VictorJuiz/thesis huggingface dataset:
Automated detection of basal cell carcinoma using polarization sensitive optical coherence tomography [electronic resource]

According to recent estimates, one in five Americans develop skin cancer in their lifetime. Basal cell carcinoma (BCC) accounts for more than 80% of total incidences of skin cancer, and while not fatal, it can grow to cause significant disfigurement and morbidity if left undiagnosed and untreated. In the current workflow of the US medical system, visual assessment of suspicious skin lesions by a primary care physician (PCP) serves as the basis for referring a patient to a dermatologist for positive determination of BCC. Biopsy and subsequent histology still remain the gold standard for skin cancer diagnostic in dermatology offices. The current medical workflow for detecting BCC suffers from the subjectivity and potential error of visual evaluations by PCPs, the invasiveness of biopsies, and the time-consuming nature of histology-based evaluations. Therefore, there is a significant clinical need for a non-invasive, real-time, automated and reliable technique for BCC detection. In this dissertation we report the development of highly sensitive classifiers, which successfully detected BCC in ex-vivo mouse and human skin. In ex-vivo mouse skin the classifier demonstrated 94.4% sensitivity and 92.5% specificity, while in ex-vivo human skin the classifier achieved 95.4% sensitivity and specificity. Our classifiers utilize features extracted from a large number of images captured by polarization-sensitive optical coherence tomography (PS-OCT), which is a form of non- invasive infrared imaging, paired with machine learning techniques that fully automate the detection process. Our proposed classifiers could be used in PCPs' and dermatologists' offices for real-time and automated detection of BCC in intact skin.

Keywords: Electrical Engineering.
Advisor: Bowden Audrey
Solgaard Olav advisor. Thesis advisor
Tang Jean (Jean Y.)
Automatic spin detection and recovery for small aircraft [electronic resource]

Spins are upset maneuvers in which an asymmetric stall over an airplane's wing causes it to enter a steep downward helical trajectory, often with reduced, annulled, or reversed control surface effectiveness. If these occur at low altitude, there might not be enough airspace to recover before colliding with the ground. Historically, this hazard has been addressed by careful aerodynamic design to suppress or minimize spin tendencies, and by flight crew training. Despite major reductions in accident rates, improvements have stagnated in recent decades, requiring new approaches to the problem. This dissertation proposes a software enabled approach, developing algorithms that can detect spins at an early stage and automatically recover with minimal altitude loss. To enable this study, a high angle of attack aerodynamic model of a typical general aviation aircraft is identified from wind tunnel and flight data. Using this model, the minimal altitude optimal control problem is investigated, and a spin recovery controller is designed. In addition, the relation between arrest delay and altitude loss is quantified, showing that altitude loss grows rapidly within the first turn. Motivated by these results, a methodology for designing spin detection schemes using different sensors is proposed. The methodology is applied to the same general aviation aircraft showing that detection at an early stage of the incipient phase is possible, resulting in as much as a fourfold reduction in altitude loss with respect to recovery from one-turn spins by a human pilot. Finally, the spin detection and recovery system is tested on small-scale UAVs, demonstrating the predicted fourfold altitude loss reduction. The results obtained indicate that such a system could help reduce spin-related accident rates by as much as 45%.

Keywords: Aeronautics and Astronautics.
Advisor: Kroo Ilan primary advisor. Thesis advisor
Pavone Marco
Rock Stephen
Automorphy, geometry, and symmetries of BPS states [electronic resource]

A host of new observations regarding BPS states in supersymmetric string compactifications point towards tantalizing new mathematical structures underlying string theory. The mathematical subjects of finite group theory, number theory (especially modular and mock modular forms), vertex operator algebras, generalized Kac-Moody algebras, enumerative geometry, and more have come to the fore in string theory of late, prompted in part by the ``Mathieu moonshine" observation in 2010 by Eguchi, Ooguri, and Tachikawa. This thesis describes progress in understanding mathematical aspects of string compactifications, with a focus on Mathieu and Umbral moonshines, automorphic forms, manifolds of special holonomy, and the algebraic and symmetric properties enjoyed by BPS subspaces of string theory. We make progress towards using string theory as an explanatory framework that ties together some of these mathematical disciplines. We also employ new mathematical ideas to constrain and describe highly symmetric string vacua.

