VictorJuiz/thesis huggingface dataset:
Reaching for “Moonshots”: Exploring the Persistence of Community College Transfer Students Who Applied to Highly Selective Universities

The American community college is currently a place where underserved populations, particularly substantial numbers of low-income and first-generation students, get a "second chance" at higher education and professional training. Many community college students opt to transfer to four-year institutions due to the rising necessity of an undergraduate education, and established pipelines of support channel students into affiliated public and/or state schools. Some students, however, decide to stray from these norms and apply to highly selective universities that have historically accepted low numbers of transfer students. This study interviewed twelve students who successfully transferred into a highly selective, research-intensive university. It explores the social relationships and interactions that transfer students perceive as contributing to their ability to apply and transfer to a highly selective university. The findings of this study revealed that the students maintained a strong drive to apply to these universities and sought out “validating agents” who willingly encouraged, affirmed, and supported their decisions. Moreover, the findings suggest that transfer students do not always attain goal support and instrumental support toward their desired goals, leading to a series of recommendations to help improve educational opportunities within this system.

Keywords: community colleges
highly selective universities
higher education
validation
persistence
social support
first-generation
low-income
transfer students
Thesis
Advisor: Stevens Mitchell
Willinsky John
O'Keeffe Jamie
A real-time framework for kinodynamic planning with application to quadrotor obstacle avoidance [electronic resource]

This thesis presents a full-stack, real-time planning framework for kinodynamic robots that is enabled by a novel application of machine learning for reachability analysis. As products of this work, three contributions are discussed in detail in this thesis. The first contribution is the novel application of machine learning for rapid approximation of reachable sets for dynamical systems. The second contribution is the synthesis of machine learning, sampling-based motion planning, and optimal control into a cohesive planning framework that is built on an offline-online computation paradigm. The final contribution is the application of this planning framework on a quadrotor system to produce, arguably, one of the first demonstrations of fully-online kinodynamic motion planning. During physical experiments, the framework is shown to execute planning cycles at a rate 3 Hz to 5 Hz, a significant improvement over existing techniques. For the quadrotor, a simplified dynamics model is used during the planning phase to accelerate online computation. A trajectory smoothing phase, which leverages the differentially flat nature of quadrotor dynamics, is then implemented to guarantee a dynamically feasible trajectory. An event-based replanning structure is implemented to handle the case of dynamic, even adversarial, obstacles. A locally reactive control layer, inspired by potential fields methods, is added to the framework to help minimizes replanning events and produce graceful avoidance maneuvers in the presence of high speed obstacles.

Keywords: Aeronautics and Astronautics.
Advisor: Pavone Marco
Rock Stephen
Schwager Mac
Real-time prefrontal cortex circuit intervention rescues social behavioral deficits in a genetic model of autism [electronic resource]

Increased cellular excitation/inhibition (E:I) balance has been suggested to represent a neural circuit activity-based final common pathway contributing to social-behavior deficits in autism-spectrum disease. For this hypothesis to be of translational significance, it should be demonstrated that acutely reducing E:I cellular balance can correct social behavior deficits. However, this crucial demonstration has not been possible in any preclinical or clinical model of autism, since currently-available drugs directly affect both excitatory and inhibitory neurons and thus cannot precisely modulate E:I balance. Even more fundamentally, it is not clear when such an intervention would have to be delivered, since if the initial maladaptive E:I balance pathology is exerted early in development, interventions delivered later could be ineffective. Here, we directly explore these questions, beginning with validated clinically-guided mice genotypically based on the human-pedigree CNTNAP2 mutation (showing social behavior deficits and stereotyped/repetitive behaviors with hyperactivity at baseline). Mice lacking CNTNAP2 gene have decreased number of parvalbumin and oxytocin neruons, as well as cortical developmental abnormalities. We achieved temporally-precise and cell-specific reduction of medial prefrontal cortex (mPFC) E:I balance by both selectively increasing the excitability of inhibitory parvalbumin (PV) neurons and decreasing the excitability of excitatory pyramidal (PYR) neurons using optogenetic approaches. Surprisingly, this real-time and reversible E:I balance modulation acutely rescued social behavior deficits and hyperactivity when delivered in the adult brain. Delving into possible mechanisms, we discovered (using fiber photometry technology to record naturally-occurring cell- specific activity signals during free behavior) that native PV neuron dynamics differed between CNTNAP2 knockout (KO) and wild-type (WT) mice in mPFC. While in WT animals the inhibitory PV cells encoded social interaction via increased activity (compared to the level in novel-object interactions), in KO animals the PV neurons failed to increase this inhibitory activity in social vs. other types of interaction. We then investigated the role of neuromodulation in mPFC on social behaviors. We found that infusion of oxytocin receptor antagonists into mPFC reduced social interactions in WT mice. More interestingly, oxytocin receptor agonist infusion rescued social behavior deficits and hyperactivity in CNTNAP2 KO mice, while not causing a significant change in WT social interactions. Together, these results demonstrate the significance of real-time mPFC E:I cellular modulation in social behavior and in rescuing autism-related symptomatology, highlighting the promise of circuit-based mechanisms and translational targets for autism.

