VictorJuiz/thesis huggingface dataset:
Electronic gene sequencing [electronic resource] : a novel method for DNA sequencing based on direct heat or pH measurement

The Human Genome Project was accomplished by a reduction in the cost of DNA sequencing by three orders of magnitude. Further cost reductions are required for sequencing to become a standard tool in clinical medicine and to enable personalized medicine via individual genome sequencing. The current cost varies between

Keywords: Electrical Engineering
Advisor: Davis Ronald W. (Ronald Wayne)
Pease R. (R. Fabian W.) primary advisor. Thesis advisor
Pianetta Piero advisor. Thesis advisor
Electronic Transport in Graphene Nanoribbons and Topological Insulators

Graphene is an atomically thin sheet of carbon atoms arranged in a honeycomb lattice. Low-energy electronic excitations in graphene behave like massless Dirac fermions, and are expected to exhibit exotic phenomena such as relativistic Klein tunneling.
While the band structure of graphene sheets is gapless, experiments have observed gap-like behavior in graphene nanoribbons, strips of graphene tens of nanometers wide. In one part of this thesis, I will present annealing experiments and electronic transport measurements on nanoribbons of varying lengths and a standardized 30 nm width. The data support a model in which quantum dots form in series along the ribbon due to charged impurities, giving rise to the observed gap-like behavior.
Recent theoretical investigations of the effect of spin-orbit coupling in graphene have led to the discovery of a class of materials known as topological insulators. A topological insulator is a three-dimensional material which has a band gap for charge carriers in the bulk, but has gapless surface states protected from disorder by time-reversal symmetry. A number of novel physical effects are expected in these materials, such as the formation of Majorana fermions in a topological insulator via the superconducting proximity effect.
In the second part of this thesis, I will describe an ongoing experiment whose first goals are to produce thin films of bismuth selenide, a material predicted to be a topological insulator, and to tune the Fermi level throughout the bulk band gap with an electrostatic gate. Films as thin as 4 nm can be produced, and show a peak in resistance as the Fermi level is moved by a gate, perhaps corresponding to the Fermi level crossing the "Dirac point" of the surface states.

Keywords: Physics
graphene
graphene nanoribbon
bismuth selenide
topological insulators
Thesis
Advisor: Goldhaber-Gordon David
Kapitulnik Aharon
Elucidation of functional and regulatory aspects of sulfate transport in Chlamydomonas reinhardtii [electronic resource]

Chlamydomonas reinhardtii (Chlamydomonas) exhibits a suite of responses to sulfur (S) deprivation, including an elevation of sulfate uptake, synthesis of extracellular arylsulfatase, down-regulation of photosynthesis and cessation of growth and cell division. One of the earliest responses to S starvation is an increase in the sulfate transport rate. Aspects of sulfate transport during S-replete and S-depleted conditions were previously studied, although the sulfate transporters had not been functionally identified. In this study, both forward and reverse genetic approaches were employed to identify sulfate transporters in Chlamydomonas. SULTR2, SLT1, and SLT2 transcripts and polypeptides increased markedly in S-starved wild-type cells, suggesting that these genes encode high-affinity sulfate transporters that function when the cells experience S limitation. Mutant strains defective for acclimation to S starvation, sac1 and snrk2.1, exhibited much less of an increase in the level of SULTR2, SLT1, and SLT2 transcripts and their encoded proteins during S deprivation compared to wild-type cells. Consequently, these two strains were unable to induce sulfate uptake to the same extent as in the wild-type strain. The SULTR2, SLT1 and SLT2 polypeptides were localized to the plasma membrane and their rates of turnover were significantly impacted by S availability; the turnover for SLT1 and SLT2 (but not for SULTR2) was demonstrated to be dependent on proteasome function. Mutants identified for each of the S-deprivation-responsive transporters were used to establish their critical role in the transport of sulfate into S-starved cells. I have also discovered a sequential, temporal regulation of the S-starvation responsive genes. The primary responses (e.g. the induction of high-affinity SO[not]42- transporters) are not dependent on protein synthesis occurring on 80S ribosomes. In contrast, the secondary responses (the induction of ARS, ECP76 and ECP88) require de novo protein synthesis. ARS73a, a putative transcriptional activator, is directly or indirectly involved in the regulation of the expression of the second tier genes, most of which encode proteins associated with the scavenging of extracellular S or the redistribution of internal S. Genetic analysis has shown that ARS73a and SAC3 kinase act in the same pathway; ARS73a is epistatic to SAC3. These new discoveries are incorporated into a model that describes S-deprivation elicited regulation in Chlamydomonas.

