VictorJuiz/thesis huggingface dataset:
Pathway discovery and engineering of pharmaceuticals from medicinal plants [electronic resource]

It is estimated that a quarter of prescribed medicines from industrialized countries are inspired or directly derived from plant small molecules. Owing to their structural complexity, large-scale synthetic methods do not yet exist for most of these plant-derived pharmaceuticals. Instead, they are extracted directly from natural sources. Industrial farming of medicinal plants, however, is susceptible to pests, diseases, and climate fluctuations, which can result in unreliable supply. In addition, many medicinal plants are difficult to cultivate and are critically endangered. One promising alternative is the engineering of faster growing organisms, such as microbes or the development of chemoenzymatic processes to produce these natural products. However, knowledge about their biosynthetic pathways -- the collection of enzymes required to produce these molecules-- is limited. Traditionally, pathway discovery in plants has been slow due to the complexity and size of their genomes, proteomes, and metabolomes. However, in the last decade, due to recent technological advances, there has been a surge in genomic, transcriptomic, and metabolomic datasets, which have provided valuable insights into plant metabolism. Here, we will present our strategy towards accelerated pathway discovery in medicinal plants, combining these new insights and more recent advances in next-generation sequencing with high-resolution mass spectrometry and a plant (tobacco) heterologous expression platform. First, we will describe our efforts in characterizing the dirigent protein family in Arabidopsis thaliana, which we suspect are involved in the biosynthesis of many unknown plant natural products that may have interesting biological activities. Second, we will describe the discovery of six enzymes from the Himalayan Mayapple for the biosynthesis of the etoposide aglycone, a precursor to the clinically used anticancer agent, etoposide. With these discovered enzymes, we engineered a non-native plant to produce this compound and other non-natural derivatives that cannot be easily accessed by chemical synthesis. Third, we will describe the elucidation of enzymes for the biosynthesis of the ester side chain of homoharringtonine, a drug used in the treatment of chronic myeloid leukemia. Lastly, we present the identification of several biosynthetic enzymes involved in the production of colchicine, a medication for the treatment of gout. This work demonstrates the efficacy of our approach towards pathway discovery in non-model plants, and enables future efforts in the engineering of alternative biological platforms for the biosynthesis of these plant-derived pharmaceuticals.

Keywords: Chemical Engineering.
Advisor: Sattely Elizabeth primary advisor. Thesis advisor
Smolke Christina D. advisor. Thesis advisor
Spormann Alfred M. advisor. Thesis advisor
Pencils of fermat hypersurfaces and Galois cyclic covers of the projective line [electronic resource]

Let $Z$ be a smooth intersection of two degree $ Fermat hypersurfaces in $\mathbb{P}^n$, and let $\pi:X\rightarrow \mathbb{P}^1$ be the pencil of hypersurfaces containing $Z$. We show that the irreducible $\mathbb{Q}$ sublocal systems of $\mathbf{R}^{n-1} \pi_*\underline{\mathbb{Q} }_X$ arise from monodromy of the Galois cyclic covers of $\mathbb{P}^1$. This can be viewed as a higher degree analog of M.\ Reid's result on the correspondence between smooth intersection of two quadrics and hyperelliptic curves.

Keywords: Mathematics.
Advisor: Vakil Ravi primary advisor. Thesis advisor
Kemeny Michael advisor. Thesis advisor
Li Jun (Mathematician)
Perceptual and social realism in virtual reality [electronic resource] : the effect of immersion on children's psychological responses

This dissertation examined the potential effects of immersive technology, like virtual reality, (VR) on young children's everyday lives. An experimental study tested the effect of technological immersion (VR versus TV) on 4-to-6-year old children's inhibitory skills, approach behaviors toward an embodied agent, and their perception of the character as a live social actor. In addition, children's emotional distress, physical distress, visual perception of the characters, and enjoyment of the virtual environments were assessed.

Keywords: Communication.
Advisor: Bailenson Jeremy primary advisor. Thesis advisor
Hancock Jeff advisor. Thesis advisor
Obradović Jelena (Education professor) advisor. Thesis advisor
Reeves Byron
PetMe: Sharing Digital Pets, Building Real Collaboration Skills

Social-emotional learning (SEL) is critical for student success. We created PetMe, a tablet game for children ages 6-8, to provide much-needed instructional materials for schools. In this two player game, children take care of a shared pet. They learn how to navigate their different perspectives and empathize with the pet’s problems in an effort to collaboratively reach their shared goal of solving the pet’s needs. Along the way, the players are taught to express their points of view and work toward resolving conflicts.

