VictorJuiz/thesis huggingface dataset:
Dynamics of Geyser systems, El Tatio, Atacama

Geysers are hot springs that periodically or episodically erupt liquid water and vapour. They are uncommon because they require a combination of abundant water recharge, magmatism to supply heat and silica, and fractures or cavities to trap rising multiphase fluids. To better understand the dynamics inside of geyser conduits, interaction between geysers, properties of the surrounding rock, and the origin of the fluid, we collected data in the El Tatio geothermal field, Atacama Desert in Chile, during October 2012 and 2014. We monitored eruption intervals, durations, and discharge through measurements of pressure and temperature within geyser conduits. At the surface, we collected samples for petro-physical and geochemical analysis. We identify that geyser systems evolve over time, including changes in the interval between eruptions, development of new thermal features, and interactions between geysers. Though geysers erupt with different styles, we recognize some common features: the conduit recharges with liquid during the quiescent period, bubbles enter the conduit before eruptions, and eruptions occur when water boils in the upper part of the conduit. Eruptions are triggered by the episodic addition of steam coming from depth suggesting that the dynamics of the eruptions are dominated by geometrical and thermodynamic complexities in the conduit and deeper reservoir. The depth where heat is added dictates the eruption style: conduits with deeper heat input are more likely to show pre-play or minor eruptions. Further evidence favoring the dominance of internal processes in controlling periodicity is also provided by the absence of responses of the geyser to environmental perturbations (air pressure, temperature and Earth tides). The thermal features interact by pressure transmission through subsurface permeable layers, which is consistent with permeability measurements of sinter in the lab. Sinter closely resembles vesicular volcanic rocks and other material formed by precipitation in geothermal settings such as travertine. We find that in fresh geyserite sinter the pore structure, and thus hydrological and geophysical properties, is controlled by the distribution of microbial matter. The geochemistry of water indicates mixing of andesitic and meteoric water. Steam separation, and dilution underground occurs as fluids rise to the surface. Evaporation at the surface seems to affect thermal pools, fountain geysers, and water in discharge channels.

Advisor: Manga, Michael
Computational approaches to understanding the genetic architecture of complex traits

Advances in DNA sequencing technology have resulted in the ability to generate genetic data at costs unimaginable even ten years ago. This has resulted in a tremendous amount of data, with large studies providing genotypes of hundreds of thousands of individuals at millions of genetic locations. This rapid increase in the scale of genetic data necessitates the development of computational methods that can analyze this data rapidly without sacrificing statistical rigor. The low cost of DNA sequencing also provides an opportunity to tailor medical care to an individuals unique genetic signature. However, this type of precision medicine is limited by our understanding of how genetic variation shapes disease. Our understanding of so- called complex diseases is particularly poor, and most identified variants explain only a tiny fraction of the variance in the disease that is expected to be due to genetics. This is further complicated by the fact that most studies of complex disease go directly from genotype to phenotype, ignoring the complex biological processes that take place in between. Herein, we discuss several advances in the field of complex trait genetics. We begin with a review of computational and statistical methods for working with genotype and phenotype data, as well as a discussion of methods for analyzing RNA-seq data in effort to bridge the gap between genotype and phenotype. We then describe our methods for 1) improving power to detect common variants associated with disease, 2) determining the extent to which different world populations share similar disease genetics and 3) identifying genes which show differential expression between the two haplotypes of a single individual. Finally, we discuss opportunities for future investigation in this field.

Advisor: Pachter, Lior
Zaitlen, Noah
High-Aspect Ratio Protein-Based Carriers for Delivery Applications

The work described in this dissertation aims to advance the early detection and therapeutic treatment of cancer. To do this, we seek to utilize protein-based carriers to deliver increased concentrations of cargo (imaging agents or drugs) to the tumor site that will allow for improved detection of early cancer states and/or a more focused delivery of therapeutics to the tumor./nDescribed herein is the production, characterization, and functionalization of two high-aspect ratio carriers: nanophage (Chapters 2-4) and a truncated IDP monomer (Chapter 5). To our knowledge, these structures have not yet been demonstrated for use in cancer delivery applications. In this work, a large emphasis was placed on the optimization of protein production and biochemical functionalization of these scaffolds for delivery applications./nThe nanophage scaffold was explored for its genetic and chemical amenability to incorporate targeting moieties (scFv and cRGD, respectively) onto the phage coat proteins to create an “active targeting” agent that would facilitate cancer cell uptake (Chapter 4). Although the chemical incorporation of cRGD onto the nanophage was met with success, recent literature studies suggest that incorporation of targeting ligands onto a scaffold may not necessarily improve the nanocarrier accumulation in the tumor environment. Therefore, to obtain a better understanding of how the physical properties of a nanocarrier affect overall tumor accumulation, in vivo biodistribution studies were employed. Here, the proficiency of different carrier morphologies (sphere, disk, rod and disordered strand) to passively accumulate in the tumor environment was compared using glioblastoma tumor models. Moreover, in silico simulations and in vitro diffusion assays were used to further evaluate how the shape and size of these carriers might affect extravasation through a pore (Chapter 6).

