VictorJuiz/thesis huggingface dataset:
Regulatory mechanisms of the anti-cancer cGAMP-STING pathway
Keywords: Medicine.
Biochemistry.

Throughout our lifetimes, our bodies encounter a plethora of threats on the cellular level, including pathogen infection, cellular damage, and the development of cancer. When these threats are not properly detected, they can lead to serious health problems, including death. Thankfully, our cells are pre-programmed with an array of innate immune pathways that can quickly respond to threats by detecting specific molecular danger signals that indicate a threat is present. Of these innate immune pathways, the cGAMP-STING pathway is on the forefront of the immune response due to its ability to detect mislocalized double stranded DNA (dsDNA). Since mislocalized dsDNA is a danger signal nearly ubiquitous with cellular threats, the cGAMP-STING pathway is essential for responding to most threats, including pathogen infection, cellular damage, and cancer. Given the extensive role of the cGAMP-STING pathway in defending against threats, regulation of the pathway is crucial to ensure its proper function. In this work, I show how intercellular pathway activation is regulated through cell-type specific transporters of the pathway's agonist, cGAMP, and how intracellular pathway activation is regulated through the E3-ubiquitin ligase PELI2
Re-imagining and expanding the diagnostic toolbox : towards robust and scalable molecular quantification
Keywords: Engineering.
Bioengineering.

Why is it that our local pharmacy only has pregnancy strips and CGMs as molecular monitors? What can we actually monitor at the doctors office reliably, and why not certain biomarkers? These are questions that underlay the body of work presented in this thesis. Particularly, I focus on some of the technical challenges of measuring and monitoring molecular biomarkers. The field of precision medicine is entering a critical phase, with unprecedented access to vast computational resources and diverse data types such as CT scans, X-rays, and electronic health records. These resources, combined with powerful algorithms, have demonstrated significant potential for disease diagnosis and treatment. Unfortunately, molecular information has yet to be used in a scalable and reliable manner, although it is a critical component to understanding disease and health status. As a result, unraveling the basis and respective markers for disease and health remains a daunting task. This thesis highlights and begins addressing some fundamental problems in scaling up the quantification of molecular biomarkers. Particularly, many current solutions assume that the intrinsic affinity between the affinity reagent and the target are the limiting factor, or view background signal and noise as an annoying feature. I will share some of our recent works that take advantage of these aspects to provide more robust and scalable molecular quantification techniques including: A method to tune molecular assays to expand the range of quantification across a larger portion of the proteomic dynamic range, a mathematical framework to relax the selectivity requirements on affinity reagents for assay design, assay development for scalable small molecule measurement, and a way to spatially minimize the effect of non-specific binding. These works take a step towards improving the way and scope of biomarkers that are measured from a fundamental level and have the potential to shift molecular quantification to be more accessible for medical diagnostics.
Reimagining youth agency and social media platforms with middle school girls and nonbinary youth
Keywords: Education.

In an effort to engender a greater will and capacity among students to act on the world (Ahearn, 2002; Giddens, 1984), this Youth Participatory Design Research (YPDR) study engaged 42 middle-school girls and nonbinary youth enrolled in an American private school in the design, building, and implementing of a social media platform for young people. Analysis of pre- and post-surveys, using a validated tool for assessing agency (Vaughn et al., 2020b), indicated that agency among participants increased by a small but significant margin during the YPDR process. Youth felt an increased sense of intentionality and choice in what they learned in school, and to a lesser degree, increased self-identification as coders. In addition, qualitative analysis of their design and platform artifacts, presentation videos, interviews, and think-alouds reveals that these student designers re-imagined social media platforms to provide themselves and other youth with opportunities for agency development through making choices safely online. Youth designed novel platform features to assist users in comfortably sharing their voices by lowering the stakes of sharing, offering novel choices around anonymity, audience selection, feedback management, and using digital spaces as a bridge between in- and out-of-school work. A self-starting after-school club then spent two academic years bringing their peers' designs to life through building and implementing a social media platform in their school. They subsequently designed their own pedagogical research projects to further test and iterate on their platform, demonstrating the extent to which agency came into play in unexpected ways. Taken together, this study's results suggest that youth may simultaneously develop agency and build agency-promoting technologies for and in schools. Pedagogical approaches that have as their purpose supporting agency development and providing students with opportunities to re-design technologies that otherwise harm them, can help, while also offering teachers a framework for repurposing their classrooms as critical hubs of change.
Reinventing the politics of literature : rediscovery, ritual, and reference as concepts of repetition in the works of Peter Handke and Lee Yangji
Keywords: Humanities and Sciences.
Comparative Literature.

