VictorJuiz/thesis huggingface dataset:
Development of a Human iPSC-based Model System for Functional Analysis of PPARγ Knockout in Patient-derived Cardiomyocytes Using CRISPR/Cas9

Diabetes is a devastating disease that affects over 400 million people worldwide. Most of those affected with diabetes have some degree of insulin resistance. Peroxisome proliferator-activated receptor gamma (PPARγ) is a key regulatory receptor often targeted by drugs such as Rosiglitazone to overcome insulin resistance, and plays a major role in cardiovascular health and metabolism regulation. This research aims to elucidate the mechanism underlying PPARγ function by knocking out the gene using CRISRP/Cas9 as well as by assessing the effects of Rosiglitazone treatment on cardiomyocytes. In this study, a human induced pluripotent stem cell (hiPSC) platform was utilized for the first time to successfully induce a PPARγ knock-out (KO) and allow for further study of the KO’s effect on cellular metabolic function in human cardiac cells. A CRISPR-based approach was employed to knockout PPARγ in an iPSC line obtained from healthy individuals. Successful KO was verified via TOPO screening and Sanger sequencing. These cells are currently being differentiated for further analysis. In parallel, cardiomyocytes treated with varying doses of Rosiglitazone were assayed for changes in gene expression and cell viability. These cells were characterized by measuring mRNA expression of PPARγ and related genes implicated in cardiovascular and metabolic regulation. qRT-PCR of these genes, including PPARγ showed a significant increase in mRNA expression in treated cardiomyocytes compared to controls. Importantly, these genes have been suggested to be regulated by PPARγ and to participate in control of cellular metabolic function. Therefore, analysis of their differential expression following Rosiglitazone treatment may provide insight into PPARγ-dependent regulation of cardiovascular health. These results contribute to the molecular and genetic understanding of PPARγ and Rosiglitazone treatment in development of cardiovascular diseases, as they show effects on key metabolic genes and cell function.

Keywords:  Department of Biology
Biology
CRISPR
Rosiglitazone
Diabetes
PPAR
Gene-editing
Stem-cell
Thesis
Advisor: Wu Joseph
Jones Patricia
Development of turbulence downstream of submerged aquatic vegetation [electronic resource]

Seagrasses modify the flow going through them by imparting drag on the flow, leading to significant mean shear at the canopy height. The lingering effects of the canopy have profound implications for propagule transport and sediment transport downstream. My results show the presence of four distinct downstream regions in unidirectional flows. These four regions are 1) the mixing layer region, 2) the transition region, 3) the decaying turbulence region, and 4) the boundary layer region. Through these regions, the velocity straightens from a mixing-layer profile towards a boundary layer profile, but the turbulence kinetic energy (TKE) takes a non-monotonic path. The remnant effects of the TKE generated by the canopy linger for up to thirty canopy heights downstream. In wave-current flows, a mean downward velocity emerges in the lee of the canopy. This downward velocity moderates the downward transport of TKE towards the bed. For larger waves, a phase-dependence of TKE emerges and mean recirculation is found. When the findings are implemented into a fruit transport model, the dispersal kernels of the fruit seem to collapse with the free-stream velocity, release height, and particle radius. In unidirectional flows, light particles are most sensitive to vertical turbulent fluctuations, while heavy particles are more sensitive to fluctuations in the horizontal velocity. For waves, the same holds true, but because of the mean vertical velocity, the fruit is not advected as far as the fruit in the unidirectional case.