Keywords: Physics.
Advisor: Kachru Shamit
Hartnoll Sean
Silverstein Eva
Axin2-positive hepatocytes in adult mouse liver homeostasis and local injury repair [electronic resource]

Wnt signaling has been implicated in the regulation of many adult stem cell populations. Using the expression of the universal Wnt target gene, Axin2, our lab has identified a privileged population of Wnt responding hepatocytes adjacent to the central vein in the uninjured adult liver. Our lineage tracing studies show that Axin2+ hepatocytes self-renew and proliferate, contributing to normal liver tissue homeostasis. These Axin2+ hepatocyte stem cells are located adjacent to Wnt secreting endothelial cells of the central vein and express Tbx3, an embryonic hepatocyte progenitor marker. Additionally, these pericentral hepatocyte stem cells are diploid in nature, but give rise to mature polyploid hepatocytes that span the rest of the liver lobule. Thus, we conclude that pericentral Axin2+ hepatocytes, under the regulation of endothelial derived Wnt signaling, behave as hepatocyte stem cells in adult mouse liver homeostasis. Our finding that Wnt signaling regulates the proliferation of hepatocyte stem cells in the uninjured liver gave rise to the hypothesis that perhaps similar mechanisms may also regulate hepatocyte proliferation following injury. Carbon tetrachloride toxicity is a well-accepted experimental injury model that induces acute centrilobular necrosis in the liver, resulting in a localized liver injury. Carbon tetrachloride injury destroys pericentral hepatocyte stem cells, but interestingly, I found that de novo Wnt signaling is initiated during the injury repair process. Hepatocytes adjacent to the injury border express Axin2 approximately 2-3 days after injury. Lineage tracing and label dilution studies show that these injury-induced Wnt responding hepatocytes proliferate, actively contributing to the repair of the local damaged tissue. Interestingly, the hepatocyte progenitor marker Tbx3 is upregulated in hepatocytes that line the injury border during the repair process. Additionally, Wnt 2, 4, 5a, and 9b expression is upregulated following injury and is observed specifically in the damaged liver tissue. Functional studies show that blockade of Wnt secretion from endothelial cells in the injured liver results in delayed hepatocyte entry into the cell cycle following injury. Furthermore, deletion of beta-catenin, the major signal transducer of the Wnt signaling pathway, in Axin2+ hepatocytes following injury leads to delayed tissue repair and increased mortality. Together, these studies demonstrate the importance of Wnt signaling in regulating hepatocyte proliferation in both homeostasis and in response to local liver injury.

Advisor: Nusse Roel
Desai Tushar
Red-Horse Kristy
Sage Julien advisor. Thesis advisor
Back into the shadows: immigrants retreat from needed services as deportation fears loom

Fear of deportation has always been a barrier to immigrants approaching law enforcement, especially those who are undocumented. Compounding the issue, domestic and sexual violence are chronically underreported from all demographics. But in recent months, that fear has multiplied to a new degree because of President Donald Trump’s pledges throughout the campaign and since taking office to crack down on illegal immigration and build a border wall with Mexico.
Immigrants have retreated not just from law enforcement, but from services of all kinds. Parents are afraid to send their children to school in case they’re taken in an ICE raid during the day and their children have no one to return to. Others fear using medical services — clinics note that some patients with chronic illnesses have stopped showing up for treatment. Even legal immigrants are afraid. In some areas, they’ve unenrolled from CalFresh, government food benefits only available to legal residents.
And, many immigrant women across Northern California are too afraid to file for restraining orders, report abuse, or seek U visas — predominately for victims of domestic and sexual violence — which require working with law enforcement.