Keywords: Biological Sciences
Advisor: Cyert Martha S.
Grossman Arthur (Arthur R.) primary advisor. Thesis advisor
Mudgett Mary Beth
Wang Zhi-Yong
Ema, display practices of Edo period votive paintings [electronic resource]

Large-scale ema (votive paintings) were commonly found at Edo period religious sites, where sacred and secular activities mingled. Ema halls functioned as art galleries, providing almost unrestricted access to paintings for any member of society. While the genre is most frequently defined through the initial act of donation, the role of ema in Edo period society is rooted in their public display. This dissertation examines the diversity of Edo period ema and contexts for their display within late Edo period society. Chapter 1 discusses the development of ema as paintings of horses in early Japanese history, including depictions in medieval handscrolls, and their role as examples of common religious practice in Japan, despite being usually described as Shinto religious objects. Chapter 2 focuses on the display and dissemination of ema during the Edo period. I examine Edo period literature about ema and how ema were understood by writers of the period. I also address the rise of ema halls and the increasing importance of ema displays within the early modern culture of public entertainment. Chapters 3 and 4 use two popular Buddhist temples in the Edo region as case studies for ema donation and display. Chapter 3 surveys ema at Sensôji temple in Asakusa, Tokyo to highlight both the continued importance of horses as subjects of ema and also the expansive diversity of subjects beyond horses. Stories told during the period about the oldest ema at Sensôji (early seventeenth-century) reveal beliefs about the efficacy of ema. Other ema display connections to the public amusements found in the Sensôji district. Chapter 4 explores the associations between ema at Naritasan Shinshôji in Chiba prefecture and the Ichikawa Danjûrô family of Kabuki actors. These actors and their fans used ema both to express religious devotion and to promote themselves in more secular ways. Naritasan was closely tied to Edo, especially through degaichô (public viewings of the temple's main statue) in the Fukagawa district of Edo, and many ema donations can be linked to the degaichô. While not denying the importance of ema as religious objects, I seek to show how their importance as objects of display and advertisement complemented their spiritual functions. They were part of a spiritual and social exchange that donors performed for both the gods and the viewing public.

Keywords: Art and Art History
Advisor: Takeuchi Melinda primary advisor. Thesis advisor
Pentcheva Bissera V. advisor. Thesis advisor
Vinograd Richard Ellis advisor. Thesis advisor
Wigen Kären
Empirical Explanation of Covered Interest Parity Deviations During Financial Crises

My paper aims to analyze the 2008 financial crisis, when Covered Interest Parity (CIP) between the U.S. dollar and the euro appears to have deviated by hundreds of basis points to historically unprecedented levels. In existing literature, this deviation is attributed to heightened credit risk spreads and dollar liquidity premiums. However, my paper shows that the Term Fed Funds explain the majority of these observed market deviations. I thus argue that covered interest parity did not fail as an economic model, but rather that panel banks underreported their true borrowing rates in the London Inter-Bank Offered Rate (LIBOR) survey. Ultimately I conclude that LIBOR, which is linked to more than $90 trillion of financial derivatives, broke down as an accurate measure of true interest rates during the 2008 financial crisis.

Keywords:  Department of Economics
Stanford Department of Economics
Covered Interest Parity
LIBOR
Term Fed Funds
Cross Currency Basis
Thesis
Advisor: Taylor John B.
An empirical study of residential developer bankruptcies in the United States 2007-2008 [electronic resource]

With falling home prices and home foreclosures currently acknowledged as a severe problem in the U.S., more attention needs to be paid to the contributing phenomenon of residential developers undergoing liquidation, which has left behind a trail of partially-completed or abandoned properties. This dissertation presents the results of an empirical investigation aimed at understanding this phenomenon. Specifically, we addressed the following research questions: How have the Chapter 11 bankruptcy cases of residential developers and home builders during this downturn been resolved? How did the actions taken by secured lenders in the course of bankruptcy proceedings shape the resolution outcome? To what extent was bank behavior during these bankruptcies affected and constrained by the banking regulatory framework and culture? This dissertation research involves the analysis of more than 200 residential developers that filed Chapter 11 bankruptcy petitions between November 2007 and December 2008. The main finding is that only a small minority of these developers confirmed a reorganization plan. The majority of the cases were dismissed or converted to Chapter 7, culminating in foreclosure or liquidation. Over 70% of the cases showed at least one instance where a secured lender sought lift-stay motions to pursue foreclosure. Among such cases, orders granting the lift-stay motions were granted most of the time. Investigating this insistence on quick foreclosure, more nuanced views of banks' lending functions, risk management and their regulatory environment are explored through a study of FDIC data, interviews with industry participants and banks' comment letters. A key finding is that, during a recession, banks may have a preference for liquidation in bankruptcy because of capital shortfalls and procyclical regulatory pressure to reduce portfolio concentrations, particularly in real estate lending. This would be inconsistent with theories that secured lenders will choose economically optimal outcomes within a bankruptcy case, as they may choose outcomes that are sub-optimal within a bankruptcy to maximize an exogenous urgent need for capital.

