VictorJuiz/thesis huggingface dataset:
Higher-genus wall-crossing in Landau-Ginzburg theory

For a Fermat quasi-homogeneous polynomial, we study the associated weighted Fan--Jarvis--Ruan--Witten theory with narrow insertions. We prove a wall-crossing formula in all genera via localization on a master space, which is constructed by introducing an additional tangent vector to the moduli problem. This is a Landau--Ginzburg theory analogue of the higher-genus quasi-map wall-crossing formula proved by Ciocan-Fontanine and Kim. It generalizes the genus-

Keywords: Mathematics.
Advisor: Li Jun (Mathematician)
Conrad Brian
Ionel Eleny
High-performance antimonide p-MOSFETs and their hetero-integration on silicon

As the benefits from scaling conventional silicon transistors start to saturate, newer structures such as gate-all-around or nanowire devices and alternate high-mobility channel materials such as III-V compound semiconductors can provide a much-needed boost to transistor performance. Antimonides are a promising group of III-V compound semiconductors being actively researched for high-speed low-power digital CMOS as well as for THz/mm wave device applications. They have the highest electron and hole mobility among all III-Vs and could potentially enable an all-antimonide CMOS solution. Antimonides are also the only viable candidate for a high-performance III-V p-MOSFET. This thesis first addresses the most critical challenge of III-V technology -- hetero-integration on a silicon substrate. The rapid-melt-growth (RMG) technique for the hetero-integration of GaSb on silicon is studied in detail, focusing on understanding the impact of film stoichiometry, purity and morphology. A low-temperature molecular beam epitaxy (MBE) process is developed to obtain pure, amorphous GaSb which is then melt-regrown into scaled high-quality single-crystal fins down to 130nm fin width. GaSb-on-insulator p-MOSFETs are successfully demonstrated and factors limiting device performance are identified. In parallel, quantum-well heterostructures were grown by the more established technique of metamorphic buffer growth to obtain high-performance InGaSb p-MOSFETs. Two different device structures are compared -- a buried channel structure and a surface channel structure. Scaled devices with ~100 nm gate length metal gate/high-κ dielectric and self-aligned Ni-alloy metal source/drain are demonstrated. Finally, the first set of studies to investigate the radiation response of antimonide p-MOSFETs for potential use in harsh environments such as space and defense applications is conducted. Laser and heavy-ion irradiation testing is performed and supported with simulations to understand the basic mechanisms of single-event-effects in these heterostructure antimonide p-MOSFETs.

Keywords: Electrical Engineering.
Advisor: Saraswat Krishna 
Griffin Peter B. 
Plummer James D.
A high-throughput screening method for engineering proteolytically stabilized growth factors

Growth factors are an important class of proteins that play a pivotal role in orchestrating many complex biological processes such as wound healing, tissue regeneration, vascularization, and tumor formation. Thus, there is immense interest in utilizing growth factors as protein therapeutics. However, although numerous recombinant growth factors have been developed as therapeutic candidates, only a few have been effective enough to receive clinical approval. This is due, in large part, to their generally poor stability. Therapeutic growth factors must remain active for an extended period to be efficacious. However, growth factors can become degraded upon exposure to enzymes known as proteases. A growth factor's susceptibility to proteases can be particularly important because these enzymes are especially active in areas relevant for disease treatment. Growth factors have previously been modified to improve their proteolytic stability, and this has been shown to enhance their biological activity. However, current methods of engineering growth factors for increased proteolytic stability are limited by low-throughput and the lack of generalizable strategies that can be used in a consistently successful manner. Thus, it can be a difficult and slow process to generate new growth factor variants with improved stability. In this work, we describe the development of a high-throughput screening method for engineering proteolytically stabilized growth factors. We validate the ability of the screen to differentiate between proteins of different proteolytic stabilities. Then, we utilize the screen to engineer a proteolytically stabilized variant of fibroblast growth factor 1 (FGF1). Finally, we characterize the ability of the engineered FGF1 protein to resist degradation, and show that this variant surprisingly antagonizes the FGFR cell signaling pathway, which may have therapeutic implications for the treatment of ocular neovascularization and tumor formation.

