VictorJuiz/thesis huggingface dataset:
Primary peripheral human plasmacytoid dendritic cell responses to rotavirus infection [electronic resource] : mechanisms of induction and consequences for pathogenesis

Rotaviruses are the leading cause of severe dehydrating diarrhea in children worldwide. Rotavirus-induced immune responses, especially the T and B cell responses, have been extensively characterized; however, little is known about innate immune mechanisms involved in the control of rotavirus infection. Although increased levels of systemic type I interferon correlate with accelerated resolution of rotavirus disease, multiple rotavirus strains, including rhesus rotavirus (RRV), have been demonstrated to antagonize type I interferon production in a variety of epithelial and fibroblast cell types through several mechanisms, including degradation of multiple interferon regulatory factors by a viral nonstructural protein. Dendritic cells (DCs), a highly specialized subset of professional antigen- presenting cells, play a central role in the initiation of innate and adaptive immunity. Plasmacytoid DCs (pDCs), which secrete the type I interferons, as well as a variety of other cytokines and chemokines, have been documented to have multiple antiviral effects. These studies characterize the primary human pDC response to rotavirus, while elucidating the viral and cellular requirements for this response. Additionally, these studies demonstrate that type I interferon derived from primary pDCs is necessary and sufficient for B cell activation by rotavirus.

Keywords: Microbiology and Immunology
Advisor: Greenberg Harry B. primary advisor. Thesis advisor
Arvin Ann M. advisor. Thesis advisor
Butcher Eugene advisor. Thesis advisor
Engleman Edgar G. advisor. Thesis advisor
Schneider David (David Samuel)
Probabilistic models for region-based scene understanding [electronic resource]

One of the long-term goals of computer vision is to be able to understand the world through visual images. This daunting task involves reasoning simultaneously about objects, regions and 3D geometry. Traditionally, computer vision research has tackled these tasks is isolation: independent detectors for finding objects, image segmentation algorithms for defining regions, and specialized monocular depth perception methods for reconstructing geometry. Unfortunately, this isolated reasoning can lead to inconsistent interpretations of the scene. In this thesis we develop a unified probabilistic model that avoids these inconsistencies. We introduce a region-based representation of the scene in which pixels are grouped together to form consistent regions. Each region is then annotated with a semantic and geometric class label. Next, we extend our representation to include the concept of objects, which can be comprised of multiple regions. Finally, we show how our region-based representation can be used to interpret the 3D structure of the scene. Importantly, we model the scene using a coherent probabilistic model over random variables defined by our region-based representation. This enforces consistency between tasks and allows contextual dependencies to be modeled across tasks, e.g., that sky should be above the horizon, and ground below it. Finally, we present an efficient algorithm for performing inference in our model, and demonstrate state-of-the-art results on a number of standard tasks.

Keywords: Electrical Engineering
Advisor: Koller Daphne primary advisor. Thesis advisor
Boyd Stephen P. advisor. Thesis advisor
Ng Andrew Y.
Procedural constraints on agency rulemaking [electronic resource] : an analysis of political control of the bureaucracy

The bureaucracy literature has long analyzed political control of administrative agencies. Such studies typically ask to what extent the president, the Congress, the courts, and interest groups influence the regulatory process? This dissertation analyzes an important but overlooked element of political control: statutory constraints on the rulemaking process such as the Administrative Procedures Act's notice and comment requirement. Almost all existing studies assume that such constraints are effective, or achieve the goals of their supporters. This assumption neglects the influence of politics, however. This dissertation challenges the conventional wisdom by analyzing the impact of politics on the likelihood that a rulemaking process constraint will be effective. Chapter 1 explains the problem and reviews the literature, showing that many studies have incorrectly assumed that all rulemaking process constraints are effective. Chapter 2 argues that opponents of proposed constraints can win concessions that undermine the odds that a constraint will be effective. Chapter 3 tests this theory with case studies of the full universe of generally applicable statutory rulemaking constraints. The chapter also analyzes whether constraints increase the amount of time required to complete a rulemaking. Contrary to common expectations, some constraints are wildly ineffective. Chapter 4 discusses the implications. The results offer new evidence regarding the extent to which the administrative process responds to the Congress, president, and courts. The results also provide insight into the goals of Congress and the president with respect to administrative law. In concluding, Chapter 5 discusses future research directions.

