VictorJuiz/thesis huggingface dataset:
The Ras proximal proteome highlights novel oncogenic effectors [electronic resource]

Characterizing the protein interactome of difficult-to-drug oncogenes, such as Ras, may identify new cancer targets. We undertook live-cell proximity-dependent protein labeling with wild type (WT) and oncogenic mutant (MT) KRAS, NRAS and HRAS isoforms in their associated tumor types, postulating that proximity-dependent protein labeling could detect interactions mediating pro-cancer functions missed by conventional approaches. This identified known, direct Ras interactors, including Raf and PI3K, as well as 130 new Ras-proximal proteins. The interactome was enriched for well-known Ras regulated roles such as cytoskeletal organization, cell junction integrity and cytoplasmic signaling pathways as well as a surprising group of small molecule transport proteins. Moreover, each Ras isoform exhibited a unique set of biological process enrichments, shedding light on isoform specific the functional pathways. A CRISPR genetic screen in 10 cell types demonstrated that 17 of these novel candidates phenocopied oncogenic Ras loss, resulting in decreased proliferation. Combined genetic and proteomic analysis identified well know oncogenic Ras effectors, Raf and PI3K; however, mTOR was the top oncogenic Ras interactor. mTOR-oncogenic Ras interaction is direct and occurs in human mutant KRAS tumors. The interaction depends upon mTORC2 constituents Rictor and MAPKAP1, but not mTORC1 component Raptor. Disruption of the oncogenic Ras-mTORC2 interaction blocked Ras-driven tumorigenesis in vivo via transcriptional regulation of cell cycle progression. Proximity-dependent protein labeling and CRISPR genetics thus synergize to identify new targets in cancers driven by Ras and other dominant oncogenes.

Advisor: Khavari Paul A. primary advisor. Thesis advisor
Elias Joshua
Oro Anthony
Sage Julien advisor. Thesis advisor
Ratcheting, competition, and the diffusion of technological change [electronic resource] : the case of televisions under an energy efficiency program

The study of the diffusion of innovation and technological change enjoys a long tradition in marketing and often places an emphasis on the role of consumer adoption. Complementing this process of diffusion are firms, which differentiate in the extent to which they provision technological change in their products. In markets with societal implications or externalities, policy is implemented to avoid the under provision of innovation. Firms have clear incentives to engage in strategic behavior in such markets because policymakers use market outcomes as a benchmark in designing regulation. This study examines a unique energy efficiency standard for television sets, under which future minimum efficiency standards are explicitly a function of current product offerings. The setting illustrates firms' dual incentives at work: Depending on the competitive environment, they have strategic incentives to both ratchet up, and ratchet down, the quality of their product offerings in order to influence future standards. These incentives affect the pace at which innovation reaches consumers. I develop and estimate a structural model of product entry and endogenous regulation to illustrate how such dynamic standards affect product release decisions, consumer purchases, and the competitive environment. My analysis provides evidence that firms are more likely to ratchet down quality when they have similar cost structures or when the market is concentrated.

Keywords: Business.
Advisor: Hartmann Wesley R. (Wesley Robert)
Nair Harikesh S. (Harikesh Sasikumar)
Seiler Stephan (Assistant professor of marketing) advisor. Thesis advisor
The reactive vega stack [electronic resource] : declarative interaction design for data visualization

