them through user experiments. Our goal is to see robot technologies make a bigger impact in peoples' everyday lives, getting robots out of the laboratory and factory, and into homes, offices, and other unstructured human spaces. Our algorithms focus on three distinct areas of telerobotic manipulation but are unified by their common reliance on 3D point cloud data obtained from emerging sensor technol- ogy; we do not depend on environment or object models known a priori since it difficult to anticipate the things a robot will encounter in unstructured settings. First, since grasp- ing is a prerequisite for many manipulation tasks, we present two algorithms for planning grasps on clusters of 3D points. Next, we explore how to perform force-feedback haptic rendering of 3D point cloud data. This enables an operator to use the sense of touch to learn about environment geometry and potential collisions. Finally, we present a controller that uses a sequence of convex optimization steps to produce constrained arm motions that follow time-varying goal poses commanded by an operator. Using 3D sensor data to form motion constraints in real-time, the robot is responsive to changing goals from the user yet also avoids collisions and unfavorable arm configurations. We demonstrate the integration of our algorithms into a telerobotic system that enables an operator to perform varied and unscripted manipulation tasks in arbitrary settings. We describe tools for navigation, perception, and manipulation, ranging from direct control of a gripper or mobile base to autonomous sub-modules that perform collision-free base navigation or arm motion planning. Most importantly, we share results from testing these interfaces in a variety of settings, including user studies with non-expert operators and a case study with a motor-impaired operator using the robot in his own home.

Keywords: Mechanical Engineering.
Advisor: Salisbury J. Kenneth primary advisor. Thesis advisor
Cutkosky Mark R. advisor. Thesis advisor
Khatib Oussama advisor. Thesis advisor
The rogue transcriptome [electronic resource] : using sequencing to track RNA regulation and identify unusual RNAs

First, we take a look at the function of a specific type of RNA editing mediated by ADAR (adenosine deaminase that acts on RNAs). We test our hypotheses on ADAR activity and target specificity through transcriptome analysis in the context of exogenous RNAi response pathway in C. elegans. By examining of small RNA and mRNA populations in adar mutants and additional RNAi defective mutants, we show that the activity and specificity of the ADAR enzyme likely precludes the detection of its targets through conventional methods of sequence capture and analysis. Based on this understanding, we develop novel computational approaches for analysis of small RNA and mRNA populations and identify a broader set of ADAR targets, leading to a deeper understanding of the ADAR pathway, the conserved functionalities of the ADAR enzyme, and its relationship with the exogenous RNAi pathway in C. elegans. Second, we examine the dynamics of the transcriptome upon and after exposure to extreme heat. We hypothesize that the recovery response after removal from heat exposure might involve alternations in transcription regulation that are more complex than a reversal of the heat-shock induced effects, and that one such form of long-term regulation might involve the endogenous RNAi pathway and regulation via synthesis of endogenous siRNAs. By examining the dynamics of the C. elegans transcriptome during time-course of heat exposure and recovery, we reach a deeper understanding of heat shock biology and explore the relationship between endogenous siRNAs and their sequence complementary mRNA targets in the context of environmentally induced perturbance.

Keywords: Genetics.
Advisor: Fire Andrew Zachary primary advisor. Thesis advisor
Kim Stuart
Montgomery Stephen
Sidow Arend advisor. Thesis advisor
The role of body mechanics in touch sensation in the nematode Caenorhabditis elegans [electronic resource]