Keywords: Tablet
Game
Children
Collaboration
Pet
Communication
Two-Player
Social-Emotional Learning
Learning Design and Technology
Graduate School of Education
Thesis
Petro-elastic interpretation of seismic impedances [electronic resource]

Success in petroleum exploration and production is closely linked to correct estimation of the properties of the subsurface. Yet, the state-of-the-art technology lacks a robust deterministic approach to integrate different physical measurements, especially if their scales are different (e.g., well versus seismic data). Such consistent integration can help in interpreting seismic data for as yet unknown petrophysical properties and conditions. I have created a new methodology to estimate the rock properties (porosity and clay content) at the seismic scale from the seismically-derived impedances: petro-elastic interpretation. The basic concept behind this methodology is a rock physics phenomenon known as self-similarity where both the P- and S-wave impedances depend on the same combination of the porosity and clay content. By examining well data, I have found that this effect often does not hold, hence allowing two elastic measurements to determine two petrophysical unknowns. This discovery allows me to go from the seismic-scale impedances to desired rock properties. I tested this methodology on a dataset from NW Australia, where the interpretation results, when compared to blind-test data, fell within acceptable error bars. The first step in this methodology is to connect two procedures: rock physics diagnostics and simultaneous seismic impedance inversion. Rock physics diagnostics is a method to find the rock physics model that quantitatively describes the measured well data. Simultaneous seismic impedance inversion uses the information from well and seismic data to obtain the elastic properties that satisfy both. The second step is to take the inversion results (P- and S- wave impedances) and interpret them together to obtain the porosity and clay content at the seismic scale. One implication of this methodology lies in the importance of S-wave velocity correction and prediction, highlighting its critical role in the accurate estimation of the subsurface properties.

Keywords: Geophysics.
Advisor: Mavko Gary
Levin Stewart A.
Zoback Mark D. advisor. Thesis advisor
Physics and applications of a plasma deflagration accelerator [electronic resource]

Pulsed, gas-fed plasma accelerators are known to operate in a mode that is characterized by ultra-high velocity, collimated plasma jets known as a ``plasma deflagration.'' Despite a degree of continuous scientific attention over several decades, both the basic underlying physics and the complex dynamics that contribute to the formation and evolution of these jets remains poorly understood. The high energy densities and inherently transient nature of these pulsed systems make for a challenging diagnostic environment, and offer an array of both physical questions and potential applications that are the focus of this dissertation. This work concerns the experimental investigation of several aspects of a pulsed plasma accelerator operated in the deflagration mode. Particular focus is given to physics governing the formation and subsequent behavior of the collimated outflowing jet, whereas prior studies have primarily engaged with the acceleration process in the inter-electrode region of the plasma gun. Three main diagnostics were implemented and are discussed, each with the aim of characterizing a specific feature of the plasma accelerator. First, an immersed probe was used to simultaneously measure multiple magnetohydrodynamic (MHD) and thermodynamic state variables at a single point in the plasma flow in order to experimentally test the MHD Rankine-Hugoniot model for plasma deflagrations and detonations. Spectroscopic methods were then applied to quantify the plasma density distribution in the near-field of the accelerator plume, using a high-resolution imaging spectrometer to spatially and spectrally resolve a transaxial slice of the plasma emission from the jet. A radial density profile was computed from the spatial variation of the observed spectral line broadening. A laser schlieren imaging apparatus was then developed, and combined with a high speed camera to capture the evolution of the plasma density structure within the jet during the entire discharge period. Finally, various applications of the deflagration-produced plasma jets were considered, including space propulsion, plasma-material interactions, and laboratory astrophysics. All three of the developed diagnostics were used, alone and in combination, to characterize the deflagration accelerator as applied to these areas. This work represents a comprehensive investigation of the detailed physics of a complex and practically useful plasma accelerator, and improves our theoretical understanding of its operation and performance.

Keywords: Mechanical Engineering.
Advisor: Cappelli Mark A. (Mark Antony) primary advisor. Thesis advisor
Edwards C. F. (Christopher Francis) advisor. Thesis advisor
Poehlmann Flavio advisor. Thesis advisor
Physiological and genetic requirements for water perception driving lateral root hydropatterning [electronic resource]

