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An Investigation of the Interplay Among CX3CR1, Immune Cells, and Gut Microbiota in Lupus-Associated Arthritis and Renal Disease using the MRL/lpr Mouse
No full textDoctor of PhilosophySystemic lupus erythematosus, or lupus, is a disease where the body's immune system attacks itself, which can lead to tissue injury and organ failure. In this dissertation, different aspects of lupus were studied to better understand the disease. CX3CR1, a surface protein that guides cell migration, was found to influence the production of inflammatory proteins IL-17A and IL-17F, as well as the gut microbiota—bacteria living in the gut. The gut microbiota was observed to influence IL-17A but not IL-17F. When examining lupus-associated kidney disease and joint inflammation arthritis, CX3CR1 was found to affect them differently. The absence of CX3CR1 worsened kidney disease but improved arthritis. Different immune cells such as T cells and myeloid cells were observed to correlate with arthritis and/or kidney disease. A new gut microbiota biomarker for lupus-associated kidney disease, the Lachnospiraceae-to-Oscillospiraceae ratio, was discovered, which may become a new method to help prescreen patients before a kidney biopsy has to be performed. Overall, these findings contribute to scientific knowledge and could lead to targeted therapies to help lupus patients
Enhancing side-channel analysis through measurement, and high-power IEMI generation
No full textIn today's interconnected world, the use of hardware security modules (HSMs) or trusted platform modules (TPMs) has been growing rapidly. These devices are the foundation of many security measures, using cryptographic algorithms to ensure the confidentiality and integrity of sensitive data. For example, an HSM in the vehicle's electronic control units (ECU) safeguards vehicle communications and functional control systems using cryptography.
However, these devices are not immune to attacks, as an adversary can gain easy physical access (or be in close vicinity) to the device or communication medium. One such attack is side-channel analysis (SCA). This work proposes an effective methodology to launch power SCA and increase the efficiency of the attack by improving the measurements. The research examines heuristics related to measurement parameters, investigate ways to optimize the parameters, determine their effects empirically, and provide a theoretical analysis to support the findings.
This work introduces a novel, measurement-focused methodology that is attack-agnostic, leveraging multi-sensor fusion with a Kalman filter to enhance SCA data resolution and significantly reduce the number of measurements needed for successful attacks. We propose and realize a low-cost, low-noise, multi-sensor measurement board to demonstrate the effectiveness of our approach. The board enables the independent but coupled measurement of both a device's power consumption and the associated electromagnetic field it produces, which we combine with a Kalman filter to improve the accuracy of the power measurement.
This enhanced data quality can significantly boost the efficiency of SCA, independent of the chosen attack method(s).
The second phase of this research investigates intentional electromagnetic interference (IEMI), a wireless attack where an adversary uses an electromagnetic field in close proximity to induce a specific secondary effect on a target device. Unlike typical cyberattacks that exploit software vulnerabilities, this attack bypass conventional cybersecurity defenses by targeting the hardware layer directly with limited or zero physical access to the target device. The research focuses on the hardware architecture and design of two distinct amplifier types:
one capable of operating across a wide range of frequencies, and a second that functions as a high-power single-tone amplifier capable of sourcing power to radiators in the kilowatts range. This work demonstrates the effectiveness of the proposed hardware through two distinct applications: wireless vehicle fingerprinting and a novel "wireless spiking" technique on smart locks, where an attacker wirelessly bypasses standard security measures to lock or unlock the device.Doctor of PhilosophyIn today's interconnected world the need to safeguard the confidentiality and integrity of sensitive data is paramount. As digital transactions and communication increasingly deprecate analog forms, protecting this information from unauthorized access or modification becomes ever more critical. Cryptography has long served as the bedrock of data security, ensuring information remains confidential and unaltered. However, with the growing sophistication of attacks, even carefully designed cryptographic implementations may be vulnerable. Adversaries with physical access or in close proximity to devices performing cryptographic operations can exploit implementation vulnerabilities through techniques like side-channel analysis (SCA) to recover sensitive information that breaks the security of these devices.
Recent efforts to boost the efficiency of SCA have focused heavily on post-processing techniques like machine learning and deep learning. However, the effectiveness of these methods is fundamentally limited by the quality of the raw data they rely on. This work introduces a novel, attack-agnostic methodology that overcomes this data bottleneck by focusing on SCA measurement improvement, which in turn improve the efficiency of the attack.
