VictorJuiz/thesis huggingface dataset:
Compliance and fragmentation [electronic resource] : who pays for public goods in China

When a government does not strictly enforce its policies, there will likely be non-compliers. What explains why some agencies and citizens comply with the state more than others? This dissertation explores the variation in compliance with public goods contribution targets in China. Although the Chinese regime is relatively capable of eliciting local contribution for public works projects, it rarely coerces compliance on a big scale due to concerns over political stability. Instead, it mostly relies on giving selective incentives, such as cutting funding and policy privileges for a few laggards. In this institutional context, theories of cooperation that emphasize the free-rider problem cannot explain compliance, because the temptation to free-ride on public goods is not sufficient for a subject to defect when the state may punish laggards. To understand compliance with public goods contribution targets in China, I present a theory of quasi-voluntary compliance: the subjects comply with the state to avoid the risks of losing resources from the state in the future; and the subjects will only offer as much contribution as their peers do to avoid punishment. This theory explains why both compliance and noncompliance could be contingent behaviors. It also implies that the state may encounter a problem of coordinated inaction—it cannot effectively use the threat of punishment to induce cooperation in a community where the majority of the members have reached a low-cooperation equilibrium. In addition, I argue that coordinated inaction is harder to sustain in fragmented bureaucratic systems or social communities, because the subjects in fragmented networks have more difficulties in predicting the strategies of their peers. This argument is in contrast with the "fragmented authoritarianism" model and social solidarity theories for explaining compliance in Chinese bureaucratic systems and rural villages. This dissertation offers two empirical tests of the relationship between organizational fragmentation and quasi-voluntary compliance. First, I use water infrastructure provision records to compare compliance from agencies in centralized and fragmented bureaucratic systems. Second, I use water tax records to compare compliance from rural households in single and multi-lineage villages. Empirical results show higher compliance for subjects in fragmented bureaucratic or social organizations. This study thus provides a cautionary tale regarding reforms that favor more centralized bureaucratic control or more small-scale social solidarity.

Keywords: Political Science.
Advisor: Oi Jean C. (Jean Chun) primary advisor. Thesis advisor
Lipscy Phillip Y. advisor. Thesis advisor
Tomz Michael advisor. Thesis advisor
Composition and mechanics of the Gram-positive bacterial cell wall and implications for cell division [electronic resource]

Most bacteria are under significant turgor pressure and surround themselves with cell walls to withstand it. This thesis mainly explores the mechanisms by which bacteria grow and divide their cell wall in the context of turgor pressure. I first discuss the plasticity and robustness of cell wall synthesis in Chapter 2 by describing the finding that the Gram-positive pathogen Staphylococcus aureus changes its cell wall composition in response to nutrient conditions. In Chapter 3, I present a collaborative study in which we characterized the cell cycle of S. aureus at single cell level and discovered a novel mechanical mechanism of daughter cell separation by which the coccoid shaped S. aureus is able to harness its turgor pressure to drive ultrafast daughter cell separation. In Chapter 4, I explore the mechanisms of daughter cell separation in a variety of bacterial species and describe the surprising observation that the fast mechanical daughter cell separation is unique to the Staphylococcaceae family in Firmicutes yet widespread in the other Gram-positive phyla Actinobacteria. In Chapter 5, I characterize the growth and division of the cell envelope in Corynebacterium and Mycobacterium, both of which polar-growing Gram-positive rods with an "outer-membrane like" mycomembrane. Finally in Chapter 6, I discuss our efforts in dissecting the roles of cell wall hydrolases in the mechanical daughter cell separation in S. aureus.

