Digital Commons Network^™

Using Environmental Dna To Evaluate The Distribution And Abundance Of Western Chicken Turtles, Kai D. Scarangella

ATU Scholars Symposium

The Western Chicken Turtle (Deirochelys reticularia miaria; WCT) is a Species of Greatest Conservation Need that is currently under review for federal listing and is assumed to be rare and declining across its range. WCT are threatened by a variety of anthropogenic challenges, including habitat loss, habitat modification, and road mortality. The conservation of this species is further hindered by a lack of understanding of its distribution, abundance, and population trends. These knowledge gaps arise largely from the species’ unique characteristics and cryptic nature. More specifically, WCT demonstrate prolonged aestivation and are notoriously difficult to capture. Environmental DNA …

Cellular And Molecular Mechanism Of Heavy Metal Phytoremediation, Kaitlin A. Edwards, Kayle Dacus, Autumn Wilbanks, Tatum Simms

ATU Scholars Symposium

Rapid urbanization and industrial activities have contributed to heavy metal contamination of several habitats thus leading to an emerging health and environmental challenge. Some heavy metals such as zinc, iron, molybdenum, manganese, copper, cobalt and nickel are found in trace amounts in biological organisms, however, most are harmful for cellular metabolism. Certain species of plants can accumulate large amounts of heavy metals and has been utilized to sustainably clean contaminated soil and water by a process called phytoremediation. Recent lab and field studies have reported promising results that could propel commercialization of this technology. The cellular and molecular mechanism involved …

Cloning The Yersinia Enterocolitica Alkaline Phosphatase For An Affinity Chromatography Ligand, Flavio E. Arellano

ATU Scholars Symposium

Alkaline phosphatase (ALP) is an enzyme responsible for the dephosphorylation of extra-cytoplasmic molecules. Conversion to a neutral molecule enhances their ability to pass through cell membranes. When microbes such as Yersinia enterocolitica are ingested, they are exposed to large changes in pH level. These changes range from ~pH6.5 in the oral cavity to pH 2 in the stomach and pH 8 in the mid-intestine. The ability of microorganisms to survive this change in pH it largely dependent on their ability to change which proteins are expressed at differing pH levels or their ability to modify those proteins to meet the …

Observing The Abundance Of Avian Families In Different Layers Of Lowland Floodplain Rainforest At Inkaterra Reserva Amazonica, Peru, Claire Costello, Melissa Curth, Andre Vu

Undergraduate Research and Engagement Symposium

This research project aims to observe the abundance and diversity of avian families and subfamilies in the Peruvian Amazon basin at Inkaterra Reserva Amazonica at Madre de Dios, Peru by performing bird surveys, fixed-radius point counts, and placing down camera traps. Over a one-week period, we will observe species of the floodplain understory and canopy to observe niche separation and specialization. In addition, we hope to see species of conservation concern and ecological importance, such as the endemic black-faced cotinga and the pale-winged trumpeter, along with indicator species, to analyze the health of the rainforest near Inkaterra Reserva Amazonica.

Seasonal And Environmental Influences On Snake Captures In Northern Indiana, Skye La Rosa, Nicholas Sekits, Sara Ruane

Undergraduate Research and Engagement Symposium

Midwestern snake populations have been declining, yet, snakes are challenging to capture and study due to their cryptic nature. We examined how the time of sampling, coverboard type, and temperature influenced the capture rates and sizes of Common Gartersnakes (Thamnophis sirtalis) and Dekay’s Brownsnakes (Storeria dekayi). We deployed coverboards (rubber or carpet) at 20 sites across northern Indiana and found that T. sirtalis captures peaked in July and August, and both species had smaller sizes in August. Coverboard type had no significant effect. These findings provide insight into snake ecology, particularly seasonal patterns, and habitat preferences, informing future conservation efforts.

