Digital Commons Network^™

Investigating The Consequences Of Conjugated And Secreted Isg15 On Coronavirus Pathogenesis, Mudassir Syed Ali

Dissertations

Coronaviruses have evolved a breadth of mechanisms to antagonize host innate immune responses. One widely studied mechanism is the ability to deconjugate ISG15 from target proteins in a process called deISGylation, which is catalyzed by the papain-like protease (PLP) domain of viral non-structural protein (nsp) 3. Since PLP activity is required for viral replication, it has been challenging to generate an infectious virus with a PLP that maintains protease activity but has lost deISGylase activity. In this study, we generated a chimeric MHV-A59 with its PLP2 domain replaced with that of the human coronavirus HKU1, which has been documented to …

Multi-Modal Emotion Appraisals Using Large Language Models, Carlos Guerrero Alvarez

Computer Science Senior Theses

This thesis investigates the capabilities of large language models (LLMs), specifically GPT4 and GPT4o, in appraising human emotional responses within strategic social scenarios. Building on the work of Houlihan et. al[7], we evaluate LLMs using a dataset of human emotion ratings from game-theoretic situations, later extending the experimental paradigm to include both text and multimodal (image and profession) inputs. Our methodology introduces novel prompting techniques for the experiment at hand, and we compare the performance of these techniques with expert perspectives to assess how different prompts influence model predictions. Results show that LLMs can approximate human emotional appraisals, with the …

Emerging Therapeutic Potential Of Fisetin For Nephrotoxicity, Kidney Injury, And Nephropathy: A Systematic Review, Saeed Mohajeri, Alizamen Salehifard Jouneghani, Saeid Heidari-Soureshjani, Catherine M.T. Sherwin, Faramarz Beigi

Pediatrics Faculty Publications

INTRODUCTION/OBJECTIVE: Kidney diseases cause high morbidity and mortality worldwide. This study investigated the mechanistic effects of Fisetin (FIS) on nephrotoxicity, kidney injury, and nephropathy induced by drugs, toxic chemicals, diabetes, lupus, diet, ureteral obstruction, and ischemic situations.

METHODS: To identify pertinent articles published before Oct 1, 2024, a comprehensive electronic search was performed across several databases, including MEDLINE/PubMed, Embase, Cochrane Library, Web of Science, and Scopus. After establishing clear inclusion and exclusion criteria, studies that met the research objectives were selected. Data were extracted and analyzed, documenting study characteristics, methodologies, and biological mechanisms.

RESULTS: Antioxidant benefits were evident with increased …

Visualizing Sustainability Data With Ai, Matthew Van Dyke, Emily Chen, Hayden Le, Dorothy Xu

Computer Science and Engineering Senior Theses

EcoVisor is a prototype system for extracting, structuring, and visualizing sustainability related metrics from natural language articles. The project integrates a FastAPI backend with a Next.js frontend to transform raw text or article URLs into structured sustainability data, detect trends over time, and generate visual outputs for users. Key capabilities include automated scraping of web articles for sustainability semantics, sustainability related metric data extraction, post-processing of extracted values into cleaned segments and sentences using HTML parsing, grouping of metrics by category and year, generation of Chart.js visualizations, and production of concise “comic brief” summaries for accessible storytelling. EcoVisor aims to …

Atp8b1 Regulates Pip2 Localization And Cleavage Of Pyroptotic Executioner Gasdermin D, Nilam Bhandari, Ashutosh Prince, Mariam R. Khan, Alicia Traughbera, Kalash Neupane, Shuhui W. Lorkowski, Gregory Brubaker, Elif G. Ertugral, Chandrasekhar R. Kothapalli

