VictorJuiz/thesis huggingface dataset:
Synchronizing Traffic Signals on Grid Networks During a Rush

A simple strategy is offered for coordinating all traffic signals on street networks arranged as grids. The strategy is based on the finding that signals of symmetric networks can be perfectly synchronized in two orthogonal directions. With this in mind, the strategy synchronizes signals in the directions that point towards the center of gravity of all workplaces in the morning rush, and away from that center during the evening. Although the strategy was initially developed for symmetric networks, it can readily be adapted to accommodate asymmetrical grid arrangements as well. The strategy is also dynamic and adaptive to real-time traffic conditions. Signals are synchronized according to the free flow motion of vehicles in under-saturated traffic, and to backward waves once street links are filled with queues. An algorithm is developed to switch smoothly between the two synchronization modes as conditions change during a rush./nThe strategy was tested via simulations of 20 x 20 signalized grids, operating in non-steady-state traffic conditions typical of rush periods, and benchmarked against a fixed zero-offset strategy commonly recommended for congested traffic. In a scenario representing a morning rush with a monocentric distribution of workplaces, the strategy was also benchmarked against the well-known SYNCHRO program. While SYNCHRO reduced the morning commute delays by 7\% relative to the fixed zero-offset strategy, the proposed strategy reduced delays by 32\% (more than four times that achieved by SYNCHRO). The strategy continued to perform well when workplaces were distributed more broadly over the network, and when workplaces were distributed in a multi-centric pattern. The strategy also performed well when tested for an evening rush, and was adapted to perform well when the grid’s original symmetry was distorted to represent a more realistic transportation network.

Advisor: Cassidy, Michael J
Neural correlates of complex communication and navigation behaviors in Egyptian fruit bats

Understanding how neural circuits control complex social and spatial behaviors in humans requires a tractable mammalian model system that allows one to probe both the appropriate behavior and its underlying neural activity. Egyptian fruit bats (Rousettus aegyptiacus) are an attractive model for studying the motor control of vocal communication and navigation. To thrive within hierarchical social structures in dark cave environments, bats evolved specialized auditory and vocal production systems to both echolocate and communicate with one another. However, to date, the detailed neural computations that support this behavior in mammals are unknown. Furthermore, in the wild, bats fly highly reproducible trajectories from their home cave to foraging sites over 20km round trip nightly. It is unclear whether the neural representation of these flight paths remains stable across days when a stable behavior is performed. In this thesis, I describe my efforts to study the behavior, anatomy, and neurophysiology of vocal communication and spatial navigation in a novel model organism./nIn Chapter 1, I provide and introduction to theories of vocal learning, mammalian motor control of vocal production, and social communication. Furthermore, I provide a focused review of the hippocampal representation of place and current theories of how this representation changes across days. In Chapter 2, I present my efforts to design a behavioral task that operantly trained the bats to produce vocalizations for reward. Additionally, I present anatomical tracing data that identified the motor cortical site of laryngeal control and supports the theory of vocal learning in bats. Finally, I discuss collaborations to probe the underlying electrophysiology in this motor region during the vocal production task. In Chapter 3, I present my work developing a wireless miniature fluorescent microscope and its use to study the longitudinal stability of spatial coding in freely flying bats performing a self-paced navigation task. This work is presented as a manuscript (currently under review) with my co-author Dr. William Liberti.