Investigating The Impacts Of Xbp1s Overexpression In Oligodendrocyte Progentior Cells In A Remylinating Mouse Model Of Multiple Sclerosis, Grace E. Newell, Kody Ellen Bruce

Undergraduate Research and Engagement Symposium

Multiple Sclerosis (MS) is a chronic autoimmune disorder that results in

the targeted destruction of myelinated axons within the central nervous system (CNS). Remyelination restores neuronal function

and prevents axonal degeneration, but remyelination is either incomplete or inconsistent in MS. Efforts to re-populate remyelinating oligodendrocytes will therefore advance reparative therapeutics for MS. Remyelinating oligodendrocytes develop and function in the presence of inflammatory environment in MS. It has been shown that inflammation diminishes the capacity of oligodendrocyte precursor cells (OPCs) to develop into mature oligodendrocytes and remyelinate demyelinated lesions. In addition, inflammation induced endoplasmic reticulum (ER) stress is one of the …

Comparing Human Skeletal Collections At Loyola University Chicago: Impacts On Education And Research, Stella Riehl

Undergraduate Research and Engagement Symposium

Collections of human skeletal remains reflect a long history of exploitation and marginalization, issues that body donation seeks to alleviate. Through comparing remains purchased from biological supply companies in the 1960-70’s by Loyola’s Anthropology Department with skeletons from the National Body Donor Program, I aim to explore whether differences impact education and research. Age at death and sex were estimated for 36 skeletons; present pathological conditions were noted. Results indicate that donor skeletons are significantly older with more chronic conditions. However, both collections display the inextricable links between lived experiences and disease processes. Emphasizing each individual’s history is essential.

Tobramycin Resistance Is Less Likely To Evolve Under Nitrogen Limitation., Anja Hofmeier

Undergraduate Research and Engagement Symposium

I am investigating whether nutrient-limited environments impact the evolution of antibiotic resistance in Escherichia coli. We evolved E. coli for 24 days in nitrogen- or carbon-limited environments with and without tobramycin. Nitrogen-limited populations were less likely to evolve antibiotic resistance as many went extinct before day 24. Growth curves for the evolved and ancestral populations showed that tobramycin-resistant populations grew more slowly than the ancestor in the absence of antibiotics. I also conducted fitness assays to evaluate the competitive ability of the evolved populations compared to their ancestor.

Stressors In Urban Ecosystems: Assessing The Challenges & Contributions Of Bee Populations In Chicago, Caitlyn Smith, Reagan Potts, Kyle Alioto

Undergraduate Research and Engagement Symposium

This presentation will evaluate the challenges that Chicago bee populations face from pesticide use and habitat fragmentation, including how urban spaces can foster pollinator populations. This presentation will also estimate the contribution of bee pollination services in Cook County as a rationale for policy recommendations. Over the course of the spring semester, we worked in a group of three students to review relevant literature, collect data, and perform a policy analysis. Through this experience, we deepened our understanding of urban bee ecology, the importance of urban planning, and community engagement.

Della Protein And Cbl-Cipk Signaling Pathway As Candidates For Genetic Engineering, Nathan F. Surles

ATU Scholars Symposium

No abstract provided.

Graphfocus: Adaptive Training Strategies To Counter Over- Globalization In Graph Transformers

Defensive Publications Series

As Transformers become more popular for graph machine learning, a significant issue has recently been observed. Their global attention mechanisms tend to overemphasize distant vertices, leading to the phenomenon of "over-globalising." This phenomenon often results in the dilution of essential local information, particularly in graphs where local neighbourhoods carry significant predictive power. Existing methods often struggle with rigidity in their local processing, where tightly coupled operations limit flexibility and adaptability in diverse graph structures. Additionally, these methods can overlook critical structural nuances, resulting in an incomplete integration of local and global contexts. This paper addresses these issues by proposing GraphFocus, …

Unizyme A Unified Protein Cleavage Site Predictor Enhanced With Enzyme Active-Site Knowledge

