Digital Commons Network^™

An Ai Approach To Differentiating Lung Squamous Cell Carcinoma From Metastases Of Other Origins, Mark G Evans, Jennifer Ribeiro, Todd Maney, Anthony Helmstetter, Jennifer Johnson, Anthony Karnezis, Casey Bales, George Sledge, David Spetzler, Ari Vanderwalde, Matthew Oberley, Balazs Halmos, Hossein Borghaei, Farah Abdulla, David Bryant, Fred Hirsch, Hassan Ghani

Department of Medical Oncology Faculty Papers

IMPORTANCE: Distinguishing primary lung squamous cell carcinoma (SCC) from squamous metastases to the lung is a clinical challenge due to histopathologic similarities. Accurate diagnosis is essential to guide treatment decisions.

OBJECTIVE: To assess the utility of an artificial intelligence (AI) approach that includes evaluation of key orthogonal evidence in distinguishing primary lung SCCs from metastatic tumors of other tissue origins.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used GPSai, a tissue-of-origin AI model run automatically on each sample submitted for molecular profiling, to flag potential misdiagnoses among research-eligible cases submitted as lung SCC. Molecularly profiled cases within the Caris Life …

(Si16-06) Equations Of Geodesics In Two-Dimensional Finsler Manifold With A Special Cubic (Α, Β)-Metric, Sejal Prajapati, Brijesh Kumar Tripathi, V. K. Chaubey

Applications and Applied Mathematics: An International Journal (AAM)

Geodesics represent the shortest path between two points in curved spacetime and are vital in the study of Finsler manifolds. Matsumoto and Park first derived the geodesic equation as a secondorder differential equation in a two-dimensional Finsler manifold with Randers, Kropina, and Matsumoto metrics. Building on this foundation, our paper presents the geodesic differential equation for a two-dimensional Finsler manifold using a special cubic power metric. In this two-dimensional setting, this work also looks at certain well-known geometric curves and analyzes their variants as solutions to the geodesic differential equation. Additionally, this work examines the geometric applications of the geodesic’s …

Alfred Russel Wallace Notes 39. What About Wallace's 'Agnosticism'...?, Charles H. Smith

Faculty/Staff Personal Papers

Alfred Russel Wallace (1823−1913) seems to have distinguished his earlier years of agnosticism from his later period as a spiritualist, but a closer look at the situation suggests he actually remained an agnostic all the way through to the end of his life. The confusion is occasioned by a lack of terminology that can be applied to his position, which most closely resembles a Spinozian manner of thinking.

An Seir Model On Time Scales With Discrete Applications To Tuberculosis, E. Akın, G. Yeni, D. Konur, S. R. Işık, M. R. Işık

Mathematics and Statistics Faculty Research & Creative Works

In this paper, we propose a novel dynamical model on time scales consisting of new parameters to investigate the transmission dynamics of tuberculosis (TB), one of the deadliest infectious diseases worldwide, characterized by a long latency stage. The dynamical TB model, governed by the Susceptible–Exposed–Infected–Recovered (SEIR) framework within a unified form, yields a continuous model with a non-saturated incidence rate on the real numbers and discrete models with saturated incidence rates when different time domains are chosen. We analyze the stability of the equilibrium points of both the continuous TB model on the set of real numbers and the discrete …

An Odd Protocol For An Agent-Based Model Of Hepatitis C Virus Transmission In A Homogeneous Syringe-Sharing Network, Seun Ale, Que Thi Nguyet Nguyen Dr., John D. Kelleher Prof., Elizabeth Hunter Dr.

Reports

The model described in this ODD is an agent-based model of hepatitis C virus (HCV) transmission among people who inject drugs (PWID). The model assumes homogeneous mixing among syringe-sharing agents, without any form of heterogeneity in the agents interactions or syringe-sharing attitude. All syringe-sharing PWID are treated as identical in terms of their interaction frequency and syringe-sharing probability. Interactions are generated dynamically using proximity-based sampling at each timestep (one day), allowing agents to form syringe-sharing interactions based on spatial closeness. The number of daily interaction events is fixed at the population level, and each syringe-sharing agent has the same probability …

An Odd Protocol For An Agent-Based Model Of Hepatitis C Virus Transmission With Inter- And Intra-Group Structural And Behavioural Heterogeneous Syringe-Sharing Networks (5), Seun Ale, Que Nguyen Dr., John D. Kelleher Prof., Elizabeth Hunter Dr.

