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Learning Paradigms For Rhythm Detection And Generation Using Mathematical Models, Biophysical And Artificial Neural Networks, Prianka Bose

Dissertations

Humans possess an inherent ability to recognize evenly-spaced rhythms, known as isochronous rhythms, owing to the brain's predisposition to entrain to external auditory stimuli with regular temporal intervals. The central focus of this research is to understand how the brain learns and retains rhythmic time intervals in the context of music. This dissertation studies rhythm detection and generation through mathematical models, biophysical networks, and artificial neural networks, addressing both isochronous and non-isochronous patterns.

A primary focus of the thesis is on isochronous rhythms. In particular, given a perturbation to an isochronous rhythm such as a tempo change or phase shift …

Machine Learning Methods For Pattern Recognition Analysis Of Genomic And Molecular Data, Kuang Du

Dissertations

While immune therapies achieve remarkable success in treating various cancers, only a subset of patients achieves a durable clinical response, and many exhibit innate or acquired resistance. Precision medicine aims to tailor treatments to individual patients based on specific biological markers, ensuring that each patient receives the therapy most likely to be effective. Predictive biomarkers and gene signatures offer potential for more personalized treatment strategies by identifying patients likely to benefit. Recent studies suggest that gene signatures, comprising sets of genes, hold predictive value for certain clinical variables. Typically derived from biological expert knowledge, these signatures demonstrate substantial predictive potential, …

Mathematical Modelling And Analysis For The Co-Infection Of Viral And Bacterial Diseases: A Systematic Review Protocol, Timothy Kiprono Yano, Ebenezer Afrifa-Yamoah, Julia Collins, Ute Mueller, Steven Richardson

Research outputs 2022 to 2026

Introduction Breaking the chain of transmission of an infectious disease pathogen is a major public health priority. The challenges of understanding, describing and predicting the transmission dynamics of infections have led to a wide range of mathematical, statistical and biological research problems. Advances in diagnostic laboratory procedures with the ability to test multiple pathogens simultaneously mean that co-infections are increasingly being detected, yet little is known about the impact of co-infections in shaping the course of an infection, infectivity, and pathogen replication rate. This is particularly true of the apparent synergistic effects of viral and bacterial co-infections, which present the …

Understanding Women, Infant And Children Feeding Decisions In Emergencies: The Case Of Covid-19 And The Formula Shortage, Davida Mensah, Edmund F. Agyemang, Constance Gewa

School of Mathematical & Statistical Sciences Faculty Publications

Background: The advantages of breastfeeding and its role in emergencies are undeniable. Studies show that many women in developed countries choose formula over breastmilk, even in emergencies. Nevertheless, no one knows if postpartum women under the Women, Infants and Children (WIC) program turned out to breastfeed or re-lactate their infants during these crises. This study aims to better understand WIC participants' perceptions about breastfeeding their babies in emergencies.

Methods: A chi-square test of independence was used to assess the association between breastfeeding choice and demographic characteristics and potential covariates of respondents. A post hoc analysis using Dunn's multiple comparisons test …

Immune Checkpoint Inhibitor-Associated Cutaneous Adverse Events: Mechanisms Of Occurrence, Abdulaziz M. Eshaq, Thomas W. Flanagan, Abdulqader A. Ba Abbad, Zain Alabden A. Makarem, Mohammed S. Bokir, Ahmed K. Alasheq, Sara A. Al Asheikh, Abdullah M. Almashhor, Faroq Binyamani, Waleed A. Al-Amoudi, Abdulaziz S. Bawzir, Youssef Haikel, Mossad Megahed, Mohamed Hassan

School of Medicine Faculty Publications

Immunotherapy, particularly that based on blocking checkpoint proteins in many tumors, including melanoma, Merkel cell carcinoma, non-small cell lung cancer (NSCLC), triple-negative breast (TNB cancer), renal cancer, and gastrointestinal and endometrial neoplasms, is a therapeutic alternative to chemotherapy. Immune checkpoint inhibitor (ICI)-based therapies have the potential to target different pathways leading to the destruction of cancer cells. Although ICIs are an effective treatment strategy for patients with highly immune-infiltrated cancers, the development of different adverse effects including cutaneous adverse effects during and after the treatment with ICIs is common. ICI-associated cutaneous adverse effects include mostly inflammatory and bullous dermatoses, as …

