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Health-Relevant Functions of the Gut Microbiome
No full textThe gut microbiome serves vital functions in host nutrition, immunity, and metabolism.Perturbations in the gut microbiome, commonly referred to as dysbiosis, have been correlated to
a wide range of diseases. However, the mechanistic basis of these relationships are poorly
understood. Here, I elucidated the enzymatic mechanisms underlying three important,
health-relevant functions of the gut microbiome using our lab’s integrated approach, combining
experimental techniques with bioinformatic analysis.
In Chapter 2, I identify the novel bilirubin reductase BilR using a fluorescence assay to
measure bilirubin reduction to urobilinogen. We delineate BilR from similar reductases via my
identification and mutation of key residues to find that BilR is primarily encoded by Bacillota
species. Our analysis of human gut metagenomes revealed that BilR is ubiquitous in healthy
adults, but shows decreased prevalence in neonates and individuals with Inflammatory Bowel
Disease (IBD). Our discovery sheds light on the role of the gut microbiome in bilirubin
metabolism and highlights the significance of the gut-liver axis in maintaining healthy serum
bilirubin homeostasis.
In Chapter 3, I demonstrate that disparate taxa can recapitulate the metabolism of
oxidized sugars utilizing enzymatically divergent, yet functionally equivalent gud/gar pathways.
We identify novel enzymes in the divergent commensal pathway, including putative 5-KDG
aldolase GudL and an uncharacterized ABC transporter GarABC that can recapitulate the
function of their nonhomologous pathogen counterparts. Our findings reveal a phenomenon
parallel to the pathogen growth promotion from inflammation-derived nitric oxide: oxidized
sugars, which are also produced during inflammation, serve as alternative carbon sources for
commensal microbes and may contribute to their increased relative abundance during gut
inflammation.
In Chapter 4, I discover SpiR, a microbial steroid Δ5-4 isomerase/3-keto reductase
responsible for cholesterol conversion to coprostanone in the gut. We verify that SpiR catalyzes
the stereospecific oxidation of both cholesterol and pregnenolone, but that it preferentially binds
to cholesterol over other related steroids. Phylogenetic analysis revealed SpiR is restricted to an
uncultured Actualibacteraceae clade, and multi-omics analysis shows SpiR is not only enriched
in cholesterol-converting individuals, but is a predictor of cholesterol conversion. Our findings
refine the enzymatic model of gut cholesterol metabolism and establish spiR as a driver for
microbial cholesterol reduction in the gut
“Yo Llevo Mi Pañuelo Amarrao”: Gen-Z Afro Dominicans exploring their ethnoracial identities in NYC
No full textWe have a great global illiteracy of Blackness (Hernández, 2024). As a global society, we
do not know or care to know the history of the global Black diaspora beyond the scope of the
Transatlantic Slave Trade period. While much literature can be found on the impact of the
Transatlantic Slave Trade, Blackness in The Caribbeans and Latin America has been
understudied. We must learn about Blackness in The Caribbeans and Latin America as it is
where most of the African enslaved people were exported to (Busey, 2017).
Furthermore, while AfroLatines are one of the fastest growing racial/ethnic groups in the
U.S., AfroLatine K-12 students/youth are underrepresented in research as compared to other
Latine students and students of color. This study aims to highlight how 7 Gen-Z Afro Dominican
youth in New York City refuse discrimination, antiBlackness, and colonial, historical
misinformation. This study aims to inform readers how some Afro Dominican Gen-Z are
changing the course of Dominican history through community, global advocacy, and education.
This study used a conceptual framework that focused on the La Casta System and
antiBlackness as foundational theories to the institutional racism in the U.S. and Latin America;
along with Afro Dominicans in New York City as a subculture and Black-imiento (Dache et al.,
2019) to explain how participants conceptualize their ethnoracial identity. It also employed
Critical Race Methodology (Solórzano & Yosso, 2022) as its methodological approach. This
study identified four key findings: (1) participants’ agency and efforts to “self-educate” on
Dominican history and interrogate antiBlack and antiHaitian narratives through historical
storytelling; (2) the methods participants used to recover from antiBlackness and racial harm; (3)
the role of schooling experiences in the formation of participants’ academic and ethnoracial
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identities; and (4) the participants’ perceptions of their generation identity and generational
advocacy as Afro Dominican Gen-Zs.
