VictorJuiz/thesis huggingface dataset:
The role of neuronal activity in glioma growth and progression [electronic resource]
Keywords: Stem Cell Biology and Regenerative Medicine.

High-grade glioma (HGG) is the leading cause of brain tumor death in both children and adults. Active neurons exert a mitogenic effect on normal neural precursor and oligodendroglial precursor cells, the putative cellular origins of HGG. Using optogenetic control of cortical neuronal activity in a patient-derived pediatric glioblastoma xenograft model, we demonstrate that active neurons similarly promote HGG proliferation and growth in vivo. Conditioned medium from optogenetically stimulated cortical slices promoted proliferation of pediatric and adult patient-derived HGG cultures, indicating secretion of activity-regulated mitogen(s). The synaptic protein neuroligin-3 (NLGN3) was identified as the leading candidate mitogen, and soluble NLGN3 was sufficient and necessary to promote robust HGG cell proliferation. NLGN3 induced PI3K-mTOR pathway activity and feed-forward expression of NLGN3 in glioma cells. NLGN3 expression levels in human HGG negatively correlated with patient overall survival. These findings indicate the important role of active neurons in the brain tumor microenvironment and identify secreted NLGN3 as an unexpected mechanism promoting neuronal activity-regulated cancer growth. We next sought to determine if neuronal activity similarly promotes invasion and migration of pediatric HGG (pHGG), and to elucidate the mechanisms that mediate this effect. Diffuse infiltration is a characteristic hallmark of pHGG, but the molecular and cellular determinants of this behavior are incompletely understood. Using in vitro invasion assays, we demonstrate that exposure to activity-regulated secreted factors in conditioned medium from optogenetically stimulated and spontaneously active cortical slices increases the degree of pHGG cell infiltration through Matrigel, but that silencing neuronal activity with tetrodotoxin abrogates the pro-infiltrative effect. This effect was observed only when pHGG cells were seeded together with conditioned medium; pHGG cells do not preferentially migrate towards conditioned medium versus plain medium, suggesting that factors secreted into conditioned medium in an activity-dependent manner influence migration/invasion by inducing a pro-infiltrative phenotype rather than acting as chemoattractants. Taken together, these data indicate that active neurons play an important role in pHGG progression as well as growth. Candidate pro-infiltrative factors identified by proteomic analyses of conditioned media, including lead candidates 78-kDa glucose-regulated protein (GRP78) and cartilage acidic protein 1 (CRTAC1, or LOTUS), are presently undergoing necessity testing, and if confirmed in vivo, may represent new approaches to targeting the diffuse spread of these devastating tumors.
The role of physical activity in facilitating affect regulation [electronic resource]
Keywords: Psychology.

Despite the known benefits of physical activity, many Americans remain physically inactive, leading to an increased risk for all-cause mortality, heart disease, and a number of other physical health consequences. While research has primarily focused on the physical health consequences associated with participating in physical activity, there are important psychological consequences as well. Research has demonstrated that physical activity can lead to beneficial changes in affect, successfully reduce symptoms of various clinical disorders, and buffer against stress. Evidence also suggests that physical activity may reduce the use of rumination, implying that physical activity may influence the ability to effectively regulate affective states in daily life. To further explore this relationship, I examined associations between physical activity and affect regulation in a series of three studies. In Study 1, I used structural equation modeling to clarify the relationships among activity levels, experienced affect, and affect regulation. Findings suggested that physical activity is both directly and indirectly related to affect regulation. Subsequent mediation analyses indicated that physical activity may directly influence affect regulation and lead to subsequent changes in experienced affect. In Study 2, I employed an intervention that increased physical activity and decreased sedentary behavior. Subsequently, I examined changes in affect and affect regulation over time. Physical activity was associated with positive affect, but not negative affect. Measures related to affect regulation increased immediately after the intervention and remained higher up to 6 months following the intervention. Sedentary behavior predicted positive affect immediately after the intervention but did not predict negative affect or affect regulation. In Study 3, I examined whether physical fitness, which serves as a marker for repeated engagement in physical activity, facilitated affect regulation in younger and older adults. Specifically, I assessed whether physical fitness was associated with better working memory performance following a negative mood induction. Results indicated that physical fitness facilitates working memory performance during a negative mood induction in both younger and older adults. Together, these findings provide initial evidence that physical activity may be associated with effectively regulating affective states.
Sampling-based motion planning for safe and efficient spacecraft proximity operations [electronic resource]
Keywords: Aeronautics and Astronautics.