Keywords: Bioengineering.
Advisor: Cochran Jennifer R. 
Kim Peter
Lin Michael Z.
History Matching Production and Displacement Data Using Derivative-free Optimization

Geomechanical simulators can be used to predict production-induced subsidence. However, the uncertainty in these predictions depends on the uncertainty in the flow and geomechanical parameters, such as permeability and Young's modulus. In this thesis, we develop a derivative-free optimization procedure for calibrating flow and geomechanical parameters. The method entails the use of the iteratively coupled flow-geomechanics module in Stanford's Automatic Differentiation General Purpose Research Simulator (AD-GPRS) combined with the mesh adaptive direct search (MADS) optimizer. Multiple sets of history matched parameters are generated using the randomized maximum likelihood (RML) procedure.
Both production and displacement (geomechanical) data can be assimilated within our framework. Data types considered in this work include well production data, surface displacement data and well displacement data, and the impact of these different types of data on predictions and parameter calibration is assessed. We first consider a three-layer model with no overburden rock. For this case, we show that assimilating either type of displacement data is useful for calibrating the harmonic average Young's modulus as well as permeability in each layer. Assimilation of either type of displacement data reduces uncertainty in both surface displacement and production predictions. Assimilation of production data, by contrast, improves permeability calibration and reduces uncertainty in production forecasts, but not in displacement predictions. We also show that history matching surface displacement data does not provide calibration of individual layer Young's moduli, though it does enable accurate calibration of the harmonic average Young's modulus over all layers. History matching well displacement data provides calibration of individual layer Young's moduli.
We next consider a more realistic (though two-dimensional) geomechanical model that includes overburden rock and bedrock. For this case we again demonstrate that both surface and well displacement data are useful for reducing uncertainty in surface displacement predictions and for estimating the harmonic average Young's modulus over all reservoir layers. Well displacement data are shown to again enable the calibration of individual layer Young's moduli.

Keywords:  Department of Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
[History Matching
Geomechanics
Derivative-free Optimization]
Thesis
Advisor: Durlofsky Louis
Holocene climate change from Fjord and Lake Sediment core and seismic records in Southern Patagonia

The Southern Hemisphere westerly wind field modulates Earth's climate by regulating Southern Ocean CO2 ventilation through wind-induced upwelling of Circumpolar Deep Water. However, past changes in the southern westerlies and the extent to which the westerlies influence global atmospheric CO2 concentrations remain relatively unknown. Southern Patagonia, the only major landmass extending into the core of the wind field, is an ideal location for reconstructing past changes in the westerlies. In Chapters 1 and 2, we present the results of sediment cores collected from Lago Sarmiento (51˚S), a large, closed-basin lake, and from Golfo Almirante Montt (GAM; 52˚S), an isolation basin in the Chilean inner-fjord system. We investigate changes in precipitation, relative westerly wind intensity, and Neoglacial events over the last 11 ka using core sedimentology, stable isotope (δ18O, δ13C and δ15N), weight percent carbonate, and elemental concentration (C & N) data. In Chapter 3, we present results of a high resolution seismic survey in GAM. Sediment core data from Lago Sarmiento and GAM identify: (1) low precipitation and weak westerlies during the early Holocene (11 -- 9.6 ka), (2) maximum Holocene precipitation and westerly wind strength in the Mid-Holocene (5.4 -- 4.1 ka), (3) low precipitation and weakening westerlies between 3.4 -- 1.5 ka, (4) and two significant regional Neoglacial events between 9.6 -- 9.0 ka and 4.1 -- 3.4 ka; we interpret Neoglacial events as a strong pulse of precipitation and strengthening of the westerlies over our field site. Our seismic survey in GAM reveals a sedimentary basin that exceeds a thickness of 100 m. We identify three seismic-stratigraphic facies, which we interpret as: (1) rapidly deposited glacio-lacustrine sediments, (2) outwash as a result of catastrophic ice-dam failure at the termination of the Last Glacial Maximum, and (3) Holocene ice-distal glacio-marine sediment. These data provide important insights into Southern Hemisphere Late Quaternary climatic variability.

