VictorJuiz/thesis huggingface dataset:
Hydromechanical modeling framework for multiscale porous materials [electronic resource]

Hydromechanical interactions between fluid flow and deformation in porous geomaterials give rise to a wide range of societally important problems such as landslides, ground subsidence, and injection-induced earthquakes. Many geomaterials in these problems possess two-scale porous structures due to fractures, particle aggregation, or other reasons. However, coupled hydromechanical processes in these multiscale porous materials, such as ground deformation caused by preferential flow, are beyond the modeling capabilities of classical frameworks. This thesis develops theoretical and computational frameworks for fully coupled hydromechanical modeling of geomaterials with two-scale porous structures. Adopting the concept of double porosity, we treat these materials as a multiscale continuum in which two pore regions of different scales interact within the same continuum. Three major developments are presented. First, we build a mathematical framework for thermodynamically consistent modeling of unsaturated porous media with double porosity. Conservation laws are formulated incorporating an effective stress tensor that is energy-conjugate to the rate of deformation tensor of the solid matrix. Based on energy-conjugate pairs identified in the first law of thermodynamics, we develop a constitutive framework for hydrological and mechanical processes coupled at two scales. Second, we introduce a novel constitutive framework for elastoplastic materials with evolving internal structures. By partitioning the thermodynamically consistent effective stress into two individual, single-scale effective stresses, this framework uniquely distinguishes proportional volume changes in the two pore regions under finite deformations. This framework accommodates the impact of pore pressure difference between the two scales on the solid deformation, which was predicted by thermodynamic principles. We show that the proposed framework not only improves the prediction of deformation of two-scale geomaterials, but also simulates secondary compression effects due to delayed pressure dissipation in the less permeable pore region. Third, we develop a finite element framework that enables the use of computationally efficient equal-order elements for solving coupled fluid flow and deformation problems in double-porosity media. At the core of the finite element formulation is a new method that stabilizes twofold saddle point problems arising in the undrained condition. The stabilized finite elements allow for equal-order linear interpolations of three primary variables—the displacement field and two pore pressure variables—throughout the entire range of drainage conditions.

Keywords: Civil and Environmental Engineering.
Advisor: Borja Ronaldo I. (Ronaldo Israel)
Kitanidis P. K. (Peter K.) advisor. Thesis advisor
Linder Christian (Engineering professor) advisor. Thesis advisor
Regueiro Richard
Iceberg profiling using autonomous underwater vehicles [electronic resource]

An improved method for creating 3D reconstructions, or profiles, of the submerged portion of free-drifting icebergs using autonomous underwater vehicles (AUVs) and simultaneous localization and mapping (SLAM) is presented. These 3D reconstructions provide context for scientific data collected around icebergs, and can aid in navigating back to points of interest on the iceberg for further study. Additionally, these reconstructions can be used to assess risk to infrastructure like oil rigs and pipelines. However, the motion of the iceberg during data collection complicates the mapping process by introducing warping and inconsistency into the reconstruction. This motion must be accounted for in order to obtain an accurate profile. The work presented here improves upon prior work in three areas. First, it enables profiling the full iceberg depth, including multiple swaths of data and many loop closure events. Second, it reformulates the motion estimation problem entirely in an iceberg-fixed frame of reference. This choice of reference frame yields computational speed increases of several orders of magnitude, and removes the need to provide an explicit estimate of the vehicle's world-relative position, which can be difficult to determine accurately. Third, it presents a method for automating the data correspondence problem, a crucial component of SLAM that is challenging in any underwater mapping task, and made even more so by the motion of the iceberg. Both simulation and field results are presented. For the simulation, a 150 meter long iceberg was modeled to an accuracy of 0.8m rms error. For the latter case, data recorded at an underwater sea cliff in Monterey Canyon was used as an analog for the vertical walls of a tabular Antarctic iceberg. The vehicle's navigation data was corrupted to simulate the effects of iceberg motion.