Keywords: Political Science.
Advisor: Moe Terry M. primary advisor. Thesis advisor
Cohen Joshua
Ferejohn John A. advisor. Thesis advisor
Eskridge William N.
Programming many-core systems with GRAMPS [electronic resource]

The era of obtaining increased performance via faster single cores and optimized single-thread programs is over. Instead, forthcoming machines are increasingly parallel and increasingly include nontraditional resources such as programmable GPUs. In this dissertation, we present GRAMPS, a programming model for heterogeneous, commodity, many-core systems that expresses programs as graphs of thread- and data-parallel stages communicating via queues. We validate its viability with respect to four design goals--broad application scope, multi-platform applicability, performance, and tunability--and demonstrate its effectiveness at minimizing the memory consumed by the queues. Through three case studies, we show applications for GRAMPS from domains including interactive graphics, MapReduce, physical simulation, and image processing, and describe GRAMPS runtimes for three many-core platforms: two simulated future rendering platforms and one current multi-core x86 machine. Our GRAMPS runtimes efficiently recognize and exploit the available parallelism while containing the footprint/buffering required by the queues. Finally, we discuss how GRAMPS's scheduling compares to three archetypal representations of popular programming models: task-stealing scheduling, breadth-first scheduling, and static scheduling. We find that when structure is present, GRAMPS's adaptive, dynamic scheduling provides good load-balance with low overhead and its application graph gives it multiple advantages for managing the run-time depths of the queues and their memory footprint.

Advisor: Hanrahan P. M. (Patrick Matthew) primary advisor. Thesis advisor
Akeley Kurt
Rosenblum Mendel advisor. Thesis advisor
A proof of the Göttsche-Yau-Zaslow formula [electronic resource]

We prove the number of r-nodal curves in [vertical line]L[vertical line] is a universal polynomial for all algebraic surface S and sufficiently ample line bundle L.

Keywords: Mathematics
Advisor: Li Jun (Mathematician) primary advisor. Thesis advisor
Ionel Eleny advisor. Thesis advisor
Vakil Ravi advisor. Thesis advisor
Property transformation, marketization and wealth inequality in urban China, 1988, 1995 and 2002 [electronic resource]

This dissertation examines the changing mechanisms of social stratification during the market transition since the end of the 1970s in urban China. Unlike most market transition literature, which assumes either a market-centered, a property-rights centered, or a state-market interaction perspective by almost exclusively studying income inequality, my property transformation perspective stresses the importance of incorporating marketization and ownership restructuring as well as state politics into a theoretical framework simultaneously by investigating the wealth accumulation and wealth disparity among different social groups, organizations/sectors during the post-socialist transformation. Post-socialist transformation is a property transformation process in which public assets are reallocated, reevaluated and reorganized. There are two trajectories of property transformation in transitional urban China: housing privatization and ownership restructuring of public enterprises. Because these property transformations are orchestrated within existing political institutions and carried out by incumbent power holders, they create greater wealth disparity between cadres and ordinary workers and between state-owned work organizations/sectors and private work organizations/sectors. Drawing on three survey datasets from the Chinese Household Income Project conducted in 1988, 1995 and 2002 in urban China, supplemented with aggregate statistics from provincial yearbooks in 2003, I find sufficient empirical evidence for my property transformation perspective and ideas on the mechanisms of wealth accumulation and inequality in urban China over the past three decades.

Keywords: Sociology.
Advisor: Granovetter Mark S. primary advisor. Thesis advisor
Walder Andrew G. (Andrew George)
Zhou Xueguang
PrPl, a decentralized social networking infrastructure [electronic resource]

We present PrPl, a decentralized infrastructure that lets users participate in online social networking without loss of data ownership. PrPl, short for private-public, has a person-centric architecture; each individual owns a Personal-Cloud Butler service that provides a safe haven for one's personal digital assets and supports sharing with fine-grain access control. A user can choose to run the Butler on a home server, or use a paid or ad-supported vendor of his choice. Each Butler provides a federation of data storage; it keeps a semantic index to data that can reside, possibly encrypted, in other storage services. It uses the standard, decentralized OpenID management system, so users can use their established personas in accessing the data. One pre-requisite to the success of a platform is the availability of applications, which means that ease of application development is essential. We have developed a language called SociaLite, based on Datalog, that allows developers to use a simple declarative database query to access the large collection of private data served up by the Butlers in our social circle running under different administrative domains. We have developed a prototype of the PrPl infrastructure and implemented a number of simple social applications on the system. We found that the applications can be written in a small number of lines of code using SociaLite. Preliminary experimental results suggest that it is viable to enable sharing of private social data between close friends with a decentralized architecture.

