VictorJuiz/thesis huggingface dataset:
Observations, causes, and potential consequences of small-scale temperature and dissolved oxygen variability in a kelp forest system [electronic resource]
Keywords: Biology.

Coastal hypoxia represents an important environmental change that has the potential to impact a wide range of species and communities in shallow subtidal habitats. While eutrophication-driven hypoxia has long been of concern in sheltered water bodies such as bays and estuaries, recently hypoxic events caused by advection of deep oceanic oxygen minimum zone waters into shallow shelf areas, have been observed. While a large component of this process is naturally occurring. Strong evidence exists which suggests that these events are also increasing due to climate change, through global deoxygenation and increases in coastal advective processes. While advective processes are commonly thought of as spatially uniform at the regional scale, this dissertation presents evidence throughout which, in fact, suggests that coastal advective processes (especially nearshore internal waves) are highly complex spatially, mostly due to their interactions with shallow topographic features such as rocky reefs. This observation is novel in two important ways. First, this small-scale spatial interaction between internal waves and rocky reefs represents novel complex habitat layer to the fluid environment, which has not been previously observed, nor considered for nearshore subtidal ecological studies. Secondly, when nearshore internal waves contain hypoxic water, the resulting small-scale spatial variability in the dissolved oxygen landscape may span super-saturated and severely hypoxic oxygen concentrations on the scale of meters within the reef. Together, the results from this dissertation suggest that small scale spatial variability in the fluid environment arising from internal wave/reef interactions, is a crucial, but poorly understood, component of nearshore habitats, which can complicate and extend hypoxic events. The results here also suggest variability at this scale may feasibly impact local organisms, especially through alterations to behavior. These dynamics are complicated, and much more work should be conducted in the future to better understand the whole impacts to shallow subtidal communities.
Observing atomic layer deposition with scanning tunneling microscopy [electronic resource]
Keywords: Applied Physics.

As modern device requirements move toward smaller and more complex architectures, ultra-thin films are playing an increasingly important role in device design and necessitate new fabrication methods. One technique that has gained prominence is atomic layer deposition (ALD) due to its surface conformality and control of material thickness and composition. But to fabricate the thinnest possible films via ALD, it is necessary to understand the early, non-uniform stage of ALD known as the nucleation phase. Because of instrument limitations, major frontiers remain both in the systematic characterization of ALD nucleation and in the degree of control of the nucleation process. This dissertation describes the utilization of a new scientific instrument that combines a nanoscale fabrication technique---ALD---with a nanoscale characterization technique---scanning tunneling microscopy (STM)---in a single vacuum chamber. The instrument has the capability to monitor individual nanostructures in situ as they are grown with ALD, tracking changes in their physical and electronic structure as they develop. It can be used to monitor the natural growth of extremely thin ALD films with sub-nanometer resolution, providing information about materials which are candidates for thin film devices. In addition, new silicon based substrates have been developed that are ideally suited for STM observation during ALD. The combination of these novel substrates and the STM-ALD instrument will allow for study of the nucleation phase of a wide range of ALD chemistries relevant for modern devices.
On correlated x-ray scattering [electronic resource] : analysis of solution diffraction images using angular intensity correlations in both the hard matter and soft matter regimes
Keywords: Applied Physics.

Correlated X-ray scattering (CXS) is a novel X-ray technique that utilizes angular intensity correlations in solution scattering patterns in order to extract a three-dimensional correlation function, which depends solely on the molecular structure factor. We report here on two of the first CXS experiments involving three-dimensional solutions of many molecules, at wide scattering angles. The first was done at a synchrotron facility, where we measured CXS arising from silver nanoparticles (NPs) embedded in a glycerol and agarose buffer. Crucially, a nitrogen jet was used to promote NP immobilization during each exposure. By averaging angular intensity correlations from on the order of 10 000 exposures, we were able to recover a CXS function that agreed well with atomic models. The second experiment was done at an X-ray free electron laser (XFEL) facility, where we measured CXS arising from gold NPs. There, we acquired on the order to 100 000 snapshots of gold NPs in solution, and were able to recover a CXS function indicating that the average NP was twinned, information that was previously unknown to us. Further, we are able to distinguish two populations of NPs present: small, twinned NPs and large, non-twinned NPs. Because CXS signal-to-noise is very low on a per-shot basis, great care must taken in order to minimize artifactual correlations that might arise during the image analysis. Artifactual correlations are a potential consequence of many experimental aspects, including sample-inhomogeneity, detector shadows, detector gain anisotropies, and beam polarization. In order to suppress these artifacts, we paired exposures that were similar in their anisotropy, and correlated their difference. By working with the difference intensities, we were able to significantly improve our signal-to-noise, and ultimately show that CXS is a viable way to extract atomic-level information from solution scattering measurements. As the technique continues to be explored, and data analysis methods are refined, CXS could reveal new pathways for studying ensemble statistics of small bio-molecules in solution, complimenting current state-of-the-art structural techniques, e.g. single particle imaging, cryo-electron microscopy, and serial femtosecond X-ray crystallography.
On the development of the direct flux reconstruction scheme for high-order fluid flow simulations [electronic resource]
Keywords: Aeronautics and Astronautics.