Advisor: Deisseroth Karl primary advisor. Thesis advisor
Luo Liqun
Malenka Robert C.
Shen Kang
Reciprocal play fuels the social construction of early altruism [electronic resource]

Altruism, the act of promoting others' welfare, is a key aspect of human life. Is altruism a phenomenon that can be counted upon to flourish in the absence of social experience? I conducted this dissertation research in the context of research suggesting that altruism is a "natural" phenomenon that arises independent of any kind of social experience. By contrast, I propose that much of young children's altruism can be fostered by a subtle aspect of social experience. Specifically, I argue that reciprocal interactions -- exemplified in early childhood by reciprocal play -- are a plausible mechanism for the rise of early altruism. As such, Section 1 uses the methodology of research on "natural altruism" to show that reciprocal play is key for the expression of altruism in infants and toddlers (Study 1 and 2), as well as in preschoolers (Study 3). Section 2 suggests why this altruism presents itself: Reciprocal play fuels expectations of benevolence (Study 4), and when these expectations are experimentally manipulated, altruism flourishes (Study 5). Section 3 moves from examining the possibility that reciprocal play is a trigger of altruism to examining whether reciprocal play is a plausible mechanism for the socialization of altruism. Indeed, Studies 6-9 suggest that when parents practice reciprocal play, altruism flourishes across a variety of contexts. All in all, I argue that reciprocal play is a key driver for the social construction of early altruism.

Keywords: Psychology.
Advisor: Dweck Carol S.
Gweon Hyowon primary advisor. Thesis advisor
Walton Gregory M. (Gregory Mariotti) primary advisor. Thesis advisor
Reconstitution of the mechano-sensitive cadherin-catenin/F-actin complex [electronic resource]

Cell-cell adhesion is essential for tissue development and maintenance. In epithelial tissue, the cadherin-catenin complex establishes this adhesion and associates with the actin cytoskeleton to do so. A long-standing hypothesis is that the cadherin-catenin complex binds actin filaments directly, but work using purified proteins challenged this idea in 2005. Since then, studies have found that the cadherin-catenin complex is sensitive to mechanical tension. As a result, we hypothesized that the complex requires tension to bind actin filaments. Results from an optical-trap assay supported this idea, and we concluded that cadherin-catenin complexes and actin filaments form two-state catch bonds, which last longer at intermediate levels of tension. Work of others suggested that association of vinculin with the cadherin-catenin complex is the molecular basis of the longer-lived catch bond state. Our follow-up work using the vinculin head domain, which binds the cadherin-catenin complex in solution but not actin filaments, demonstrated that association of vinculin lengthens the duration of actin bonds. Full-length vinculin, however, is an autoinhibited molecule that binds the cadherin-catenin /actin complex weakly. Thus, based on other studies, further work sought to test whether or not actomyosin-generated tension and abl-mediated phosphorylation were sufficient to increase this binding. Experiments conducted using a microscopy-based filament-binding assay showed that while tension and phosphorylation were not required for association of vinculin, they had an additive effect on the amount of bound vinculin. Altogether, my thesis work provided mechanistic insights into how mechanical tension affects the kinetics and composition of the cadherin-catenin/F-actin complex.

