Digital Commons Network^™

Structural Evolution Of Nitrogenase Over 3 Billion Years, Bruno Cuevas Zuviría, Franka Detemple, Kaustubh Amritkar, Amanda K. Garcia, Lance Seefeldt, Betül Kaçar

Chemistry and Biochemistry Faculty Publications

Previously, we identified the only dinitrogen reduction mechanism known to date as an ancient feature conserved from nitrogenase ancestors, which we directly tested by resurrecting and integrating synthetic ancestral nitrogenases into the genome of Azotobacter vinelandii (Garcia et al., 2023), a genetically tractable, nitrogen-fixing model bacterium. Here, we extend this paleomolecular approach to investigate the structural evolution of nitrogenase over billions of years of evolution by combining phylogenetics, ancestral sequence reconstruction, protein crystallography, and deep-learning based predictions. This study reveals that nitrogenase, while maintaining a conserved multimeric core, evolved novel modular features aligned with major environmental transitions, suggesting that subtle …

Mechanistic Rationale For Toxic Aerosol Formation From Vaping And Dabbing With A Focus On Ketene Formation From Semi-Synthetic Cannabinoids, Kaelas Ryan Munger

Dissertations and Theses

Cannabis vaping is a relatively new route of administration that is increasingly common among youth and young adults. Cannabis vaping has been associated with cases of acute lung injury, especially among youth, and most often involves the heating and aerosolization of high-potency products having cannabinoid concentrations of ~ 50 % - 98 % w/w. Proponents argue that vaping is safer than smoking due to the characteristically lower temperatures and fewer plant materials. However, the extreme cannabinoid concentrations, along with non-natural formulations having undisclosed additives, require studies of the health effects of these products. Despite the popularity of cannabis concentrate vaping, …

An Adaptive Force Matching Potential For Alanine Developed With Møller-Plesset Perturbation Theory And Smooth Fourier Transform Correction Map, Ying Yuan, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

Developing accurate force fields for biomolecules remains a significant challenge due to the subtle energetic differences between various conformational states. We present a novel force field model for polyalanine, ALAMP2_25, developed using adaptive force matching (AFM) with M & oslash;ller-Plesset perturbation theory at the second order (MP2) as the reference method. By fitting smaller model compounds and transferring parameters to larger peptides, we overcome the limitations of traditional AFM approaches and enable the use of more accurate electronic structure methods. The ALAMP2_25 model incorporates a new correction scheme, Smooth Fourier Transform-based phi, psi correction map (SFT-CMAP), which efficiently describes phi, …

Bayesian Survival Analysis For High-Dimensional Compositional Data, Zhenying Ding

All ETDs from UAB

Survival analysis integrating microbiome and clinical data offers powerful insights into human health. The microbiome influences immunity, inflammation, and cancer outcomes. Combining microbial profiles with clinical factors like tumor stage, treatment, and demographics enhances understanding of how host-microbe interactions affect survival. To analyze these complex datasets, advanced statistical methods, including Bayesian models, penalized Cox proportional hazards models, and machine learning techniques are employed. These approaches can uncover novel biomarkers and therapeutic targets, leading to personalized treatment strategies that optimize patient survival. However, challenges arise due to the compositionality, high-dimensionality, and phylogenetic relation between taxa in microbiome data. In this dissertation, …

Calibrating A Holling-Tanner Model With Applications To S&P500 Forecasting, Jonathon Knowles

All ETDs from UAB

The primary goal of this thesis is to improve upon existing dynamical system models in economics. Existing models utilizing Lotka-Volterra dynamics display a tendency to suffer from unrealistic forecasts dominated by exponential growth and decay. Additionally, current inverse methods are only applicable in differential equation systems with linear coefficients. In this body of work, we propose novel methods for handling these challenges.

Controlling Properties Of Pmaa Multilayer Hydrogel Microparticles Through Network Structure, Daniel Inman

All ETDs from UAB

Advancements in the fabrication of “smart” stimuli responsive hydrogel microparti-cles have been pivotal in their optimization for applications. The responsiveness of hydro-gel networks to external stimuli enhances the intrinsic properties of hydrogels to increase functionality. Through layer-by-layer assembly, the internal composition, network struc-ture, and surface chemistry of multilayer hydrogels can be directly controlled to introduce new and unique properties. Applicable to a wide variety of shapes and sizes; hydrogel mi-croparticles are versatile for biological interactions, such as, cellular internalization, tissue regeneration, biosensors, and more. Thus, this dissertation will discuss the synthesis of shaped pH-responsive hydrogel microparticles and the investigation of …