Keywords:  Department of Communication and Journalism
Communications
Journalism
Virginia Fay
Immigration
Sexual Assault
Domestic Violence
Food Benefits
Medical Services
School Attendance
Driver's Licenses
Deportation
Thesis
Advisor: Zacharia Janine
Backpack [electronic resource] : towards practical mix-in linking in Haskell

In this thesis, we describe an evolution of the Backpack mixin package system which respects the division between package manager and compiler in the Haskell ecosystem: Backpack'17. Programs written in Backpack'17 are processed in two phases: first, a mixin linking phase which computes a "wiring diagram'' of components indifferent to the actual Haskell source code, and then a typechecking phase on the output of mixin linking which processes Haskell source. This is not merely a paper design: our architecture was principally motivated by our experiences implementing Backpack'17 in the GHC compiler and the Cabal package system.

Advisor: Mazières David (David Folkman)
Dreyer Derek
Mitchell John C. advisor. Thesis advisor
Bacterial morphology in the Sinorhizobium/Medicago nitrogen-fixing symbiosis [electronic resource]

In this thesis, I explore how bacteria change shape. I used the model bacterial symbiont Sinorhizobium meliloti, which undergoes significant changes in cell shape during its nitrogen-fixing symbiosis with legume plants. Nitrogen is a limiting nutrient in the environment, and nitrogen-containing fertilizers are heavily used in agricultural systems. Organically available (fixed) nitrogen is energetically expensive to produce. Legume plants, in symbiosis with rhizobia soil bacteria, are able to fix nitrogen and do not require nitrogen-containing fertilizers. The model system of Medicago sativa (alfalfa) and the soil bacterium S. meliloti permit laboratory study of this process. As the human population continues to grow, it is essential to understand the conditions that are required for biological nitrogen fixation. M. sativa and S. meliloti initiate symbiosis by exchanging chemical calling cards. S. meliloti cells then invade plant roots. M. sativa forms nodules -- specialized root organs -- to house the bacteria. S. meliloti cells within the nodules differentiate to form nitrogen-fixing bacteroids. These bacteroid cells can be ten times larger and contain twenty times more genomic DNA than free-living cells, and they are often branched in contrast to the rod shaped bacteria found in the soil. The purpose of this dramatic morphological switch is not well understood but appears to be essential for nitrogen fixation. I used different culture media and environmental conditions and examined bacterial mutants to investigate what external factors are involved in S. meliloti free-living cell shape. I tested multiple conditions including microaerobic versus aerobic, salt concentrations in culture media, a range of temperatures, and different carbon sources. Of all these conditions, I discovered that only the presence of phosphate in growth media was strongly correlated to branching and an increase in cell size. This morphology is specifically related to the activity of a phosphate transporter-encoding gene, pstC. This result was confirmed through whole genome sequencing and epistatic expression of mutated and full-length pstC in different laboratory strains of S. meliloti. I hypothesize that an increase in extracellular phosphate concentration may be present within root nodules and may contribute to bacteroid differentiation. More work remains to be done to determine the role of phosphate in legume/rhizobia symbiosis and uncover the mechanism by which phosphate affects cell morphology.

Keywords: Biophysics.
Advisor: Long Sharon R. primary advisor. Thesis advisor
Huang Kerwyn Casey
Mudgett Mary Beth
Theriot Julie advisor. Thesis advisor
Banking Regulation and Policy Recommendations for Chile

The purpose of this document is to discuss risks that affect financial institutions, in particular banks, and to make policy recommendations related to Chilean Banks General Law. Though most industries exhibit equity over assets ratios above 35%, banks show in general levels below 10%. Deposit insurance and bailout promises are explicit and implicit subsidies, respectively, that allow banks to obtain cheap debt and to hold lower equity ratios than those that they would hold without those subsidies. The Basel Accords have been international attempts to improve banking soundness, but capital requirements have been set at insufficient levels to prevent generalized banking distress. During the subprime mortgage crisis, poorly capitalized financial institutions were unable to cope with generalized house-price drops and massive mortgage failures. Chilean banks were not affected by the financial crisis, in part because of their low dependency on external debt and low exposure to complex securities. The Chilean Congress is discussing a new Banking Law that will fully adopt the Basel III accords. Our proposal is to include an equity over assets requirement of 9%, which is equivalent to the current average of Chilean banks. Setting a higher capitalization means a guarantee that banks’ solvency will not fall below current levels. It would place Chile at the international vanguard of banking regulation.