The second phase of this research investigates intentional electromagnetic interference (IEMI), a wireless attack where an adversary uses an electromagnetic field in close proximity to induce a specific secondary effect on a target device. Unlike typical cyberattacks that exploit software vulnerabilities, this attack bypass conventional cybersecurity defenses by targeting the hardware layer directly. The research focuses on hardware architecture and design of the amplifier that can work across wide range of frequencies. This work demonstrates the effectiveness of the proposed hardware through two distinct applications: wireless vehicle fingerprinting and a novel "wireless spiking" technique on smart locks, where an attacker wirelessly bypasses standard security measures to lock or unlock the device
Are We on the Same Page? Examining Developer Perception Alignment in Open Source Code Reviews
No full textCode reviews are a critical aspect of open-source software (OSS) development, ensuring quality and fostering collaboration. This study examines perceptions, challenges, and biases in OSS code review processes, focusing on the perspectives of Contributors and Maintainers. Through surveys ( = 289), interviews ( = 23), and repository analysis ( = 81), we identify key areas of alignment and disparity. While both groups share common objectives, differences emerge in priorities, e.g, with Maintainers emphasizing alignment with project goals while Contributors overestimated the value of novelty. Bias, particularly familiarity bias, disproportionately affects underrepresented groups, discouraging participation and limiting community growth. Misinterpretation of approach differences as bias further complicates reviews. Our findings underscore the need for improved documentation, better tools, and automated solutions to address delays and enhance inclusivity. This work provides actionable strategies to promote fairness and sustain the long-term innovation of OSS ecosystems.Published versio
Tertiary Phosphorus Removal Hampton Roads Sanitation District (HRSD) Virginia Initiative Plant (VIP): Technology Selection and Operational Considerations
No full textMaster of ScienceExcess phosphorus and nitrogen released in treated wastewater can harm rivers and coastal ecosystems by promoting algal blooms and reducing water quality. Beginning in 2032, the Hampton Roads Sanitation District (HRSD) must meet a much stricter limit for phosphorus in treated wastewater at its Virginia Initiative Process (VIP) facility. This change requires both improvements to existing biological treatment and the addition of advanced treatment steps to remove the remaining nutrients before discharge. To identify effective solutions, HRSD tested two different treatment technologies that remove phosphorus using chemicals and physical separation. Both approaches successfully met the new phosphorus limit, but one option, the cloth media filtration system, required fewer chemicals and eliminated the need for an additional additive, making it simpler to operate. However, this system produced more return flows to the plant, which could increase hydraulic demands during certain operating conditions. In parallel, this research evaluated ways to improve nitrogen removal reliability by upgrading an existing treatment process that protects beneficial bacteria from toxic cyanide. A pilot system using attached-growth microorganisms was tested and showed strong performance even under high loading, elevated temperatures, and after operational disturbances. The system recovered quickly and exceeded design expectations. Overall, this study demonstrates practical, scalable strategies to help HRSD meet future nutrient limits while minimizing new construction, reducing chemical use, and improving treatment reliability. The results provide guidance for selecting technologies that protect water quality while maintaining efficient and resilient wastewater treatment operations
Leading in Place with Teams: Building Better Collaboration
No full textWorkshop for the Provost's Leadership Development Program: 2025-26 Leading in Place Cohor
Journal of Biomechanics
No full textOccupational arm-support exoskeletons (ASEs) can reduce shoulder muscle activity during overhead work, but their effects on muscle synergy structure and temporal activation remain limited. We examined the effects of using three different exoskeletons on muscle synergies during simulated overhead tasks. Muscle activity from 18 participants (gender-balanced) performing both pseudo-static and dynamic tasks across 24 conditions (three ASEs and a control condition) was analyzed using non-negative matrix factorization to extract synergy number, structure, and activation coefficients. Dynamic tasks recruited more muscle synergies (interquartile range: 2–5) than pseudo-static tasks (interquartile range: 1–3), with some task combinations showing modest increases with ASE use compared to the control condition. Synergy structure and temporal activation were generally similar across interventions (mean cosine similarity 0.74–0.92), but certain ASE-task combinations produced significant local changes in synergy structure. Using exoskeletons generally altered muscle weightings, shifting from primary arm-elevating and shoulder-stabilizing muscles toward modules involving neck and back muscles, suggesting compensatory strategies for device-imposed biomechanical demands. Activation time courses remained highly similar across most interventions during pseudo-static tasks, though dynamic tasks showed reduced peak magnitude with exoskeleton use. Our results indicate that while modular motor control is largely preserved with ASE use, device- and task-specific adaptations in synergy structure and temporal activation can occur. Future research should explore how ASE design features influence neuromuscular strategies and assess long-term adaptation of muscle synergies in occupational settings.Accepted versio
From Hyperspectral Indices to Global Fluorescence: PACE Vegetation Indices as Predictors of Terrestrial Photosynthesis
No full textSolar-induced chlorophyll fluorescence (SIF) serves as a direct remotely sensed indicator of photosynthetic activity, making it a valuable tool for assessing terrestrial productivity. However, the practical application of satellite-derived SIF is hindered by spatial resolution limitations and data gaps. The NASA Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission presents an opportunity to overcome these challenges through its hyperspectral Ocean Color Instrument and globally distributed Land Vegetation Index (LANDVI) product suite. This study's primary contribution lies in demonstrating that PACE vegetation indices alone can reliably predict SIF from global retrievals obtained using data from the Copernicus Sentinel-5P Tropospheric Monitoring Instrument (TROPOMI), even in the absence of PACE BRDF and albedo products (and their associated corrections).