This research provides a timely and necessary study of how researchers, curriculum
writers, policymakers, and other stakeholders can draw from the experiences of Afro Dominican
and Dominican youths in New York City and support their schooling experiences. It also
provides ways we, as educational scholars, can present research in disaggregated ways to help
advance research on understudied populations.
Note: After completing a full draft of this dissertation, I used Grammarly, an AI writingassistance application to assist with final editing
MORSE FUNCTIONS WITH C^{1,1} REGULARITY
No full textMilnor’s Lectures on the h-cobordism theorem [7], Theorem 2.7 states: If M is a compact manifold without boundary, the Morse functions form an open dense subset of C∞ (M, R) in the C2 topology. In this thesis, our main work is generalizing this theorem. We build up the weakly Morse function and show that the set of weakly Morse functions is open and dense in C^ {1,1} (T^n , R). In order to prove the Main Theorem, this thesis is divided into five chapters. Chapter 1 provides an introduction to Morse theory and the motivation behind this problem. Chapters 2 and 3 present important properties of Morse functions and Lipschitz functions that are needed throughout the thesis. In Chapter 4, we list and prove several important results related to convex hulls. In particular, Carathéodory’s Theorem 4.5 on convex hulls, Theorem 4.6 on compact preserving property of the convex hull operator, and Theorem 4.10 and 4.12 will provide the necessary tools to separate compact sets away from closed sets. In the final chapter, we use the theorems discussed earlier to establish a series of containment relationships and apply the Clarke Inverse Function Theorem 5.10 to prove the main theorem 5.15
Data sets for "Effects of nonresonant instability and magnetic reconnection on ion heating and acceleration in quasi-parallel shock waves"
No full textData set of 2D and 3D particle-in-cell simulations for a research paper "Effects of nonresonant instability and magnetic reconnection on ion heating and acceleration in quasi-parallel shock waves"
Evolving Language Patterns on the Web: Community Influence, Model Adaptation, and Bias Mitigation
No full textThe language of the Web is in constant evolution, shaped by the dynamic interplay between social interaction, symbolic innovation, and shifting cultural norms. Online communities actively drive this evolution by introducing novel expressions, reinterpreting existing tokens, and constructing meanings that challenge traditional linguistic assumptions. Among the most illustrative of these transformations are emojis—visual symbols whose interpretations vary widely across users and contexts. As emojis evolve from standardized Unicode definitions into contextually rich social symbols, they reveal the complexity and fluidity of digital communication. However, this rapid pace of linguistic change presents major challenges for both human communication and natural language processing (NLP) systems, which struggle to adapt to the semantic drift of tokens over time.
This dissertation investigates the interconnections between language evolution, social meaning construction, and computational modeling. It centers on three key areas that reflect different facets of this linguistic transformation.
First, we examine the diffusion and semantic adaptation of newly introduced emojis in digital discourse. By analyzing usage patterns and leveraging large language models (LLMs), we develop an interpretation framework to decode the evolving meanings of new emojis and assess their impact on downstream NLP tasks.
Second, we explore how biased associations embedded in training data lead to spurious correlations at the concept level. We demonstrate that LLMs tend to internalize these associations, which can skew their predictions and reinforce societal stereotypes. By identifying the mechanisms behind such biases, we highlight the importance of mitigating shortcut learning in both pre-training and fine-tuning stages.
Third, we investigate how emojis, originally designed for neutral or positive expression, are repurposed for offensive communication. We develop a multi-step LLM-based pipeline to identify and replace offensive emojis in social media content while preserving the original semantic intent. Our human evaluations demonstrate that this approach reduces perceived offensiveness without sacrificing clarity or meaning.
