VictorJuiz/thesis huggingface dataset:
Integrated characterization and optimization approach for groundwater engineering systems [electronic resource]

As the reliability of water supply is threatened by climate change, increasing demand and potential contamination, sustainable management of groundwater resources is more important than ever. The current crisis calls for the development of a systematic and integrated management approach that employs a predictive modeling of complex subsurface physical, chemical and biological processes, utilizes a large volume of hydrogeological and geophysical measurements for accurate subsurface characterization, quantifies uncertainty regarding model prediction, and makes a series of optimal decisions for economic and reliable aquifer management plans. In this dissertation, I make contributions in three important topics, which are pivotal components of integrated groundwater resources management: groundwater flow modeling tailored for managed aquifer recharge and recovery, subsurface characterization methods using various types of measurements, and dual control strategy for remediation design. First, variably saturated groundwater flow modeling with a commercial software, FEFLOW, is presented especially designed for managed aquifer recharge and recovery (MAR) projects. This modeling approach is then used to design and construct an intermediate-scale laboratory aquifer at the Center for Experiment Study of Subsurface Environmental Processes at Colorado School of Mines, Colorado, which aims at testing and validating an integrated sensor-based MAR management framework. Next, a computationally efficient stochastic inversion approach, Principal Component Geostatistical Approach, is introduced to characterize large-scale subsurface properties with various types of measurements. Then, a novel subsurface characterization method, Bayesian total variation inversion approach, is developed with an emphasis on the discrete geologic feature identification. Lastly, an integrated simulation-optimization program tool, Stochastic Cost Optimization Toolkit (SCOTOOLKIT), is applied for the reliable and cost-efficient remediation plans to a DNAPL contaminated area at a U.S. Air Force Base in Dover, Delaware.

Keywords: Civil and Environmental Engineering.
Advisor: Kitanidis P. K. (Peter K.) primary advisor. Thesis advisor
Freyberg David L. advisor. Thesis advisor
Knight Rosemary (Rosemary Jane)
An integrative model of chromatin and expression variation across human cell types [electronic resource]

Although all cells in our body contain the same genetic material, they can perform vastly different functions by selectively expressing subsets of their genes. Cell-type-specific gene regulation is achieved through interactions between regulatory proteins and epigenetic mechanisms, which affect the structural organization of the genome. Characterizing these interactions is important for understanding the causes of genetic diseases and for identifying potential targets for medical intervention. The amount and complexity of genomic data being generated nowadays imply that many of the challenges that the field of genomics is currently facing are purely computational. The goal of this thesis is to demonstrate how machine learning approaches that account for the inherent heterogeneity and combinatorial complexity of gene regulatory mechanisms can be successfully used to provide novel biological insights. This thesis starts by presenting two studies that use computational techniques to investigate the variation in epigenetic state across genomic contexts and individuals. These studies demonstrate that the effects of epigenetic variation on gene regulation are highly combinatorial. Motivated by these results, and by the wealth of data generated by the ENCODE and Roadmap Epigenomics projects, I present a machine learning framework for discovering cell-type-specific regulatory mechanisms. This framework integrates several data sources including gene expression, DNA sequence information, cell-type-specific epigenetic state, and information regarding protein interactions. The proposed model achieves high predictive power and discovers novel cell-type-specific regulatory features and context-specific interactions between them.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Kundaje Anshul
Snyder Michael
Interacting effects of physical disturbance and ocean acidification stress on the California mussel, Mytilus californianus

One of the main impacts of human carbon dioxide emission is the decline of oceanic pH. The concomitant reduction in carbonate ion concentration has proven deleterious to range of calcareous marine species, many of which are also subject to habitat loss and disturbance due to human exploitation of the coast. Here, I examined the interaction of pH and dislodgment stress on the California mussel, Mytilus californianus. First, pH was found to be the dominant stress affecting growth; however, due to pseudoreplication, a second experimental run was conducted, which suggested that pH and disturbance act synergistically to reduce growth rates. Further analysis determined that pH and disturbance did not significantly differ between experiments, but that potential compensatory effect had been acting in the tanks: increased pCO2 in tank water may have allowed mussels to offset the metabolic demand of hypercapnia and byssogenesis. These results highlight the difficulty of simulating the intertidal environment in a controlled fashion and the necessity of continued study of compound stress effects for the management of coastal resources under climate change.