Advisor: Koseff Jeffrey Russell primary advisor. Thesis advisor
Fringer Oliver B. (Oliver Bartlett) advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
Ouellette Nicholas (Nicholas Testroet)
Development of X-ray absorption diagnostics for gas-phase reacting flows [electronic resource]

Accurate experimental measurements are critical to the design and understanding of efficient combustion systems. While new heterogeneous combustion technologies such as Porous Media Burners (PMBs) have demonstrated favorable combustion properties including an extended lean flammability limit, low emissions, and wide dynamic power range, they also pose challenges for traditional experimental techniques. Because combustion occurs within a porous ceramic matrix, physical probes can disturb the combustion environment while engineering optical access becomes difficult. Further, data provided by existing methods is generally of insufficient spatial dimensionality to fully describe complex internal PMB physics. In this context, the development of new diagnostics that can provide measurements of relevant physical quantities non-intrusively, without optical access, and with high spatial resolution becomes a challenge in creating experimental datasets that improve fundamental physical understanding of PMB systems. In this work, a diagnostic for gas-phase reacting flows is developed based on the principles of X-ray computed Tomography (XCT) at clinical energies, and applied to three different systems of interest. Clinical fan-beam XCT is first applied to a turbulent gas-phase krypton jet, and it is shown that X-ray attenuation measurements can resolve krypton mole fraction within the jet in three dimensions with high quantitative accuracy. A cone-beam X-ray system is then used to image a krypton-diluted, premixed Bunsen flame via XCT. Simultaneous data series describing visual emission and X-ray attenuation are performed, and scanner noise trends are evaluated via both experiment and simulation. Comparison of experimental data to an axisymmetric simulation with detailed chemistry is demonstrative of both the utility and phenomenology of the X-ray attenuation signal as a density surrogate in reacting flow measurements. Effects of the krypton contrast agent on important combustion quantities such as flame speed and temperature are also evaluated. Finally, measurements of a porous media burner are performed with cone-beam XCT, and theory is developed to relate X-ray attenuation to gas-phase temperature. Using this method, experiments are performed to demonstrate temperature measurement of a krypton-diluted flame within the optically opaque porous ceramic matrix of the PMB. Temperature measurements in the gas phase are contrasted with direct thermocouple measurements, and the effect of imaging artifacts and experimental uncertainties is analyzed in detail.

Keywords: Mechanical Engineering.
Advisor: Ihme Matthias
Bowman Craig T. (Craig Thomas)
Eaton John K. advisor. Thesis advisor
Pelc Norbert J. advisor. Thesis advisor
Die Suche nach dem Glück [electronic resource] : Gottfried Keller's psychology of flourishing

Is it possible to live a flourishing life in modern post-industrial society? Self-cultivation has a rich and enduring history in humanistic discourse since the Renaissance. In the last century, however, "flourishing" has increasingly become the domain of the social sciences—psychologists and educators. This dissertation seeks to articulate how the humanities contribute to this vital cultural discourse. The project aims to integrate literary and social scientific models of flourishing into a cohesive framework through an interdisciplinary case study. It outlines Gottfried Keller's nineteenth-century model of human flourishing and demonstrates its pertinence to twenty-first century educational psychology. It argues that Keller prefigures key frameworks of contemporary psychological complexity. A close analysis of the novella cycle, "Die Leute von Seldwyla, " demonstrates that Keller's educational psychology prefigures key frameworks of contemporary psychological complexity, including adolescent development (Chapter I), resilience (Chapter II), attachment (Chapter III), and post-traumatic stress (Chapter IV). The first two chapters highlight the ongoing dialogue between literary and empirical approaches to individual growth. Chapter I situates Keller in the historical trajectory from organic vitalism in the Age of Goethe to the emergence of empirical psychology in the late 19th century, with close readings of "Pankraz der Schmoller" and "Frau Regula Amrain und ihr Jüngster" and parenthetical readings of Bildungs-narratives by Goethe and the Jena Romantics. Chapter II focuses on Keller's depiction of resilience and self-directed learning, demonstrating his uniqueness among his contemporaries, through analysis of "Romeo und Julia auf dem Dorfe" and "Kleider machen Leute" in the context of a survey of German, French, English, and Russian realism. The third and fourth chapters reevaluate the last two novellas of the "Seldwyla" cycle in light of Keller's educational psychology. Chapter III, focusing on "Das verlorne Lachen, " considers the mingling of romantic love and religion as analogous frameworks for spiritual meaning-making in modernity. Chapter IV traces Keller's portrait of trauma and the violence of history in "Dietegen." This project argues that Keller's educational psychology posits story-telling as the core prerequisite skill that enables flourishing in modern society and makes self-actualization democratically accessible.