Mcl1 And Hexokinase 2 Form A Glucose Metabolic Regulatory Axis, Robert Lee

All ETDs from UAB

Hexokinase 2 (HK2) initiates glucose metabolism by catalyzing the conversion of glucose to glucose-6-phosphate providing the starting substrate for a vast array of metabolic pathways such as glycolysis, pentose phosphate pathway (PPP), amino acid biosynthesis and others. While HK2’s metabolic role in normal physiologic function (such as in cardiomyocytes) and cancers (through driving the Warburg Effect) are well established, there is emerging evidence that supports HK2 is also a critical mediator of protein-protein interactions that regulate cell survival. Through comprehensive review, we explore how HK2 contributes to cell survival through metabolic and protein scaffolding roles. We also investigate a novel …

Modeling The Basal Ganglia Network Using Leaky Integrate-And-Fire Neurons To Explore Its Role In Facilitating Purposive Saccades, Saarth Anjali Chitale

All ETDs from UAB

Saccadic eye movements provide a well-defined behavioral readout for investigating how the basal ganglia (BG) contribute to action selection. While saccades are controlled by multiple brain regions, including direct excitatory inputs from various cortices, the BG exerts a key inhibitory influence. Decades of experimental work using saccadic behavioral paradigms in non-human primates have yielded important insights into the activity of BG populations. These include the caudate nucleus, subthalamic nucleus, globus pallidus externus, and substantia nigra pars reticulata, as well as dopaminergic afferents from the substantia nigra pars compacta and efferent projections to the superior colliculus, which controls eye movements. Despite …

Intelligence Architectures And Machine Learning Applications In Contemporary Spine Care, Rahul Kumar, Conor Dougherty, Kyle Sporn, Akshay Khanna, Puja Ravi, Pranay Prabhakar, Nasif Zaman

SKMC Student Presentations and Publications

The rapid evolution of artificial intelligence (AI) and machine learning (ML) technologies has initiated a paradigm shift in contemporary spine care. This narrative review synthesizes advances across imaging-based diagnostics, surgical planning, genomic risk stratification, and post-operative outcome prediction. We critically assess high-performing AI tools, such as convolutional neural networks for vertebral fracture detection, robotic guidance platforms like Mazor X and ExcelsiusGPS, and deep learning-based morphometric analysis systems. In parallel, we examine the emergence of ambient clinical intelligence and precision pharmacogenomics as enablers of personalized spine care. Notably, genome-wide association studies (GWAS) and polygenic risk scores are enabling a shift from …

Data From: Nek4 Suppresses Cell Proliferation In Bt20 Triple-Negative Breast Cancer Cells By Diminishing Expression Of Cell Cycle Genes, While Its Depletion Mitigates Proliferation In Other Cell Lines, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

09.08.2025 Ored Connect, Liz Williamson

ORED Newsletter

• Researcher training opportunities
• Project to increase PhD student success
• ORED online training opportunities

Sagebrush, Wildfire, And Homeowners Associations: Climate Adaptation Opportunities In Summit County, Utah, Rebecca Ivans, Kendall Becker, Wesley Crump, J. Bradley Washa, Lewis Kogan, Scott Hotaling

All Current Publications

Environmental changes and rapidly expanding suburban developments are amplifying wildfire risk in Utah, including in mixed-sagebrush habitats like those in Morgan, Summit, and Wasatch counties along the Wasatch Back. Wildfire risk to people and structures is especially high in the wildland-urban interface (WUI), where homes and buildings intermingle with undeveloped wildlands and natural vegetation that can fuel wildfire. Much of this urban expansion is occurring in the form of large, dispersed developments managed by homeowners associations (HOAs), which often dictate standards for the homes and properties within their purview. Thus, HOAs can play a critical role in supporting wildfire mitigation …

The Next Frontier In The Study Of Noncovalent Bonding: Transition Metals, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

As work continues unabated in the study of noncovalent bonding, particularly σ-hole bonds, new challenges have emerged as the participation of transition metals in interactions of this sort is fast becoming appreciated. While there are certain similarities with the halogen, chalcogen, etc, bonds, in which the main group elements participate, there are certain unique properties of these metal atoms that must be analyzed before a complete understanding can be attained. As one example, these atoms tend to act simultaneously as both electron donors and acceptors, a synergistic action that amplifies the overall bond strength. Ideas are expressed in this paper …

