VictorJuiz/thesis huggingface dataset:
Investigation on diagnostic biomarkers and protein-protein interactions by using giant magnetoresistive biosensors [electronic resource]

In the past decade, our research group has been developing giant magnetoresistive (GMR) biosensors and demonstrated that this sensor platform has great potential for application to many fields of nanomedicine, especially diagnostics and drug development. In this dissertation, I present major development and several new applications of GMR biosensors. First of all, the history of magnetic biosensors and GMR biosensors are introduced. Then, a new technique to longitudinally monitor immune response via antibody isotypes is described. This technique is used, in conjunction with bioluminescent imaging, to measure both firefly luciferase (FL) specific and total antibody response, and to find the upregulated IgG2a response in the regression mice. Cytokine measurement shows interferon-gamma signature in the regression mice. These results indicate that the immune response is predominantly involved with T-helper-1-cell-mediated immune response. Secondly, the use of protein and peptide microarrays for autoantibody detection is demonstrated. System lupus erythematosus is an autoimmune disease, characterized by the existence of autoantibodies. A chemokine score was previously proposed to assess disease severity. The correlation between autoantibodies measured by the microarray and the chemokine score is found, and the reactivity of autoantibodies to histone 2B peptides in chemokine high patients is higher than in chemokine low patients. Thirdly, a new kinetic assay using GMR biosensors is presented. The current gold standard, Surface Plasmon Resonance (SPR) is sensitive to changes in pH and salt concentration and is typically single-plex in nature. The GMR biosensor platform is insensitive to pH and salinity, and has an added ability to multiplex. By using magnetic nanoparticles conjugated with proteins and microfluidic chips, the interactions between programmed cell death 1 (PD-1) protein and its ligands are measured utilizing bivalent interactions and a Langmuir isotherm binding model. Lastly, the use of GMR biosensors as point-of-care (POC) devices is demonstrated in a Eigen Lifescience platform.

Keywords: Mechanical Engineering.
Advisor: Santiago Juan G. primary advisor. Thesis advisor
Wang Shan
Mallick Parag
Iterative convex methods for control [electronic resource]

This thesis examines ways to leverage the techniques of convex optimization for control problems (and other problems) that are not necessarily convex by using iterative procedures. Often we can find very good solutions to hard problems by solving a series of simpler problems. As the techniques for convex optimization have improved over the past couple decades, the qualifications for simple problems have expanded dramatically allowing for these simple steps to be remarkably complicated. By leveraging this increased complexity we develop algorithms that are more efficient and capable of handling more complex models. In the first chapter of this thesis we examine the problem of trajectory optimization, in particular the minimum-time traversal of a fixed path. This is a problem that arises in machining, automated racing, surveillance, and other applications. We explore a change of variables that makes the problem convex. We exploit the structure of the problem to efficiently find solutions. This speed allows the algorithm to be used in online settings as part of model predictive control (MPC) loops. The algorithm can also be used to rapidly evaluate different trajectories to identify the fastest one. This evaluation splits the minimum time trajectory problem into a series of fast trajectory evaluations. In the second section of the thesis we examine a technique called the convex-concave procedure (CCP) which addresses difference of convex (DC) problems. This iterative procedure finds local minima of DC problems by solving a sequence of convex problems. We present a number of extensions to this algorithm to allow a much wider range of problem classes to be considered, including a vector form of the problem and extensions to address large scale problems. We then present a series of examples to highlight various aspects of these algorithms. In the last section of the thesis we leverage CCP to address the antagonistic control problem. Whereas a typical control problem attempts to minimize an objective, the antagonistic control problem maximizes an objective. This simulates an aggressor taking control of a system to do it harm. Having knowledge of how and when harm can be done to a system, allows for better defense of the system. We also demonstrate how the S-procedure can be used to get an upper bound on the negative behavior to pair with the lower bound provided by CCP.

Keywords: Mechanical Engineering.
Advisor: Boyd Stephen P. primary advisor. Thesis advisor
Gerdes J. Christian primary advisor. Thesis advisor
Lall Sanjay advisor. Thesis advisor
'La gran dolor que llengua no pot dir' [electronic resource] : ausiàs March and the poetics of private pain