Together, these three investigations provide a comprehensive account of how language evolves in digital environments—and how NLP systems can better keep pace. Our findings underscore the need for adaptive, socially aware computational frameworks that account for linguistic fluidity, community-specific conventions, and evolving symbolic practices. By aligning NLP models more closely with the dynamics of human communication, this dissertation contributes to the development of more inclusive, responsive, and semantically grounded language technologies
ENHANCING ACCESS TO CULTURAL ARCHIVES THROUGH DATA SCIENCE, GENERATIVE AI, AND KNOWLEDGE GRAPHS
No full textCultural archives hold invaluable historical records, yet outdated cataloging methods and access barriers limit their usability. My dissertation addresses these challenges by integrating data science, generative AI, and knowledge graphs to enhance engagement with Maryland’s Legacy of Slavery (LoS) project collections. My two-pronged strategy focuses on (1) developing computational tools to empower researchers and students to access and perform detailed data analysis on archival datasets independently and (2) leveraging generative AI and knowledge graphs to improve accessibility and contextual analysis. This dissertation synthesizes five interconnected studies conducted between 2021 and the present, structured under three research objectives. Research Objective I supports the first prong, while Objectives II and III collectively support the second.Research Objective I – Empowering Archival Practitioners through Data Science and Computational Thinking: In Study 1 (published, 2021), I used a mixed-method exploratory case study approach to develop interactive Digital Computational Notebooks (iDCNs) as educational tools for archival studies through a step-by-step data science based analysis on one of the LoS datasets. Designed based on a well-established computational thinking (CT) framework, iDCNs integrate Python scripts, narrative explanations, and visualizations to guide students and archivists in cleaning, analyzing, and interpreting LoS datasets. An IRB-approved user survey among students and educators confirmed that iDCNs enhance technical proficiency and critical thinking, making archival data more accessible for independent data analysis.
Research Objective II – Designing and Evaluating Generative AI Solutions for Enhanced Access: Addressing the second prong of my strategy, in Study 2 (peer-reviewed, 2023; to be published, 2025), I employed design science and an exploratory case study approach to develop ChatLoS, a chatbot powered by Retrieval-Augmented Generation (RAG) and OpenAI’s GPT models, allowing users to query one of the LoS datasets in natural language. By chunking text for retrieval, ChatLoS preserved contextual relevance and eliminated the need for users to understand data schemas. While it significantly improved accessibility, its reliance on RAG introduced limitations, including ethical concerns, bias, data privacy risks, and constraints that restricted the chatbot’s ability to handle complex, multi-step analytical tasks beyond targeted
searches. To address these, in Study 3 (published, 2024), I explored a comparative empirical design in leveraging a generative AI Agent that enables dynamic complex data analysis beyond targeted semantic search retrieval. Findings revealed that while RAG-based retrieval is optimal for targeted semantic search with explainability, an AI agentic approach enhances exploratory analysis, trend identification, and multi-step reasoning also with explainability. However, both studies highlighted concerns about limited scalability across more extensive archival collections, inaccuracies, inconsistencies, usage of proprietary GPT models, including ethical risks, and data control.
Research Objective III – Evaluating and Optimizing Generative AI for Ethical and Scalable Archival Access: To address issues identified in Objective II, the first study in this objective focused on completing the development of a Knowledge Graph-based Retrieval-Augmented Generation (KG-RAG) enhanced ChatLoS. This system integrates multiple LoS datasets—Certificates of Freedom, Domestic Traffic Advertisements, and Manumissions—into a unified knowledge graph
that supports explainable, multi-hop reasoning grounded in archival provenance and explainability. This ChatLoS version was further enhanced to promote transparency by providing source links to scanned archival documents and surfacing internal query logs in a human-readable format. This design enables users to understand how answers are generated and to verify the archival trail. Following this, two systematic user evaluations were conducted using an evaluation rubric
grounded in the Activity Theory framework. These evaluations compared the current LoS access systems to the three evolving versions of ChatLoS, revealing how each Gen-AI enhanced iteration progressively mediated user interaction and resolved long-standing usability and interpretability contradictions. This study demonstrated how a KG-RAG enhanced generative AI system can resolve key contradictions in existing access methods by aligning tool behavior with archival
principles such as context, trust, and traceability. This also identified opportunities for future work by introducing new contradictions. The second part of this objective evaluated four leading LLMs—GPT-4o, Claude, Llama, and Gemini—across criteria such as security, accuracy, guardrail customization, and multi-user deployment capabilities. Findings identified enterprise-grade models like Azure OpenAI GPT-4o as more appropriate for sensitive archival applications.