Reports

The model described in this ODD is an agent-based model of hepatitis C virus (HCV) transmission among people who inject drugs (PWID). The model incorporates structural heterogeneity through a three-group interaction framework and behavioural heterogeneity through group-specific syringe-sharing rates with additional intra-group variability. The syringe-sharing population in the model is divided into core, inner, and outer circle groups representing individuals with high, moderate, and low levels of syringe-sharing interaction intensity, respectively. In addition to differences in the number of daily interaction opportunities across groups, agents in each group are assigned syringe-sharing probabilities that vary at the individual level around their …

Neurosymbolic Counterpoint Generation, Paul D. Jarski

Master's Theses

Recent advancements in generative artificial intelligence have revolutionized music generation, yet research has predominantly focused on raw audio synthesis over music in symbolic form, i.e. a score. This thesis presents the first neurosymbolic model designed to generate imitative Renaissance counterpoint in symbolic (MIDI) format. By leveraging an autoregressive Transformer architecture, this research explores the capacity of deep learning models to manage independent voices and strict stylistic constraints.

We compare multiple data representation strategies with distinct tokenization methods. The proposed model incorporates a symbolic component that enforces fundamental contrapuntal rules. Additionally, this thesis contributes a preprocessed dataset of Renaissance polyphony, in …

College Of Natural Sciences 2025 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Dean's Message 
Page 3 Department Highlights 
Page 4 One Day for State 
Page 5 Ice cores reveal volcanic eruptions in 13th century 
Page 5 How do our cells interpret stress 
Page 6-7 Faculty Excellence
Page 8 New chemical biology consortium will accelerate cancer research
Page 9 SDSU to combat crop disease, biofilms in new NSF-back project 
Page 9 Science as Art Competition 
Page 10-11 Student Excellence  
Page 12 SDSU researcher developing natural alternative to synthetic dyes
Page 12 Browning Retired
Page 13 Quantum technologies through NSF-backed project
Page 13 NASA Funds CNS Development of Model
Page 14 GGS …

An Odd Protocol For An Agent-Based Model Of Hepatitis C Virus Transmission In A Two-Group Structural Heterogeneous Syringe-Sharing Network (M2), Seun Ale, Que Nguyen Dr., John D. Kelleher Prof., Elizabeth Hunter Dr.

Reports

The model described in this ODD is an agent-based model of hepatitis C virus (HCV) transmission among people who inject drugs (PWID). The model extended a baseline homogeneous model by incorporating structural heterogeneity via a two-group interaction framework. The syringe-sharing population in the model is divided into inner and outer circle groups representing individuals with differing levels of syringe-sharing interaction intensity. While all agents share the same syringe-sharing probability and epidemiological processes remain identical across agents, the number of daily interaction opportunities differs between the two groups. Interactions in the model are generated dynamically using proximity-based sampling at each timestep …

An Odd Protocol For An Agent-Based Model Of Hepatitis C Virus Transmission In A Three-Group Structural Heterogeneous Syringe-Sharing Network (M3), Seun Ale, Que Nguyen Dr., John D. Kelleher Prof., Elizabeth Hunter Dr.

Reports

The model described in this ODD is an agent-based model of hepatitis C virus (HCV) transmission among people who inject drugs (PWID). The model incorporates structural heterogeneity through a three-group interaction framework. The syringe-sharing population in the model is divided into core, inner, and outer circle groups representing individuals with high, moderate, and low levels of syringe-sharing interaction intensity, respectively. While the syringe-sharing rate and all epidemiological processes remain identical across agents, the number of daily interaction opportunities differs by agent grouping, capturing variation in structural position within the syringe-sharing network. Interactions are generated dynamically using proximity-based sampling at each …

An Odd Protocol For An Agent-Based Model Of Hepatitis C Virus Transmission With Inter-Group Structural And Behavioural Heterogeneous Syringe-Sharing Networks (M4), Seun Ale, Que Nguyen Dr., John D. Kelleher Prof., Elizabeth Hunter Dr.

