VictorJuiz/thesis huggingface dataset:
Population genetic analyses of gene expression and complex traits

A central goal of human genetics is to understand how the genome contributes to complex traits like height, BMI, and risk for many common diseases. This question is particularly challenging to answer in that analyses of human complex traits rely largely on observational data. In this dissertation, I present several projects that utilize statistical models and careful interpretation of data to infer features of latent process from observational data. First, I aim to improve our understanding of human complex trait architecture by exploring the effects of selective constraint on gene expression. I demonstrate that, while there is clear evidence of widespread constraint on gene expression, this selection is weak. Much of the variance of gene expression across individuals is, therefore, attributable to common genetic variants. Consistent with existing literature, this suggests that the genetic architecture of complex traits is highly polygenic. I also consider the role of previously under-studied contributors to genetic variance (e.g., epistatic interactions, somatic variation, and short tandem repeats) in complex traits. In addition, I apply the same careful consideration of confounders and data interpretation to measure, and understand possible drivers of, gendered differences in behavior between men and women scientists at academic meetings.

Keywords: Biology.
Advisor: Feldman Marcus W. 
Pritchard Jonathan (Jonathan K.) 
Fraser Hunter B. 
Montgomery Stephen
Portfolio management and optimal execution via convex optimization

We study three related applications, in the field of finance, and in particular of multi-period investment management, of convex optimization and model predictive control. First, we look at the classical multi-period trading problem, consisting in trading assets within a certain universe for a sequence of periods in time. We develop a framework for single- and multi-period optimization: the trades in each period are found by solving a convex optimization problem that trades off expected return, risk, transaction cost and holding cost. Second, we look at the classical Kelly gambling problem, consisting in repeatedly allocating wealth among bets so as to maximize the expected growth rate of wealth. We develop a convex constraint that controls the risk of drawdown, i.e., the risk of losing a certain (high) amount of wealth. Third, we look at an optimal execution problem, consisting in buying, or selling, a given quantity of some asset on a limit-order book market. We study the case when the execution is benchmarked to the market volume weighted average price, and the objective is to minimize the mean-variance of the slippage. In all three cases, we provide extensive numerical simulations (using real-world data, whenever possible), developed as open-source software. In practice, these problems are solved to high accuracy in little time on commodity hardware, thanks to strong theoretical guarantees from modern convex optimization and a rich and growing ecosystem of open source software.

Keywords: Management Science and Engineering.
Advisor: Boyd Stephen P. 
Borland Lisa Marina
Ye Yinyu
Portraits of the West: Representations of California in Nineteenth-Century Japan

Japan saw many changes in the 1800s, one of which was an increase of knowledge about the West. After more than two hundred years of restricting the information that came into Japan from foreign lands, the Japanese state began to actively study Western countries in order to learn from them; the goal was for Japan to become a modern nation like those in the West, which were the most powerful in the world at the time. This thesis will look into the types and amount of knowledge available in Japan during the nineteenth century regarding one specific region of the West – California. It will study maps, travelers’ accounts, and geography textbooks that were available to Japanese during the 1800s in order to examine the development of knowledge regarding California in Japan. This thesis will address the following questions: What sort of image of California did Japanese people hold during the 1800s? How did perceptions change as the nineteenth century progressed and more accurate information about California and the West entered Japan? Depictions of California found in late Edo and early Meiji maps, travelers’ accounts, and geography textbooks ultimately portrayed a land of wealth and success by the end of the nineteenth century.

Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
Japan
California
San Francisco
Japanese maps
Castaways
Iwakura Mission
Japanese geography textbooks
Japanese perceptions of the West
Interactions between Japan and the West
Japanese travelers to America
Thesis
Advisor: Wigen Kären
Pound-Drever-Hall Frequency Stabilization for Atom Interferometry

We present the development and implementation of a Pound-Drever-Hall laser frequency stabilization system for two lasers for use in a prototype of an atom interferometric gravitational wave detector. Techniques of coupling our lasers into an optical cavity, a measurement of our optical cavity finesse employing an optical cavity transient simulation fit, a measurement of the transfer functions of our stabilization components, a design of our locking circuitry, and our analysis of the lock stability are presented. We also present an outlook describing implementing these stabilized lasers into our larger experimental setup.