This dissertation examines concepts of repetition in the literary works of Austrian-Slovene writer Peter Handke (1942-) and Japanese-Korean writer Lee Yangji (1955-92). The concept of repetition is, in its everyday usage, bound to past traumas, psychological compulsions, and retributive resentments; at the same time, repetition plays a critical role in the development of motor and cognitive skills, the acquisition of new knowledge, and the deepening of understanding. Against the tendency of writers of German- and Japanese-language literature during the twentieth century to draw from socially- and psychologically-oriented understandings of repetition, the literary works of Peter Handke and Lee Yangji reimagined repetition as a portal to renewals of inheritance, rites of healing, and rearticulations of moral and aesthetic commitments. This dissertation argues that the partially overlapping, parallel processes by which Handke and Lee made their rediscoveries of their respective Slovene and South Korean minority heritages during the 1980s -- returns to roots in order to restore a sense of identity ruptured by the Second World War -- were mediated by the literary modes of translation, performance, and allusion; and moreover, these literary modes brought both writers into closer proximity to an enriching and edifying experience of repetition. This dissertation thus neither decouples politics from literature nor lays out a political agenda for literature, but rather takes repetition as a starting point for reconfiguring the political assumptions we bring to reading, writing, and language more generally
Relating outcrop and subsurface expressions of the Magallanes-Austral Basin: Provenance of the eastern Magallanes-Austral Basin from detrital zircon U-Pb sediment core ages, Southern Patagonia
Keywords: Malkowski, Matthew
Dobbs, Stephen
McHargue, Timothy
Detrital Zircon
Maximum Depositional Age
Magallanes-Austral Basin
Patagonia
Springhill Formation
La Anita Formation
Piedra Clavada Formation
Text
Thesis

Analyzing how provenance signatures of tectonically complex ancient sedimentary basins vary between the outcrop and the subsurface is crucial to understanding basin filling history. The 500+ km-long outcrop belt of the Magallanes-Austral Basin in southern Patagonia and its subsurface to the east allows us to constrain relationships between longitudinal and transverse sediment sources feeding the basin. New detrital zircon U-Pb ages (n=2558) from nine subsurface core samples from the Springhill, Piedra Clavada, and La Anita Formations along a 140 km east-west seismic reflection transect (50°S latitude; 71.5-69.5°W longitude) reveal provenance and filling history of the basin’s eastern subsurface extent. Detrital zircon ages (n=1068) were also collected from four outcrop Springhill Formation samples 140 km northwest from the transect near Lago San Martin. Maximum depositional ages (MDAs) from the Springhill Formation cores range from 154.9–146.8 Ma, which are older than correlative outcrop ages of 144.6–126.7 Ma. MDAs from the Piedra Clavada and La Anita Formations range from 93.4–91.4 Ma and 78.9–78.3 Ma, respectively, and overlap in age or are slightly younger than outcrop ages. The unimodal Late Jurassic age distribution from the Springhill Formation suggests that it almost exclusively was sourced by recycling of its underlying El Quemado Complex and highlights the underfilled nature of the Rocas Verdes Basin. By the Early Cretaceous, detritus supplied to the basin was derived from the arc, fold and thrust belt, and distal synrift volcanic sources. The occurrence of Early–Middle Jurassic ages in the Piedra Clavada Formation samples suggest either the basin was sourcing from the North Patagonia Massif to the north-northeast and from the Deseado Massif to the northeast or recycling exhumed volcaniclastic sequences in the northern margin of the basin. By the Late Cretaceous, the basin fill was more locally sourced, as suggested by the muted signal of Early–Middle Jurassic ages in La Anita Formation samples and a second mode of Late Jurassic–Early Cretaceous ages locally derived from recycling exhumed El Quemado Complex from the fold and thrust belt. We suggest that the longitudinal and local transverse drainages that sourced the Magallanes-Austral Basin outcrop belt also propagated eastward across the basin (what is now subsurface strata). Distal sourcing from the North Patagonian Massif is determined by subsidence and bypass in the Golfo San Jorge Basin and existence of Albian–Turonian fluvial transport systems capable of transporting Jurassic sediment to the Magallanes-Austral Basin.
Relational work, post-bureaucracy, and inequality in Silicon Valley
Keywords: Humanities and Sciences.
Communication.

