Washington University Medical Center
Washington University St. Louis: Open ScholarshipNot a member yet
26344 research outputs found
Sort by
Generic FPGA Preprocessing for Astrophysics Instruments in HLS
Get PDFFPGAs are widely deployed on high-energy astroparticle physics instruments to preprocess large volumes of streaming data from various sensors. Increasingly, these deployments are finding their way to space-borne instruments, where constraints on size, weight, and power (SWaP) require careful balancing of speed and resource utilization. Although telescope designs vary widely, they often share common preprocessing elements, including channel-level readout, pedestal subtraction, waveform integration, and zero suppression from front-end ADCs, as well as identification and centroiding of signal islands across groups of multiple channels. High-Level Synthesis (HLS) tools allow these designs to be expressed at a conceptual level, which automates a significant amount of the workload in FPGA design and development; compared to traditional hardware description languages, this enables rapid prototyping and redeployment of common logic across different instruments. Nonetheless, prior work lacks sufficient generality to be applied in a broader context, requiring logic to be rewritten from scratch for a new instrument. In this work, we explore generic programming paradigms in the context of HLS, demonstrating that this allows sufficient flexibility of specification to create a pipeline that can be recompiled to automatically accommodate distinct instruments from a manifest of their unique properties and requirements. We apply this to two diverse instrument designs: scintillator-based detectors with 1D pixel arrays, and imaging atmospheric Cherenkov telescopes with 2D pixel arrays. In doing so, we also present a novel HLS-based two-pass connected-component labeling (CCL) implementation that can be easily switched between 4-way and 8-way CCL
The Kinship of Creatives
No full textThis research essay contends that artists and creative individuals must recognize their agency in shaping societal narratives, particularly during times of technological and political upheaval. The essay draws on the insights and contributions of visionaries like Walter Benjamin, Ursula K. Le Guin, and Tomm Moore to emphasize the power of imagination and creativity in addressing real-world issues. It argues that previous technological advances have often reinforced hierarchical and oppressive systems, benefitting a select few while neglecting the masses. As we enter the fourth Industrial Revolution, this essay calls the artists to reclaim their tools from being co-opted for exclusionary and destructive purposes. By resonating with the moral and ethical considerations of past visionaries, contemporary creatives can build a defense against the misuse of technology and narrative. This essay highlights the responsibility of artists as direct contributors to the world order, urging them not to be passive spectators but active participants in the fight for inclusivity and justice
The Liminal Space of Dreams: Narration of Dreams in Graphic novel and Comics
No full textThis essay explores the dream as a narrative in graphic novels and comics, examining its character as a subconscious experience depicted by means of visual storytelling. Focusing on psychological, symbolic, and aesthetic functions of dream narrative, I demonstrate that dream narration offers an allegory by means of which both creator and reader can explore issues of identity, desire and trauma in an intimate and healing way. In analyzing these functions of dream narration, I draw upon ideas from theorists such as C.J Jung, Freud and other scholars who have engaged their work on the psychological perspective of the experience of dreams; Roland Barthes on the structuralism and Post-Structuralism, semiotic language narration; Scott McCloud and other comic scholars on the visual aesthetic of dreams and history of dream comics. This essay unravels the storytelling of dreams to create a non-linear logic of storytelling, My research engages comics all of which focus on author and reader collaboration, mid-20th-century American golden age comics, to autobiographical graphic novels from Julie Doucet and Una. Ultimately, I seek to show that dream narratives provide a safe space for both artists and readers. I argue that dream narration in comics is not only an artistic exploration of the unconscious but also a collaborative meaning-making that evolves across social context
Trans-dimensional Coexistence: I No Longer Hold You But I See You
Get PDFWe live in a world where impermanence is the only lasting truth. Fleeting moments and fading relationships reoccur in our lives, but the journey continues, nonetheless. My practice projects my individuality onto universal connections between humans through depicting worlds full of colorful imaginations, experiences, creatures, and figures. I draw inspiration from work by Inka Essenhigh, Yoko Ono, and Pipilotti Rist, studying contemporary artists’ use of colors, materials, and audience participation to make an array of works from paintings to an interactive installation as my final work. Additionally, I look into historical sources about mythical creatures and religious beliefs to enhance my understanding of various perspectives of humans’ interests in illusions and faiths. Bridging the worlds I created together, this thesis explores my concept of trans-dimensional coexistence, where everything will be reconnected in the end
Hot Girls Don\u27t Worry About Copyright: Trans/Formative Works and the Femmage Lifestyle
Get PDFThis thesis examines the ways in which collage is an ontologically transgender medium due to its freedom from traditional artistic formal and narrative structures. Considering that many trans experiences center around dichotomies, juxtaposition, and self-definition, collage is the best equipped to communicate these experiences in innovative ways. Through interrogations of feminized labor and the ways in which the art world upholds harmful gender binaries, as well as discussions of Femmage, maladjustment, and obsession, I argue that the fragmentary nature of photomontage, digital collage, and videomontage can externally express the multitude of feelings and identities contained within a body, to a greater extent than that of other forms of art
Places, Please!