The present dissertation explores how the poetry of Ausiàs March (1400-1459) problematizes the view of fifteenth-century Iberian literature as part of a linear transition from the medieval to the early modern period. More specifically, I examine notions of body, pain, and subjectivity that emerge in the lyric poetry of the late medieval Crown of Aragon and trace their trajectory through the 128 cants of the Valencian poet and into the literary milieu of sixteenth-century Castile. I argue that the unique way in which March draws upon so-called medieval tropes and source material, the way his poetics theorize on the essence of private pain before pain was private, paradoxically fashions what so many scholars point to as his strikingly modern, subjectively emotional "self." Focusing on the themes of language, love, community, and pleasure and pain, my first chapter excavates March's complicated relationship with his troubadour predecessors, focusing on what he takes from the Provençal tradition and what he abandons. In the second chapter, I examine the work of Giorgio Agamben, David Bakan, Ariel Glucklich, and Elaine Scarry to offer a new reading of March's verses that focuses on his treatment of bodily pain and what it implies vis-à-vis theories of the self. Chapter three is a close comparative analysis of March's original cants and their most widely disseminated sixteenth-century Castilian translation, that of the Portuguese Jorge de Montemayor (1560); in this final chapter, I pay special attention to the ways in which Montemayor transforms and even eliminates March's frequent presentation of the poetic self, the body, and pain. By situating my study within a trans-linguistic (and trans-national) framework, I am able to arrive at a more nuanced understanding of textual constructions of subjectivity and experience in fifteenth- and sixteenth-century Iberia.

Keywords: Iberian and Latin American Cultures.
Advisor: Barletta Vincent primary advisor. Thesis advisor
Alduy Cécile advisor. Thesis advisor
Greene Roland
Resina Joan Ramon advisor. Thesis advisor
Lagrangian Tori in R4 and S2xS2 [electronic resource]

We study problems of classification of Lagrangian embeddings of a torus in a symplectic 4-manifold. First we complete the proof of a claim that all Lagrangian tori in R^4 are isotopic. Next we present a construction of Lagrangian tori and Klein bottles in monotone S^2xS^2. Finally we show that all monotone tori may be produced from such a construction, and outline a new approach to the problem of finding the Hamiltonian isotopy classes of monotone tori in S^2xS^2.

Keywords: Mathematics.
Advisor: Eliashberg Y.
Ionel Eleny advisor. Thesis advisor
Vakil Ravi advisor. Thesis advisor
Large-eddy simulation of span-periodic and three-dimensional shock/turbulent boundary layer interactions [electronic resource]

Shock-turbulent boundary layer interaction (STBLI) remains a critical phenomena in the design and performance of supersonic and hypersonic vehicles. This investigation utilizes high-fidelity large-eddy simulation (LES) to better understand the physics involved in compression ramp STBLI. Specifically, streamwise oriented counter-rotating vortices in the recovery region and low frequency unsteadiness of the shock are explored in detail. A parametric variation on ramp angle is performed to explore the behavior of STBLI at a wide range of interaction strengths. An assessment of wall-modeled LES using a simple equilibrium wall-model for compression ramp STBLI at high Reynolds number is performed and deficiencies in the model are explored in detail. A first-of-its-kind LES calculation of a compression ramp STBLI with flow confining aerodynamic fences is performed to explore the three-dimensional aspects of this configuration including changes in the low frequency unsteadiness near the fences.

Keywords: Aeronautics and Astronautics.
Advisor: Lele Sanjiva K. (Sanjiva Keshava)
Alonso Juan José
Moin Parviz advisor. Thesis advisor
Laser field control of 1,3-cyclohexadiene isomerization [electronic resource]

Conical Intersections play a crucial role in quantum molecular dynamics, especially in polyatomic molecules where they are ubiquitous due to large degrees of freedom. We have explored the effects of light fields on conical intersections and multidimensional nonadiabatic dynamics in 1,3-cyclohexadiene (CHD). These experiments have demonstrated control of the photoinduced isomerization dynamics of CHD to 1,3,5-hexatriene in the presence of an ultrafast laser pulse. We have found that the laser field maximally suppresses isomerization if it is both polarized parallel to the excitation dipole and present 50 fs after the initial photoabsorption, at the time when the system is expected to be in the vicinity of a conical intersection that mediates this structural transition. A modified ab initio multiple spawning method was developed that showed that the laser induces a resonant coupling between the excited state and the ground state, i.e., a light-induced conical intersection. These calculations explain both the optimal timing of the control, and the photochemical process behind it.

