VictorJuiz/thesis huggingface dataset:
Gibbs measures and phase transitions on locally tree-like graphs [electronic resource]

In this thesis we consider Gibbs measures defined on sparse, locally tree-like graphs. We investigate the asymptotic behavior of these measures in the limit of graph size tending to infinity. In the first part we study replica symmetric heuristics for the asymptotic free energy density. We develop an interpolation scheme for proving replica symmetric bounds, and apply it to establish new results on the free energy of some classical models of statistical physics, including the Ising, Potts, and hard-core models. In particular, for d even we explicitly determine the asymptotic free energy density of ferromagnetic Potts models on graphs converging locally to the d-regular tree. This result covers, for example, any sequence of d-regular graphs with diverging girth. In the second part of this thesis we study random constraint satisfaction problems in which replica symmetric heuristics are expected to fail. For a large class of these problems, the one-step replica symmetry breaking cavity heuristic yields exact predictions of the satisfiability transition. We give the first rigorous confirmations of this prediction for two problems in this class, not-all-equal-SAT and maximum independent set, both in the setting of random regular graphs. In the second problem we furthermore establish tight concentration of the maximum independent set size.

Keywords: Statistics.
Advisor: Dembo Amir primary advisor. Thesis advisor
Chatterjee Sourav advisor. Thesis advisor
Montanari Andrea advisor. Thesis advisor
Global civil society [electronic resource] : altering pathways to empower the marginalized

Increased cross-national exchanges and the rise of global civil society have captured the attention of scholars and practitioners alike. In the three papers that comprise this dissertation, I use different analytic and methodological approaches to explore the features of global civil society and its effects on domestic civic and political affairs. The central focus is on the ability of global civil society actors and agendas, and transnational movements to reshape domestic contestations and empower those who are generally among the most marginalized: minority groups, indigenous peoples, and women and girls. Two important trends emerge from the research. First, NGOs, as key actors of global civil society, may strengthen local civil society organizations generating new systemic and sustainable opportunities for marginalized communities. The political economy of aid, though, remains a predominant feature of global civil society, strongly influencing where NGOs locate and biasing who is—and is not—supported. Marginalized groups, thus, have new pathways to recourse, but those opportunities may be constrained by geopolitics and global hierarchies.

Keywords: Sociology.
Advisor: McAdam Doug primary advisor. Thesis advisor
Powell Walter W. advisor. Thesis advisor
Snipp C. Matthew advisor. Thesis advisor
Soule Sarah Anne
Global quantification of proteostasis regulation [electronic resource]

Protein homeostasis, or proteostasis, is the result of protein synthesis, folding, degradation, and other quality control mechanisms which work in unison to establish and maintain desired levels of proteins. Deficiencies in proteostasis have been linked to aging and a number of diseases such as Alzheimer's disease, Huntington's disease, and cancer. Although individual mechanisms within the proteostasis network have been studied at length, the extent to which each process is responsible for overall protein maintenance has yet to be uncovered. Genomic and proteomic techniques developed in the last decade and are now capable of measuring proteostasis regulation, particularly protein synthesis and degradation. Chapter 1, the introduction to this dissertation, covers the techniques currently available for studying the dynamics of proteostasis on a systems-level. These techniques were applied in Chapters 2 and 3 to explore proteostasis regulation. Chapter 2 includes a global analysis of four aspects of proteostasis regulation -- transcript abundance, translation, proteins abundance, and degradation. This four dimensional approach to characterizing proteostasis under unperturbed conditions allowed for the detection of several distinct modes of regulation that reflect underlying biological mechanisms notably, non-degradative ubiquitination and mTOR-dependent translation regulation. Expanding our fundamental and quantitative understanding of these and other processes will support future mechanistic studies and will aid in the development of predictive models of proteostasis dynamics. Chapter 3 describes a project, in collaboration with the Kim lab at Stanford, aimed characterizing the aging proteome. Proteostasis collapse has been linked to aging in several of model organisms, however research focused on the systems biology of aging has largely relied on genomic and transcriptomic techniques. Here, we used mass spectrometry to quantify the changes in protein abundance that occur from adulthood to old age in the nematode, C. elegans. We identified over three thousand proteins and reproducibly measured changes in protein abundance for over 60 proteins. Some of these proteins were previously shown to play a role in the aging process, thus supporting our results. Proteins that signify the aging phenotype will serve as candidates for future experiments toward deciphering the mechanisms of aging.

