Digital Commons Network^™

An In-Silico Investigation Of Induced Target Neural Activity Through Simulation-Based Inference Informed Deep Brain Stimulation, James Lee, Ty Roachford

Florida Atlantic Undergraduate Research Journal

Deep Brain Stimulation (DBS) is clinically effective for various neurological disorders, yet its underlying neuronal mechanisms remain unknown. Building on previous studies, we used an in-silico Hodgkin-Huxley biophysical model to investigate hippocampal CA1 responses to DBS. Our simulations replicate key experimental findings, confirming robust somatic depolarization at 140 Hz and a more gradual ramp at 40 Hz, alongside distinct transient and sustained voltage profiles. Both frequencies modulated firing rates, supporting the notion that DBS disrupts pathological network activity. Beyond frequency-specific effects, we employed Simulation-Based Inference (SBI) to identify the DBS features needed to suppress spiking and match a quiescent target …

Copyright, Editorial Team

Florida Atlantic Undergraduate Research Journal

No abstract provided.

Biographies, Editorial Team

Florida Atlantic Undergraduate Research Journal

No abstract provided.

Table Of Contents, Editorial Team

Florida Atlantic Undergraduate Research Journal

No abstract provided.

Man, Cut The Crop: Effects Of Cropectomies On Survival And Behavior In Drosophila Melanogaster, Emily Peraza

Florida Atlantic Undergraduate Research Journal

The gut-brain axis mediates communication between the digestive and nervous systems to regulate physiology and behavior. Its dysfunction profoundly impacts human health and causes disease. Region-specific hormones and neurotransmitters in the digestive system respond to several processes to signal the brain, but the mechanisms of gut-brain signaling are not fully defined. Drosophila melanogaster is a powerful model for studying gut biology by showing remarkable similarity to mammalian digestive systems, as both regulate energy by distributing nutrients. We refined a minimally invasive surgical protocol to remove the crop from adult flies. We then utilized the Activity Recording CAFE (ARC) and Drosophila …

Artist Statement, Zarina Mason

Florida Atlantic Undergraduate Research Journal

No abstract provided.

Letter From The Editor, Ana Tyulmenkova

Florida Atlantic Undergraduate Research Journal

No abstract provided.

Exploring Gender Differences In Perceptions Of Ai's Impact On Social Media, Samkit Bothra

Florida Atlantic Undergraduate Research Journal

Artificial Intelligence (AI) is increasingly shaping social media through content personalization and moderation, raising questions about its influence on public opinion and trust in digital news. Gender plays a key role in shaping perceptions of AI’s impact, with men and women potentially viewing its applications differently. This study explored gender-based perspectives on AI’s role in social media, focusing on its effects on information credibility and privacy. Data from 155 participants, collected via Amazon Mechanical Turk, were analyzed using IBM’s SPSS. The first hypothesis proposed that women would be more skeptical than men about AI's use in news, citing greater concerns …

A Comprehensive Overview Of The Quantum Approximate Optimization Algorithm, Vincent Stafford

Florida Atlantic Undergraduate Research Journal

As quantum computing research advances, the Quantum Approximate Optimization Algorithm (QAOA) has emerged as a leading approach to harnessing current quantum hardware for solving complex combinatorial optimization problems. This pedagogical, expository paper outlines the mathematical foundations of QAOA, explains its step-by-step implementation from first principles in a manner accessible to advanced undergraduate students and non-specialists, and explores real-world applications such as protein folding and job scheduling. We also examine the algorithm’s performance challenges, including barren plateaus and circuit depth limitations.

Evaluating Fungicide Programs For Grapevine Disease Management And Fungicide Sensitivity Monitoring, Abraham Ahumada

Master's Theses

Grapevine diseases, such as powdery mildew and Botrytis bunch rot, require repeated fungicide applications to maintain fruit quality and reduce yield losses. However, fungicide performance can vary among products, application programs, disease pressure, and pathogen sensitivity. This thesis evaluated fungicide programs for control of powdery mildew in ‘Chardonnay’ grapes and assessed fungicide sensitivity of Botrytis cinerea isolates collected from California vineyards.

