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A Community's Fight for Justice: The Creosote Contamination Collection
No full textThis item is a presentation detailing work conducted in Fondren Library's Fondren Fellows Program.This presentation highlights documents and oral histories related to the creosote contamination of Houston's Fifth Ward and Kashmere Gardens. From 1899 to 1984, Southern Pacific Transportation Company used creosote as a wood preservative, leading to groundwater and soil contamination. The area was determined to be a cancer cluster in 2019, and community members have worked with the EPA, Houston Health Department, the Texas Commission on Environmental Quality, and other organizations to address the harm caused by the contamination. This presentation aims to preserve information and, importantly, highlight personal narratives from community members. Members of the Fondren Fellows gathered and described these materials
Atmospheric chemistry and aerosol associated with the coastal urban environment
No full textThis study aims to understand the dynamics of atmospheric secondary organic aerosol (SOA) in Houston, Texas. It (1) explores the relationship between sea breeze and air quality, (2) investigates the spatiotemporal characteristics of aerosols and SOA formation rates, and (3) analyzes factors that impact new particle formation (NPF).
Long-term monitoring demonstrated that PM2.5 (particles with diameters of 2.5 m or smaller) concentrations are ~30% larger on days with southerly wind or sea breeze recirculation compared to those under other wind patterns. On southerly wind days, 53% of PM2.5 was attributed to long-range transport of soil. In contrast, on sea breeze recirculation days, 60% of PM2.5 was attributed to anthropogenic sources and only 15% to soil sources. SOA also appeared to be important on sea breeze recirculation days.
To investigate in-situ SOA mechanisms and NPF in Houston, aerosol composition and size distribution were measured during the TRACER field campaign from July to September 2022. During this campaign, OA contributed the most significant fraction of aerosol. Assuming two OA factors - less-oxidized oxygenated OA (LO-OOA), and more-oxidized oxygenated OA (MO-OOA) - represent SOA, a mass balance model was used to estimate the SOA formation rate. For MO-OOA, the largest formation rates aligned with intense photo-oxidation processes. For LO-OOA, the most significant formation rates occurred at night, likely associated with nitrate radical chemistry.
Substantial differences in particle compositions and concentrations were observed on NPF and non-NPF days. PM1 mass concentrations were 7% to 76% lower on NPF days compared to non-NPF days across all sites. However, the fractional increase in the contributions of sulfate and MO-OOA on NPF days allows enhanced uptake of gases. These results suggest that, given similar condensation sinks, other atmospheric conditions play a critical role in determining the occurrence of NPF.
This study provides a comprehensive investigation of SOA formation, NPF, and impacts of meteorological conditions in Houston. These findings contribute to efforts to improve air quality in coastal urban areas in order to meet the National Ambient Air Quality Standards
Data@Rice Text Analysis Workshops - Fondren Fellows Program 2025
No full textThis item is a presentation detailing work conducted in Fondren Library's Fondren Fellows Program.This submission includes slide decks for two workshops presented as part of the Spring 2025 Data@Rice series, designed to introduce and deepen participants' skills in text analysis using accessible tools. The workshops cater to different experience levels, offering both foundational and intermediate instruction.
Introduction to Text Analysis with Voyant:
This beginner-friendly workshop introduces key concepts in text analysis and demonstrates how to use Voyant, a free online tool, to explore textual patterns. Participants learn to create concordances, examine word frequencies and trends, and identify co-occurring terms. The session also covers basic terminology, real-world applications, and ethical considerations.
Intermediate Text Analysis with Python:
Designed for participants with prior experience in Python and basic text analysis, this workshop dives into hands-on techniques using libraries like NLTK, SpaCy, and Gensim. After a brief refresher on text analysis, the course explores sentiment analysis and topic modeling with real-world data
Engineering synthetic phosphorylation signaling networks in human cells
No full textProtein phosphorylation signaling networks have a central role in how cells sense and respond to their environment. This thesis outlines a comprehensive approach to designing and implementing synthetic phosphorylation networks in mammalian cells, using modular protein domain parts to construct reversible phosphorylation cycles and assemble customizable circuits. By leveraging model-guided tuning, these engineered circuits enable precise signal processing and facilitate the creation of diverse network connections. The synthetic pathways can be linked to upstream cell surface receptors for rapid sensing of extracellular ligands and downstream elements that regulate gene expression.