Keywords:  Public Policy Program
Stanford University
Humanities and Sciences
Public Policy Program
banks
capital regulation
Basel accords
solvency
insolvency risk
equity over assets ratio
leverage ratio
risk weighted assets
subprime mortgage crisis
financial crisis
Chilean Banking Law
Thesis
Advisor: Admati Anat Ruth
A Bayesian framework for quantifying fault network uncertainty using a marked point process model [electronic resource]

Faults are one of the building-blocks for subsurface modeling studies. Incomplete observations of subsurface fault networks lead to uncertainty pertaining to location, geometry and existence of faults. In practice, gaps in incomplete fault network observations are filled based on tectonic knowledge and structural interpreter's intuition pertaining to fault relationships. Modeling fault network uncertainty with realistic models that represent tectonic knowledge is still a challenge. Although methods that address specific sources of fault network uncertainty and complexities of fault modeling exists, a unifying framework is still lacking. In this paper, a rigorous approach to quantify fault network uncertainty is proposed. Fault pattern and intensity information pertaining to fault networks are expressed by means of a marked point process, namely a marked Strauss point process. Fault network information represented using marked Strauss point process is constrained to fault surface observations (complete or partial) within a Bayesian framework. A structural prior model is defined to quantitatively express fault patterns, geometries and relationships within the Bayesian framework. Structural relationships between faults, in particular age-based fault abutting relations, are represented with an implicit, level-set based approach to represent abutting relations between fault surfaces. A Markov Chain Monte Carlo sampler is used to sample posterior fault network realizations that reflect tectonic knowledge and match fault observations. We apply the methodology to a field study from Nankai Trough and Kumano Basin. In this illustrative study, the target for uncertainty quantification is a deep site with attenuated seismic data with only partially visible faults and many faults missing from the survey or interpretation. A structural prior model is built from shallow analog sites that are believed to have undergone similar tectonics compared to the site of study. Fault network uncertainty for the field is quantified with fault network realizations that are conditioned to structural rules, tectonic information and partially observed fault surfaces. The proposed methodology generates realistic fault network models conditioned to data and a conceptual model of the underlying tectonics. In the second part of the thesis, an approach to incorporate fault network uncertainty in fluid flow problems is proposed. The main challenge is creating multiple structural frameworks and creating deformable grids prior to fluid flow simulation. Proxy-based workflow are presented in order to choose fault network realizations that result in most dissimilar fluid-flow responses. Thus, the computational load of evaluating exhaustive set of fault network realizations is reduced to a select few. The proxy-based approach is illustrated using a field case.

Keywords: Energy Resources Engineering.
Advisor: Caers Jef primary advisor. Thesis advisor
Aydin Atilla advisor. Thesis advisor
Mukerji Tapan
Belief Map

The internet dramatically changed who can get access to information and in turn who can talk about it. However, spend just a few minutes online and it becomes apparent how little critical analysis is actually taking place. Motivated reasoning prevents most people from being able to evaluate evidence about controversial issues in an unbiased manner. (Kahne and Bowyer, 2016) The illusion of explanatory depth emboldens extreme opinions about systems that are more complicated than they seem. (Rozenblit and Keil, 2002) Social media algorithms create echo chambers that distort one’s capacity to perceive the world at large. Choices of convenience-- as in the choice not to fact-check, not to explain your reasoning, not to survey opposing viewpoints even if it means having to search-- all undercut one’s ability to reason with rationality. We aim to create a learning tool, in concert with a series of modules, that does a better job of engendering these skills with the intent of providing an alternative to the essay typically deployed in schools to teach critical thinking. Students analyze and map sources for credibility and strength of effect focused around a given issue to create a pseudo-meta-analysis, and reconcile their findings with their own opinions with support built in to our solution design. The goal is that learners recognize the value of engaging with opposing ideas and evidence and demonstrate these behaviors outside of the learning system. Additionally, learners will soften extreme views that lack grounded evidence. This can be measured by looking at heat maps of movement along our charts, as well as investigating the level of reasoning and engagement with evidence that disagrees with their view.

