VictorJuiz/thesis huggingface dataset:
Novel astrophysical signatures of beyond the standard model physics

Astrophysical systems provide novel opportunities to search for new physics in regions of parameter space inaccessible to Earth-based experiments. Supernovae, for example, are some of the hottest environments in the Universe, achieving temperatures upwards of tens of MeV; they are consequently uniquely suited to test models of new physics at the MeV scale. In this dissertation, I will show that supernovae (and other astrophysical systems) allow us to probe a wide range of models of new physics, both placing new constraints and suggesting future signals by which we might one day uncover what lies beyond the Standard Model

Keywords: Physics.
Advisor: Graham Peter (Peter Wickelgren)
Dimopoulos Savas
Toro Natalia
Novel biomaterials for enhanced spatiotemporal control of adjuvant delivery to improve immune activation

While prophylactic vaccines and immune checkpoint inhibitors are two of the greatest medical feats of all time, they have come nowhere near fully eradicating infectious disease or cancer, respectively. The primary challenge to developing immunotherapies that work for all patients and across all disease states is that our immune system is incredibly complex. Many cues must be provided to our immune system in a coordinated manner -- considering both timing and location -- to realize the full effects of immunotherapy. Fortunately, our understanding of how our immune system interacts with pathogens and vaccines has grown enormously over recent decades, allowing for the development of more targeted immunotherapies. For example, we now have a thorough understanding of the downstream changes that follow activation of a wide array of pattern recognition receptors (PRRs) that recognize different danger signals, or adjuvant molecules. By combining our understanding of immunology with our understanding of novel biomaterials that can provide levers for controlling presentation, biodistribution, and kinetics of therapeutics, we can incorporate adjuvants into vaccines and cancer therapies in a manner that overcomes limitations of canonical immunotherapy. In my thesis, I have focused on engineering methods for polymer-based delivery of adjuvants to both improve the efficacy of and reduce the toxicity of subunit vaccines and immune checkpoint inhibitors

Keywords: Biochemistry.
Advisor: Appel Eric (Eric Andrew)
Kim Peter
Li Lingyin
A novel diffuse-interface model and numerical methods for compressible turbulent two-phase flows and scalar transport

Compressible two-phase flows and the transport of scalars in two-phase flows have a wide range of applications in natural and engineering processes. In this thesis we first present a novel diffuse-interface model for the simulation of compressible two-phase flows. We start with the baseline five-equation model that consists of equations for the transport of volume fraction, mass of each phase, momentum, and total energy. It is known that this model cannot be used with a non-dissipative scheme as is, and the direct solution of these equations with a dissipative scheme results in artificial diffusion of the interface which results in poor accuracy. We, therefore, propose interface-regularization (diffusion--sharpening) terms to this five-equation model in such a way that the resulting model can now be used with a non-dissipative central scheme, and the model also maintains the discrete conservation of mass of each phase, momentum, and total energy of the system. For stable numerical simulations of compressible flows, it is known that a discrete entropy condition needs to be satisfied, and the discrete conservation of kinetic energy alone is not a sufficient condition, unlike in incompressible flows. To achieve this, we first propose discrete consistency conditions between the numerical fluxes, and then present a set of numerical fluxes--which satisfies these consistency conditions--that results in an exact discrete conservation of kinetic energy and approximate conservation of entropy (a KEEP scheme) in the absence of pressure work, viscosity, and thermal diffusion effects. Next, we also propose a novel scalar-transport model for the simulation of scalar quantities in two-phase flows. In a two-phase flow, the scalar quantities typically have very different diffusivities in the two phases, which results in effective confinement of the scalar quantities in one of the phases, in the time scales of interest. This confinement of the scalars leads to the formation of sharp gradients of the scalar concentration values at the interface and could result in artificial numerical leakage of the scalar and negative values for the scalar concentration values, presenting a serious challenge for its numerical simulations. To overcome this challenge, we propose a new consistent scalar-transport model that prevents artificial numerical leakage of the scalar at the interface. The proposed model also maintains the positivity property of the scalar concentration field, a physical realizability requirement for the simulation of scalars. Finally, we present numerical simulations to verify and validate the models presented in this work in a wide range of settings and regimes, spanning laminar to turbulent flows; and assess the accuracy, robustness, and scalability of the models