Advisor: Yartsev, Michael M
Metabolic Flux Signature Perturbations: Endoplasmic Reticulum Stress, Diet, and Aging

The unfolded protein response in the endoplasmic reticulum (UPRER) is involved in a number of metabolic diseases, including non-alcoholic fatty liver disease. Here, we first characterize the UPRER induced metabolic changes in mouse liver through in vivo metabolic labeling and mass spectrometric analysis of proteome and lipid fluxes. We induced ER stress in vivo via tunicamycin treatment and measured rates of proteome-wide protein synthesis, de novo lipogenesis and cholesterol synthesis serially over a three-day period, thereby generating a metabolic “signature” of the UPRER over time. Synthesis of most proteins was suppressed under ER stress conditions, including proteins involved in lipogenesis, consistent with reduced de novo lipogenesis at 48 and 72 hours. The reduction in de novo lipogenesis was explicable by reduced food intake, shown in pair-feeding studies. Despite the lower de novo lipogenesis rates, electron microscopy revealed striking morphological changes to ER and H&E staining showed lipid droplet enriched livers under ER stress. Pre-labeling of adipose tissue prior to ER stress induction revealed mobilization of lipids from adipose to the liver. Interestingly, the source of these lipids in liver was uptake of free fatty acids, not whole triglycerides or phospholipids from lipoproteins, as demonstrated by replacement of the triglyceride-glycerol moiety in liver concurrently with increased incorporation of labeled palmitate from adipose tissue. We also induced ER stress by a high-fat diet and observed similar metabolic flux signatures, suggesting that this mechanism may play a role in the progression of fatty liver disease. Using these same stable isotope labeling approaches, several changes in protein synthesis across ontologies were noted with age, including a more dramatic suppression of translation under ER stress in aged mice as compared to young mice. De novo lipogenesis rates decreased under ER stress conditions in aged mice, including both triglyceride and phospholipid fractions. In young mice, a significant reduction was only seen in the triglyceride fraction. These data indicate that aged mice have an exaggerated response to ER stress, which may indicate less effective mechanisms of protein clearance after inducing the UPRER. These flux-based approaches provide a powerful tool to identify novel regulators of ER stress and potential targets for pharmacological intervention. We applied the same stable isotope labeling techniques to generate region-specific metabolic flux signatures of mouse brains. Assessing how metabolic flux signatures of the brain are perturbed through different interventions, including anti-aging therapeutics and preventative lifestyle interventions, could provide a powerful tool to assess cell-specific and region-specific changes with age, and provide a kinetic metric to assess intervention effectiveness.

Advisor: Hellerstein, Marc
Combinatorics of polytopes, orthogonal polynomials, and Markov chains

We study various combinatorial formulas arising in the asymmetric exclusion process, orthogonal polynomials, and Ehrhart theory. In particular, we give combinatorial formulas for polynomials with positive coefficients. Explaining the positivity of such polynomials is an interesting problem by itself, and giving combinatorial formulas is useful as they provide a fast and compact way to compute those polynomials./nThe asymmetric exclusion process (ASEP) is an important model from statistical mechanics which describes a system of particles on a lattice hopping left and right. This process was introduced in the 1970s independently in the context of biology and mathematics. Since then, this model has many variants and was studied extensively in various fields. The ASEP on a line is a Markov chain on a one- dimensional lattice of length $N$ with open boundaries. A particle can hop to the right with the rate 1 and can hop to the left with rate $q$, as long as the neighboring site is empty. And on each boundary, a particle can enter from the left or right with rate $\alpha$ or $\delta$ respectively and can exit to the left or right with rate $\gamma$ or $\beta$ respectively. Papers of Sasamoto \cite{SS} and subsequently, Uchiyama, Sasamoto, and Wadati \cite{MU} revealed a surprising connection between the ASEP on a line and orthogonal polynomials, in particular the Askey-Wilson polynomials which lie in the top hierarchy of (basic) hypergeometric orthogonal polynomials in the sense that all other polynomials in this hierarchy are limiting cases or specializations of the Askey-Wilson polynomials. In Chapter 2, we give combinatorial formulas for the Al-Salam-Chihara polynomials, which are related to the ASEP when $\gamma=\delta=0$. The totally asymmetric exclusion process (TASEP) on a ring is a Markov chain on a periodic one-dimensional lattice of length $N$ where each lattice site can be either occupied by a particle or empty. A particle can hop to its right (when it is empty) with the rate 1. In Chapter 3, we study the inhomogeneous version of the TASEP and show that many steady-state probabilities are proportional to the product of Schubert polynomials./nIn the 1960s, Ehrhart introduced Ehrhart polynomials and Ehrhart series to study the number of lattice points inside polytopes. Since then, there has been a lot of study on Ehrhart polynomials and Ehrhart series of many well-known polytopes. The $(k,n)$-$th$ $hypersimplex$ $\Delta_{k,n}$ is a lattice polytope inside $\mathbb{R}^n$ whose vertices are (0,1)-vectors with exactly $k$ 1's. The hypersimplex can be found in several algebraic and geometric contexts, for example, as a moment polytope for the torus action on the Grassmannian, or as a weight polytope for the fundamental representation of $GL_n$. In Chapter4, we prove the first combinatorial formula for the Ehrhart series of the hypersimplex, proving a conjecture of Early \cite{Early1}.