Reports

The model described in this ODD is an agent-based model of hepatitis C virus (HCV) transmission among people who inject drugs (PWID). The model incorporates structural heterogeneity through a three-group interaction framework and behavioural heterogeneity through group-specific syringe-sharing rates. The syringe-sharing population in the model is divided into core, inner, and outer circle groups representing individuals with high, moderate, and low levels of syringe-sharing interaction intensity, respectively. In addition to differences in the number of daily interaction opportunities across groups, agents in each group are assigned distinct syringe-sharing probabilities, reflecting variation in risk-taking behaviour across structural groups within the syringe-sharing …

The Modern Sisyphus Blows Leaves: Attitudes And Impacts Regarding Leaf Litter Removal On A Suburban Campus, A. C. Nony, M. R. Mcclung, M. L. Reid

Journal of the Arkansas Academy of Science

Leaf litter habitat disruption in suburban spaces stems from the prevalence of “lawn culture,” that is, the accepted societal norm that land immediately surrounding humans or meant for human recreational use should be clean, tidy, controlled, and aesthetically pleasing, above other considerations. When leaf litter on residential and recreational lawns is cleared, it removes vital habitat for organisms of several taxa, especially species that rely on litter as a moisture and temperature-controlled substrate for overwintering. We administered an opinion survey to students, staff, and faculty at Hendrix College, a highly residential and suburban campus in Conway, Arkansas, to assess views …

Identification Of Microplastics And Additives From The Lake Erie Watershed And The Cuyahoga River Via Maldi-Ms And Dart-Ms, Chrys Wesdemiotis, Calum Bochenek, Luciana Rivera Molina, Robert Brand

University Research

Micro(nano)plastics have received increased attention as environmental contaminants due to their harmful effects on ecosystems and human health. Conventional extraction methods for microplastic analysis are often lengthy and complicated, resulting in the loss of important chemical components such as additives. In this study, we provide a complementary approach, utilizing matrix-assisted laser desorption/ionization (MALDI) and direct analysis in real time (DART) mass spectrometry (MS) techniques, with minimal extraction and sample preparation to preserve both polymer and additive information. MALDI-MS was applied to aqueous samples collected along the shores of Lake Erie and the Cuyahoga River, successfully identifying the base polymer(s) in …

Time-Dependent Amplification Of Growth Rates In A Plankton-Oxygen Model, Rapha Coutin

Master's Theses

Near-bottom hypoxia occurs when dissolved oxygen levels drop to a level that is harmful to marine biology, creating biological dead zones along the ocean floor. Recent years have seen a dramatic increase in the percentage of coastal, near-bottom, hypoxic water, with the average in 2021 nearly double that of the average from 2009 to 2018 and about twenty-eight times the average from 1950 to 1980. Recent literature has linked this increase in oceanic hypoxia to the increase in upwelling-favorable winds caused by climate change. Upwelling brings low-oxygen, nutrient-rich water up to the surface, leading to plankton blooms and mass consumption …

Plm-Effector: Unleashing The Potential Of Protein Language Models For Bacterial Secreted Protein Prediction, Dandan Zheng, Lihong Chen, Guansong Pang, Jian Yang

Research Collection School Of Computing and Information Systems

Bacterial secreted proteins, particularly effectors delivered by specialized secretion systems, are key mediators of virulence and host-pathogen interactions. However, accurate computational identification remains challenging, as many existing methods rely heavily on sequence similarity or handcrafted features, and often focus on a single secretion system. Recent studies have reported that some bacterial effectors may be associated with more than one secretion system, highlighting the complexity of secretion system annotation and motivating the development of system-aware computational prediction approaches. Here, we present PLM-Effector, a hybrid deep learning framework that integrates modern protein language models (PLMs) with multiple neural architectures via a two-layer …