Using 8-day global composites from 2024, we establish a temporal and spatial correlation between PACE indices and TROPOMI SIF (TROPOSIF) across fifteen biome-stratified study regions, including forests, grasslands, agricultural systems, and xeric landscapes. Simple univariate linear models reveal that the Enhanced Vegetation Index (EVI) and the Chlorophyll Index Red Edge (CIRE) are the most reliable global predictors of SIF, accounting for 80% and 77% of the variance, respectively. Notably, the stability of the EVI-SIF and CIRE-SIF relationships across seasons further emphasizes the significant role of canopy structure and chlorophyll information captured by these two indices in explaining global SIF variability. Seasonal analyses indicate that while EVI and CIRE are most effective in most forests and agricultural systems, moisture-sensitive indices and pigment indices perform better during dry seasons and transitional periods in water-limited ecosystems. Spatial residual analyses suggest minimal global bias but systematic underestimation in boreal forests and selected tropical regions, which aligns with established effects of canopy architecture and fluorescence escape probability. Considering that EVI, in particular, is available even from moderate-resolution Earth resource satellite missions such as Sentinel-2 and Landsat, there is substantial potential for SIF downscaling to management and policy-relevant scales.Master of ScienceNew satellite technology from NASA's PACE mission helps us study Earth's plants from space. This project uses PACE data to measure how much plants glow faintly when they photosynthesize, a process called SIF, which shows how active and healthy plants are worldwide. By combining PACE data with information about different landscapes, like forests and grasslands, we created a way to predict this plant glow across the globe. Our findings show that certain measurements, like the greenness of plants, strongly match the glow, especially when looking at seasonal changes, plants behave differently in spring versus winter, for example. These results could help us monitor how plants respond to climate change, improve farming, and better understand how plants store carbon, which is vital for a healthy planet
Asian long-horned tick distributions in Virginia pastures and evaluating the horn fly as a possible vector of Theileria orientalis Ikeda
No full textThe Asian longhorned tick (Haemaphysalis longicornis) is an invasive ectoparasite of growing concern in the U.S. due to its role as the primary vector of the emerging cattle parasite, Theileria orientalis Ikeda. To better understand the transmission landscape in Virginia, this study first evaluated the fine-scale environmental drivers of H. longicornis density. Across two field seasons (2023–2024), 25,929 ticks were collected and analyzed using negative binomial generalized linear mixed models. Results indicated that vegetation height was the most consistent predictor of density, with short vegetation supporting significantly fewer ticks than medium-height vegetation. While relative humidity was positively associated with nymphal density, landscape features like distance to trees or water sources were not significant predictors. These findings suggest that fine-scale pasture management may be a viable tool for reducing tick populations.
However, because T. orientalis outbreaks have been observed in regions with no or low tick density, investigating alternative transmission pathways is essential. To address this, the second phase of this study evaluated the potential for the horn fly (Haematobia irritans), the most economically significant fly pest of U.S. beef cattle, to act as a vector. A total of 2,365 horn flies (254 pools) were collected from nine Virginia counties and screened using conventional and quantitative PCR. T. orientalis Ikeda DNA was confirmed in flies from four counties (Augusta, Bland, Culpeper, and Nottoway), with remaining samples either negative or below the limit of detection.
Collectively, these findings provide a comprehensive look at the ecology of T. orientalis in Virginia. While vegetation management remains a key strategy for controlling the primary tick vector, the detection of Ikeda DNA in horn flies provides the first evidence of this pathogen in a novel arthropod species. This suggests that horn flies may serve as vectors, highlighting a critical need for further experimental studies to determine their epidemiological significance in cattle health management.Master of Science in Life SciencesThe Asian longhorned tick is an invasive species that was first detected in the U.S. on livestock in 2017 (retrospectively shown to be in the country since 2010) and has been rapidly spreading since. Although we are only beginning to fully understand the role of this invasive tick in transmitting pathogens to mammals, it has already shown to cause severe problems for livestock, particularly cattle. It is the only known organism to transmit a protozoan pathogen called Theileria orientalis Ikeda to cattle, which can cause them to become anemic, lose weight, become lethargic, and in rare cases cause death. On top of that, the tick can reproduce asexually, meaning one tick can start an entire population by themselves, a factor which has contributed to their rapid spread. Land managers are having a hard time managing these ticks, but this study offers data that may help them.