Keywords: Chemistry.
Advisor: Theriot Julie primary advisor. Thesis advisor
Boxer Steven G. (Steven George)
Huang Kerwyn Casey
Comprehensive image and transcriptomic analysis of circulating tumor cells [electronic resource]

The presence of circulating tumor cells (CTCs) in the blood of metastatic cancer patients can be an indicator of poor prognosis and survival. However, CTC detection assays that enable non-invasive "liquid biopsy" are generally limited by the lack of high-throughput, high-efficiency enrichment of CTCs from whole blood and rapid, accurate enumeration of the collected CTCs. Moreover, molecular analysis of single CTCs, which may recapitulate primary and metastatic tumor biology, remains challenging because current platforms have limited throughput, are expensive, and are not easily translatable to the clinic. This doctoral dissertation describes research work that aims to address these challenges by enabling a comprehensive image and transcriptomic analysis of CTCs from cancer patients. Image analysis of CTCs by immunocytochemistry comprises the immunofluorescent staining of CTCs followed by image analysis to identify CTCs. After CTCs were immunomagnetically enriched from whole blood samples by MagSifter and immunofluorescently stained, fluorescence microscope images of CTCs were then acquired on prepared cytospin slides. To achieve automated image cytometry of CTCs, CTC candidate images were first identified using an automated cell image segmentation method. Subsequently, a Random Forest machine learning algorithm was developed to classify each CTC candidate image as positive or negative, based on parameters such as size, shape, and fluorescence intensities in different channels. This approach was applied to identify and enumerate CTCs enriched from non-small cell lung cancer (NSCLC) patients' blood samples with high correlation to pathological assessment. This approach for automated image cytometry has demonstrated high-throughput CTC identification with excellent accuracy and reproducibility. For downstream molecular analysis of CTCs at the single-cell level, a massively parallel, multiplex gene expression profiling platform has been developed to enable compartmentalization and analysis of hundreds of single CTCs. After magnetic collection of CTC from blood, a single-cell Nanowell assay performs CTC mutation profiling using modular gene panels. Using this approach, multigene expression profiling of individual CTCs from NSCLC patients has been demonstrated with unprecedented sensitivity. These results represent the first demonstration of a high-throughput, multiplexed strategy for comprehensive single-cell mutation profiling of individual lung cancer CTCs toward non-invasive cancer therapy prediction and disease monitoring.

Keywords: Electrical Engineering.
Advisor: Wang Shan
Diehn Maximilian
De la Zerda Adam
Computation, mechanisms, and optimal coding in retinal adaptation [electronic resource]

Sensory systems face the problem of encoding sensory signals that vary greatly, exceeding the operating range of individual neurons. As a consequence, neural systems dynamically adapt to the current sensory environment by changing their response properties. While this adaptive coding and its underlying mechanisms have been studied over decades, a lack of quantitative, biophysical models limits our understanding both of the mechanisms of adaptation and the principles by which the nervous system has been optimized through evolution. Synaptic transmission and spiking are two key mechanisms thought to contribute to adaptation in the retina and elsewhere in the brain. To understand how the computation of contrast adaptation arises, we developed an accurate dynamical, multi-stage model that included bipolar cell synaptic transmission and ganglion cell spiking. Using this model, we show that, paradoxically, spiking alone is anti-adaptive, but that synapses and spiking act synergistically to generate adaptation. We further analyzed the parameters of the model to understand how the retina balances the conflicting requirements of information transmission and energy conservation in a rapidly changing environment. We show that synergistic adaptation from synapses and spiking creates an optimal balance of information transmission and energy eciency in a dynamically changing environment. Our findings reveal synapses as the essential source of adaptation, with spiking enhancing that adaptation, and the two mechanisms together acting to maximize information transmission while conserving energy.