Advisor: Williams, Lauren
Human-Centered Circuit Board Design With Flexible Levels of Abstraction and Ambiguity

Printed Circuit Board (PCB) design tools are critical in enabling users to build non-trivial electronics devices.However, mainstream tools work at the lowest level of design --- schematics and individual components --- which can make design difficult for beginners and tedious for experts./nIn this work, we start by examining current board design practices to learn how a variety of users approach the process, what tools they use, what works well, and where things are lacking.From those results, we focus on building tools to support the system architecture level of design --- a representation that we believe captures the most important design decisions without getting mired in the details./nTaking inspiration from software engineering and chip design languages, we implement a hardware construction language (HCL) that supports users at multiple levels of abstraction (from system to subcircuits), enables mixed-ambiguity design through abstract components (such as a generic resistor instead of a particular part number), and encodes the methodology for subcircuit design instead of static instances (for example, automatically sizing a resistor in a LED circuit).To support users working with this very different interface to board design, we also build an integrated development environment (IDE) plugin that adds a linked graphical view and editor to the standard textual code editor./nSmall but in-depth user studies on these tools indicate that this approach can provide benefits over mainstream flows, but also suggests avenues for continued work.

Advisor: Hartmann, Björn
Alon, Elad
Hopf Monoids and the Theory of Valuations

Many families of combinatorial objects have natural ''merging" and ''breaking" operators which endow the family with a Hopf algebra structure. The theory of Hopf monoids is a refinement of the Hopf algebras that appear in combinatorics that are better equipped to deal with labeled objects and produce stronger results. Since their inception, these objects have unified various disparate results in combinatorics. In this dissertation, we present three results in this direction./nIn the second chapter, we initiate the study of an extension of Hopf monoids to the category of posets. These objects model combinatorial families with a poset structure compatible with the Hopf structure. This compatibility is best understood as the multiplication maps and comultiplication maps forming an adjunction - a fact generalizing the restriction-induction adjunction of the representations of the symmetric group. With this, many aspects of Hopf monoids, such as duality, primitives, and the antipode, simplify to purely poset-theoretic aspects such as Galois connections, Mobius inversion, and characteristic polynomials. With this method, we give new calculations of the primitives of hypergraphs, set partitions, and simplicial complexes as well as giving formulas for their antipodes./nThe third chapter presents joint work with Ardila that gives a new Hopf-theoretic framework for the theory of valuations on generalized permutahedra. Valuations are functions on polytopes which generalize measures. In particular, they satisfy certain inclusion-exclusion relations coming from polytope subdivisions. Using this new framework, we give a powerful method for constructing valuations from simpler ones. With this, we recover many of the previously studied valuations on matroid polytopes as well as construct new valuations for matroid polytopes, poset cones, and nestohedra. Of particular note, we show that many algebro-geometric invariants arising from the theory of wonderful compactifications of hyperplane arrangements are valuations. These include the Kazhdan-Lusztig polynomial of a matroid, the motivic zeta functions of a hyperplane arrangement, and the Eur's volume polynomial of the combinatorial Chow ring of a matroid./nIn the final chapter, we discuss the relationship between Hopf monoids and the type A_n root system as well as efforts to extend Hopf monoids to arbitrary root systems. While properly defining Coxeter Hopf monoid is currently out-of-reach, we present joint work with Eur and Supina that describes a universal valuation for Coxeter matroids. In the type A_n case, this valuation is a Hopf monoid morphism - a fact which is responsible for the relationship between Hopf monoids and valuations. Extending this result to arbitrary root systems would lead to new applications in Coxeter combinatorics and in the geometry of the flag varieties of arbitrary Lie type.

