VictorJuiz/thesis huggingface dataset:
Huddle: Building Your Circle of Support
Keywords: mental health
Learning Design and Technology
Graduate School of Education
Wellness Education
peer support
conversation
Residential Education
peer health educator
depression
suicide
supportive conversational strategies
Thesis

Peers are often first-responders to mental health crises for college students. Peers are also often insufficiently prepared to respond effectively in these situations. College campuses are more reactive than preventative in their approach to mental health care. However, college freshmen are undergoing a significant period of transition when it is most critical to have the skillset to manage their own and support other’s mental health. Undergraduate freshmen need to recognize symptoms of depression and suicidal ideation, feel comfortable responding to a peer in need, and prioritize a healthy mind.
Huddle is an online learning experience for undergraduates on college campuses. This is an immersive experience integrated with peer health educator or residential advisory programs in residential dorm settings for students to build skills through a 3-step approach: 1) informing students about the warning signs of depression and suicidal ideation, 2) identify cues to appropriately support a peer in need, and 3) effectively navigate a conversation with a peer as a medium of support. If students can practice these skills in a safe, low-consequence environment, then they should feel more prepared to transfer these skills to real life and, in turn, have greater control over their own mental health care.
I anticipate that students will see an evident increase in confidence and comfort in acting as first-responders to mental health problems by their peers after engaging with Huddle over a few weeks in their first-year in college. A high functioning prototype of Huddle has been tested with freshmen for success in learning and usability. This feedback will inform the design of Huddle as a fully functioning product.
Huddle cultivates supportive college communities by empowering college freshmen to navigate difficult conversations about mental health with their peers.
Hybrid ionic liquid - boron nitride gates for clean, high carrier density transistors [electronic resource]
Keywords: Physics.

Using gates to change carrier density via the electric field effect is a cornerstone of condensed matter physics. Gating using ionic liquid electrolytes has recently generated considerable interest as a method to achieve large carrier density modulations in a variety of materials, opening routes to devices based on physics accessible only at carrier densities beyond the breakdown limit for oxide dielectrics. However, electrolyte gates can chemically modify the channel due to electrochemically driven reactions and increase carrier scattering due to the proximity of the ions in the electrolyte to the carriers in the channel. In this work, I discuss how inserting a thin layer of hexagonal boron nitride between the electrolyte and the channel prevents chemical modification and suppresses scattering, while still allowing carrier densities significantly beyond those possible with oxide dielectrics. I begin with a brief introduction to electrolyte gating using ionic liquids, including the use of reference electrodes in three terminal measurements. In the second chapter, using a combination of in situ x-ray spectroscopy and electrochemical techniques, I show that trace impurities in the ionic liquids can cause reversible electrochemical oxidation of a gold channel and that a thin boron nitride layer prevents this oxidation. I then take a brief digression to discuss how x-ray scattering can be used to learn about surface and interface structure. I develop a new model for analyzing crystal truncation rods from miscut surfaces that can be used to learn about terrace morphology and that has a simple roughness factor to account for disorder from terrace steps in the truncation rod intensity. In the fourth chapter, I use x-ray reflectivity to probe the spatial arrangement of the ions on a strontium titanate channel, and show that the timescale for ion rearrangement matches the timescale for the onset of electrical conduction, suggesting an electrostatic gating effect. Finally, I show that boron nitride spacers significantly improve carrier mobility in graphene channels and that the remaining scattering arises primarily from ions in the bulk liquid.
Hybrid modeling of engine core noise [electronic resource]
Keywords: Mechanical Engineering.