Keywords: German Studies.
Advisor: Berman Russell A.
Damon William
Daub Adrian advisor. Thesis advisor
Starkey Kathryn advisor. Thesis advisor
Digital Attachments to Life After Death: Grieving in the Age of Technology

As technology continues to expand, so does the presence of digitization in society. With the ease and accessibility of digitization, individuals of Western society have begun to assume a virtual presence. The countless hours of curating online profiles have created digital shadows of real lives. If digital profiles become embedded with the “spirits” and memories of their users, what happens to their virtual existence after death? America’s cremation movement demonstrates society’s complex perception of life and death. As the scattering of ashes displaces a person, what becomes of the role of the body? What becomes the role of a virtual presence? Researchers have observed how the bereaved have used technology, but there is limited study of the implications of these digital tools. This thesis examines the role of technology on the ways in which society grieves. Case studies are analyzed to identify the patterns and characteristics of grieving in the age of technology. These first hand accounts from the bereaved support the thesis that digital profiles allow the bereaved to maintain a connection to the departed, and social networks help them realize the impact the deceased had on others. However, some of the bereaved believe that when the person is gone, so too should their profile fade. If digital profiles prolong the relationship between the deceased and the bereaved, is the ability to visit the deceased online helpful to the bereaved? Through meta-analysis of psychology studies, the innate attachment style of the bereaved is the essential marker for the value of the digital presence of the deceased. By Freudian logic, social media profiles would inhibit successful mourning as they prolong detachment. However, according to Bowlby and the continuing bonds theory, digital profiles can be used as helpful tools to reconstruct a relationship with the deceased.

Keywords:  Department of Science
Science Technology and Society
Stanford University
grief
bereavement
digital media
profile
chatbots
death
evolution of mourning
cremation
virtual afterlife
grief work
continuing bonds
Thesis
Advisor: Kieschnick John
Sato Kyoko
Digital Editing Theory in Practice: Matthew Parker’s A Testimonie of Antiquitie

This thesis examines theoretical issues in the field of digital scholarly editing, and the execution of that theory through the creation of a digital edition of Archbishop Matthew Parker's 1566 book "A Testimonie of Antiquitie".

Keywords:  Department of English
Department of English
scholarly editing
matthew parker
archbishop parker
parker
digital humanities
digital editing
digital edition
testimonie of antiquitie
old english
anglo-saxon
early print
Thesis
Advisor: Treharne Elaine
Albritton Benjamin
The digital learning ecosystem [electronic resource] : finding a path toward innovation in a land of stagnation

This dissertation seeks to explain whether and how technology could be better utilized to support learning by underserved students. It affords readers with actionable information about optimizing technology to support learning by underserved students in US public schools. The sum total of these learnings, read against the backdrop of our history, tells a grim story about the likelihood of an equitable school system fueled by technology. While this illusion plays a role in structuring the conversation about of what is possible in American education, in reality, the potential for technology to systemically improve equitable access to high quality education is profoundly limited by the constraints of our fundamentally broken school system.

Keywords: Education.
Advisor: Goldman Shelley
Garcia Antero advisor. Thesis advisor
McDermott Ray (Raymond Patrick)
Digitally-assisted if-sampling ADC with background-calibrated dynamic distortion compensation [electronic resource]

