VictorJuiz/thesis huggingface dataset:
Convex methods for radiation treatment planning
Keywords: Bioengineering.

Upwards of 1.6 million cases of cancer are diagnosed each year in the US alone, and two-thirds of those patients receive radiation therapy (RT). For each such patient, clinicians design an individualized treatment plan based on anatomy scans and the capabilities of their clinic's radiation delivery hardware. Treatment planning involves fundamental tensions between tumor coverage and toxicity to surrounding healthy tissues. Increasingly sophisticated RT hardware and planning algorithms have been designed to address these challenges, but come with commensurate increases in computational burden. This thesis addresses two planning challenges common to all modern RT modalities: (1) efficiently solving large scale intensity optimization problems, and (2) satisfying the (nonconvex) radiation dose constraints derived from clinical trials. We formulate the treatment planning problem as a convex minimization. We introduce methods for approximately solving treatment planning problems at dramatically reduced computational cost, and appeal to our convex problem formulation and duality theory to obtain bounds on the suboptimality of these approximations. We then present a framework for handling all desired clinical objectives via convex surrogates. We implement these methods as open-source software packages that make use of modern, general purpose convex solvers. Collectively, this thesis lays the groundwork for a core, modality-agnostic, intensity optimization module that can incorporated as-is into virtually all planning algorithms used in current practice or proposed in the literature.
Coordinating on meaning in communication
Keywords: Psychology.

How do we manage to understand each other? Human languages are a powerful solution to this challenging coordination problem. They provide stable, shared expectations about how the words we say correspond to the beliefs and intentions in our heads. However, to handle an ever-changing environment where we constantly face new things to talk about and new partners to talk with, linguistic knowledge must be flexible: we give old words new meaning on the fly. My dissertation investigates the cognitive mechanisms that support this balance between stability and flexibility. Chapter 1 introduces the overarching theoretical framework of communication as a meta-learning problem. Computational models of semantic meaning must explain both the speaker's initial conventional expectations about how words will be understood by novel partners and the dynamics of how these expectations may shift over the course of a particular conversation. Chapter 2 proposes a computational model that formalizes the problem of coordinating on meaning as hierarchical probabilistic inference, which I argue satisfies both of these conditions. Community-level expectations provide a stable prior, and dynamics within an interaction are driven by partner-specific learning. Chapter 3 exploits recent connections between this hierarchical Bayesian framework and continual learning in deep neural networks to propose and evaluate a computationally efficient algorithm implementing this same model at scale in an adaptive neural image-captioning agent. In Chapter 4, I provide an empirical basis for further model development by quantitatively characterizing convention formation behavior in a new corpus of natural-language communication in the classic Tangrams task. By using techniques from natural language processing to examine the (syntactic) structure and (semantic) content of referring expressions, we find that pairs coordinate on equally efficient but increasingly idiosyncratic solutions to the problem of reference. Chapter 5 uses an artificial-language reference game paradigm to test the hypothesis that communicative context systematically shapes which conventions form. Finally, Chapter 6 investigates the generality of the proposed computational mechanisms by examining convention formation in a graphical communication task. Taken together, this line of work builds a computational foundation for a dynamic view of meaning in communication.
Coordination of junction biogenesis and epithelial integration during differentiation
Keywords: Biology.

The adult Drosophila midgut, like other epithelial tissues, undergoes dynamic self- renewal. The intestinal stem cells are the only mitotic cells in the midgut and they generate new cells, which are small and localize on the basal side of the epithelium. These daughter cells, enteroblasts, have to mature and integrate into the tissue as they differentiate into intestinal cells, called enterocytes. These new cells, as they integrate, have to form septate junctions with the surrounding fully differentiated intestinal cells to ensure the epithelial barrier is maintained. For my thesis work I have dedicated my research to investigating how the septate junction network is maintained during cellular differentiation. I have explored how a wide variety of cellular differentiation events such as establishment of apical polarity, integration into the tissue and expression of transcription factors, are coordinated with generation of septate junctions de novo in enteroblasts to ensure that the intestinal barrier is maintained during turnover.
Core-shell nanomaterials for enhanced oxygen electrocatalysis
Keywords: Chemical Engineering.

