VictorJuiz/thesis huggingface dataset:
Social and ecological change in the Gulf of California : an investigation of small-scale fisheries in the Anthropocene

As global environmental and socioeconomic change impacts resource-dependent societies worldwide, small-scale fisheries are increasingly exposed to local threats and external pressures. Marine scientists and natural resource managers have devoted substantial research effort to describing the emergent phenomena impacting specific marine organisms, populations, and food webs. Yet comparatively little attention has been dedicated to investigating the consequences for coastal fishing communities and livelihood practices. In this dissertation, I investigate the cross-scale interactions and feedbacks shaping patterns of marine resource abundance and extraction within modern small-scale fisheries in the Gulf of California. Recognizing that the delineation between marine ecosystems, natural resources and associated social systems is increasingly artificial and arbitrary, I adopt an integrated systems science approach to identify the oceanographic, ecological, and socioeconomic drivers transforming regional small-scale fisheries. Leveraging theory and methods from diverse disciplines, I identify processes of social and ecological change that are rapid, intensive, and intertwined and suggest that fishers' interactions with the marine environment are increasingly dictated by the contextual factors mediating their perception of and response to external stimuli. Analysis of in situ decision-making, behavior, and response following system perturbation is used to provide insight concerning the design and development of locally relevant adaptation and mitigation strategies. In illustrating the value of diverse and participatory methods, I argue that marine resource management and conservation in the human-dominated epoch known as the Anthropocene requires the integration of different types of knowledge and the use of inclusive research approaches.

Keywords: Biology.
Advisor: Broad Kenny
Crowder Larry B.
Gilly William 
Micheli Fiorenza
Social Connection, Loneliness, and Social Burdens as Experienced by Participants in the WELL for Life Project

Background and objectives: Social connectedness is a key component of health and well-being, yet certain subdomains of social connectedness deserve closer attention in certain populations. This report examines three subdomains of social connectedness in different age and gender groups.
Research Design and methods: Participants (n=4043) completed an online survey as part of the Stanford WELL for Life project. The survey included 13 items tapping social connectedness. Factor analysis was used to construct three subscales from these items. Linear regressions were used to evaluate associations between age and scores on these subscales among all participants and stratified by gender. Transcripts from semi-structured interviews (n=102) in which participants described periods of high and low well-being were reviewed in order to further illuminate the regression results.
Results: Three sub-domains of social connectedness were identified: social support and belonging; loneliness; and social burdens. Female gender was significantly linked to greater experiences of social burdens. Qualitative data from interviews extended this finding: women were more likely to discuss experiences of being drained by helping care for others (particularly family) than men, though men talked more about difficulty in meeting others’ expectations. Older age was significantly linked with lower experiences of loneliness and more social connectedness regardless of gender.
Discussion and implications: Studies of social connectedness and well-being may benefit from including measures of social burdens. Interventions to improve the well-being of those with low social connectedness might focus on high loneliness among young people and high social burdens among women.

Keywords: Stanford School of Medicine
Community Health and Prevention Research
Stanford Prevention Research Center
Social Connectedness
Social Support
Gender
Age
Well-being
Thesis
Advisor: Heaney Catherine
Social movement participation and public opinion : an experimental approach

Do racial structures in contemporary U.S. society create bias and obstacles for the support of minority activists? How does the experience of being a minority activist in this environment impact one's social psychology? My dissertation examines the role of racial bias in opposition to black activism. First, I find that racial bias exists in the value a victim of wrongful police use of fatal force has on the public's attitudes toward protests against police brutality and respect for police. However, our ability to detect this bias is strongest before beliefs crystalize along ideological lines. I also find that opposition to minority activists is driven, in part, by the perception that claims are being made on the basis of racial group membership, rather than across racial lines. While this belief is itself fraught with racial inequality implications, outright racial discrimination against the composition of the activist group is not a significant motivator for opposition. Finally, I find that salient activist experiences can indeed lead to increased emotional feelings of anger, collective identification with the content of activism, and feelings of self-efficacy. Throughout this entire dissertation, a novel contribution is an experimental approach to provide some causal evidence in the areas of race and social movements. Taken together, this dissertation breaks new ground in providing compelling evidence on how racial bias impacts the perception of minority victims of police violence and social movements seeking to alleviate race-specific inequalities, as well as how participation in those social movements changes the activists themselves.