The work further explores the application of these synthetic networks in therapeutically relevant settings. We demonstrate how engineered circuits can detect physiologically significant biomolecules, such as inflammation markers, and respond with targeted actions, including the controlled secretion of therapeutic proteins. The successful integration and functional testing of these synthetic pathways in primary human cells highlight a significant step toward their use in cell-based therapies. This adaptability illustrates the potential for engineering customized cellular responses tailored to specific disease states, paving the way for innovative treatment strategies.
By providing a robust toolkit and showcasing its versatility, this thesis lays the groundwork for future advancements in synthetic biology. The modular design and adaptability of these synthetic signaling networks create opportunities for developing programmable cellular systems capable of addressing a wide range of biotechnological and medical challenges. This work contributes to the growing field of synthetic biology by establishing a foundational framework for integrating engineered pathways into cellular systems, enhancing their ability to perform complex, tailored functions and expanding the scope of potential applications in biosensing and therapeutic development
Sustainable Thermal Soil Remediation Engineering: Catalytic Advances to Treat Pollution by Heavy Hydrocarbons
No full textPolycyclic aromatic hydrocarbons (PAHs) are among the most pervasive soil pollutants. These compounds, found naturally in oil or formed during the incomplete combustion of organic matter, resist natural degradation, and pose serious health risks, including cancer, preterm births, and neurocognitive defects. Pyrolysis, a thermal remediation technology, can effectively remove PAHs to meet regulatory standards and preserve soil components critical for water and nutrient retention, making it possible to use treated soil for environmental restoration. However, this approach requires the use of moderately high temperatures (350-550°C), leading to high energy demands, which remain a significant cost driver and a sustainability challenge. This dissertation explores how clays modified with non-toxic transition metals can be used as an amendment to catalytically decrease the required pyrolytic treatment temperature and time (and thus energy) needed for PAH removal from soils and sediments.
To assess the potential for clays and their transition metals to enhance pyro-catalytic treatment of PAH-contaminated soils, the addition of 10% (by weight) of bentonite clay modified via ion-exchange with Fe or Cu was mixed with a weathered crude oil contaminated soil containing PAHs and pyrolyzed at several different temperatures. The addition of Fe-bentonite and Cu-bentonite significantly lowered the total petroleum hydrocarbon (TPH) content to below regulatory compliance standards at a pyrolysis temperature of 300°C with a 15 min treatment time, which is 2-4 times lower than temperatures typically required for incineration. Thermogravimetric analysis coupled with mass spectrometry revealed the release of key pyrolysis degradation products, hydrogen and propyl ion fragments, at lower temperatures than those observed for unamended soil, highlighting the catalytic effect.
To identify the reaction mechanisms and transformation pathways of PAH pyro-catalytic treatment, we explored the pyrolysis of several different PAHs spiked on various ion-exchanged clays. Bentonite modified with Fe3+, Cu2+ or Zn2+ catalyzed the decomposition of naphthalene, pyrene, benz(a)anthracene, and benzo(g,h,i)perylene at temperatures as low as 100°C in 15 min. This is the lowest pyrolysis temperature that has been reported to rapidly achieve significant PAH degradation. Combining experimental studies with computational modeling of PAH interactions with transition metals in clays, our analysis revealed that PAHs with lower ionization potential exhibit greater susceptibility to thermal-catalytic treatment, likely due to a direct electron transport (DET) mechanism facilitated by cationic Fe3+ in Fe-enriched bentonite. The formation of aromatic radicals via this DET mechanism initiates a cascade of aromatic polymerization reactions, ultimately converting PAHs into a non-toxic, fertility-preserving char.
