VictorJuiz/thesis huggingface dataset:
Approximation techniques for mixed-integer quadratic programs [electronic resource]

This thesis studies the class of NP-hard mixed-integer optimization problems with quadratic objective function and constraints that are not necessarily convex. We propose the Suggest-and-Improve framework, which encapsulates and generalizes a number of known techniques and provides heuristics for computing approximate solutions to quadratically constrained quadratic programs, for which no specialized methods are available. Using numerical examples, we show that the Suggest-and-Improve framework can yield strong upper and lower bounds on the optimal value. We also show a provable bound on the semidefinite relaxation applied to the NP-hard problem of minimizing a convex quadratic function over the integer lattice. Finally, we discuss the family of concave quadratic inequalities that can be added to general mixed-integer quadratic programs. This technique allows the Suggest-and-Improve framework to be applied to any mixed-integer quadratically constrained quadratic problems.

Advisor: Boyd Stephen P. primary advisor. Thesis advisor
Charikar Moses advisor. Thesis advisor
Valiant Gregory advisor. Thesis advisor
The archaeology of Danish healthcare legislation and local healing practices, 1803-1848, St. Croix, US Virgin Islands [electronic resource]

This archaeological research project examines the practical negotiations between colonial healthcare policy and local healthcare practices during the 19th century in St. Croix, US Virgin Islands. In order to understand how enslaved individuals approached issues of health and well-being within the context of institutionalized medicine, archaeological excavations were conducted at a former plantation hospital at Estate Cane Garden. Targeted analyses of ceramics, faunal remains, and macrobotanical remains from the hospital indicate that enslaved caregivers and patients utilized a wide range of plant and animal resources and that foodways served as important conduits of healing. While Danish physician reports and Board of Health documents indicate a deep investment in maintaining the health of enslaved people by creating a comprehensive healthcare network, archaeological excavations highlight a lack of material objects commonly associated with medical practice. Archaeological research suggests that: 1) the centrally administered healthcare system envisioned by the colonial government was not implemented at the local level, and 2) everyday care at the hospital may have encompassed broader interpretations of healthcare and wellness than those mentioned in the medical documents. This research emphasizes the historical rootedness of "health" and argues that "health" is a simultaneously institutionalized and highly individual/subjective state of being.

Keywords: Anthropology.
Advisor: Voss Barbara L.
Ebron Paulla A.
Hauser Mark W. advisor. Thesis advisor
Seetah Krish advisor. Thesis advisor
Aristotle on ontological priority [electronic resource]

Aristotle's ambitions for ontology extend beyond determining what beings there are: he also thinks there is an order among the beings, i.e. that some things are prior in being to others. I argue that priority in being is a causal relation: one thing is prior in being to another when it is a cause of being for the latter. My causal view gives us new interpretive resources for understanding how Aristotle's apparently diverse claims about what is prior in being to what are unified: in each case, what is prior in being is a cause of being for what is posterior in being, but different prior entities make different causal contributions to the being of different posterior entities. My causal view also gives us insight into how Aristotle came to accept the claims about priority in being that he does. It allows us to draw on Aristotle's criticisms of his predecessors' views about the causes and principles of being, as well as on Aristotle's statement of the puzzles that must be solved in first philosophy, to see what philosophical pressures shaped Aristotle's view.

Keywords: Philosophy.
Advisor: Code Alan Dodd
Bobonich Christopher advisor. Thesis advisor
Netz Reviel advisor. Thesis advisor
As America grows more diverse, fashion magazine covers are slow to show progress

Over the past three decades, American Vogue has featured five times as many white models on its covers than minority models, while Harper’s Bazaar U.S. has shown nearly seven times as many white models. At the same time, the United States has seen an increase in the minority population, which grew nearly 30 percent from 2000 to 2010 alone. The white population grew 1.2 percent over that same period.
This look at fashion magazine covers comes at a time when diversity in the fashion and entertainment industries is increasingly under watch. A number of outlets, including theFashionSpot, Vogue, NYMag and Fashionista, covered diversity on the runways of New York Fashion Week this past year, while ABC’s announcement of Rachel Lindsay as the first black bachelorette also made headlines.