Autonomy has demonstrated success in many vehicle control problems, but has yet to show significant breakthroughs for spacecraft guidance during proximity operations. In part due to a costly verification and validation process as well as from limited access to formally-safe guidance algorithms, mission planners have instead had to rely on maneuver plans with straightforward, easily-verified trajectories and extensive human oversight. Unfortunately, this strategy often introduces propellant inefficiencies, adds significant labor overhead, and limits missions to Earth proximity where two-way communication times are short. This dissertation seeks to remedy these issues by developing a provably-safe and propellant-efficient sampling-based motion planning framework for fully-autonomous spacecraft proximity operations. The framework is designed for a wide range of hazardous guidance scenarios, including autonomous orbital rendezvous and inspection, pinpoint small-body descent, and on-orbit satellite servicing. Due to the dangers associated with operating near other objects, special care is taken to enable real-time guidance as well as ensure the availability of safe abort trajectories so that spacecraft can respond quickly and safely to control failures and sudden environmental changes. Through its generality, efficiency, and speed, the proposed approach offers the potential to enable entirely new capabilities for next-generation space missions, while also increasing the frequency, flexibility, and reliability of present-day operations in space.
Saxitoxin-derived probes for labeling voltage-gated sodium channels [electronic resource]
Keywords: Chemistry.

Voltage-gated sodium channels (NaVs) are obligatory membrane proteins responsible for the initiation and propagation of bioelectricity in excitable cells. A desire to study channel trafficking and regulatory mechanisms inspires the development of molecular tools for labeling channels patterned after the bis-guanidinium neurotoxin, (+)-saxitoxin (STX). The synthesis and electrophysiological evaluation of a novel class of cysteine-reactive, trifunctional STX-maleimide conjugates are described herein. These probes covalently inhibit wild-type NaVs, and contain a fluorophore, affinity, or bioorthogonal tag for visualizing and/or isolating toxin-bound channels. STX-maleimide derivatives were also demonstrated to covalently inhibit cysteine mutant channels, enabling the development of an orthogonal ligand-receptor pair. In addition, the preparation and characterization of reversible fluorescent STX conjugates are also described, which display excellent potency against neuronal NaV subytpes. Such reagents therefore represent valuable imaging agents for the visualization of NaVs in cultured neurons.
Scalable techniques for quantum network engineering [electronic resource]
Keywords: Applied Physics.

In the quest for creating ``quantum enhanced'' systems for information processing many currently pursued design strategies are difficult to scale significantly beyond a few dozen qubits. The dominant design paradigm relies on starting with near perfect quantum components and a vast overhead of classical external control. In my thesis I present tools and methods for a more integrated framework which treats quantum and hybrid quantum-classical systems on equal footing. We have recently defined a Quantum Hardware Description Language (QHDL) capable of describing networks of interconnected open quantum systems. QHDL is compiled to symbolic and numerical system models by a custom software tool suite named QNET. This allows us to rapidly iterate over quantum network designs and derive the associated equations of motion. Building on a recently developed model reduction technique for describing networks of nonlinear oscillators in the semi-classical regime, I present a library of nonlinear optical circuit designs useful for all-optical computation. I further present an end-to-end theoretical proposal to create all-optical neuromorphic circuits capable of supervised learning. The system is hierarchically composed of tunable linear amplifiers, analog phase memories and thresholding non-linear circuits which can be used to construct more general quantum feedback networks for nonlinear information processing. Finally, I introduce a novel model transformation capable of dividing the description of quantum states into a low-dimensional quasi-classical part coupled to a lower complexity quantum state. This approach is exact and naturally tailored to simulating coupled quantum systems with varying degrees of dissipation.
"Se svou neúnavnou prací" [electronic resource] : Antonín Salac̆ and classics at the margins
Keywords: Classics.

In this dissertation, I give an account of the history of classical studies in Czechoslovakia, focalized through the life and career of the philologist, epigrapher, and archaeologist Antonín Salač (1885-1960). Salač was born, educated, and habilitated in Prague, in the center of Europe but the margins of classicism. What does the study of Graeco-Roman antiquity look like in circumstances like these? Because of the relative geopolitical marginality of Czechoslovakia, as well as the relative marginality of classical studies in Czech culture, in order to facilitate their scholarly work, Salač and his colleagues were compelled to leverage a host of strategies to which our histories of classical studies rooted in great powers and "source nations" have failed to acquaint us—strategies running the gamut from theories of "small nations" to quasi-core-periphery economic relations, subtended by historical forces like Pan-Slavism and Czech nationalism. I also integrate into my dissertation people—women, diggers, "local enablers"—and narratives—dead ends, false starts, unanswered questions—not typically accorded space in our histories of classical studies. Thus, the life and career of Antonín Salač become an opportunity for a new perspective on the people and practices that create both classical studies and its histories.
Searches for light scalar dark matter [electronic resource]
Keywords: Physics.