Fuel cells and electrolyzers are emissions-free, electrochemical devices for the interconversion of electricity and chemical energy that hold significant promise towards clean electrification of the transportation sector and carbon-neutral fuel generation, respectively. Unfortunately, both devices suffer from kinetic limitations of the oxygen electrochemical reactions, resulting in performance inefficiency and high catalyst costs and prompting the search for economical, high-performance oxygen electrocatalysts. Core-shell nanostructured catalysts have the potential to decrease precious metal loading requirements over their monometallic counterparts and improve activity via electronic and geometric modifications induced by the core material. This thesis investigates the benefits of the core-shell electrocatalyst motif for both the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER) across several materials systems and electrolyte conditions. First, the performance advantages of Pt-based core-shell nanostructured catalysts for the ORR (occurring at the fuel cell cathode) in acidic media is explored. Utilizing a systematic methodology for catalyst design, we identify Ir@Pt (core@shell) nanoparticles as a promising system for enhanced ORR performance, synthesize Ir@Pt core-shell nanoparticles, and demonstrate an activity and stability enhancement over the commercial state-of-the-art Pt/C catalyst. Building on this demonstration of the core-shell catalyst platform, this thesis further explores core-shell materials for the OER (occurring at the electrolyzer anode). Inspired by the established beneficial effects of Au supports for thin-film OER catalysts, Au@metal-oxide nanoparticles were synthesized and characterized for alkaline OER. These mixed-metal oxide catalysts demonstrated a general activity enhancement with the inclusion of a Au-core, illustrating the successful translation of catalyst/support effects to the core-shell nanoparticle architecture. Finally, the last part of this work focuses on further extending the core-shell morphology to the OER in acidic media. A perspective on the past, present, and future state of OER catalysis in acid is first provided to reveal trends and opportunities for improved catalyst design. Finally, investigations of Sr iridate particles and bimetallic Ir-based thin films are presented and catalysts with significantly improved intrinsic activity over pure Ir-oxide are identified. Overall, this work demonstrates the versatility and promise of the core-shell morphology to achieve high performance catalysts across various reactions, electrolytes, and material chemistries.
Cosmic noise : Juan Downey and the postcolonial politics of Cold War communication
Keywords: Art and Art History.

As colonial rule crumbled after World War II, a new imperial power struggle emerged with the Cold War, one waged with the science and technology of communication. In the past fifteen years, art and media historians have examined the impact of Cold War communication sciences -- cybernetics, computation, and information theory -- on dominant cultural production of the North Atlantic. They have been slower, however, to engage the aesthetic entanglements of these sciences with global processes of decolonization, modernization, and imperialism for artists hailing from the Third World. This dissertation examines the postcolonial politics of Cold War communication through a case study of artist and architect Juan Downey (1940-1993), a Chilean-born intellectual who pioneered artistic advances in architecture and communications alongside collectives such as Groupe International d'Architecture Prospective, Raindance Corporation, and MIT's Center for Advanced Visual Study in the 1960s and 1970s. Downey shared his international contemporaries' enthusiasm for designing communications architecture that could advance social utopian goals, yet he distinguished himself with the application of cybernetic principles such as feedback, systems analysis, and information transmission to artworks that interrogated and challenged colonial legacies and imperial projections in the Cold War Americas. Departing from the scholarly literature that explores his artwork in the context of the video medium, this first dissertation-length monograph on Downey contextualizes his wide-ranging interdisciplinary practice as an extension of his cybernetic view of the world. Surveying his drawings, paintings, prints, sculptures, videos, installations, and performances produced between 1959 and 1979, it establishes an alternative genealogy of cybernetic and systems-based art in the formal, philosophical, and political concerns of the Chilean avant-garde of the late 1950s and 1960s and demonstrates how Downey's adaptation and application of cybernetic principles in his artworks of the late 1960s and 1970s came to dramatize the utopian ambitions and material struggles over technology and communication during the Cold War, particularly in relation to histories of imperialism and dependence and the possibilities of socialist revolution in Latin America. Positioning Downey within a field of tensions around aesthetics, techno-politics and cultural difference, this dissertation proposes the study of his work as a new perspective from which to rethink how Cold War communication technologies and discourses were mobilized to create visions of a more democratic participatory world inclusive of ways of knowing and being in the South.
Cosmological simulations for precision dark energy measurements with wide field galaxy surveys
Keywords: Physics.

Current and upcoming cosmological surveys are turning their eyes towards the late time universe in an attempt to answer fundamental questions about its composition and the physical laws that govern it. Given the non-linear nature of the observables studied by these surveys, perturbative modeling approaches have limited faculty. Thus, non-perturbative simulation approaches are necessary in order to connect theory with observation and harness the statistical power contained in the deluge of data that will be collected in the coming years. In this thesis, I discuss a number of efforts, all centered around using simulations to interpret data and aid analyses with wide field galaxy surveys. The first part of this thesis will focuses on a model for galaxy formation based on the evolution of dark matter halos and subhalos in high resolution N-body simulations, and its extension to large volume, low resolution lightcone simulations. I then show the application of this model to the Dark Energy Survey (DES), the most precise weak lensing survey to date. In particular, I present the suite of simulations that I created with this model and show that it agrees well with the first year of DES (DES Y1) data. I will then demonstrate how this suite was used to test the analysis choices made in the DES Y1 analysis of weak lensing and galaxy clustering. Finally, I discuss an effort to use cosmological simulations as models for highly non-linear observables in galaxy surveys. First I will present a well validated suite of simulations suitable for this type of modeling, which efficiently spans a large cosmological parameter space. I will then overview the models that we built from these simulations, and the outlook for applying them to upcoming data in order to use it to its fullest capacity.
Cosmology with robust galaxy cluster weak lensing mass measurements
Keywords: Physics.