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …

Rna Structural-Dynamical Hierarchy: Sars-Cov, Sars-Cov-2, And Delta/Omicron Variant S2m Monomers, Kissing Complexes, And Extended Duplexes, Adam Kensinger

Electronic Theses and Dissertations

The power and promise of ribonucleic acid (RNA) molecules are only beginning to be realized in living organisms and pharmaceutical intervention. Specifically, defining the chemical physics of RNA’s heterogenous structural ensemble and dynamics, which has experienced expansive growth over the last few years, is central to a complete understanding, yet continues to be a significant challenge. A 41-nucleotide hairpin called the stem-loop II motif (s2m), present in the viral genomes of severe acute respiratory syndrome (SARS), SARS-coronavirus-2 (SARS-CoV-2), and the Delta and Omicron variants responsible for the COVID-19 pandemic, is a potential antiviral target due to its high sequence conservation …

A Clustering-Based Location Allocation Method For Delivery Sites Under Epidemic Situations, Yaqiong Zhou, Junqi Chen, Weishi Li, Sihang Qiu, Rusheng Ju

Journal of System Simulation

Abstract: To address the poor performance of commonly used intelligent optimization algorithms in solving location problems—specifically regarding effectiveness, efficiency, and stability—this study proposes a novel location allocation method for the delivery sites to deliver daily necessities during epidemic quarantines. After establishing the optimization objectives and constraints, we developed a relevant mathematical model based on the collected data and utilized traditional intelligent optimization algorithms to obtain Pareto optimal solutions. Building on the characteristics of these Pareto front solutions, we introduced an improved clustering algorithm and conducted simulation experiments using data from Changchun City. The results demonstrate that the proposed algorithm outperforms …

Emergency Vehicle Dispatching Model Considering Demand Urgency And Delivery Fairness, Long Kejun, Liu Jia, Gao Zhibo, Chen Suqian, Zhang Zhonggen

Journal of China & Foreign Highway

In emergency vehicle dispatching after unexpected events，it is crucial to prioritize critical nodes with high demand urgency while minimizing excessive delivery delays at other nodes to prevent secondary impacts.On this basis，this study developed an emergency vehicle dispatching model that considered demand urgency and delivery delay fairness.Firstly，the entropy weight-TOPSIS method was used to calculate the demand urgency for each node，and a delivery delay balance index was introduced to minimize disparities in delivery delays between nodes.Secondly，a multi-objective optimization model was established with total delivery time，overall cost，and delivery delay balance as objectives，while considering constraints such as inventory levels at distribution centers and route …

Comparing Multivalent Cross-Linked Sodium Alginate/ Montmorillonite Beads Containing Curcumin Or Cayenne Pepper As Drug Carriers And Their Antimicrobial Resistance, Shionainn Traynor, Shubham Sharma

SURE Journal: Science Undergraduate Research Experience Journal

The aim of the following work was to investigate and compare curcumin and cayenne pepper in microbeads composed of sodium alginate (SA) crosslinked with montmorillonite (MMT) to act as drug carriers and their antimicrobial resistance. The microbeads were prepared through ion-exchange in multivalent solutions of CaCl₂, MgCl₂ and AlCl₃. The microbeads were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive X-ray analysis (EDX) and the time required for intercalation of curcumin and cayenne pepper with MMT. Simulated intestinal fluid (pH 7.3) and gastric fluid (pH 1.2) at 37°C were used for comparison in swelling studies. …

Mathematical Modelling Of Disease Outbreak, Favour Christian, Matthew Molloy

SURE Journal: Science Undergraduate Research Experience Journal

Establishing a model framework for more research necessitates a thorough understanding of the causes, distribution, prevalence, and evolution of infectious illnesses. The main mathematical concept used in this modelling simulation is ordinary differential equations (ODEs). The purpose of this study was to investigate the significance of the many criteria linked to a zombie virus spread. The zombie framework provides an accessible and relatively simple representation of the nature of infectious disease spread, allowing for tractable assumptions and the development of more complex situations.