Chemical & Biomedical Engineering Faculty Publications

Mutations in ATP8B1 cause progressive familial intrahepatic cholestasis, with symptoms including pruritus, pancreatitis, fat malabsorption, intestinal inflammation, and failure to thrive. High-throughput studies showed interconnection between ATP8B1 and phosphoinositide (PIPs), but the mechanism linking ATP8B1, lipid metabolism, and inflammation remains unclear. Atp8b1G308V/G308V mouse model, unbiased RNAseq, high-resolution-stimulation emission depltion (STED)-microscopy, and Crispr-Cas9 generated ATP8B1-/- knockouts in hepatocytes/monocytes/macrophages were used to determine role of ATP8B1 in phosphatidylinositol,4-5-bisphosphate (PIP2) trafficking and inflammation. Human ATP8B1, purified from Sf9 insect cells and reconstituted in proteoliposomes, was used to test cell-free PIP2 flip. Various in-vitro techniques were used for testing direct interaction between PIP2 and …

Biomarker-Guided Imaging And Ai-Augmented Diagnosis Of Degenerative Joint Disease, Rahul Kumar, Kyle Sporn, Aryan Borole, Akshay Khanna, Chirag Gowda, Phani Paladugu, Alex Ngo, Ram Jagadeesan, Nasif Zaman, Alireza Tavakkoli

Department of Medicine Faculty Papers

Degenerative joint disease remains a leading cause of global disability, with early diagnosis posing a significant clinical challenge due to its gradual onset and symptom overlap with other musculoskeletal disorders. This review focuses on emerging diagnostic strategies by synthesizing evidence specifically from studies that integrate biochemical biomarkers, advanced imaging techniques, and machine learning models relevant to osteoarthritis. We evaluate the diagnostic utility of cartilage degradation markers (e.g., CTX-II, COMP), inflammatory cytokines (e.g., IL-1β, TNF-α), and synovial fluid microRNA profiles, and how they correlate with quantitative imaging readouts from T2-mapping MRI, ultrasound elastography, and dual-energy CT. Furthermore, we highlight recent developments …

Shedding Light On Inequities Of Power Outages Through Data Transparency, Kelly A. Stevens, Sanam K. Aksha, Mohammed Siddiqur Rahman, Elizabeth Trader, Herbert Longenecker, Rebecca Entress

Faculty Publications

In a changing climate, the electricity grid is increasingly exposed to more extreme weather that results in significant power outages. Further, lower income and racial-ethnic minority households are more likely to experience a higher frequency and duration of power outages compared to less socially vulnerable groups. The literature on the unequal impacts of power outages is a new, growing area of research that has been stymied in part due to the difficulty acquiring high spatial resolution, historical power outage data from utilities. In this Perspectives article, we review the availability of power outage data, and what can be learned from …

Shedding Light On Inequities Of Power Outages Through Data Transparency, Kelly A. Stevens, Sanam K. Aksha, Mohammad Siddiqur Rahman, Elizabeth Trader, Herbert Longenecker, Rebecca Entress, Thomas Wahl, Christopher Emrich, Kristopher O. Davis

Faculty Publications

In a changing climate, the electricity grid is increasingly exposed to more extreme weather that results in significant power outages. Further, lower income and racial-ethnic minority households are more likely to experience a higher frequency and duration of power outages compared to less socially vulnerable groups. The literature on the unequal impacts of power outages is a new, growing area of research that has been stymied in part due to the difficulty acquiring high spatial resolution, historical power outage data from utilities. In this Perspectives article, we review the availability of power outage data, and what can be learned from …

Electrochemical Three-Dimensional Printing And Soldering, Arash Takshi, Sabrina Marie Rosa-Ortiz

USF Patents

A hydrogen evolution assisted electroplating nozzle includes a nozzle tip configured to interface with a portion of a substructure. The nozzle also includes an inner coaxial tube connected to a reservoir containing an electrolyte and an anode, the inner coaxial tube configured to dispense the electrolyte through the nozzle tip onto the portion of the substructure. The nozzle also includes an outer coaxial tube encompassing the inner coaxial tube, the outer coaxial tube configured to extract the electrolyte from the portion of the substructure. The nozzle also includes at least one contact pin configured to make electrical contact with a …