Get PDFGrowing up in the American South as the daughter of a scenic designer, I frequently found myself on both the physical stage of the theatre and the metaphorical stage of gender performance. Through immersive oil paintings, I seek to visually represent where these two experiences merge, depicting imagery and characters from my childhood staged in theatrical and uncanny environments. In this thesis I explore the canine motif as my primary subject, positioning the Dalmatian as a self-insert and exploring the show dog as a foil to the Southern beauty. Building upon Judith Butlers theory of gender performance, and Laura Mulvey’s theory of the male gaze, I position the application of paint as a parallel to women’s altering of personal appearance and self-surveillance. I harness the beauty and tactility in both my paintings’ imagery and the medium of oil paint to direct the viewer inward, intimating complicity. In my large-scale paintings, I employ the visual interruption of the stage curtain and the spotlight as painted tactics of the Brechtian alienation effect, to distance viewers from the immersive qualities of an oil painting and remind them to engage with the aestheticized imagery critically. Through Sigmund Freud’s concept of the uncanny, and Jean Baudrillard’s idea of the simulacrum, I question how the constructed nature of a stage set or staged scene can reflect our constructed culture. Ultimately, my work examines the antithetical nature of girlhood and asks the viewer to consider whether there can be room for both celebration and critique of femininity
Optimizing Massively Parallel Reporter Assays for In Vivo Neurogenomics: Tools to Decode Enhancer Function in the Brain
No full textNeurodevelopmental disorders like autism spectrum disorder affect millions globally, with substantial personal, medical, and societal consequences. While genome-wide association studies have implicated thousands of genetic variants in disease risk, the vast majority reside in non-coding regulatory regions where their functional mechanisms remain unclear. This challenge is exacerbated by the inability of existing massively parallel reporter assays (MPRAs) to distinguish transcriptional regulation from post-transcriptional control, and their poor performance in living tissue where cell-type-specific and developmental contexts are critical. This dissertation presents the Inferred Stability Optimized Massively Parallel Reporter Assay (ISOMPRA), a redesigned MPRA platform that independently quantifies nascent and mature RNA to disambiguate regulatory mechanisms while maintaining compatibility with in vivo applications. Chapter 1 establishes the conceptual foundation of this dissertation, demonstrating how non-coding regulatory variation in enhancers and untranslated regions converge on shared neurodevelopmental pathways despite remarkable genetic heterogeneity, followed by an investigation into MPRAs and their history. Chapter 2 validates ISOMPRA through systematic in vitro benchmarking, revealing that conventional approaches misclassify 60% of elements as transcriptionally functional enhancers or repressors when effects arise from altered RNA stability. Testing 466 autism-associated enhancer variants and 3,325 3′ UTR variants demonstrated that regulatory elements frequently exhibit dual functions—simultaneously modulating transcription and post-transcriptional processes. ISOMPRA achieved superior reproducibility with 8-fold reduced sequencing requirements compared to traditional barcoded methods. Chapter 3 implements ISOMPRA in developing mouse brain via AAV delivery, demonstrating substantially improved performance over conventional approaches in complex neural tissue. Using Cre-dependent designs in cortical excitatory neurons enabled cell-type-specific regulatory measurements from single tissue samples, revealing that most variants exhibit context-dependent effects, with regulatory function determined by cellular environment rather than being an intrinsic sequence property. Chapter 4 systematically investigates how promoter architecture shapes regulatory landscapes—an often-overlooked design parameter in MPRAs. Motivated by the reduced dynamic range and lower replicate correlation observed in vivo with minimal promoters (Chapter 3), I evaluated whether promoter identity could account for this variability and improve assay performance in neural contexts. Testing seven distinct promoters across human and mouse cell lines revealed that promoter choice alone explained nearly 40% of expression variance—far exceeding contributions from cell type or RNA processing. Strikingly, the majority of tested variants exhibited promoter-dependent regulatory effects, underscoring that variant interpretation cannot be divorced from promoter context. Moreover, neuronal-like cell types displayed a more restrictive, repression-dominated regulatory architecture relative to the more permissive expression profiles of non-neuronal cells. These findings establish promoter architecture as a critical determinant of regulatory activity and provide key design principles for optimizing in vivo MPRA performance. Chapter 5 translates these findings in vivo, demonstrating that strategic promoter selection substantially improves assay performance: optimized promoter choice increased correlation among biological replicates and enhanced detection sensitivity in brain tissue. Beyond these technical advances, systematic promoter comparison revealed that cell-type tropism determines which neural populations are functionally sampled. Only a small percentage of variants showed promoter-independent effects, with the majority exhibiting complex interactions between promoter choice and sex. Collectively, this dissertation establishes that regulatory variant function represents context-dependent phenomena shaped by promoter architecture, cellular environment, developmental timing, and biological sex. ISOMPRA provides essential infrastructure for translating genetic discoveries into mechanistic understanding of how non-coding variation disrupts neurodevelopmental gene expression programs, offering a framework for systematic variant interpretation in complex biological contexts
Synthesis of Well-defined Acrylamide-based Polymers and Related Materials for Water Treatment and the Fabrication of Carbon Fiber