The mechanics of our skin determine how our skin and specialized mechanically-sensitive neurons within it are stressed and strained when touched. Understanding the interplay between skin mechanics and touch sensitivity is paramount in uncovering the fundamental molecular mechanisms underlying touch sensation and in understanding and treating touch insensitivity due to diseases like peripheral neuropathy. Despite this importance, the interplay between skin mechanics and sensitivity is poorly understood. The organism Caenorhabiditis elegans is an excellent model system in which to test the hypothesis that skin mechanics affect touch sensitivity. C. elegans detects body touch with just six mechanically-sensitive neurons. These neurons are embedded in the outer shell (consisting of the cuticle, hypodermis and body wall muscles) of the body plan, which dominates the overall body mechanics. If skin mechanics are important in touch sensitivity in C. elegans, stiffening or softening the outer shell should alter the ability of the animal to detect applied mechanical stimuli. I demonstrate that a piezoresistive cantilever force clamp system and methods that alter C. elegans body mechanics can be combined to directly test the hypothesis that mechanics modulate touch sensitivity. In particular, I build on prior work demonstrating that genetic mutation of cuticle proteins alters body stiffness, and use optogenetic modulation of body wall muscle tone to demonstrate that the body wall muscles modulate C. elegans body mechanics. Combining piezoresistive cantilevers capable of applying minute forces with these techniques to alter the mechanics of the body allows us to directly quantify the affect of body stiffening or softening on force or indentation depth sensitivity in C. elegans. I find that even small shifts in body stiffness have a significant effect on force sensitivity, with body stiffening leading to a reduction in force sensitivity and vice versa. Further, I demonstrate that indentation depth sensitivity is less affected by changes in body mechanics, suggesting that the mechanically-sensitive neurons involved in body touch in C. elegans respond more directly to applied indentation than to applied force. These findings emphasize the importance of considering skin mechanics in understanding the sense of touch and insensitivity due to diseases like peripheral neuropathy.

Keywords: Mechanical Engineering
Advisor: Pruitt Beth primary advisor. Thesis advisor
Dunn Alexander Robert advisor. Thesis advisor
Goodman Miriam Beth advisor. Thesis advisor
Saxitoxin-derived probes for the study of voltage-gated sodium channels in living cells and animals [electronic resource]

Voltage-gated sodium channels (NaV) serve an essential role in physiology. Accordingly, their dysfunction is associated with a number of human diseases and disorders, including epilepsy, cardiac arrhythmias, and chronic pain conditions. Designed by Nature as a chemical weapon, the naturally occurring channel blocker (+)-saxitoxin (STX) can be repurposed as a tool for studying these large integral membrane proteins. Access to new toxin derivatives through de novo synthesis offers a unique strategy to probe NaV structure and function, circumventing key limitations associated with existing methods for studying these proteins. The preparation and electrophysiological evaluation of an expanded library of N21-modified STX analogues is described herein. Characterization of the binding properties of these nanomolar NaV inhibitors has contributed to the development of an enhanced model for the structure of the inner pore of the channel. A select set of STX-fluorophore conjugates that bind reversibly to NaV with submicromolar potency serve as fluorescent markers of channels in living cells to study channel motility in the cell membrane. By contrast, maleimide-conjugated STX derivatives can be engineered to act as irreversible inhibitors of ion conductance when applied to wild-type NaV isoforms. The unique binding behavior of these derivatives has been leveraged to develop a new class of NaV probes for use in live cell imaging experiments and protein profiling studies. Maleimide-toxin conjugates with bioorthogonal reactive groups have been synthesized and can be employed for ligation of visualization and isolation tags to covalently modified channels. Appendage of fluorine-18 to a modified STX affords a probe for studying NaV expression in living subjects. An efficient synthetic route yields a derivative that binds with nanomolar affinity to several NaV isoforms. Biodistribution, autoradiography, and PET-MRI imaging studies demonstrate accumulation of the radiotracer at the site of injury in a rat model of neuropathic pain. This uptake correlates with the previously reported upregulation of NaV isoforms at this site, validating the utility of this probe as a NaV imaging agent. Collectively, these STX derivatives, uniquely available through chemical synthesis, represent a novel set of molecular probes for studying NaV function in vitro and in vivo.