The models are designed around a zombie outbreak in which the zombie virus is spread through a …

Editorial - Sure Journal Vol 6, Anne M. Friel, Eva Campion, Sinead Loughran

SURE Journal: Science Undergraduate Research Experience Journal

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Engineering Functionalized Nanomaterials For Targeting And Ablating Biofilms On Surfaces, Dhanush Lakmal Yapa Amarasekara

Theses and Dissertations

Biofilms on both the surface and interior of medical devices pose major challenges, including hindering device performance and serving as infection sources. These biofilms form a protective layer around bacteria, shielding them from the body’s immune system and antibiotics. This makes infections difficult to treat, as the bacteria within the biofilm are resistant to both antibiotics and immune defenses. Additionally, biofilms can induce inflammation and irritation in nearby tissues, leading to further health complications. Antibiotic resistance raises concerns about the emergence of multi-drug resistant (MDR) pathogens. MDR infections are difficult to treat, leading to prolonged hospital stays and the need …

Fisheries Management In Mississippi State-Operated Fishing Lakes: A Review And Look To The Future, Hayden Gregory Funk

Theses and Dissertations

The Mississippi Department of Wildlife, Fisheries and Parks currently manages 18 State Lakes and 17 State Park Lakes to provide public fishing opportunities. My goal was to conduct a comprehensive analysis of monitoring and management activities in State Lakes to enhance understanding of lake dynamics, further develop existing management initiatives, and identify alternative avenues for effective management. To achieve this objective, I have undertaken a comprehensive examination and synthesis of the historical background pertaining to State Lakes and conducted an analysis of pertinent data regarding lake characteristics such as the physical and chemical attributes of the lakes, the features of …

Design, Synthesis, And Nmr-Guided Characterization Of A Targeted Covalent Inhibitor-Like Molecule Against Ivyp1 From P. Aeruginosa, Samuel Taylor Moore

Master's Theses

Multi-drug resistance poses a serious threat to future generations and historical antibiotic pipelines; consequently, the medical and economic burdens associated with treating multidrug-resistant bacteria are substantiated. In this context, P. aeruginosa (PA) emerges as one of the most significant healthcare challenges, being a leading cause of resistance-associated mortality worldwide. Despite modern efforts to combat these poor outcomes, drug-resistant cases continue to rise, and the need for novel antibiotic treatment is apparent. To this end, we investigated relevant resistance mechanisms and past antibiotic targets within PA, and in doing so, we identified relationships between peptidoglycan biology and a periplasmic protein, Inhibitor …

The Mongolian Remodeling And The Structure Of Anoplocephalid Cestode Diversity, Mackenzie Grover

All NMU Master's Theses

Ecological disruption plays an important role in structuring diversity of flora, fauna, and their parasites. At the end of the Eocene, climatic change across Asia resulted in a faunal turnover (the Mongolian Remodeling) as rodents diversified and larger mammals declined. Throughout the Oligocene, the landscape in Asia was characterized by episodic climatic and landscape changes resulting in pulses of rodent diversification. The role of historical ecological disruption in Central Asia in structuring the diversity of parasites of small rodents has not been thoroughly investigated. The hyper-diverse Paranoplocephala species complex (family: Anoplocephalidae) infect rodents throughout the Holarctic and present an opportunity …

Estimating Medium-Term Regional Monthly Economic Activity Reductions During The Covid-19 Pandemic Using Nighttime Light Data, Ma Flordeliza P. Del Castillo, Toshio Fujimi, Hirokazu Tatano

SOSE Affiliate: Manila Observatory

Economic impact estimates of the initial lockdowns due to the COVID-19 pandemic showed a significant reduction in economic activities globally. However, the succeeding impacts and their spatiotemporal distribution within countries remain unknown. Studies showed that nighttime light data (NTL) has effectively revealed the spatiotemporal dimensions of the economic effects of COVID-19. Thus, this study used NTL data to determine the medium-term regional monthly economic impacts of the pandemic in the Philippines in terms of the Economic Activity Reduction (EAR) index. We generated a spatial error model, regressing pre-pandemic NTL on mean temperature, maximum rainfall, and built-up area. This model explained …

Synthesis Of Novel Chromenone Esters For Biochemical Assays, Andrew Dean Helmerich