Defensive Publications Series

Enzyme-catalyzed protein cleavage is essential for many biological functions. Accurate predic tion of cleavage sites can facilitate various appli cations such as drug development, enzyme de sign, and a deeper understanding of biologica mechanisms. However, most existing models are restricted to an individual enzyme, which ne glects shared knowledge of enzymes and fails generalize to novel enzymes. Thus, we introduce a unified protein cleavage site predictor named UniZyme, which can generalize across diverse enzymes. To enhance the enzyme encoding for the protein cleavage site prediction, UniZyme em ploys a novel biochemically-informed model ar chitecture along with active-site knowledge of pro …

Probabilistic Graph Circuits Deep Generative Models For Tractable Probabilistic Inference Over Graphs

Defensive Publications Series

Deep generative models (DGMs) have recently demonstrated remarkable success in capturing complex probability distributions over graphs. Al though their excellent performance is attributed to powerful and scalable deep neural networks, it is, at the same time, exactly the presence of these highly non-linear transformations that makes DGMs intractable. Indeed, despite representing probability distributions, intractable DGMs deny probabilistic foundations by their inability to answer even the most basic inference queries with out approximations or design choices specific to a very narrow range of queries. To address this limitation, we propose probabilistic graph circuits (PGCs), a framework of tractable DGMs that provide …

Offline Model-Based Optimization Comprehensive Review

Defensive Publications Series

Offline optimization is a fundamental challenge in science and engineering, where the goal is to optimize black-box functions using only offline datasets. This setting is particularly relevant when querying the objective function is prohibitively expensive or infeasible, with applications spanning protein engineering, material discovery, neural architecture search, and beyond. The main difficulty lies in accurately estimating the objective landscape beyond the available data, where extrapolations are fraught with significant epistemic uncertainty. This uncertainty can lead to objective hacking (reward hacking)—exploiting model inaccuracies in unseen regions—or other spurious optimizations that yield misleadingly high performance estimates outside the training distribution. Recent advances …

Development Of A Transitive-Based Netework Clustering Methodology For Unweighted, Directed Networks, Collin Jacob Matthews

Honors Capstone Projects and Theses

No abstract provided.

April 29, 2025, Council On Graduate Studies

Minutes

No abstract provided.

Neuroarts And Neuroaesthetics, James Hutson, Piper Hutson

Faculty Scholarship

Recent advancements in neuroarts and neuroaesthetics have elucidated the relationship between artistic engagement and neural processes, emphasizing the impact of aesthetic experiences on cognitive and emotional well-being. Central to this exploration is the NeuroArts Blueprint initiative, which consolidates interdisciplinary research to better understand the impactful role of the arts on brain function and health outcomes. Empirical studies highlight how exposure to art, such as music or visual stimuli, activates neural circuits involved in emotion regulation, memory, and reward processing, particularly engaging the medial orbitofrontal cortex. Innovations such as haptic and electro-tactile devices have introduced novel sensory modalities that not only …

Analyzing The Chemical Composition & Morphology Of Hydroxyapatite Coating On Magnesium Biomaterials, Khaoula Kamal

Honors Theses

The purpose of this thesis is to further explore the capabilities of magnesium metal to serve in biodegradable orthopedic implant applications. Current standards for orthopedic implants involve metals that cause many issues such as high risk of infection due to the need for secondary surgery. Despite magnesium’s biocompatibility, it presents a challenge that will be addressed in this thesis: a fast degradation rate. To combat this problem, hydroxyapatite (HA), an integral component of bone, was used to coat the surface of magnesium scaffolds and offer a slower degradation rate. Previous Priddy Lab studies have confirmed the presence of HA coating …

Glycosylation Of Serine/Threonine-Rich Intrinsically Disordered Regions Of Membrane-Associated Proteins In Streptococci., Mohammad M Rahman, Svetlana Zamakhaeva, Jeffrey S. Rush, Catherine T Chaton, Cameron W Kenner, Yin Mon Hla, Ho-Ching Tiffany Tsui, Vladimir N Uversky, Malcolm E Winkler, Konstantin V Korotkov, Natalia Korotkova