Core noise, or the noise generated by unsteady combustion, is a growing concern for aircraft engine designers. Core noise is typically divided between direct noise, the acoustic fluctuations generated by the flame, and indirect noise, the noise created as unsteady flow structures are distorted and accelerated downstream of the flame. This thesis develops new modeling tools for predicting both direct and indirect noise behavior and also analyzes the mechanisms by which core noise arises. The problem of indirect noise generation in turbomachinery applications is considered in detail. Existing low order, acoustically compact models for indirect noise prediction are reviewed. A new correction to the compact model is then proposed which renders new predictions rotationally invariant, a property that previous models do not possess. Ultimately, an acoustically noncompact model is developed which incorporates geometric and frequency-dependent effects and and is compared against higher order numerical results. It is then demonstrated that fluctuations in mixture composition can act as a previously unconsidered source of indirect noise. Additionally, the sensitivity of the mechanism to fuel choice and thermodynamic operating considerations is explored. The model is then expanded to account for acoustically noncompact effects in nozzle flows. Lastly, the impact of core noise on the total downstream acoustic signature of an aircraft engine is examined. The study focuses on a representative engine flowpath, constructed of a test stand combustor, single stage turbine, nozzle, jet and acoustic farfield. The modeling approach couples high fidelity Large Eddy Simulation of the combustor, nozzle and jet with low order models for the turbomachinery stages in order to capture both the generation and propagation of acoustic and turbulent fluctuations as they pass from the combustor downstream to the acoustic farfield of the device. It is found that the coupling between core noise and jet noise is quite complex, with low frequency sound amplified by core noise effects while high frequency noise is slightly suppressed. Ultimately, a physical mechanism for this coupling is proposed, positing that the presence of upstream fluctuations excites an instability in the jet, leading to the observed changes in acoustic response.
Hypoxic regulation of C5aR1 in colorectal cancer
Keywords:  Department of Biology
biology
cancer
hypoxia
complement system
HIF
C5aR1
Thesis

Hypoxia, or low oxygen tension, is a common feature of the tumor
microenvironment that is linked to tumor resistance to radiation therapy, and thus, is also
associated with poor patient prognosis. The complement system, a set of serum proteins
which has traditionally been understood as part of the immune system, has also been
found to be tumor-promoting when upregulated. However, the interaction between
hypoxia and the complement system is not fully understood. In patients with colorectal
cancer, an increased level of complement component C5a receptor (C5aR1) expression is
strongly correlated with poor patient prognosis, and we have found that C5aR1
expression is also increased in hypoxia. We predicted that the hypoxia inducible factors
(HIFs) may be playing a role in the transcriptional upregulation of C5aR1. We assessed
at what level the induction was occurring at—transcriptional or translational—and
produced complicating data. In a subset of experiments, hypoxic induction was observed
with dependence on HIF-1α, which was predicted to bind upstream of the C5AR1
promoter. We also observed that induction was lost in some cells and absent in different
cell lines. We conclude that C5aR1 may be induced in hypoxia but also depends on other
cellular factors. The results of this study provide novel insight into how the upregulation
of C5aR1 occurs in colorectal cancer. Given the relationship between C5aR1 levels and
patient outcome, understanding how receptor expression is regulated may allow for the
development of new therapeutic approaches to treating colorectal cancer.
Identification of single barium atoms with resonance ionization mass spectroscopy for the nEXO neutrinoless double beta decay experiment [electronic resource]
Keywords: Physics.

The mechanism for neutrino mass generation is an open question in particle physics, with implications for new physics at higher mass scales. If neutrinos are their own antiparticle, meaning they have Majorana masses, this property can be measured through a rare process called neutrinoless double beta decay. EXO-200 is an experiment searching for neutrinoless double beta decay of xenon-136 using a liquid xenon time projection chamber. The first part of this work describes a search for the two-neutrino double beta decay of xenon-136 to an excited state of barium-136 with EXO-200 data using machine learning techniques. A measurement of the half-life of this decay can provide valuable input to nuclear models and reduce systematic uncertainties of the neutrinoless double beta decay process. The second part of this work describes efforts to greatly improve the sensitivity of a future experiment similar to EXO-200 through the identification of the barium-136 daughter produced in the double beta decay of xenon-136. In the technique explored here, barium ions are adsorbed onto a substrate, where they neutralize, and are then transported to a separate identification chamber. They are subsequently desorbed using laser-induced thermal desorption (LITD) and selectively ionized using resonance ionization spectroscopy (RIS), followed by identification using a time of flight mass spectrometer. Improvements in understanding of the LITD and RIS processes, backgrounds to the technique, and substrate cleaning methods are presented, bringing the technique closer to single barium atom sensitivity.
Identifying the causal effects of early life socioeconomic exposures on health over the life course [electronic resource]
Keywords: Health Research and Policy.