Galaxy clusters—the largest nodes on the cosmic web of dark matter—compress the mass of 10^15 Suns into a volume of order ∼Mpc^3. Their extreme gravitational influence gives rise to several unique observational signatures, such as X-ray emission from diffuse baryonic matter that is heated and ionized by the cluster's gravitational squeeze, and the prominent weak lensing signal imprinted upon the shapes of background galaxy images as light travels through a cluster's gravitational field. These and other measurable cluster properties can be used to obtain cluster masses and constrain cosmology. Clusters are powerful dark energy probes, both as tracers of cosmic structure growth and the universe's geometry. The former experiment counts the number of clusters in mass and redshift bins using large astronomical surveys like the forthcoming Large Synoptic Survey Telescope (LSST). The latter is based upon the gas mass fraction f_gas=M_gas/M_total of clusters. Leveraging the fact that clusters are so large they contain a representative sample of the universe, the mass fraction of intracluster gas, the dominant baryonic component of clusters, can be related to the cosmic baryon fraction (Ω_b/Ω_m) using a small correction factor from hydrodynamic simulations. Since the absolute f_gas of massive clusters is redshift-independent, while its measured apparent f_gas depends on distance, it serves as a standard quantity to constrain dark energy. The key challenge for both experiments is measuring cluster masses accurately. In this thesis we address this need for accurate galaxy cluster masses with robust weak lensing measurements. We focus on a subset of 10 clusters from the forthcoming fgas cosmology sample (in prep.). These are relaxed galaxy clusters—undisturbed, symmetric systems, with no signs of recent merging activity—which enables reliable M_total measurements based on the assumption of hydrostatic equilibrium. Chandra X-ray imaging yields precise measurements of relative M_total and M_gas between clusters in the sample, however they suffer from an unknown bias. Accurate weak lensing masses measured from wide-field SuprimeCam photometry provide the needed absolute calibration, enabling robust f_gas measurements, as well as constraints on Ω_m and dark energy properties.
A country without culture is destroyed : making Rwanda and Rwandans through heritage
Keywords: Anthropology.

In 1994, the people of Rwanda suffered genocidal violence and the destruction of their homes and nation. In the years since, the process of reconstruction led by the Rwandan Patriotic Front government has pursued transformation of the country's economy, justice system, politics, and even sociocultural characteristics such as identity. In the process of building the New Rwanda, the RPF embraces the potential of heritage to reshape national identity and to establish key characteristics of the new country. In particular, the government deploys heritage to revitalize culture, drawing on the pre-colonial Rwandan past, in order to establish a new national identity and re-situate the country in the international context of power. A Kinyarwanda proverb, "A country without culture is destroyed", indicates the necessity of embracing the past—source of Rwandan identity and culture—in order to create a better future of resilience and resistance to the potential resurgence of genocidal violence. This dissertation examines four thematic ways heritage is involved in the RPF's nation- and state-building efforts in the post-genocide era: the production and deployment of ideals of value, dignity, unity, and development. Using the varied methods of heritage ethnography, including interviews, participant observation, site visits, and analysis of texts, the dissertation argues that heritage both shapes and is shaped by the demands of contemporary governance in Rwanda as the RPF seeks to make a new country with new citizens to people it. This focus on the internal processes of heritage production demonstrates the interrelation of heritage with national and international politics and techniques of governance. Ethnographic and historical analysis also reveals the numerous pressures on heritage production, such as those which pull it into exclusionary social processes that privilege certain groups over others, flatten narratives of the past, and undercut the government's stated goals of domestic development and unification. At the same time, heritage has been effectively integrated into initiatives to resist international influence via assertions of dignity and national pride. Through attention to the processes of heritage-making in the post-conflict context, this dissertation reveals the internal systems of state heritage production and its multiply intersecting power dynamics as the government seeks to remake both Rwandans and their country.
The creation and impact of British colonial armies in Africa
Keywords: Political Science.