Keywords:  Department of Physics
Pound-Drever-Hall Frequency Stabilization
Atom Interferometry
Thesis
Advisor: Hogan Jason
Moler Kathryn A.
Practicing on the moon : globalization and the practice of foreign corporate lawyers in Myanmar

This dissertation presents a case study of Myanmar's emerging corporate legal bar dominated by foreign law firms and lawyers after its abrupt exposure to economic globalization in 2011. The emerging business demand from the economic opening of the country coupled with the lack of native corporate lawyers and absence of protectionist barriers explain the dominance of foreign lawyers and law firms during this formative stage. The study finds a diverse group of foreign law firms in Myanmar: global law firms, local law firms established by Western expatriates, and law firms from neighboring Asian countries. Foreign lawyers have not only taken the lead in transnational legal practice, but have also gained precedence even in providing local law advice to companies seeking to invest in the country. The highly discretionary and indeterminate government policy and practice, along with inadequate business laws and outdated common laws reflect the lack of legal certainty in Myanmar. Most foreign corporate lawyers who are newcomers that came into the country after 2011 perceive Myanmar's legal system as having "a void of law." Their deconstruction and marginalization of the authority of local law paves the way for a new type of hegemonic law based on globalized business norms and legal practices. Foreign corporate lawyers in Myanmar, regardless of their civil or common law background, all share a common mode of legal practice -- suggesting that a globalized identity of corporate lawyers has emerged. This practice focuses on stabilizing business, amidst Myanmar's legal uncertainty, by combining both technical legal practice and relational practice. Foreign lawyers in Myanmar serve as producers of legal structures -- their technical legal practice creates both de-facto hard legal structures along with soft legal structures as normative frameworks for business. They also assume the role of relational intermediaries -- serving as communication intermediaries, information intermediaries, and reputation intermediaries. By analyzing firsthand interview data with practitioners and other informants at a formative moment in Myanmar's history, I claim that the practice of foreign corporate lawyers is central to the transplantation of, first, a new conception of the legal profession; second, a new mode of legal practice; and third, a new mode of production of law into this previously closed society. In considering the nature of Law and Development as well as the process of legal transplant into a newly emerging economy, I place the roles of pioneering foreign lawyers front and center.

Keywords: Law.
Advisor: Hensler Deborah R.
Gordon Robert W. (Robert Watson)
Pérez-Perdomo Rogelio
The predictable case of Faroese

This thesis concerns case-marking phenomena in Icelandic and Faroese. I argue that the best approach to case distinguishes the levels of abstract, morphosyntactic and morphological case, and permits mismatches between levels in some grammars (Linking Theory, Kiparsky 1997, 2001); these mismatches are best handled by an Optimality Theoretic output harmonisation on the mapping from argument structure to morphosyntax (Prince and Smolensky 1993 et seq.). Such a theory provides a cogent account of predicates with non-nominative subjects in Insular Scandinavian, which present an interesting puzzle: in Icelandic, dative-subject verbs occur with nominative objects that trigger number agreement, whereas in Faroese the object in such sentences is marked accusative and occurs with default third person singular agreement. To date this difference has been poorly understood, and calls for in-depth analysis. The central hypothesis explored in this thesis is that the patterns observed are not language-specific idiosyncrasies, but the outcome of constraint interactions of a typical kind: namely, a pressure to index a nominative argument in the clause by number agreement, and a pressure to express structural accusative case on the object. I argue that similar constraint conflicts are responsible for the loss of lexical case in phenomena such as nominative substitution and case non-preservation, and correctly predict the availability of the passive in dative-subject predicates. I include a substantial amount of new data from surveys conducted on the Faroe Islands and Iceland, which are consistent with my hypothesis, and shed new light on the case systems of these languages beyond simple monotransitives. Moreover, I propose a Competing Grammars Model of intra-linguistic variation (cf. Kroch 1989 et seq.), which finds empirical support in corpora, and offers a plausible framework for explaining the diachronic trajectory of these languages. Finally, the model of grammar proposed here is also cross-linguistically tractable, generating realistic typologies of case-related phenomena, and can easily be extended to other language families.

Keywords: Linguistics.
Advisor: Gribanova Vera 
Kiparsky Paul 
Harizanov Boris 
Zaenen Annie E. (Annie Else)
Predicting the transmission of ultrasound through the skull : estimation of the acoustic properties of bone using computed tomography and magnetic resonance imaging

Interest in transcranial magnetic resonance guided focused ultrasound (tcMRgFUS) is being driven by an ever increasing number of applications. tcMRgFUS uses ultrasound transmitted through the intact skull to achieve a therapeutic outcome. Therapies under investigation include ablation as an alternative to surgery, targeted drug delivery through the temporary opening of the blood brain barrier, or the modulation of neurons. All of these applications rely on simulations of the propagation of ultrasound through the skull in order to compute the patient specific corrections necessary to efficiently transfer acoustic energy into the brain. In turn, these simulations rely on patient specific estimates of acoustic properties such as velocity and attenuation. These estimates are usually made using CT images of the patient. In this thesis I examine current models of predicting acoustic velocity and attenuation and propose modifications to these models. My analysis relies on experiments performed using 100 samples taken from two ex-vivo skulls. Each fragment is imaged using clinical CT, micro CT, and MRI and the acoustic velocity and attenuation of each fragment are measured. The velocity data are used to show that variations in the x-ray energy and reconstruction algorithm used to acquire a CT scan have a significant impact on the relationship between Hounsfield units (HU) and velocity that is not adequately accounted for in existing transformations of HU to velocity. Further, HU provide an incomplete estimate of velocity because they do not provide information about the pore structure in the skull. My results show that MR has the potential to provide this missing information. The attenuation results show that attenuation monotonically decreases with HU and that both CT and MR can predict acoustic attenuation in the human skull.