Keywords: Mechanical Engineering.
Advisor: Moin Parviz
Lele Sanjiva K. (Sanjiva Keshava)
Mani Ali (Professor of mechanical engineering)
Urzary Javier
Novel rechargeable batteries of sodium/chlorine, lithium/chlorine and aluminum/graphite

This dissertation presents two main works accomplished during my PhD research on rechargeable batteries. In the first part of the dissertation (chapter 2-3), new types of rechargeable sodium and lithium batteries, called sodium/chlorine and lithium/chlorine batteries, are introduced and their performances and working mechanisms are discussed. In the second part of the dissertation (chapter 4), the study of two different ionic liquid electrolytes, one being the mixture of aluminum chloride and 1-ethyl-3-methylimidazolium chloride and the other being the mixture of aluminum chloride and 1-methyl-1-propylpyrrolidinium chloride, for aluminum/graphite battery is presented

Keywords: Chemistry.
Advisor: Dai Hongjie
Solomon Edward I.
Zare Richard N.
Novel regulators of learning and plasticity in motor system circuits

Motor learning is the process by which animals integrate sensorimotor information from the world in order to update future motor actions and improve desired outcomes. Neuroscience research in the past decades has identified brain structures and neuronal circuits involved in this process, and revealed that motor learning is a highly distributed process that involves precise spatiotemporal coordination and refinement throughout the corticobasal ganglia network. Reflecting this widespread involvement of brain circuitry, experimental approaches to study motor learning encompass a wide array of scope and techniques including in vivo electrical recordings or imaging, synaptic-level electrophysiology, genetic pathway analyses, and more. The work presented in this dissertation focuses on understanding two key activity-dependent mechanisms by which the synapses of circuits involved in motor control and motor learning change. Chapter 1 provides an overview of the motor learning field, with particular focus on the literature surrounding functional and structural synaptic plasticity of the synapses that I primarily focused on for my PhD work: (a) the synapses on neurons in primary motor cortex and (b) their projections into the striatum. In Chapter 2, I show that the stability of newly formed dendritic spines in motor cortex is the greatest predictor of motor learning, and that artificially increasing their stability in wildtype mice is sufficient to enhance the acquisition of motor skills. To do this, I studied PirB-/- mice and used chronic in vivo two-photon imaging of dendritic spine dynamics (in M1) while training mice on a reaching task. I showed that pharmacologically increasing the stability of newly formed spines in M1 (by selectively blocking PirB function genetically or with a decoy receptor) during training is sufficient to improve their learning of this task. In Chapter 3, I show that mice lacking all 3 isoforms of Synuclein (Syn-tKOs) exhibit an abolishment of endocannabinoid (eCB) plasticity in the striatum. Combining electrophysiological recordings with pharmacology and viral strategies, I dissected this synaptic phenotype and found that synucleins are required postsynaptically for eCB release, where activity-dependent membrane interaction of synucleins (likely with SNAREs) is needed for retrograde eCB signaling. In Chapter 4, I touch on conclusions and future directions based on this work. I place my findings in the context of the larger fields of motor learning and synaptic plasticity, and end with implications for promising translational therapeutic science

Advisor: Ding Jun (Jun B.)
Shatz Carla J.
Buckwalter Marion
Luo Liqun 
Malenka Robert
Nuclear aPKC-Mediated Mechanisms of Drug Resistance in Basal Cell Carcinoma