Two British colonial armies in Africa----the West African Frontier Force and the King's African Rifles----formed the basis for the independent armies of Ghana, Nigeria, Kenya, Uganda, Sierra Leone, Tanzania, Malawi, and Zambia. The new governments directly inherited the soldiers and officers of these colonial forces. Decisions made by the British in shaping these colonial forces influenced the post-independence histories of these nations. The rank and file and native colonial officer corps were ethnically biased, not representative of the general population of the colonies. The British argued that the soldiers that made up the rank and file were drawn from the Martial and Hamitic Races of Africa, since these groups were claimed to be natural soldiers. Instead, I argue, these groups came from the margins of both the territory and economy of the colony. Commissioned native officers came from groups with a higher missionary presence. Missionaries were the main providers of colonial education so that these groups could respond to the educational needs of command. The unbalanced officer corps impacted the early histories of these African nations. If the government engaged in actions that hurt the political standing of groups that made up a large proportion of the officer corps, coups occurred. If the officer corps was small, or the government only exploited groups that were minorities in the officer corps, coups did not occur.
CRISPR/Cas9 Gene Replacement in Hematopoietic Stem Cells as a Novel Therapy for Gaucher Disease
Keywords: Biology
CRISPR/Cas9
Hematopoietic Stem Cell Transplantation
Macrophage
Gaucher Disease
Stanford University Department of Biology
Stanford University Department of Pediatrics
Stanford University
Stanford Undergraduate Advising and Research
Porteus Lab
Gomez-Ospina Lab
Thesis

Gaucher Disease (GD) is a severe genetic disorder caused by mutations in the gene GBA1 encoding the lysosomal hydrolase glucocerebrosidase (GCase). GCase deficiency leads to glycolipid storage in the lysosomes of macrophages, triggering their transformation in pathological “Gaucher Cells” that infiltrate tissues and promote immune deregulation, ultimately initiating progressive disease in the spleen, liver, bone and brain. Hematopoietic stem cell (HSC) transplantation (HSCT) is known to cure GD through replacing patient blood cells – including macrophages – with donor blood cells, yet comorbidities arising from histoincompatibility between patient and donor prevent its widespread application. Owing to recent advancements in gene-editing technologies, a promising new alternative is ex vivo gene-correction and transplantation of patient-derived HSCs. To this end, we present stable and efficient targeting of GBA1 expression cassettes to a “safe harbor” locus in primary human HSCs using a CRISPR/Cas9 and AAV6 platform. In vitro differentiation of GBA1-targeted HSCs produces functional macrophages with elevated GCase expression, demonstrating the potential for GBA1 gene-targeting to restore GCase activity in GD macrophages. Moreover, we show that it is possible to constrain GBA1 transgene expression to macrophage-lineage cells using a tissue-specific promoter, thereby minimizing ectopic transgene expression in HSCs. Importantly, GBA1-targeted HSCs sustain human hematopoiesis at least 32 weeks in a murine xenograft model and produce circulating monocytes capable of differentiation into macrophages, indicating that they retain proper self-renewal and multi-lineage reconstitution capabilities in vivo. Taken together, these studies provide proof-of-principle for genome-engineered autologous HSCT as a novel therapy for Gaucher Disease and set the stage for the clinical translation of ex vivo genome-editing therapies.
Crossing a Bridge of Memory: Historical Memory and Populist Rhetoric in the Czech and Slovak Republics, 1990-2004
Keywords: historical memory
populism
political rhetoric
Czech Republic
Slovakia
Vladimír Mečiar
Václav Klaus
Miloš Zeman
Stanford Department of History
CDDRL
Thesis

From the first protests of the Velvet Revolution in November 1989 to the present day, leaders of the Czech and Slovak Republics have invoked historical memory in their political messaging. The recent success of populist parties in Europe has provoked a great deal of scholarship, and prompted questions about the history of populism across the continent, including the Czech and Slovak Republics. This study asks the question: How have politicians used historical memory and populist rhetoric in the Czech and Slovak Republics after the fall of communism? Through archival research and interviews, buttressed by existing literature, this work examines Czech and Slovak politics in the first half of their post-communist life to date: from 1990 to 2004. This thesis concludes that during this period, Czech and Slovak politicians used different rhetorical strategies in accordance with the most pressing political challenges they each faced. Historical memory was a resource that all politicians drew upon, but historical memory was utilized in populist rhetorical structures only when the political challenge in question was one which required politicians to divide, or distinguish between, two groups said to hold different ideologies. Examples include the 1990-1992 Czech political debate over the communist regime’s legacy, and the 1992 and 1994 campaigns of Slovak Prime Minister Vladimír Mečiar. In contrast, populist rhetoric was not employed when the challenge at hand was one which required politicians to build accord in service of pursuing a shared ideal future, namely that of European Union membership. This paper concludes by exploring future avenues for research on this and related topics.