Systems, Methods, And Media For Monitoring The Production Process Of A Product, Chris Peter Tsokos, Lohuwa Mamudu

USF Patents

In accordance with some embodiments, systems, methods, and media for monitoring a production process of a product are provided. In some embodiments, a system comprises a remote server, a communications connection between the remote server and a facility database, at least one processor coupled to the communication system, and a memory device having stored thereon a set of computer readable instructions. The set of computer readable instructions cause the at least one processor to: receive a first set of data related to the production process, calculate a first monitoring index indicator for the production process based on the first set …

Systems And Methods For Providing Active Contraction Properties Of The Myocardium Using Limited Clinical Metrics, Igor Nobrega, Wenbin Mao

USF Patents

A deep learning model can be used for the identification of active contraction properties of the myocardium using limited clinical methods. A method for identifying the active contraction properties can include inputting a plurality of clinical metrics into a deep learning model. The method can further include inputting a representation of a cardiac cycle through a pressure volume-loop into the deep learning model. The deep learning model can include a first process layer with a first intermediate output and a second process layer that receives the first intermediate output as a first intermediate input. The method can further include outputting …

Gamma Irradiation Effects On Physical And Electronic Properties Of Monolayer Cvd Grown Graphene, Chintan P. Chavda, Ashok Srivastava, Erin Vaughan, Jianwei Wang, Manas Ranjan Gartia, Georgios Veronis

Faculty Publications

Two-dimensional material graphene has proven to have remarkable electrical and photonic properties, opening the door to a wide range of uses, including employment under the harsh conditions of space. The creation of graphene on various substrate types is known to be possible via a number of approaches, including direct deposition and the substrate transfer process. In this work, we used an argon plasma, methane as a carbon source, and a nanoCVD-8G graphene reactor to deposit monolayer graphene (MLG) on transition metal substrates for studying the effects of gamma irradiation on the physical and electronic properties. Graphene's crystalline structure is investigated …

Machine Verification Of Correctness For A Concurrent Union-Find Object, Karun Ram

Computer Science Senior Theses

We consider a family of near-optimal randomized multiprocessor implementations for the union-find problem due to Jayanti and Tarjan–known as the Jayanti-Tarjan Randomized-Linking (JT-RL) union-find objects–and provide the first formal and fully machine-verified proof of their strong linearizability (i.e., correctness). Their algorithms are efficient both in theory and in practice: numerous benchmarking works demonstrate that they perform faster, or as fast, as all other known implementations for the union-find object on both CPUs and GPUs.

The correctness of the JT-RL algorithms is subtle, which motivates the need for formal verification. To this end, we first specify the JT-RL objects in TLA+, …

The Case For Visual Art In Overcoming The Double Empathy Problem, Katelyn Milea Rose Nilson

Theses and Dissertations

A person's cognitive environment--made up of their thoughts, experiences, and tendencies--can affect how they empathize with others. Those with significantly different cognitive environments, such as autistic and neurotypical individuals, may have a difficult time empathizing with one another. This study aimed to facilitate empathy between the two groups by aligning their cognitive environments through discussion about visual art. Five autistic neurotypical dyads completed three discussion sessions where they observed and journaled about a piece of art, discussed their thoughts with each other, and filled out a questionnaire about their experience. All participants also completed a post-study interview. Data from questionnaires, …

Level Of Service Criteria For Urban Arterials With Heterogeneous And Undisciplined Traffic Streams, Afzal Ahmed, Farah Khan, Syed Faraz Abbas Rizvi, Fatma Outay, Muhammad Faiq Ahmed, Muhammad Adnan

