VictorJuiz/thesis huggingface dataset:
Understanding the effects of nanostructuring on gold catalysis [electronic resource] : a study of morphology, electronic structure, and electrocatalytic activity

The main objective of this thesis is to disentangle the myriad of factors that can potentially explain the origins of catalysis on gold nanostructures. Our approach to sort out these effects is to synthesize supported and unsupported gold nanostructures within a suitable nano-scale size range and measure their morphologies, electronic structures with and without reactants present, and electrocatalytic activities for several oxidation reactions. Using this approach, we can best attempt to relate the geometric and electronic nature of gold to its electrocatalytic activity, thereby lending insights into the origins of gold catalysis in general. The work delineated in this thesis provides evidence that surface structure is a key determining factor in gold catalysis, particularly for gold nanocatalysts with feature sizes 3.4 nm or greater. Undercoordinated atoms at the surface of Au nanostructures as well as surface strain are the likely contributors to significant, measurable changes in the electronic structure for Au nanoparticles, as evidenced by measuring their valence band using hard X-ray photoemission spectroscopy (HAXPES), though size dependent band structure changes may also play a role as well. At smaller sizes such as 1.6 nm, additional factors may come into play, as shown through ambient pressure photoemission spectroscopy (APPES) measurements. This thesis also details the sintering behavior of Au nanoparticles in electrochemical environments, and in particular differences observed in acid versus base. Recognizing and understanding these effects is critical to elucidating the intrinsic catalytic activity of nanoparticulate gold samples, highlighting the importance of accurately measuring gold surface area before/during/after electrochemical measurements. It was found that sintering is more prominent for gold samples with smaller feature sizes, particularly in basic environments, and higher oxidative potentials. Finally, unsupported, nanostructured Au thin films were synthesized and examined for the electro-oxidation of methanol in acid. The high activity of these nanostructures confirms the importance of surface structure in dictating the catalytic activity of Au at nano-scale dimensions.

Keywords: Chemical Engineering.
Advisor: Jaramillo Thomas Francisco primary advisor. Thesis advisor
Nilsson Anders
Noerskov Jens
Understanding the molecular mechanisms of cardiomyopathy-causing mutations in sarcomeric proteins [electronic resource]

Heart disease is one of the leading causes of morbidity and mortality in the developed world. As such, significant amount of resources and energy are funneled into developing treatments and therapeutics. While genetically caused cardiovascular diseases manifest at the tissue level, the fundamental mechanism that triggers the secondary effects and tissue remodeling generally occurs at the protein level. It is therefore critical to understand the molecular changes on the basic biochemical and biophysical level and connect these to the cellular and developmental disease processes. One such cardiovascular disorder is hypertrophic cardiomyopathy or HCM, which has been estimated to affect approximately 1 in 500 individuals. It disproportionately affects young adults and is the leading cause of sudden cardiac death. Since the first case of genetically linked HCM was identified in the early 1990s, a significant amount of work has been done to understand the molecular mechanism of the disease. Mutations have been identified in the proteins comprising the contractile apparatus of the muscle, the sarcomere. One such protein is [beta]-cardiac myosin, which has been recognized as a significant culprit of genetically linked HCM (~30-50%). Many studies have been performed to understand how single point mutations can alter the enzymatic and mechanical properties of this motor protein, but there is no clear consensus about the molecular mechanism. This has been due mainly to the lack of available human [beta]-cardiac myosin and the use of non-human and non-[beta]-cardiac myosin. Non-human and non-[beta]-cardiac myosin from common animal models differ by >30 residues, and as clearly evident from the disease and from previous studies on myosin, a single amino acids mutation can significantly alter and disrupt myosin function. During my thesis work, I have performed the first biochemical and biophysical work in the field looking at cardiomyopathy mutations using human [beta]-cardiac myosin. I have shown that HCM-causing [beta]-cardiac myosin mutations result in a gain of function, increasing the power or work output of the myosin. I have also examined HCM-causing mutations in troponin T, a component of the thin filament regulatory unit, using human [beta]-cardiac myosin. In the muscle, the interaction of myosin and actin is regulated by calcium through the thin filament proteins, namely the troponin complex and tropomyosin. HCM-causing mutations in troponin T increase calcium sensitivity or the number of force-producing heads that can interact with actin, thereby also increasing force or power output in the muscle. My work not only sheds light on fundamental properties of thick and thin filament function in the human sarcomere and presents the first studies of HCM-causing mutants in a human background, it also establishes a new approach to the problem of cardiomyopathy that will be critical in truly understanding and targeting the disease.