Powdery mildew, caused by the fungal pathogen Erysiphe necator, is a major threat to the production of Vitis vinifera grapes worldwide. Because powdery mildew management relies heavily on fungicide applications, field evaluations are needed to compare the efficacy …

Birds Of A Tether Flock Together: Examining Centromere Tethering And Chromosome Segregation In Caulobacter Crescentus, Jake Dwyer, Simon Kruczak, Rodrigo Arana-Garrido, Paola Mera

MICRO-CCS student projects

Introduction:

Chromosome segregation is essential for all domains of life. Caulobacter crescentus is a key model for studying this process. It divides asymmetrically into two morphologically distinct cells. Proteins can be seen directly with fluorescent tags.

Research done on Caulobacter can apply to many different bacteria. The ParABS system is integral to chromosome segregation in Caulobacter.

ParS – DNA sequence on the chromosome

ParB – CTP-binding protein that specifically recognizes parS

ParA – ATP-binding protein that non-specifically binds DNA and provides the force for segregation.

PopZ – Polar tethering protein via interactions with ParB.

TipN - Polar protein that …

Has Plant Domestication Compromised Plant Defensive Chemistry? Aphid Induced Stress In Tomatoes, Nhi Do, Satinderpal Kaur, Minxing Zhu, Esther N. Ngumbi

MICRO-CCS student projects

Tomato plants have natural defensive mechanisms.

Direct: Phenolics are secondary metabolites that can protect the plant by intoxicating the herbivores and/or producing strong repulsive odors.

Indirect: VOCs, Volatile Organic Chemicals, are gas phase signals that attract the predators of the attacking herbivore to the plant.

Domestication of plants may chemically alter these defenses by prioritizing fruit production over defensive traits.

We hypothesize that wild/ancient tomato plants would have a greater quantity of volatiles and increased concentration of leaf total phenolics compared to cultivated tomatoes during aphid herbivory.

How Does High-Oil Sorghum Change Potential Extracellular Enzyme Activity Across Soil Depth Profiles Under Drought Conditions?, Krystal Monique Role, Rounak Patra, Wendy Yang

MICRO-CCS student projects

Transgenic oil sorghum reallocates photosynthate-carbon (C) into vegetative lipids, accumulating nonstructural lipids in both shoot and root tissues. Altered plant C allocation and root lipid accumulation may shift root exudate chemistry, belowground C inputs, and microbial nutrient demand throughout the soil profile. While aboveground productivity in high-oil sorghum is well-characterized, its belowground impacts on soil microbial enzyme activity and exchangeable cation dynamics, especially across soil horizons under drought stress remain unknown.

Project objective was to find out how transgenic high oil sorghum (Tx-HO1) influences CNP acquiring extracellular enzyme activities and soil exchangeable cation dynamics across soil horizons under drought and …

Investigation Of Biological Denitrification Inhibition By Specific Anthocyanins, Kristin Palazzo, Holly Anderson, Aislinn Geedey, Angela Kent

MICRO-CCS student projects

Nitrogen fertilizers are applied to corn fields to support high crop yields, but some nitrogen is lost through microbial denitrification, producing nitrous oxide (N2O), a potent greenhouse gas. Some plants produce certain flavonoids that can suppress microbial denitrification, a trait known as biological denitrification inhibition (BDI). Maize produces flavonoids in the form of anthocyanins, including cyanidin-3-glucoside (C3G), the major anthocyanin produced by maize.

The goals of this project were to determine whether C3G:

is produced in maize roots

inhibits microbial denitrification

Recovering Plasmid-Id Barcoded Strains Of Sinorhizobium Meliloti From A Native Soil Microbiome, Kenny Sacks, Hannah Murray, Katy Heath

MICRO-CCS student projects

Introduction

Legume-Rhizobia Mutualism: Nitrogen is an essential nutrient for plant growth. Plants can’t produce nitrogenous compounds. Rhizobia fix atmospheric nitrogen gas into bioavailable forms. Rhizobia form a nutrient exchange mutualism with leguminous plants.