All Works

Accurate evaluation of the prevailing traffic operations plays an important part in developing sustainable transport systems. This research examines the suitability of the level of service (LOS) criteria developed by the Indian and United States (US) Highway Capacity Manuals (HCM) for heterogeneous and undisciplined traffic streams and proposes new criteria using a data-driven approach. Traffic data were collected from a selected major arterial in Karachi, and fundamental diagrams were developed using these data. These fundamental diagrams and field-collected data were analyzed using the K-mean clustering approach to examine the actual traffic states at various LOS bands used in practice. Associating …

Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map Of The Human Kidney Across The Lifespan, Liam Mclaughlin, Bo Zhang, Siddharth Sharma, Amanda L Knoten, Madhurima Kaushal, Jeffrey M Purkerson, Heidie L Huyck, Gloria S Pryhuber, Joseph P Gaut, Sanjay Jain

2020-Current year OA Pubs

The human kidney maintains homeostasis through a complex network of up to a million nephrons, its fundamental tissue units. Using innovative tissue processing and light sheet fluorescence microscopy, we mapped the 3D neurovascular connectivity of nephrons to understand how their structural organization enables coordinated functions like filtration, absorption, and blood pressure regulation. Our analysis revealed developmental changes in glomerular orientation, density, volume, and innervation from birth through aging. We discovered an extensive nerve network connecting different nephron segments and organizing glomeruli into distinct communities. These communities are linked through "mother glomeruli" that serve as control centers, creating a repeating pattern …

An Isometry Theorem For Persistent Homology Of Circle-Valued Functions, Nathan Broomhead, Mariam Pirashvili

School of Engineering, Computing and Mathematics

This paper explores persistence modules for circle-valued functions, presenting a new extension of the interleaving and bottleneck distances in this setting. We propose a natural generalisation of barcodes in terms of arcs on a geometric model associated to the derived category of quiver representations. The main result is an isometry theorem that establishes an equivalence between the interleaving distance and the bottleneck distance for circle-valued persistence modules.

Convergence Research For Microplastic Pollution At The Watershed Scale, Heejun Chang, Elise F. Granek, Amanda Gannon, Jordyn M. Wolfand, Janice Brahney

Geography Faculty Publications and Presentations

Microplastics are found in Earth’s atmosphere, lithosphere, hydrosphere, pedosphere, and ecosphere. While there is a growing interest and need to solve this grand challenge in both the academic and policy realms, few have engaged with academics, policymakers, and community partners to co-identify the problem, co-design research, and co-produce knowledge in tackling this issue. Using a convergence research framework, we investigated the perception of microplastic pollution among different end users, delivered educational materials to K-12 teachers and practitioners, and identified key sampling points for assessing environmental microplastic concentrations in the Columbia River Basin, United States. Three community partner workshops identified regional …

A Heterogeneous Kinetic Monte Carlo Model Of Maleic Anhydride Grafting Onto Polypropylene, Tomás Romero Pietrafesa, Jorge Guapacha, Mariano Asteasuain

Polymer Reaction Engineering XII

Please click Additional Files below to see the full abstract

Safe Human–Robot Collaboration With Risk Tunable Control Barrier Functions, Vipul K. Sharma, Pokuang Zhou, Zhengtong Xu, Yu She, S. Sivaranjani

School of Industrial Engineering Faculty Publications

In this article, we consider the problem of guaranteeing safety constraint satisfaction in human–robot collaboration (HRC) with uncertain human position. We pose this problem as a chance-constrained problem with safety (chance) constraints represented by uncertain control barrier functions, where the probability of safety constraint satisfaction under uncertainty is bounded by a tunable user-defined risk. We solve this stochastic optimization problem using a sampling-based approach and obtain a risk-tunable controller to safely accomplish HRC tasks. We demonstrate the safety and performance of this approach through both simulation and hardware experiments on a 7 degree-of-freedom Franka–Panda manipulator and characterize the tradeoff between …

Phage-Induced Protection Against Lethal Bacterial Reinfection, Yikun Xing, Haroldo J Hernandez Santos, Ling Qiu, Samantha R Ritter, Jacob J Zulk, Rachel Lahowetz, Kathryn A Patras, Austen L Terwilliger, Anthony W Maresso

