VictorJuiz/thesis huggingface dataset:
The development of conceptual representations of mental life

Attributions of thoughts, beliefs, desires, intentions, emotions, perceptions, and sensations are at the core of human social life—but "mental life" is a complex concept, encompassing a wide range of experiences and abilities that vary along many dimensions. This makes ordinary people's representations of mental life a fascinating case study of abstract reasoning and its development: How do children come to represent this complex conceptual space? In this dissertation I describe a series of large-scale studies designed to explore this question among children (4-9y) and adults in the modern US context, using an empirical approach that unites recent work on the "dimensions of mind perception" with rich traditions of research on the development of the animate-inanimate distinction, lay biology and psychology, and theory of mind. These studies address three ontological questions about ordinary people's representations of mental life: (1) What are the conceptual units that anchor representations of mental life at different points in development? (2) How are these conceptual units organized in relation to each other, and how does this organization change over development? and (3) How do people of different ages deploy their conceptual representations of mental life to reason about specific entities in the world—namely, animate beings vs. inanimate objects? Results suggest that, over the course of early and middle childhood, US children's representations of mental life undergo substantial development in all three of these respects. These findings have important implications for children's social cognitive development.

Keywords: Psychology.
Advisor: Dweck Carol S.
Markman Ellen M.
Gweon Hyowon
Development of novel methods for the formation of C-C and C-N bonds

Carbon-carbon and carbon-nitrogen bonds are some of the most common motifs in organic molecules and as a result, the invention of new methods for selectively forming these bonds is highly important. The first half of this thesis describes the discovery of two novel and unexpected carbon-carbon bond forming reactions, and also includes a review on the unique chemistry of geminal and vicinal bis(sulfones). The second half of this work deals with enantioselective carbon-nitrogen bond formation, and describes the development of two transition metal-catalyzed asymmetric allylic alkylation reactions. It also contains a review on annulative allylic alkylation reactions between dual electrophiles and dual nucleophiles and their applications in complex molecule synthesis.

Keywords: Chemistry.
Advisor: Trost Barry M. 
Burns Noah
Kanan Matthew William
Development of real time calibration for an integrated additive manufacturing platform for tissue engineering constructs

Next generation development of tissue engineering scaffolds increasingly leverages the ability of additive manufacturing methods in order to generate highly complex designs that can be customized to unique conditions found in the patient. Specifically, the development of integrated manufacturing methods, whereby multiple additive processes are utilized in conjunction with one another represent a potentially novel solution for how to create bio-mimetic scaffolds that can replicate natural tissue structures. In this paper, we discuss the development of a novel integrative manufacturing platform that aims to create next generation scaffolds for tissue engineering. Specifically, we discuss the overall design of the platform and our creation of a real-time calibration scheme that corrects for error during our manufacturing process.

Keywords: Yang, Yunzhi
tissue engineering
scaffolds
biomechanical
mechanical
calibration
additive manufacturing
orthopedic surgery
3d printing
computer vision
Thesis
Advisor: Pan Chi-chun
Levenston Marc
Development of synthetic and semi-synthetic transporters for drug and gene delivery