In this dissertation, I explored the role of relational labor in Silicon Valley post-bureaucratic workplaces through two cases: the implementation of AI ethics in technology companies, and the role of employee's relational work at WeWork. I examine the growth of the field of AI ethics, also referred to as "responsible AI, " which has developed in response to criticisms following investigations of algorithms that revealed disproportionate harms on marginalized groups. I agrue that legitimacy shapes organizational similarity, or isomorphism, in the field and show that this constrains corporate practices related to ethics. Next, I examine ethics workers through the lens of institutional entrepreneurship to understand the barriers to implementing responsible AI in technology organizations. I focus on the diplomatic and interpersonal skills ethics entrepreneurs must engage in on a case-by-case basis in order to effect change, due to the lack of organizational infrastructure and support they receive. I find that ethics entrepreneurs face three major barriers to their work: the product-centered institutional environment, the difficulty of quantifying ethics in metrics-driven organizations, and frequent reorganizations of teams which make it difficult to access knowledge and maintain relationships central to their work. As a result of these barriers, ethics workers, who are often from marginalized backgrounds, take on great personal risk when raising ethics issues. Finally, I aim to understand what motivates the reaggregation of decentralized knowledge work in coworking spaces like WeWork. In recent years, coworking has exploded in popularity amongst knowledge workers. How can we understand the social and cultural forces that precipitated this shift from disaggregated to reaggregated work? I focus on the emotional labor and relationship labor performed by culture workers at WeWork, and I argue that this labor sustains decentralized capitalism. Despite the underlying spirit of techno-utopianism in Silicon Valley (Turner, 2006) and what Karppi and Nieborg (2021) describe as "an almost pathological belief in their corporation's ability to make the world a better place, " diversity in the technology industry remains stagnant or even regressive (Gee and Peck, 2015). This dissertation examines the stakes of changes to knowledge work, by outlining the consequences for workers at large but especially the implications on racial and gender inequality at work. These stakes have potential to affect not only the workplace, but also companies' products and society at large
Relativistic jets in the era of X-ray polarimetry
Keywords: Humanities and Sciences.
Physics.

Measuring X-ray polarization has been a major goal in astrophysics for the last 40 years. With the launch of NASA's Imaging X-ray Polarimetry Explorer (IXPE) in December 2021, soft X-ray polarimetry (1-10 keV) is now possible. In this thesis, I introduce an optimal signal extraction method for X-ray polarimeters based on gas pixel detectors. Using IXPE's thus improved sensitivity, I make progress towards identifying the high-energy emission processes and magnetic field geometries responsible for radiation in blazar jets. First, I develop a simulation-based inference framework for measuring X-ray polarization as a function of time, energy, and position in gas pixel detectors, proving that for a fixed model budget the framework is optimal. Second, I propose a simple geometrical jet model to study the polarization properties of leptonic blazar jets, including their observed EVPA rotations and their detection prospects with IXPE. Finally, I interpret IXPE's measurements of BL Lacertae across the synchro-Compton transition region to suggest leptonic-dominated emission processes in blazars, and of Mrk 421 to provide evidence for helical magnetic fields as the source of EVPA rotations
Removing black boxes in materials science : two-component droplet tilings and distributed manufacturing of fibrous media
Keywords: Engineering.
Materials Science and Engineering.

The interaction of liquids with materials is fundamental to many areas of science, industry, and human health. The first half of this thesis explores how a specific type of liquid (specifically, Marangoni-contracted, two-component liquids) can be used to create a new class of deliberately designed lattice system at the macroscale. The second half builds an experimental context for distributed manufacturing of fibrous materials used in essential products such as face filtering respirators and menstrual pads. Advances in material fabrication have made it possible to produce materials with an increasing range of geometries, including those with no precedent in nature. However, the relationships between geometry and state or the dynamics governing transitions between states in condensed material systems are not well understood and remain difficult to observe. Here, we have developed a system that exploits the properties of two-component, marangoni-contracted droplets to rapidly explore the properties of systems with novel geometries. In particular, the ability to move in response to vapor gradients over long distances enables the observation of the dynamics of many body systems governed by a non-additive potential energy function subject to non-trivial geometric constraints. The resulting systems are highly frustrated and display relaxation dynamics over two-timescales, a characteristic feature of systems with long-ranged interactions. We show further that the system is amenable to control by a global gravitational field, enabling partial reduction in frustration through the implementation of hysteretic annealing. Finally, we show that specific geometric configuration can give rise to non-reciprocal interactions, a property common to many non-equilibrium systems but with few artificial realizations. The availability of many essential products are determined by access to engineered materials. While the production of many materials is highly efficient, this often comes at the cost of robustness, resiliency, and distribution. During the COVID-19 pandemic, production of raw material for personal protective equipment could not quickly respond to surge demand and left many in low and middle income countries without adequate resources. Here, we explored the potential for centrifugal melt spinning for the production of non-woven air filtration media. Meanwhile, access to another essential product, disposable menstrual pads, suffers from many of the same constraints. We develop a mild delignification chemistry for the small scale production of absorbent medium for use in disposable menstrual pads. We show that Agave sisalana, a drought tolerant succulent that can be grown on marginal land, can be treated under mild conditions to yield an absorbent material with an absorption and retention capacity meeting and exceeding performance of absorbents found in commercially available products.
Resilience in the face of trauma : how sexual violence shapes economic well-being
Keywords: Humanities and Sciences.
Sociology.