Keywords: Chemical and Systems Biology.
Advisor: Elias Joshua
Kopito Ron Rieger
Meyer Tobias advisor. Thesis advisor
Wandless Thomas advisor. Thesis advisor
Governing trade beyond tariffs [electronic resource] : the politics of multinational production and its implications for international cooperation

While tariffs have been effectively eliminated over the last 50 years, a number of regulatory barriers to commerce persist. This thesis explains this persistence as a consequence of the interests of firms and governments and the limits of existing international institutions. This thesis develops three general findings. First, unlike with tariffs, the elimination of regulatory barriers to trade is not in the competitive interests of the most internationalized firms. Second, governments have an interest in using regulations to attract investment and retain the profits of that investment. Third, the existing institutions that govern trade, while able to resolve tariffs, are ill suited to address the challenges of regulatory protection. These three findings, illustrated with formal and empirical analysis, explain why cooperation in the area of regulatory protection remains difficult.

Keywords: Political Science.
Advisor: Goldstein Judith primary advisor. Thesis advisor
Bagwell Kyle advisor. Thesis advisor
Lipscy Phillip Y. advisor. Thesis advisor
Tomz Michael advisor. Thesis advisor
Gradient boosting machine for high-dimensional additive models [electronic resource]

The gradient boosting machine proposed by Friedman (2001) represents a fundamental advance in statistical learning. Although previous studies have shown the effectiveness of this algorithm on fitting additive models when the sample size is much bigger than the number of covariates, its properties in the high-dimensional case, where the number of covariates exceeds the sample size, are still an open area of research. We extend the application of the gradient boosting machine to a high-dimensional censored regression problem, and use simulation studies to show that this algorithm outperforms the currently used iterative regularization method. Buhlmann (2006) proved the convergence and consistency of the gradient boosting machine for high-dimensional linear models. We establish the same asymptotic theory for nonlinear additive models by showing that the set of basis functions is highly redundant. Then we discuss the properties of the 10-fold cross validation, which can be used in practice to define a criterion for choosing the number of iterations for the gradient boosting machine. We illustrate the effectiveness of the gradient boosting machine plus this stopping criterion on fitting high-dimensional additive models through numerical examples.

Advisor: Lai T. L. primary advisor. Thesis advisor
Saunders Michael
Shih Mei-Chiung advisor. Thesis advisor
Green fluorescent protein and its 10th [beta]-strand [electronic resource] : controlling protein-peptide interactions with light

Truncated green fluorescent protein (GFP) that is refolded after removing the 10th [beta]-strand (s10) can readily bind to a synthetic strand to recover the absorbance and the fluorescence of the whole protein. This allows rigorous experimental determination of thermodynamic and kinetic parameters of the split system including the equilibrium and the association/dissociation rate constants, which enables residue-specific analysis of protein-peptide interactions. The equilibrium constant obtained from the ratio of the two rate constants agrees with that directly estimated from the binding isotherm, which supports the one-to-one binding model. In measuring the dissociation rate of s10, it was discovered that the strand can photodissociate, where the dissociation rate is greatly increased by light irradiation. We found that in the overall photodissociation process, a thermal step follows light-activation of the molecule, and the thermal activation barrier was determined through an Arrhenius plot of the rate constants acquired at a saturating light intensity. The thermal step could be selectively affected by mutating residue 209 on s10 and by changing the solvent viscosity, which suggests that the thermal step is the actual dissociation of s10. In the process, we found that the quantum yield of photodissociation can be enhanced by increasing the temperature or lowering the viscosity of the solvent, or by introducing mutations such as K209Q or Y203T. For the light-activation step, cis-trans isomerization of the chromophore could be suggested as the underlying mechanism referring to the previous work on truncated GFP with strand 11 removed (Kent and Boxer, 2011). Photodissociation links photoexcitation of the protein to its conformational change, which opens the possibility of using GFP in caging. Finally, GFP variants carrying one extra s10 were created and characterized, and their possible applications were explored. These proteins can fold with either one or the other s10, and the ratio of the two folded forms, unambiguously distinguished by their resulting colors, can be systematically modulated by mutating the residues on s10 or by changing the lengths of the two inserted linker sequences that connect each s10 to the rest of the protein. Exploiting studies on photodissociation, ratiometric protease sensors were designed from the construct by engineering a specific protease cleavage site into one of the inserted loops, where the bound s10 is replaced by the other strand upon protease cleavage and irradiation with light to switch its color. Since the conversion involves a large spectral shift, these genetically encoded sensors display very high ratiometric dynamic range. Further engineering of this class of proteins guided by mechanistic understanding of the light-driven process will enable interesting and useful applications of the protein.