In the past few years, there have been several emerging challenges facing the advancement of computational fluid dynamics (CFD) for aerospace design applications. Firstly, there is an growing interest in simulating unsteady, vortex-dominated flows over complex geometries, a problem for which existing second-order Reynolds-averaged Navier-Stokes (RANS) methods have had limited success. In addition to this, shifts in modern computing hardware towards highly data-parallel architectures, such as graphics processing units (GPU) and similar accelerators, have created another hurdle, as many existing CFD applications and methods are not well suited to draw compute performance efficiently from these increasingly dominant computing technologies. To address these challenges, there has been an increased interest in high-order CFD methods, in particular those based within a discontinuous finite element (DFE) framework. The high-order nature of these methods makes them well-suited to simulating vortex-dominated flows due to a limited introduction of numerical dissipation. Furthermore, the element-wise discretizations found within DFE methods result in tightly-coupled degrees of freedom within each element, a trait that maps well to modern computing hardware due to an increased potential for data reuse and high arithmetic intensity. A popular DFE method that is particularly suitable for solving the compressible Navier-Stokes equations is the flux reconstruction (FR) method. The FR method is based on the differential form of the governing equations and provides a general framework that can recover other similar high-order schemes, such as the nodal discontinuous Galerkin (DG) scheme and the spectral difference (SD) scheme. While existing FR methods are commonly touted as simple relative to comparable DFE methods, they still remain fairly complex relative to existing lower order alternatives. In this thesis, a simplified variation of the flux reconstruction scheme, named the direct flux reconstruction (DFR) scheme is developed which streamlines the existing flux reconstruction procedure, on tensor-product and simplex elements. The first part of the thesis contains the development of the DFR scheme in 1D and its extension to tensor-product elements for advection-diffusion type problems. The DFR formulation in this context is proven to be linearly stable and shown to recover the nodal DG method for 1D and tensor product elements. In latter chapters, an extension of the DFR scheme to simplex elements is developed beyond this which provides a new approach for FR on simplices that naturally extends many of the ideas from the 1D scheme. In addition to theoretical developments, this thesis includes details of a GPU implementation of the DFR scheme that achieves high-performance on modern computing hardware.
On the emergence of spacetime and semi-classical dynamics [electronic resource]
Keywords: Physics.

The quantum physics of black holes and advances in string theory indicate that our contemporary notion of space—a continuous dynamical geometry obeying Einstein's equations—is an emergent concept. Gravitational physics appears instead as an effective description of a lower-dimensional quantum mechanical theory. This idea is called the holographic principle. In this thesis, we make steps towards developing a mathematical language for describing the emergence of geometry in the AdS/CFT correspondence, a string-theoretic realization of the holographic principle. The key idea we exploit is the curious relation between spacetime geometry and quantum entanglement discovered by Ryu and Takayanagi. We import mathematical tools from the field of integral geometry to connect questions such as "What is a point?" and "What is a distance?" in AdS space with the entanglement pattern of the CFT wavefunction. We then utilize the previous formalism to propose a new way of linking the degrees of freedom on the two sides of the AdS/CFT duality.
On the front lines of mental crisis: Dealing with mentally ill a growing challenge for SFPD
Keywords:  Department of Communication and Journalism
Department of Communication
mental health
San Francisco Police Department
5150
CIT
Thesis

This reporting examines San Francisco Police Department interactions with mentally ill people. The department receives dozens of calls for service related to mental health each day, making these encounters a major part of its workload. An incident in early 2017 in which an officer shot mentally ill San Francisco resident Sean Moore highlights the challenges of handling mental-crisis encounters as well as some of the department’s shortcomings.
A growing homeless population and a shortage of mental health services have contributed to a rise in serious mental-crisis incidents. Incidents where officers conclude a person is a danger to himself or others have increased nearly 50 percent since 2003. The police department’s approach to interacting with the mentally ill revolves around the Crisis Intervention Team model, and protocols for dispatching CIT-certified officers are still evolving.
On the mod p derived Hecke algebra of a p-adic group [electronic resource]
Keywords: Mathematics.