Faculty, Staff and Students Publications

Bacteriophages, or phages, are viruses that target and infect bacteria. Due to a worldwide rise in antimicrobial resistance (AMR), phages have been proposed as a promising alternative to antibiotics for the treatment of resistant bacterial infections. Up to this point in history, phage use in preclinical animal studies, clinical trials, and emergency-use compassionate care cases has centered around the original observation from 1915 showing phage as lytic agent, and thus a treatment that kills bacteria. Here, we describe an activity associated with phage therapy that extends beyond lytic activity that results in long-term protection against reinfection. This activity is potent, …

Moderating Role Of Locus Of Control On The Relationship Between Self-Efficacy And Trust In Ai, Amelia Gillies

Walden Dissertations and Doctoral Studies

The rapid integration of artificial intelligence (AI) into essential sectors, including healthcare, customer services, and defense, has underscored the importance of user trust in AI systems. Psychological traits such as locus of control (the extent to which individuals attribute outcomes to internal or external factors) and self-efficacy (individuals’ confidence in their ability) have been identified as significant factors influencing trust in these automated systems. Previous studies have independently linked these psychological traits to trust in technology; however, there has been limited exploration of potential moderating effects of locus of control on the relationship between digital technology self-efficacy and trust in …

Pyruvate Dehydrogenase Kinase 4 Mediates Sex Specific Outcomes In Sepsis Induced Cardiomyopathy, John Yap

Dissertations

During sepsis, males often experience worse cardiac outcomes than females. Here, we identified pyruvate dehydrogenase kinase 4 (PDK4) as a key contributor to this disparity. PDK4 is a mitochondrial protein that regulates glucose utilization by inhibiting pyruvate dehydrogenase (PDH). Using a mouse model of endotoxemia, we induced acute inflammation with a sublethal dose of lipopolysaccharide (LPS), which caused cardiac dysfunction and significantly increased myocardial PDK4 expression in males but not females. Cardiac-specific PDK4 overexpression promoted LPS-induced cardiac dysfunction in both sexes, whereas cardiac-specific PDK4 knockout provided protection. In wild-type males, LPS disrupted cardiac metabolism by decreasing PDH activity and fatty …

Interrogating The Dispersal Process And Relevant Genes In Vibrio Fischeri, Jeremy Esin

Dissertations

Biofilms are aggregates of bacteria encased in a matrix that shields bacteria from environmental hazards. These structures are formed in response to cues from the environment and drive colonization of new niches. Biofilms can be both beneficial and detrimental. Largely, research focuses on biofilms that have negative outcomes in clinical, environmental, and economical settings. However, the value of beneficial biofilms is recognized and studied. The marine bacterium Vibrio fischeri is part of a model system for studying symbiotic biofilms in a eukaryotic host. V. fischeri produces a transient biofilm at the surface of a specialized light organ and then disperses …

Marketing De Moda Predictivo E Inclusivo: Estrategias De Segmentación Avanzada Para Audiencias Diversas Con Inteligencia Artificial, Oscar Barroso Huertas

GDI. Revista de investigación de Género, Diseño e Innovación

Introducción: El marketing predictivo, impulsado por la inteligencia artificial (IA), está transformando cómo las marcas anticipan las necesidades de sus audiencias. En Moda, la personalización es clave para conectar emocionalmente con los consumidores, pero también es esencial que las marcas sean inclusivas, respetando la diversidad y la privacidad. Este artículo explora cómo las marcas de moda usan el marketing predictivo para segmentar audiencias diversas, garantizando campañas personalizadas e inclusivas. Metodología: Este estudio adopta un enfoque mixto, combinando revisión documental y análisis cualitativo. Se revisan fuentes académicas y casos de marcas que aplican marketing predictivo inclusivo, utilizando tecnologías como machine learning …