Transcription factor trafficking requires a highly regulated process involving numerous structural proteins in the nucleus. Disruptions to these processes have been implicated in a number of diseases including the development of drug resistance in basal cell carcinoma (BCC). BCC, one of the most common forms of skin cancer, is driven by high levels of Hedgehog (Hh) signaling, a critical pathway in development that has been associated with several cancers. Previous studies have identified atypical protein kinase C (aPKC) as a key regulator of drug resistance in BCCs, which functions to maintain a high Hedgehog pathway signal in order to promote tumor growth and therefore evasion of treatment. However, while aPKC appears to alter nuclear structure, the specific mechanism through which it regulates the Hh pathway and its transcriptional output remains unclear. One hypothesis proposes that aPKC interacts with the nuclear lamina, and through this interaction can release transcription factors from the nuclear envelope. Lamins are classically involved in nuclear structural maintenance and recent findings have also elucidated their important role in transcriptional regulation, especially upon post-translational modifications. In order to analyze how aPKC interacts with the nuclear lamina, we conducted biochemical and phosphoproteomic analyses of a murine BCC cell line (ASZ0001) upon small-molecule inhibition of aPKC. Specifically, we analyzed aPKC’s phosphorylation residues in lamina via mass spectrometry of fractionated cell nuclei and evaluated the ability of nuclear lamina co-regulatory protein, LAP2α, to disrupt higher order phospho-lamin structure formation by co-immunoprecipitation-based lamin oligomerization assay. Notably, we found that interactions between aPKC and the nuclear lamina regulate the Hh pathway in BCC. In the nucleus, aPKC phosphorylates lamin A at residues near its IgG fold, including S390 and S392. Additionally, phosphorylation at these residues promotes association of lamin with LAP2α and the GLI1 transcription factor, which drives Hh signaling. These findings will aid in the discovery of future targeted therapeutics for BCC and further our understanding of transcription factor regulatory mechanisms, specifically the importance of movement between different nuclear compartments.

Keywords:  Department of Biology
Hedgehog
transcription factor
basal cell carcinoma
lamin
atypical protein kinase c
biology
Thesis
Advisor: Oro Anthony
Stearns Tim
Nuclear resonance vibrational spectroscopic studies of the biferric and high-valent states of binuclear non-heme iron enzymes

Binuclear non-heme iron (NH2Fe) enzymes play significant roles in all realms of life including human health, drug discovery, and antibiotic biosynthesis. These enzymes reductively activate dioxygen to form reactive intermediates that go on catalyze a wide variety of chemical reactions including hydroxylation, N-oxygenation, and electrophilic aromatic substitution. Defining the geometric and electronic structure of these enzymes in their resting biferric and intermediate states is critical in understanding their reaction mechanisms. Nuclear resonance vibrational spectroscopy (NRVS) probes the vibrational quanta of the 57Fe Mössbauer transition and is thus well-suited for selectively probing the NH2Fe center of this enzyme class. NRVS does not possess an optical selection rule, and the partial vibrational density of states (PVDOS) spectrum obtained from NRVS exhibits intensity for all modes containing 57Fe iron motion, yielding rich vibrational data. Calculation of the NRVS PVDOS spectra for candidate structural models using quantum mechanical methods permits modeling and assignment of the NRVS data, leading to elucidation of the geometric structure of a target molecule. In this thesis, NRVS is applied to the biferric states of class Ia ribonucleotide reductase (RnR) and soluble methane monooxygenase (sMMO), as well as the methane-reactive intermediate Q in sMMO, to define their geometric structures and understand how these structures influence their function

Keywords: Chemistry.
Advisor: Solomon Edward I.
Karunadasa Hemamala
Stack T. (T. Daniel P.)
"Nunca más una educación del Estado": (re)imaginando el sistema educativo en Iximulew