Keywords: Aeronautics and Astronautics.
Advisor: Rock Stephen
Alonso Juan José
Mitiguy Paul
Identification and characterization of inhibitors of amyloids and amyloid-based biofilm in E. coli through cell-based high-throughput screening [electronic resource]

Biofilms are multicellular microbial communities that consist of the cells plus a self-produced extracellular matrix (ECM), a complex, heterogeneous housing that protects the cells from environmental insults. In the human host, biofilms can result in persistent infections that are difficult to treat, leading to further health complications and longer hospital stays. Additionally, environmental persistence through biofilm formation can contribute to foodborne outbreaks by pathogenic strains. Identification of compounds that inhibit biofilm formation would provide a valuable tool for reduction of pathogenesis resulting from biofilms. In natural biofilms, adhesive amyloid fibers are abundant and employed by a wide variety of bacteria, suggesting a crucial role in biofilm formation and persistence. The most well-studied bacterial amyloid adhesins are the curli fibers produced by Escherichia coli and Salmonella species. In the laboratory, the coproduction of curli and cellulose by E. coli enables the formation of bacterial biofilms on agar, characterized by the hallmark wrinkled colony morphology. Amyloid fibers are highly ordered protein aggregates formed by the non-covalent polymerization of a single protein with the polypeptide chains aligned in the cross-β-configuration. Originally considered to be exclusively the result of protein misfolding, many examples of amyloid fibers that perform physiologically useful and specialized functions for the organism producing them have been identified and termed functional amyloids. Understanding the mechanism of formation of these functional amyloids not only provides insight into the prevention of biofilm formation, but also the prevention of diseases associated with amyloids produced by protein mis-folding. We developed a cell-based high-throughput screen to identify inhibitors of curli-dependent biofilm formation by the uropathogenic E. coli clinical isolate UTI89, and, in parallel, curli-dependent cell adhesion by the laboratory strain MC4100. In screening the compound libraries available at Stanford's High Throughput Bioscience Center, several potential inhibitors were identified and subsequently characterized.

Keywords: Chemistry.
Advisor: Cegelski Lynette primary advisor. Thesis advisor
Boxer Steven G. (Steven George)
Khosla Chaitan
Identification of a novel regulator of synapse formation and Neuronal Specification in C. elegans

The formation of neuronal synapses in the nematode Caenorhabditis elegans (C. elegans) is a highly regulated process dependent on the recruitment of synapse assembly proteins to the presynaptic active zone. Other proteins involved in the synaptogenic process, as well as the molecular mechanisms through which they act, remain unknown. Recent work has shown that essential genes play important roles in synaptogenesis (P. H. Chia, Li, & Shen, 2013; Firnhaber & Hammarlund, 2013). Previously, the role of essential genes in the C. elegans nervous system has been difficult to study due to lethality associated with loss of function mutations in functional domains of essential genes. However, recent advances in RNAi have allowed the generation of C. elegans strains that facilitate targeted neuron-specific RNAi.
Here, we employ a tissue specific RNAi strategy to identify ztf-11, a zinc finger transcription factor, as an essential gene involved in synaptogenesis in the Hermaphrodite Specific Neuron (HSN). To determine the ZTF-11 expression pattern as well as its tissue specific requirements we inserted a conditional degradation motif (ZF1) fused to a C-terminal GFP tag via the CRISPR/Cas9 genome editing system. Using fluorescence microscopy we found that that ZTF-11::ZF1::GFP was highly expressed in neural progenitor cells and neurons in a highly regulated spatiotemporal fashion. Cell-specific degradation of ZTF-11 in HSN demonstrated that ZTF-11 is essential for proper synapse formation. Taken together, our study provides new mechanistic insights into the role of ztf-11 in synapse assembly through regulation of downstream genes that may directly influence assembly of active zone proteins and their functional roles in synaptogenesis and neurogenesis.