Interactive visualization is an increasingly popular medium for analysis and communication as it allows readers to engage data in dialog. Hypotheses can be rapidly generated and evaluated in situ, facilitating an accretive construction of knowledge and serendipitous discovery. Crafting effective visualizations, however, remains difficult. Programming toolkits are typically required for custom visualization design, and impose a significant technical burden on users. Moreover, existing models of visualization relegate interaction to a second-class citizen: imperative event handling callbacks that are difficult to specify, and even harder to reason about. This thesis introduces the Reactive Vega stack: two new declarative languages for interactive visualization that decouple specification (the what) from execution (the how). At the foundation is Reactive Vega, an expressive representation that models user input as streaming data. Its underlying dataflow runtime handles the complexity of event propagation and state management, freeing users to focus on interaction design decisions. Vega-Lite builds on Vega to provide a high-level grammar for rapidly authoring interactive graphics for exploratory analysis. Its concise specification format decomposes interaction design into semantic units that can be systematically enumerated. Critically, these languages offer JSON syntaxes to simplify programmatic generation of interactive visualization and enable novel interactive data systems. This thesis develops one such system, Lyra, a direct manipulation tool for visualization design. Drag-and-drop operations in Lyra generate statements in Vega and Vega-Lite, allowing users to author a diverse range of visualizations without any textual specification. These systems have been released as open-source projects, have been widely adopted, and have given rise to an ecosystem of interactive visualization tools. Users can author an exploratory visualization in the Jupyter Notebook, export it to Lyra via Vega-Lite and add an explanatory annotation layer, and then embed the resultant Reactive Vega visualization within a Wikipedia article. As a result, rather than a single monolithic system, the Reactive Vega stack facilitates development of targeted applications, and allows users to work at the level of abstraction most suited for the task at hand.

Advisor: Agrawala Maneesh primary advisor. Thesis advisor
Heer Jeffrey Michael
Landay James A.
"Real people, real events" [electronic resource] : actuality and mass politics in Maoist documentary cinema

Documentary filmmaking in Mao's China involved intricate and often unpredictable negotiations between the reporting of historical facts and the transmission of ideological messages, as well as between interpreting the world and changing it. As a study of Chinese documentarian practice during the 1950s and 60s, this dissertation will illuminate how its representations and transformations of lived reality reflected broader societal tensions. The political salience of Mao-era documentary cinema, I contend, can be thrown into relief by following how the terms of debate over its engagement with social reality were successively revised against a shifting ideological and technological terrain. The first half of this study interrogates the decisive critical concept of zhenshixing (truthfulness, authenticity), concentrating on the contest over creative and organizational agency that hung in the balance amidst 1950s disputes concerning how filmmakers should and should not go about addressing themselves to "real people, real events". The second half of my project then turns to the textual analysis of key motion pictures released at the onset of the Great Proletarian Cultural Revolution: the nuclear test film Great Triumph of Mao Zedong Thought (1966) and the documentary series celebrating the historic Red Guard rallies in Beijing (1966-67). I show how the imagery and aesthetic choices found in these cinematic works point to contending visions of social mobilization and political subjectivity, visions that called into question prior media production arrangements and espoused new logics of form, giving expression to essential conflicts between anarchic mass-political exuberance and the grey rationality of technocratic control. This dissertation reveals the surprising theoretical depth and formal innovativeness of a cinematic corpus that has been dismissed as dogmatic and devoid of aesthetic interest. Moreover, it brings into focus what was productively aberrant and exceptional about Cultural Revolution culture, underscoring fractures and scissions in Mao-era documentary cinema, as reframed in terms of a "politicizing of art" deeply indebted to Maoist notions of truth and aesthetic production, representation and reality, knowing and doing.

Keywords: Art and Art History.
Advisor: Ma Jean
Levi Pavle advisor. Thesis advisor
Mullaney Thomas S. (Thomas Shawn) advisor. Thesis advisor
Wang Ban
Real-time decision support with reinforcement learning for dynamic flowshop scheduling [electronic resource]

The dynamic flowshop scheduling problem has attracted a lot of attention from both academia and industry because of its nature of NP-hardness in computation on the one hand, and its great value for optimization of manufacturing systems on the other. Traditionally, effective heuristic methods have been widely adopted in the industry to solve this problem. In recent years, machine learning has also exhibited great potential in the field. In this paper, we propose a reinforcement learning approach to this problem. We discuss settings for orders, performance measurements, and learning methods in detail to construct a controlled environment for this research. We then establish a manufacturing simulation system to compare the performance of the reinforcement learning approach and three heuristic approaches. While the experimental results revealed the superiority of the reinforcement learning method, investigations into dispatching decisions exposed its limitations in actual industry applications. Hence, two strategies were designed and employed to improve the reinforcement learning approach. After validating the reinforcement learning method with the improved strategies, we summarized and presented the dispatching rules of the reinforcement learning method as one type of complementary decision for supporting real-time flowshop scheduling problems.