If the dark matter is made up of a bosonic particle, it can be ultralight, with a mass potentially much below 1 eV. Moduli fields, whose values could set couplings and masses of known particles, are good candidates for such light dark matter. Their abundance in our Universe would manifest itself as tiny fractional oscillations of Standard Model parameters, such as the electron mass or the fine-structure constant, in turn modulating length and time scales of atoms. Rods and clocks, used for gedanken experiments in the development of relativity theory, have since transformed into actual precision instruments. The size of acoustic resonators and the frequency of atomic transitions can now be measured to 1 part in 10^24 and 10^18, respectively, and thus constitute sensitive probes of moduli. Atomic gravitational wave detectors can have a time-domain response to modulus dark matter, and sense temporal oscillations of atomic frequencies down to 1 part in 10^25. This thesis gives an overview of the parameter space of modulus dark matter, and compares the sensitivity of various experimental proposals relative to existing constraints from searches for new forces. I will focus on two classes of experimental strategies in particular: resonant-mass detectors (rods), and atomic spectroscopy and interferometry (clocks).
Searching for heavy photons in the HPS experiment [electronic resource]
Keywords: Physics.

The Heavy Photon Search (HPS) is a new experiment at Jefferson Lab that searches for a massive U(1) vector boson (known as a heavy photon or A') in the MeV-GeV mass range and coupling weakly to ordinary matter through a kinetic mixing interaction. The HPS experiment seeks to produce heavy photons by electron bremsstrahlung on a fixed target, is sensitive to heavy photon decays to electron-positron pairs, and targets the range in heavy photon mass from 20 to 600 MeV, and kinetic mixing strength epsilon^2 from 1E-5 to 1E-10. HPS searches for heavy photons using two signatures: a narrow mass resonance and displaced vertices. This dissertation presents the theoretical and experimental motivations for a heavy photon, the design and operation of the HPS experiment, and the displaced vertex search. The data used in this dissertation is the unblinded fraction of the 2015 HPS run, for the period of operation where the HPS silicon vertex tracker (SVT) was operated at its nominal position. This data was recorded from May 13 to May 18, 2015, at a beam energy of 1.056 GeV and a nominal beam current of 50 nA. The integrated luminosity is 119 inverse nanobarns, which is equivalent to 0.172 days of ideal running at the nominal beam current. This dissertation presents results (signal significance and upper limits) from the displaced vertex search in the mass range from 20 to 60 MeV, and kinetic mixing strength epsilon^2 from 2E-8 to 1E-10. This search does not have sufficient sensitivity to exclude a canonical heavy photon at any combination of mass and mixing strength. The strictest limit achieved in this analysis on the production of a particle that decays like a heavy photon is 115 times the expected production cross-section for a heavy photon. Factors limiting the sensitivity of this analysis are discussed. Projections of HPS performance with the full 2015 data set, and with planned improvements to the analysis, are presented. Comparisons are also made to earlier reach estimates.
Sediment transport due to river plumes in stratified, rotationally-influenced lakes [electronic resource]
Keywords: Civil and Environmental Engineering.

River inflows are often the dominant source of sediment, contaminants, and nutrients into an aquatic system and the dynamics of these flows dictate the fate of introduced constituents and their impact on the lake. The form of the river plume depends on the density of the river flow relative to the ambient surface waters. For instance, a dense river plume will plunge beneath the surface and, in a deep stratified system, will intrude into the water column at a depth of neutral buoyancy. While near-field (momentum-dominated) mixing between the plume and ambient water masses dictates the depth of an inflow intrusion, once the intrusion forms, the plume is influenced by buoyancy and rotational forces. The far-field plume is characterized by a balance between rotation and buoyancy forcing and the mid-field is defined as the adjustment region between the near-field momentum dominated region and the far-field geostrophic plume region. We have employed both field observations and numerical modeling to investigate sediment transport dynamics from intrusive plumes in the mid- and far-field regions. Field observations of multiple river inflows were collected in Pallanza Bay of Lake Maggiore, Italy, a stratified, rotational lacustrine system. We verified that the measured inflow intrusion speeds in Pallanza Bay were well characterized by a simple buoyancy-driven plume scaling. The effective sediment settling speed was shown to be one order of magnitude larger than the expected settling speed based on particle size, which can be due to effects such as particle flocculation and convective sedimentation. We also investigate the role of ambient stratification on the plume dynamics in the mid and far-field regions with a three-dimensional numerical model that was extensively validated with observations. An analytical expression was developed to predict the extent of sediment (in the along-plume direction) using the flow rate and ambient stratification. Finally, an idealized numerical model was employed to extend the range of conditions and to investigate the role of the lateral boundary in a lake on the plume transport dynamics. The lateral boundary modifies the amount of material that is trapped in a recirculating region near the mouth relative to the amount transported along the boundary. The plume propagation speed and thickness, which differ for buoyant and intrusive plumes, are shown to dictate the extent of sediment transport across a wide range of conditions. The timescale of sediment settling relative to the timescale of plume development will dictate sediment transport in a lake. In particular, the sediment settling timescale relative to the timescale of far-field plume development will dictate whether the sedimentation extent increases or decreases with the basin Rossby number.
SEDIMENTOLOGY AND STRATIGRAPHY OF A PART OF THE UPPER CRETACEOUS PIGEON POINT FORMATION, SAN MATEO COUNTY, CALIFORNIA
Keywords:  Department of Geological and Environmental Sciences
School of Earth Energy &amp; Environmental Sciences
Pigeon Point Formation
sedimentology
stratigraphy
Thesis