Modern digital-beamforming phased-array systems enable cost-efficient common technology platforms that can be quickly deployed in many airborne or ground radar and communication applications. At the heart of the phased array receiver chain, multi-channel IF-Sampling Analog-to-Digital Converters (ADCs) serve the important purpose of down-converting the Intermediate Frequency (IF) signal to baseband and digitizing it for post-processing. The main design challenge of such ADCs is maintaining a good linearity performance across a wide input signal bandwidth while minimizing power consumption. In this thesis, we present an IF-Sampling ADC that consumes less power in the performance-limiting frontend and leverages the power of modern digital technology to post-correct the signal distortion in the digital domain. To satisfy the requirement of the target phased-array system, the ADC converts signals with 8-bit resolution at 1.25 GS/s sample rate. Our digital post-distortion filter uses a compact, derivative-based dynamic distortion model and enables ADC SFDR improvements of 10 dB for 2.5 GHz inputs. This ADC is the first to demonstrate correction model update in the background, in order to adapt to environmental variations (e.g., temperature variation). This continuous background calibration is enabled through a low sampling rate, on-chip auxiliary ADC that acquires high-linearity reference samples in real-time. Temperature sweeps from 10 °C to 80 °C confirm the scheme's robustness.

Keywords: Electrical Engineering.
Advisor: Murmann Boris primary advisor. Thesis advisor
Horowitz Mark (Mark Alan) advisor. Thesis advisor
Wooley Bruce A.
Digitized Cultural Production and Its Effects on Diversity and Innovation in Popular Music

Internet technologies, from Napster to Spotify, have changed the musical tastemaking process dramatically over the past fifteen years. Popular narrative assumes that these platforms have democratized musical tastemaking by diminishing major record labels’ monopoly over mass distribution. This same narrative predicts that the democratic forum afforded by these platforms should foster diversity and innovation in popular music, relieving us from the typical formulaic, standardized fare. But is this really true? Have these platforms enabled democracy, or have technology companies usurped the hegemonic power that major labels once held? Furthermore, have these new platforms diversified popular music and eliminated barriers to entry for marginalized artists, or do these platforms hold biases of their own? By conducting interviews with top executives, and mapping trends in key indicators of diversity and innovation across Billboard charts, viral charts, human-curated Spotify charts, algorithmic recommendations, and record label rosters, I examine the impact of digitized tastemaking on popular music. In my interviews, I found that music executives unanimously sense a loss of power, but are conflicted about the effect of streaming platforms on diversity and innovation. They remain skeptical of streaming as a democratic tool, fearing that streaming statistics can be manipulated, and that online platforms may advantage certain artists and consumers over others. In my statistical analysis, I find mixed results: increased representation for specific demographics (Asian men, Scandinavian bands, and openly gay performers), but decreased representation for others (African-American, Hispanic, and Female performers). Biases within Internet communities, curators, and algorithms, have created barriers, rather than eliminated them, for certain artists. Most notably for Female artists, representation appears to decrease significantly as labels rely more on streaming and social media statistics. Innovation—measured by number of genres represented, as well as standard deviation of tempo and chord structures—has increased in the 2010’s, but has yet to fully recover from massive declines in the 2000’s, which are likely linked to risk-averse scouting required by dramatic declines in music revenues. Meanwhile, the types of innovation most rewarded by the Internet, including shock-value and aggressive self-meming, are considered by some to be a step backward in product quality.

Keywords:  Technology and Society
Music
Diversity
Innovation
Stanford
Science Technology &amp; Society
Thesis
Advisor: Christin Angèle
Disavowing attachments [electronic resource] : maladjustment in trans[masculine] thought

"Disavowing Attachments" identifies and thinks with forms of trans maladjustment in twentieth and twenty-first century literature and theory. Whereas work in transgender studies has long emphasized agency, self-sameness, and contentment in order to untangle trans identity from mental illness, I argue that this tactic has limited trans studies' ability to respond to the very lives and texts that early trans scholars sought the authority to interpret. Consequently, this project returns to texts central to the field—including the Brandon Teena archive, the secluded life of early trans man Michael Dillon, and Sandy Stone's inaugural manifesto—in order to argue for and model trans theory that thinks with, rather than against, the bad feelings that persist in transphobic discourse and trans cultural production alike. To that end, the project opens with an account of the entanglement of trans and disability history in the nineteenth to twentieth-century United States, in order to put forward maladjustment as a resource for doing trans theory. Each subsequent chapter meditates on how prevalent, disavowed narratives of trans maladjustment—the depressed transsexual, the raped transgender man, and the trans recluse—allow for imaginative routes around old theoretical impasses, as well as offer a version of trans theory that is more able to engage with other minority discourses, especially feminist, disability, and critical race theory, to which it is indebted and indelibly attached.