Re: Butte Priority Soils Operable Unit (Bpsou) Final Reclamation Improvement Sites Field Sampling And Investigation Plan (Fsp): Bres No. 18 – Walkerville Ballfield, Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

The Influence Of Defects: Oxidation Of Non-Planar Transition Metal Model Catalysts, Maxwell Gillum

Dissertations

Metal-catalyzed oxidation reactions are a major application of heterogeneous catalysis and are a widely applied synthetic route for the production of chemicals and reagents essential to modern society. However, as the intricacies of heterogeneous surface catalysis are slowly being unraveled, minute details of the catalytic environment have been revealed to play outsized roles in the catalytic activity of the surface. The experiments herein further investigate the interplay between surface geometry and the formation oxygen-induced surface structures. Understanding how defects influence surface reactivity is a necessary step in gaining the ability to accurately model heterogeneous catalytic environments. Two different aspects of …

Air Pollution And Diseases: Signaling, G Protein-Coupled And Toll Like Receptors, Isabella Cattani-Cavalieri, Katrina F. Ostrom, Jordyn Margolis, Rennolds S. Ostrom, Martina Schmidt

Pharmacy Faculty Articles and Research

Air pollution is a significant public health issue that impacts lung health, particularly in vulnerable populations such as children, the elderly, and individuals with pre-existing respiratory conditions. Both natural and anthropogenic sources of air pollution give rise to a variety of toxic compounds, including particulate matter (PM), ozone (O₃), sulfur dioxide (SO₂), nitrogen dioxide (NO₂), carbon monoxide (CO), and polycyclic aromatic hydrocarbons (PAHs). Exposure to these pollutants is strongly associated with the development and exacerbation of respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), lung cancer, and idiopathic pulmonary fibrosis (IPF). Notably, early life exposure to pollutants such as …

Re: Butte Priority Soils Operable Unit (Bpsou) Final Insufficiently Reclaimed Sites Field Sampling And Investigation Plan (Fsp): Bres No. 120 – Bonanza Dump, Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Deep Learning-Driven Proteomics Analysis For Gene Annotation In The Renin-Angiotensin System, Mortaza Eivazi, Kamran Hosseini, Shahin Alipanahi, Huijing Xia, Luke Restivo, Ayushi Patel, Mahdieh Gozali, Tahereh Ebrahimi, Amy Scarborough, Vahideh Tarhriz, Eric Lazartigues

School of Medicine Faculty Publications

The renin-angiotensin system (RAS) is central to cardiovascular diseases such as hypertension and cardiomyopathy, yet the functions of many RAS genes remain unclear. This study developed a multi-label deep learning model to systematically annotate RAS gene functions and elucidate their roles in biological pathways. A total of 39,463 RAS-related publications from PubMed and PMC were processed into text format. Feature matrices were generated using TF-IDF and token processing, followed by dimensionality reduction via Principal Component Analysis (PCA). A Multi-Layer Perceptron (MLP) was applied for multi-label classification, with performance evaluated using Precision, F1-Score, Ranking Loss, and ROC-AUC metrics. The model outperformed …

Resource Assessment Report No. 5: West Coast Deep Sea Crustacean Resource 2024 Assessment, Emma-Jade Tuffley, Simon De Lestang

Resource Assessment Reports

The West Coast Deep Sea Crustacean resource consists of crystal crab (snow) (Chaceon albus), champagne crab (spiny) (Hypothalassia acerba) and giant crab (Pseudocarcinus gigas). The resource is mainly accessed by the commercial West Coast Deep Sea Crustacean Managed Fishery (WCDSCMF), which primarily targets crystal crabs. The West Coast Rock Lobster Managed Fishery (WCRLMF) also retains a small amount of champagne crabs as byproduct of deep-water rock lobster fishing. The WCDSCMF is a pot-based fishery using baited pots operated in a long-line formation in shelf edge waters ( > 150 m in depth) off the West …

Resource Assessment Report No. 3: Gascoyne Demersal Scalefish Resource 2024 Assessment, Emily A. Fisher, Rachel Marks, Sybrand A. Hesp, Ainslie Denham, Gary Jackson, David V. Fairclough

Resource Assessment Reports

The Gascoyne Demersal Scalefish Resource (GDSR) comprises over 80 species inhabiting inshore (20-250 m deep) and offshore ( > 250 m deep) waters in the Gascoyne Coast Bioregion (GCB; south of Onslow to north of Kalbarri). The GDSR is primarily targeted by commercial, charter and recreational boat-based line fishers. Snapper and Goldband Snapper are the indicator species selected for monitoring and assessing the status of the inshore suite of the GDSR, while Ruby Snapper and Greybanded Grouper are the indicators for the offshore suite.