The dissertation concludes with a synthesis of findings that integrates the results of the three research objectives. It also highlights promising directions for future work, including participatory community studies and interface enhancements to ensure equitable, transparent, and culturally sensitive access to digital archives
Short-lived subduction interface fluid transport at the depths of episodic tremor and slow slip [dataset]
No full textGeophysical observations and geologic evidence suggest the source region of deep episodic tremor and slow slip (ETS) at the subduction interface is fluid rich and subject to high pore fluid pressure, however the mechanistic role of fluid in producing this seismic phenomenon remains debated. Previous studies have linked fluid movement and seismicity through diffusion chronometry, capable of resolving fluid transport durations at timescales comparable to the seismic cycle, but none have directly constrained the timescales of fluid transport at the subduction interface, the inferred source region of ETS. We invert measured Li concentration and isotope profiles using a Monte Carlo Li advection-diffusion model to constrain the duration (and associated uncertainties) of fluid transport around two partially-reacted metamafic blocks from an exhumed subduction interface (Amphibolite Unit, Catalina Schist, California). Both blocks yield time-integrated durations of fluid transport of ~40 years (years to centuries at 95% confidence) much shorter than the lifetime of these rocks in the subduction zone and comparable to, or longer than, the longest slow slip events. This suggests that fluid transport does not occur continuously at the subduction interface but rather reflects transport through fracture permeability consistent with fault-valve type models of fluid transport and related pore pressure fluctuation and frictional instability. The presence of peak metamorphic quartz + garnet veins in the rinds supports the formation and healing of fracture permeability as the process controlling fluid transport at the subduction interface. The fluid transport recorded by these blocks may be the geologic record of geophysically-observed variations in Vp/Vs during the slow slip cycle in modern subduction zones.NSF-EAR-091110, NSF-OISE-1545903, NSF-EAR-212251
“WOMEN IN THE STRUGGLE”: WOMEN OF COLOR COALITIONAL RELATIONALITIES IN THE COLD WAR ERA
No full textThis dissertation revisits the 1970s as a key period of unprecedented radical left organizing to explore the complex modes of solidarity integral to the political thought and activism of Black women and Latinas engaged in radical left grassroots movements during the Cold War. In doing so, this project complicates existing investigations of that period and notions of solidarity by exploring the fundamental role that coalition played in the work of the Third World Women’s Alliance (TWWA), a Marxist-Leninist, anti-imperialist Third World women’s organization. Utilizing the primary methods of qualitative expert interviews and archival research, I conduct a relational, interdisciplinary, and intersectional study of the coalitional organizing of the Black women and Latinas who spearheaded the Third World Women’s Committee to Celebrate International Women’s Day (1974-1980) stewarded by the Bay Area, California chapter of the TWWA and El Comité Lolita Lebrón (1974-1977), a committee of the New York City chapter of the TWWA. Through this analysis, I theorize coalitional relationalities as a broad framework for understanding the interconnected political, economic, affective, aesthetic, and ontological relationships that these organizers forged over racial/ethnic lines, time, and multiple scales, to resist colonial categories of difference and hierarchies of power toward freedom. Original interviews with Dr. Vicki Alexander, Frances Beal, Linda Burnham, Rebecca Carrillo, Dr. Concha Delgado-Gaitán, Cheryl Perry League, Dr. Patricia Romney, Dr. Melanie Tervalon, and Dr. Ana Celia Zentella, bring to the fore the everyday coalitional organizing practices and theories of Black women and Latinas who were active as rank-and-file members and leaders in both chapters of the Third World Women’s Alliance. Through archival research I layer into my analysis, close readings of Triple Jeopardy: Racism, Imperialism, Sexism, organizational records, internal position papers, and notes, along with other English and Spanish language movement ephemera of the TWWA and adjacent groups.