Sexual violence can be physically, emotionally, relationally, and financially devastating, resulting in major disruption to survivors' everyday lives. However, about 70% of trauma survivors will be resilient—defined as maintaining a stable equilibrium in one's everyday life in the months and years following a traumatic event. Given that over half of women will experience sexual violence at some point in their lifetime, my dissertation asks: How are women doing well, despite the sexual trauma they face? I directly intervene in this debate by highlighting the roles that social support and social institutions play in facilitating and constraining survivors' resilience trajectories. I do this by examining the case of sexual violence and economic resilience. In the first paper of my dissertation, I provide a theoretical framework for explaining how economic resilience is empowered and constrained through an integration of micro-level, meso-level, and institutional-level social processes. This integration of a survivor's agency at the micro-level with the social structure in order to be resilient is a social process I term integrated resilience. The second dissertation paper zooms in on resilience in the context of educational persistence. Despite the high rates of sexual violence that school-aged women face, I explain how women are doing academically well through their strategic deployment of institutional support. The third dissertation paper traces how the workplace can be a site of both constraint and empowerment for survivors of sexual violence. In this paper, I show how these constraining and empowering experiences in the workplace shape survivors' future job search processes and occupational destinations. My body of work aims to show not only the harms done to women, but their strength and ingenuity in response to social constraint.
Resonances and symmetries in photonics
Keywords: Humanities and Sciences.
Applied Physics.

Resonances and symmetries are fundamental concepts in physics. This thesis presents my research on resonances and symmetries in photonics. The first part of this thesis investigates Fano resonances in nonlocal metasurfaces, including their basic principles and potential practical applications such as all-optical edge detection, free-space squeezing, and the generation of light bullets. The second part of this thesis focuses on the internal symmetries of linear photonic systems, particularly Lorentz reciprocity. I propose an extended Kirchhoff's law of thermal radiation applicable to all thermal emitters. I also investigate the impact of Lorentz reciprocity on reflection. I hope this thesis will contribute to a better understanding of resonances and symmetries in photonics and their practical applications
Responsibility and cooperation
Keywords: Humanities and Sciences.
Philosophy.

This work begins with methodological issues upstream of traditional questions about moral responsibility, starting with just what the problem of responsibility is and why it matters. Articulating and motivating my interest in the problem shapes and constrains other methodological choices, such as how to delimit the subject matter and how to inquire into it. The approach I develop is functionalist: if we want to understand the nature and value (or lack thereof) of holding one another responsible, we should think about holding one another responsible does -- what needs or interests (if any) it serves; what functions it has in our lives. The answer, I suggest, is that our practices of holding one another responsible function to sustain and promote cooperation: the different ways in which we hold one another responsible function as solutions to different kinds of distinctively interpersonal obstacles that living and working together often face
Rethinking power dynamics in software tools for artists
Keywords: Engineering.

Computation has become an essential tool for art and design. Yet many creative software tools limit users to preset options and filters, which may be restrictive for professional artists who have unique goals and workflows. While artists can learn to code to circumvent this preset functionality, the structured and abstract nature of programming is in tension with the exploratory and concrete nature of visual art making. From Photoshop to Processing, tools give artists the power to create, but the designers of such tools also exert power over artists by dictating what is available to them. This dissertation offers three contributions towards understanding, enabling, and questioning power relationships in software tools for visual art. First, through a thematic analysis of interviews with over a dozen professional artists, I show that pre-existing software tools are most powerful when they enable fine grain aesthetic control and adaptable to artists' idiosyncratic workflows, and that artists learn to program their own tools to gain various forms of power. Second, to support visual artists in programming, I present the Demystified Dynamic Brushes (DDB) system. DDB is a creative coding environment that visualizes program information on the ongoing artwork and grounds debugging interactions with stylus inputs, giving artists the power to understand their programs in a way aligned with their existing expertise. Finally, I argue that the traditional way software tools empower their users---through defining abstractions and representations that align with user needs---also disempower them by exerting a ``normative ground'' that structures and limits how users can and should act, think, and express themselves. Backed by interviews with creative practitioners and tool designers, I build a preliminary theory of how power relationships manifest in creativity support tools, and what tool designers can do, both technically and methodologically, to mitigate imbalances in power relationships. Taken together, it is my goal to show that supporting creative practices beyond accomplishing tasks with more efficiency or lower mental load----supporting wonderful creative practices that are unpredictable, emergent, and messy---means taking power relationships---and creative practitioners themselves---more seriously in software design.