Resumen:
Veinticinco años después de que se firmaran los Acuerdos de Paz que terminaron con 36 años
de conflicto armado en Guatemala, no se ha llevado a cabo la implementación del Acuerdo de
Identidad y Derechos de los Pueblos Indígenas. Los poderes que controlaban el Estado que
ejecutó el genocidio del Pueblo Maya-Ixil, entre otros crimenes de lesa humanidad, aún
controlan las tres ramas del gobierno. Incluyendo el Ministerio de Educación, dentro de la rama
ejecutiva. Cuando las instituciones educativas son entendidas como espacios que reproducen
las estructuras coloniales capitalistas, se hace necesario (re)imaginar la educación. Semillas de
Atitlán localizado en Sololá y, el Proyecto Luis de Lión en Sacatepéquez, han traído a la
práctica el desafío de (re)imaginar la educación. Estos proyectos liderados por mujeres Mayas
y Mestizas son un nuevo estándar de lo que puede ser la educación y nos muestran que las
relaciones con los estudiantes, las familias y la comunidad pueden ser transformadas cuando la
enseñanza y el aprendizaje se hacen desde las perspectivas comunitarias. A través de esta tesis,
voy a yuxtaponer las condiciones dentro de las cuales el Estado provee la educación y los
proyectos transformadores que Anita Waxqi y Mayarí de León están liderando en sus
comunidades, el impacto que tiene en los estudiantes y las dificultades a las que se enfrentan
al desafiar el poder normativo del Estado.
Abstract:
Twenty-five years after the Peace Accords that ended the 36-year armed conflict in Guatemala,
there has not been an adequate implementation of the Agreement on Identity and Rights of
Indigenous Peoples. The powers that controlled the state during the genocide of the pueblo
Maya-Ixil, amongst other crimes against humanity, still holds power over the three branches of
government. This includes the Ministry of Education in the executive branch. When formal
education institutions are understood as sites that reproduce capitalist and settler-colonial
structures, another way of (re)imagining education is needed. Semillas de Atitlán located in
Sololá, and the Proyecto Luis de Lión in Sacatepéquez, have brought to praxis the challenge of
(re)imagining education. These projects led by Mayan and Mestiza women are setting a new
standard of what education can be. They are also demonstrating that the relationships amongst
students, families and the community at large can be transformed when teaching and learning
are carried out through a community perspective. Through this thesis, I will juxtapose the
conditions under which the state provides education and the transformative projects that Mayarí
de León and Anita Waxqi, respectively, are leading in their communities, the impact that it has
on the children, and the struggles they face by defying the normative rule of the state.

Keywords: community education, (re)imagination of futures, Iximulew,
Text
Thesis
Objective and subjective sleep quality in adolescence : relations With pubertal stage, affect, and functional brain connectivity

Sleep quality decreases dramatically during adolescence. Part of this reduction is due to pubertal-related changes, which in combination with social and psychological factors can lead to long-lasting impairments in sleep quality and affective functioning, particularly during a developmental period when the brain is maturing. In this dissertation, I measure a diverse set of objective and subjective sleep parameters using ecological momentary assessment and actigraphy in a community sample of mid- to post-pubertal adolescents. Given relatively few reports of subjective and objective sleep quality in relation to pubertal stage in a single sample, my first aim is to characterize associations of pubertal stage with subjective sleep satisfaction, objective sleep efficiency, objective and subjective sleep duration, and circadian preference. We found that, regardless of age, pubertal stage was associated with subjective sleep satisfaction, but not with any of the other sleep measures. Based on these findings, in my second aim, I investigate whether positive and negative affect (PA and NA, respectively) are associated with subjective sleep satisfaction, as opposed to sleep duration, and whether pubertal stage is related to PA and NA. We found that 1) higher NA and lower PA were related to poorer sleep satisfaction, but were not related to subjective sleep duration; and 2) advanced pubertal stage was associated with NA, but not with PA. Finally, given brain-based explanations for the association between puberty and affective difficulties, and because sleep is controlled by the brain, in my third aim I test whether measures of sleep are correlated with patterns of resting-state functional connectivity (FC) that have been previously found to be associated with impairments in sleep. I expand on previous reports linking experimentally-induced sleep restriction and FC by examining the relation between naturalistically-assessed objective and subjective sleep quality and intrinsic brain networks in this sample of mid- to post-pubertal adolescents. We found that higher FC within the anterior default mode network was associated with a circadian preference towards morningness. These findings are consistent with previous reports that objective and subjective sleep quality, including circadian preference, have different psychological and biological correlates. Longitudinal data are needed to test a mechanism by which sleep and the brain interact to explain the association between pubertal stage and affective difficulties. The findings from this project may help researchers generate testable hypotheses for understanding how intervention might best be possible during this vulnerable developmental period