Keywords: Biochemistry.
Advisor: Spudich James A.
Krasnow Mark
Straight Aaron
Unfolding of systems of inductive definitions [electronic resource]

This thesis is a contribution to Solomon Feferman's Unfolding Program which aims to provide a general method of capturing the operations on individuals and predicates (and the principles governing them) that are implicit in a formal axiomatic system based on open-ended schemata. The thesis in particular studies the unfolding of the classical system for one generalized positive arithmetical inductive definition. The main result is an ordinal analysis of this theory. The resulting ordinal has been known since Heinz Bachmann, and has been studied by Peter Aczel, who felt it should be of proof-theoretic interest. Solomon Feferman conjectured specifically that it should be the strength of the theory under consideration here, and this thesis verifies his conjecture. The upper bound proceeds via a system of numbers, inductive definitions and ordinals that is analyzed with a combination of operator-controlled derivations and asymmetric interpretation. The lower bound is established through a well-ordering proof that uses the unfolding machinery to construct hierarchies based on jump operators. This part highlights a new ingredient needed in the unfolding at this level, namely a dependent version of the join operator, producing disjoint unions of predicates indexed by a predicate. The thesis also includes an appendix detailing the history and motivation of the unfolding program, as well as an appendix describing previous work on the Aczel-Bachmann ordinal.

Keywords: Mathematics.
Advisor: Feferman Solomon primary advisor. Thesis advisor
Mint͡s G. E.
Strahm Thomas (Thomas Adrian) advisor. Thesis advisor
Unleashing health rights in Argentine courts [electronic resource] : from the myth of rights to the politics of rights

Demands for the protection of social rights, and health rights in particular, have become a distinctive feature of judicialization in Latin American countries, including Argentina. Although a growing number of studies have begun to document the new relationship between the courts and health rights generated after almost two decades of litigation, little is yet empirically known about the versatile struggles undertaken in domestic courts and their consequences beyond the judgments. More specifically, given the scarcity of domestic empirical explorations, much remains to be discovered about legal mobilization experiences and courts' roles in the adjudication of conflicts regarding the intersection of health policies and rights. This dissertation takes a step toward filling that gap by exploring a set of conceptual, theoretical, and methodological questions that are critical to advancing current debates on health and the role of courts in bringing justice and expanding the rule of law in Argentina. With that aim in mind, this dissertation proceeds in two stages. First, it offers a basic assessment of the context and magnitude of the judicialization of health in the country, relying on multiple secondary sources and descriptive statistics obtained from databases of court decisions and dockets generated for this dissertation. Second, to complement the broader picture, the project proposes a qualitative study of strands of health rights litigation, offering a process-based observation of diverse patterns of judicialization while helping identify and compare the broader impacts of courts' roles in adjudicating health rights demands. Through these narrative studies, this dissertation tells the story of how once-dormant health rights clauses have come to life through the work of litigants, judges, and policy makers. It also shows how, in the process of unleashing health rights, courts have played contradictory roles throughout the nonlinear trajectories of different patterns of judicialization that can be located along a spectrum in which an atomistic and routinized style of judicialization is at one extreme, a bureaucratizing form of judicialization is in the middle, and a cooperative style of judicialization is at the other extreme. Ultimately, throughout these rich and variegated experiences of judicialization, courts' adjudication of right-to-health claims has sometimes reinforced ineffective or unequal arrangements, while at other times exhibiting potentially transformative capacities.

Keywords: Law.
Advisor: Hensler Deborah R.
Friedman Lawrence
Stacy Helen advisor. Thesis advisor
Unraveling the genetics of disease using structured probabilistic models [electronic resource]