Keywords: Phillips, Cheryl
fashion
modeling
tori
owens
models
diversity
race
america
vogue
harper's bazaar
Thesis
As demand for genetic counseling grows, the profession struggles to keep up

As genetic testing becomes more common and an increasing number of new tests become available, demand is growing for genetic counselors who can help people correctly interpret results and make informed decisions. But there is a shortage of genetic counselors who work directly with patients, according to a recent study by the National Society of Genetic Counselors. Assuming a demand of one genetic counselor for every 75,000 people, supply is not expected to match demand for more than a decade. At the same time, the science of gene sequencing is quickly outpacing genetic counselors’ ability to understand and interpret each new genetic variation that is discovered.

Keywords:  Department of Communication
genetic counseling
Stanford University
Department of Communication
Thesis
Advisor: Phillips Cheryl
Aspects of cosmology and black hole physics in string theory [electronic resource]

Over the past few decades string theory has provided us with many novel ideas and models of physics where the interplay of gravity and quantum mechanics is crucial. In particular it has been widely used in the study of black hole physics and cosmology. This thesis describes three aspects of string theory's application in these two fields. First we consider open string pair production effects near hyperbolic black holes in Anti-de Sitter space (AdS). It is shown that these black holes can decay by radiating D-branes and there can be non-adiabatic pair production of open strings stretched between those radiated branes. In the second part we switch to cosmology, where we consider two models inspired by axion monodromy, which is very natural in string theory. First we study heavy fermion production effects, which come from the assumption that the fermion mass is modulated by the inflaton field, and its signature on primordial N-spectra. A detailed comparison between this effect and the effect of boson production is made. Lastly, we consider the case where there are a large number of axions that collectively drive inflation. It is shown that the spectral index and the tensor-to-scalar ratio depend on the distribution of parameters of the axion fields. This thesis is based on papers [1, 2, 3].

Keywords: Physics.
Advisor: Silverstein Eva
Kachru Shamit
Shenker Stephen Hart
Assembly and allostery in group II chaperonins [electronic resource]

Proteins must achieve their native conformations in order to function and avoid aberrant interactions within the cell. The folded state is formed rapidly for proteins with simple topologies. However, the folding of many large proteins with complex folds is assisted by the diverse array of molecular chaperones. The chaperonins are a unique class of essential protein chaperones found in all domains of life. These complexes are comprised of two 7-9 membered rings that undergo dramatic conforma- tional changes upon ATP binding and hydrolysis. Two classes of chaperonins exist, termed group I and group II. Group I chaperonins exist in bacteria and endosymbiotic organelles, while group II chaperonins are found in all eukaryotes and archaea. Both families promote the folding of substrates in an ATP dependent manner by encapsulating them within discrete central chambers. This thesis focuses on detailing the mechanism of a model group II chaperonin from the archaea Methanococcus maripaludis. Work was performed to define the native folding substrates of the complex as well as to detail the cooperative mechanism that controls all group II chaperonin cycling. A key allosteric interface was identified using a mathematical approach that predicts functionally important residues based on patterns of covariation found in multiple sequence alignments of a protein. Biochemical dissection of mutations at this interface reveal that the chaperonins have evolved to be less cooperative than attainable. Early evidence will be presented that suggests the N- and C-terminal tails of the chaperonin likely serve as coordinators of nucleotide cycling.