Advisor: Francis, Matthew B.
The tradition of Greek and Latin incantations and related ritual texts from antiquity through the medieval and early modern periods

Based on a large corpus of texts, presented in catalogue form as an appendix, I analyze the tradition of a set of Greek ritual utterances defined here as incantations from classical antiquity through the early modern period. The foci are late antiquity and Byzantium, with perspectives forwards into modern Greece and a consideration of the influence of Greek material on Latin incantations in the medieval West. The textual evidence is organized typologically, first by intended purpose (healing and apotropaic; erotic; cursing and other aggressive functions), then by internal compositional motifs. This typology is intended to facilitate the tracing of continuity and change. I argue that incantations, and related ritual practices for erotic compulsion and cursing, represented precious traditional knowledge for those who chose to make use of them. This knowledge in turn was not passively received but rather selectively transmitted, augmented, and adapted for maximum relevance and efficacy in the contemporary context of use. The backbone of the tradition as a whole is a broad and diverse circulation of technical literature in the form of practical recipes, intersecting with and reinforced by popular oral transmission, in which learned practitioners of medicine, and some ecclesiastics, took an occasional interest.

Advisor: Mavroudi, Maria
Enantioselective Construction of C-N and C-C Bonds via Chiral Anion Phase-Transfer Catalysis

The ability to control absolute stereochemistry is a powerful tool in organic synthesis. Given the utility of enantiopure molecules in a number of industries, the pharmaceutical perhaps most prominent, many research efforts have focused on asymmetric catalysis. Recently, the Toste Group has developed and implemented a chiral anion phase-transfer strategy to achieve high enantioselectivity in a number of transformations. This thesis describes new reactivity discovered within this manifold and also discusses the design and synthesis of new phase-transfer catalysts to improve enantioinduction./nChapter 1 details an asymmetric aminocyclization reaction of tryptamine derivatives enabled by chiral anion phase-transfer of aryldiazonium salts. The immediate products, C3-diazenated pyrroloindolines, can be converted directly to cyclotryptamine natural product derivatives, providing an efficient entryway into a complex scaffold that has been previously accessed by much longer synthetic sequences./nChapter 2 is a natural extension of the work presented in Chapter 1 and describes an enantioselective α-amination of activated ketone derivatives, again employing aryldiazonium salts as aminating reagents. Obtaining high enantioselectivity initially proves to be very difficult, as use of our traditional library of BINOL-derived chiral phosphoric acids leads to poor enantioinduction. Eventually, we overcome this challenge through the design and synthesis of a new library of chiral phosphoric acids, specifically those derived from a 1,1′-binaphthyl-2,2′-diamine (BINAM) backbone. Chapter 2 also presents potential advantages of our methodology over more commonly used α-amination reactions that utilize dialkyl azodicarboxylates./nChapter 3 discusses the use of aryldiazonium salts in a more traditional role as cross coupling electrophiles. By merging chiral anion phase-transfer and palladium catalysis, we report an enantioselective Heck-Matsuda arylation of cyclic olefins. Through the process of reaction optimization, we observe counterion dependent reactivity and are ultimately able to avoid the formation of undesired olefin isomers by judicious choice of phosphate. While chiral anions have almost exclusively been used to optimize enantioselectivity, this result indicates that counterions can also be used to modulate chemical reactivity in transitional metal catalyzed processes.

Advisor: Toste, Dean F
A Spectroscopic Investigation of Photoelectrochemical Reactions at the Semiconductor - Electrolyte Interface for Artificial Photosynthesis

The mechanism of water oxidation to molecular oxygen at the surface of strontium/ntitanate, a representative transition-metal oxide photocatalyst, was investigated/nusing ultrafast pump-probe spectroscopy and accompanying characterization methods./nThe dependence of the rate of initial charge transfer on applied potential was investigated/nwith transient absorption spectroscopy, revealing a phenomenological transfer coefficient/nfor this single step of the multi-step water oxidation reaction. Time resolved/ninfrared spectroscopy provided the first direct evidence of the molecular character of the/nfirst intermediate to be a titanium-bound oxyl radical, and revealed interfacial Fano coupling/nbetween the electrolyte, surface species, and catalyst electronic continuum. Further/nwork combining both transient absorption and time-resolved mid-infrared spectroscopy/nexposed a minimum of three distinct surface states at the strontium titanate surface,/nproviding insight into the rich chemistry mediated at the catalyst surface. These results/nhighlight the intricacies of charge transfer at the surface of these promising materials,/nprovide insight into an important but difficult reaction necessary for any artificial/nphotosynthetic system, and offer a generalizable paradigm for considering heterogeneous/nphotochemistry. Finally, preliminary groundwork was done to uncover the mechanism/nof the carbon dioxide reduction half reaction in a novel inorganic-biological bacterial/nsystem with potential to produce green chemicals such as carbon-neutral liquid fuels.