Advisor: Ardila, Federico
Williams, Lauren
A History of Electroacoustics: Hollywood 1956 – 1963

This dissertation argues that a cinematic approach to music recording developed during the 1950s, modeling the recording process of movie producers in post-production studios. This approach to recorded sound constructed an imaginary listener consisting of a blank perceptual space, whose sonic-auditory experience could be controlled through electroacoustic devices. This history provides an audiovisual genealogy for electroacoustic sound that challenges histories of recording that have privileged Thomas Edison’s 1877 phonograph and the recording industry it generated. It is elucidated through a consideration of the use of electroacoustic technologies for music that centered in Hollywood and drew upon sound recording practices from the movie industry. This consideration is undertaken through research in three technologies that underwent significant development in the 1950s: the recording studio, the mixing board, and the synthesizer. The 1956 Capitol Records Studio in Hollywood was the first purpose-built recording studio to be modelled on sound stages from the neighboring film lots. The mixing board was the paradigmatic tool of the recording studio, a central interface from which to direct and shape sound. Finally, the electronic synthesizer offered the potential for total control over sonic timbre, as can be seen in the use of the Trautonium in Alfred Hitchcock’s The Birds (1963). Together, these histories advance an understanding of recorded sound that de-centers the idea of reproduction, and emphasizes instead twentieth-century cybernetic ideals of influence, and, ultimately, control, through the recorded medium of sound.

Advisor: Davies, James Q.
Advanced concepts in prompt gamma-ray imaging for ion-cancer verification

The major paradigm in the treatment of cancer has been to develop and improve methods for more focused targeting of cancerous cells while reducing the toxicity to healthy tissue. In radiation oncology, that effort has been focused recently on the use of proton beams. The dose kinematics of protons – namely the Bragg curve – allows for better conformity to tumors. However, as protons do not escape the patient, additional safety margins are added to treatment plans which undermine the theoretical therapeutic benefits of protons unless reliable in vivo range verification tools are found.This dissertation describes advanced techniques and concepts as applied to a multi-knife edge slit collimator 2D imaging system. First, the physics of proton therapy is reviewed and a survey is given of current ongoing system designs for proton range verification. Next, an overview is given of the system as well as new improvements to the hardware and software of the data acquisition system. New measurements were then conducted using a 67.5 MeV proton beam at an order of magnitude higher beam current than has been done previously. Details of additional gain and crystal segmentation adaptation algorithms developed to correct for beam-induced effects on the photomultipliers are then described. The incorporation of a separate detector to provide timing information about the arrival of the beam is then discussed: both the potential benefits as well as limitations found in its use here that will inform future iterations of the design. Lastly, a physics kernel is introduced based on published angular excitation functions to further enhance image quality. The system was found to be able to determine the range of the proton beam to within 1 mm (2σ) with the delivery of 10^10 protons across a 6 cm FOV. Future investigations utilizing the techniques proposed here should only enhance this sensitivity and contribute to efforts to better patient outcomes.