Water is necessary for all known forms of life. Due to their sessile lifestyle, land plants employ an array of physiological and developmental responses to enhance uptake of water from the environment and limit its loss in times of water deficit. These responses occur at several spatial scales of organization, including at the level of single cells, multicellular tissues, organs, and organ systems. Despite the importance of these acclimatory processes to plant survival, the mechanisms of water perception upstream of acclimation responses are poorly understood. To gain a better understanding of these processes, I performed experiments to examine the genetic and physiological basis for hydropatterning, a recently discovered developmental response to water availability. During hydropatterning, lateral root branches are induced in regions of the main root directly contacting sources of available water, and are inhibited in regions exposed to low water availability. I used hydropatterning as a model to understand water perception in plants using two experimental strategies. In my first approach, I asked whether developmental competence to respond to water was limited, and if so, what biological processes were required to establish competence. Through a combination of physiological and mathematical-modeling experiments, I revealed growth to be a requirement for competence, and demonstrated that growth-associated changes in tissue biophysical properties were predictive of future lateral root patterning decisions. In my second approach, I sought to identify genetic loci required for hydropatterning. I uncovered phenotypic variation in hydropatterning through a mutant screen and a survey of natural maize accessions, and identified a 1-Mb interval of the maize genome associated with this phenotype. I conclude with a discussion of how my findings will inform future studies on water sensing, and what key experimental and technological advances will be necessary to move this field forward.

Keywords: Biology.
Advisor: Long Sharon R. primary advisor. Thesis advisor
Ehrhardt David
Peay Kabir
Walbot Virginia
"Placing the history of advertising": A spatial history of advertising in modern Shanghai (1905-1949)

Directly inspired by Philip Ethington's proposal on "placing history", my dissertation offers a spatial approach to the history of advertising in modern Shanghai (1905-1949). Based on various materials (press, archives, photos, sketches, graphs, maps, trees), this spatial trend aims to shift the gaze from mainstream cultural approach (focused on representations visible on press advertisements) to a spatial and material approach of advertising, with a genuine concern for the physical aspects of advertisements. The first part (chapter 1 and 2) is devoted to mapping and measuring the populations and territories of advertising in Shanghai, both in the local press (Chinese newspaper Shenbao and British North-China Daily News), as well as within the city. The second part examines the actors who made and inhabited these spaces, namely the emerging advertising profession (chapter 3) and the actors involved in the production or consumption of advertised products (advertisers/manufacturing companies, brands/products, markets/consumers) (chapter 4). Chapter 5 is devoted to advertising “landscapes” - a term that I used as an operative concept to replace the overused, and often misused, notion of representation - in order to cover every dimension of advertisements (their physical environment at various scales, the copy surface, the discourses they carried). Chapter 6 offers to take advertising spaces as an ideal observatory for examining tensions, conflicts and other forms of relationships surrounding advertising, as well as a "laboratory" for inventing urban modernity – that is, new ways of conceiving and living the city in modern Shanghai. As spatial approaches are often blamed for “freezing” history, my dissertation eventually attempts to trace the circulations and rhythmic patterns between the printed and urban spaces, within and outside Shanghai (chapters 7 and 8). Beyond the "terrain", my dissertation strives to take advantage of the new resources available to historians in the digital age. The digital platform MADspace, which has been especially designed as a digital companion to this PhD project, makes the assumption that the digital ecology offers unexpected opportunities for renewing research questions and methodologies in the field of (Chinese, urban) history.

Keywords: actor
advertising
city
digital history
ENS Lyon
map
outdoor
press
space
spatial history
urban history
representation
rhythm
Shanghai
Thesis
Advisor: Henriot Christian
Benedict Carol
Plasmonic gold nanomaterials for medical diagnosis and biological imaging [electronic resource]

This thesis describes the development, optimization and application of plasmonic gold nanomaterials in medical diagnosis and biological imaging. Gold nanoparticles undergo unique localized surface plasmon resonances in the visible and near-infrared (NIR). Coupling of the scattering nanoparticle plasmon modes result in enhanced local electric field and NIR fluorescence emission rate, which can lead to NIR fluorescence enhancement (NIR-FE) under certain conditions. Here, the application of this NIR-FE effect is discussed in the context of protein microarray immunoassays. Multiplexed protein assays are constructed on the nanostructured plasmonic gold film that display up to 100-fold fluorescence enhancement and ~3 orders of magnitude extension of the protein detection dynamic range, compared to conventional assays on commercial substrates such as glass. Immunoassays performed on the plasmonic gold films afford more sensitive measurements of proteins over a broader dynamic range with higher signal-to-noise ratio. The aim of this thesis is to develop novel protein microarray immunoassays for biomedical diagnostics on the plasmonic gold platform to conquer some of the most challenging healthcare problems faced by global population. The clinical application of plasmonic substrates is demonstrated from the diagnosis of infectious diseases and the early detection of hypertensive heart diseases. The application of the plasmonic gold nanomaterials for sensitive imaging and detection of cellular proteins is also presented.