Recent technological advances have allowed us to collect genomic data on an unprecedented scale, with the promise of revealing genetic variants, genes, and pathways disrupted in clinically relevant human traits. However, identifying functional variants and ultimately unraveling the genetics of complex disease from such data have presented significant challenges. With millions of genetic factors to consider, spurious associations and lack of statistical power are major hurdles. Further, we cannot easily assess functional roles even for known trait-associated variants, particularly for those that lie outside of protein-coding regions of the genome. To address these challenges in identifying the genetic factors underlying complex traits, we have developed probabilistic machine learning methods that leverage biological structure and prior knowledge. In this thesis, we describe four applications of such models. First, we present a method for reconstructing causal gene networks from interventional genetic interaction data in model organisms. Here, we are able to identify intricate functional dependencies among hundreds of genes affecting a complex trait. We have applied this method to understanding the genetics of protein folding in yeast, where we demonstrate ability to recapitulate the details, including ordering, of known pathways, and make novel functional predictions. Second, we present PriorNet, a method for incorporating gene network and path- way information into the analysis of population-level studies of genetic variation in human disease. PriorNet utilizes a flexible, Markov Random Field prior to propagate information between functionally related genes and related diseases, in order to improve statistical power in large-scale disease studies. We demonstrate a significant improvement in the discovery of disease-relevant genes in studies of three autoimmune diseases. Next, we extend the intuitions of PriorNet in a method for identifying interactions between genetic variants in human disease, to begin to understand how genes work together in complex disease processes. Our method, GAIT, leverages gene networks, network structure, and other patterns to adaptively prioritize candidate in- teractions for testing, and dramatically reduce the burden of multiple hypothesis correction to identify a large number of interactions in diverse human disease studies. Finally, we discuss the identification of functional variants on a large scale through the use of gene expression as a high-resolution cellular phenotype. We have sequenced RNA from 922 genotyped individuals to provide a direct window into the distribution, properties, and consequences of thousands of regulatory variants affecting diverse gene expression traits including splicing and allelic expression. From the identified variants, we also train a model, LRVM, for predicting regulatory consequences based on location and genomic properties of each variant.

Advisor: Koller Daphne primary advisor. Thesis advisor
Batzoglou Serafim advisor. Thesis advisor
Levinson Douglas advisor. Thesis advisor
U.S. courts and international trade policy [electronic resource]

This dissertation examines how and to what extent the United States Court of International Trade and the United States Court of Appeals of the Federal Circuit give weight to the General Agreement on Tariffs and Trade (GATT) and the World Trade Organization Agreement (WTO) when reviewing agency implementations of U.S. trade remedy laws. The analysis in this dissertation shows that domestic courts in the United States have, over time, decreased their reliance on GATT/WTO law in spite of the more legalized and more powerful dispute settlement system after the Uruguay Round Agreement (1994). I argue that the function of an institution is not enough to understand how a court decides a case and whether or not a court chooses to endorse international agreements to which the United States has committed. A better predictor for the tendency of an institution to promote compliance with international agreements or laws is the origins of the institution--in particular, how it derived its authority to adjudicate particular issues. Because Congress conferred the authority to adjudicate international trade disputes to the Court of International Trade (CIT), that court's treatment of GATT/WTO law reflected Congress's attitude on the matter of compliance with GATT/WTO law. Congress had an interest in enforcing U.S. trade remedy laws against foreign firms, and the CIT inherited such an attitude. This led to the CIT giving less weight to GATT/WTO law when adjudicating disputes with regards to the enforcement of U.S. trade remedy laws. Ultimately, I argue that U.S. courts are unlikely to be the source of compliance with the United States' obligation under the GATT and WTO agreements.

Keywords: Political Science.
Advisor: Weingast Barry R. primary advisor. Thesis advisor
Goldstein Judith advisor. Thesis advisor
Yoo John advisor. Thesis advisor
Using all networks around us [electronic resource]

Our smartphones are increasingly becoming loaded with more applications and equipped with more network interfaces---3G, 4G, WiFi. The exponential increase in applications for mobile devices has powered unprecedented growth for mobile networks. Mobile operating system and mobile network infrastructure are struggling to cope with this growth. In this thesis, I advocate that we use all of the networks around us. Our smartphones are already equipped with multiple radios that can connect us to multiple networks at the same time. By using those connections, we can open up tremendous capacity and coverage to better serve users, applications, and network operators alike. If done right, this will provide mobile users with seamless connectivity, faster connections, even lower charges and smaller energy footprints. To do so, we must first overcome several technical challenges that I will be describing in this dissertation, along with their proposed solutions. 1. I design a client network stack that allows the applications to migrate flows from one network to another, aggregates bandwidth across multiple networks to achieve faster connections and provides applications with flexible control over interface choices. I also present a prototype of this client network stack---called Hercules---to demonstrate its viability and usefulness. 2. I develop the theoretical foundation for scheduling packets across multiple networks while taking into account that applications have interface preferences. Using this theoretical foundation, I design a packet scheduling algorithm---multiple interface Deficit Round Robin (miDRR)---that is formally shown to provide weighted max-min fair packet scheduling. 3. Finally, I outline a programmable open network architecture that supports users making use of multiple networks simultaneously. The architecture also enable the operators to continually innovate and provide better services. By deploying and operating this network on the Stanford campus, the design is validated and the architecture's benefits affirmed. All in all, I show that making use of multiple networks at the same time is both technically possible and beneficial for users, applications, and network operators.