Does Genetic Testing Influence Outcomes: Early Experience In Melanoma Case Series, Ryan Reyes, George Skenteris, Stella Coker Watson Self Ph.D., Ms, Christine Marie-Gilligan Schammel, Steven D. Trocha

Faculty Publications

Background:

The treatment and prognosis of melanoma have historically been based on histologic stage and Breslow depth; however, due to the increase in surveillance, melanomas are being identified at an earlier stage and lower Breslow depth. Advances in genetic testing, such as Decision Dx®, mean that melanoma diagnostic decisions and prognosis can now be directed by genetics. The purpose of this project was to assess the influence of a Decision Dx® high-grade (Class 2A/B) classification on the treatment of melanoma patients at a regional medical center, particularly those not deemed high risk by conventional classification methods, including Breslow depth and …

Empirical Comparisons Of Partial Dimension Reduction Algorithms In High-Dimensional Regression, Nathan Greenfield

Master's Theses

In high-dimensional regression problems, dimension reduction methods are often used to address the challenges of multicollinearity and estimation instability. Partial dimension reduction extends these ideas by applying dimension reduction to a subset of the predictors, while the remaining predictors are modeled without compression. This approach is particularly useful when it is important to retain variability and interpretability in certain predictors.

This thesis investigates the empirical performance of partial dimension reduction algorithms and introduces a novel algorithm, Iterative Partial Residual (IPR). Two algorithms are considered: a baseline algorithm, Marginal Residual (MR), and the proposed IPR method. Their predictive performance is evaluated …

Trophic Structure And Mercury Bioaccumulation In Walleye And Yellow Perch In The Upper And Lower Red Lake Basins, Marissa Pribyl

Biology Graduate Theses

Mercury is a persistent global contaminant that biomagnifies through aquatic food webs, with dietary and environmental factors serving as the primary drivers of accumulation in fishes. Trophic structure and methylmercury dynamics in Walleye (ogaa; Sander vitreus) and Yellow Perch (asaawens; Perca flavescens) were investigated in the Upper and Lower Red Lake basins in Red Lake, Minnesota, during 2024-2025. Diets of Walleye and Yellow Perch were assessed through stomach dissections, and tissue samples from both species were analyzed for total mercury concentrations. Additional analyses included shiners (gigoozens; Notropis spp., Hudsonius spp.) along with a variety of freshwater fish and …

Comparison Of Analytical Techniques From The Extraction Of Bioactive Compounds From Kratom, Curry, Ginger, And Turmeric, Riley Bruno

Honors Program: Senior Projects (Public)

Plants, herbs, and spices have been used as medicines for thousands of years. Early civilizations often attributed healing properties of plants to magical or divine forces. However, as chemistry and analytical technology advanced between the 16th and 18th centuries, scientists began to understand that bioactive compounds within the plants actually caused these effects. Today, natural products remain extremely important in drug discovery. As the number of newly developed synthetic drugs declines, there has been renewed interest in identifying biologically active molecules from plants. Bioactive molecules are a group of diverse chemical compounds that stimulate a response in living tissues. The …

The Application, Construction, And Validation Of Hidden Markov Model Profiles For Carbonic Anhydrase Enzymes, Samuel F. Kaplan

Master's Theses

Carbonic anhydrases (CAs) catalyze the reversible hydration of CO2 and have evolved independently at least eight times, resulting in structurally distinct enzyme families (α, β, γ, δ, ζ, η, θ, ι). Traditional sequence alignment methods struggle to classify these convergently evolved proteins because their sequential similarity does not reliably indicate functional or evolutionary relationships. Many CA sequences in public databases are annotated generically without family assignments, and prior computational approaches have focused predominantly on the three well characterized families (α, β, γ), leaving the five recently discovered classes without robust classification tools. Family level assignment is often a prerequisite for …

Environmental Impact Of Preventative Fire-Retardant Applications On Soil Water Chemistry, Patrick C. Michelsen

