VictorJuiz/thesis huggingface dataset:
Alone on The Ridge: Life in Paradise after the Camp Fire
Keywords: Camp Fire
environment
MA Journalism
Stanford
Paradise
water
insurance
fire
natural disasters
Thesis

The Camp Fire took 86 lives and 14,000 homes in a town nicknamed “The Ridge” that sits in the foothills of the Sierra Nevada Mountain range. Thousands of people lost everything and are trying to find ways to start over whether it’s through rebuilding, moving far away or finding a home in a neighboring town. But the Camp Fire also left people and structures behind. About 1 percent of the homes in Paradise remain standing, most of which are reoccupied, said Paradise Mayor Jody Jones. The fire caused over 1,000 businesses to immediately close for months, but the Chamber of Commerce estimates 150 have now reopened.
This story paints a picture of what life is like in a town trying to clean up and rebuild. It has four sections that detail this reality: a couple who live in a mostly-empty neighborhood, a business owner fighting to stay open, a church that has become a community center and Paradise Intermediate’s experience finishing out the school year in an emptied hardware store and plans to return to Paradise next August.
Those left face a struggle against undrinkable water. They fight to get insurance coverage for their homes since almost every major insurance company has stopped reinsuring houses in Paradise. They drive through the charred landscape getting stuck in the construction or losing their way without the familiar landmarks to guide their paths. Everything has changed on The Ridge.
Alveolar stem cells and niches in aging, injury and evolution
Keywords: Biochemistry.

The lung is the primary organ of respiration and the site of diseases that cause 7 million deaths annually. Although relatively understudied at the turn of the century, the field of lung stem cell biology is experiencing a renaissance due to advances in the ability to monitor and genetically mark and manipulate cells in mice. This dissertation focuses on two major topics in the field. In the first part, I focus on the identification of the alveolar stem, its niche and the signals regulating alveolar stem cell identity. I show that alveolar stem cells display active Wnt signaling, which imparts upon them the ability to proliferate and inhibits their transdifferentiation. Wnt signaling is activated by a juxtacrine signal from a single, neighboring fibroblast. I also describe how alveolar stem cells react to injury and the increased need for regeneration. I show that quiescent AT2 cells are recruited as emergency stem cells during injury through a transient autocrine source of Wnt signaling. I then describe the probing by single cell transcriptomics of the molecular underpinnings of alveolar stem cells and how they differ from other alveolar epithelial cells. Last, I describe a cellular transplantation assay developed for future study of these cells. The second part of my dissertation focuses on creating molecular cell atlases of mouse and human lungs. As a member of the Tabula Muris consortium, I led a team that captured lung tissues and analyzed data for the lung, spleen and kidney. I then describe my collaborative effort to create a molecular cell atlas of the human lung by single cell RNA sequencing (scRNAseq), for which we sequenced > 70,000 cells and molecularly characterized 58 molecular cell types including 14 novel populations. I then use these data to analyze mammalian lung evolution at single cell resolution. Finally, I describe my efforts to discover the molecular program responsible for the unique flat morphology of AT1 cells, which comprise one side of the gas exchange surface and enables efficient exchange of gases.
Amino Acid Withdrawal Engages ATF4-mediated Transsulfuration and Protects Cancer Cells from Oxidative Death
Keywords:  Department of Biology
Biology
ferroptosis
cell death
tumor suppression
amino acids
mTOR
ATF4
transsulfuration
Thesis

Ferroptosis is a form of regulated cell death which can be triggered by starvation of the amino acid cysteine. Its role in human physiology is poorly understood, but evidence suggests some tumor suppressors act by restricting cellular import of cysteine, thus inducing ferroptosis and preventing cancer growth. Here, I show that the supraphysiologic concentration of arginine in culture medium promotes sensitivity to ferroptosis, and that tumor-physiologic levels of arginine do not permit ferroptosis induction by cysteine starvation. This was observed in a broad panel of cancer cell lines, but not in two non-cancer cell lines. Mechanistically, arginine withdrawal induces Activating Transcription Factor 4 (ATF4) expression, which drives de novo cysteine biosynthesis via the transsulfuration pathway. Treatment with the transsulfuration inhibitor propargylglycine abrogated the protective effects of arginine starvation and direct ATF4 stimulation with thapsigargin also suppressed ferroptosis. Thus, cysteine interconversion from methionine downstream of cystine import suppresses ferroptosis. These data suggest a mechanism by which ATF4 permits cancer cell evasion of tumor suppressive, non-apoptotic cell death. Inhibitors of ATF4 or transsulfuration should be evaluated for their ability to slow tumor growth and induce cancer cell ferroptosis in in vivo models.
Analyzing the Impact of Advanced Maternal Age and Inflammation on Pregnancy Outcomes
Keywords:  Department of Biology
Advanced maternal age (AMA)
maternal immune activation
pregnancy complications
inflammation
Thesis