In this thesis we explore the structure of the derived Hecke algebra of a p-adic group, a graded associative algebra whose degree 0 subalgebra is the classical Hecke algebra. Working with Z/p^a coefficients, we will establish a Satake homomorphism relating the degree 1 component of this algebra, and the corresponding component for the algebra of a maximal torus. Generalizations and extensions of this construction are also discussed.
On Treaties and Taboos: US Responses to the Norms in the NPT and Genocide Convention (1946-1999)
Keywords: Center for International Security and Cooperation
International Relations Program
genocide
Genocide Convention
nuclear weapons
Nuclear Nonproliferation Treaty
norms
international norms
international order
international society
Thesis

Tens of millions of people perished during the Second World War. The deaths caused by the Holocaust and the nuclear bombing of Hiroshima and Nagasaki, however, attained a special prominence in the collective memory of humanity. The leader of the post-war international order, the United States, was simultaneously liberator of the Nazi concentration camps and the state that had used atomic weapons against Japanese civilians. Nevertheless, during the remainder of the 20th century, United States responded very differently to the norms that developed around nuclear weapons and genocide—specifically the nuclear nonproliferation norm and the international prohibition against genocide. This thesis investigates the reasons behind the difference in the United States’ responses to the nuclear nonproliferation norm and the international prohibition against genocide during the 20th century. Four case studies are examined: the drafting of the Genocide Convention (1944-1948); the drafting of the NPT (1958-1968); the United States’ response to India's nuclearization (1947 - 1999); US intervention during the Kosovo War (1998-1999). The results of this research find that the norm against nuclear proliferation reinforces the post-war international order—one led by the United States and organized under the United Nations system. In contrast, the international prohibition against genocide highlights contradictions embedded in the UN Charter and threatens to disrupt the foundation of the UN society of states. The implications of these findings suggest that there are limits to the kinds of international norms that can be constructed and endorsed by the United States within the structure of the current UN society of states.
Online active learning with linear models [electronic resource]
Keywords: Mathematical and Computational Engineering.

In this thesis we address online decision making problems where an agent needs to collect optimal training data to fit statistical models. Decisions on whether to request the response of incoming stochastic observations or not must be made on the spot, and, when selected, the outcomes are immediately revealed. In particular, in the first part, we study scenarios where a single linear model is estimated given a limited budget: only k out of the n incoming observations can be labelled. In the second part, we focus on active learning in the presence of several linear models with heterogeneous unknown noise levels. The goal is to estimate all the models equally well. We design algorithms to efficiently solve the problems, extend them to sparse high-dimensional settings, and derive statistical guarantees in all cases. In addition, we validate our algorithms with synthetic and real-world data, where most of our technical assumptions are violated. Finally, we briefly explore active learning in pure exploration settings for reinforcement learning. In this case, an unknown Markov Decision Process needs to be learned under a fixed budget of episodes.
Online and distance instruction in lower income countries [electronic resource] : evidence from three field experiments
Keywords: Education.

In recent decades, the advancement of computing technologies has resulted in a proliferation of new educational resources -- from computerized learning software to fully online courses, offered free of charge and available to anyone with Internet access. While excitement around the new technologies has ebbed and flowed, there is no slowdown in the creation of computerized and online teaching products, many which target disadvantaged populations, including those in lower income countries. However, little rigorous evidence exists about whether online and distance instruction is effective these settings where student needs may differ considerably from those in higher income nations, where most research in this area is conducted. My dissertation offers some of the first evidence in this area of inquiry through three field experiments on the use of online and distance-learning instruction in two lower-middle income countries, Ghana and Mongolia. I begin by examining the demand among Ghanaian educators for online sources of professional development and identifying barriers for effective implementation. I then investigate the effectiveness of a blended online instructional pilot in STEM courses in Mongolia and finally evaluate an interactive model of distance learning in Ghanaian primary schools that could represent the future of online learning.
Opening Up Open Access: Investigating Alternate Funding Models to Stimulate Open Access Publishing
Keywords: Science Technology and Society
Open Access Publishing
Thesis