Keywords:  Department of Biology
Biology
synapse formation
neurogenesis
transcription factor
RNAi
Thesis
Advisor: Shen Kang
Feldman Jessica
Identification of the Coronary Artery Disease Causal Variant and Gene at 15q22.33

Genome wide association studies (GWAS) have uncovered a number of SNPs associated with a range of diseases including coronary artery disease (CAD). We focus on one particular variation in the SMAD3 gene (rs17293632) that is a key factor in the pathophysiology of CAD. The purpose of this research is to investigate how allelic variation affects gene expression at the SMAD3 gene within 15q22.33, provide validation for the causality of coronary artery associated variant rs17293632, and explore how SMAD3 expression looks in developing cells of mouse models. This called for 1) quantitative investigation of allelic variation at rs17293632 using a dual-luciferase assay and eQTL analysis, 2) validation of causality of rs17293632 through genome editing using a CRISPR/Cas9 system followed by SMAD3 TaqMan qPCR expression analysis, and 3) validation of SMAD3 enhancer in vivo through generation of SMAD3 specific transgenic mice followed by X-gal staining of LacZ reporters. Using these methods we found the SMAD3 expression has allelic dosage dependence at rs17293632, with higher expression of SMAD3 in cells correlated with the number of C alleles at this loci. Through genome editing we confirmed that this variation altered SMAD3 expression in cultured HEK cells. Lastly, in vivo data showed that transgenic lines of C/T mice display different patterns of SMAD3 expression during embryonic development in different tissues. These results indicate the importance and strong causal relationship between allelic variation at rs17293632 and the expression of our CAD relevant gene. In vivo analysis then suggests that this expression is regulated by a wide range of tissue-specific mechanisms that, through further research, may be uncovered. Overall, the data presented here demonstrates the great potential of variant investigation in understanding biological nuances on the smallest scale. These biological insights in turn provide the foundation for the exploration of related genes and the potential development of gene-targeted therapies.

Keywords:  Department of Biology
Genetics
biology
cardiovascular medicine
Thesis
Advisor: Quertermous Thomas
Fraser Hunter
Identifying a new driver of aging in C. elegans [electronic resource]

Aging is a fundamental biological process seen in nearly all organisms. While research has discovered hundreds of genes whose dosage can modify lifespan, it is unclear how many of these genes play a role in the normal transition from the young state to the old state. To better understand aging, it is critical to identify which processes are driving aging in wildtype organisms. Our approach is to search for direct regulators of molecular changes that appear over time in the nematode worm Caenorhabditis elegans. This is a quantitative, global, and relatively unbiased way to find potential drivers of aging. We begin with a set of over 1,000 gene expression changes between young and old worms. In this work, we used a computational screen to identify transcription factors that directly bind to our list of age-regulated genes. The top hit from our screen is a conserved GATA transcription factor called ELT-2 that functions during development to effect the terminal differentiation of the intestine. The expression of ELT-2 and its direct transcriptional targets decline during aging. Lifespan can be either extended or shortened by increasing or decreasing the dosage of ELT-2. Together, these findings provide strong evidence to support the idea that changes in the expression of ELT-2 drive transcriptional changes during aging and limit lifespan.

Keywords: Genetics.
Advisor: Kim Stuart
Brunet Anne
Fire Andrew Zachary advisor. Thesis advisor
Villeneuve Anne
Identifying Pancreatic Islet Cell Fate Changes in Type 1 and Type 2 Diabetes Mellitus