Keywords: Chemistry.
Advisor: Du Bois Justin primary advisor. Thesis advisor
Wandless Thomas advisor. Thesis advisor
Wender Paul A. advisor. Thesis advisor
Scalable wireless monitoring systems with passive sensors for biomedical applications [electronic resource]

Continuous wireless monitoring of in vivo biopotential, biochemical, and biomechanical properties has the potential to yield breakthroughs in our understanding of human health and disease. In particular, current technology does not yet allow us to do so at micron (i.e., cellular) scales. We look to create a scalable system of chronically implantable passive sensors with a wireless detection platform to individually address and continuously monitor them. Scaling down the size of resonant sensors poses significant challenges for passive wireless detection. In particular, inherently higher resonant frequencies at smaller sizes push our operation into regimes where traditional approaches fail. Two schemes based on power reflection distortion (PRD) and group delay distortion (GDD) are proposed to operate over a wide range of frequencies. They are shown to be capable of operating in high frequency regimes near and above the readout circuit self-resonance. In addition, we describe a generic finite-difference time-domain (FDTD) framework for analyzing electromagnetic (EM) wave propagation and scattering in an anatomically realistic human phantom with an inhomogeneous dispersive model. Interactions with implantable resonant sensors are studied within this framework. We demonstrate a wireless real-time monitoring system with passive, flexible sensors, which scale down to unprecedented dimensions of 1×1×0.1 cubic mm. This level of scaling is enabled by the presented GDD detection scheme, which overcomes the operating frequency limits of traditional strategies and exhibits insensitivity to lossy tissue environments. We apply this system to capture human pulse waveforms in real-time as well as to continuously monitor in vivo intracranial pressures with sensors down to 2.5×2.5×0.1 cubic mm in proof-of-concept mice studies. Furthermore, printable wireless sensor arrays are introduced and their use in concurrent spatial pressure mapping is shown. Our vision is to extend the passive sensing approach and scale the resonant sensor platform down to intracellular dimensions at the intersection of intracellular delivery limits and integrated circuit fabrication capabilities. We demonstrate a family of 3D multilayer micro-Tag (µTag) structures as a potential platform for resonant tagging and sensing at the cellular level. As a stepping stone towards chronic cellular monitoring, we demonstrate the delivery of µTags into living cells and viability of internalized µTags over a 5-day period. Looking forward, this technology creates exciting opportunities to use remote physiological monitoring as a routine part of biomedical research and patient care. In the future, we foresee that such monitoring will be possible even at the cellular level.

Keywords: Electrical Engineering.
Advisor: Wong Hon-Sum Philip
McConnell Michael advisor. Thesis advisor
Pauly John (John M.) advisor. Thesis advisor
Scales of diversity in thermophilic microbial communities [electronic resource] : from metagenomes to individual cells and viral metagenomes

Microbial diversity can be queried at several scales within natural environments. On a macroscopic scale, microbial communities are capable of incredible feats: from colonizing the most inhospitable habitats imaginable, to creating ancient stromatolites, or living in intimate symbioses with the human body, inside and out. These complex microbial assemblages are comprised of different microscopic populations, which interact as a whole to stabilize the community ecosystem: selective evolutionary pressures work to shape each population, exquisitely adapting it to succeed in the current environmental conditions. In turn, these populations are comprised of millions of individual cells, each struggling to survive a variety of environmental stressors, to outcompete their closely-related neighbours, and carve out a distinct niche. Single cells wage constant war against predators such as viruses, which exist in large numbers and can effect entire populations, and ultimately the community as a whole. With such a range of complexity within a microbial community, it is essential to view microbial diversity through several tiers, in order to achieve a more complete picture. Only when diversity is viewed from several hierarchical levels, can the connections be made between the biology that is occurring on very fine scales and its effect on the entire system. Thus, this thesis has characterized microbial diversity in the hot spring microbial mats of Yellowstone National Park at multiple scales. There are several reasons why the microbial mats represent the ideal model system in which to query microbial diversity (Chapter 1). The evolution and adaptation of thermophilic Synechococcus sp. across a temperature gradient is queried by the creation of a targeted deep sequencing dataset, revealing statistically significant SNPs that correlate with thermal adaptation (Chapter 2). A second targeted deep sequencing dataset of 90 loci was generated to investigate the microdiversity present between two closely related thermophilic Synechococcus species, confirming the presence of micro-niches in stabilizing diversity across several years (Chapter 3). Successful gene amplification of the T1B CRISPR loci from a single cyanobacterial cell was achieved with the goal of investigating diversity at the single cell level (Chapter 4). Lastly, host-virus co-evolution is characterized by creation of a virome and a novel pipeline to assemble and analyze viral sequences: matching potential host-viral pairs by using CRISPR spacers (Chapter 5).