Social and economic factors during childhood are known to influence health later in life. These include factors like poverty and education. The objective of this dissertation is to apply cutting-edge methods to study the effects of early life social and economic conditions on health and mortality. This will help guide the development of interventions and policies to address these risk factors. This dissertation is made up of three studies with the following goals: (1) characterize the impacts of childhood family income on child development; (2) examine the effects of state-level social and economic factors during childhood on later health and mortality; (3) identify the effect of educational attainment on chronic disease outcomes and biomarkers. Each of the three projects involves the linkage of multiple large data sets including thousands of individuals spanning years or decades. The unifying theme of these projects is the use of cutting-edge rigorous methods. In each of these studies, I find that the childhood social and economic factors described above are associated with later health. I review the implications of these projects for the development of relevant policies and interventions. In a time when discussions around inequality are increasing, research such as this will better inform policy decisions to improve health among disadvantaged groups.
Identifying the Cellular Origin and Enzymatic Mechanism of Activity-regulated Neuroligin-3 Secretion
Keywords:  Department of Biology
biology
neurobiology
high-grade glioma
neuroligin-3
ADAM10
tumor proliferation
Thesis

High-grade gliomas (HGG) are the leading cause of brain tumor death. Despite advancements in therapeutics, prognoses for patients remain poor with current treatment methods. Recently, it has been shown that neuronal activity promotes HGG growth via the activity-dependent cleavage and secretion of neuroligin-3 (Nlgn3), an important synaptic molecule and newly recognized glioma mitogen. However, the mechanisms of its cleavage and secretion are largely uncharacterized. Understanding both the cell-of-origin of Nlgn3 and the mechanism of enzymatic cleavage would shed light on the molecular interactions occurring in the glioma microenvironment, which in turn could inform therapeutics. Using a genetic knockout mouse model, this study demonstrates that Nlgn3 is necessary for glioma growth in vivo. Analyses of conditioned media generated from acute cortical slices in the presence of specific protease inhibitors showed that Nlgn3 is secreted from neuron and oligodendrocyte precursor cell populations, and cleaved enzymatically by the ADAM10 sheddase. Furthermore, administration of an ADAM10 inhibitor robustly blocks the growth of xenografted HGG cells in vivo. The results of this study highlight the therapeutic potential of targeting Nlgn3 cleavage and secretion in the glioma microenvironment and offer a novel and promising way to limit the proliferation of this group of deadly brain tumors.
Identifying the gene modifier of twinning in indeterminate gametophyte1 (ig1) Zea mays mutants
Keywords:  Department of Biology
Biology
Maize
Zea mays
Corn
Genetics
Carnegie Institution for Science Department of Plant Biology
Thesis