Molecular and Cellular Biochemistry Faculty Publications

Proteins harboring intrinsically disordered regions (IDRs) lacking stable secondary or tertiary structures are abundant across the three domains of life. These regions have not been systematically studied in prokaryotes. Here, our genome-wide analysis identifies extracytoplasmic serine/threonine-rich IDRs in several biologically important membrane-associated proteins in streptococci. We demonstrate that these IDRs are glycosylated with glucose by glycosyltransferases GtrB and PgtC2 in Streptococcus pyogenes and Streptococcus pneumoniae, and with N-acetylgalactosamine by a Pgf-dependent mechanism in Streptococcus mutans. The absence of glycosylation leads to a defect in biofilm formation under ethanol-stressed conditions in S. mutans. We link this phenotype to the C-terminal IDR …

A Bivalent Self-Amplifying Rna Vaccine Against Yellow Fever And Zika Viruses, Peter Battisti, Matthew R. Ykema, Darshan N. Kasal, Madeleine F. Jennewein, Samuel Beaver, Abbie E. Weight, Derek Hanson, Jasneet Singh, Julie Bakken, Noah Cross, Pauline Fusco, Jacob Archer, Sierra Reed, Alana Gerhardt, Justin G. Julander, Corey Casper, Emily A. Voigt

Animal, Dairy, and Veterinary Science Student Research

Introduction: Yellow fever (YFV) and Zika (ZIKV) viruses cause significant morbidity and mortality, despite the existence of an approved YFV vaccine and the development of multiple ZIKV vaccine candidates to date. New technologies may improve access to vaccines against these pathogens. We previously described a nanostructured lipid carrier (NLC)-delivered self-amplifying RNA (saRNA) vaccine platform with excellent thermostability and immunogenicity, appropriate for prevention of tropical infectious diseases.

Methods: YFV and ZIKV prM-E antigen-expressing saRNA constructs were created using a TC-83 strain Venezuelan equine encephalitis virus-based replicon and complexed with NLC by simple mixing. Monovalent and bivalent vaccine formulations were injected intramuscularly …

Students In The Gardner-Webb University College Of Arts And Sciences Recognized In Awards Ceremony, Office Of University Communications

Gardner-Webb NewsCenter Archive

Faculty in the College of Arts and Sciences recently presented awards to students in recognition of their hard work, dedication and excellence.

Integrative Systems Approach To Cell Line Design: From Bistability To Metabolic Byproduct Reduction To Amino Acid Prototrophy, Bhanu Chandra Mulukutla, Chris Mccready

Cell Culture Engineering XIX

Please click Additional Files below to see the full abstract

Assessment Of Biotransformation Rates, Biomagnification, And Bioconcentration Factors Of Difficult-To-Test Substances Using In Vitro Rainbow Trout Liver Subcellular Fractions, Mark A Cantu, Beatrice Chee, Talia R Cole, Yung-Shan Lee, Frank A P C Gobas

Faculty and Staff Publications

In vitro hepatic biotransformation assays have been proposed as methods for expediting and improving bioaccumulation assessment for substances that are difficult to test in conventional in vivo bioaccumulation assays and to reduce animal testing. However, to date, there has been no convincing evidence to demonstrate the ability and limitations of in vitro assays to estimate in vivo biotransformation rates and corresponding bioconcentration and biomagnification factors of difficult-to-test substances in fish. The present study presents the first measurements of in vitro biotransformation rates of superhydrophobic and highly volatile linear and cyclic siloxanes in rainbow trout liver S9 subcellular fractions and the …

Insights Into Cortical Organization And Executive Dysfunction In Pediatric Traumatic Brain Injury, Madeleine Reading

Theses and Dissertations

Cortical gyrification is essential for cognitive development, yet its relationship with executive functioning (EF) in pediatric traumatic brain injury (TBI) remains unclear. This study examined whether children with TBI exhibit atypical cortical folding in EF-related regions and whether these differences relate to EF performance. Using FreeSurfer 7.1.1, we analyzed local gyrification index (LGI) in 206 participants (ages 5-18) from 14 sites within the ENIGMA Pediatric msTBI Working Group. Vertex-wise regression revealed that longer time since injury (TSI) was associated with increased gyrification in the right fusiform gyrus and multiple left-hemisphere regions, suggesting region-specific neuroplasticity. Contrary to expectations, higher GCS scores …