Open access, or the publishing practice of making a printed work available to anyone, embodies the idea that the world is better off when we freely share knowledge. As it stands, only a small percentage of academic articles are published under such a license, meaning that new, emerging, and exciting research is often inaccessible to many who might benefit from it. This is, in part, due to the cost of publishing; those journals that do offer open access as an option must shift the cost of lost revenue to the authors. As a result, the author usually must spend thousands of dollars of their grant money to make an article open access. In this thesis, I explore the question: is it economically feasible for publishers to make a revenue-neutral move to open access by realigning funding pathways? I propose a new model which shifts the monetary burden of open access from publishers and authors to funding agencies through the direct support of article publishing. This thesis shows how such a model can be revenue-neutral for a journal moving from closed subscription to open access. The results demonstrate that funding agencies are already involved in sponsoring research articles, and that a revenue-neutral shift is possible due both to a reduction in transaction costs and the proposed redistribution of publishing costs across several stakeholders. The data collected for the purpose of this thesis from publicly available sources indicates which groups of agencies play large roles in funding research, and addresses various concerns raised about the proposed system. My analysis shows that a revenue-neutral move from subscriptions to open access system is feasible, while pointing to potential cost savings and advantages for each stakeholder in the academic publishing industry.
Optimization, random graphs, and spin glasses [electronic resource]
Keywords: Statistics.

This thesis studies a class of optimization problems on sparse random (hyper-)graphs. Of central focus is the optimum value of these problems on graphs with a large number of vertices. The first part introduces a general framework to study the typical value of some combinatorial optimization problems on sparse random graphs, via a connection with mean-field spin glasses. An an application, we derive novel bounds on various combinatorial quantities such as Max-Cut, min-bisection, max XORSAT etc. The second part of this thesis studies a semi-definite relaxation of the min-bisection problem on sparse random graphs. As a consequence, we provide near optimal recovery guarantees for a natural semi-definite programming based algorithm for the community detection problem.
Optimizing technology R&D and adoption with adaptive adversaries [electronic resource] : a Markov game approach with cyber and biosecurity applications
Keywords: Management Science and Engineering.

Decision makers in government, industry, and academia need to consider adversaries with harmful intentions when planning the development and adoption of some new technologies. Typical decision models for technology focus on commercial applications where patent law or market economics strongly influence competition. Existing models do not address all cases where adversaries can co-opt or misuse even a tightly regulated technology. This dissertation extends the technology adoption literature to consider technology decisions with adversaries in conflict scenarios where technology determines outcomes for the decision makers. We develop a general framework and model that is intended to capture strategic issues in technology decision making using a Markov game. Then we use the model to answer contemporary risk management questions in two diverse fields: cyber operations (a high-obsolescence technology field) and synthetic biology (a case study on dual-use influenza viral research). Technology R& D, conflict events, and external random events are modeled as stochastic processes for each player. These cases seem unrelated—but they share mathematical features that benefit from analysis with our model.
Orbital diversity for global navigation satellite systems [electronic resource]
Keywords: Aeronautics and Astronautics.

The underlying theme of this dissertation is the utilization of new orbits to improve the Global Navigation Satellite System (GNSS) we rely upon in nearly all facets of modern life. This includes new orbits for safety-critical augmentation systems as well as for navigation core-constellations. Today, safety-oriented augmentation is placed in geosynchronous orbit while navigation core-constellations such as GPS are placed in medium Earth orbit. This lack of diversity leads to certain pitfalls. Augmentation systems are limited in platforms on which they can piggyback and do not reach users at high latitude. Navigation systems have limited geometric diversity as well as faint signals, leaving them vulnerable to interference and limited in urban and indoor environments. The orbital diversity introduced here improves the service, reliability, and functionality of GNSS. In the present work, new orbital representations are developed to enable orbits such as medium, inclined geosynchronous, and highly elliptical for augmentation with a tenfold improvement in orbit description accuracy compared to service today. This, along with constellation and frequency diversity on the horizon, is shown to enable safety-critical services for both aviation and maritime operations in the entire northern hemisphere. This is of great importance in the Arctic where commerce and traffic is on the rise due to decreasing sea ice. The addition of these orbit classes also increases SBAS visibility in urban canyons where safety critical systems like autonomous automobiles are beginning operation. For navigation, we propose leveraging the wealth of low Earth orbiting (LEO) satellites coming in the near future. This unprecedented space infrastructure is planned by the likes of OneWeb, SpaceX, and Boeing to deliver broadband Internet globally. These LEO constellations offer a threefold improvement on geometry compared to navigation constellations today, relaxing constraints on other aspects while still maintaining the positioning performance of GPS. Closer to Earth, LEO offers less path loss than MEO, improving signal strength by 1000 fold (30 dB). This strengthens us to interference and aids substantially in urban and indoor environments.