Keywords: Sociology.
Advisor: Soule Sarah Anne
Willer Robert Bartley 
Olzak Susan
Solid-state NMR studies of peptidoglycan and teichoic acids in the bacterial cell wall and bacterial biofilms

Gram-positive bacteria surround themselves with a cell wall that is essential to cell survival and serves as a major target for antibiotics. The cell wall is composed primarily of two polymeric macromolecules: peptidoglycan (PG) and teichoic acid (TA). During infection, bacteria can further elaborate a multi-component extracellular matrix beyond the cell wall to form a biofilm community, enmeshing many cells, that improves adhesion, increases virulence, and helps avoid host immune responses. Cell walls and biofilm matrices are insoluble and heterogeneous materials that pose a challenge to analysis with biophysical techniques like X-ray crystallography, solution NMR, and mass spectrometry. We are implementing solid-state NMR methods to access atomic-level compositional parameters of cell walls and the extracellular matrix, particularly doing so in the context of intact biofilms to address questions that cannot be answered by attempted digestions and solution-based analysis. I will report on our new approach to quantify the relative proportions of PG and TA in isolated cell walls through 13C analysis, and how we have extended this approach to intact whole cells and protoplasts to identify several characteristic spectral features of cell walls. These allow us to gauge cell wall levels quantitatively. Further 15N analysis revealed a uniquely shift-resolved peak in whole cells entirely attributed to TA D-alanylation. We use these markers alongside isotopic-labeling experiments to characterize the distinct mode of actions of a panel of cell wall synthesis inhibitors. Through our analysis, we also found that cells in stationary phase exhibit reduced levels of TA with increased PG. We have now discovered that TA D-alanylation decreases significantly in cells that make a robust extracellular matrix, as visualized by EM. Similarly, cells treated with a small molecule inhibitor of teichoic acid synthesis appear to make more developed biofilms. Our solid-state NMR measurements are integrated with proteomic and microscopic analysis of biofilm cells and reveal direct composition-function relationships. Together, our results demonstrate that S. aureus PG and TA production are tunable, and that decreased TA production or modification occurs as cells form biofilms.

Keywords: Chemistry.
Advisor: Cegelski Lynette 
Boxer Steven G. (Steven George)
Solomon Edward I.
Some hierarchical and group regularization methods and applications

We analyze methods to model data with group effects that may be hierarchical. We begin by introducing a problem inferring human results from experiments done on mice in Chapter 2. Since we have paired experimental results across many genes and diseases, this suggests a hierarchical random effects model. Alternatively, we can also simplify the generative assumptions and consider a fixed effect model with regularization. While these basic models can outperform the baseline estimate of using the results on mice directly, they do not take full advantage of the two factors in the data. We impose either a hierarchical model or an additive model to account for the two effects. In Chapter 3, we propose a two factor random effects model with a more general covariance structure, which captures correlation across related genes and diseases and thus, allows interactions between the factors. The benefit of this model extends to general linear regression problems with networked data. Finally, in Chapter 4, we analyze pliable lasso, which extends the lasso, for regularizing two factor fixed effects with potential interactions between them. While the lasso can be used for all terms, including interactions, the large amount of coefficients introduces variance into the estimator. Pliable lasso imposes a hierarchical structure, that allows variance reduction. Since pliable lasso is a more general method for estimating interaction effects and not just fixed effects, our analysis is done with general main and interaction effects.

Keywords: Statistics.
Advisor: Tibshirani Robert 
Imbens Guido 
Taylor Jonathan E.
A source rock first approach to petroleum system analysis in the middle Magdalena Valley, Colombia

The Middle Magdalena Valley (MMV) is an intermontane basin and petroleum province in northern Colombia. A succession of organic-rich source rocks deposited in the Cretaceous show excellent petroleum potential and have generated economic oil and gas accumulations within the valley. However, understanding the chronology of source rock maturation and generation with respect to the other petroleum system elements is complicated by the impact of the Andean orogeny on northern South America. To help resolve the MMV petroleum system, biomarker chemometrics of oil samples from discoveries in the basin are used to identify distinct petroleum tribes with characteristics indicating the presence of multiple source rocks. An examination of pyrolysis data from MMV wells finds six Cretaceous intervals with favorable organic matter quality and quantity within the Tablazo, La Luna, and Umir formations. Finally, a 3-D model of source rock maturation and generation from the Cretaceous to the present-day enables the incorporation of all petroleum system elements within the context of the basin evolution. The timing of maturation-generation for the Cretaceous interval and the petroleum tribes identified both support that the upper members of the La Luna Formation and the Umir Formation generated the majority of hydrocarbons discovered in the MMV

Keywords: Geological and Environmental Sciences.
Advisor: Graham S. A. (Stephan Alan)
Scheirer Allegra Hosford 
Moldowan J. M. (J. Michael)
Spatial multiplexing in optical communications