Keywords: Biophysics.
Advisor: Dunn Alexander Robert primary advisor. Thesis advisor
Nelson William primary advisor. Thesis advisor
Theriot Julie advisor. Thesis advisor
Weis William I. advisor. Thesis advisor
Recovering a Kantian analytic/synthetic distinction through incompatibility [electronic resource]

This dissertation seeks to recover a viable analytic/synthetic distinction that retains a distinctly Kantian heritage. It is formulated with distinctly metametaphysical intent, to be part of another philosophical project that Kant initiated: the critique of metaphysics. In my view, to take or treat a claim as analytic is to, at least implicitly, to undertake a commitment to its being deducible merely from our commitments about object-general, non-localized incompatibility and entailments claims; to treat a claim as synthetic is, at least implicitly, to undertake an implicit commitment to its not being so deducible. The account of the analytic/synthetic divide I provide is cleaved in terms of alethically modal concepts which, traditionally, have been seen as metaphysically-loaded and hence problematic for my purposes. This is because the dominant philosophical tradition for understanding alethic modality rests its account on the metaphysically and epistemically fraught notion of a continuum of inter-accessible possible worlds. To avoid this, my account draws on resources found in Robert Brandom's incompatibility semantics, which offers an alternative account of necessity and possibility in terms of the less-problematic notion of incompatibility (Brandom 2008). My appropriation of Brandom's incompatibility semantics incorporates several changes. First, I reinterpret Brandom's semantics using an intensional notion of schematic generality, which helps me to clarify the semantic interdependence of general and particular therein and resolve several epistemological and methodological concerns. I also discuss the complicating factor of nonmonotonicity by reference to the Michael Thompson's work on "natural-historical judgments" (2008), showing how the generality and modality expressed in nonmonotonic, modally-sophisticated claims can fit within my revised understanding of incompatibility semantics and the analytic/synthetic divide. Next, I modify Brandom's incompatibility semantics by formally extending it to equal the expressive power of Kripke Semantics by incorporating an analog of accessibility relations therein, and thereby rectifying formal and intuitive impoverishments of Brandom's formalism. I also provide an interpretation of what accessibility relations, transposed into incompatibility semantics, can be taken to mean by invoking a logical notion of meta-compatibility, and I provide a pragmatic explication of what linguistic practitioners must do in order to take or treat matters as meta-compatible.

Keywords: Philosophy.
Advisor: Taylor Kenneth Allen
Crimmins Mark advisor. Thesis advisor
Lawlor Krista advisor. Thesis advisor
Recovery of resources and energy using methane-utilizing bacteria [electronic resource] : synthesis and regeneration of biodegradable, tailorable bioplastics and production of nitrous oxide

Methane is a familiar and abundantly available gas with both natural and anthropogenic sources. Aerobic methanotrophs (methane-utilizing bacteria) use methane as their sole carbon and energy source. Use of methanotrophs for biotechnological applications to convert methane into value-added products is attractive since methane is cheap, abundant, and in the case of anaerobic digestion is a renewable carbon source. One such potential application is production of biodegradable bioplastic, polyhydroxyalkanoates (PHAs), a sustainable alternative to petroleum-based plastics. Previously, poly(3-hydroxybutyrate) (P3HB) was the only type of PHAs reported to be produced by methanotrophs. However, applications for P3HB are limited by its narrow melt processing windows and lack of flexibility. This research present a methodology to produce various PHAs having a wide range of thermophysical properties using methane as a primary feedstock and added co-substrates. This research also focuses on a recycling strategy to regenerate waste PHA products into new PHAs using "abiotic-biotic PHA recycling" that is rapid and efficient, and can avoid downcycling (i.e., it can avoid decrease of molecular weights each cycle). Methanotrophs can also be used to remove nitrogen from wastewater and generate nitrous oxide, a potential co-oxidant of biogas methane to increase energy production. Finally, this research demonstrates a novel methanotroph fermentation scheme, an emulsion-based fermentation, which enables enhanced mass transfer of insoluble methane substrates to methanotroph medium without the need for vigorous agitation.