The delivery of small molecules, probes, and nucleic acids across impenetrable biological barriers represents a challenge for many current clinical strategies. Nucleic acids are of particular interest for delivery with potential clinical applications in cancer immunotherapy, gene editing and vaccines. Chapters 2-5 describe the development and use of charge-altering materials for the delivery of nucleic acids. The charge-altering materials described are dubbed Charge-Altering Releasable Transporters (CARTs), diblock or triblock oligomers consisting of a lipid-modified oligocarbonate block(s) followed by a charge-altering block. The charge-altering blocks, derived from either morpholinones or poly(serine esters), are initially cationic for complexation of the polyanionic nucleic acid cargo but degrade under basic conditions over time to neutral byproducts, providing a mechanism for nucleic acid release. These chapters describe the use of CARTs to deliver a range of nucleic acid cargos (plasmid DNA, messenger RNA, small interfering RNA) across a variety of cell types, including lymphocytes, as well as for in vivo gene delivery. Chapter 6 explores vault proteins as another scaffold for drug or probe delivery. Vaults are naturally occurring, large (13 MDa), hollow ribonucleic protein complexes. These proteins have the potential to be promising delivery agents based on their biocompatibility, size, and internal compartment that can encapsulate hundreds to thousands of molecules. In this chapter, we systematically study the chemical modification of vault proteins and used the developed strategies to prepare vaults modified with cell penetrating peptides for enhanced uptake into cells. Chapter 7 describes the synthesis and evaluation of prodrugs of PKC modulators. Prostratin, bryostatin 1, ingenol esters and their analogs, are potent PKC modulators and have been identified as latency reversing agents (LRAs) for HIV eradication. LRAs can be used to activate the HIV provirus in latent viral reservoir cells, which can then be subject clearance using a "kick and kill" approach. While promising agents, a major challenge associated with the clinical use of LRAs is sustaining therapeutically meaningful levels of the active agent while minimizing side effects. In this chapter, we describe the synthesis of PKC modulator prodrugs designed to slowly release the active drug over time. These PKC modulator prodrugs exhibit comparable but delayed in vitro activity relative to the parent compounds and avoid the problems associated with bolus administration in vivo.

Keywords: Chemistry.
Advisor: Wender Paul A. 
Dassama Laura 
Khosla Chaitan
Development of the capsule ultrasound (CUS) device

Currently, there is a lack of medical imaging tools required to investigate the multiple layers of the entire small intestine in the gastrointestinal (GI) tract. Some of the existing imaging modalities, such as computed tomography (CT) and magnetic resonance imaging (MRI), used for examining the GI tract, expose the patient to radiation and/or are expensive. To make GI tract assessment easier, doctors use endoscopic ultrasound (EUS) and capsule endoscopy (CE). While EUS provides adequate penetration depth, it is unable to look at the entire small bowel. On the other hand, while CE is able to survey the entire small bowel, it only observes at the superficial layer due to its use of optics. To increase the prevalence of GI tract screening, with particular emphasis on small bowel, we propose to develop the capsule ultrasound (CUS) device, a diagnostic capsule with ultrasound imaging capability. Our envisioned device will measure 2.5 cm in height and 1 cm in diameter. Upon being swallowed by the patient, the CUS device will collect images of the GI tract with 360 degrees field-of-view (FOV) and wirelessly transmit the images to an external recorder for image reconstruction and display. To accomplish this goal, the CUS device will be equipped with a cylindrical transducer array around its perimeter and the associated imaging electronics, for regulating the image acquisition process, as well as a wireless transmitter, for wirelessly sending the ultrasound data to the external recorder, inside the capsule. This thesis highlights research towards the development of the CUS device, which, once developed, could be a revolutionary product for diagnosis of diseases in the GI tract, in particular the small intestine. Even though the development of the CUS device is a collaborative research project involving several students, in this thesis I demonstrate and share aspects of the research onto which I have contributed. In this thesis, I first discuss the system-level optimization of the CUS device through image simulations. Next, I highlight the transducer array fabrication process and the characterization results. Moreover, I demonstrate preliminary imaging results of the CUS device through wire and small bowel phantoms. Lastly, I share an integration scheme for the transducer array to increase patient safety. The research presented in this thesis for the design and development of the CUS device can be used to produce other wearable, disposable, and wireless-based medical devices to improve healthcare.