Project description

Can our bacteria persist within the rhizosphere and into the nodule when faced with native microbial competitors? The Medicago-Sinorhizobium mutualism is used as a model system. Survival of strains post competition is difficult to measure due to identical 16S rRNA sequences and similar marker genes. Plasmid-ID barcoding sequences may provide a way of testing strains against a community.

Soil Microbiome Effect On Seedling Diseases And High Throughput Isolate Identification, Annalaysia Smith, Mara Krone, Santiago Mideros

MICRO-CCS student projects

The soil microbiome has a substantial effect on disease suppression. Organic farming is a practice used to create a more diverse microbiome which can create disease suppression. Different agricultural practices such as fertilization and rotation system are known to affect the microbiome (Schlatter et al 2017). Therefore, it is important to study the effects of different microbiomes on disease suppression. Furthermore, methods are necessary for quantifying the effect of disease suppression on specific pathogen populations. To do this, it is important to properly identify the pathogens.

Objectives:

1. Test if different nitrogen treatments cause variations in organic soils disease suppression. …

Effects Of Varying Ph Levels On Prophenoloxidase Activity And Hemocyte Recruitment In Daphnia Dentifera, Yusra Siddiqi, Carla Caceres

MICRO-CCS student projects

Anthropogenic activities and natural processes are responsible for changing the pH of freshwaters which can impact aquatic life. D. dentifera is a keystone species found in midwestern lakes that is susceptible to a parasitic yeast called Australozyma monospora. A. monospora spores puncture the Daphnia gut into the hemolymph and begin using the host’s resources. Invertebrate immunity is under researched.

Research objective: How will different pH impact prophenoloxidase (proPO) activity and hemocyte recruitment in Daphnia dentifera?

Screening A Random Hile Mutant Library To Characterize Hild Regulation In Salmonella, Danista Kannah, Gracious Donkor, James M. Slauch

MICRO-CCS student projects

Salmonella is a leading cause of gastrointestinal diseases globally. It utilizes a type three secretion system (T3SS) encoded on Salmonella Pathogenicity Island 1 (SPI1) to invade host intestinal epithelial cells during infection.

HilE directly regulates HilD via a direct protein-protein interaction. The Slauch lab identified two HilD variants, A141V and A141T, which are blind to HilE. These variants activate hilA expression even in the presence of HilE, indicating that the binding of HilE to these mutants is compromised.

Hypothesis: Performing random mutagenesis of hilE could lead to changes at the protein level which could compensate for the loss of interaction …

Fungal Diversity In Lespedeza Cuneata Roots, Gwendolyn Happ, Sophia Mcdade, Anthony Yannarell

MICRO-CCS student projects

Background

• Plants form a relationship with fungi that can be beneficial or harmful
• Fungi may grow on the plant surface, within plant tissues, or around roots
• Plants release compounds that invite fungi to their roots and chemicals  that can diminish unwanted fungi

Why Lespedeza cuneata? 

• Invasive that competes with native plants and damages biodiversity within plant and animal communities
• Alters soil microbiome
• Expansive seed bank and deep root system
• Understanding its microbiome can help in understanding invasive species success and ecology

Efficacy And Evolutionary Dynamics Of 222 Nm Far-Uvc Against Vibrio Cholerae, Kadicha Madakimova, Angus Wu, Nkrumah Grant

MICRO-CCS student projects

The Far-UVC light at 222 nm wavelength (UV222) is one of the emerging methods of disinfection of bacteria in public spaces such as hospitals and labs.

• Does not penetrate human skin and does not cause harm to eyes making it a safer alternative to conventional UV systems.

• Primarily targets proteins preventing regrowth and repair pathways.

However, the potential for bacterial adaptation following sublethal UV222 exposure remains largely unknown.

Central question: How does QS transcriptional state influence the efficacy and resistance profile of V. cholerae to UV222 nm irradiation?