The indeterminate gametophyte1 (ig1) gene in maize is an important regulator in the transition from proliferation to differentiation in embryo sac development. ig1 mutant embryo sacs lack the ability to limit proliferation, which leads to structural defects. These defects include embryo sacs with extra egg cells, extra central cells, and extra polar nuclei, which give rise to abnormal seed phenotypes post-fertilization. Extra egg cells in an embryo sac can be fertilized producing kernels with multiple viable embryos. The ig1-O mutation results in different frequencies of multiple embryos, or “twinning,” in different maize inbred backgrounds. Confocal microscopy confirmed that Mo17 embryo sacs carrying the ig1-O allele have a significantly higher frequency of multiple egg cells than ig1-O embryo sacs in a B73 inbred background. The frequency of twinning is intermediate in the ig1-O/+ Mo17/B73 hybrid compared to ig1-O inbred lines. This suggests that a genetic modifier(s) may be responsible for the difference in phenotypic frequency between these inbred lines. Based on Genotyping by Sequencing (GBS) data analysis and further fine mapping, there are two major enhancers of twinning on chromosome 8 and 9. Carrying the Mo17 allele of either one of these is sufficient to increase the frequency of twinning caused by the ig1-O mutation.
Identifying the role of an oxytocin-like neuropeptide in A. burtoni social behavior
Keywords:  Department of Biology
Isotocin
Prostaglandin F2α
Astatotilapia burtoni
knockout
ascent
descent
aggression
reproduction
social behavior
Thesis

The neuropeptide oxytocin plays a role in generating social behavior appropriate to context. Although pharmacological studies have implicated the peptide in a wide range of behaviors, oxytocin knockout studies in mice have shown that the peptide is not necessary for many of its associated behaviors. Mice, however, have a limited behavioral repertoire and cannot alone provide a complete picture of the peptide’s necessity in regulating various social behaviors. In this study, we used the cichlid fish Astatotilapia burtoni to characterize the social behavior role of isotocin, the oxytocin homolog found in teleost fish. Females of this species perform unique reproductive behaviors, whereas males adapt their social status to match their changing social environment. We first analyzed the role of isotocin in female spawning behavior by studying a line of A. burtoni carrying a CRISPR-generated null mutation in the isotocin gene (IT-/-). We then described the activity of isotocin neurons by quantifying the coexpression of isotocin with egr-1, an immediate-early gene and proxy for neural activity. Finally, we described the behavior and reproductive success of male IT-/- A. burtoni to evaluate the peptide’s role in male status and behavior. Our data show normal rates of typical social behaviors in both male and female IT-/- fish, as well as potential involvement of isotocin neurons in social descent. These results provide insight into the role of isotocin in female spawning behavior and male social status, and they also suggest possible signaling pathway redundancy.
Identity, threat, and belonging in online learning environments [electronic resource]
Keywords: Communication.

Psychological threats to people's social identity and sense of belonging can undermine motivation and performance in in-person learning environments. I argue that these social psychological processes can also apply in technology-mediated environments and limit the potential of online environments to provide more affordable, personalized, and effective learning experiences at scale. Many online learning environments face the unique challenge of serving people around the world from diverse cultural and socio-demographic backgrounds. To create psychologically inclusive environments that afford equal opportunities to diverse learners, the content and design of online environments can be manipulated strategically. A synthesis of verbal and visual cues that can reduce threats to social identity and belonging specifically in online learning environments is presented. Discussion focuses on when to tailor the learning environment to different people, how the effects of different cues interact, and how to assess online psychological inclusivity.
Imaging of electron forces, interactions, and topological states in designer quantum materials [electronic resource]
Keywords: Physics.