Keywords: Bioengineering.
Advisor: Khuri-Yakub Butrus T.
Arbabian Amin 
Dahl Jeremy J.
Pelc Norbert J.
Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures

Investigating human oligodendrogenesis and the interaction of oligodendrocytes with neurons and astrocytes would accelerate our understanding of the mechanisms underlying white matter disorders. However, this is challenging due to limited accessibility of functional human brain tissue. Here, we developed a novel differentiation method of human induced pluripotent stem cells (hiPS cells) to generate three-dimensional (3D) neural spheroids that contain oligodendrocytes as well as neurons and astrocytes, called human oligodendrocyte spheroids (hOLS). We demonstrate that oligodendrocyte-lineage cells derived in hOLS transition through developmental stages similar to primary human oligodendrocytes and that the migration of oligodendrocyte-lineage cells and their susceptibility to lysolecithin exposure can be captured by live imaging. Moreover, their morphology changes as they mature over time in vitro and start myelinating neurons. We anticipate that this method can be used to study oligodendrocyte development, myelination, and interactions with other major cell types in the central nervous system.

Keywords: Stem Cell Biology and Regenerative Medicine.
Advisor: Pasca Sergiu 
Gitler Aaron D. 
Monje-Deisseroth Michelle
Palmer Theo
Diffusion encoding waveform design for mapping microstructure in the human brain

Diffusion MRI is a non-invasive method of measuring the diffusion of water molecules in biological tissue. The patterns of water diffusion reflect the underlying tissue microstructure, which hinders or restricts the displacement of water. Changes in diffusion reflect microstructural changes that can be critical for clinical diagnosis, disease monitoring, and the study of neurodegenerative processes. The diffusive motion of water is encoded through the interaction of time-varying magnetic field gradients and the diffusive motion of water molecules. The design of these gradient waveforms can be tailored to the diffusion regime of interest and the capabilities of the MR scanner. Diffusion gradient waveforms can be designed to separate the effects of tissue heterogeneity, orientation dispersion, and microscopic diffusion anisotropy within the constraints of the limitations and imperfections of the gradient systems. In this dissertation, a parsimonious sampling scheme for double diffusion encoding (DDE) MRI is presented, which optimizes the measurement of microscopic diffusion anisotropy on a whole- body clinical MRI scanner. The proposed scheme was used to demonstrate the improved ability of DDE compared to conventional MRI to characterize normal and damaged tissue in a cohort of multiple sclerosis patients. Next, an optimization framework is presented for the design of generalized diffusion encoding waveforms which are robust to imperfections in the gradient system caused by eddy current and concomitant fields. Finally, the adaptation of these methods to a novel high- performance head-only gradient system is described.

Keywords: Electrical Engineering.
Advisor: Hargreaves Brian Andrew 
McNab Jennifer (Jennifer A.)
Pauly John (John M.)
DIGGING DEEPER INTO A COMMUNAL GARDEN NETWORK: UNEARTHING CULTURAL KNOWLEDGE OF URBAN KNOWLEDGE OF URBAN AGRICULTURE TO CULTIVATE WELL-BEING

This community-based participatory research study partnering with the Buena Vista Mobile Home Park honed in on a representative sample of ten participants across varying ages and levels of involvement within the greater community. Semi-structured interviews were conducted with the sample population to explore culturally and personally based knowledge surrounding urban agriculture and the role of an interconnected communal garden network in mediating this knowledge and other educational and social functions. Specifically, the following sub-questions were explored: (1) What are the origins and sources of local knowledge of urban agriculture and how do community members learn and share this knowledge? (2)Within this community, how do members perceive these garden spaces from an individual and communal perspective? (3) What are the social and educational functions of the community garden network, if any? Substantial knowledge exists within Buena Vista, especially surrounding how to cultivate urban agriculture. The communal garden network exists as a collection of spaces for knowledge and vegetation to be shared. This network also facilitates the maintenance of well-being and social interactions within a highly cohesive community. The home gardens hold substantial value in an area where space is contested, and represent an opportunity to further cultivate already existing pride and the flow of inter-community and intergenerational knowledge transfer.