Keywords: Electrical Engineering.
Advisor: Baccus Stephen A. primary advisor. Thesis advisor
Ganguli Surya
Weissman Tsachy advisor. Thesis advisor
Computational limits in statistical estimation [electronic resource] : hidden clique and related problems

Characterizing computational costs of statistical estimation and inference is a fundamental challenge. In many modern applications a confluence of both large-scale and high-resolution data has highlighted the computational challenges in extracting information and performing inference. For a number of reasons, the hidden clique problem from theoretical computer science has emerged as a prototypical example of the impact computational considerations can have on statistical estimation problems. In particular, the computational phenomena observed in the hidden clique problem are intimately related to analogous phenomena in other problems like sparse principal components analysis and learning communities in graphs. In this thesis, we study algorithm-based computational limits for the hidden clique problem and related problems. We use the popular approaches of the belief propagation heuristic, and convex programming relaxations for two aims: 1. We propose new algorithms that provably improve over the prior state-of-the-art methods for the hidden clique problem and sparse principal components analysis (PCA). 2. We provide hardness evidence for the hidden clique problem based on local algorithms, which generalize the belief propagation heuristic, and the powerful Sum-of-Squares hierarchy of convex programming relaxations.

Keywords: Electrical Engineering.
Advisor: Montanari Andrea primary advisor. Thesis advisor
Boyd Stephen A.
Candès Emmanuel J. (Emmanuel Jean) advisor. Thesis advisor
Computational methods for unbiased risk estimation [electronic resource]

In many engineering applications, one seeks to estimate, recover or reconstruct an unknown object of interest from an incomplete set of measurements. In recent years it has been shown that it is possible to recover the true object by exploiting a priori information about its structure, such as sparsity in Compressed Sensing or low-rank in Matrix Completion. However, in practice the measurements are corrupted by noise and exact recovery is not possible. A popular approach to address this issue is to solve a convex optimization problem that trades off between fidelity to the measurements and resemblance to the known structural characteristics of the true object. This tradeoff is usually controlled by a single regularization parameter. A possible criterion is to select the value of this regularization parameter by minimizing an unbiased estimate for the prediction error as a surrogate for the true prediction risk. However, evaluating this estimate requires knowledge of the regularity of the solution to the convex optimization problem with respect to the measurements. In this work we introduce a conceptual and practical framework to study the regularity of the solution to a popular class of such optimization problems. This framework leads to a disciplined approach for obtaining closed-form expressions for the derivatives of the predicted measurements that are amenable to computation. These expressions establish a connection between the geometry of the convex optimization problem and the unbiased estimate for the prediction risk.

Advisor: Candès Emmanuel J. (Emmanuel Jean) primary advisor. Thesis advisor
Murray Walter advisor. Thesis advisor
Ryzhik Leonid advisor. Thesis advisor
Conceptual complexity and the evolution of the lexicon [electronic resource]

Natural languages are filled with regularities. Where do these regularities come from? A parsimonious explanation is that these regularities emerge as a consequence of pressures within the broader context in which language is used: Communication among many cognitive systems. In this dissertation, I consider one particular regularity as a case study in how the dynamics of language use might shape language structure. Specifically, I focus on a bias in natural language to map long words on to conceptually complex meanings and short words on to conceptually simple meanings, or a complexity bias. Across a series of experimental and corpus studies, I explore whether languages and their speakers have a complexity bias, what conceptual complexity is, and what pressures might have lead to this bias over the course of language evolution. In the final chapter, I consider a broader range of linguistic phenomena and examine how aspects of language use might influence these structures.

Keywords: Psychology.
Advisor: Frank Michael C. (Professor of human biology) primary advisor. Thesis advisor
Goodman Noah (Noah D.) advisor. Thesis advisor
Markman Ellen M.
Conflict and the Cross-Border Pipeline: Revisiting the "Commercial Peace"