Keywords: Environmental Earth System Science
Advisor: Dunbar Robert
Chamberlain C. Page 
Guilderson Tom
Maher Katharine
Hot-electron devices and physics based on oxide heterostructures

Today, we live in the age of nanomaterials with discovery of novel properties at nanometer length scales. In this thesis, we focus on perovskite oxides at such length scales in the form of thin films and heterostructures, which represent rapidly emerging class of nanomaterials significant for a rich variety of emergent phenomena. Until now, research has mostly focused on using easily accessible in-plane experimental probes to study these systems. The goal of this thesis is to expand upon this approach by establishing a solid vertical device platform and to probe the dynamics of the strongly correlated electron systems therein. As part of this goal, we focus on the fabrication of vertical hot-electron transistors based on oxide heterostructures down to the two-dimensional limit with atomic-scale precision and then the study of non-equilibrium dynamics of hot electrons across phase transitions using these device platforms. Further, we probe the spectroscopic evolution of hot-electron dynamics in oxide heterostructures using internal photoemission spectroscopy. These studies open up new avenues for probing and utilizing emergent phenomena at oxide interfaces and heterostructures using vertical device geometry.

Keywords: Electrical Engineering.
Advisor: Hwang Harold Yoonsung
Nishi Yoshio
Suzuki Yuri (Applied physicist) 
Wang Shan
The household thru time : the paracas to nasca transition at Uchuchuma, Aja Valley, Peru

This dissertation focuses on the emergence of the prehispanic Nasca (AD 1-- 700) culture during the transition from the Late Terminal Formative (200 BC -- AD 1) to the Early Intermediate Period (AD 1 -- 700) in the Rio Grande de Nasca Region, Peru. The Paracas culture (800-100 BC), a federation of various ethnic groups from the Ica region that shared pottery, textile, and funerary practices, migrated to the Nasca region sometime during the Late Terminal Formative. Andean archaeologists suggest that Paracas groups living in the Nasca region came together to form a centralized society and ethnicity -- Nasca -- that shared a common religion and pottery style. To better understand the nature of this transition from Paracas to Nasca from a household perspective, my project systematically compared both Paracas and Nasca domestic practices (e.g. ceramic production, stone tool making and food consumption) using data from a residential archaeological site called Uchuchuma, located in the Aja Valley, Peru. While my excavations confirm a Paracas and Nasca occupation at Uchuchuma, they also demonstrated that these occupations were not continuous and that the two groups lived in different areas of the site. Artifact analyses demonstrate that food consumption, stone tool making, and ceramic production were much more varied in Paracas households, while Nasca households were more homogeneous. I conclude that Paracas people living at Uchuchuma were highly influenced by the broader social changes occurring in the Nasca region, as architecture, pottery styles, and stone tool making traditions were abandoned and replaced with new ones. I argue that the abandonment of certain Paracas traditions such as house form and ceramic technology were abandoned intentionally, as participation in the developing Nasca architectural and pottery style would have connected this community with a broader network of interaction. Finally, I suggest that the continuation in settlement, some pottery forms, and plaza use were subtle practices that allowed the Uchuchuma community to maintain ties with their past.

Keywords: Anthropology.
Advisor: Rick John W. 
Vaughn Kevin
Voss Barbara L.
How mechanical properties of the pancreas signal the immune system in type 1 diabetes

Inflamed tissues experience a change in stiffness compared to their healthy state. This could be partially a result of accumulation of the glycosaminoglycan hyaluronan (HA). T cells can sense external mechanical forces, as seen in stiff and soft matrix. The goal of this work is to investigate the role of mechanobiology in type 1 diabetes (T1D) using HA-based hydrogels that mimic the physiological mechanics and biophysical cues in pancreatic islets.