The information capacity of optical communication systems can be increased by multiplexing signals in co-propagating spatial and polarization modes of multimode or multicore fibers. In this dissertation, we discuss some fundamental aspects of spatial multiplexing in long-haul and short-reach transmission systems. We describe methods for modeling the temporal dynamics of modes in the presence of random environmental vibrations and show, both theoretically and experimentally, that the rate of channel dynamics increases with the number of coupled modes. We study the implications of fast channel dynamics on the adaptive multiple-input multiple-output digital signal processing at the receiver. Furthermore, we discuss the combined impact of mode-dependent gain and modal dispersion on the capacity of spatially multiplexed links, and derive the requirements for optical amplifiers in ultra-long-haul systems. We propose techniques for optical equalization using meshes of Mach-Zehnder interferometers. In particular, we evaluate the performance of the self-configuration method to configure mesh phase shifters and propose variants of this method that can track microsecond timescale channel dynamics. Finally, we propose novel design algorithms to optimize fiber refractive index profiles for various applications. Our algorithms enable effective control of fiber properties such as mode coupling, chromatic and modal dispersions.

Keywords: Electrical Engineering.
Advisor: Kahn Joseph M. (Joseph Mardell) 
Miller D. A. B. 
Solgaard Olav
A stability framework for the Galerkin approximation of multifield saddle point principles with applications to irreversible problems

This dissertation addresses the development of a variational-based stability framework and finite element design for the approximative description of a broad class of materials which in their mathematical description are expressed as saddle point principles. The primary focus lies in the treatment of standard dissipative solids for which the energetic response can be expressed by two scalar functions, a free energy density and a dissipation function. As these materials show a time-dependence, the variational problem may be related to a potential function in incremental form. A fundamental challenge lies in the proper approximation of interpolated field variables due to a possible lack of the uniqueness of the approximated solution. The presented framework aims to generalize the so-called discrete inf-sup theory and its numerical verification in the context of general problems in an arbitrary number of fields for both linear and nonlinear problems and to provide a basis for multi-fold inf-sup conditions in the presence of vanishing parameters. Its novel character lies in the notion of Hessian matrices through which the requirement, that a perturbation of a functional possesses the desired properties, is met. This framework is then applied to a number of examples for which new discretization techniques are developed and tested. The first example represents a two-field displacement-pressure saddle point principle for porous materials that governs the interaction of a deforming porous solid matrix with an inter-penetrating solvent, a description that is of interest in the context of many geotechnical problems, the study of polymeric gels, and a large variety of biological materials. For the study of this problem a subdivision-technique is proposed in the context of isogeometric analysis and the satisfaction of stability requirements is shown. The second example represents a description of the same problem derived from a three-field principle with an additional incompatible field for the deformation gradient. It is shown that a reduced formulation of previously used incompatible modes provides the desired stability and the accompanied smoothness of the pore pressure in a much larger range of deformations due to its capability to avoiding hourglassing in the finite deformation range. Finally, a recent four-field variational formulation in the context of gradient plasticity, that overcomes drawbacks regarding mesh sensitivity, and the corresponding finite element design is investigated based on the proposed framework and a test is conducted for three different element types.

Advisor: Linder Christian (Engineering professor) 
Borja Ronaldo I. (Ronaldo Israel)
Lew Adrian
Stability of oil/water interfaces

The stability of oil/water interfaces affects the manufacture of many different products in industries ranging from pharmaceuticals to oil industry. In the first part of the talk, the stability of asphaltene-laden interfaces will be discussed. Asphaltene molecules are complex molecules from crude oil that are defined by their solubility in hydrocarbons. These molecules have the propensity to adsorb onto oil/water interfaces where they create a viscoelastic network and stabilize oil/water emulsions. This causes difficulties, for instance, in the desalting process, one of the first processes in an oil refinery. During the desalting process, high concentrations of salt in crude oil are reduced by a liquid-liquid extraction where crude oil is mixed with water. Then, this mixture is brought to a settling tank called desalter where the two phases are expected to separate. However, the presence of asphaltenes may negatively impact this separation process as they stabilize oil/water emulsions. We built an experimental setup in the Fuller laboratory to reproduce in a smaller scale and in a controlled way the separation process that occurs in a desalter. Our goal was to study the impact of asphaltenes on the coalescence of both water and oil drops against a flat oil/water interface. We found that water drops are more stable than oil drops upon coalescence. In addition, the time it takes for water drops to coalesce as a function of the aging time of the interface presents a maximum due to a spontaneous appearance of micron-sized droplets at the oil/water interface. This spontaneous appearance of droplets is a phenomenon known as spontaneous emulsification and, in our system, the majority of the droplets formed consist of asphaltene-laden water droplets. In the second part of the talk, the spontaneous emulsification phenomenon in the presence of asphaltenes will be discussed. We used a co-flow microfluidic device to study the shrinkage due to spontaneous emulsification of suspended water drops in asphaltene/heptane-toluene solutions. The initial size of water drops and the concentration of solvents used in the oil phase are varied in our study. We found that drops will only decrease in size in the presence of asphaltenes. In addition, we found that drops shrink faster as their initial drop size decreases. In fact, the drop's radius decreases linearly with time and the angular coefficient of this relationship is a strong function of the drop's initial size. Finally, we found that the internal pressure of asphaltene-coated water drops does not follow a simple Young-Laplace equation and its internal pressure is inversely proportional to the drop's initial surface area. The internal drop pressure was found to be a potential force for spontaneous emulsification. An understanding of the spontaneous emulsification phenomenon in the presence of asphaltenes has strong implications in the oil industry, as it may affect problems ranging from oil refining to oil spill cleanups.