Keywords: Physics.
Advisor: Bucksbaum Philip H. primary advisor. Thesis advisor
Martinez Todd J. (Todd Joseph)
Reis David A.
Latent variable models for visual activity understanding [electronic resource]

One of the important goals of computer vision is to categorize and understand human actions in images and video. The ability to automatically solve this problem opens the door to a host of impactful applications such as search and retrieval, surveillance, medical research, automatic annotation, and human-computer interfaces. Approaches for action recognition have involved increasingly rich modeling with hidden variables, which are often required to capture the properties of and interactions between components in a scene that distinguish one action from another. Learning models with hidden variables accurately and efficiently can be a difficult problem that poses great computational challenges. In this work, we address two related problems: developing computational methods to accurately and efficiently learn models with latent variables from data, and constructing models of sufficient richness to solve high-level human action recognition tasks. To address the first problem, we turn to Self-Paced Learning, which is designed to avoid bad local minima while learning latent variable models. We show that we can use Self-Paced Learning in combination with data with varying levels of annotation to achieve superior levels of performance. To address the second problem, we propose a latent variable model that explicitly represents human pose, object trajectories, and the interactions between them in video sequences. Since labeling all of these components in training data is onerous and such labels are not available in test data, the model uses latent variables and takes advantage of data with varying levels of annotation. It also takes advantage of recent progress in both the quality of combined video and depth sensors and the accuracy of pose trackers that are based on these measurements. With these technologies in hand, we are able to leverage accurate pose trajectories in our model without the need for any additional annotation or human intervention. By combining a pose-aware action model with successful discriminative techniques in a single joint model, we are able to recognize complex, fine-grained human action involving the manipulation of objects in realistic action sequences. For our adaptation of Self-Paced Learning to diversely and noisily labeled datasets, we demonstrate that we can improve on the results of a state-of-the-art action recognition technique with still images by augmenting a labeled dataset with images gathered from the internet without any annotation. Furthermore, to showcase both the ability of our human action model to capture complex human actions and the efficacy of our learning approach, we introduce a novel Cooking Action Dataset and show that our model outperforms existing state-of-the-art techniques.

Advisor: Koller Daphne primary advisor. Thesis advisor
Li Fei Fei
Ng Andrew Y.
Learning Belonging in the Classroom: The Experience of Mexican-Heritage Students in California's Central Valley

This paper is the result of a research project that explores how a sample of Mexican-heritage students situated themselves in the dual language program at a California public elementary school, in which students received roughly half their daily instruction in English and the other half in Spanish. These 48 students were part of a student body in which more than 95% of students were Latino and 100% of students were considered “socioeconomically disadvantaged” by the state. Close ethnographic study through classroom observation, interaction with students, and staff interviews illuminate how students experienced finding a sense of belonging (or not) at school, with emphasis on two areas of their background: beliefs regarding the role of parents in the education experience and language use. Spanish-speaking students generally formed relationships with peers who shared the same primary language. Although the school as an institution and the staff as representatives of the school vocalized support of family involvement and Spanish as an academic or public language, day-to-day interactions did not necessarily guarantee that this message or standard of belonging was upheld. Rather, it was in connections with peers of similar backgrounds that students found acceptance. This belonging is situated in the context of a broader cultural citizenship, and implications for the individual extend to future negative social or economic effects of students not having their "right to belong" upheld by a public institution that represents the dominant national community.

Keywords:  Department of Anthropology
Anthropology
education
language
Spanish
cultural citizenship
belonging
Thesis
Advisor: Tambar Kabir
Learning from electronic health records [electronic resource] : enabling the learning healthcare system

The widespread adoption of Electronic Health Records (EHRs) is an unprecedented opportunity to expand the evidence base of clinical medicine by embedding data generation and capture in routine clinical care. We present two case studies in which we demonstrate how to use the free text of clinical notes, in combination with domain knowledge, to address problems in post-marketing drug safety and surveillance. We then present evidence that, surprisingly, very simple and scalable methods work as well as more complex methods of extracting information from clinical text for purposes of clinical research.

Advisor: Shah Nigam
Mackey Lester
Musen Mark A. advisor. Thesis advisor
Learning human history from sequenced Y chromosomes [electronic resource]