Keywords: Community gardens
Urban agriculture
Experiential environmental education
Graduate School of Education
Thesis
Direct detection and characterization of exoplanets

Direct imaging is a method to detect and study extra solar planets, which consists in spatially resolving the light of the planet from the light of the star around which it is orbiting. The method is currently sensitive to young gas giant exoplanets that still radiate the heat from their formation, at orbital separation similar to the gas giants in our solar system. A recurring theme in this work is the application of maximum likelihood and Bayesian inference to the detection and characterization of directly imaged planets. In particular, I have designed and implemented the planet detection scheme for the Gemini Planet Imager Exoplanet Survey, which is a 531-star direct-imaging survey spanning 2014-2018. In addition to improving the statistical standards of the field, the detection limits set by this work have allowed the derivation of planet occurrence rates for giant planets and informed their formation history. Additionally, I have demonstrated how Bayesian inference can be used to constrain the mass of undetected exoplanets, in particular those potentially carving the gaps of proto-planetary disks, which is the disk of orbiting gas a dust from which planets form. Finally, I developed a statistical framework for the analysis of medium resolution spectroscopic data, which I have used to characterize the planets orbiting the star HR 8799. In 2008, HR 8799 b, c and d were the first directly imaged exoplanets, and is still the only multi-planet system observed with this method. From these data, I derived the first radial velocity measurement of HR 8799 b and c and detected water and carbon monoxide in the atmosphere of HR 8799 d for the first time.

Keywords: Physics.
Advisor: Macintosh Bruce
Allen Steven W. (Steven Ward) 
Roodman Aaron J. (Aaron Jay)
Dirty Diplomacy: An Analysis of U. S. Foreign Policy Towards the Salvadoran Civil War and the Massacre at El Mozote

The 2016 Salvadoran Supreme Court decision to remove the 1993 Amnesty Law and the current legislative battle in El Salvador over the introduction of yet another amnesty proposal has catapulted the case of the El Mozote massacre to the forefront of the human rights discussion. At its core, this paper asks, what was the role of the United States in the Salvadoran Civil War, particularly at the massacre at El Mozote? Additionally, it explores the significance of this involvement in 2019, as prosecutions in the case move forward. The existing literature on human rights during the Salvadoran Civil War predominantly focuses on the culpability of Salvadoran military government members in committing human rights abuses between 1979 and 1992. Meanwhile, there seems to be relatively less attention paid to the role of the U.S. during this period—it is commonly only acknowledged in passing. Thus, using a descriptive analytic framework, this paper explores the U.S. economic and military contributions, political involvement, and judicial reforms that arguably hurt rather than helped the search for justice in El Salvador’s civil war and in particular at the 1981 massacre at El Mozote.

Keywords: Salvadoran Civil War
American Foreign Policy
Human Rights
El Mozote
Stanford University
Center for Latin American Studies
Thesis
A discontinuous galerkin method with enrichment for boundary layers

A discontinuous Galerkin method with enrichment and Lagrange multipliers (DGLM) is proposed for the solution of problems with boundary layers. Specifically, this includes the steady and unsteady advection-diffusion equation with a spatially-varying advection field and the steady incompressible Navier-Stokes equations. The standard finite element method (FEM) is susceptible to the issue of spatial instability at practical mesh resolutions, typically observed as non-physical oscillations in the numerical solution to these problems. This is especially the case in the advection-dominated regime in which the boundary layers have steep gradients. Like the discontinuous enrichment method (DEM), the DGLM overcomes this issue through the use of novel shape functions designed to resolve boundary layers. These are chosen here element-wise as polynomials that are additively enriched with approximate free-space solutions of the governing differential equation. The enrichment functions are inspired by the boundary layer theory and are derived using an asymptotic analysis for different types of boundary layers. Inter-element solution continuity is weakly enforced using polynomial Lagrange multipliers. The method is shown to be stable in the inf-sup sense. Numerical results reveal that the DGLM has a lower error constant than the FEM and outperforms it for both the advection-diffusion equation in the high Peclet number regime and the incompressible Navier-Stokes equations in the laminar flow regime.