Cross-border pipelines are pipelines that cross at least one international boundary in order to transport natural gas or crude oil from one state to another. States and multinational enterprises are planning and building new cross-border pipelines to prepare for rising long-term energy demand, to facilitate oil and natural gas production in reserves located in landlocked countries, and to integrate regional energy markets. To build and operate a cross-border pipeline, states and firms must agree upon a breadth of terms, including ownership, operation, financing, right-of-way, contracted volumes, arbitration processes, and transit fees. Therefore, cross-border pipeline projects involve significant interaction among the participating states.
This thesis seeks to determine whether the interaction that enables cross-border pipelines to exist and operate increases or decreases conflict among the participating states. This thesis uses brief case studies to demonstrate that two opposite trends from existing literature may explain the effect of cross-border pipelines on interstate conflict. First, cross-border pipelines introduce additional economic interdependence between states, which empirical studies have already shown to decrease interstate conflict. Second, cross-border pipelines exhibit high asset specificity and are thus vulnerable to the hold-up problem, which increases interstate conflict. Converting a novel and comprehensive database of cross-border oil and natural gas pipelines to a dyad-year dataset, this thesis shows through empirical analysis that cross-border pipelines have no robust effect on the incidence of interstate conflict from 1946 to 1992.

Keywords: Center for International Security and Cooperation
pipelines
energy transit
cross-border
conflict
economic cooperation
Thesis
Advisor: Scheve Kenneth F.
The conformational cycle of the chaperonin termini [electronic resource]

Chaperonins are an essential family of molecular chaperones present in all three domains of life. They are large oligomeric complexes comprising two rings of 7-9 subunits related by twofold symmetry. Chaperonins engage unfolded or misfolded client proteins and encapsulate them in an isolated folding chamber in an ATP-dependent manner. The chaperonins are subdivided into two phyla, known simply as group I and group II. The group I chaperonins are found in bacteria and the endosymbiotic organelles mitochondria and chloroplasts, whereas group II chaperonins are principally encoded by archaeal and eukaryotic genomes. Less frequently, group II chaperonins may be found in bacterial genomes. The two groups of chaperonin share the same domain architecture, differing primarily in complex stoichiometry, inter-ring register, and the requirement of cofactors for client folding. This thesis concerns the structural dynamics of the terminal regions of both the group I and group II chaperonins. In particular, this work presents evidence from molecular dynamics simulations that the C-termini of the group I chaperonin undergo an ATP dependent conformational cycle with implications for substrate binding. Using a combination of crystallography and solution state nuclear magnetic resonance spectroscopy, the final chapter of the thesis establishes that the C-terminal conformational cycle hypothesized for the group I chaperonin is observed in a model group II chaperonin. Furthermore, that chapter introduces a heretofore unobserved N-terminal conformation of the group II chaperonin and demonstrates that both the N and C-termini influence the nucleotide usage of the enzyme.

Advisor: Frydman Judith primary advisor. Thesis advisor
Pande Vijay primary advisor. Thesis advisor
Bryant Zev David advisor. Thesis advisor
Puglisi Joseph D. advisor. Thesis advisor
Conformational transitions within an RNA enzyme [electronic resource]

Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes (ribozymes). Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers and must undergo structural rearrangements to assume functional structures. Here I describe a series of projects that uncover conformational transitions within the active site of the group I ribozyme. Most generally, the results described in this thesis underscore RNA's tendency to form alternative structures, even within an RNA active site, and highlight the important of RNA conformational changes in allowing RNA to navigate a rugged conformational landscape. Despite the apparent difficulties that RNA faces in specifying a unique structure that would be optimal for catalysis, RNA enzymes have persisted to the modern day, and several of them, including the spliceosome and ribosome, coordinate complex multistep processes. Perhaps RNA's folding "problem" has been harnessed by Nature to evolve dynamic ribonucleoproteins such as the ribosome and spliceosome, which undergo local and global conformational changes during their functional cycles.