Keywords:  Department of Biology
Micheli Lab
Hopkins Marine Station
Stanford University
Mytilus
Ocean Acidification
Stress Interactions
Biology
Thesis
Advisor: Micheli Fiorenza
Palumbi Stephen
Interactions between innate immune cells and the brain vasculature in development and injury in zebrafish

Innate immune cells and vasculature are known to interact in both development and in injury. The CNS has specific macrophages, microglia, dedicated to protecting it, but the mechanisms by which resident immune cells interact with the vasculature in the brain are not well understood. How do microglia and another key innate immune cell type, neutrophils, help or impair neurovascular development and healing? To address the roles of these immune cell types in the brain, our study used zebrafish mutants lacking microglia and macrophages to elucidate the interactions of these cells with vasculature during normal development and after blood vessel severing. Zebrafish are used as simple vertebrate model organisms because their embryos are translucent, allowing for real-time imaging of fluorescently marked cells. We characterized injury, immune response, and healing in mutants lacking microglia, and mutants lacking microglia and having uncontrolled inflammation.
Our findings show that immune cells in the brain respond in similar temporal patterns as in previous studies of injury in other tissues . Neutrophils persist after injury for an abnormally long time period in nlrc3-like mutants, which were shown previously to have excess inflammation and greatly reduced microglia. Our studies also show that normal early vasculature development is not disrupted by macrophage deficiency. The inflammatory conditions in nlrc3-like mutants may impair vasculature re-growth after injury compared with wildtype and with mutants in interferon regulatory factor 8 (irf8), which lack macrophages but, in contrast to nlrc3-like mutants, appear to have a normal inflammatory response. Taken together, these findings point to a possible role of cells of the innate immune system in neurovasculature healing. Our data suggest that immune dysregulation by hyperinflammation or deficiency in macrophage production may have negative consequences on the body’s ability to respond to neurovascular disruption. These studies provide a framework for future studies that may shed light on the pathophysiological process involved in stroke, cancer, and traumatic brain injury.

Keywords:  Department of Biology
Biology
Neuro
Neurobiology
Immunology
Innate
Vasculature
Blood
Vessels
Developmental
Dev
DevBio
Microglia
Neutrophil
Neutrophils
healing
heal
injury
recovery
Development
Neurovascular
Interactions
Thesis
Advisor: Talbot William
Red-Horse Kristy
Shiau Celia
Interactive sound source separation [electronic resource]

In applications such as audio denoising, music transcription, music remixing, and audio-based forensics, it is desirable to decompose a single-channel recording into its respective sources. One of the most promising and effective classes of methods to do so is based on non-negative matrix factorization (NMF) and related probabilistic latent variable models (PLVMs). Such techniques, however, typically perform poorly when no isolated training data is given and offer no mechanism to improve upon unsatisfactory results. To overcome these issues, we present a new interaction paradigm and separation algorithm for single-channel source separation. The method works by allowing an end-user to roughly paint on time-frequency displays of sound. The rough annotations are then used to constrain, regularize, or otherwise inform an NMF/PLVM algorithm using the framework of posterior regularization and to perform separation. The output estimates are presented back to the user and the entire process is repeated in an interactive manner, until a desired result is achieved. To test the proposed method, we developed and released an open-source software project embodying our approach, conducted user studies, and submitted separation results to a community-based signal separation evaluation campaign. For a variety of real-world tasks, we found that expert users of our proposed method can achieve state-of-the-art separation quality according to standard evaluation metrics, and inexperienced users can achieve good separation quality with minimal instruction. In addition, we show that our method can perform well with or without isolated training data and is relatively insensitive to model selection, thus improving upon past methods in a variety of ways. Overall, these results demonstrate that our proposed approach is both a general and powerful separation method and motivates further work on interactive approaches to source separation. To download the application, code, and audio/video demonstrations, please see http://ccrma.stanford.edu/~njb/thesis.