Advisor: Vetter, Kai
Privacy-Preserving Computation for Nuclear Safeguards

Nuclear safeguards are a key component in international efforts to prevent the proliferation of nuclear weapons. The International Atomic Energy Agency (IAEA) and its nuclear inspectors are tasked with administering these safeguards measures, ensuring to the best of their ability that weaponizable nuclear material is not created or diverted without the knowledge of the international community. However, no safeguards system is invincible, and so it is necessary for the IAEA to be constantly advancing and expanding its capabilities. At the same time, despite the vast majority of the international community agreeing that the proliferation of nuclear weapons should be avoided via their commitments permitting the IAEA to administer safeguards within their jurisdictions, it is expected that some States will be hesitant to allow the agency to significantly expand the scope of implemented safeguards. This leaves large quantities of potentially insightful data unavailable to safeguards administrators evaluating compliance with international regulations./nThis dissertation proposes a solution to reconcile these competing interests in the form of privacy- preserving computation. Using privacy-preserving algorithms, IAEA inspectors and IAEA Mem- ber States may realize a new paradigm where nuclear facility data can be analyzed for safeguards purposes without that data ever being revealed to anyone other than the facility operators. These algorithms open the possibility that entirely new data streams may become accessible to IAEA inspectors, especially those that lend themselves to modern data analytics techniques./nThis work represents the culmination of recent efforts to showcase for the first time how nuclear safeguards could be implemented in a privacy-preserving context. It includes a proof-of-concept demonstration of how the privacy-preserving technique of garbled circuits could be used for a safe- guards analysis of real nuclear data, highlighting the present feasibility of such algorithms. It also introduces CypherCircuit, a new software framework for building and evaluating garbled circuits that is intended to facilitate the adoption of privacy-preserving technologies by skeptical or non- expert audiences. The CypherCircuit Python package is designed to cultivate an understanding of garbled circuits through an intuitive, transparent, and accessible design, encouraging the application of privacy-preserving techniques to novel challenges—in this case nuclear safeguards.

Advisor: Slaybaugh, Rachel N
What Does the Fox Say? A Cross-Cultural Analysis of Aesop and the Talking Animal Tradition

Aesop’s fables are sometimes dismissed as stories for children, and not worthy of serious study. This dissertation argues that fables are an important part of understanding cultural world views of animals, and that the relationships between humans and animals depicted in Aesop’s fables are question the binary division between humans and animals. Talking animals are not just laughable tales for children, but they provide a method for exploring human identity as one species among many, interacting with other beings in a way that depends upon relationship rather than possession of human speech. I use theoretical approaches from Indigenous Studies and Human-Animal studies, and I use Indigenous animal stories, in particular, those collected by William Jones in the earlier twentieth century and published in his two-volume Ojibwa Texts. The Ojibwe stories demonstrate alternative methods of understanding anthropomorphism and the relationship between humans and animals./nIn chapter 1, I first look at an Aesopic fable that may have been translated into Ojibwe as a case study for my methods. Next, I look at several famous fables quoted by other Greek authors, and I demonstrate that the talking animals in these accounts can be read as destabilizing the idea of human exceptionalism and human exclusivity in the realm of justice. In chapter 2, I explore human relationships with other animals, specifically with canine species. I focus on Aesopic fables about wolves and the Ojibwe story “Nenabozho and the Wolves” for this investigation. In chapter 3, I look at trickster figures: the fox in Aesop’s fables, and Nenabozho and other animals in Ojibwe stories./nThis project makes two important contributions to the field. First, it looks at fables for their own sake, arguing that they are more than just allegories of human experience, but that they demonstrate cultural attitudes toward animals and allow human beings to better understand their relationship with other species. Second, this dissertation relies upon Indigenous stories and Indigenous scholars to provide interpretive methods for better understanding of Aesop’s fables. This is in contrast to previous scholarship which used Classical mythology to explain Indigenous stories./nI have chosen this interpretive method because I believe that Indigenous stories and methods afford valuable perspectives that are often ignored or forced to fit into Western paradigms. By adopting this cross-cultural methodology, I hope to both open a new method of interpretation and also recognize the value of Indigenous stories and language within the humanities in general.

Advisor: Kurke, Leslie