Keywords: critical thinking
polarization
belief
Thesis
Better donors: a non-monetary incentives mechanism to increase kidney market participation

Patients that need a kidney transplant and have a potential donor that is not compatible often participate in centralized kidney exchanges to find a match for a successful transplant. A significant challenge for kidney matching exchanges involves the over-representation of patients that are not compatible with most donors. The presence of these highly sensitized patients decreases the number of possible exchanges amongst incompatible pairs, hence decreasing total successful transplants. This paper proposes a non-monetary mechanism that would decrease the sensitivity of kidney exchange pools. Specifically, the mechanism would encourage compatible pairs with old, low sensitivity donors to participate in centralized kidney exchanges with the objective of exchanging the old donor’s kidney with a kidney from a younger donor, hence improving the health outcomes of the patient. The paper uses Monte Carlo simulations to show that, in a kidney exchange pool with real-world characteristics, very two added compatible pairs lead to an additional kidney transplants. Furthermore, the simulations show that 94% of participating compatible pairs were matched with a younger donor. Given 2016 donor demographics, the introduction of this mechanism could have increased US annual paired kidney donations by up to 10%, or 72 new transplants. If implemented, the proposed a mechanism would lead to both an increase the life expectancy of patients from compatible pairs and a significant increase in total kidney transplants - all without any notable tradeoffs.

Keywords:  Department of Economics
Stanford Department of Economics
Thesis
Advisor: Clerici-Arias Marcelo
Between revolutionary motherland and death [electronic resource] : art and visual culture in socialist Ethiopia

This dissertation examines the role of art and visual culture in the Ethiopian revolution of 1974, and the ensuing years of Marxist Leninist military dictatorship that followed. It argues that revolutionary change hinged upon a process of visual revelation, and that this process, although begun in earnest by artists and students who sought to challenge authority, was ultimately hijacked by those who would use images not to liberate, but to control. As such, this dissertation examines the positions of art and its makers both at the heart of radical domestic political change, and on the final frontier of the Cold War in Africa. Whilst exploring the ways in which the military sought to harness and utilize artists, this research stresses the survival of creativity even under duress. Four chapters examine, respectively, the centrality of art, photography and film in the downfall of Emperor Haile Selassie, the rapid growth and unexpected trajectory of graphic art, the push for realism and the import of Soviet art concepts, and the politics of cultural heritage both as propaganda and resistance. Addis Ababa is positioned as the main cultural hub, yet the sojourns of young artists to Moscow, Leningrad, Pyongyang and Havana offer insights into the complex global networks of cultural exchange in which Ethiopia's artists were enmeshed. Between 1974 and 1991 Ethiopia was a dictatorship, but Ethiopia's artists were not simply passive propagandists. Their works provide a rich, visual chronicle of an era rife with wavering ideological positions, rampant disillusionment and manifold acts of creative disobedience.

Keywords: Art and Art History.
Advisor: Lee Pamela M. primary advisor. Thesis advisor
Martinez-Ruiz Barbaro
Meyer Richard
Roberts Richard L.
Between Tito and Stalin [electronic resource] : Enver Hoxha, Albanian communists, and the assertion of Albanian national sovereignty, 1941-1948

This dissertation offers a new interpretation of the beginning of the Yugoslav-Soviet rift in 1948, examines its relationship with Albania's communist takeover and Yugoslavia's enlargement policies from 1941 through 1948, and lends fresh perspective on the establishment of communist regimes in Eastern Europe. While it challenges views that the Stalinist transformation of Eastern Europe was determined by the nature and outlook of Soviet despotism under Stalin, it argues that ideology and domestic politics were entwined, and that Bolshevism was related to wider political cultures and practices in the region, including citizenship, class, early Cold War discourse, political mobilization, nationalism, and bilateralism.

Keywords: History.
Advisor: Naimark Norman M. primary advisor. Thesis advisor
Jolluck Katherine R.
Weiner Amir