No full textPolyacrylamide-based materials are of interest due to their unique properties, namely their hydrophilicity. Polyacrylamides can be readily synthesized in both linear and crosslinked architectures via many different chain growth methods, and multi-component copolymers imbued with additional functionality is possible. While many commercial applications exist for polyacrylamides, their breadth of utility has not yet been discovered. Many gaps still remain; however, this dissertation serves as a report of improved properties and functionality of PAN-based carbon fiber precursors and TCA functional materials via incorporation of polyacrylamides. In this dissertation, I introduce polymers and their distinctive qualities to serve as a basis for the research described herein, followed by a discussion of the history and uses of polyacrylamides, the polymer that ties together this body of work (Chapter 1). In the same chapter, I introduce carbon fiber and supramolecular polymers, two areas of research this dissertation will cover. This is followed by an account of a novel post-polymerization method of producing both atactic and isotactic PAN/PTBAM precursors for the production of high-performance carbon fiber (Chapter 2). Next, my research on a supramolecular TCA-based polyacrylamide hydrogel designed for metal sequestration in water treatment applications is described (Chapter 3). Lastly, I conclude my dissertation with a summary and future directions of both projects (Chapter 4). Within the field of carbon fiber, over 90% of fibers are produced from PAN-based precursors, due to the high-performance capabilities this precursor allows. While much research has been done on these fibers to improve properties, there has been less focus on the precursor polymer than on fiber production and processing. Although the fiber production processes greatly affect the resultant carbon fiber’s performance, the precursor polymers used to generate fibers play a large role in these properties, as well. Currently, PAN is produced via an uncontrolled free radical polymerization, which limits control over properties like tacticity and dispersity. To reach the ultimate trifecta of simultaneous stereochemical, molecular weight, and tacticity control, we developed a novel two-step chemical process in which PTBAM is first synthesized in a manner that can yield isotactic, relatively high molecular weight (~150 kDa), and low dispersity polymers. This polymer is then subjected to a post-polymerization modification of a pseudo-dehydration reaction capable of converting the majority of amide sidechain groups to nitriles, creating a PAN/PTBAM copolymer. This conversion is stereoretentive and does not greatly affect the molecular weight distribution defined in the first step, leading to better PAN-based precursors for carbon fiber production. Both atactic and isotactic PAN/PTBAM polymers were spun into fibers and thermally processed, which were observed to have dramatically enhanced mechanical properties (e.g., stiffness and strength, and counterintuitively the elasticity) compared to commercially purchased Sigma PAN precursors of a similar molecular weight treated in the same manner. In terms of supramolecular chemistry, TCAs have garnered attention for their binding ability of soft metal ions. This leads to questions of whether these compounds could be useful in remediation of metal-laced water sources. Two highly toxic metals, mercury and lead, have shown to be compatible with TCA binding. While research has been done into these types of interactions, many of these technologies have not been realized as functional materials. A need for robust and selective materials capable of metal binding is seen in water treatment applications. Within, I describe functionalization of a thiacalix[4]arene core to improve soft metal binding and hydrophilicity, as well as addition of an acrylamide polymerizable group, allowing for incorporation into a polyacrylamide-based hydrogel network. This allowed for production of a functional proof- of-concept material that is able to selectively sequester metal ions, specifically silver, mercury, and lead ions from water sources. Overall, this dissertation demonstrates the scope of polyacrylamide architectures and applications that are readily accessible and presents two novel applications that illustrate this breadth
Spatial Patterns in Electronic Health Record Data-Based Predictive Modeling: A Case Study of Prenatal Care and Preeclampsia
No full textThe electronic health record (EHR) documents interactions between patients and healthcare systems and is widely used for secondary research on health outcomes due to broad adoption. While EHR data support efficient clinical informatics research, they are subject to biases stemming from healthcare seeking behavior, health system attributes, and individual or environmental characteristics. Place-based characteristics, in particular, strongly influence when and how patients access care and shape health outcomes. These biases in EHR data can affect predictive modeling pipelines which leverage them, contributing to variation in model performance across groups. In healthcare, where predictive models are increasingly used to guide care, uneven performance may result in inadequate or inequitable care provision. This dissertation focuses on prenatal care as a critical use case, given the large patient population it serves and the rising rates of maternal and fetal morbidity and mortality in the U.S. Prenatal care access is shaped by persistent disparities across racial, socioeconomic, and geographic lines, which makes predictive modeling in this domain especially vulnerable to bias in EHR data. Preeclampsia, a serious pregnancy complication, is a target outcome where early diagnosis through predictive modeling could improve care and reduce adverse outcomes. To better understand and address spatial bias, this work investigates how such bias manifests across the predictive modeling pipeline. Specifically, it examines spatial bias at the stages of data collection, cleaning, and model training and evaluation in the context of a preeclampsia prediction task. The findings demonstrate notable spatial patterns in geographic representativeness of EHR data, EHR data quality, and model performance. These patterns suggest that spatial bias is not isolated to a single phase but embedded throughout the pipeline. As EHR data continue to be used in clinical research and decision-making, increased attention to spatial bias is critical. Transparency around these issues is essential to ensuring that predictive models support equitable and effective healthcare delivery