Keywords: Biochemistry.
Advisor: Herschlag Daniel primary advisor. Thesis advisor
Das Rhiju
Krasnow Mark
Conjuring cane [electronic resource] : the art of William Berryman and Caribbean sugar plantations

This dissertation examines the depiction of sugar plantations in the colonial Caribbean, with a specific focus on Jamaica during the late eighteenth and early nineteenth centuries. Over the course of the eighteenth and early nineteenth century, there were few better examples of modern industrial labor systems than those found on Caribbean slave labor plantations, specifically those that produced sugar. These plantations were the nexus of the slave, sugar and rum trades. Though protected by mercantilist policies, these trade networks, and their arbiters, incredibly wealthy merchants based in the metropole, were capitalist at their core. The very functioning of the sugar plantation, with its state-of-the-art technology, and coordination of an enormous, highly disciplined labor force in the field with a highly skilled labor force the sugar mill under a rigorous, time-sensitive, and detailed schedule, was the epitome of modern labor. In addition to its economic and industrial impacts, the plantation was a site where new cultures were created through the process of what has at times been called creolization, hybridization, or cultural syncretism. Although crucial to modernity, the history of sugar plantations has often been overlooked in its histories in lieu of events like the Industrial Revolution or French Revolution. In this dissertation, I argue that the images produced and widely circulated of West Indian plantations, usually in the Picturesque style, created an impression of the plantation as a pastoral site, which, like the pastoral and Georgic images of rural British estates, not only placed these sites in a distant past, but also extracted them from their modern reality. The theories behind the Picturesque found their roots in the idea of the omniscient eye produced by property surveys, one of the first visual strategies aimed at representing land as privately owned capital. Thus, the Picturesque reinforced and naturalized European ownership and control over plantations at a time when, in many cases, that ownership was in peril. Countering this narrative is the work of artist William Berryman. Although his work has remained relatively unknown, his paintings and drawings of Jamaica in the early nineteenth century present a view of the inner workings of plantation society. This dissertation is the first extensive study of his archive, which contains approximately three hundred images from his eight year sojourn in Jamaica.

Keywords: Art and Art History.
Advisor: Wolf Bryan Jay primary advisor. Thesis advisor
Brody Jennifer DeVere advisor. Thesis advisor
Marrinan Michael advisor. Thesis advisor
Nemerov Alexander advisor. Thesis advisor
Connecting the Drops: The Negotiation of the Indus Water Treaty

In a world burdened by burgeoning populations and faced with declining water resources, water is likely to trigger conflict. Since the partition of British India in 1947 and the creation of the modern states of India and Pakistan, the two South Asian countries have been involved in four wars (one undeclared), as well as many border skirmishes and military stand-offs. Yet despite being strong adversaries, India and Pakistan have had a comprehensive water treaty, the Indus Water Treaty, active for over 50 years. This thesis explores the complex, drawn-out negotiation of the treaty, from its beginnings in 1950 to its eventual creation in 1960. Furthermore, this thesis looks into the significance of the final agreement, and its implications for India and Pakistan’s overall relationship.

Keywords:  Program in International Relations
Indus Water Treaty
Thesis
Advisor: Stedman Stephen
Considered opinions and better citizens [electronic resource] : public spiritedness, collective decisions, and issues of measurement

This dissertation explores the efforts to promote considered opinions and better citizens. The first chapter examines the relationship between deliberation and public spiritedness with scientific samples of the public who participated in seven Deliberative Polls on utility choices, and attempts to answer: a) do people become more public spirited after deliberation in the sense that they are willing to support the provision of public goods; and b) do they do so for identifiable reasons that are about the state of the community and not just the state of their own pocketbook? The second chapter of this dissertation attempts to explain the individual-level preference changes that underpin the aggregate phenomenon of deliberation-induced single-peakedness, which precludes majority cycles -- what individuals come to adopt single-peaked preferences, and more importantly, what underlying mechanisms cause the individuals to move closer to single-peakedness after deliberation? The final chapter of this dissertation examines four types of questions in six national or regional telephone surveys, and attempts to answer whether offering or omitting the middle alternative is good or bad in term of improving measurement validity and promoting more considered opinions.

Keywords: Communication.
Advisor: Fishkin James S. primary advisor. Thesis advisor
Bailenson Jeremy advisor. Thesis advisor
Krosnick Jon A. advisor. Thesis advisor
List Christian