VictorJuiz/thesis huggingface dataset:
Scalable wireless monitoring systems with passive sensors for biomedical applications [electronic resource]
Keywords: Electrical Engineering.

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.
Scales of diversity in thermophilic microbial communities [electronic resource] : from metagenomes to individual cells and viral metagenomes
Keywords: Biology.

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).
Scanning SQUID microscopy of magnetic cells
Keywords:  Department of Physics
SQUID
microscopy
magnet
magnetic
cell
Thesis

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.
Searching for dwarf spheroidal galaxies and other Galactic dark matter substructures with the Fermi Large Area Telescope [electronic resource]
Keywords: Physics.

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.
Searching for function [electronic resource] : signals of purifying selection in polymorphism and divergence
Keywords: Genetics.

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.
Secondary flows and dispersion in channel junctions [electronic resource]
Keywords: Civil and Environmental Engineering.

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.
Seeding survival: The value of school gardens in under-resourced communities in Cape Town
Keywords: school garden
environmental education
nutrition
garden-based learning
youth development
self-sufficiency
Cape Town
Thesis

Amid the growing effort in environmental education to foster links between children and nature, school gardens are one focus of increasing attention. Research on school gardens suggests positive outcomes for students in academic achievement, personal development, health and nutrition, community development, and environmental attitudes. Although the World Bank categorizes South Africa as an upper-middle income country, the country remains plagued by stark disparities in quality of life, health and education. Because of the aforementioned benefits, under-resourced areas of South Africa would seem to benefit from school garden programs, yet evidence from research and practice indicate that school gardens may be expensive and challenging to maintain. This tension raises a question: are school gardens worth the financial and human resources required to create and maintain them? This study addresses this tension by asking: in what ways do teachers, principals and caretakers in under-resourced schools in Cape Town value school gardens? The data were collected through interviews with 44 teachers, principals, and caretakers from 7 schools. Findings suggest that interviewees valued the following, in decreasing order of salience: teaching students skills to grow food, immediate and long-term nutrition, academic achievement, and environmental education-related outcomes. Participants also suggested that school gardens are one of the only places for students to gain certain experiences and skills. The data constellated around one theme: the garden spoke to the importance of greater self-sufficiency for all involved. In this way, the school gardens, helped conceptions of environmental education to converge with everyday living. These findings call attention to the diverse values held by school communities and provide insight into the future implementation, design, and framing of school gardens in South Africa and beyond.
Seismic hazard analysis using the ambient seismic field [electronic resource]
Keywords: Prieto, Germán A., 1979-
Geophysics.

With the recent occurrence of unexpectedly large earthquakes, seismic hazard analysis is now at a critical point, for which ground motion prediction is a key element. Traditionally, ground motion intensity is predicted using the empirical ground motion prediction equations, relations developed from observed ground motion measurements. There is a clear shortage of data for large events at short distances, and seismologists increasingly turn to physics based approaches to simulate ground shaking. Ground motion prediction is commonly divided into three main components: source characterization, wave propagation through a three-dimensional crustal structure, and non-linear site response. Each of these represents a challenging research endeavor, with significant source of uncertainty. In this thesis, I develop the foundation for using ambient-noise seismology to predict ground motion, and apply the methods I build to data in California and Japan. The cross-correlation of the ambient noise recorded simultaneously at two seismic stations has similar properties to the Green's function between the two stations. In this thesis, I develop techniques for robust estimation of reliable Green's functions. Once stable Green's functions are obtained, I use a newly established surface-wave eigen problem solver to correct the surface impulse response for source depth and mechanism to construct a virtual earthquake. I validate the virtual earthquake seismograms against data from nearby moderate earthquakes and demonstrate that strong basin amplification occurs at the same locations in both data sets. I expand the virtual point sources to extended ruptures and characterize the Los Angeles sedimentary basin amplification sensitivity to M7+ scenarios on the San Andreas Fault. In Japan, I use the ambient seismic field Green's functions to characterize basin resonance, identify virtual sources that have for strong shaking potential and recover detailed and complex wave propagation effects due to the basin structure that affect seismic amplification in central Tokyo. This thesis demonstrates the powerful opportunities that weak signals like the ambient seismic field bring to seismic hazard analysis, and gives rise to new research questions that will contribute to improve our understanding of the seismic hazard in populated areas.
The semantics of syntactic choice an analysis of English emotion verbs [electronic resource]
Keywords: Linguistics.