Keywords: Law.
Advisor: Friedman Lawrence M. (Lawrence Meir)
Cole G. Marcus advisor. Thesis advisor
Jagolinzer Alan D.
Energetics and dynamics of internal tides in Monterey Bay using numerical simulations [electronic resource]

Mixing processes in the ocean play a key role in controlling the large-scale circulation and energy distribution of the ocean. Internal tide-driven mixing is most important among the processes to mix the ocean interior. In the past decade, significant efforts have been made to understand tidal mixing processes. However, more details and better understanding are still required for some fundamental problems, such as the mechanisms that govern internal tide generation, radiation, and dissipation processes and the associated energy partitioning. This research aims to understand the energetics and dynamics of tidal mixing processes through both theoretical analysis and numerical simulations. The complete form of barotropic and baroclinic energy equations are derived and employed as the theoretical framework for analyzing the tidal energy budget. These equations provide a more accurate and detailed energy analysis because they include the full nonlinear and nonhydrostatic energy flux contributions as well as an improved evaluation of the available potential energy. This approach has been implemented in the hydrodynamic SUNTANS model, which is being employed to study the energetics of barotropic-to-baroclinic tidal conversion over complex bathymetry in the real ocean. Three-dimensional, high-resolution simulations of the barotropic and baroclinic tides in the Monterey Bay area are conducted using the SUNTANS model. A detailed analysis of the energy budget is performed to address the question of how the barotropic tidal energy is partitioned between local barotropic dissipation and local generation of baroclinic energy. After that, we then assess how much of this generated baroclinic energy is lost locally versus how much is radiated away and made available for open-ocean mixing. The mechanism of internal tide generation is investigated by examining the dependence of barotropic-to-baroclinic energy conversion on three nondimensional parameters, namely the steepness parameter, the tidal excursion parameter, and the Froude number. Finally, a simple parametric model is presented to estimate the barotropic-to-baroclinic energy conversion.

Advisor: Fringer Oliver B. (Oliver Bartlett) primary advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
Street Robert L. advisor. Thesis advisor
Enumerating invisibility, humanizing numbers [electronic resource] : public health and the production of inequities 1948-1974

"Enumerating Invisibility, Humanizing Numbers: Public Health and the Production of Inequities 1938-1974" is directed at answering one question: Why in spite of intensive study that has resulted in a wealth of numerical and statistical information on public health does the San Joaquin Valley and the residents therein remain, among one of the most underfunded, overlooked, impoverished and unhealthy regions? Through an examination of historical materials--surveys, reports, occupational surveillance, and decision making--this dissertation seeks to better understand how data and policy, through the social processes of classification and quantification, may have contributed to the production of inequities in the San Joaquin Valley. There are few studies to date that systematically examine the relationship between knowledge and numbers and even fewer that address the concerns of frequently overlooked communities of agricultural laborers in the San Joaquin Valley. This dissertation begins to fill these gaps by reviewing a diverse array of source material to trace how institutions counted and measured agricultural laborers, how the institutions shaped these counting practices, and how numbers shaped policies. Given that institutional identities and strategies of governance are at stake in the production of these numbers, the story of agricultural laborers their health, social, and scientific visibility must be told alongside the stories of state bureaucracies. In tracing how institutions counted and measured agricultural laborers, how the institutions shaped these counting practices, how numbers shaped policies and decisions, there is an opportunity to understand historically the potential consequences of these counting practices. Together they reveal how institutional identities contributed to the making of public health data--its production, content and interpretation. This data, meant to reveal patterns of disease and improve public health, has paradoxically played a role in concentrating health inequities in the San Joaquin Valley because it has often made invisible the relationships between material deprivation and health or the environment and health. This dissertation does not advocate that we cease to use numbers in science and in policy. Rather, it is meant to recognize that every system of data collection and surveillance, regardless of the institution producing the data, is subjective and is shaped by particular values that have material consequences on populations As a result, the analysis intends to render numbers and their production more transparent and therefore open to critical analysis, and to provoke reflection on how the human elements- history, culture, and experiences --can explain the inequities that data alone can conceal.