Keywords: Music.
Advisor: Wang Ge
Abel Jonathan (Jonathan Stuart)
Chafe Chris advisor. Thesis advisor
Smith Julius O. (Julius Orion) advisor. Thesis advisor
Interpreter-driven automatic image segmentation and model evaluation [electronic resource]

This dissertation addresses a major bottleneck in iterative seismic imaging projects: interpretation and modeling of large, subsurface salt bodies. These salt structures are ubiquitous in many of the world's most active areas for seismic exploration, and are extremely time-consuming and difficult to interpret -- a process that is conventionally undertaken manually, with little automation. In this thesis, I propose two tools that can help interpreters increase the degree of automation in the salt interpretation workflow, while allowing them to maintain control of the process through expert guidance and scenario testing. The first of these tools is an interpreter-guided, graph-based image segmentation algorithm. This method allows interpreters to provide limited salt boundary interpretations on one more 2D sections of a 3D seismic image; the manual picks are then incorporated into the automatic 3D segmentation process. The second tool is an efficient, wavefield-based scheme to evaluate several potential velocity models. This method synthesizes source and receiver wavefields from an initial image; these wavefields can then be imaged very quickly using velocity models based on different salt interpretation scenarios. Finally, I use a 3D example from the Gulf of Mexico to demonstrate how these tools can be integrated in a streamlined salt interpretation workflow. After using image segmentation to generate velocity models, the model evaluation scheme identifies one superior to the one used to create the initial image. A subsequent full migration with the new velocity model produces an image with improved clarity and continuity of subsalt reflectors.

Keywords: Geophysics.
Advisor: Biondi Biondo
Claerbout Jon F. advisor. Thesis advisor
Clapp Robert G. (Robert Graham) advisor. Thesis advisor
Mavko Gary
Intersectionality as a Tool for Student Activism

I argue that we need an intersectional analysis of organizing in order to form a sustainable activist coalition that is capable of making demands of both the institution and the student body. I used Black Feminist theory to shape my work, both to contextualize and problematize my findings.
My research questions include: Does an intersectional framework enhance the work of student activists in their individual organizations? What are the different ways in which student activist leaders understand the role of the organization in a larger framework for social justice? In what ways can we use these findings to made recommendations for furthering the work of intersectionality? In what ways can we use these findings to forge strong coalitions with student activist organizations?
I prove that the accommodations of Stanford as an institution hinder radical student activism, limiting cross-community work and intersectional understanding. I suggest Stanford student activism could strengthen their political power and advance social justice by grounding collaborative efforts in intersectional frameworks. I argue that an intersectional framework is necessary for the advancement of a strong anti-oppression student movement. As community is the focus of my work, I conducted in-depth interviews with student activists, along with participant observation. The activists I engaged with guided my inquiry and ultimately dictated the direction of my findings. My research adds to the body of literature on intersectionality and social movements. I explore the process that activists go through when engaging in collaborative work with other organizations, outlining best methods for coalition building and strategic planning with the help of intersectional frameworks.

Keywords: Feminist Studies
Feminist Gender and Sexuality Studies
Stanford
student activism
activism
intersectionality
black feminism
revolutionary
organizing
community organizing
college organizing
college activism
social movements
black feminist theory
coalitions
coalition-building
Stanford activism
hunger strike
takeover of the president's office
students of color coalition
SOCC
MEChA
MEChA de Stanford
identity politics
Occupy Stanford
Divestment
Thesis
Advisor: Yarbro-Bejarano Yvonne
Intracellular recording of single cell action potentials by nanoelectrodes [electronic resource]

Many biological cells use electricity to control their physical and chemical functions. Some cells do so by generating action potentials, which are rapid rises and falls in the electric potential difference across their cell membrane. In particular, muscle cells, neurons, and endocrine cells use action potentials to initiate mechanical contraction, perform signal processing, and trigger chemical release, respectively. Action potentials are generated by the rapid opening and closing of ion channels on the cell membrane. Malfunctions of these ion channels are the cause of many diseases and toxicity in humans. Therefore, understanding the electrophysiology and pathology of these cells requires accurate recording of their action potentials. In this thesis I will present our results in developing nanoelectrodes for accurate, minimally invasive, and high-throughput intracellular recording of single cell action potentials. Using mammalian cardiac cells as the target system, we first demonstrate intracellular recording by platinum nanopillar electroporation. We discover that the tight cell membrane-electrode interface allows recording with high signal-to-noise ratio. I will then move on to the development of a new nanoelectrode topology, namely iridium oxide nanotubes, which give more than an order of magnitude increase in recording duration. At the same time we also verify that our nanoelectrode recording is accurate compared to the patch clamp recording standard. Finally, I will present application of our nanoelectrodes to record human stem cell derived cardiomyotyes for drug screening assays and disease monitoring.