Periodic assessments of GDSR indicator species demonstrated that historical fishing of Snapper led to stocks being below …

Resource Assessment Report No. 2: West Coast Demersal Scalefish Resource 2025 Assessment, Emily A. Fisher, David V. Fairclough, Elaine Lek, Jeremy Briggs, Sybrand Alex Hesp, Ainslie Denham

Resource Assessment Reports

The West Coast Demersal Scalefish Resource (WCDSR) comprises over 100 species inhabiting inshore (20-250 m deep) and offshore ( > 250 m deep) waters of the West Coast Bioregion (WCB; north of Kalbarri to east of Augusta). The WCDSR is primarily targeted by commercial, charter and recreational boat-based line fishers, including the commercial West Coast Demersal Scalefish (Interim) Managed Fishery (WCDSIMF). Indicator species selected for monitoring and assessing the status of the inshore suite of the WCDSR include Snapper, WA Dhufish and Baldchin Groper, while indicators for the offshore suite include Hapuku, Bass Groper and Blue-eye Trevalla.

The WCDSR is more …

Cysteine Oxidation Of A Redox Hub Within Complex I Can Facilitate Electron Transport Chain Supercomplex Formation, Runtai Chen, Seyed Amirhossein Tabatabaei Dakhili, Rokas Gerulskis, Yuan Yuan Zhao, Steven Lockhart, Lusine Tonoyan, Arno G. Siraki, Guocheng Huang, Adam Kinnaird, Darren H. Freed, Shelley D. Minteer, Evangelos D. Michelakis, John R. Ussher

Chemistry Faculty Research & Creative Works

The mitochondrial electron transport chain (ETC) is a four complex unit that could be considered the most essential infrastructure within the mitochondria, as it primarily functions to generate the mitochondrial membrane potential (ΔΨm), which can then be utilized for ATP synthesis or heat production. Another important aspect of ETC function is the generation of mitochondrial reactive oxygen species (mtROS), which are essential physiologic signaling mediators that can be toxic to the cell if their levels become too high. Currently, it remains unresolved how a highly utilized and functioning ETC can sense excessive mtROS generation and adapt, to enhance ΔΨm. Here, …

Comprehensive Review Of In Vitro Approaches For Environmental Heavy Metal Exposure, Manas Warke, Madeline English, Camila Padilla, Lexie Gasco, Wendy Leisner, Rupali Datta, Smitha Rao

Michigan Tech Publications

Heavy metals are ubiquitous environmental pollutants, contaminating air, soil, and water via the erosion of natural deposits, as well as originating from anthropogenic sources, such as agriculture, industries, transportation, and landfills. The increasing utilization of heavy metals over the years, combined with the persistent nature of metals in the environment poses a direct threat to human and environment health. Although regulatory limits have been established for toxic metals, assessing the associated health risks using real-life exposure scenarios remains challenging. In this review, we summarize the development and use of in vitro models based two- and three-dimensional cell culture systems, focusing …

Multi-Fidelity Machine Learning Modeling For Aerodynamic Response Prediction Of Aerospace Vehicles, Ethan S. Jackman

Theses and Dissertations

Hypersonic vehicle design requires understanding complex aerodynamic phenomena across the full flight regime. This study presents a novel MF surrogate modeling methodology that enables the prediction the full field response across a vehicle’s surface. A Space-Filling Curve (SFC) is used to convert unstructured data into 1D vectors. The a Convolutional Autoencoder is used with transfer learning to reduce the dimensionality of the data. An Emulator-Embedded Neural Network (E2NN) combines multi-fidelity data for fast, accurate predictions. A benchmark analytical example and hypersonic application are used to evaluate the methodology. Using various numbers of samples and sampling strategies it is found that …

Regioselective C-Allylation Of Indole With Potassium Allyltrifluoroborate In The Presence Of Pd-Catalyst, Milton Kumar Kundu

Tennessee State University Alumni Theses and Dissertations

Indole is a versatile heterocyclic scaffold renowned for its wide range of pharmacological activities and strong potential as a successful drug candidate. These attributes continue to inspire researchers to explore indole derivatives as promising leads in drug development. In this project, we report the development of a cross-coupling reaction of indoles and potassium allyltrifluoroborate to the corresponding 3-allylindoles in the presence of PdCl2(dtbpf) and PdCl2(dppf)CH2Cl2 catalyst under microwave heating, offering a rapid, regioselective, and high-yielding synthetic route. This methodology provides a valuable platform for generating structurally diverse indole-based compounds, which could serve as promising leads for further pharmacological evaluation and …