Keywords: Chemical Engineering.
Advisor: Fuller Gerald G.
Qin Jian (Professor of Chemical Engineering) 
Spakowitz Andrew James
Statistical methods for adaptive data analysis

We consider the problem of inference for parameters selected to report only after some algorithm, the canonical example being inference for model parameters after a model selection procedure. After defining the selected parameters, the conditional correction for selection requires knowledge of how the selection is affected by changes in the underlying data. We address two important issues arising in selective inference methodology: statistical power of selective inference methods and generality of the selection procedures addressed by the methods. We provide two methods that improve on the power of the original selective inference methods. The first way to improve statistical power after data exploration is to do selection on a noisy version of the data, thus using less information in selection and leaving more for inference. We also introduce the bootstrap version of this method and prove asymptotic guarantees. By redefining the selected parameters to require as little as possible information from selection, the second method we introduce here improves greatly on the power of the original selective inference methods. We apply the method to conduct powerful inference after Lasso in high-dimensional settings. The third method enables inference after black box model selection algorithms, without having explicit selection. In this work, we assume we have in silico access to the selection algorithm. We recast the inference problem into a statistical learning problem which can be fit with off-the-shelf models for binary regression. We apply this method to stability selection, which was previously out of reach of this conditional approach.

Keywords: Statistics.
Advisor: Taylor Jonathan E. 
Romano Joseph P.
Tibshirani Robert
Stereospecific functionalization of vicinal dihalides and efforts toward the total synthesis of archaeal lipids

Chapter 1 shows that while nucleophilic substitution reactions are universally taught, they are often much more complicated than we think. A huge amount of work has been done to understand neighboring-group participation in SN1-type reactions both in a qualitative and quantitative sense. Studying the reactivity of dibromides and their surrogates led to important insights in physical organic chem-istry. However, the enantiospecificity and potential synthetic use of such processes are underexplored. Chapter 2 is a reprint of a review I coauthored entitled "Chiral Alkyl Halides: Un-derexplored Motifs in Medicine". While alkyl halides are valuable intermediates in synthetic organic chemistry, their use as bioactive motifs in drug discovery and me-dicinal chemistry is rare in comparison. This is likely attributable to the common misconception that these compounds are merely non-specific alkylators in biologi-cal systems. A number of chlorinated compounds in the pharmaceutical and food industries, as well as a growing number of halogenated marine natural products showing unique bioactivity, illustrate the role that chiral alkyl halides can play in drug discovery. Through a series of case studies, we demonstrate in this chapter that these motifs can indeed be stable under physiological conditions, and that halogenation can enhance bioactivity through both steric and electronic effects. Chapter 3 demonstrates that dihalides could be used to generate a configurational-ly stable bromonium ion either through Lewis acid activation or by using a strongly ionizing solvent. This bromonium ion can then be trapped by a host of nucleophiles inter- and intramolecularly. Using this strategy, a variety of natural products and natural product relevant motifs were synthesized in our laboratory. Chapter 4 describes the importance of studying archaeal lipids and the ongoing efforts toward their total syntheses. Archaeal lipids are structurally unique, their biosynthesis has several unanswered questions, and their biophysical properties have not been studied on pure compounds. Our work describes a highly convergent strat-egy toward GDGT-0, which exploits the molecule's C2 symmetry. We have shown the feasibility of a key enantioselective hydrogenation step, and alternative strategies have been described that may circumvent certain challenges.

Keywords: Chemistry.
Advisor: Burns Noah
Trost Barry M. 
Wender Paul A.