Advanced maternal age (AMA; ≥ 35 years in humans) is associated with an increased risk of severe pregnancy complications, including miscarriages and stillbirths. These risks are also elevated in circumstances of infection and elevated inflammatory signaling in the mother. Given that older individuals frequently develop chronic inflammation that worsens with age, it is possible that the immune system may contribute to poor pregnancy outcomes in AMA mothers. This study characterized the immunological profiles of young and aged pregnant mice in order to identify the role of inflammation on AMA pregnancy outcomes. Older pregnant mice (aged 6–8 months) exhibited prolonged and elevated cytokine levels compared to young controls (aged 2–4 months) following mid-gestation challenges of either saline or lipopolysaccharide (LPS), a bacterial mimetic. Analyses of embryonic development from these pregnancies later demonstrated that the percentage of inviable, hemorrhaged or otherwise affected fetuses was significantly increased in litters from AMA dams. This effect tended to be exacerbated following a mild immune challenge by LPS. Finally, embryonic brains from AMA litters tended to exhibit reduced neural stem cell proliferation in the neocortex compared to those from control litters, and placentas from AMA dams tended to display greater degrees of necrosis than placentas from young dams. These findings not only highlight inflammation as a potentially relevant risk factor in AMA pregnancies but also implicate maternal age as a possible confounder in studies on maternal immune activation.
Anisotropic full-waveform inversion with pore pressure constraints
Keywords: Geophysics.

Anisotropy can arise as an intrinsic property of rocks (for example shales) and minerals (for example clay), but most commonly as an effective property of layered or fractured media. Anisotropy provides a better description of the subsurface and seismic wavefields. To include anisotropy in Full-Waveform Inversion (FWI), however, one needs to extend the search space and invert for not only a single velocity model but also anisotropic parameters that describe how velocity varies with direction. Sadly, there is often an ambiguity in determining whether a change in the seismic data recorded on the surface comes from a perturbation in velocity or anisotropic parameters in the subsurface. This means there may be a number of subsurface anisotropic models that, for a given objective function, t the observed data equally well. To address this uncertainty problem in anisotropic FWI, I constrain the inversion with bounds derived from a rock physics workflow that models the relationship between velocity and pore pressure. This workflow combines various sources of data such as well logs, drilling data, basin history, and shale diagenesis to build velocity templates which are consistent with our rock physics models and understanding of pore pressure behavior in the subsurface. In a 3D eld data application, enforcement of the derived constraints improves the final seismic image in terms of focusing and continuity of reflectors and better flattens the common image gathers we use to assess velocities. In addition, the resulting anisotropic velocity models are more physically plausible and better suited for subsequent exploration workflows such as pore pressure prediction and geo-hazard prevention.
Applications of atomic layer deposition for next-generation nanoscale devices
Keywords: Mechanical Engineering.

Atomic Layer Deposition (ALD) is a thin film deposition technique that has gained prominence in recent years due to its ability to synthesize highly conformal and uniform films, with precise thickness control and for a wide range of materials. This work explores how the unique properties of ALD films can be leveraged through novel nanofabrication processes to enable higher performance devices. First, a comprehensive characterization of the etch rates of 9 oxide ALD films in 20 wet chemicals and vapor etchants is presented, as knowing the films' etch rates and their compatibility with commonly used processing chemicals is crucially important when integrating them into nanofabrication processes. Second, a new process is described that, by taking advantage of ALD films' excellent properties as etch stop layers for vapor releases, allows the simultaneous release of suspended structures of varying sizes and arbitrary shapes with high accuracy. This so-called "sandbox" process can be incorporated into the fabrication of many kinds of devices, and has been successfully employed for aluminum nitride piezoelectric resonators, resulting in a record high figure of merit. Finally, the development of thermal accelerometers featuring ultrathin suspended platinum thermistors with thicknesses down to 8 nm is presented. Using plasma-enhanced ALD of platinum for the first time in a thermal accelerometer enables a 100x reduction in beam cross-section compared to previous work. Plasma treatments and nucleation layer dependencies of ALD platinum are investigated to further enhance material properties. Novel fabrication processes allow large cavity sizes of up to 500 μm depth and 4000 μm length, resulting in unprecedentedly high aspect ratios exceeding 100,000:1, which confer many benefits such as increased heating efficiency and decreased thermal time constants.
Applications of convex optimization in metabolic network analysis
Keywords: Electrical Engineering.