Diabetes mellitus is a complex group of diseases characterized by impaired glucose homeostasis due to insufficient insulin secretion by pancreatic islet beta cells. Diabetes occurs when the pancreatic beta cells are destroyed by autoimmune attack (type 1 diabetes) or when their function is impaired (type 2 diabetes). Therefore, intensive research efforts are focused on developing a therapeutic strategy to replace functional beta cells. Glucagon-producing pancreatic alpha cells have demonstrated the ability to express insulin and other beta cell genes in mice when endogenous beta cells are experimentally ablated. However, the extent to which such cellular changes occur in the context of human diabetes is unclear. Moreover, it is unknown which molecular mechanisms regulate the fate of adult human alpha cells. To determine the degree of pancreatic islet cell fate change in diabetes, we examined human type 1 and type 2 diabetic pancreas samples for alpha cells that lost the expression of hallmark alpha cell genes and acquired the expression of beta cell genes. In type 1 diabetic samples, we found a subset of cells that expressed both glucagon (GCG) and key beta cell genes and lost the expression of the alpha cell gene ARX. In type 2 diabetic samples, we found cells that co-expressed GCG and beta cell genes, as well as INS+ cells that lacked the expression of the beta cell gene NKX6.1. To create methods to dissect genetic mechanisms maintaining human alpha cell identity, we developed a cell-purification strategy to isolate human alpha cells, and a method to label human alpha cells for lineage tracing. My work reveals profound changes in alpha and beta cell fate in diabetic islets, and provides new techniques for isolating and lineage-tracing human alpha cells.

Keywords:  Department of Biology
Biology
diabetes
alpha and beta cells
glucagon
insulin
ARX
DNMT1
Thesis
Advisor: Kim Seung
Jones Patricia
Ignorance, capacitarian control, and responsibility [electronic resource]

This work is about the connection between ignorance and responsibility. It addresses the questions of what it takes for agents to be responsible for their ignorance of morally relevant considerations (both normative and factual) and for the unwitting wrongdoing prompted by it. This topic has recently commanded a great deal of attention in light of some skeptical arguments purporting to show that agents are rarely (if ever) blameworthy for their ignorance and their unwitting wrongdoing. In the dissertation I address these arguments, diagnose their weak points, and propose a conception of responsibility-relevant control—the capacitarian account—that not only is able to rebut those arguments but also provides a fruitful way to explain responsibility for ignorance and unwitting wrongdoing. Along the way I also touch on a variety of related topics such as the epistemic condition on responsibility, the capacities that matter for responsible agency, how we attribute unexercised capacities to wrongdoers, the content and justification of judgments of blameworthiness, the structure of negligence, the distinction between factual and moral ignorance, and whether the latter sometimes exculpates.

Keywords: Philosophy.
Advisor: Bratman Michael primary advisor. Thesis advisor
Vargas Manuel
Bobonich Christopher advisor. Thesis advisor
Dannenberg Jorah
Schapiro Tamar
Image and orality [electronic resource] : vision, voice and modernism in the literature of new worlds

This project takes a sensory approach to the question of literary voice in the Americas. Drawing from sensory philosophy, semiotics, theories of literacy and orality, psychoanalysis, and a touch of neuroscience, I argue that American literature exists in a state of dynamic tension between image, as the textual byproduct of vision, and orality, as the textual imprint of voice. Using Columbus's account of his first voyage as an origin story, I argue that modernity -- especially in the New World -- is based on and imposes a visual bias that has favored image at the expense of genuine orality (or the authentic voice), which is lost, or covered over, at the moment of encounter. My project reads American modernism as a return to the site of this lost voice, and a confrontation with the images that replaced it. Orienting my argument around four points -- early, proto-, high, and late modernism -- my project explores how writers at each of these moments approached and worked through image in order to restore contact with the voice.

Keywords: Comparative Literature.
Advisor: Saldívar Ramón
Greene Roland
Rocha Marília Librandi advisor. Thesis advisor
Image processing for novel and efficient quantification of neuronal transport [electronic resource]

Biological research is highly visual, as advances in imaging technologies over the last few decades have enabled biologists to discern increasingly specific structures using fluorescence microscopy. However, two obstacles limit the amount of information that can be extracted from images. The first is the diffraction limit, the fundamental limit that dictates how small of an object can be resolved by light waves. The second challenge is the necessity to efficiently and objectively process the large numbers of images that today's technology can acquire. Current research in the fields of image processing and computer vision is not directly applicable to biological images, because it focuses primarily on extracting information from natural images with strong features. This dissertation leverages some of these engineering techniques to create two tools to address the challenges of visual biological research in the context of neuronal transport. These tools incorporate techniques from image processing and machine learning to effectively extract information about various molecules associated with neuronal transport, including structures ten times smaller than the diffraction limit. With the computational methods described in this dissertation, biologists can quantify various biological phenomena rapidly and robustly, and in turn, accelerate neuroscience research.