Keywords: Chemistry.
Advisor: Boxer Steven G. (Steven George)
Cui Bianxiao advisor. Thesis advisor
Lin Michael Z. advisor. Thesis advisor
Gurus on loan [electronic resource] : an ethnographic study of an intercultural knowledge-transfer program in a multinational company

Transferring knowledge and practices across cultural boundaries has become increasingly important for today's multinational companies (MNCs). Yet, knowledge and practice transfer is often difficult to achieve, and management scholars insufficiently understand how individuals accomplish this transfer in their everyday work. Using ethnographic methods, I closely studied how some knowledge transfer rotations in an MNC unfolded over time. My analysis unearthed multiple types of challenges in transferring knowledge and practices—challenges that existing theories of knowledge and practice transfer cannot adequately explain. To account for my empirical findings, I propose a practice-based framework of knowledge transfer that integrates the perspectives of both the knowledge sender and the knowledge receiver. The framework identifies two necessary components of knowledge transfer: knowledge reenactment by the sender and knowledge reconstruction by the receiver. I highlight three practices that are important yet challenging for the parties involved: Entry point identification for the sender to reenact knowledge, active observation and meaning reconstruction for the receiver to accurately process the knowledge that is enacted by the sender. I conclude by discussing (a) some theoretical implications of the study for the literature on knowledge and practice transfer and the literature on international assignment, and (b) some practical implications for managing knowledge transfer within MNCs.

Keywords: Management Science and Engineering.
Advisor: Hinds Pamela primary advisor. Thesis advisor
Barley Stephen R. advisor. Thesis advisor
Markus Hazel Rose advisor. Thesis advisor
Gyro-based multi-image deconvolution for removing handshake blur [electronic resource]

In low-light situations, long exposures are inevitable to improve the image quality, but, in turn, handshake blur becomes significant. Although image deblurring techniques have been intensively studied, most methods are brittle and computationally expensive, making them hardly usable in practice. This dissertation presents a new gyro-based multi-image deblurring system that handles various challenges in real-world situations. Instead of capturing a single long exposure image, a burst of shorter exposure images is captured along with gyroscope data being recorded at the same time. Then, any camera shake that occurred during the capture is removed to obtain a sharp and noise-free image of the scene. Because both camera motion and the scene are accurately measured with a better capture method, gyro-based multi-image deblurring is more robust than previous approaches while its computational burden is significantly reduced. In addition to the implementation, an important property of multi-image deblurring is presented: Multi-image deconvolution does not benefit from increasing exposure time beyond a certain threshold. The noise reduction granted by increasing exposure time is mostly offset by the noise amplification incurred by the more extreme deblurring. Based on this analysis, different capture strategies are compared in various photographic situations, demonstrating that multi-image deblurring is a robust approach that works in low-light situations when other methods fail.

Keywords: Electrical Engineering.
Advisor: Levoy Marc primary advisor. Thesis advisor
Horowitz Mark (Mark Alan) advisor. Thesis advisor
Rock Stephen M. advisor. Thesis advisor
Happy meals [electronic resource] : animals, nature, and the myth of consent

In describing man as an "animal rationale, " Aristotle argued for a "myth of consent, " i.e. that slaves, barbarians, women, and animals have all "agreed" to be owned and controlled by Greek male citizens for their own "protection." Therefore, there are two main themes in Aristotelian thought in the original definition of man, which became inscribed in later thinkers. The first is that the exclusion of the slave, and later of the colonized, as biological inferiors is rendered possible in part because of these pre-existing caesuras in politics, ethics, and philosophy which exclude animals, women, and slaves, based on their shared equation with the human body and supposed lack of reason. And second, this domination is justified via a rhetoric of care and benevolent protection. Based on a critique of this "myth of consent, " in the first half of the dissertation I argue that the practices of "locavorism, " "humane slaughter, " and being a "compassionate carnivore" obscure the reality of the death and suffering that such practices entail. I argue that the effect of the so-called "humane farming" movement is not a critique of anthropocentric privilege, but instead the restatement and re-entrenchment of the most basic claims of the factory farm system. In the second half of the dissertation, I explore the "myth of consent" for marginalized populations which have been oppressed, in part, based on a supposed belief in the need to "protect" them (even when this "protection" involves their death) as well as a belief in their supposed "animalistic" nature. Underlying all of these arguments, I argue that that the question "what is man?" (as opposed to the animal) is not a question philosophy should attempt to answer, but a power dynamic that we should, instead, seek to critique.

Keywords: Modern Thought and Literature.
Advisor: Fishkin Shelley Fisher primary advisor. Thesis advisor
Heise Ursula K. primary advisor. Thesis advisor
Kohrman Matthew
Haptic fMRI: Visually Guided Movement & Force Experiments for Understanding Human Neuromuscular Control