Keywords: Electrical Engineering
Advisor: Lam Monica S. advisor. Thesis advisor
Public purpose, common good [electronic resource] : constitutional property in the democratic state

This dissertation concerns the status of property as a constitutional guarantee in a democratic state. With the exception of libertarian views, the contemporary legal theory literature resists treating property on par with other constitutionally protected liberties and goods on the grounds that constitutional property rights are fundamentally at odds with democracy. Constitutionalizing property, critics hold, is tantamount to insulating privately held interests from public deliberation and decision-making—something that is neither possible nor desirable. I defend two arguments against this position. First, I argue that the conflict is not between property and democracy, but between property and a particular understanding of democratic constitutionalism. The constitutional property debate assumes that the purpose of constitutional guarantees is protecting individuals from political majorities, acting as trumps against majority-enacted legislation. However, while property serves many purposes that are important for human liberty, none can be plausibly described as fulfilling this kind of role since property is inherently conventional and requires political definition. Second, I argue that libertarian theories of property are more complicated than the literature lets on. While libertarians are typically thought to defend just the kind of rights-based view that critics associate with constitutional property, I show that this is not a fair characterization. Libertarians care about rights, but social ordering and the rule of law are their more basic concerns, and it is this set of concerns that better explains property's importance for democracy on the libertarian view.

Keywords: Philosophy
Advisor: Satz Debra primary advisor. Thesis advisor
Cohen Joshua
Fried Barbara
Quantum dot spins and microcavities for quantum information processing [electronic resource]

Semiconductor quantum dots are attractive building blocks for scalable quantum information processing systems. The spin-up and spin-down states of a single electon, trapped inside a quantum dot, form a single quantum bit (qubit) with a long decoherence time. The electron spin qubit can be coupled to excited states using an optical field, which provides an opportunity to quickly manipulate the spin with optical pulses, and to interface between a stationary matter spin qubit and a 'flying' photonic qubit for quantum communication. The quantum dot's interaction with light may be enhanced by placing the quantum dot inside of an optical microcavity. Finally, the entire system is monolithically integrated, and modern semiconductor fabrication technology offers a path towards scalability. This work presents experimental developments towards the utilization of single quantum dot electron spins in quantum information processing. We demonstrate a complete set of all-optical single-qubit operations on a single quantum dot spin: initialization, an arbitrary gate, and measurement. First, initialization into a pure spin state (logical 0) is accomplished on a nanosecond timescale by optical pumping. Next an ultrafast single-qubit gate, consisting of a series of broadband laser pulses, rotates the spin to any arbitrary position on the Bloch sphere within 40 picoseconds. Finally, the spin state is measured by photoluminescence detection. We then combine these operations to perform a 'spin echo' sequence on the quantum dot. The spin echo extends the qubit's coherence (memory) time from a few nanoseconds to a few microseconds, more than 10^5 times longer than the single-qubit gate time. We next investigate a feedback mechanism between the electron spin and nuclear spins within the quantum dot, which leads to dynamical pumping of the quantum dot's nuclear magnetization. Finally, we take the first step towards interfacing a stationary matter quantum bit with a flying photonic qubit by strongly-coupling a quantum dot exciton to a pillar microcavity. An anti-crossing of the cavity and excitonic modes indicates that the exciton and cavity modes are coupled more strongly to each other than to the rest of their environment, while photon statistics prove that we have successfully isolated and coupled a single quantum dot exciton.

Keywords: Applied Physics
Advisor: Yamamoto Yoshihisa primary advisor. Thesis advisor
Mabuchi Hideo advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
Rab GTPase-activating proteins at the Golgi:endosome interface [electronic resource]