Master's Theses

Between 1992 and 2012, 84% of all documented wildfires were started by humans. These fires often start around high-risk locations such as power lines and roadsides where fuel loads are near these potential human-caused ignition sources. Point source ignition sites that are surrounded by shrubs or grasslands are especially important because fires that occur within these biomes are responsible for far more destruction of property than forest fires. One strategy that is effective at mitigating the spread of fires from ignition sites that are within grassland or shrub biomes are preventative fire-retardant products (PFRPs). These PFRPs differ from traditional fire-retardant …

Molecular Lung Imaging Following Exposure To Radiation Predicts Long-Term Survival In Rats, Anne V. Clough, Kathrina Mpala, Taheri Pardis, Laura Norwood Toro, Andreas M. Beyer, Tracy Gasperetti, Ming Zhao, Sarah Kerns, Heather A. Himburg, Said H. Audi

Mathematical and Statistical Science Faculty Research and Publications

Delayed effects of acute radiation exposure (DEARE), including radiation pneumonitis (lung-DEARE), develop weeks to months after radiation exposure. Pathway-targeted biomarkers that capture early oxidative stress and cell death could improve risk stratification and provide objective measures of mitigator efficacy. The objective was to test whether molecular lung imaging predicts long-term survival and mitigator response after irradiation. Rats received 13.5 Gy leg-out partial-body irradiation with a subset treated with the radiation-injury mitigator lisinopril. Rats underwent lung imaging at weeks 2 and 4 post-irradiation with ^99mTc-duramycin (cell death) and ^99mTc-HMPAO (oxidative stress). Plasma mitochondrial damage-associated molecular patterns (mtDAMPs) were also …

N-Dqn: Neutrosophic Deep Q-Network For Uncertainty-Aware Forecasting And Decision Optimization, Rania Lutfi

Neutrosophic Systems with Applications

Uncertainty remains a critical challenge in dynamic spatiotemporal forecasting. This study proposes the Neutrosophic Deep Q-Network (N-DQN), a framework that integrates neutrosophic logic with deep reinforcement learning to enhance decision optimization under uncertainty. Features are modeled through truth, indeterminacy, and falsity membership functions, enabling robust handling of ambiguous data. The framework incorporates attention-guided preprocessing and horizon-aware optimization to adapt predictions across short- and long-term intervals. Experiments on benchmark traffic datasets (METR-LA and PEMS-BAY) demonstrate improved forecasting accuracy and reduced error rates compared with established baselines. The results highlight the scalability and resilience of N-DQN, positioning it as a promising approach …

An Electrochemiluminescence-Based Arsenic (Iii) Sensor Using Luminol On Screen-Printed Gold Electrodes, Harmesa Harmesa, Isnaini Rahmawati, Andrea Fiorani, Yasuaki Einaga, Eny Kusrini, A’An Johan Wahyudi, Asep Saefumillah, Tribidasari A Ivandini

Journal of Electrochemistry

Electrochemiluminescence (ECL) of luminol has been studied on a screen-printed gold electrode for a simple and sensitive detection of arsenic ions (As(III)). Cyclic voltammetry (CV) was applied as the proposed technique to study luminol’s electrochemical behavior and to evaluate the arsenic’s effect in the ECL system, while hydrogen peroxide (H₂O₂) served as a co-reactant to enhance luminol’s light emission under alkaline conditions. To achieve optimal electrode performance, key parameters including pH, scan rate, and the concentrations of H₂O₂ and luminol were carefully optimized. The presence of As(III) induced a quenching effect on the …

Exosome Engineering For Blocking Gut Dysbiosis And Inducing Cell Death Mechanisms In Glioblastoma Multiforme, Ahalya Muraleedharan, Karthik Rangavajhula, Swapan K. Ray

Faculty Publications

Glioblastoma multiforme (GBM) is the most lethal primary brain tumor in adults. Emerging evidence endorses that gut dysbiosis contributes to GBM progression through the gut–brain axis (GBA), promoting inflammation and therapeutic resistance via abnormal short-chain fatty acid production and cytokine dysregulation. Exosomes, naturally occurring nanovesicles (30–150 nm), offer promising therapeutic potential due to their blood–brain barrier permeability, biocompatibility, and versatile cargo capacity. This review examines exosome engineering strategies for dual targeting: inhibiting alterations in gut microbiome and inducing regulated cell death mechanisms such as apoptosis and ferroptosis in GBM. We describe exosome engineering with detailed focus on cargo loading approaches …