Recent advances in combining haptic interfaces with functional magnetic resonance imaging (Haptic fMRI) have enabled motor neuroscientists to design complex experiments that investigate how the human brain coordinates the musculoskeletal system. The human body's numerous and redundant degrees-of-freedom necessitate complex experiments to probe their dynamic range. In this thesis, we present a modular experiment design whose components can be combined to create arbitrarily complex Haptic fMRI experiments that include three-dimensional motor planning, unconstrained reaching, position holding, and visually guided trajectory tracking. Our experiment design achieves consistent response latencies, minimal hand jitter, and stereotypical goal-directed reaches and visually-guided motion trajectories across subjects. Moreover, the intuitive nature of our experiments helped subjects minimize head motion to less than half the spatial resolution of our fMRI scans, and decorrelated hand and head motions. We also establish criteria for including force-based haptic interaction in motor neuroimaging experiments by characterizing how well humans perceive forces. Finally, we determined that Haptic fMRI experiments conducted with the Stanford Haptic fMRI Interface (HFI) avoid task-correlated artifacts---simultaneously imaging a subject's brain with a brain-like phantom revealed no task-correlated noise. The phantom served as an ideal control because it was devoid of physiological activity but could still be affected by experimental artifacts. The experimental framework presented in this thesis sets the stage for future artifact-free motor fMRI experiments with Haptic fMRI that can help us understand how neuromuscular control works in the brain.

Keywords: Program in Biomedical Computation
Stanford Robotics
fMRI
motor neuroscience
haptic fMRI
HFI
functional magnetic resonance imaging
Thesis
Advisor: Menon Samir
Boahen Kwabena
Khatib Oussama
Haptic rendering of medical image data for surgical rehearsal [electronic resource]

This thesis investigates the problem of haptic rendering of medical image data for applications in surgical simulation. Surgical rehearsal is an emerging concept where an immersive simulation environment is created from patient-specific, pre-operative image data. Surgeons and trainees would then have an opportunity to rehearse procedures before operating on that patient. Patient-specific surgical simulation requires not only real-time visualization, but also a means of touching and manipulating a virtual model of that patient's unique anatomy. Haptic devices provide a means of achieving touch-enabled interaction. Thus computer haptics, the discipline concerned with generating and rendering haptic stimuli, is integral to high-fidelity surgical rehearsal. Haptic rendering algorithms to enable force-feedback interaction with pre-operative image data are presented in this work. These methods enabled the creation of virtual surgical environments for temporal bone surgery and for endoscopic sinus surgery. The systems were validated by comparing the experience in the simulation environment with observations from the actual procedure. Findings in the virtual surgical environment bore a high resemblance to images captured from intra-operative video of the same patients, indicating the predictive value of the simulation.

Advisor: Salisbury J. Kenneth primary advisor. Thesis advisor
Blevins Nikolas H. advisor. Thesis advisor
Hanrahan P. M. (Patrick Matthew) advisor. Thesis advisor
Hedgehog signaling in urogenital regeneration and neoplasia [electronic resource]

The Hedgehog (Hh) signaling pathway functions in embryonic development to control cell growth, cell fate and pattern many aspects of the vertebrate body plan. The role of the pathway in adult tissue homeostasis, regeneration and cancer, however, is still emerging, especially in the context of epithelial/stromal interactions. Previous work on the adult bladder demonstrated the importance of stromal Hh pathway response in mediating homeostatic response to injury by eliciting production of stromal factors that act on the epithelium; in this dissertation I investigate the role of epithelial/stromal interactions involving the Hh pathway in prostate regeneration and bladder cancer. In the adult prostate, Hh pathway response occurs in a subset of stromal cells. Prostate regeneration involves the formation of new prostate branches, and I showed that stromal cells at the tips of nascent buds lacked Hh pathway response. Decreased pathway activity in stromal cells leads to increased branching, and this correlates with increased secretion of hepatocyte growth factor (Hgf), which acts on the epithelium to induce prostate branching. In regions that are not budding, stromal Hh pathway response down-regulates expression of Hgf. Hence, the spatial organization of stromal Hh pathway response in combination with the negative regulation of secreted hepatocyte growth factor (Hgf) levels by Hh pathway activity, together modulate branching morphogenesis during prostate regeneration. I also examined the role of Hh pathway activity in development of invasive urothelial carcinoma and find, despite its initial presence in the cancer cell of origin, that Sonic hedgehog (Shh) expression is lost during progression. Genetic blockade of stromal response to Shh furthermore dramatically accelerates progression. This cancer-protective effect is associated with Shh-induced stromal expression of BMP signals, which stimulate urothelial differentiation, and progression is reduced by pharmacological activation of BMP pathway activity. Taken together, the results of this dissertation highlight the importance, in regeneration and cancer, of epithelial/stromal interactions in which the Hh pathway is a key mediator. In both models examined, Hh ligand produced by the epithelium stiumates pathway response in the stroma, which regulates the secretion of factors that act on the epithelium. In a broader context, this work provides a conceptual framework for understanding epithelial/stromal interactions involving Hh signaling in other organ systems, a more detailed understanding of which will enable better therapeutic strategies for the treatment of disease.

Keywords: Developmental Biology.
Advisor: Beachy Philip Arden primary advisor. Thesis advisor
Clarke Michael F.
Krasnow Mark
Talbot William