Hypothesis: Qurom-sensing transcriptional state determines V. cholerae susceptibility to UV222 nm UV …

A Tale Of Two Symbionts: Comparative Cellular Localization Of Two Manipulative Rickettsiella Strains In A Spider, Kaitlyn Costanza, Thea Bliss, Matthew Doremus

MICRO-CCS student projects

Many arthropods harbor maternally transmitted endosymbionts that manipulate host reproduction to increase their transmission. One such manipulation is cytoplasmic incompatibility (CI), in which embryos produced by infected males and uninfected females fail to develop.

Rickettsiella has recently been discovered to cause CI in Mermessus fradeorum. Two geographically distinct Rickettsiella strains infect this spider: R1 causes strong CI, whereas R2 causes weaker CI.

Hypothesis: H1: Both Rickettsiella strains will localize within or near developing sperm cells in the testes. H2: The stronger R1 strain will exhibit more consistent localization within infected adult reproductive tissues than the weaker R2 strain.

Association Of Ultra-Processed Food Intake With Insulin Secretion And Sensitivity In Mexican American Children: Results From The Safari Study, Hemant Kulkarni, Rector Arya, Srinivas Mummidi, Sharon P. Fowler, Roy G. Resendez, Juan C. Lopez-Alvarenga, Vidya Farook, John Blangero

Human Genetics Publications

Background/Objectives: There is increasing interest in and evidence for the role of ultra-processed foods (UPFs) in cardiometabolic risk. We tested the hypothesis that UPF intake score derived from dietary history is associated with measures of insulin secretion and sensitivity in a family setting even when the process of type 2 diabetes is still to ensue. Methods: We used data from our well-characterized San Antonio Family Assessment of Metabolic Risk Indicators in Youth (SAFARI) study cohort of nondiabetic children (aged 6–17 years). Dietary history was assessed using the Block Food Frequency Questionnaire. Outcomes of interest were 19 clinically useful indexes of …

Mosaic Loss Of Y Chromosome Associates With Lung Function, Emphysema, And Epigenetic Aging, Woei Yuh Saw, Kangjin Kim, Yichen Huang, Jeong H. Yun, Xiaolong Ma, Jason Bacon, Yash Pershad, Daniel Levy, George T. O’Connor, John Blangero

Human Genetics Publications

Rationale: As the global population ages, identifying risk factors for age-related diseases, such as COPD, is crucial for public health. Mosaic loss of Y chromosome (mLOY) in blood cells is an age-related somatic mosaicism event, but its relationship with pulmonary health remains undercharacterized. Objectives: To examine the association between mLOY and pulmonary outcomes in men. Methods: Leveraging mLOY assessment (cell fraction ≥ 5%) in over 12 000 men, including 5097 from the COPDGene Study and 7235 from six additional cohorts in the Trans-Omics for Precision Medicine program, we investigated mLOY associations with respiratory outcomes and epigenetic aging using multivariable cross-sectional, …

Investigation Into Molecular Bases Of Pregnancy-Associated Malaria, Nicole Pozo

Biochemistry and Molecular Biology

Plasmodium falciparum causes the most severe and deadly form of malaria and remains a major global health problem, especially in sub-Saharan Africa (Milner, 2018). The parasite infects and multiplies inside red blood cells, leading to fever, anemia, organ damage, and death if untreated (Milner, 2018; Song et al., 2022). It is especially dangerous because it avoids the immune system by changing surface proteins called Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), which are encoded by more than 60 var genes. By switching between these genes, the parasite hides from immune detection and creates repeated waves of infection (Deitsch & Dzikowski, …

Acute Intermittent Hypoxia And Acute Intermittent Hypercapnic Hypoxia Elicit Cortico-Diaphragmatic Plasticity In People With Chronic Spinal Cord Injury, Alysha Bogard, Michela Mir, Tommy Sutor, Jessica Dunn, Kathryn Cavka, Arian Vistamehr, Hannah Snyder, Joseph Welch, Jayakrishnan Nair, Gina Brunetti, Gordon Mitchell, Emily Fox