Twenty years ago, the first genome-scale metabolic network reconstruction of the cellular metabolism of an organism was published, shortly after the first genome was sequenced. From that time on, the ever-increasing advances in the high-throughput omics technologies have allowed for the comprehensive reconstructions of exponentially growing sizes. However, the vast amount of data can be a two-edged sword which makes many essential tasks computationally intractable. To overcome the demands of systems biology, even while they are outpacing Moore's law, faster computational techniques are needed to enable the current methods to scale up to match the progress of data generation in a prospective manner. In this dissertation, we go over several different areas of systems biology from flux coupling analysis to context-specific reconstruction and propose efficient computational methods for several tasks separately. Then we work towards a more holistic approach and discuss the idea of a canonical metabolic network reduction to reduce the number of reactions for any general task. In analogy to the concept of lossless compression in information theory, we will show that the well-known emergent redundancies of flux distributions are the key concept. Additionally, we will derive the minimum reduced metabolic network and prove a converse that any further reduction loses some information on the elementary modes.
Applications of Lagrangian field theory in the computational modeling of beam-wave interactions
Keywords: Electrical Engineering.

Modeling the non-linear interaction between intense charged particle beams and electromagnetic fields in beam-based radiation sources, from klystrons to free electron lasers, has historically been addressed using semi-analytical simulation tools. Through recent advances in manufacturing and materials science, we can now realize structures and interaction topologies which are vastly more complex than in current devices -- unintuitive configurations with the potential to overcome traditional limits in interaction efficiency and output power. These device concepts lie beyond the assumptions of semi-analytical models, however. Their multi-scale nature, spanning time scales from picoseconds to milliseconds, also renders them computationally intractable to model with more general, transient solvers (particle-in-cell codes). To address this issue, we have developed a steady-state solver which applies abstract concepts from Lagrangian mechanics, classical and quantum field theory and differential geometry to the concrete challenge of full-wave electromagnetic finite element analysis. Through this unique field theory perspective, we overcome several open problems in beam-wave modeling, from the interpolation of the current density from particle trajectories (where we demonstrate an 80 fold improvement in accuracy over existing state of the art approaches), to the revival of the traditional nodal finite element framework for the solution of electromagnetic fields. This approach is also computationally efficient, converging to the steady-state solution in less than ten iterations compared to the thousands to billions of time steps required by a transient solver.
Applications of metallic nanoparticles for in-situ combustion : delivery and enhanced performance
Keywords: Energy Resources Engineering.

The advantage of using nanoparticles to influence reaction kinetics in hydrocarbon reservoirs is two-fold: nanoparticles are better catalysts for oxidation reactions because of their large surface-area-to-volume ratio and have increased transportability through porous media because of their small size. In-situ combustion (ISC) is a thermal recovery method used to access light and heavy crude oil deposits by physically and chemically altering the oil in place. Success, among a host of factors, depends on the nature of oxidation and non-oxidative reactions and the combustion fuel. Metal nanocatalysts, specifically, can improve the process by providing a way to alter those critical parameters beneficially. This work explains why and how specific metal nanoparticles enhance heavy-oil ISC and develops a new method for the emplacement of those nanoparticles in porous media. The effects of seven different transition metal nanoparticles on Colombian, Venezuelan, and Mexican crude oil samples were investigated. Experiments were used to measure the change in burning characteristics with additives at two different length scales. At the small-scale, select nanoparticles decrease the apparent activation energy for combustion, change the limiting gateway reaction, make combustion fuel more reactive, increase fuel quality, and alter low-temperature oxidation products. During reactive flow, the improvements as mentioned above are critical to helping sustain combustion when excessive fuel deposition causes premature quenching. For ISC candidates that burn well, increased efficiency leads to greater oil production. Considering these benefits, emplacement of nanoparticles into the hydrocarbon system needs to be handled appropriately. The most critical feature of any transport mechanism is its ability to maximize catalytic surface area; however, due, in large part, to a lack of understanding of the fundamental science governing delivery and emplacement of nanoparticles on or near solid-liquid and liquid-liquid interfaces, this is a nontrivial undertaking. Therefore, a new method is developed in order to achieve the result mentioned above. The mechanism decreases particle interactions with other elements in the reservoir by encapsulating nanoparticles in the dispersed phase of an oil-in-water emulsion. The hydrophilic-lipophilic difference, a semi-empirical formulation, provides the means to calculate the temperature (phase inversion temperature) that the emulsion destabilizes and releases nanocatalysts in the pore space. Direct visualization and injection experiments confirm delivery efficacy and show that the technique delivers a relatively equitable distribution of nanoparticles to the porous medium.
Applying genome editing and genomics for novel cellular tracking and measurement
Keywords: Bioengineering.