Advisor: Leckie Jim
Reason-product (in)compatibility [electronic resource] : implications of consumer reasoning for post-choice satisfaction

This dissertation challenges and extends longstanding research on the topic of deliberative reasoning in consumer choice, a decision strategy whereby consumers carefully consider or articulate their arguments for or against making a choice. This literature has accepted that such reasoning (versus not reasoning) leads to less satisfying choices. I argue that this view is too narrow. Instead, I propose that reasoning does not lead to reduced satisfaction as a rule, but rather as a function of a mismatch between the content of consumers' reasons and the types of products under their consideration. I refer to this as "reason-product (in)compatibility." This framework proposes that deliberative consumer reasoning includes two broad types: reasoning which relies on "cognition-based" reasons, grounded in defensible evaluations and beliefs; and reasoning which relies on "affect-based" reasons, grounded in feelings and emotional reactions. In hedonic product choice contexts, only cognition-based reasoning leads to reduced satisfaction, while in utilitarian contexts, only affect-based reasoning leads to reduced satisfaction. The mechanism behind these results is a change in consumers' choice behavior: the type of reasoning (cognition- or affect-based) influences how consumer evaluate their options, and ultimately, what kind of product they choose (utilitarian or hedonic). Thus, deliberative reasoning appears to lead to less satisfying choices not as a rule, but rather as a result of when the reasons and products are incompatible. By contrast, when reasons and products are compatible, deliberative reasoning does not reduce post-choice satisfaction. I note that much of the extant literature has focused only on the effect of relying on cognition-based reasoning in hedonic contexts. I confirm these patterns of results both in surveys of real world purchase retrospections, and in experimental studies. Finally, I cover the contributions of the work, identify and address alternative accounts and limitations, and outline future research directions.

Keywords: Business.
Advisor: Khan Uzma Aslam
Simonson Itamar primary advisor. Thesis advisor
Shiv Baba
Re-centering C-Pop: The Sinification of K-pop through Cultural Hybridity, Mimicry, and Gender Bending

This thesis tells the story of the development of a new form of contemporary mainland Chinese C-pop that has been created through mimicry, cultural hybridization, and gender-bending. K-pop has had a strong influence in the creation of this new form, but C-pop is uniquely Chinese in that the performers are Chinese and sing in Chinese, and their efforts are supported by the Chinese government. Chapter 1 introduces the background of K-pop in China, explains the structure of the K-pop industry, and explains the concept of mimicry, which is a key theoretical concept in this thesis. Chapter 2 examines the popularity of K-pop in China using data from Chinese social media and news outlets, analyzes why K-pop is popular, and addresses the sentiments of anti-fans. Chapter 3 focuses on FFC-Acrush, a new mainland Chinese C-pop group, which demonstrate how Chinese “boy bands” are mimicking and hybridizing K-pop, creating a new form of music in the third space. This chapter will provide a visual analysis of how FFC-Acrush is similar to and distinguished from Korean K-pop, particularly in the way that gender is performed. Chapter 4 investigates the high-level actors who affect the reception of K-pop and C-pop in China, namely the Chinese state and entertainment companies, and analyzes their motives for and means of emulating South Korea, featuring another the C-pop group, TFBOYS, as an example. The conclusion assesses whether or not China can become a center of ‘cool’ and provides concluding remarks.