Keywords: Materials Science and Engineering.
Advisor: Bollyky Paul
Heilshorn Sarah 
Melosh Nicholas A.
How prepared do I have to be for a job? : gender differences in the desire for preparedness

While some people jump into taking on a new challenge, others feel like they need to be more "prepared" before they take the first step. Such a desire to be highly prepared could hold one back from embarking on a new journey, such as applying for a new job. Is there a gender difference in how much people want to be prepared for a job before applying? In this dissertation, I systematically examine this phenomenon and seek a solution that could reduce the gender difference. Study 1a and 1b revealed that women wanted to have a greater level of job-related knowledge and skills before applying than men. Studies 2-4 explored boundary conditions for the gender difference in the desire for preparedness. Study 2 investigated whether women would believe other women should also be highly prepared. Women wanted a high level of preparedness for themselves but not for others, and the gender difference disappeared when people made judgments about others rather than themselves. Study 3 presented jobs in gender-typed and gender-neutral industries to test whether the gender difference varied across jobs in different fields. The gender difference was not significant overall, but both women and men wanted to be more highly prepared for male-typed jobs than female-typed jobs. Study 4 presented jobs that varied in level of career-related risk. Both women and men wanted to be prepared to an equal extent, not only when the job was explicitly described as safe, but also when it was described as risky. The difference was significant only when there was no overt mention of a risk involved. Finally, Study 5 tested a potential solution for organizations to reduce the gender difference. I presented job descriptions that portrayed the recruiting company as valuing either employees' learning, ability, or health (control). When the company valued learning, compared to health, women's desire for preparedness decreased, and the gender difference was closed. This research suggests that women may set a higher standard than men early in their career when they consider applying for jobs. Importantly, this work proposes a practical organizational solution that may equalize the psychological standing of women and men when they apply for a job and encourage women to take opportunities they might be well qualified for.

Keywords: Psychology.
Advisor: Dweck Carol S.
Gross James J. (Professor of psychology)
Walton Gregory M. (Gregory Mariotti)
Human Induced Pluripotent Stem Cells Reveal Mitophagy as an Essential Process Against Diabetic Cardiomyopathy

Diabetic cardiomyopathy is a common consequence of diabetes and is associated with mitochondrial pathology. Using human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) as an in vitro model of diabetes, we sought to understand the role of mitophagy, a process that selectively degrades mitochondria through the autophagy-lysosome pathway, as a crucial quality control pathway against diabetic cardiomyopathy. We first showed that iPSC- CMs exposed to a diabetic milieu demonstrated increased hypertrophy, impaired calcium signaling, and higher oxidative stress. Flow cytometry analysis of iPSC- CMs subjected to diabetic conditions revealed two distinct populations of cells (normal and hypertrophied), suggesting a heterogeneous response to hyperglycemia. In these cells, hypertrophied iPSC-CMs were found to have reduced mitophagy compared to normal cells when exposed to hyperglycemia. In addition, we showed that mitochondrial fragmentation was also decreased in the hypertrophied iPSC-CMs compared to normal cells upon exposure to hyperglycemia, demonstrating a link between mitochondrial fragmentation and mitophagy. Surprisingly, pretreatment of iPSC-CMs with a non-selective antioxidant, N-(2-mercaptopropionyl)-glycine, not only failed to limit the deleterious effects of hyperglycemia but actually led to increased hypertrophy and cell death. We found that mitophagy was significantly reduced in iPSC-CMs following antioxidant treatment, suggesting the need for mild oxidative stress as a trigger for mitophagy. Future studies are warranted to further investigate the association between oxidative stress, mitochondrial fragmentation, and mitochondrial fission as targets against diabetic cardiomyopathy.