Keywords: Modern Thought and Literature.
Advisor: Moya Paula M. L. primary advisor. Thesis advisor
Jain Sarah S. Lochlann
Ngai Sianne advisor. Thesis advisor
Discourse and Deceit: Native Advertising, Influencer Marketing, and the Increasing Corrosion of Public Trust

This thesis analyzes the deceptive promotional practices of native advertising and influencer marketing, examining how existing literature on the former may be applied to the understudied latter. The thesis argues that both practices engender public skepticism towards public discourse, thus undermining democratic self-governance. Building on this argument, the thesis suggests influencer marketing may be an even more pernicious threat to public discourse than native advertising by virtue of undermining public trust not only in media content but also in the common person. Turning to the issue of regulation, the thesis argues that given the severity of the threat these deceptive promotional practices pose to public discourse, the Federal Trade Commission both can and should take a significantly more prescriptive regulatory approach. To conclude, the thesis emphasizes the dangers of failing to adequately address novel forms of commercial deception as technology advances.

Keywords:  Department of Communication
marketing
deception
influencer
ethics
native advertising
FTC
regulation
Thesis
Advisor: Glasser Theodore
Discovery of a novel protein complex essential for toxoplasma effector transport into the host cell [electronic resource]

The ability of Toxoplasma to infect and successfully manipulate its host is dependent on its ability to transport "GRA" proteins that originate in unique secretory organelles called dense granules into the host cell in which they reside; however, the essential transport machinery has not been identified. GRAs have diverse roles in Toxoplasma's intracellular lifecycle including co-opting crucial host cell functions and proteins such as the cell cycle, c-Myc and p38 MAP kinase. To identify proteins necessary for the transit of GRAs across the parasitophorous vacuole (PV) membrane, we screened mutants defective in c-Myc upregulation for their ability to export GRA16 and GRA24 to the host cell nucleus as well as modulate host cell processes associated with this and other proteins. This led to the discovery that novel proteins MYR1 (Myc regulation 1), MYR2, and MYR3 play a crucial role in translocation of a subset of GRAs into the host cell. MYR1 is cleaved by ASP5 into two fragments that interact with each other in a disulfide-dependent manner and associate with the PV membranes; interestingly, cleavage is dispensable for MYR1 function. MYR3 likewise associates with PV membranes and co-localizes and interacts with MYR1. Finally, MYR2 is secreted into the PV and associates with PV membranes. Overall, MYR1-3 are the first identified membrane-localized components in Toxoplasma that are required for effector transport across the PVM, and may constitute a novel protein translocon that is essential for hijacking host cell pathways.

Keywords: Microbiology and Immunology.
Advisor: Boothroyd John C. primary advisor. Thesis advisor
Bogyo Matthew
Carette Jan
Einav Shirit advisor. Thesis advisor
Pringle John R.
The disease of commerce [electronic resource] : yellow fever in the Atlantic world, 1793-1805

In 1793 an outbreak in Saint Domingue (modern Haiti) grew into a global crisis. The violent illness swept through the West Indies, the United States, and southern Europe traveling as far as Livorno, Italy. The scourge was a viral, hemorrhagic fever known as yellow fever. This outbreak was not the first attack of yellow fever, but it was the largest up to that date. The pandemic lasted twelve years (1793-1805) and killed tens of thousands of people situated on the Atlantic rim. This dissertation is the first study of the crisis from a global perspective. While taking a broad view, it centers on the United States and explores the impact of yellow fever on American trade, politics, and diplomacy.

Keywords: History.
Advisor: White Richard
Gould Eliga H. advisor. Thesis advisor
Winterer Caroline