Self-Supervised Learning And Its Applications In Medical Image Analysis, Siladittya Manna

Doctoral Theses

Self-supervised learning (SSL) enables learning robust representations from unlabeled data and it consists of two stages: pretext and downstream. The representations learnt in the pretext task are transferred to the downstream task. Self-supervised learning has appli- cations in various domains, such as computer vision tasks, natural language processing, speech and audio processing, etc. In transfer learning scenarios, due to differences in the data distribution of the source and the target data, the hierarchical co-adaptation of the representations is destroyed, and hence proper fine-tuning is required to achieve satisfactory performance. With self-supervised pre-training, it is possible to learn repre- sentations aligned …

If You Can’T Beat Hemp, Join Hemp: A Policy Argument For A Federal Regulatory Framework Encompassing Intoxicating Hemp Derivatives And Marijuana And Why Re-Scheduling Marijuana Isn’T The Answer, Frances Alaina Rodriguez

University of Miami Business Law Review

The Agriculture Improvement Act of 2018 (2018 Farm Bill) legalized industrial hemp and its downstream uses by removing hemp from the definition of marijuana under the Controlled Substances Act (CSA). Its enactment led to the explosion of a multi-billion dollar intoxicating hemp derivatives (IHD) market. This boom, combined with growing state–level marijuana legalization, presents a unique opportunity for comprehensive federal cannabis reform.

This Note argues that the traditional pathways for marijuana legalization—rescheduling through the Controlled Substances Act or state-by-state legislation—are inadequate given the emergence of a federally legal but largely unregulated IHD industry. Instead, this Note proposes a unified federal …

Lsab Minutes April 29, 2025, Shawna Battle, Maryke H. Barber

WRL: Library Student Advisory Board Minutes

No abstract provided.

Non-Finite Clause Use In Disciplinary Research Writing: A Formulaic Sequence-Based Functional Comparison Between Expert And Student Writers, Xixin Qiu

Faculty Scholarship

Non-finite clauses (NFCs), despite their increasingly recognized role in second language (L2) acquisition and academic writing as part of a multidimensional conceptualization of syntactic complexity, have not been analyzed in functional and discipline-specific perspectives. This study addresses this gap by providing a linguistic-descriptive account of NFC use in expert and advanced student English research writing. Using a 2.26-million-word corpus of published research articles and student manuscripts in Agricultural Science, this study profiles the distribution of NFC subtypes and identifies frequent discoursal functions realized by non-finite verb-centered formulaic sequences. The findings reveal significant differences in NFC use across writer groups, with …

From The Ground Up: Community-Based Participatory Research Reclaiming The Science Of Lead, Juan Manuel Rubio, Bavisha Kaylan, Anthony Diaz, Patricia Flores, Maya Cheav, David C. Bañuelas, Ashley Green, Annika Hjelmstad, Ariane Jong-Levinger, Tim Schütz, Maya Carrasquillo, Alana M. W. Lebron, Jun Wu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

For decades, the dominant approach to lead poisoning has been to focus on homes affected by lead paint and to treat children who are already suffering from lead poisoning. This individualizing approach developed in the context of the defunding and deregulation of government agencies in the 1980s. In recent years, however, community–academic partnerships have reframed lead as an environmental issue produced by the development of the lead industry in the twentieth century and connected to overlapping histories of exploitation, discrimination, and inaction. These community-based projects have contributed to shifting research agendas (by emphasizing historical analysis and the study of the …

Voices Raised, Spring 2025, University Of Dayton. Women's Center

Women’s Center Newsletter

Newsletter editor: Gabby Campana

In this issue:

• Leading with Purpose, by Ajá McMichel
• Women and Religion: Resistance, Reverence, and Radical Faith, by Meg Cole
• “One is Not Born, But Rather Becomes, A Woman”: Revisiting The Second Sex, by Nikita Khasgiwale
• Women's History Month, Spring Semester Events
• From the Director's Desk, by Leah L. Ward, Ph.D.