Undergraduate Honors Thesis Collection

This project details the synthesis of a variety of novel chromenone esters to be used as enzymatic probes. A robust, initial library of 22 chromenone esters was successfully synthesized with differences in chain length, branching, and the incorporation of cyclic and heteroatomic moieties. These new chromenones were fully characterized by 1HNMR, 13CNMR, DEPT HRMS, 19FNMR, and HSQC. The utility of these compounds comes from the fact that they will fluoresce upon cleavage of the ester; thus, this property makes them ideal candidates to be used in the monitoring of enzymatic activity of esterases. Elucidating the enzyme-substrate structure activity relationship (SAR) …

Use Of Equine H3n8 Hemagglutinin As A Broadly Protective Influenza Vaccine Immunogen, David Verhoeven, Brett A. Sponseller, James E. Crowe, Sandhya Bangaru, Richard J. Webby, Brian M. Lee

Chemistry

Development of an efficacious universal influenza vaccines remains a long-sought goal. Current vaccines have shortfalls such as mid/low efficacy and needing yearly strain revisions to account for viral drift/shift. Horses undergo bi-annual vaccines for the H3N8 equine influenza virus, and surveillance of sera from vaccinees demonstrated very broad reactivity and neutralization to many influenza strains. Subsequently, vaccinating mice using the equine A/Kentucky/1/1991 strain or recombinant hemagglutinin (HA) induced similar broadly reactive and neutralizing antibodies to seasonal and high pathogenicity avian influenza strains. Challenge of vaccinated mice protected from lethal virus challenges across H1N1 and H3N2 strains. This protection correlated with …

The Impact Of Wild Pigs (Sus Scrofa) On Avian Occupancy And Vegetation Structure, Kenneth Wilson

Graduate Theses and Dissertations

Invasive species, particularly wild pigs (Sus scrofa), pose a significant threat to native ecosystems through both direct and indirect impacts. Wild pigs are large-bodied omnivorous species that can consume a wide variety of plants and animals and are known for destructive foraging behaviors, which likely threatens avian communities through habitat alteration and can impact the long term structure of ecosystems where they are present.

In chapter 1, we used a combination of avian point count surveys, vegetation assessments, and camera trap surveillance to quantify how the occupancy of breeding birds in bottomland hardwood forests changed in relation to …

(R2102) Chaos Measure In A Discrete Sir Epidemic Model With Constant Recovery, Sonia Aneja, Itendra Kumar, Sada Nand Prasad

Applications and Applied Mathematics: An International Journal (AAM)

A discrete SIR epidemic model with constant recovery and bilinear incidence rate is investigated for emergence of regular and chaotic behaviour in the context of non linear dynamics and different viable settings. The Euler’s discretization method is employed to transform the continuous epidemic model into discrete model which has been used as the study model. Attention is paid to various bifurcation plots obtained by varying certain system parameters while keeping other parameters constant. Bifurcations indicate regular evolution followed by chaos. Regular and chaotic attractors have been drawn in the process. As part of chaos measure, numerical studies are extended to …

Establishment Of Structure-Property-Processing Relationships For Design Of Sprayable Hydrogels And Amyloid/Peo Electrospun Composites, Xianjun Wang

Dissertations

The focus of this dissertation is the design, synthesis, characterization, and prototyping of bio-inspired materials to understand the role of structure, intermolecular interactions, and processing technique on the self-assembly, bioactive properties, and mechanical properties of the biomaterials. This work is divided into three research areas: 1) sprayable and adhesive glycopolymer based hydrogels; 2) decapeptide-based composite nanofiber mats; and 3) prototyping sutures and meshes via electrospinning. The established structure-property-processing relationships provide a foundation for designing biomaterials in the future.

The first chapter provides an introductory overview of the requirements necessary for the development of hydrogels, glycopolymers, and peptides, including relevant processing …

Hurricane Evacuation: Navigating Uncertainty During Covid 19 And With Existing Communication Scales, And Considering Public And Expert Perception Of Alternative Scales, Leilani D. Paxton

USF Tampa Graduate Theses and Dissertations

This dissertation investigates the effectiveness of current hurricane warning products and communication strategies, exploring factors influencing public perception of risk and decision-making during evacuations. The study employs a mixed-methods approach, combining survey data, focus group discussions, and interviews with meteorologists and emergency managers. The first paper examines the impact of the COVID-19 pandemic on hurricane risk perception and evacuation decisions. Findings indicate that while COVID-19 concerns played a role in some individuals' decisions, particularly those with pets or concerns about shelter conditions, the majority of participants evacuated for Hurricane Ian. The study highlights the importance of providing clear, consistent, and …