Keywords: Biology.
Advisor: Bhaya Devaki
Fukami Tadashi
Batzoglou Serafim advisor. Thesis advisor
Grossman Arthur (Arthur R.) advisor. Thesis advisor
Spormann Alfred M. advisor. Thesis advisor
Scanning SQUID microscopy of magnetic cells

Scanning Superconducting Quantum Interference Device (SQUID) microscopy is a minimally invasive tool normally used to study magnetic fields in condensed matter systems. We apply the techniques of scanning SQUID microscopy to biological samples that exhibit strong magnetic properties. These biological samples are part of a larger interdepartmental project to produce magnetically labeled stem cells for use as tracers in MRI. Using our SQUID magnetometers, we hope to better characterize individual cells so that their growth can be optimized for use as contrast agents. This thesis is divided into two major parts. The first concerns the problem of fitting the dipoles measured with the SQUID magnetometer to extract their dipole moments. We determine that the most desirable way to determine the magnetic moment of a SQUID measured dipole is to fit two superconducting vortex images to the dipole data. The second describes preliminary experiments in which we measure individual magnetic cells using scanning SQUID microscopy. We find that, in the two types of cells measured, the magnetic moment per cell as determined by Quantum Designs Magnetic Property Measurement System (MPMS) measurements is higher than that determined by scanning SQUID microscopy. We speculate that the reason for this is that scanning SQUID is a low field technique, and so the magnetic moments of the many individual magnetic particles do not line up in the same direction to produce a large overall magnetic moment as they do in the high field environment of an MPMS.

Keywords:  Department of Physics
SQUID
microscopy
magnet
magnetic
cell
Thesis
Advisor: Moler Kathryn A.
Osgood Brad
Searching for dwarf spheroidal galaxies and other Galactic dark matter substructures with the Fermi Large Area Telescope [electronic resource]

Over the past century, it has become clear that about a quarter of the known universe is composed of an invisible, massive component termed ``dark matter''. Some of the most popular theories of physics beyond the Standard Model suggest that dark matter may be a new fundamental particle that could self-annihilate to produce gamma rays. Nearby over-densities in the dark matter halo of our Milky Way present some of the most promising targets for detecting the annihilation of dark matter. We used the Large Area Telescope (LAT) on-board the Fermi Gamma-ray Space Telescope to search for gamma rays produced by dark matter annihilation in Galactic dark matter substructures. We searched for gamma-ray emission coincident with Milky Way dwarf spheroidal satellite galaxies, which trace the most massive Galactic dark matter substructures. We also sought to identify nearby dark matter substructures that lack all astrophysical tracers and would be detectable only through gamma-ray emission from dark matter annihilation. We found no conclusive evidence for gamma-ray emission from dark matter annihilation, and we set stringent and robust constraints on the dark matter annihilation cross section. While gamma-ray searches for dark matter substructure are currently the most sensitive and robust probes of dark matter annihilation, they are just beginning to intersect the theoretically preferred region of dark matter parameter space. Thus, we consider future prospects for increasing the sensitivity of gamma-ray searches through improvements to the LAT instrument performance and through upcoming wide-field optical surveys.