Keywords: Psychology.
Advisor: Gotlib Ian H.
Poldrack Russell A.
Zaki Jamil
Observation of center of mass momentum in 7Li Bose-Einstein condensates

In this thesis I report on the observation of center of mass (CM) energy of a 7Li Bose-Einstein condensate far above the zero-point energy of the confining trap. This measurement is made possible by the attractive interactions of 7Li which prevent dispersion of the atomic cloud and create a soliton within a quasi-1D waveguide. This soliton behaves like a single particle and carries with it the CM momentum of the condensate from which it was formed prior to release from the initial trap. We observe soliton CM energies significantly larger than the above the ground state energy of the trap. This is a novel observation of condensate CM energy not explained by motion of the trap, thermalization, or mean-field effects in the condensation process. This data provides insight into the condensation process and places limits on the usefulness of solitons in other metrology applications

Keywords: Applied Physics.
Advisor: Kasevich Mark A.
Hogan Jason
Schleier-Smith Monika
Offline Norms and Online Behaviors: A Study of How Audience Perception Shapes Online Black Political Engagement

The study of Black American’s involvement in politics has been parsed with literature emphasizing the role historical and social contexts have had on black political behaviors—from Jim Crow segregation, to the Civil Rights movement, to the election and reelection of the first Black President. White and Laird have supplied extensive research to this discipline by using black American’s support for the Democratic Party as a proxy to answer how group unity in political choices is maintained. Yet, the perception of our online audience as a variable for enforcing racial group norms has been understudied in this discipline. The goal of this thesis is to bridge the conforming mechanisms present in our offline networks to those in our online networks, observing whether racial pressures in online spaces push for conformity around norms of black political behaviors. To do this, I design a survey experiment that tests whether black users’ engagement with anti-black or pro-black messages are contingent on whether they perceive the racial make-up of their online network to be black or white. Overall, data from the survey is consistent with the idea that the perceived race of our online network does influence black users’ engagements to group-based messages. These findings suggests that our online behaviors are motivated, in part, by our attachment to racial and social group identities.

Keywords: racial group norms
social identity
audience perception
online networks
black political norms
Text
Thesis
Advisor: Jefferson Hakeem
On hyperbolic cone metrics, PSL(2, R)-character varieties, and branched coverings

We study hyperbolic cone metrics on closed surfaces whose cone angles are integer multiples of 2 pi. The first part of this thesis focuses on local deformations of these cone metrics. We show that these cone metrics depend smoothly on their underlying complex structures and conical data, and that their holonomy representations define a smooth submersion to the PSL(2, R)-character variety. Furthermore, given any tangent vector in the image of this submersion, we construct a natural horizontal lift to the space of hyperbolic cone metrics and describe this lift in terms of harmonic forms and holomorphic quadratic differentials. The second part of this thesis focuses on hyperbolic cone metrics with a prescribed holonomy representation of Euler class 2 - 2g + 1. We study the space of these cone metrics when the prescribed holonomy representation is discrete, and describe a connection between the topology of this space and the Birman-Hilden lifting properties of branched coverings between closed surfaces

Keywords: Mathematics.
Advisor: Kerckhoff Steve 
Danciger Jeffrey
Trettel Steve J.