Furthermore, I examine state responses to their organizing employing close readings of redacted FBI files, interviews, and organizational documents. I analyze the state’s racializing surveillance (Browne 2015), and repression of these activists as connected to capital’s routinized exploitation and surveillance of US Third World women workers. Additionally, I map the resistance strategies that these activists employed to survive and challenge such violence. State surveillance of the TWWA demonstrated the decolonial potentialities of coalitional organizing among poor and working-class women of color as the state engaged in a violent Cold War project of capitalist nation-building
Cinema Paradiso: Enhancing Urban Life through Film
No full textThe rise of streaming services has revolutionized the film industry, shifting the primary viewing experience from movie theaters to home settings. This trend, amplified by the COVID-19 pandemic, has led to decreased occupancy rates in cinemas and diminished the communal aspects of film watching. To reverse this trend, public environments need to analyze what is keeping the occupant at home and use these findings to create spaces suitable to the occupant’s needs. This thesis explores how revitalizing a dying typology can inherently improve economically struggling urban areas and restore a sense of community that is becoming increasingly lost in the new digital age. The focus will analyze how art and film can educate and provide various services to the community to encourage intercultural competence. By analyzing the eco-psychological traits between humans and the environments they occupy and exploring various case studies that prioritize the human experience, this study will demonstrate strategies to create a space that uses digital media as a tool to foster physical social interactions and connections. This thesis contributes to the broader discourse of how urban spaces can stimulate job creation, enhance social activity, and improve media literacy, thereby reversing economic decline and reinvigorating the urban landscape
Execution of Complex Action Sequences Under Various Cognitive Demand With and Without Hand Biomechanics Alterations
No full textMany previous studies have investigated the effects of compromised limb biomechanics oncognitive-motor performance. However, many have focused on lower rather than upper extremities
while disregarding problem-solving tasks achieved under various demands. Additionally, limited
efforts have examined performance and mental workload concurrent to the completion of a
complex sequential task utilizing upper extremities and particularly when their biomechanics are
altered. However, the examination of cognitive-motor performance when upper limb
biomechanics are compromised would inform the relationship between cognitive and sensorimotor
control processes. This work aims to examine the effects of altered hand biomechanics on
performance and mental workload as individuals solve a sequential task under two cognitive
demands. In the current work, participants completed the Tower of Hanoi task under both low and
high cognitive demand while the hand effector was biomechanically altered or not. Biomechanics
alterations were achieved via a brace, in which degrees of freedom and effector sensorimotor
capabilities were substantially diminished. The sequential task performance was examined via
Levenshtein Distance (LD), which assesses the optimality of participant sequencing along with
sequence completion time, which was subsequently segmented to measure time during which hand
movement is being executed or paused, and the number of disk drops. Mental workload and
physical demand were assessed via NASA-TLX survey, while visual analog scale surveys
evaluated physical as well as cognitive effort and fatigue. Results revealed that compared to the
unbraced condition, brace usage led to an increase of the hand motion time along with an elevation
of both perceived mental workload as well as cognitive fatigue and effort without affecting the
structure of the sequence (i.e., LD) nor the time during which movement was paused. The same
findings were obtained in response to an elevation of cognitive task demands with the only
difference being that of a deterioration of sequence structure (i.e., increased LD) and an elevation
of the time during which movement was paused were also observed. Furthermore, enhanced
cognitive task demand under the brace condition led to an elevation of the number of disk drops
and perceived physical demand accompanied by an increase of physical effort and fatigue whereas
this was not observed for the unbraced conditions. These findings suggest the alteration of the
upper-extremity biomechanics, or an elevation of cognitive-task demand resulted in a decrement
of performance along with an elevation of the engagement of cognitive-motor processing resources
resulting in a greater mental workload and ultimately leading to a decrease of cognitive-motor
efficiency. Further, an increase of cognitive task demand leading to greater errors of fine
sensorimotor coordination (disk drops) while maintaining the action sequence structure when
individuals performed with compromised but not normal limb biomechanics suggest that
individuals may have prioritized the completion of the action sequencing at the expense of the
accurate motor execution. In turn, these greater sensorimotor errors would have required further
movement regulation leading to an increase of the perceived physical demand, effort and fatigue.
This work provides further insight into the understanding of adaptive human behavior and has the
potential to inform rehabilitation of individuals with compromised upper-extremity biomechanics