Keywords: Physics.
Advisor: Bloom E. (Elliott)
Allen Steven W. (Steven Ward) advisor. Thesis advisor
Funk Stefan
Searching for function [electronic resource] : signals of purifying selection in polymorphism and divergence

During my graduate career, my research has focused on studying signals of purifying selection, using the tools of population genomics and molecular evolution to elucidate the underlying function of sites across the genome. In this thesis, I first focus on the theoretical implications of the interplay between weak constraint and mutational biases for divergence data between species. By explicitly incorporating the selective fitness of nucleotides into DNA substitution models, weak selection and mutational biases under this model can together have unexpected effects on the pattern of DNA sequence evolution over a phylogeny. In the next chapter, I investigate the selective forces acting on the synonymous sites of D. melanogaster, taking advantage of the high quality, deep population sequencing data available for that species. Within-species polymorphism data can allow for the detection of strong purifying selection using a combination of SNP density and allele frequency. Synonymous sites are generally assumed to be subject to weak selective constraint. However, contrary to this expectation, I demonstrate in Chapter 2 that a substantial proportion of synonymous sites in D. melanogaster are evolving under very strong selective constraint while few, if any are evolving under weak or moderate constraint. I conclude by examining the power and properties of using divergence and polymorphism to search for functional elements in a genome. There is a large potential gain in power from having deep samples of population variation in multiple related species, which, combined with divergence data, should allow for the estimation of selection coefficients on relatively few sites. Comparative population genomics, the analysis of large-scale population data within and between species, represents a powerful extension to current approaches using the evolutionary signatures of purifying selection to detect functional elements and ascertain their functional importance.

Keywords: Genetics.
Advisor: Petrov Dmitri Alex
Sherlock Gavin advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Tang Hua (Geneticist) advisor. Thesis advisor
Secondary flows and dispersion in channel junctions [electronic resource]

Existing parameterizations for channel junctions often assume complete mixing and naturally arise from oversimplifications of junction physics. These models often use one computational cell to resolve channel junctions and neglect localized, supertidal flow features which may determine junction mixing via shear, separation, flow bifurcations, turbulent mixing layers, and secondary circulations induced by curvature. The hydrodynamics and dispersion in tidal junctions is largely unstudied and increased knowledge of junction hydrodynamics is needed to model transport for accurate ecosystem modeling. This dissertation determines numerical modeling techniques necessary to simulate the hydrodynamics of tidal river junctions and utilizes these results to perform a study of dispersion in the Georgiana Slough Junction of the Sacramento-San Joaquin Delta. First, techniques are developed to simulate secondary flows within a channel junction. Second, the hydrodynamics of the Georgiana Slough Junction are simulated and validated with field-data. Third, dispersion studies are performed using the validated model to assess the role of intra-junction flow features on dispersion in a channel junction.

Keywords: Civil and Environmental Engineering.
Advisor: Fringer Oliver B. (Oliver Bartlett) primary advisor. Thesis advisor
Fong Derek advisor. Thesis advisor
Koseff Jeffrey Russell advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
Security for mobile devices [electronic resource]

In recent years mobile devices have truly taken the stage as the dominant computing modality. The transition to mobile has brought about new opportunities to innovate but also new risks to user privacy and system security. This thesis investigates computer security concepts and techniques in the context of mobile computing. How can we implement traditional security measures such as Address Space Layout Randomization in a mobile environment? How does the use of mobile devices impact password management? Do the myriad sensors in modern smartphones have privacy implications? The work presented here was carried out over several years, weaving together traditional security concepts that could be carried over from the PC world, and novel challenges and solutions unique to mobile devices. The field is still evolving: we are certain to see exciting new developments soon, some of them I hope inspired by findings in the use of sensors or perhaps cloud-based threat detection and response discussed here.

Advisor: Boneh Dan
Lam Monica S. advisor. Thesis advisor
Mitchell John C. advisor. Thesis advisor