The Upper Cretaceous Pigeon Point Formation (PPF) is exposed for 16 km along the Pacific coast of San Mateo County, California, from just south of Pescadero Beach to just north of Año Nuevo Point. This study focuses on the area from Pescadero Point to Pebble Beach and explores the stratigraphy, process sedimentology and the depositional environments of the formation. The PPF is part of the Salinian terrane, the basement block of granitoid and metasedimentary rocks lying immediately west of the San Andreas Fault in central California. The Salinian block is thought to be the major source of the PPF sediments. The study area includes a stratigraphic section about 500 meters in thickness that is composed of three main lithofacies: thick-bedded sandstone, interbedded mudstone and sandstone, and mudstone. The formation has both syn-depositional (planar lamination, cross sets, ripples) and post-depositional (soft sediment deformation such as water escape structures, dish structures, flame structures and a sandstone dike) sedimentary structures. S3/Ta divisions form the most of the sedimentation units in the thick-bedded sandstone units, which were deposited by high-density turbidity currents, whereas thin-bedded sandstone and mudstone beds are interpreted as partial or complete Bouma sequences deposited by low-density flows. The facies associations suggest that the overall depositional setting of Pigeon Point rocks in the study area was a channel mouth or upper splay for the thick-bedded sandstones and a laterally related levee-overbank and possible lobe fringe areas for the interbedded sandstone and mudstone and mudstone lithofacies.
Selecting the dimension of a subspace in principal component analysis and canonical correlation analysis [electronic resource]
Keywords: Statistics.

It is common practice in statistical data analysis to perform dimension reduction, as modern data sets grow larger and more complex. Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA) are two of the most popular methods for dimension reduction. Despite the popularity of these methods, there is no widely adopted standard approach to select the proper dimension of the subspace to be obtained by PCA or CCA. To address this issue, we propose a novel method utilizing the hypothesis testing framework and test whether the currently selected subspace via PCA or CCA captures all the statistically significant signals in the given data set. While existing hypothesis testing approaches do not enjoy the exact type 1 error property and lose power under some scenarios, the proposed method provides exact type 1 error controls along with decent size of power in detecting signals. Central to our work is the post-selection inference framework which facilitates valid inference after data-driven model selection; the proposed hypothesis testing method provides exact type 1 error controls by conditioning on the selection event which leads to the inference.
Self interferometry [electronic resource] : self interference cancellation and its applications
Keywords: Electrical Engineering.

Wireless radios are typically half-duplex radios, and hence, the current wireless networks are Time Division Duplex(TDD) or Frequency Division Duplex (FDD). Full-duplex for wireless communications is considered impossible i.e. radios cannot transmit and receive at the same frequency at the same time. If we could achieve full duplex radios we won't need TDD or FDD strategy, we could potentially double the spectral efficiency. The fundamental challenge in achieving full duplex radios, when a radio is transmitting while simultaneously trying to receive (hear another radio) on the same frequency, it cannot. It's own transmission acts as a very strong self-interference. In this dissertation, we present the design, prototype and implementation of full duplex mimo radios. In particular, we built the first single antenna per chain full-duplex MIMO radios for 2.4 GHz WiFi-PHY i.e. to achieve an m-chain MIMO transceiver we need only m antenna. We design novel cancellation algorithms and circuits that reduce all self-interference to the noise floor and enable full-duplex MIMO PHY with almost no loss. The cancellation algorithms designed for full duplex themselves are of independent interest and apply to many other interference problems in wireless. We exploit this to build a full duplex relay which is the first one to provide both range extension and increase the capacity, is oblivious to ongoing transmission the source and the destination don't even realise that relay exist. Further, we build on top of the cancellation BackFi; a system that provides high throughput connectivity using backscatter to IoT devices at a very lower power. BackFi backscatters all ubiquitous ongoing WiFi signals to provide connectivity. Thus, providing connectivity without using extra spectrum just leveraging full duplex link. The cancellation, in essence, cancels all the reflections from the environment of self transmitted signal, inferring the reflection from cancellation provides us information about the environment. Towards the end, we abstract this information with a platform of Self-Interferometry, which provides with a unique way of looking at environment using wireless signals instead of light. Thus building a camera with wireless radios.