Keywords: Electrical Engineering.
Advisor: McKeown Nick primary advisor. Thesis advisor
Katti Sachin advisor. Thesis advisor
Parulkar Gurudatta M. advisor. Thesis advisor
Using Empirically Estimated Efficiency Frontiers to Gauge Central Bank Performance and Effectiveness

The tradeoff efficiency frontier between the variability of inflation and the variability of output has served as an important tool for evaluating monetary policy, used recently by Mervyn King (2012), the Governor of the Bank of England, and Ben Bernanke (2004), the Chairman of the Federal Reserve. However, these previous studies focus on the theoretical versions of the tradeoff curve, whereas this paper, by using dynamic stochastic optimal control methods, empirically estimates and calculates the optimal tradeoff curves between output and inflation for the three key periods of 1983-1990,1991-2000, and 2001-2010. In the findings, an inward shift in efficiency frontiers is observed between the periods of 1983-1990 and 1991-2000, pointing to increased output and inflation stability; this macro improvement is unfortunately reversed in the 2000’s, shown by a drastic outward shift in efficiency frontiers between the periods of 1991-2000 and 2001-2010. Upon further examination, this outward shift can be attributed to more intense shocks, specifically the interest rate shocks caused by discretionary monetary policy and compromised central bank independence. Indeed, though the de jure independence of the central bank has stayed constant over time, discretionary policy making had led to a deterioration of de facto independence in the 2000’s, explaining the higher output and inflation variabilities as illustrated by the outward shift in optimal tradeoff curves.

Keywords:  Department of Economics
Stanford Department of Economics
inflation
output
monetary policy
tradeoff efficiency frontier
Thesis
Advisor: Taylor John
Using fractional derivatives as a degree of symmetry to characterize natural shapes [electronic resource]

The main pursuit of this thesis is to model shapes and features in natural data, such as interstellar neutral hydrogen images, in order to recognize the unusual, or novel, in the presence of the ordinary. The presented approach develops on an abstraction we call the degree of symmetry. We assert that any feature or shape decomposes into two orthogonal components: one signifies a fractional degree of symmetry, and the other a corresponding, fractional degree of anti-symmetry. This framework conflates measure of symmetry with fractional-order derivatives, such that every feature is an instantiation of a linear model consisting of the orthogonal components. Each component is a fractional derivative of a symmetric function. The parameters of our model induce a 3-D representation space for the purpose of detection, classification, and characterization of features. The Wavelet transform of the features, particularly the decay of the coefficients and the coefficients' footprint on the scale-translation plane, provides sufficient information to determine the parameters of the model. In a representative application of the method, analysis of 21-cm interstellar neutral hydrogen spectra collected synoptically by the 150-foot Stanford radio Telescope demonstrates the performance of the proposed method in search for unusual structures. Additional examples such as roughness analysis of silicon deposition surface images, using our fractional symmetry transformations, also illustrate the utility of the proposed approach.

Keywords: Electrical Engineering.
Advisor: Tyler G. Leonard (George Leonard) primary advisor. Thesis advisor
Carlsson Gunnar
Linscott Ivan advisor. Thesis advisor
Zebker Howard A. advisor. Thesis advisor
Using network knowledge to improve workload performance in virtualized data centers [electronic resource]

The scale and expense of modern virtualized data centers motivates running them as efficiently as possible. These data centers are primarily composed of physical machines running virtualization software, with each physical machine hosting many virtual machines (VMs) simultaneously. The performance of the workload running inside a VM is affected not only by other VMs on the same physical machine, but in the case of a workload that uses the network, the location of the VM and other VMs it is communicating with in the network topology, and the utilization of all network links in between. This thesis explores how the performance of workloads running inside VMs can be improved when network traffic and topology data informs the assignment of VMs to physical machines (VM placement). To answer this question, I built a network control system based on the OpenFlow control protocol, Beacon, and a cluster control system that managed the Xen virtualization layer, resource measurement, experiments, and the VM placement algorithms used to optimize experiments. This system is named Virtue, and was used to run and monitor experiments on an 80 server cluster. The VM placement algorithms evaluated in this thesis were able to improve the median performance of network-heavy, scale-out workloads by over 70% compared to random initial placements in a multi-tenant configuration. Performance improvements of 33% to 129% were observed when running the same experiment and varying both the edge link speeds between 100Mb/s and 750Mb/s, and the core network oversubscription ratio between 16:1 and 1:1.

Advisor: McKeown Nick
Kozyrakis Christoforos
Rosenblum Mendel