Department of Physical Therapy Faculty Papers

Respiratory impairment is a leading cause of morbidity and mortality after spinal cord injury (SCI), highlighting the need for interventions that improve breathing function. In people with SCI, acute intermittent hypoxia (AIH) elicits respiratory motor plasticity and improves inspiratory function. However, in uninjured people facilitation of corticospinal diaphragm motor evoked potential (MEP) amplitude occurs only when AIH is combined with mild hypercapnia (acute intermittent hypercapnic hypoxia; AIHH). It remains unclear whether AIHH similarly enhances diaphragm corticospinal excitability after SCI. We tested the hypothesis that AIHH increases diaphragm MEP amplitude and reduces MEP onset latency in individuals with chronic SCI, whereas …

Interpretable Machine Learning Of Plasma Proteomics Reveals Stage-Specific Signatures Across The Alzheimer's Disease Continuum, Hemshankar Laugi

2026 Spring Honors Capstones Projects

Alzheimer’s pathology begins years before clinical symptoms, starting early with amyloid-β accumulation, followed by tau deposition and neurodegeneration. Although existing tools, such as cerebrospinal fluid (CSF) screening and PET/MRI imaging, can accurately track disease progression, they are invasive, expensive, and not scalable for population-level screening. So, there is a growing interest in using blood-based plasma biomarkers as a scalable alternative. While recent studies demonstrate strong predictive performance with plasma biomarkers, most rely on a small set of canonical blood-based protein biomarkers such as amyloid-β, p-tau, and neurofilament light. These biomarkers primarily reflect downstream brain pathology and may fail to capture …

Personalizable Metabolic Models To Enable Immune Characterization And Drug Discovery, Joshua Loecker

Department of Biochemistry: Dissertations, Theses, and Student Research

Cellular metabolism is reshaped by disease and physiological state, and genome-scale metabolic networks (GSMNs) offer a systematic way to interrogate this biology and identify therapeutic targets. Building a GSMN from expression data, however, requires a sequence of stages including read processing, normalization and gene-activity classification, multi-omic integration, model reconstruction, simulation, and biological interpretation. These are typically handled by disconnected tools spanning multiple programming languages, file formats, and databases. The resulting reliance on heterogeneous interfaces and manual steps threatens reproducibility. This work develops an ecosystem of computational tools that carry an analysis from raw sequencing reads to mechanistic biological interpretation. First, …

Using Zebrafish To Investigate The Innate Immune Response To R132h Mutant Glioma, Mikaela L. Fairbanks

All NMU Master's Theses

Gliomas are the most commonly occurring brain tumor found in adults. The most dominant mutation found in glioma is in the isocitrate dehydrogenase 1 (IDH1) gene. IDH converts isocitrate into α-ketoglutarate (α-KG), but the mutated form of it will take α-KG and further convert it into D-2-hydroxyglutarate (D-2-HG). Mutated IDH1 glioma (mIDH1) produces a higher concentration of D-2-HG than the wild-type IDH1 glioblastoma (wtIDH1). These mIDH1 tumors tend to have a better prognosis, growing slower and having less inflammation than the wtIDH1 counterpart, potentially due to the increased D-2-HG. However, the effects of mIDH1 and D-2-HG on the innate immune …

Assessing The Relationship Between The Degree Of Static And Dynamic Quadricep Angle And Kinetic Asymmetry Index % In Females During The Follicular Phase Of Menstruation, Madeline Grace Poirier

All NMU Master's Theses

The quadriceps angle (q-angle) quantifies lateral pull on the knee. Females have greater static and dynamic q-angles due to anatomical factors including a wider pelvis and more lateral tibial tuberosity, which may influence ACL injury risk. The kinetic asymmetry index (KAI %) measures limb-to-limb differences in ground reaction force (GRF) impulses during dynamic tasks including countermovement jumps (CMJs), with values > 10% linked to injury risk. During the follicular phase of the menstrual cycle, fluctuating hormones increase joint laxity, further heightening biomechanical vulnerability in females.

This cross-sectional study examined the relationship between static and dynamic q-angle and KAI % in active, …

Developing Solvent-Based Recycling Methods At Ambient Conditions To Regenerate Bisphenol A Diglycidyl Ether And Recover Metal Oxides From Epoxy Nanocomposites, Heaven Smith

Rose-Hulman Undergraduate Research Publications

No abstract provided.