Keywords:  Stanford Global Studies
Center for East Asian Studies
C-pop
K-pop
East Asian Pop Culture
Thesis
Advisor: Zur Dafna
Recruiting for Excellence: International Hiring and Enrollment in Recent Russian Higher Education Reforms

Higher education has increasingly become a marker of national prestige, as well as a key instrument of national development. In the past 15 years, developing and developed countries alike have engaged in a series of “excellence initiatives” to pump money into higher education institutions. China, France, Germany, and Russia have all introduced these excellence initiatives as a critical step toward “world-class” status. Higher education reform has been an ongoing project in Russia in the past ten years, as the country strived to overcome setbacks in academia following the collapse of the Soviet Union. In 2009, the state invested in 40 universities as a means of creating world class research institutions across the country. Like most countries, Russia has now turned toward world university rankings as a guide to gauge its global success, which are based on a series of metrics, including publications, collaborations, and the recruitment of foreign scholars and students.
This research focuses specifically on internationalization and recruitment efforts at a funded public university, a private university, and a state technical institution, to better understand the differing motives of recruitment. Institutions included in the 5-100 Project are assisted by the government, and so have the largest incentive to recruit internationally. All the same, public institutions throughout the country are governed by nationwide monitoring, although their recruitment occurs at a much more “grassroots” level because they are not provided any special budget. By promoting internationalization across the spectrum, Russia seeks to improve its brand and reputation around the world and expand its reach to students beyond developing countries, in addition to creating a competitive economic good. However, the effect of disproportionately investing in one university over another remains an issue in how higher education reforms are structured, not only in Russia but internationally. The study also examines the impact of implementing reforms quickly on individuals who are recruited by these universities, both to study and teach.

Keywords:  Center for Russian
international higher education
higher education
Russian higher education
internationalization
Russian universities
Stanford Global Studies
Center for Russian
East European
and Eurasian Studies
Thesis
Advisor: Stoner Kathryn
Weiner Amir
Redundancy and awareness in discourse [electronic resource]

Rational speakers should not be redundant. This is a view on language use that is both widely held and intuitively compelling. It is also wrong. This dissertation shows that speakers routinely produce redundant utterances and explores the reasons why they do so. In particular, it focuses on rational motivations for redundancy as they relate to a speaker's desire to raise a listener's awareness of or draw a listener's attention to some issue. At a high level, this dissertation demonstrates that the models standardly assumed by linguists for modelling discourse are insufficient to make sense of the full range of functions that language use serves. These models typically make the idealizing assumptions that all speakers and listeners have perfect memories, are fully rational, and are logically omniscient. The arguments in the following pages show the necessity of thinking of linguistic discourse in a more nuanced way. This more elaborate model of discourse recognizes that speakers are well aware of the cognitive limitations of their interlocutors, but also that they have well-developed strategies to deal with such limitations.

Keywords: Linguistics.
Advisor: Lassiter Daniel primary advisor. Thesis advisor
Condoravdi Cleo A.
Frank Michael C. (Professor of human biology) advisor. Thesis advisor
Potts Christopher
Regent [electronic resource] : a high-productivity programming language for implicit parallelism with logical regions