Keywords: Biology.
Advisor: Frydman Judith primary advisor. Thesis advisor
Cyert Martha S.
Wandless Thomas advisor. Thesis advisor
Weis William I. advisor. Thesis advisor
Assessing lifecycle costs and benefits of integrated sanitation and energy recovery strategies in low-income countries [electronic resource]

By mid-century, the global urban population is projected to increase by 2.4 billion people with 60% of growth expected to take place in cites of sub-Saharan Africa (SSA) and South Asia (SA) (UN-DESA, 2015). These regions have some of the lowest rates of urban sanitation coverage and modern fuel access, with only 41% and 67% estimated to have access to improved sanitation and 19% and 55% estimated to use modern fuels for cooking in SSA and SA, respectively (WHO/UNICEF, 2015a; Legros, et al. 2009). In recent years, decentralized sewered and non-sewered sanitation management approaches have gained traction in low-income SSA and SA cities as alternatives to expensive and resource intensive conventional wastewater treatment. Energy recovery from domestic waste has also received increasing attention as a strategy to offset operational costs of sanitation services, provide alternative energy resources and reduce environmental impacts of waste treatment systems. Waste-to-energy technologies may simultaneously contribute to multiple Sustainable Development Goals (SDGs) including achieving universal access to safely managed sanitation; universal access to modern, clean fuels; and integration of climate change measures into national policies, strategies and planning including fostering low emissions development (UN, 2015). However, despite increasing adoption of alternative sewered and non-sewered sanitation approaches and growing interest in energy recovery, little empirical evidence exists regarding the extent to which energy recovery may offset costs of sanitation systems and the long-term resource requirements, environmental impacts and financial costs and benefits of alternative sanitation approaches. This dissertation (1) provides empirical evidence on the costs and benefits of integrated sanitation and energy recovery strategies in low-income countries, (2) develops a lifecycle based framework to enable sanitation planners to systematically investigate the resource use, environmental impacts and financial costs and benefits of decentralized sewered and non-sewered sanitation approaches and (3) demonstrates application of this framework using primary data from operational sanitation systems in Zambia and India, thus also generating the first comprehensive analyses of decentralized sewered and non-sewered sanitation management in urban SSA and SA.

Advisor: Davis Jenna (Professor)
Lepech Michael primary advisor. Thesis advisor
Levitt Raymond E. advisor. Thesis advisor
McCarty Perry L. advisor. Thesis advisor
Atomic layer deposited Al2O3 and TiO2 for high-k dielectric and memory applications [electronic resource]

Atomic layer deposited (ALD) metal oxide thin films have promising application in future logic and memory nano-devices. For beyond Si n-channel metal-oxide-semiconductor (MOS) devices, InGaAs and ALD deposited Al2O3 are strong candidates for the high-k dielectric and the channel layer, respectively, due to the high electron mobility of InGaAs, large conduction band off-set between Al2O3 and InGaAs, and a low defect density at the interface. Besides the growth of high-k dielectrics for MOS device scaling, ALD is also widely used to deposit transitional metal oxide, including TiO2 and HfO2, for fabrication of resistive random access memory (RRAM) as a high performance non-volatile memory. The first main section of the dissertation focuses on the ALD Al2O3 as the dielectric layer for InGaAs MOS devices, and the passivation of the interface traps and border traps in the gate stacks as a key issue to improve the device performance. With quantitative analysis by theoretical modelling, we find that by lowering the Al2O3 ALD temperature from 270 °C to 120 °C, combined with large dose TMA pre-exposure prior to ALD and optimized post-metal forming gas anneal (FGA), the border traps can be reduced effectively while interface trap density maintains low. The reduction of border traps is associated with the incorporation of atomic hydrogen that passivates the dangling bonds in the Al2O3 during the FGA. While the FGA treatment effectively reduces both the interface traps and border traps, it also increases the capacitance-voltage hysteresis, indicating a degradation of device stability. This device stability issue is confirmed to be caused by the depassivation of hydrogen from the Al2O3/InGaAs interface under bias stress. In the second section, we report the first use of vertical-field ionic liquid (IL) and aqueous electrolyte gating to study the resistance switching mechanism of ALD TiO2 for RRAM application. A large electric field applied during IL gating induces a conductivity increase in ALD-grown thin TiO2 films caused by the formation and electromigration of oxygen vacancies in the oxide at room temperature. Nevertheless, conductive filaments are not formed during IL gating, presumably because the low programming current minimizes local Joule heating. This hypothesis is supported by experiments in which the ionic liquid is replaced by a conductive salt solution. With significantly increased programming current, electrolyte contact biasing generates a single dominant conductive filament. The reported results indicate the necessity of combined field-driven oxygen ion motion and local kinetic enhancement of oxygen vacancy assembly due to Joule heating to achieve conductive filament formation and dimensionally scalable resistance switching.