Root Exudates: The Rhizospheric Frontier For Advancing Sustainable Plant Protection, Muhammad Rahil Afzal, Misbah Naz, Youbo Yu, Lisha Yan, Peiyi Wang, Janaki Mohotti, Gefei Hao, Jing-Jiang Zhou, Zhou Chen, Libo Zhang, Qian Wang

Faculty Publications

Root exudates (REs), a diverse array of bioactive metabolites secreted by plant roots in response to environmental stimuli, serve as key mediators of rhizosphere ecology and plant defense responses, offering a promising avenue for sustainable pest management and eco-friendly plant protection. While earlier reviews primarily focus on root exudates in the context of general rhizosphere dynamics and plant-microbial interactions, critical knowledge gaps persist in REs-plant-pest tripartite interactions, the mechanistic basis of REs-mediated plant defense, and their practical integration with integrated pest management (IPM) frameworks. This review provides a synthesis of the latest literature on the biochemical diversity and functions of …

Single-Molecule Orientation And Localization Microscopy, Sophie Brasselet, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Single-molecule localization microscopy (SMLM) offers enhanced spatial resolution in optical microscopy, providing detailed insights into the spatial organization of proteins in cells at the nanoscale. Over the past decade, SMLM has progressively incorporated the capability to retrieve the orientations of single molecules using their polarized dipolar emission pattern. Here we explore recent advancements in single-molecule orientation and localization microscopy (SMOLM), which yields super-resolved images of molecular three-dimensional (3D) orientations, wobble and 3D positions. This advancement opens possibilities to explore the nanoscale organization and conformation of biological molecules as well as to monitor and design local 3D optical fields in nanophotonics. …

Long-Term Patterns In The Relative Abundance Of Common Snook As A Factor Of Shifting Environmental Conditions In The Florida Coastal Everglades, Jordan A. Massie, Ryan J. Rezek, Rolando O. Santos, W. Ryan James, Natasha M. Viadero, Ross E. Boucek, Jennifer S. Rehage

Marine Science

Objective Environmental variability as a factor of climate change and water management can result in fluctuations in the abundance and distribution of fish populations from year to year, with either negative or positive effects depending on behavioral and physiological requirements and the ability to adapt to changing conditions. Variability in water levels can also influence prey availability, affecting predator abundance in seasonal foraging areas. In this study, our objective was to better understand how environmental variation has affected the relative abundance of Common Snook Centropomus undecimalis in the freshwater/estuarine habitats of Everglades National Park. Methods Electrofishing data over 17 years …

Linking Hydrology, Temperature, And Energetics: Global Change Implications For The Foraging Ecology Of A Generalist Predator, Mack White, W. Ryan James, Justin S. Lesser, Ryan J. Rezek, Jonathan R. Rodemann, Ross E. Boucek, Rolando O. Santos, Jennifer S. Rehage

Marine Science

Objective: The objective of this study was to quantify the effects of temperature, hydrology, and body size on the diet and energy requirements of a generalist predator, Common Snook Centropomus undecimalis (hereafter, “snook”), to gain a better understanding of predator–prey dynamics in the wake of global change. We first ask how temperature, hydrology, and body size influence the occurrence of fish, invertebrates, and empty stomachs in the diet of snook. Next, we model the energetic requirements of snook as a function of body size and temperature. Last, we use predation simulations to test how changes in prey quality, together with …

Quantification Of Terpenes In Various Commercial Cannabis Products By Gas Chromatography-Flame Ionization Detection And Gas Chromatography-Mass Spectrometry, Kaitlyn M. Ignaszak

Forensic Science Master's Projects

The goal of this research project was to identify and quantify the terpenes in five commercial cannabis products (dried bud, kief, two tinctures, and a pain cream) using gas chromatography-flame ionization detection (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Terpene identification and quantification were conducted using GC-MS and GC-FID, with a standard sample containing 21 terpenes of known concentrations. To determine the most effective extraction conditions, three organic solvents (ethanol, acetonitrile, and ethyl acetate) were employed. Additionally, the effects of extraction time on terpene yield were investigated by analyzing aliquots collected at five different time intervals, ranging from one hour to …