Keywords: Civil and Environmental Engineering.
Advisor: Criddle Craig primary advisor. Thesis advisor
McCarty Perry L. advisor. Thesis advisor
Waymouth Robert M. advisor. Thesis advisor
Recurrent Point Mutations in the Kinetochore Gene KNSTRN in Cutaneous Squamous Cell Carcinoma

Cutaneous squamous cell carcinoma (SCC) is the second most common cancer, with an annual global incidence in excess of 1 million. To identify recurrent genomic aberrations that underlie the development of this malignancy, single nucleotide variant (SNV) determinations from whole-exome sequencing of 12 SCC-normal pairs was used to distill a list of 336 candidate genes that were then sequenced in 100 SCC-matched normal pairs with an average depth exceeding 1200X. KNSTRN ranked third behind CDKN2A and TP53 among recurrently mutated genes in SCC after normalizing for gene length. KNSTRN encodes a kinetochore protein that has not previously been implicated in cancer. Somatic mutations in KNSTRN were present in 2 of 12 (17%) and 19 of 100 (19%) SCCs analyzed by whole exome and targeted sequencing respectively, and most mutations occurred around a UV-signature hotspot serine to phenylalanine substitution present at codon 24 (S24F). KNSTRN S24F was detected in SCC precursors, consistent with an early event in tumorigenesis. Cancer-associated mutant KNSTRN disrupted chromatid cohesion in normal cells, and using whole-genome copy number analysis, SCCs with KNSTRN S24F were determined to be significantly associated with an increase in copy number aberrations. Mutant KNSTRN also enhanced Ras-driven tumorigenesis in vivo. Thus, we report the first cancer-associated missense mutations in the kinetochore gene KNSTRN with dominant, pro-tumorigenic consequences in cutaneous SCC.

Keywords:  Department of Biology
Biology
cancer
KNSTRN
squamous cell carcinoma
SCC
genetics
sequencing
molecular genetics
Thesis
Advisor: Khavari Paul
Lee Carolyn
Bergmann Dominique
Refashioning Napoletanità: Identity, Corporeality, and Value Creation in the Neapolitan Bespoke Tailoring Industry

Despite Naples' gritty, dangerous image being incongruous with conventional bourgeois aesthetics of Italian luxury fashion, Neapolitan bespoke tailoring is regarded as one of the most prestigious sectors of global luxury menswear. Editorial attention on these tailoring firms (sartorie) fail to fully unpack the complex interplay between Neapolitanness (napoletanita') and commercial value. Drawing on two summers of fieldwork in Naples and Florence, I argue that the sartorie conceive of their work's value as deriving from their napoletanita', understanding Neapolitan cultural identity's multiplicity of meanings and contradictions in ways that cohere with their ascendancy in luxury fashion. I first consider how history, renegotiated, is a powerful modality through which sartorie experience and express their napoletanita'. Naples' storied Greek, Roman, and Enlightenment past resolves tensions between the sartoria's cultural prestige and contemporary Naples' lack thereof, while "traditional" Neapolitan narratives of labor and handcraftsmanship resolve the luxury industry's inherent tension between commerce and exclusivity. The Mafia's violent 20th century legacy is understood as testifying to the enduring spirit of Neapolitans for having survived. Second, I outline how for sartorie artisanship rests upon a productive tension between the eye's perfect judgment and the hand's imperfect unmechanicality. Artisanship breaks down the traditional dichotomy between Maussian gift and Marxian commodity, by incorporating inalienable napoletanita', creating producer-client social obligations, and obscuring certain social relations of production in the sartoria. After Douglas, I suggest that the sartorie's corporeal concerns about the lack of artisanal eye or handcraftsmanship i competing menswear sectors evince social concerns about the gift of napoletanita's susceptibility to being threatened by industrialization. The final section centers a value-based understanding of labor processes and cultural commodification in safeguarding the future of waning artisanal industries, suggesting how the EU might implement geographical indication protection schemes beyond agricultural produce and foodstuffs industries.