This study collected ALT within cattle pastures in Virginia. Field collections were done several times over the summer of 2023 and 2024. A systematic collection enabled analyses aimed at predicting where in a pasture the ticks would be most likely to congregate according to certain physical and environmental conditions. The analyses showed that environmental variables such as vegetation height and relative humidity at ground level were important for predicting how many ticks would be in that area. In general, the ticks avoided shorter vegetation in favor of taller vegetation. This may seem like common knowledge, but we previously lacked hard data that backed up such assumptions. The presence of ticks was not influenced by proximity to trees or water, which was not expected, as proximity to trees and water are usually associated with higher relative humidity levels, which ticks are known to prefer.
The second half of this study investigated the horn fly, a notable cattle pest in the U.S., as a possible alternative vector of T. orientalis. There are cases of T. orientalis Ikeda, where cattle are getting this disease despite no ALT being detected in the pasture. This implies that another organism could be responsible for transmission. Horn flies were chosen to be studied because, like ticks, they also feed on cattle blood, meaning that they could potentially feed on an infected cow and transmit the pathogen to a susceptible cow. This first step aimed to determine if the pathogen is present within horn flies that were feeding on cattle. Horn flies were collected from nine cattle farms in Virginia, some of which had a high rate of T. orientalis Ikeda within the herd. DNA was extracted from collected flies and tested for evidence of T. orientatlis by conventional PCR, and type confirmed via qPCR. Results showed that in four of the nine farms, T. orientalis Ikeda was present in the tested flies. This does not mean that horn flies are actively transmitting the disease, but it does show evidence of infection and lays the groundwork for a future study to examine vector competency. Results from subsequent studies could change the way that horn flies are managed on cattle farms and reveal why pastures without ticks are resulting in cattle contracting the disease
Geothermics
No full textIn this study, we apply control theory to mitigate earthquake hazards to a stress-based model of enhanced geothermal stimulation. The model considers pore pressure diffusion as the main stressing mechanism and rate-and-state friction as the shear failure mechanism. The controller is designed to follow a given average pressure and the probability of exceedance of a red-light earthquake (the magnitude at which the stimulation would have to stop by regulation) within chosen volumes surrounding the injection source and within a target time. We rigorously prove that the proposed controller can effectively force two output types within the system to given references, despite the presence of model uncertainties, and with minimal system information, using a continuous control signal. This framework is applied to a validated model of the 2018 Otaniemi geothermal stimulation. We use a suite of simulations to identify injection scenarios that outperform the 2018 Otaniemi stimulation. The optimal stimulation achieves higher average pressure in a shorter time with lower seismic hazard. The controller can help determine whether a combination of safety thresholds and optimization targets is feasible and economical. The control framework could be used to design stimulation schedules for enhanced geothermal systems.Accepted versio
Quantile Connectedness and Tail Risks: Interactions between Agricultural and Energy Markets
No full textThis study examines the return spillovers and tail-risk dynamics between energy and agricultural commodity markets using a quantile vector autoregression (QVAR) model. We investigate connectedness in the futures contract returns of ten commodities, including energy products (crude oil, heating oil, gasoline, natural gas) and agricultural products (corn, soybeans, wheat, live cattle, lean hogs, cotton), across different market conditions. Our findings indicate that return spillovers intensify significantly in the tails of the return distribution compared to the median, with total connectedness approximately doubling in these tail regions. Energy commodities, particularly crude oil and heating oil, act as net transmitters across most quantiles, while agricultural commodities generally function as net receivers. Corn is an exception, consistently acting as a net transmitter across the entire conditional return distribution. These findings have important implications for investors in risk management and portfolio diversification, as well as for policymakers aiming to manage commodity price risk.Master of ScienceThis study examines how price changes in energy and agricultural commodities spread across markets, with a focus on periods of unusually large gains or losses. We analyze futures returns for ten commodities: crude oil, heating oil, gasoline, natural gas, corn, soybeans, wheat, live cattle, lean hogs, and cotton. We find that energy and agriculture markets become much more tightly linked during extreme market conditions than during typical periods. Energy commodities, especially crude oil and heating oil, most often trigger price changes that ripple through other markets, whereas agricultural commodities typically respond to these shocks. Corn is a notable exception because it frequently influences price movements in other markets. These findings are useful for investors and firms managing commodity risk, as well as for policymakers concerned with market instability and food and energy price pressures