A Dynamical Systems Approach For Modeling Malware Propagating Through A Network And Potential Solutions Towards Mitigating Spread, James Johnson

Cybersecurity Undergraduate Research Showcase

Many people draw close parallels between malware propagating through a network and an epidemic spreading through a population. Epidemics are often modeled by a Susceptible-Infected-Recovered (SIR) model, in which a similar system of equations can model the spread of a virus through a computer network, and can be simplified when making assumptions about the network itself and its fixed number of nodes and edges. In this instance, malware propagating in a network also should reflect the network it is propagating through, in which the dynamical system will factor in the nodes of the network and their properties. The system itself …

Implementing Bernstein Operational Matrices To Solve A Fractional‐Order Smoking Epidemic Model, Jalal Al Hallak, Mohammed Alshbool, Ishak Hashim

All Works

This paper leverages the Bernstein operational matrices method for the first time in order to resolve the nonlinear fractional smoking epidemic model presented in terms of Caputo’s fractional derivative. An approximate solution is derived using Bernstein’s operational matrices and strategically chosen collocation points. This is followed by the validation of the proposed method’s accuracy and reliability against the established Runge–Kutta fourth‐order method. Furthermore, a comprehensive comparative analysis is conducted against two prominent techniques: the fractional differential transform method (FDTM) and the q‐homotopy analysis transform method (q‐HATM). The results show a superior and significant performance regarding accuracy as well as approximation. …

Alabama Agricultural Producers’ Experiences With Wild Pigs (Sus Scrofa) And Their Preferences Concerning Wild Pig Management, Hailey E. Ellis, Luren M. Jaebker, Alan D. Bright, Mark D. Smith, Keith M. Carlisle

United States Department of Agriculture Wildlife Services: Staff Publications

Government agencies and landowners use a variety of lethal methods to reduce invasive wild pig populations and resulting agricultural damages. To provide decision-makers with information regarding Alabama farmers’ experiences with wild pigs and their preferences for management actions, we surveyed Alabama Farmers Federation members in 2020. We found that wild pigs were commonly present on livestock, timber, and crop production acreage, but wild pig damages and costs were much more common among crop producers. Respondents' wildlife acceptance capacity for wild pigs was low and all lethal control methods were considered aceptable by most reposndents, particularly those performed by landowners. While …

Internet Of Medical Things: Integrating Machine Learning And Wearables For Healthcare, Jingwen Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

The Internet of Medical Things (IoMT), which integrates Internet of Things technologies into healthcare, has become a powerful tool for enhancing health monitoring and predicting clinical outcomes. By leveraging wearable devices, IoMT facilitates continuous, cost-effective, and convenient tracking of patients' health conditions over time. This dissertation applies data-driven methods to address critical clinical challenges involving wearable devices. Specifically, it focuses on three significant clinical problems: (1) indoor contact tracing for healthcare workers using Bluetooth Low Energy (BLE) beacons, (2) predicting surgical outcomes using wearable data, and (3) developing robust models for surgical outcome prediction that account for patient variability using …

Internet Of Medical Things: Integrating Machine Learning And Wearables For Healthcare, Jingwen Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

The Internet of Medical Things (IoMT), which integrates Internet of Things technologies into healthcare, has become a powerful tool for enhancing health monitoring and predicting clinical outcomes. By leveraging wearable devices, IoMT facilitates continuous, cost-effective, and convenient tracking of patients' health conditions over time. This dissertation applies data-driven methods to address critical clinical challenges involving wearable devices. Specifically, it focuses on three significant clinical problems: (1) indoor contact tracing for healthcare workers using Bluetooth Low Energy (BLE) beacons, (2) predicting surgical outcomes using wearable data, and (3) developing robust models for surgical outcome prediction that account for patient variability using …

Kreig: Quantifying The Relationship Between Sars-Cov-2 Viral Load And Infectiousness, Aurelien Marc

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Kreig: Examining Affinity Maturation And Antigenic Drift With An Agent-Based Model, Jasmine Af Kreig, Jannatul Ferdous, Ruian Ke, Ruy M. Ribeiro

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.