The three projects comprising this thesis explore and apply genetic diversity to various biological processes. In the first project, I engineer updatable and diverse CRISPR-based sequence barcodes for lineage tracing applications. I demonstrate the potential of such CRISPR-based barcoding methods by illustrating the agreement between the fully known lineage of C. elegans and that obtained using dynamic sequence barcodes, delve into the challenge presented by sequence dropouts through a simulation-based approach, and underscore the technique's promise by establishing its information content. In the second project, I add a new tool to the CRISPR/Cas9 toolbox by exploring the genetic diversity of CRISPR systems and discovering IgnaviCas9, a Cas9 from a hyperthermophilic Ignavibacterium. IgnaviCas9 expands the temperature range at which targeted nucleic acid cleavage is possible, thus speeding the development of new biotechnological techniques. I demonstrate one such application by using IgnaviCas9 to deplete undesired amplicons during the amplification step of library preparation in sequencing workflows. In the final project, I enable the examination of how genetic diversity is created during the processes of sperm development. I apply microfluidic methods to capture and amplify DNA from single sperm cells. I then perform whole genome sequencing to understand selection processes during spermatogenesis.
An archaeology of europeanization : transnationalism, heritage, and communities in post-communist Albania
Keywords: Anthropology.

Albania, a European Union (EU) candidate country since 2014, has struggled with a turbulent post-communist period (1991-present) defined by civil unrest, political corruption, a struggling economy, and extremes in socio-economic inequalities (Elbasani & Šabić 2018; Abrahams 2015; Vickers & Pettifer 2013). The built environment of the entire Albanian landscape has held no exception to such social and political mayhem. Albania's heritage landscape in particular has been subject to diverging episodes of destruction and material manipulation, each dependent on current political needs and visions to enforce a national narrative of prosperity and democratic success. This dissertation is particularly concerned with Albania's process of Europeanization and cultural heritage's role within it. In this dissertation I argue that the Albanian government has been negotiating its cultural heritage, from its archaeological sites to its memorials and museums, in a dramatic and tumultuous process of heritage erasure, promulgation, and reconfiguration; yet, it is doing so not only as part of a need to create a new Albanian narrative, but as a response to growing international pressures to shape its socio-political system into one that is democratic to Western standards, economically thriving, and socially stable with tight political borders that protect Europe from a growing immigration crisis. Yet, as Albania's heritage landscape is altered, the communities that are connected to that landscape are impinged upon as well. While this dissertation explores how the Albanian government manages its material past within its ever-present Europeanization process, it also investigates the social consequences of such a heritage negotiation at the whim of international agendas and global tensions. Examining diverse types of heritage, including museums, memorials, religious buildings, and archaeological sites, as well as investigating heritage from several periods of Albania's past, be it the remains of its Roman or communist periods, this research underscores Albania's struggle with managing a past that has been largely defined by foreign occupations. Based upon more than 24 months of ethnographic fieldwork, my research shows that the valorization of cultural heritage in Albania comes almost exclusively from the outside, from international agencies and nation-states that the Albanian government holds in its highest esteem and may even seek to emulate. Ultimately, this dissertation argues that in order for Albania to shed a past of foreign dependencies, Albania will need to own its past.
Architectural Energetics for Byzantine Chancel Screen Construction: The Case of the Marzamemi II "Church Wreck"
Keywords:  Department of Civil and Environmental Engineering
chancel screens
Marzamemi
architectural energetics
Stanford University
School of Engineering
Byzantine empire
Architectural Design
religious architecture
Thesis

The present work introduces the first architectural energetics analysis of a Byzantine chancel screen from the Marzamemi II shipwreck. Emerging technologies in digital modeling present new opportunities for research in architecture, archaeology, and classical studies. The burgeoning technological resources of today's world, coupled with new 3D digital modeling programs, have the potential to ease the research of archaeological sites and artifacts. For this thesis I digitally recreated an “ideal” version of a Byzantine chancel screen (a religious architectural artifact) from the fragments recovered at the Marzamemi II shipwreck. This reconstruction represents the state of the artifact when it was loaded onto the ship after leaving the quarry approximately 1500 years ago.
Over the course of the 2018 field season, I took measurements, created sketches, and used digital Artec models of conserved and recently recovered architectural artifacts to begin re-creating their original shape prior to the wreck of the ship. These calculations can help the researchers at the Marzamemi Maritime Heritage Project to better understand the possibility of standardization within the recovered architectural elements. Following the 2018 field season, I used 3D models of the recovered chancel screen fragments to digitally produce the “ideal” chancel screen. During this time, I also explored the architectural energetics of the chancel screen in regards to religious symbolism, Byzantine economics, and labor estimates for the carving of one screen.