Keywords: Materials Science and Engineering.
Advisor: McIntyre Paul Cameron primary advisor. Thesis advisor
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Salleo Alberto
Atomic layer deposition physics at the nucleation stage [electronic resource]

Three dimensional complex chip architectures are gaining more widespread usage as computing devices continue to shrink. These complex architectures are necessary in order to continue scaling down the size of each individual transistor and make them more efficient. In manufacturing such complex architectures, traditional material deposition methods such as physical or chemical vapor deposition are no longer as effective as they are somewhat directional. A method that is gaining widespread use is atomic layer deposition (ALD). ALD allows multiple advantages such as exquisite thickness control of deposited films, three dimensional film conformality and control over composition. However, certain useful films grown via ALD have an initial growth nucleation stage which is not well understood. This limitation prevents us from growing the thinnest possible pinhole-free films. Gaining an understanding of the nucleation stage would allow us to continue scaling our devices down further and even perform selective area deposition. In order to shed some light on the nucleation stage, in this dissertation, we have utilized the unique capability of a custom built combined scanning tunneling microscope (STM) and ALD system to observe topographically the nucleation stage of ALD in-situ. We used existing wet etch techniques to create atomically flat hydrogen terminated silicon, and created a method for using remote plasma to create atomically flat suboxide terminated silicon, both for use as suitable flat substrates for STM observation of ALD nucleation. With these atomically flat substrates available to us, we observed, using a variety of characterization techniques, the nucleation stage of two ALD systems: ALD ZnO and ALD Ru. Though we selected two specific systems to study, this technique could be further used on any other desired chemistries for study. We further demonstrate the ability of this STM-ALD tool to perform both bottom up and top down lithography, by activating sites for ALD, or decomposing ALD precursors at specific locations, or by etching away deposited layers using the STM tip.

Keywords: Applied Physics.
Advisor: Prinz F. B. primary advisor. Thesis advisor
Suzuki Yuri (Applied physicist) primary advisor. Thesis advisor
Bent Stacey advisor. Thesis advisor
Atomistic modeling of high-pressure silica crystallization under dynamic compression [electronic resource]

Understanding the kinetics of shock-compressed SiO2 is of great importance for mitigating optical damage for high-intensity lasers and for understanding meteoroid impacts. Experimental work has placed some thermodynamic bounds on the formation of high-pressure phases of this material, but the formation kinetics and underlying microscopic mechanisms are yet to be elucidated. In this study, by employing multi-scale molecular dynamics studies of shock-compressed fused silica and quartz, we find that silica transforms into a poor glass former that subsequently exhibits ultrafast crystallization within a few nanoseconds. We also find that, as a result of the formation of such an intermediate disordered phase, the transition between silica polymorphs obeys a homogeneous reconstructive nucleation and grain growth model. We construct a quantitative model of nucleation and grain growth, and compare its predictions with high-pressure silica crystal grain sizes observed in laser-induced damage and meteoroid impact events. Moreover, we have studied the quantum nuclear effects for high-pressure silica crystallization. While quantum nuclear effects play important roles in shock-induced chemical reactions and phase transitions, they are absent in classical atomistic shock simulations. To address this shortcoming, we couple the shock simulation with a colored-noise Langevin thermostat. We find that this semiclassical approach gives shock temperatures as much as 7% higher than classical simulations near the onset of crystallization in silica. We have also studied the impact of this approach on the kinetics of crystallization and the position of high-pressure silica melt line.