Modern supercomputers are dominated by distributed-memory machines. State of the art high-performance scientific applications targeting these machines are typically written in low-level, explicitly parallel programming models that enable maximal performance but expose the user to programming hazards such as data races and deadlocks. Conversely, implicitly parallel models isolate the user from these hazards by providing easy-to-use sequential semantics and place responsibility for parallelism and data movement on the system. However, traditional implementations of implicit parallelism suffer from substantial limitations: static, compiler-based implementations restrict the programming model to exclude dynamic features needed for unstructured applications, while dynamic, runtime-based approaches suffer from a sequential bottleneck that limits the scalability of the system. We present Regent, a programming language designed to enable a hybrid static and dynamic analysis of implicit parallelism. Regent programs are composed of tasks (functions with annotated data usage). Program data is stored in regions (hierarchical collections); regions are dynamic, first-class values, but are named statically in the type system to ensure correct usage and analyzability of programs. Tasks may execute in parallel when they are mutually independent as determined by the annotated usage (read, write, etc.) of regions passed as task arguments. A Regent implementation is responsible for automatically discovering parallelism in a Regent program by analyzing the executed tasks in program order. A naive implementation of Regent would suffer from a sequential bottleneck as tasks must be analyzed sequentially at runtime to discover parallelism, limiting scalability. We present an optimizing compiler for Regent which transforms implicitly parallel programs into efficient explicitly parallel code. By analyzing the region arguments to tasks, the compiler is able to determine the data movement implied by the sequence of task calls, even in the presence of unstructured and data-dependent application behavior. The compiler can then replace the implied data movement with explicit communication and synchronization for efficient execution on distributed-memory machines. We measure the performance and scalability of several Regent programs on large supercomputers and demonstrate that optimized Regent programs perform comparably to manually optimized explicitly parallel programs.

Advisor: Aiken Alexander primary advisor. Thesis advisor
Levis Philip advisor. Thesis advisor
Olukotun Oyekunle Ayinde advisor. Thesis advisor
Regulation of axonal transport mediates in vivo en passant pre-synapse formation [electronic resource]

In order for the brain to function, neural circuits must be wired to form appropriate connections, called synapses, during development. In order to assemble the synapse at a given location, all the materials which comprise the pre-synaptic neurotransmitter release apparatus and post-synaptic receptors must be assembled in opposition to each other. Since neurons are specialized types of cells, understanding these processes requires us to understand how materials are synthesized by the cell, travel from their sites of synthesis to the axons/dendrites, where the majority of synapses are located, and then come together to form a synapse. This thesis will focus on these key cell-biological questions as they pertain to the assembly of the pre-synaptic neurotransmitter release apparatus. More specifically, in my thesis I ask how do two key components of synapses, Synaptic Vesicles (SVs) and Active Zone proteins (AZs) travel to the synapse from their sites of synthesis? What motors are responsible? How are cargoes dropped off at synapses, both during development and during later stages of maintenance and plasticity when synaptic materials must be re-supplied? In Chapter 1 of my thesis, I introduce more detailed conceptual and molecular background to frame these questions, including what is currently understood about the axon cytoskeleton and axon transport of pre-synaptic materials. The second part of chapter 1 consists of a review I wrote on what is currently known about AZ protein axonal transport. In Chapter 2 of my thesis, I describe work I did to contribute to a project that investigated this process of SVP cargo drop-off. Specifically, we find that auto-inhibition of the Kinesin-3 motor by an intra-molecular binding interaction between the motor head and motor tail domain is essential to get SVs that are properly distributed among many en passant synapses. Chapter 3 of my thesis is a study that I initiated with Kang to understand how pre-synaptic terminals first form behind an extending growth cone during development, and how SVs and AZ proteins are transported from the cell body to these nascent synaptic sites. In this study, I investigate the development of pre-synaptic terminals in PDE dopaminergic neurons in C. Elegans. First, I show that PDE dopamine neurons contain bona fide active zones, characterized by the presence of canonical AZ proteins. Then, focusing on the development of these synapses, I find that PDE pre-synapses, characterized by SVs clustered at active zones, form rapidly behind the extending growth cone, in many cases, appearing in as little as a few minutes. SVs are clearly dependent upon Kinesin-3 for transport down the axon and to synapses, and pausing of the Kinesin motor by auto-inhibition is crucial to deposition of these SVs at en passant synapses, even during the earliest stage of development. In contrast, different AZs exhibit differential dependence on Kinesin-3 for transport, with most AZ proteins being Kinesin-3 independent.

Advisor: Shen Kang
Clandinin Thomas R. (Thomas Robert)
Luo Liqun
McConnell Susan