Keywords:  Department of Bioengineering
Stanford School of Engineering
Department of Bioengineering
Stanford Cardiovascular Institute
Undergraduate Advising and Research (UAR) Major Grant
stem cell
diabetes
diabetic cardiomyopathy
cardiology
mitophagy
proteomics
Thesis
Advisor: Wu Joseph
Qi Stanley Lei
Human rights, borders, and asylum [electronic resource] : translating distant wrongs into domestic rights

In Human Rights, Borders, and Asylum, I examine the complex and contradictory relationship between the professed universality of human rights and the lived experiences of asylum seekers in our bordered world, a world in which they are routinely subjected to detention, discrimination, deportation, and even death. Through a variety of methods - including legal and documentary analysis, historical research, 120 in-depth interviews, and participant observation at immigration detention centers, asylum offices, and immigration courts in nine U.S. cities - this dissertation looks at how the multitude of actors involved in the process of seeking asylum (or refugee status) declare, recognize, and deny rights claims. To understand how asylum seekers come to be recognized or denied as human rights subjects, I pay particular attention to groups who have been historically excluded from international refugee law and its enactment into U.S asylum and immigration law - namely women and children from Central America as well as sexual minorities - and how these claims interact with and have the potential to transform the law. I refer to this process as translating distant wrongs into domestic rights. While the continual expansion of the international human rights regime plays an important role in advancing certain minimum standards of treatment toward marginalized and vulnerable populations through legislation and enforcement, ultimately this dissertation highlights how normalized states of exception, arbitrary adjudication, and selective implementation leave asylum seekers in a precarious state. Thus, I argue that the juridical idea of dignity - the foundation of the international human rights regime - must be supplemented with recourse to the ethical principle of hospitality, that is, the notion of welcoming the "other" into one's home as a guest. Hospitality can reduce initial apprehensions in the host-guest encounter, constructing a liminal zone that is the starting point for an engaged dialogue between the citizen and non-citizen. From this space, dynamic alliances and transnational solidarities have the potential to emerge and thus stimulate social and political movements and legal strategies to challenge sovereign power and illegal/immoral state policy, recalibrating society's moral compass and pointing us in a direction toward recognizing the dignity of asylum seekers.

Advisor: Jiménez Tomás R. (Tomás Roberto)
Stacy Helen
Hansen Thomas Blom
Tambar Kabir advisor. Thesis advisor
Human-centric machine learning : enabling machine learning for high-stakes decision-making

Domains such as law, healthcare, and public policy often involve highly consequential decisions which are predominantly made by human decision-makers. The growing availability of data pertaining to such decisions offers an unprecedented opportunity to develop machine learning models which can help humans in making better decisions. However, the applicability of machine learning to such scenarios is limited by certain fundamental challenges: a) The data is selectively labeled i.e., we only observe the outcomes of the decisions made by human decision-makers and not the counterfactuals. b) The data is prone to a variety of selection biases and confounding effects. c) The successful adoption of the models that we develop depends on how well decision-makers can understand and trust their functionality, however, most of the existing machine learning models are primarily optimized for predictive accuracy and are not very interpretable. In this dissertation, we develop novel computational frameworks which address the aforementioned challenges, thus, paving the way for large-scale deployment of machine learning models and algorithms to address problems of significant societal impact. We first discuss how to build interpretable predictive models and explanations of complex black box models which can be readily understood and consequently trusted by human decision-makers. We then outline novel evaluation strategies which allow us to reliably compare the quality of human and algorithmic decision-making while accounting for challenges such as selective labels and confounding effects. Lastly, we present approaches which can diagnose and characterize biases (systematic errors) in human decisions and algorithmic predictions.

Advisor: Leskovec Jurij 
Liang Percy 
Rudin Cynthia
Hunting down host targets for host-directed therapies through forward genetic screens

Infectious diseases have plagued humans for centuries, and with the rise in antimicrobial resistance, there is a pressing need to develop novel strategies for combating pathogens. Host-directed therapies offer a promising alternative to traditional antimicrobials that directly target the pathogen. Furthermore, the identification of targets for the development of host-directed therapies has been accelerated by the advent of next-generation screening technology. This thesis presents examples of applying forward genetic screens to the identification of novel and attractive host targets for the development of host-directed therapies.

Keywords: Microbiology and Immunology.
Advisor: Carette Jan
Kim Peter
Kirkegaard Karla 
Yeh Ellen