Keywords: Chemistry.
Advisor: Dai Hongjie
Cui Bianxiao advisor. Thesis advisor
Xia Yan
Plastic companions [electronic resource] : posthuman intimacy in twenty-first-century Latin America

"Plastic Companions: Posthuman Intimacy in Twenty-First-Century Latin America" examines how representations of gender expression and sexual practice in post-2000, Southern Cone literature interpolate the influence of technological advances on modern intimacy. "Plasticity" and "posthumanism" are two central, organizing principles of this research. Functioning as both noun and adjective, the word "plastic" refers to that which is easily shaped, but it can also signify something that gives shape, as in the case of plastic surgery. This bidirectional term—one that both gives and takes form—serves as a useful hermeneutic for reading posthuman intimacy in contemporary Latin American print and cinematic culture. By posthuman, I mean a way of understanding the irreversibly connected relationship between our species and a natural world that is rapidly being reshaped by technological interventions. This project is invested in both the flesh-and-blood impacts of these interventions and the symbolic influence of high-tech sexual allure on everyday intimacy. With a posthumanist perspective that shifts focus away from the human to highlight the agency of the rest of the material world, this analysis investigates how the literary expression of our growing reliance on technology reflects the more-than-human aspects of so-called "human" sexuality. From the shapely sex dolls in Ariel Magnus's Muñecas, to the thwarted, scalpel-sculpted ideals in Lucía Puenzo's XXY and Gabriela Cabezón Cámara's Romance de la negra rubia, and, finally, the fluid performances of online dating in Alberto Fuguet's Sudor—the plastic companions featured in this study demonstrate not only the malleability of humans as sexually desirable objects but also the elasticity of posthuman desire, which finds intrigue and satisfaction beyond the organic strictures of the species. The present dissertation also explores how narrative, itself, can be a technology of posthuman intimacy. One unifying feature of the archive is an explicit invitation to find these alternative forms of companionship desirable and actionable. These texts generate readerly complicity in taboo sexual intimacy by instilling knowledge of and perhaps appreciation for these once culturally marginalized relations. Each of the three chapters in "Plastic Companions" thus describes one formal feature that contributes to readerly complicity, naming plaesthetics, cyborg writing, and Grindr narrativity as the narrative attributes that distinguish these stories of posthuman intimacy. In summary, the project shows that the literary ramifications of integrating modern technology into Latin American stories of love and desire often undermine humanist depictions of intimacy and widen the pool of eligible significant others.

Keywords: Iberian and Latin American Cultures.
Advisor: Hoyos Ayala Héctor primary advisor. Thesis advisor
Daub Adrian advisor. Thesis advisor
Rocha Marília Librandi advisor. Thesis advisor
Plutonium Management and Disposition in the United States: History and Analysis of the Program

Signed in 2000, the Plutonium Management and Disposition Agreement between the U.S. and Russia required each nation to dispose of at least 34 metric tons of weapon plutonium. Nonetheless, the U.S. Plutonium Disposition Program still remains incomplete as of 2017. This thesis analyzes the failure of the Pu disposition program through the assessment of information from the scientific and technical literature, the U.S. government, and NGOs in order to answer the following question: Why has the United States been unable to implement its own policy as agreed to with Russia in the 2000 Plutonium Management and Disposition Agreement? The analysis revealed that the failure of the U.S. policy is primarily a consequence of placing uncritical faith in the U.S. Government’s ability to implement the MOX fabrication technology. The program was unsuccessful because a multitude of problems compounded, including structural organization and communication issues, a waste standard that constrained disposition options, fundamental misunderstandings of the technology by those in policy-making positions, insufficient appreciation for the challenges of transferring a plant design from France to the U.S. with regard to regulatory and procurement issues, an underdeveloped contractor base, political complexity that affected the funding profile, and the attempt to implement a program that did not align with the U.S. National nuclear fuel strategy. This thesis proposes that a broad-based, reorganized U.S. nuclear waste and weapon material disposition program should combine the plutonium disposition program and other U.S. nuclear waste disposal projects into a unified national strategy. This plan should be implemented by a single-purpose organization focused on disposal of the entirety of the Nation’s nuclear waste, including excess weapons plutonium.

Keywords: Center for International Security and Cooperation
Plutonium Management and Disposition Agreement
Spent Fuel Standard
plutonium
MOX
nuclear waste form
program management
nuclear security
Thesis
Advisor: Ewing Rodney