We have developed atomic manipulation with a scanning tunneling microscope (STM) into a compelling new tool to investigate the fundamental properties of condensed matter systems. Our new capability to assemble and fine-tune essentially any two-dimensional lattice combined with the ability to probe density of states at subatomic scale allows us to investigate the physics of electronic states with unprecedented freedom and precision. Here I aim to answer questions that so far proved too elusive for traditional material synthesis and measurement methods, in particular, questions about topological states in complex non-periodic systems and about many-body instabilities driven by electron interactions. In this thesis, I focus on corrals and lattices created by patterning a free electron gas of a Cu(111) surface with carbon monoxide (CO) molecules. The CO molecules provide act as potential wells and constrain the surface state electrons to an effective lattice or corral pattern. In the first part I explain a series of quantum force measurement experiments, where I try to shed some light on the quantum force distance dependence and focusing inside several corral structures. Next part describes charge fractionalization in molecular polyacetylene as well as in Kekule distorted molecular graphene. I discuss how a domain wall or a vortex defect in a bond strength wave, leads to an emergence of a mid-gap state, and the fractional charge associated with it. Following that, I talk about effective gauge fields in graphene induced by strain as well as through direct modulation in bond strength and on-site potential. I explain how these induced perturbations to the lattice can be described by gauge fields, equivalent to the ones associated electromagnetic fields. One remarkable consequence of this equivalence is strain gauge invariance that allows one to produce lattices with the same electronic energy spectrum, but very different local structure. In the next part, I show how electron-electron interactions lead to instabilities as the lattice constant changes. In particular, I show that in a honeycomb lattice doped to the Van Hove singularity, the instability leads to a spontaneous nematic and polarized pseudospin phase. I also research investigate the instability in the flat band of a honeycomb 5-5-8 grain boundary where the leading phase is likely magnetic. Next, I describe quasicrystalline molecular lattices based on Penrose tilings and the electron fractalization that happens in them. I show the deep connection between penteract and electrons in a Kite-and-Dart quasicrystal that form localized states at energies related by the golden ratio. I end by briefly discussing some possible future experiments that can exhibit an even larger variety of effects such as an emergence of a quantum spin Hall state or topological currents can be expected. These effects might show when one introduces stronger interactions and stronger spin-orbit coupling present for example on surfaces of gold and topological insulators.
Impact of common and rare regulatory variation on human disease [electronic resource]
Keywords: Genetics.

The rate at which we have identified human genetic variation has greatly outpaced our capacity to characterize the functional significance of individual variants. This interpretation bottleneck is the product of several distinct challenges that ultimately hinder our ability to link individual variants with specific phenotypes. One challenge is that the vast majority of variants are found in non-coding regions of the human genome and have no immediately obvious functional consequences. Another challenge is the overwhelming abundance of rare and novel variants that are found in a given individual - these variants are difficult to interpret because we cannot be certain of their association with any particular phenotypic effect. In this thesis, I address several questions regarding the interpretation of genetic variants, with a focus on those that are found in non-coding regions of the genome. After providing a general overview of the variant interpretation problem, I discuss one of the primary risks associated with clinical genome sequencing - namely the problem of dealing with incidental findings. I then discuss how we can improve our ability to identify common and rare regulatory variation using isolated populations and family-based study designs. Finally, I provide several examples demonstrating the clinical utility of RNA sequencing for patients with rare, undiagnosed genetic disorders.
Implications of grazing for the internal distribution of Macrocystis pyrifera chemical defense compounds
Keywords:  Department of Biology
grazer
chemical defense compounds
polyphenols
life stage
Macrocystis pyrifera
blade
Thesis

Grazing organisms can negatively affect giant kelp (Macrocystis pyrifera) individuals and ecosystems by consuming large amounts of biomass. M. pyrifera, however, serves important ecosystem functions, providing food, habitat, shelter, and nursing grounds for a suite of organisms. Thus, it is crucial to understand M. pyrifera’s mechanisms of defense in order to predict how M. pyrifera responds to heavy grazing events and how M. pyrifera protects itself on a day-to-day basis. Little is known about the distribution of M. pyrifera’s chemical defense compounds (polyphenols) across life stages and within a blade. To test this, M. pyrifera blades were subjected to grazing by Chlorostoma brunnea. This was repeated for juvenile, adult, and apical blades. Polyphenol levels of each blade were tested and compared. Polyphenol concentrations were found to be highest in apical blades, lowest in juvenile blades, and moderate in adult blades. Within juvenile blades, the tip contained the lowest concentration of polyphenols, whereas the base contained the highest. Polyphenol distributions were found to align with distributions of compounds and biological processes that may enhance the individual’s fitness.