Egain Tube Memristors Offering Reliable Switching On A Biological Time Scale, Yuriy V. Pershin, Liya Patel, Bapi Bera, Doug Aaron, Stephen A. Sarles

Faculty Publications

Memristive devices have been considered promising candidates for nature-inspired computing and in-memory information processing. However, experimental devices developed to date typically show significant variability and function at different time scales than biological neurons and synapses. This study presents a memristive device comprised of liquid-metal eutectic gallium indium (EGaIn) contained within a mm-scale tube that operates via a bulk, voltage-dependent switching mechanism and exhibits distinct unipolar resistive switching characteristics that occur on a biological time scale (tens of milliseconds). The switching mechanism involves voltage-controlled growth and dissolution of an oxide layer on the surface of the liquid metal in contact with …

Urban–Rural Disparities In Metabolic Risk Factors For Hypertension Among The Elderly In Indonesia, Susiana Nugraha, Puri Wulandari

Kesmas

Hypertension remains a major public health challenge among the elderly in low- and middle-income countries. This cross-sectional study examined demographic and metabolic factors associated with hypertension among the elderly living in urban and rural areas of West and Central Java Provinces, Indonesia. This study included 1,920 adults aged ≥60 years who had resided in the study areas for at least six months, were able to communicate effectively, and provided informed consent. Data were collected between March and August 2023 using stratified multistage random sampling, structured questionnaires, and biochemical measurements. Multivariable logistic regression revealed distinct patterns of association across settings. In …

Plants Have A Chemical Defense To Protect Themselves From Herbivory, Isis Cordova

Research on Capitol Hill

All plants produce compounds for survival. My work focuses on how plants remember past attacks and whether that memory leads to stronger/faster responses.

Rapid Single-Cell Measurement Of Transient Transmembrane Water Flow Under Osmotic Gradient, Hong Jiang, Jinnawat Jongkhumkrong, Y. J. Chao, Qian Wang, Guiren Wang

Faculty Publications

Aquaporins (AQPs) are critical for transmembrane water transport in response to osmotic gradients, but their gating and regulatory mechanisms remain poorly understood. A central challenge is the lack of methods to measure water flow across AQPs from individual cells with the spatiotemporal resolution and sensitivity equivalent to patch-clamp recordings of ion fluxes—a limitation stemming from the electrically silent nature of water flow. Here, we present a novel optical technique—Flow-Induced Fluorescence Increase Velocimetry (FIFIV) based on Laser-Induced Fluorescence Photobleaching Anemometry (LIFPA)—that enables direct, real-time monitoring of cytoplasmic flow induced by transmembrane water transport under osmotic pressure gradients. Using small molecular fluorescent …

Association Between Dietary Folate And Prostate Cancer Aggressiveness Among African Americans And European Americans, Lihchyun Joseph Su, Sarah O'Connor, Daniela Ramirez Aguilar, Minjae Lee, Harrison Wong, Hui-Yi Lin, Jeannette T. Bensen, James L. Mohler, Lenore Arab, Longgang Zhao, Ebonee N. Butler, Laura Farnan, Susan E. Steck Phd, Mph, Rd

Faculty Publications

Background: Despite the confirmed beneficial effects on preventing neural tube defects, concerns about high intakes of synthetic folate, or folic acid, in promoting cancer progression have been raised. This study evaluated the association between folate intake and prostate cancer (PCa) aggressiveness among African-American (AA) and European-American (EA) males. Methods: This study included 722 AA and 775 EA men with prostate cancer. Folate intake (dietary folate equivalent (DFE), synthetic folate, natural folate) was estimated using the National Cancer Institute Dietary History Questionnaire and detailed dietary supplement use questionnaire. Analyses included univariable comparisons of demographic and clinical characteristics of the two racial …