Advisor: Harris, Charles B
Strange and Unstable Fabrication

In the 1950’s a group of artists led by experimental composer John Cage actively engaged chance as a means to limit their control over the artworks they produced. These artists described a world filled with active and lively forces, from the sounds of rain to blemishes in paper, that could be harnessed in creative production to give rise to new aesthetics and cultivate new sensitivities to the everyday. This approach to making was not simply act of creative expression but active attempt at creative expansion—a way of submitting to a world of creative forces beyond the self for the sake of seeing, hearing, or feeling things anew. I use these practices as a lens to reflect on the way human-computer interaction (HCI) researchers think about and design for making, specifically as it relates to the present day “maker movement.” I focus on how the design of digital fabrication systems, like 3D printers, could make room for creative forces beyond the maker and why such modes of making are worth considering in HCI research. Since digital fabrication technologies have catalyzed the maker movement and are often described as key instruments for “democratizing” manufacturing, this project joins broader efforts to reflect on values in maker technology as a means of expanding the design space of digital fabrication in ways that could potentially increase the diversity of participants associated with the movement./nBy weaving through post-anthropocentric theories of the new materialisms, design practice, art history, and HCI, I contribute a theory of making that accounts for the creative capacity of nonhumans as well as design tactics to make room for nonhuman forces in the design of digital fabrication systems. I argue that nonhumans exert material-semiotic forces upon makers that shape their perspectives on stuff and culture in tandem. I then suggest that tools that are both strange and unstable create a space for makers to perceive and work with these forces in ways that honor the unique life and agency of nonhuman matter. As a whole, this work adds dimensionality to HCI’s existing focus on making as a process of self-expression by suggesting new design territories in fabrication design, crossings between critical reflection and creative production. I close this work by speculating on how tools that trade control, mastery, and predictability for chance, compromise, labor, and risk could become valuable within a broader landscape of making.

Advisor: Ryokai, Kimiko
Three Essays on Legitimacy and Organizational Outcomes

This research demonstrates that CEO dismissal can be one form of activism utilized by a board of directors against CEOs’ prior records of violating institutional logics (i.e., cultural beliefs, norms, and assumptions about appropriate conduct) especially during poor performance. To this end, it examines two organizational outcomes of CEO dismissal and post-dismissal strategic changes in large U.S. Fortune companies between 1984 and 2007. During this period, the field of large firms was characterized by the rise of a shareholder-value logic, in which maximizing shareholder returns was the ultimate goal of the firm and corporate refocusing and employment downsizing were appropriate and necessary means to that end. According to event-history analyses, poor performance generally led to an increase in the CEO dismissal rate, but this effect was even stronger for CEOs who were reluctant to refocus and downsize during their tenures in the position. Moreover, when their predecessors were dismissed, new CEOs were more inclined to refocus and downsize, especially during their early tenures. These results indicate that when firms deviating from logics perform poorly, directors attribute the performance problem to the deviation itself, and thus seek the removal of the CEO as a means of strategically reorienting towards prevailing logics. This study contributes to institutional theory and upper echelon research.

Advisor: Haveman, Heather
Audio Hashprints: Theory & Application

We rely heavily on search engines like Google to navigate millions of webpages, but a lot of content of interest is multimedia, not text data. One important class of multimedia data is audio. How can we search a database of audio data? One of the main challenges in audio search and retrieval is to determine a mapping from a continuous time-series signal to a sequence of discrete symbols that are suitable for reverse-indexing and efficient pairwise comparison. This talk introduces a method for learning this mapping in an unsupervised, highly adaptive way, resulting in a representation which we call audio hashprints. We will discuss the theoretical underpinnings that determine how useful a particular representation is in a retrieval context, and we show how hashprints are a suitable representation for tasks requiring high adaptivity. We investigate the performance of the proposed hashprints on two different audio search tasks: synchronizing consumer recordings of the same live event using audio correspondences, and identifying a song at a live concert. Using audio hashprints, we demonstrate state-of-the-art performance on both tasks.