Exploring Educator Psychological Capital Through Participation In A Coordinated School Violence Prevention Approach, Stephanie Lorraine Neff

Walden Dissertations and Doctoral Studies

This study is a description of how educators’ participation in a coordinated approach to violence prevention contributed to employee wellness and school climate. Using principles of psychological capital (PsyCap) theory, archival focus group and interview data were used to describe educator experiences during implementation of a 3-year coordinated approach to school violence in a mid-sized public school district. Findings of the analysis revealed consistent references to feelings of hope, efficacy, resilience, and optimism throughout the study, but with slight shifts in frequency each year based on both internal (i.e. skill development, relationship-building), and external (i.e. administrative support, policy directives, broader …

Dynamics Of Urban Heat And Green Infrastructure, Yunjae Ock

Dissertations and Theses

This dissertation provides a comprehensive analysis of the interaction between urban heat and green infrastructure (GI) in terms of dynamic aspects, spatiotemporal variation across various spatial scales, temporal phases, and socioeconomic contexts. By integrating a national-scale longitudinal analysis, street-level structural assessments, and neighborhood-specific resilience frameworks, this study enhances our understanding of how cities can utilize existing ecological assets to mitigate increasing heat risks while addressing systemic inequities.

Urban areas face unprecedented thermal challenges due to climate change and the urban heat island effect, with marginalized communities disproportionately affected. Although cities are increasingly adopting GI expansion for heat mitigation, significant knowledge …

A Survey Of Feature Attribution Techniques In Explainable Ai: Taxonomy, Analysis And Comparison, Mohd Amril Nazir, Edmund Evangelista, Syed Muhammad Salman Bukhari, Ravishankar Sharma

All Works

The feature attribution methods have become central to explainable artificial intelligence (XAI), providing critical insights into how machine learning (ML) models make individual and aggregate decisions. This survey presents a complete taxonomy of feature attribution techniques, organizing them into model-agnostic and model-specific categories while highlighting extensions such as rule-based and attention-based explanations. We analyze formal definitions of each method, mathematical formulations, application contexts, strengths, and limitations. A comparative analysis highlights key trade-offs among model flexibility, computational cost, explanation fidelity, and interpretability. In addition to theoretical perspectives, we provide practical comparisons of selected methods on benchmark tasks to guide real-world applicability. …

Mutant P53 Gain Of Function: Why Many See It, Why Some Do Not, Guillermina Lozano, Carol Prives, Kanaga Sabapathy

Faculty, Staff and Student Publications

Mutations in the TP53 tumor-suppressor gene in human cancer are unique in that 60% to 70% are of the missense variety, resulting in a full-length protein that is often highly expressed in patients' tumors. These missense mutant proteins often exhibit pro-oncogenic activities (referred to as gain of function) in mouse models and human cell lines and correlate with poor cancer prognosis in some cases.

A Novel Cardiomyopathy Phenotype Linked To A Chd7 Missense Variant, In Young Park, Chih-Wei Hsu, Karim Bouazoune, Christina E Espindola, Madeline Hannah Mclaughlin Armond, Cristian Coarfa, Sandra L Grimm, James F Martin, Donna M Martin, Cheryl Lyn Walker

Center for Medical Ethics and Health Policy Staff Publications

Loss of function in the chromatin remodeler CHD7 causes CHARGE syndrome, characterized by variable penetrance and diverse abnormalities. However, establishing genotype-phenotype correlations has been challenging, as most CHD7 inactivating mutations are null alleles. Through CHD7 missense variant analysis at potential phosphorylation sites, we identified T730 (T720 in mice) as a critical residue associated with pathogenesis. Using a CHD7 T730 missense variant (Chd7T720A) and a frameshift null allele (Chd7fs) in a mouse model, we found that Chd7fs/fs mice were non-viable, while Chd7fs/+ mice exhibited haploinsufficiency-related circling behavior. Notably, Chd7fs/T720A mice died before postnatal …