The Y chromosome harbors the longest stretch of non-recombining DNA in the human genome--by orders of magnitude. Consequently, the molecule a man transmits to his son bears a record of mutations that occurred in their paternal-line ancestors. We can therefore utilize variation within a sample to build a detailed phylogenetic tree that is a rich source of information about historical migrations and extant population structure. Two decades of scholarship have revealed many aspects of the tree's topology and the geographic distribution of its clades, but little was known about its branch lengths. The advent of high-throughput sequencing unlocked the chromosome's full potential as an evolutionary marker. With full sequences, we could, in principle, discover variants free of ascertainment bias and with great sensitivity, but the Y chromosome's uniquely complex structure presented challenges for short-read sequencing analysis. In this dissertation, I describe my work developing methods to analyze, interpret, and extract insight from Y-chromosome sequences. Upon segmenting the chromosome to delineate regions amenable to short-read sequencing and developing a pipeline to reliably call genotypes, I characterized the full structure of the tree and used its branch lengths to estimate split times. I first applied these methods to a collection of 69 individuals sampled from nine globally diverse populations and to a study of the phylogenetic and geographic structure of a common yet poorly characterized clade. Second, I extended these methods to gain insight from ancient-DNA (aDNA) specimens. To estimate a split time related to the initial colonization of the Americas, I utilized missing evolution on the lineage of a 12,600-year-old individual buried in direct association with Clovis tools, implementing a Poisson process model for mutations on the tree. I also analyzed the Y-chromosome sequence of Kennewick Man, a 9,000-year-old individual whose population affinities had been the subject of scientific debate and legal controversy. Finally, I used Y-chromosome sequence data to help identify the likely origin of a 17th-century enslaved African whose remains were excavated in the Caribbean, and I developed a method to leverage the Y-chromosome phylogeny to estimate the genotyping error rate. I then scaled the methods I had developed in order to apply them to two large-scale sequencing projects. In the third part of this dissertation, I detail my analysis for the Y-chromosome subgroup of the 1000 Genomes Project, whose sample includes 1,244 males from 26 populations. To conclude, I discuss an ongoing effort to investigate the population history of Africa by capturing and sequencing the Y chromosomes of several hundred Africans sampled from diverse populations across the continent.

Advisor: Bustamante Carlos (Carlos D.)
Pritchard Jonathan (Jonathan K.) advisor. Thesis advisor
Tang Hua (Geneticist)
Legislation and anticipation: Consequences for the measurement of the minimum wage employment effect

When Congress or a state legislature passes a minimum wage increase, there is often a period of several months between the passage of the increase and its implementation. During this period, employers know the level of the current binding minimum wage, but they also know the level of the minimum wage at a defined future date. Although this “future wage,” as I call it, is not yet binding, employers may take action to decrease their employment in anticipation of the coming increase. Using monthly CPS data from California, Oregon and Washington in the years 1994- 2014, I estimate the effect of both the current minimum wage and the future wage, when it exists, on the teen employment-population ratio. I divide the observations into two regimes: a “limbo” period during which there is a future wage, and a “normal” period during which there is not. I find that while a strong correlation exists between the minimum wage and teen employment in the normal regime, this correlation disappears in the limbo regime when a future wage exists. This indicates that although employers make employment decisions based on the current wage when no future wage exists, it is not clear whether they continue to do so when a future wage is present.

Keywords:  Department of Economics
Stanford Department of Economics
minimum wage
legislation
employment
lead effects
teenagers
Thesis
Advisor: Pencavel John
Leveraging socioemotional goals to increase physical activity in older adults [electronic resource]

Physical inactivity is prevalent among Americans, particularly in older citizens, so much so that it poses a major threat to public health. My research examined two potential reasons for low levels of activity in older adults grounded in motivation: first, older adults may be inactive because they do not accrue benefits in valued domains, and second, interventions may be ineffective because they do not align with older adults' goals. Reasoning from socioemotional selectivity theory, I predicted that older adults would be motivated to engage in physical activity to the extent that it was perceived and experienced as an emotionally meaningful or satisfying activity. I posited that if older adults do not experience meaningful benefits from physical activity in the short-term, they are unlikely to maintain physical activity. To examine this possibility, I designed Studies 1 and 2 to test how physical activity influences emotional experience and cognitive performance in younger and older adults, first in a controlled, experimental setting (Study 1), then in daily life (Study 2). Findings from both studies suggest that older and younger adults experience comparably potent benefits from physical activity. I reasoned from these findings that experiencing benefits from physical activity could support maintenance of physical activity in older adults, and, therefore, initiation of physical activity, rather than maintenance, may be a key barrier to increasing physical activity in older adults. Because interventions aimed at initiating physical activity have met with limited success, particularly in older adults, the second aim of this research was to test whether interventions could be tailored to motivate younger and older adults to be more active. In Studies 3 and 4, I approached this question using values affirmation (Study 3) and an incentives framework (Study 4), in order to test the effects of reducing threat surrounding physical activity participation through socioemotional goals, and the efficacy of incentivizing physical activity through socioemotional goals. Findings from Study 3 indicated that older and younger adults responded positively and comparably to an intervention that emphasized personal values to promote physical activity. Similarly, findings from Study 4 indicated that older adults were comparably responsive to goal-based incentives as younger adults, although, once initiated, older adults better maintained the increase in physical activity relative to younger adults. Together, findings from these four studies suggest that older adults may benefit from goals-based interventions aimed at promoting and maintaining physical activity.

Keywords: Psychology.
Advisor: Carstensen Laura L. primary advisor. Thesis advisor
Gotlib Ian H.
Tsai Jeanne Ling advisor. Thesis advisor