Keywords: Physics.
Advisor: Doniach S. primary advisor. Thesis advisor
Reed Evan J. primary advisor. Thesis advisor
Cai Wei
Authenticity in Context: Examining Folk Theories of Online and Offline Authenticity through Computerized Text Analysis

This study examined folk notions of authenticity through a computerized text analysis of participant responses, and connected them to conceptual pillars in the philosophical literature on authenticity. Participants (N=178) were asked to describe an experience in which they felt authentic or inauthentic, and either prompted to recall an experience on social media or offline (no specific prompt for social media). Their responses were analyzed using LIWC (Linguistic Inquiry and Word Count) 2015, and the results were examined through Kernis and Goldman’s four-part framework for authenticity (2006). Recall of authentic events involved more unbiased processing and confidence, while recall of inauthentic events revealed higher self-awareness. Social media responses were negatively linked with family-words, weakly positively-linked with friend words, and more pro-social in drives. These findings affirm Kernis and Goldman’s framework, and offer insight into current folk notions of authenticity in an era of social media.

Keywords:  Department of Communication
authenticity
folk psychology
folk notions
LIWC
social media
analytical thinking
cognitive complexity
confidence
social concern
Department of Communication
School of Humanities and Sciences
Thesis
Advisor: Hancock Jeffrey T.
Autism Prevalence Trends by Birth Year and Diagnostic Year: Indicators of Etiologic and Non-Etiologic Factors - an Age Period Cohort Problem

The primary objective of this study is to characterize the etiological and non-etiological components of the observed increase in incidence of diagnosis of autism in California from 1980 to 2015. We show that the time trends of autism prevalence by birth year and diagnostic year correspond directly to trends in etiologic (causal) and non-etiologic (non-causal) factors respectively and endeavor to estimate the coefficients of both trends. The primary dataset is incidence of autism diagnosis data from the California Department of Developmental Services (CA-DDS). It provides the numbers of clients newly enrolled for services under an autism classification for each diagnostic year from 1980 through 2015 with separate observations for each birth year and gender. The analysis estimates cumulative incidence to age 10 as a more appropriate measure than prevalence. Knowledge of the birth year and diagnostic year trends is important for elucidating the combined effect of variable etiologic factors, that is, environmental effects broadly defined, which may lead to an understanding of potential prevention and treatment strategies. The birth year trend, controlling for diagnostic year trend, could also be used to predict the future case load of adults with autism needing support, which may inform policy decisions and associated funding requirements for care of these individuals, which already consumes an estimated 1.5% of US GDP. It is straightforward to estimate the sum of the birth year and diagnostic year coefficients, which corresponds to a growth of 12.82% per year from 1980 to 2015, but intractable to estimate the allocation of individual coefficients within that sum. The problem of estimating the birth year and diagnostic year trends falls within the class of age period cohort (APC) problems, because the age factor affects the analysis and the three variables are collinear; there is a lack of identifiability, which prevents reliable estimation of the key variables. We investigated novel methods of analyzing this type of problem and demonstrate a new way to understand the problem. We show that estimating the age factor correctly is both more important and more difficult than indicated in previous APC literature because estimates of the age factor are inherently functions of the coefficients of the period (diagnostic year) and cohort (birth year) effects, which are unknown, and biases in the age factor estimate based on implicit assumptions of these two effects directly affect the resulting estimates.

Keywords:  Department of Health Research & Policy
Stanford Department of Health Research &amp; Policy
autism
prevalence
cumulative incidence
California Department of Developmental Services
birth cohorts
etiologic
non-etiologic
age period cohort
APC
age factor
Thesis
Advisor: Nelson Lorene
Sainani Kristin