Keywords: Electrical Engineering.
Advisor: Pauly Kim Butts (Kim Rosemary Butts)
Dahl Jeremy J.
Ghanouni Pejman
Khuri-Yakub Butrus T.
Principles of artificial synaptogenesis

The process by which synapses in the vertebrate brain are formed has eluded neuroscience for decades. Despite tremendous advances in understanding how synapses facilitate signaling, the cellular processes that direct synaptogenesis are still a mystery. To understand the mechanistic basis of synaptogenesis I have focused attention on a family of molecules known as neuroligins. Neuroligins have a paradoxical relationship to synapse formation. Although genetic deletion of all neuroligin genes has no effect on synapse density, overexpression of neuroligin molecules by neurons in culture results in a dramatic increase in synaptic contacts made onto the overexpressing neuron. My approach has been to leverage neuroligin overexpression and study this artificial form of in vitro synaptogenesis under the assumption that the principles of artificial synaptogenesis are likely similar to the principles of synaptogenesis in vivo. Collectively, this work shows that artificial synaptogenesis induced by neuroligin overexpression is dependent primarily on extracellular interaction with neurexin and suggests that the synaptogenic effect may not be due to any specific signaling pathway, but instead may be attributable to high-affinity adhesion in general.

Keywords: neurosurgery) degree committee member.
Molecular and Cellular Physiology.
Advisor: Südhof Thomas C. 
Brünger Axel T.
Shen Kang
Private contributions and public opinion

Previous research has shown that government spending can crowd out private contributions to public goods, such as charitable giving. This dissertation explores whether, conversely, private contributions also crowd out public support for government spending. The results of several experiments suggest that, at least under certain conditions, crowding-out in public opinion may occur. This crowding-out effect may be especially likely when private contributions are framed as progress rather than commitment toward a particular goal.

Keywords: Political Science.
Advisor: Tomz Michael 
Haber Stephen H.
Sniderman Paul M.
Proactive communication for human-robot interaction

As robots move from isolated industrial settings into everyday human environments, we need to consider how they should interact with people. Emerging applications range from delivery and support in warehouses, to home and social services. Compared to isolated workspaces, human environments impose more challenges. For example, in social navigation, the robot needs to reach its destination while avoiding people and navigating in a socially compliant way. However, human behaviors are usually complex, stochastic, and hard to predict, which creates difficulties for the robot to plan appropriate actions. To address these challenges, this thesis focuses on the use of simple, proactive haptic communication to facilitate interactions with humans in various scenarios. The core research idea is that, instead of reacting to humans in the environment, the robot should proactively use communication to exchange information and affect human behaviors. This thesis addresses the following topics: (1) the effects of communication on human behavior, (2) mathematical models that predict these effects and human actions, and (3) algorithms to plan for communications that improve efficiency and performance of the human-robot system. We study these topics in the context of three applications. We first present the design and application of a bidirectional communication scheme for a person-following robot. Then we discuss the use of implicit and explicit communication in a mobile robot social navigation scenario. Finally, we present methods for communicating directional information for human navigation guidance.

Keywords: Mechanical Engineering.
Advisor: Okamura Allison 
Follmer Sean 
Sadigh Dorsa
A probabilistic analysis of the risk of nuclear deterrence failure

This research develops a quantitative risk analytic method to assess the risk of deterrence failure given modern nuclear weapon arsenals and policies. The model includes multiple antagonist behaviors, levels of conflict escalation, weapon capabilities and effects, and a spectrum of policies, both for protagonists and antagonists. It is based on infinite-horizon, risk-sensitive Interactive Partially Observable Markov Decision Processes. This model allows multiple agents to identify optimal policies in the management of conflict scenarios given the trade-offs between their political goals and the consequences of various forms of conflict. We develop a set of metrics for deterrence effectiveness based on the probability of specific opponent actions and on the evaluation of different conflict outcomes. The model and analysis capture complex behaviors and escalation dynamics, identify approximately optimal policies in specific conflicts, and can be extended to a large spectrum of possible scenarios. An illustration is presented, based on the analysis of fictitious data for a bilateral conflict scenario between two nuclear-armed, peer states. In this example, we evaluate various nuclear arsenals and stated policies about their use, based on the results of the model, including optimal conflict management and comparison of deterrence-effectiveness metrics. The results can provide valuable insights to policy and decision makers by allowing them to consider a spectrum of consequences involved in various alternatives.