Keywords: Applied Physics.
Advisor: Cui Bianxiao primary advisor. Thesis advisor
Mabuchi Hideo primary advisor. Thesis advisor
Cui Yi
Intrinsic and extrinsic factors influencing presynapse number and location in C. elegans [electronic resource]

The number of connections formed between neurons and their targets is dynamic. In vertebrate systems the number peaks in young animals and then reduces with age. Throughout life, the connections are plastic and can change in response to activity. Misregulation of synapse number is associated with mental retardation and some degenerative diseases. Few studies have focused on using an in vivo system with a stereotyped synaptic circuit to understand the mechanisms regulating synapse number. To better understand factors influencing synapse number we studied the C.elegans motorneuron DA9, which has a highly stereotyped number and location of synapses. We found that loss of function of the myotubularin family member mtm-6 reduces the number of synapses in the DA9 motorneuron. MTM-6 is a lipid phosphastase whose human homologs MTMR 6-8 are capable of acting on phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate. We found that mtm-6 is expressed in nervous system of the worm as well as the previously reported tail cells. The reduction of synapse number is due to two different functions of MTM-6 reflected by its expression pattern. MTM-6 regulates secretion of the C. elegans Wnt ligand EGL-20 in a fairly specific manner due in part to their mutual expression in non-neuronal tail cells. Loss of egl-20 causes a reduction in synapse number that appears to be the result of DA8 and DA9 maintaining a synaptic border. While mtm-6 regulation of egl-20 is non-autonomous, mtm-6 also causes a reduction in synapse number due to intrinsic mechanisms in the neuron. MTM-6 impacts endocytosis through its dephosphorylation of phosphatidylinositol 3-phosphate. In the process of studying whether or not synapse number was impacted in endocytosis and exocytosis mutants we discovered that these mutants affect the localization of presynaptic material. unc-26/synaptojanin caused synaptic vesicle puncta to localize into the normally synapse-free region of DA9. This phenotype was not observed in the alleles used for other endocytosis mutants, such as unc-57/endophilin, itsn-1/intersectin, amph-1/amphiphysin, or dyn-1/dynamin. In contrast loss of the exocytosis genes unc-13/Munc-13 or unc-18/Munc-18 caused mislocalization of presynaptic material to the dendrite. The mislocalization phenotype of unc-13/Munc-13 was suppressed by loss of unc-57/endophilin. Our results indicate that proper distribution of presynaptic material is impaired in different ways depending on which part of the synaptic vesicle cycle is targeted.

Keywords: Molecular and Cellular Physiology.
Advisor: Shen Kang
Clandinin Thomas R. (Thomas Robert)
Meyer Tobias advisor. Thesis advisor
Smith Stephen J.
Investigating Post-translational Modification of p53: Effects on p53 Interaction with the Long Noncoding RNA DINO

The p53 tumor suppressor is a central component of the DNA damage response, mediating its effect on cell cycle progression and cell death through a myriad of gene expression regulation patterns. A novel long noncoding RNA, DINO, has been recently discovered as an intricate part of the p53 damage response pathway, providing a feed-forward mechanism for p53 activation and stabilization following sustained DNA damage. While DINO promotes post-translational modifications of the p53 C-terminal domain in order to enhance protein stability, it is not yet know whether the post-translation modifications can impact the binding of p53 and DINO. In this study, we set out to identify the amino acid residues critical for p53’s binding of DINO. We were motivated by the observations that the basic residues of the C-terminus, which are likely involved DINO binding, are subjected to extensive post-translational modifications. We generated eighteen point mutations of p53, selectively targeting basic residues in the p53 C terminal domain to identify their role facilitating binding of DINO and p53. Here, we identify six basic lysine residues in p53’s C-terminal domain that we hypothesized to impart critical function in RNA mediated binding of p53. Using site-directed mutagenesis, we successfully synthesized 18 mutant constructs in total, with mutations to alanine, glutamine, and lysine at each of the six lysine residues. To best characterize the functionality of these various p53 mutants, we developed a high-throughput method of RNA immunoprecipitation to characterize their impact on the protein’s ability to bind DINO. qRT-PCR analysis provided us with initial insight into the success of this in vitro RNA binding assay, imparting us with a foundation to better assess the role of post-translation modification of basic lysine residues in p53’s C-terminal domain in the future. A deeper understanding of how p53 modifications impact lncRNA interaction provide a deeper understanding of the mechanism by which p53 post-translational modification “barcode” can elicit distinct cellular phenomenon (1).

Keywords:  Department of Biology
DINO
long noncoding RNA
p53
RNA binding
post-translational modification
tumorigenesis
Biology
Stanford
Thesis
Advisor: Chang Howard Y.
Simoni Robert D.