Rab GTPases are master regulators of membrane trafficking in eukaryotic cells. With GTP bound, they regulate trafficking by recruiting effectors to specific membrane-bound compartments. GTPase-activating proteins (GAPs) stimulate a Rab's intrinsic rate of GTP hydrolysis, thus inactivating the Rab by converting bound GTP to GDP. Regulation of Rab proteins links the formation and breakdown of sequential, Rab-regulated membrane domains in the secretory and endocytic pathways. This thesis presents the characterization of a novel RabGAP, RUTBC1. RUTBC1 binds Rab9 in vitro and in cells through interactions with its N-terminus. Overexpression of RUTBC1 only slightly disrupts MPR trafficking and RUTBC1 does not function as a GAP for Rab9. In vitro biochemical screening of Rab proteins revealed that RUTBC1 has GAP activity toward Rab33b and Rab32. These data suggest that RUTBC1 might function to link inactivation of these Rabs in relation to a Rab9 microdomain, in support of the existence of a Rab cascade at the interface between the Golgi apparatus and endosomes. Depletion of RUTBC1 unexpectedly led to concomitant depletion of Atg16L1. Atg16L1 has an established and essential role in macroautophagy, a highly conserved cellular recycling process. Overexpression of Atg16L1 caused the formation of large puncta in the cytoplasm, which are also labeled by endogenous RUTBC1 and may represent autophagosomes. Atg16L1 is a known Rab33b effector, suggesting that Rab33b, RUTBC1 and Atg16L1 function together to regulate autophagosome formation. Finally, RUTBC2, which is highly related to RUTBC1, also binds specifically to Rab9. In vitro biochemical screening for RUTBC2's Rab substrates showed that RUTBC2 had highest GAP activity toward Rab34 and Rab36, two very similar Rabs thought to play a role in secretion. The difference in substrate specificity between RUTBC1 and RUTBC2 further exemplifies the highly complex integration of diverse membrane trafficking pathways in mammalian cells.

Keywords: Biochemistry
Advisor: Pfeffer Suzanne primary advisor. Thesis advisor
Chu Gilbert advisor. Thesis advisor
Harbury Pehr advisor. Thesis advisor
Race cues in the news, racial attitudes, and the politics of criminal justice punitiveness [electronic resource]

Individuals are often called upon to form opinions about phenomena that they have limited first-hand experience with; in many of these instances, they turn to the news media as a vicarious source of information. Is the news media a central and influential cultural root force that directly shapes audience members' attitudes and beliefs, or is it a cultural conduit whose messages are selectively accepted or rejected by audience members based on their individual tastes and preferences? This dissertation grapples with this question by focusing on the nature and scope of the relationship between crime news exposure and audience members' racial attitudes and criminal justice policy preferences. It uses nationally representative survey data to assess the relationship between news exposure patterns, demographic and social psychological characteristics, and public opinion about race and crime. It also employs several survey-based experiments to directly gauge the impact that the type of crime presented and the race and gender of actors featured in crime news has on audience members' attitudes and beliefs. The findings indicate that various types of news have differing relationships with audience attitudes, with some being more potent than others, and that individuals' demographic and social psychological characteristics are important factors shaping the relationship between news exposure and attitudes. Overall, the results suggest that the news media acts as a cultural conduit as opposed to a cultural root force; its messages are not written on a tabula rasa, instead, audience members' characteristics play a key role in determining media effects. In short, while crime news is at times influential on audiences' attitudes about race and punishment, this is not always the case.

Keywords: Sociology.
Advisor: Bobo Lawrence
Cook Karen S. primary advisor. Thesis advisor
McDermott Monica
Racial contours [electronic resource] : theorizing racial identities through variation in responses among the multiracial population

In the 1990's, a small but influential social movement advocating for the inclusion of a multiracial category on the U.S. Census changed the way we collect data on race in the United States. Now, instead of prioritizing single race categories, the Census Bureau, under the directive of the Office of Management and Budget, encourages the expression of a more subjective meaning of racial identity by allowing people to choose more than one race. This new method of measuring race is a closer approximation to a social constructionist view of race and is a significant departure from centuries of racial categorization largely determined by rules of descent. While some people herald this new era of "multiraciality" as an era of post-racialism, I argue that the emergence of a "mark one or more race" category does not necessarily signal the end of race but is significant for other reasons. Indeed, an unintended consequence of the shift in enumeration strategies was that it allowed researchers for the first time to empirically measure how race still matters. In this dissertation, I argue that the variability in responses to questions about race helps us understand how racial ideologies and social structures continue to influence the way people identify. This variability is important to study not because it represents a weakening of racial and ethnic boundaries, though in some cases it may, but because it informs our knowledge of the contemporary and historical boundaries associated with racial and ethnic identities. After analyzing racial and ethnic self-identification across several datasets, I show that racial descent rules and social structures are important predictors of racial self-identification. Furthermore, the knowledge gleaned from models in this dissertation provides a glimpse of the future racial composition of the United States and allows us to gauge the potential impact of a growing multiracial population on race in America.

Keywords: Sociology.
Advisor: Snipp C. Matthew primary advisor. Thesis advisor
Bobo Lawrence
McDermott Monica