Keywords: Management Science and Engineering.
Advisor: Paté-Cornell M. Elisabeth (Marie Elisabeth) 
Hecker Siegfried S. 
Kochenderfer Mykel J.
Nacht Michael
Probabilistic estimates and theoretical controls of earthquake size : applications to Southern California and induced seismicity

Earthquakes are complex, stochastic processes. They occur throughout the world, and even though we know so much about them, more often than not we learn something new each time a large event occurs. In California, where much time and money has been spent on monitoring, measuring, and forecasting seismicity, there is little evidence to suggest when the next San Andreas-rupturing earthquake will occur, or exactly how big it will get. However, earthquakes do obey the laws of physics. Some of these laws, friction in particular, are stochastic in their very nature; it is imperative to couple physics-based understanding with quantitative stochastic modeling to obtain a complete description of how earthquakes work. To do this, I look at two problems. The first problem is to develop a method to quantify uncertainty in the moment deficit rate (MDR) for regional-scale fault systems. There are three sources of uncertainty: with the data itself, in how well our models of the crust reflect its actual properties, and in the sensitivity of the data to the fault at depth. Prior to this work, no rigorous methods have existed to measure how uncertain any particular MDR estimate is. I show how a method termed the Constrained Optimization Bounding Estimator (COBE) rigorously quantifies uncertainty in the MDR related to the data and resolution of a given model, and that the current MDR in southern California is larger than expected given the historic moment release. The second problem I address is what controls the size of earthquakes in the context of induced seismicity. I consider how the restriction of seismicity to the pressurized zone would alter the frequency-magnitude statistics of induced events, and whether or not such changes have been or could be observed in real data. The last chapter uses fully dynamic rupture simulations on 2-D rough faults to characterize maximum earthquake size with and without pressure perturbations. The results indicate that earthquake hazard is governed more by the background stress conditions and less by injection-related parameters.

Keywords: Geophysics.
Advisor: Segall Paul
Dunham Eric 
Ellsworth William L.
Probing and tuning far-from-equilibrium oxygen exchange kinetics on electrochemical solid-gas interfaces

The oxygen exchange reaction, which involves the transformation of an oxygen gas molecule to two lattice oxygen ions, is ubiquitous and fundamental in solid-state electrochemistry. During this reaction, the oxide catalysts could change the stoichiometry, surface morphology, electronic structure etc. Without a well-defined surface and in situ probing techniques, the in-depth study of this solid-gas catalysis reaction is complicated. Moreover, to understand the reaction pathway and to identify the rate-determining step, near-equilibrium measurements have been employed to quantify the exchange coefficients. Because the exchange coefficient contains contributions from both forward and reverse reaction rate constants and depends on both oxygen partial pressure and oxygen fugacity in the solid, unique and definitive mechanistic assessment has been challenging. In this thesis, we derive a current density equation as a function of both oxygen partial pressure and solid oxygen fugacity and consider both near and far-from-equilibrium limits. Rather than considering specific reaction pathways, we generalize the multi-step oxygen incorporation reaction into the rate-determining step, preceding and following quasi-equilibrium steps, and consider the number of oxygen ions and electrons involved in each. By evaluating the dependence of current density on oxygen partial pressure and solid oxygen fugacity separately, one obtains the reaction orders for oxygen gas molecules and for solid-state species in the electrode. This model was then applied to (La1-xSrx)FeO3-δ (LSF), a promising candidate for solid-oxide fuel cell (SOFC) cathodes. We fabricated thin film LSF electrochemical cells whose surface morphology, structure, and chemistry were well controlled. We first investigated the surface defect chemistry using in operando synchrotron techniques. Combining the defect concentration results and the away-from-equilibrium rate equation model, we simulated many reaction pathways and compared with experimental data to determine the rate-determining steps. It was revealed from TEM that varying the (La+Sr)/Fe ratio changes the surface structure and shifts the rate-determining step from the molecular pathway to atomic pathway. The individual reaction steps were also simulated by DFT. The surface double Fe-O2 structure causes a substantial incorporation barrier and explains the experimental results. More applications to other LSF thin films showed how the reaction kinetics were influenced by the material composition and the vacancy formation energy. Some deviation on kinetics parameters were also observed and explained by generalizing the rate equation to non-ideal conditions.

Keywords: Applied Physics.
Advisor: Chueh William
Hwang Harold Yoonsung
Clemens B. M. (Bruce M.)