Keywords:  Department of Anthropology
artisanship
cultural commodification
gift
geographical indication protection
Naples
value
Thesis
Advisor: Yanagisako Sylvia
Regulation of lysosomes in myelination and microglia function [electronic resource]

The central nervous system, composed of the brain and the spinal cord, is made up of two broad classes of cell types: neurons and glia. The interaction between glial cells and neurons is crucial for proper development and function of the nervous system. The first type of glial cells, macroglia, includes astrocytes and oligodendrocytes. Oligodendrocytes are the cells that form myelin, an evolutionary adaptation that allows rapid and efficient propagation of action potentials along axons. Diseases of myelin include multiple sclerosis, in which damage to the myelin sheath in the central nervous system disrupts flow of information between the brain and the body, often leading to debilitating symptoms. The second glia cell type, microglia, performs a variety of roles in the CNS including phagocytic clearance of dead neurons and debris. Microglia have been implicated in neurodegenerative diseases such as Alzheimer's Disease, which is characterized by memory loss, neuronal death and accumulation of abnormal amyloid plaques. By understanding the pathways that control microglia and oligodendrocyte development and function, novel therapies for CNS diseases may be developed by harnessing the capabilities of these cell types. In this dissertation, I focus on the roles of the Rag-Ragulator complex and other lysosomal-associated proteins in microglia and oligodendrocytes. In Chapter 2, I describe the identification of mutations that disrupt the Rag-Ragulator complex in a screen for myelin mutants. In mutants lacking RagA and Lamtor4, components of the Rag-Ragulator complex, myelinated axons are reduced compared to wildtype siblings, despite the presence of oligodendrocytes. The absence of Rag-Ragulator function prevents oligodendrocytes from maturing and ensheathing exons. These results point toward a key function of lysosomes in myelination. In Chapter 3, I describe the microglial function of the Rag-Ragulator complex. RagA and Lamtor4 mutants have a reduced number of microglia. The few microglia that are present have an expanded lysosomal compartment - yet are unable to properly clear debris that they have engulfed. In Chapter 4, I characterize Tcirg1b mutants, which exhibit a similar microglia phenotype to RagA mutants. Tcirg1b encodes a component of the vacuolar proton pump that acidifies the lysosome. Tcirg1b mutants have microglia that are engorged with undigested apoptotic neuronal debris. Together, this work defines new roles of lysosomal genes in oligodendrocytes and microglia, thereby highlighting the importance of lysosome function in different glial cell types.

Keywords: Developmental Biology.
Advisor: Talbot William
Bejerano Gill
Meyer Tobias advisor. Thesis advisor
Nusse Roel
Regulation of the ARL6 GTPase cycle within the primary cilium [electronic resource]

Primary cilia organize cellular signaling cascades by dynamically concentrating signaling receptors in response to extracellular cues. In particular, the removal of signaling molecules from cilia tunes the sensitivity of major signaling pathways but remains a poorly understood process. A major sorting complex for the cilium is the BBSome, a coat-like complex of eight Bardet-Biedl Syndrome (BBS) proteins, which directly recognizes signal receptors and co-moves with the intraflagellar transport (IFT) machinery within cilia. Importantly, recruitment of the BBSome to membranes relies on GTP loading onto the ARF-like GTPase ARL6/BBS3, but no regulators for the nucleotide state of ARL6 have been identified so far. Identification of the guanine nucleotide exchange factor (GEF) and GTPase-activating protein (GAP) for ARL6 is key to pinpointing the locations where BBSome coats assemble and disassemble, respectively, and will further shed light on the pathomechanisms of BBS. Because mutations in the Rab-like GTPase and IFT-B subunit IFT27/RABL4 were recently identified in a BBS family, we sought to characterize the function of IFT27 in BBSome-mediated trafficking. Strikingly, ARL6, BBSome and the candidate BBSome cargo GPR161 accumulated in IFT27-deficient cilia, and photokinetic assays on stable cell lines expressing fluorescently tagged BBSome revealed that IFT27 perturbation reduces BBSome exit rates ~3-fold while leaving BBSome entry rates unaffected. At the molecular level, IFT27 disengages from the rest of IFT-B to directly associate with and stabilize the nucleotide-free form of ARL6 against aggregation. Thus, we propose that within cilia, IFT27 dissociates from IFT-B to directly participate in GTP loading onto ARL6, promoting the assembly of exit-bound and cargo-laden BBSome coats. Additional mechanisms for the regulation of IFT27 and ARL6 within cilia are discussed.

Keywords: Biochemistry.
Advisor: Nachury Maxence
Beachy Philip Arden advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Straight Aaron