Advisor: Morgan, Nelson
Chip-Scale Lidar

The superiority of lidar compared to radio-frequency and ultrasonic solutions in terms of depth and lateral resolution has been known for decades. In recent years, both application pull such as 3D vision for robotics, rapid prototyping, self-driving cars, and medical diagnostics, as well as technology developments such as integrated optics and tunable lasers have resulted in new activities./nPulsed, amplitude-modulated continuous-wave (AMCW), and frequency-modulated continuous-wave (FMCW) lidars can all be used for ranging. The latter option enables excellent depth resolution at the micron level. Achieving this level of performance is contingent on a precision light source with accurate frequency modulation. This thesis presents a fully integrated solution realizing an electro-optical phase-locked loop (EO-PLL) fabricated on separate complementary metal-oxide-semiconductor (CMOS) and silicon-photonic wafers interconnected with through-silicon vias (TSVs)./nThe system performs 180,000 range measurements per second, with a root-mean square (RMS) depth precision of 8 μm at distances of ±5cm from the range baseline increasing to 4.2 mm RMS error at a range of 1.4 m, limited by the coherence length of the laser used in these experiments. Optical elements including input light couplers, waveguides, and photodiodes are realized on a 3 mm by 3 mm silicon-photonic chip. The 0.18 μm CMOS application-specific integrated circuit (ASIC) of the same area comprises the front-end trans-impedance amplifier, analog electro-optical PLL, and digital control circuitry consuming 1.7 mA from a 1.8-V supply and 14.1 mA from a 5-V supply. The latter includes 12.5 mA bias current for the distributed Bragg reflector (DBR) section of the tunable laser./nAlso presented in the thesis is a novel dual mode lidar that combines FMCW and chirped-AMCW operation to simultaneously achieve precision depth resolution and a longer operating range not limited by Laser coherence length.

Advisor: Boser, Bernhard E
Essays in the Value of Intermediaries in the Real Estate Market

The thesis consists of two chapters on real estate economics./nIn the first chapter, I study the impact of intermediaries in the real estate transactions. In many markets, intermediaries collect a substantial amount of commission in exchange for their expertise. Real estate is a prominent example—Americans paid more than $60 billion for real estate brokerage services in 2014. In this paper, I find a significant positive relationship between listing agents with greater recent experience and sales price, which is entirely driven by the sorting of more experienced agents into better houses. Once both observed and unobserved house characteristics are controlled for, there is no significant effect of experienced listing agents on average sales price. However, I present a novel finding that there is a significant negative relationship between recent listing agent experience and the variance of the sales price, which means that experienced listing agents add value to risk- averse sellers. Moreover, I investigate the mechanism that drives this negative relationship. Looking at individual performance, I show that a listing agent’s past performance predicts his future performance, and that good past performance leads to more listings in the future. The relationship is driven by the survivorship of better agents over time rather than the accumulated expertise of the agents. The channel is consistent with survivorship bias and decreasing returns to the number of listings for listing agents, similar to Berk and Green (2004)[8]./nIn the second chapter, I geocode a rich real estate repeated sales dataset and map each property to its school district and neighborhood. I study how big data algorithms differ from OLS regression in predictive power and how robust those algorithms are to data stratification. I find that it is computationally expensive for the random forest algorithm to use step functions to approach the linear data generating process. Once there are fewer predictors, the RF algorithm outperforms other algorithms. This is robust to different model specifications. In addition, the random forest algorithm provides similar results under different stratifications. I also study the effect of keywords on sales price and how informative they are in predicting sales price. I find that certain keywords can be valuable in explaining variation in the data but have insignificant impact on the average sales price, suggesting that the interaction between such keywords and other house features together should be considered when we specify our models. Lastly, I am able to exploit cross time variation in school academic performance index to identify the effect of school quality on house prices controlling for neighborhood fixed effect. I find school quality has a robust significantly positive effect on property sales price.

Advisor: Wallace, Nancy
DellaVigna, Stefano
Enchanting Disciplined Selves and Secular Publics: Ethics and Politics in a Mexican Charismatic Christian Brotherhood

Drawing on 17 months of ethnographic research, Enchanting Disciplined Selves and Secular Publics examines everyday attempts of a brotherhood of charismatic Christian businessmen in Mexico to reconceive of what it means to be religious and what it means to be secular. This Christian brotherhood adopts a hybrid organizational identity that allows its members to operate on both sides of the religious/secular divide. In examining the brotherhood’s quest for a more potent relationship with the Holy Spirit than those of conventional religion the dissertation shows how a brother’s quest for experience and evidence of God’s supernatural intervention in the details of everyday life serve as a means of methodically scrutinizing, evaluating and exhorting the self. The dissertation also shows how the brotherhood’s distinction from “religion” enables brothers to make use of the meaning-laden character the “secular” to reclaim and celebrate the Christian origins of the concept. Growing numbers of scholars theorize co-constitutive relationships between the religious and the secular; this dissertation examines public actors’ attempts to wrestle with these nebulously intertwined relationships on the ground.

Advisor: Riley, Dylan J