Keywords: Aeronautics and Astronautics.
Advisor: Farhat Charbel 
Alonso Juan José
Lele Sanjiva K. (Sanjiva Keshava)
The discovery and design of bivalent, small-molecule glucose-6-phosphate dehydrogenase activators and tetramethyleneethane equivalents for the convergent synthesis of the bicyclo[4.4.0]decane core

This dissertation covers work carried out independently in both the Mochly-Rosen and Wender Labs. Chapters 1 and 2 focus on the relevant background and development of a novel class of enzyme activators to treat G6PD deficiency (Mochly-Rosen Lab). Chapter 3 (Wender Lab) focuses on the development of novel synthetic methods for the construction of the bicyclo[4.4.0]decane core. The application of this method in the construction of novel dyes is outlined. Chapter 1 provides a historical perspective on the discovery of mutated glucose-6- phosphate dehydrogenase (G6PD) as the underlying cause of favism and related diseases (e.g. primaquine sensitivity). A discussion follows which highlights certain pathologies associated with G6PD deficiency along with the consequences of reduced NADPH synthesis. The tertiary and quaternary structure of G6PD is discussed along with the functional consequences of altering the oligomeric state of the enzyme. Chapter 2 begins with background on small-molecule activators and protein-protein interaction (PPI) stabilizers. The high-throughput screening (HTS) campaign to find a small- molecule activator of G6PD is described, followed by a mechanistic investigation of the initial 'hit' molecule, AG1. This mechanistic understanding enabled the design of new analogs without the reactive liability of AG1 (disulfide) and led to the understanding of the general pharmacophore of these compounds. A discussion of the relevant synthetic methods and properties of these molecules is presented. Chapter 3 details the development of a novel class of reagents which enable two conjunctive cycloadditions for the synthesis of the bicyclo[4.4.0]decane core (naphthalene, higher acene and heterocyclic products). This class of reagents is a synthetic equivalent to the tetramethyleneethane (TME) diradical. These reagents use the vinylogous Peterson elimination for reactivity generation after the first cycloaddition between a dienophile and the novel diene. One reagent, DMTB, was found to enable the construction of bicyclic systems resulting from all thermal Diels-Alder (DA) cycloadditions or a mixture of DA cycloadditions followed by a transition-metal-catalyzed [4+2] reaction. Ultimately, DMTB was used in the synthesis of a new solvatochromic dye, 6-DMA in 69% overall yield. To enable back-to-back transition- metal-catalyzed [4+2] products, another reagent (THP-DMTB) had to be utilized due to decomposition of the original reagent under these conditions. In order to enable the formal synthesis of hetero-Diels-Alder products, AcDMTB was developed, which expands the methodology outside the constraints of Diels-Alder or metal-catalyzed cycloadditions.

Keywords: Chemistry.
Advisor: Mochly-Rosen Daria 
Du Bois Justin 
Kanan Matthew William
Displaced landscape : the art and life of Ni Zan (1301-1374)

This dissertation, "Displaced Landscape: The Art and Life of Ni Zan (1301-1374), " retrieves the lived experiences of underrepresented, displaced people during the Yuan-Ming dynastic transitional era. By using Ni Zan's paintings as counter-memories, my project raises new questions about the dominant mythology surrounding Ni Zan. Mainstream historiographies in China define him as a loyal recluse, which limits understandings of the variety of his life experiences. Instead, my research shows that Ni Zan was an active agent who coped with turbulent times by means of artistic practice, and reconstructs the forgotten local history of the Wu region (today's Suzhou and its surrounding area) in the late Yuan period. My analysis of Ni's paintings shows how art objects can operate as a creative social force and spotlights two previously overlooked potentialities in Chinese painting. First, it can function as, what I term, a "communal space" of memory, communion, or personal/political mourning. Second, it can function as "objectified charisma, " the sedimentation of an individual's virtues and powers into objects embedded with iconic and indexical properties.

Keywords: Art and Art History.
Advisor: Vinograd Richard Ellis 
Egan Ronald
Kwon Marci 
Lewis Mark Edward