Psychological verbs ('`psych-verbs'') such as admire, amaze, fear, and frighten, have long been known to exhibit marked syntactic behavior in many languages. This behavior has inspired numerous analyses which assume that there is a unified explanation for the observed patterns. In this dissertation, I focus on the more problematic class of psych-verbs, the so-called Object-Experiencer (Obj-Exp) verbs (e.g. amaze, depress, frighten, fascinate) and argue, as some others have, that the explanation for their unusual character is primarily semantic in nature, and can be traced back to the ways in which humans conceptualize psychological events and processes. It is commonly argued that the special behavior of these verbs obtains only in their stative and/or more controversially non-agentive readings. Through qualitative and quantitative analyses of the semantic properties of Obj-Exp verbs and their arguments, I explore a controversial topic in previous research: the interaction of stativity and passivization among different subclasses of Obj-Exp verbs in English. Analysis of corpus data shows that eventive and stative uses are available to all Obj-Exp verbs in both the active and passive. I show that the choice between active and passive uses is particularly sensitive to the causal role of the stimulus and the nature of the emotion denoted by the verb; together these determine the linguistic construal of the situation as either a causative process or an attitudinal state. Additionally, I examine the variable (un-)acceptability of English Obj-Exp verbs in agentive contexts, and offer experimental and corpus data showing that a given verb's acceptability in an agentive context directly correlates with the tendency for its emotion to be iv associated with a controllable antecedent. These facts argue against analyzing differences in agentivity among psych-verbs at the level of lexical semantic structure, and instead suggest treating agentivity as an inference arising from the total integration of semantic, syntactic, and contextual information in the clause. Overall, the findings of these linguistic studies align well with recent theories developed in the psychological literature on emotion.
Sensing conformational dynamics of single trapped proteins in solution [electronic resource]
Keywords: Physics.

Proteins are macromolecular nanomachines that perform a wide variety of essential functions in living organisms. Distinct types of proteins in the cell serve as molecular sensors and signalers, sunlight-harvesting antennas and transducers, molecular motors for transport and metabolic energy storage, and oxidizers and reducers of physiological metal ions, to name a few. To achieve these complex functions, proteins are not static building blocks, but instead adopt multiple conformations in distinct functional states. These functions are inherently dynamic, meaning that methods capable of resolving dynamic behavior are necessary to fully elucidate protein function. Many bulk fluorescence methods have been used to study proteins by averaging together the signals from many copies of the same protein. However, such methods fail to capture distributions in protein conformations (e.g. mixtures of active and inactive states) and unsynchronized dynamics among these conformations (e.g. transition rates from inactive to active states under various conditions). Single-molecule fluorescence spectroscopy of proteins, on the other hand, allows direct observation of distributions and dynamics by watching only one protein at a time. In particular, a special device known as the Anti-Brownian ELectrokinetic (ABEL) trap can hold single fluorescently labeled proteins in solution for several seconds of spectroscopic observation without surface attachment, encapsulation, or the use of large beads. The ABEL trap combines fluorescence-based position estimation obtained by scanning a laser spot with the application of electrokinetic feedback forces to counter the Brownian motion of single proteins, one at a time. In this Dissertation I will describe my use of the ABEL trap technique to study dynamics of a variety of biomolecules, with emphasis on two proteins: the [beta]2-adrenergic receptor ([beta]2AR), an essential cellular signaling protein, and the peridinin-chlorophyll-protein (PCP), a sunlight-harvesting pigment-protein complex found in algae. In [beta]2AR, I observed a shift in protein conformation and in time scales of protein dynamics upon binding of an activating drug. In PCP, I observed two distinct classes of conformational change, indicating light-induced conformational flexibility, which may play a physiological role. Ongoing projects include resolving conformational substeps in FoF1 ATP synthase and measuring electron transfer kinetics of the multicopper oxidase Fet3p.
Serine integrases for non-viral gene & [and] cell therapy [electronic resource]
Keywords: Genetics.

The "integrase" enzyme of the bacterial virus phiC31 mediates the unidirectional fusion of the phiC31 and host-bacterium genomes. This recombination reaction occurs between two specific DNA sequences (att-sites), and can be performed by the enzyme without accessory factors in a wide variety of cellular environments, including human cells. Although its primary application to date in eukaryotes has been in organisms where the native phiC31 integrase (C31-int) att-sites have been pre-introduced, C31-int can also function on certain endogenous sequences (pseudosites) in animal genomes, albeit with significantly reduced activity. The ability of C31-int to perform pseudosite integration has made it the focus of several whole-animal and tissue-culture gene-therapy studies over the past decade, as there is currently no means to safely maintain the therapeutic DNA that is delivered for gene-therapy. The focus of my graduate work has been to assist these efforts to apply C31-int for gene-therapy. Specifically, I have sought to increase our basic scientific understanding of DNA recognition by C31-int through deletion and chimera studies (Chapters 2-3), and I have also attempted to improve the implementation of C31-int applications in mammals through my contributions to applied C31-int projects (Chapters 4-6). The results from my deletion and chimera studies have helped to clarify that C31-int employs DNA binding domains that are largely modular and have also helped to lay the groundwork for a potential means to derive serine integrases with novel specificities. The results from my contributions to applied C31-int projects have made it possible to reverse the wild-type reaction in mammalian cells (Chapter 4), to produce high-quality mouse induced-pluripotent-stem cells (iPSC) with C31-int (Chapter 5), and to genetically engineer mouse iPSCs (Chapter 6). Although C31-int will still require significant engineering before it is suitable for use in human gene therapy, and although additional work will be required to fully realize the potential of our iPSC-production and -engineering scheme in human cells, my experience with C31-int and related enzymes that I describe in this dissertation has left me optimistic that these are not unreasonable goals.