Keywords: Modern Thought and Literature.
Advisor: White Richard
De Genova Nicholas advisor. Thesis advisor
Kohrman Matthew
Epistasis and evolution [electronic resource]

Most biological traits depend on the interactions among many different genes; these genetic interactions are known as "epistasis." In the first part of this thesis, I examine the evolution of the general pattern of epistasis among deleterious mutations. I find that recombination and population structure create selective pressures favoring different forms of epistasis. In the second part, I consider a particular form of epistasis, known as a "fitness valley, " in which a possible adaptation requires a combination of multiple individually deleterious of neutral mutations to provide a fitness benefit. I find that large populations can rapidly cross shallow fitness valleys, especially if there is a small amount of recombination among the necessary mutations, while they cannot cross deep valleys if recombination is too frequent.

Keywords: Physics
Advisor: Feldman Marcus W. primary advisor. Thesis advisor
Fisher Daniel S. primary advisor. Thesis advisor
Kivelson Steven advisor. Thesis advisor
Petrov Dmitri Alex
Tuljapurkar Shripad
Equilibrium and control in complex interconnected systems [electronic resource]

Large-scale complex systems such as power grids, transportation systems, and social networks are reshaping every aspect of modern society. Despite their ubiquitous nature, the design and understanding of such complex networks is still very challenging. Decision making in such systems is complicated by the fact that an agent's optimal choice depends on the choices made by other agents in the system. In a smart grid, the power consumption of an individual user could depend on the demand profile of other users, some of who may be physically far away. An investment decision by an agent in an online auction is affected by the strategic choices of other agents participating in the auction. Thus, a node's decision is affected by the presence and the actions of other nodes in the system. The multitude of dependencies arising in such environments lead to an extremely complicated decision making process for a single agent. Often in complex systems, the decision maker has partial information about the state of the system. For example, a centralized load balancer in a server farm obtains the state of the queues via a communication network. This network introduces delays and losses which result in partial information at the decision maker. This further complicates the decision making process. In this thesis, we study equilibrium and control in complex interconnected systems. In the first part of the thesis, we investigate centralized decision making in a networked system in presence of delays. Specifically, we show that even in the presence of delays, a centralized decision maker can make optimal decisions with only a subset of the past history of the system.This history depends on the structure of the system as well as the associated delay pattern. From a practical point of view, these results show that one can make optimal decisions with only finite memory about the past, thus eliminating the need to store the entire history. Thus, for example, a centralized load balancer in a server farm can use algorithms based on only a finite past to evenly distribute load across multiple servers. In the second part of the thesis, we look at decentralized decision making in a reactive environment. We describe a mean field approach to decision making in large-scale systems. The basic premise of this approach is to treat other agents as a single entity with some aggregate behavior. We develop a unified framework to study mean field equilibrium in large-scale stochastic games. Under a set of simple assumptions, we prove the existence of a mean field equilibrium. A key insight developed from our result shows that the existence result is closely related to the approximation of mean field equilibrium to the actual behavior. Thus, a single agent can make near optimal decisions based only on aggregate behavior of other agents. We conclude the thesis with various interesting extensions and open challenges in the design and understanding of complex interconnected systems.

Keywords: Electrical Engineering
Advisor: Goldsmith Andrea
Johari Ramesh
Lall Sanjay advisor. Thesis advisor
The equivariant motivic cohomology of varieties of long exact sequences [electronic resource]

A perfect field, $, is fixed throughout. The aim of the present work is to compute the equivariant motivic cohomology of a certain variety, $X$, which represents the space of long exact sequences of given length and with prescribed ranks, all in the category of finite dimensional $-vector spaces, equivariant with respect to an action of the multiplicative group scheme of $. In order to calculate this, it is necessary to establish a number of results pertaining to the motivic cohomology of the general linear group scheme, and to introduce a spectral sequence for deriving the motivic cohomology of homogeneous varieties. We then present the variety $X$ as a homogeneous variety, and so obtain the cohomology. As an application, we show that the cohomology furnishes obstructions to equivariant maps from punctured affine $-spaces to $X$, which amounts to the same thing as obstructions to the existence of certain differential graded modules over polynomial rings over $. The obstructions so found are a generalization of the Herzog-K\"uhl equations, which are well-known in the particular case where the differential graded module is in fact a resolution of an Artinian module.

Keywords: Mathematics
Advisor: Carlsson G. (Gunnar)
Cohen Ralph L.
Vakil Ravi advisor. Thesis advisor