Overall, pyro-catalytic treatment using natural, earth-abundant materials like clays as catalysts can decrease the temperature and treatment time needed for removal of heavy hydrocarbons (resulting in lower energy consumption), avoid destruction of soil fertility, and increase throughput capacity. This approach addresses the need for more sustainable, reliable, cost-effective and broadly applicable soil remediation, and connects public health protection with the energy-environment nexus by transforming contaminated soil from a liability into a commodity (i.e., fertile soil for ecosystem restoration)
Microwave Transitions and Synthetic Dimensions in Rydberg Atoms
No full textThe marriage between Rydberg physics and ultracold atomic systems have hatched so many fascinating achievements. The exaggerated properties of Rydberg states, combined with the pristine environments provided by the ultracold atoms, can lead to realizations of exotic physical systems. One particularly innovative direction that
emerged recently is to use microwave-frequency transitions between Rydberg levels to simulate the dynamics of a particle hopping between lattice sites. Such approach,
referred to as Rydberg synthetic dimensions, falls under the broad scheme of quantum simulations. Here we present description of the infrastructure used for Rydberg excitation and coherent microwave transitions, which are essential to the realization of Rydberg synthetic dimensions. We will also present experimental results on simulating the Su-Schireffer-Heeger Hamiltonian, a canonical model with paradigmatic importance in topological physics
Closed Loop Solute Transport in Blood Vessels and Organs
No full textHypoplastic left heart syndrome (HLHS) is a congenital heart disease that causes oxygenated blood to mix with deoxygenated blood, resulting in death. This raises a critical need to accurately model the transport of oxygen in blood vessels and organs throughout the human body to improve outcomes in patients with HLHS. Previously, numerical reduced models have been created to solve for blood flow and concentration of one solute. These models reduce the dimensions of the vessels and organs to improve computational efficiency. This work extends the models from open network of blood vessels to closed loops and includes organs. Appropriate transmissibility conditions at each vessel junction and organ bed are constructed, that are based on balance laws. The class of interior penalty discontinuous Galerkin methods is used for the spatial discretization of the models. The blood flow equations are discretized in time using a two-stage Runge-Kutta scheme and we solve for the momentum of the blood and cross-sectional area of the vessel first. We then discretize the solute transport equation in time using a forward Euler scheme and solve for the oxygen concentration. The conservation of solute mass is of important consideration and the proposed method and numerical results are indeed shown to conserve solute mass
A Federated Learning Framework For Personalized and Privacy-Preserving Biosignal Interfaces
No full textBiosignal-controlled interfaces—using data collected from sensors in, on, or around the body such as cameras, accelerometers, or electromyography sensors—offer a richer way to serve individual abilities, preferences, and behaviors in mobile human-computer interactions. However, the centralized machine learning paradigm has several shortcomings which prevent us from realizing this vision. Centralized training demands that users share their sensitive biosignal data to train a one-size-fits-all model, which may lack accessibility and fail to generalize to novel or out-of-distribution users. Personalizing to improve performance via finetuning requires even more user data, further increasing the privacy risk. Personalized federated learning balances this privacy-personalization trade-off by leveraging information from peer users to enhance performance via personalized models without requiring users to upload their sensitive data. This work introduces a framework for researchers working with sensitive biosignal data to incorporate federated learning into their applications. We apply our framework to both an open-loop simulation and a closed-loop user study for an EMG interface. We show that traditional algorithms outperform our modified sequential FL algorithm in terms of performance, but have a substantially higher privacy risk. Finally, we highlight the need for more federated learning theory to support the sequential scenario inherent to many wearable applications
What Is It?
No full textThere is an existing attitude towards architecture revolving around the obsession with the specificity and perfection of design. This approach is necessary when working closely with a client who is also the singular user group of the space being designed. However, once a wide group of users are to be accommodated in a designed space, specific design moves can lose significance and impact. This thesis acknowledges how different user groups redefine the way designed spaces and objects are used and challenges how to design for unexpected multiplicities
1.1 Towards frameworks for evaluation and governance of Biotechnologies Beyond Conventional Containment
Full text linkThis entreaty was created as part of The Spirit of Asilomar and the Future of Biotechnology summit (February 23-26, 2025) in Pacific Grove, CA.At the Spirit of Asilomar meeting, one working group met to discuss whether a consistent framework for categorizing and providing guidance for the use of Biotechnologies Beyond Conventional Containment (BBCCs), similar to how the Biosafety Level framework operates for the laboratory use of biological agents, could be developed. This document presents some of the major conclusions from these discussions, outlines the general structure of what a framework might look like, and states some open questions that still need to be addressed to develop any concrete implmeentation of such a framework