Keywords: Electrical Engineering.
Advisor: Shen Kang
Girod Bernd advisor. Thesis advisor
Horowitz Mark
Imaginal renaissance [electronic resource] : desire, corporeality, & rebirth in the work of Jacob Böhme

Böhme is an important figure who connects the histories of early modern religious dissidence to Continental philosophy and later countercultural movements, yet he remains understudied. Challenging prevalent views that Böhme's writings are exercises in irrationality or "primitive" religious speculation, I argue that his work provides the theory for a practice aimed at (a) relocating religious authority in the body and (b) fostering an experience of the world that rejects contemporaneous theological and scientific cosmologies in favor of an ontology of human/world co-constitution. I demonstrate that many of Böhme's concepts do not "make sense" when approached as theology, philosophy, or theory, because his texts are indexed to the body: they are meant to catalyze existential transformation rather than convey purely conceptual content. My dissertation attempts to rectify the tendency to "disembody" Böhme, by approaching him first and foremost as a praxis-oriented thinker. I analyze Böhme's work, not as an example of introspective mysticism or speculative philosophy, but as the framework for a praxis meant to be performed in real time: an "existential paradigm" that is simultaneously (a) a phenomenology of desire; (b) a theory, method, and practice of self and world creation; and (c) a creative action aimed at disrupting the social imaginary and influencing the larger body politic.

Keywords: Religious Studies.
Advisor: Sheehan Thomas primary advisor. Thesis advisor
Bashir Shahzad
Pentcheva Bissera V. advisor. Thesis advisor
Imagined voices [electronic resource] : Amerindian oralities and new world poetics

How did colonial linguistic exchanges between Amerindians and Europeans shape early modern conceptualizations of language itself--its locus and limits, its ideological plasticity or inflexibility? While oral traditions are persistent objects of scholarly attention, the concept of orality in itself has often been taken for granted, receiving less theoretical examination in comparison to the extensive scholarly corpus devoted to interrogating categories such as writing, literacy, text, and media. My research addresses the pending question of the complexities of orality in the New World by arguing that colonial encounters produced multiple oralities: a series of semiotic, aesthetic, and material phenomena that often emerge through the gestures of suckling and singing, in the regimes of grammar and taste, and in the performance of combat and proselytization. This study addresses early modern linguistic and cultural encounters in the Americas, focusing on the role of Amerindian languages in the development of what I call a New World poetics. I adopt an inter-American and transatlantic framework in order to compare how multilingual actors narrated and reinvented indigenous languages in historical, linguistic, lyric, and missionary works. The corpus under consideration includes the Nahuatl-language poetry collected in the Cantares Mexicanos manuscript, the Tupi grammar authored by Jesuit José de Anchieta, linguistic and missionary tracts and translations by Roger Williams and John Eliot, and the treatise on Incan history and customs by El Inca Garcilaso de la Vega. I demonstrate that these texts, written in and concerning languages such as Nahuatl, Narragansett, Quechua, Tupi, and Wampanoag, all evince sustained attention to the complexities of orality, conceived through the somatic and material qualities of speech, song, and alphabetic writing. Addressing these distinct forms of orality in colonial American literatures provides a vocabulary and framework for thinking about the oral in plural terms, related but not restricted to its relationship with written and spoken expression. In navigating the intersections of major Amerindian and European languages and traditions within a unified theoretical framework, my project integrates both comparative American and transatlantic encounters as the coordinates within which to critically revise traditional notions of orality used to interrogate the early colonial world.

Keywords: Comparative Literature.
Advisor: Greene Roland
Briceño Ximena advisor. Thesis advisor
Rocha Marília Librandi advisor. Thesis advisor
Saldívar Ramón