Open Access. Powered by Scholars. Published by Universities.®

Other Computer Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

Medicine and Health Sciences

Institution
Keyword
Publication Year
Publication
Publication Type

Articles 1 - 30 of 84

Full-Text Articles in Other Computer Sciences

Developing A Comprehensive Resource Guide For Caregivers Within The Area Agency On Aging, Aiden R. Murphy May 2026

Developing A Comprehensive Resource Guide For Caregivers Within The Area Agency On Aging, Aiden R. Murphy

Public Health Capstone Projects

This project developed a new universal caregiver resource guide for caregivers within the Area Agency on Aging, in order to improve resource navigation and workflow efficiency. Resources were collected, verified, and organized into a new, streamlined guide via the ARIA chatbot, covering multiple needs. Caregiver resources were collected and verified by the capstone student and mentor, Michael Kroeker, and organized into a centralized knowledge base within the ARIA chatbot. A mixed methods evaluation was conducted utilizing a 5-point Likert scale with three quantitative questions and one open-ended qualitative question. The data was given to the SeniorLine staff, who wanted to …


Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker May 2026

Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Computational prediction of allosteric binding sites in protein structures remains a persistent challenge, as these regulatory pockets evade detection by both sequence-based and structure-based algorithms. Both computational and physical origins of this predictive asymmetry remain insufficiently understood. In this study, we systematically examine the determinants of binding site predictability using a dual framework that integrates a fine-tuned protein language model and the structure-based method P2Rank as complementary tools probing a diverse data set of 453 human kinases, together with a physics-based interpretability layer derived from energy landscape frustration analysis. Both predictors exhibit a sharp and reproducible dichotomy on protein kinases, …


Integrative Approaches And Data Analysis For Single-Cell Rna Sequencing Data, Teng Long Jan 2026

Integrative Approaches And Data Analysis For Single-Cell Rna Sequencing Data, Teng Long

Computer Science and Engineering Dissertations

The rapid growth of single-cell RNA sequencing and transcriptomic datasets has created major computational challenges in causal discovery, representation learning, and biologically faithful data generation. To address these challenges, this dissertation presents three complementary deep learning frameworks for the analysis and modeling of transcriptomic data. Together, these methods form an integrative computational toolkit for understanding complex biological systems from high-dimensional and heterogeneous gene expression data.

First, this dissertation introduces DAG-VAERL, a causal discovery framework that integrates variational autoencoders, graph neural networks, reinforcement learning, and attention mechanisms to infer directed acyclic graphs for gene regulatory network analysis. DAG-VAERL improves causal structure …


Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Aug 2025

Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ongoing evolution of SARS-CoV-2 variants has underscored the need to understand not only the structural basis of antibody recognition but also the dynamic and allosteric mechanisms that could underlie complexity of broad and escape-resistant neutralization. In this study, we employed a multi-scale approach integrating structural analysis, hierarchical molecular simulations, mutational scanning and network-based allosteric modeling to dissect how Class 4 antibodies (represented by S2X35, 25F9, and SA55) and Class 5 antibodies (represented by S2H97, WRAIR-2063 and WRAIR-2134) can modulate conformational behavior, binding energetics, allosteric interactions and immune escape patterns of the SARS-CoV-2 spike protein. Using hierarchical simulations of the …


Multiscale Modeling And Dynamic Mutational Profiling Of Binding Energetics And Immune Escape For Class I Antibodies With Sars-Cov-2 Spike Protein: Dissecting Mechanisms Of High Resistance To Viral Escape Against Emerging Variants, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Jul 2025

Multiscale Modeling And Dynamic Mutational Profiling Of Binding Energetics And Immune Escape For Class I Antibodies With Sars-Cov-2 Spike Protein: Dissecting Mechanisms Of High Resistance To Viral Escape Against Emerging Variants, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The rapid evolution of SARS-CoV-2 has underscored the need for a detailed understanding of antibody binding mechanisms to combat immune evasion by emerging variants. In this study, we investigated the interactions between Class I neutralizing antibodies—BD55-1205, BD-604, OMI-42, P5S-1H1, and P5S-2B10—and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein using multiscale modeling, which combined molecular simulations with the ensemble-based mutational scanning of the binding interfaces and binding free energy computations. A central theme emerging from this work is that the unique binding strength and resilience to immune escape of the BD55-1205 antibody are determined by leveraging a broad epitope …


Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker May 2025

Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we conducted a comprehensive analysis of the interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and four neutralizing antibodies—S309, S304, CYFN1006, and VIR-7229. Using integrative computational modeling that combined all-atom molecular dynamics (MD) simulations, mutational scanning, and MM-GBSA binding free energy calculations, we elucidated the structural, energetic, and dynamic determinants of antibody binding. Our findings reveal distinct dynamic binding mechanisms and evolutionary adaptation driving the broad neutralization effect of these antibodies. We show that S309 targets conserved residues near the ACE2 interface, leveraging synergistic van der Waals and electrostatic interactions, while S304 focuses on …


Preserving Privacy In Senior Care At Home Monitoring Systems, Sam Russel, Ryan Benton, Amy Campbell, Scott Sittig Mar 2025

Preserving Privacy In Senior Care At Home Monitoring Systems, Sam Russel, Ryan Benton, Amy Campbell, Scott Sittig

Shelby Hall Graduate Research Forum Posters

Many seniors prefer to live at home which necessitates research into the application of technologies to provide a safer environment with less caregiver resources. However, the application of home health care (HHC) monitoring for seniors is still in an evolutionary stage. Present HHC systems are produced by private companies with general regulatory guidelines lacking specific care of the elderly. As such, each company that produces such a system claims to have better safety, privacy, and security that their competitors. A pressing issues is devising and applying a general framework for the application of technologies that delivers safety while preserving privacy. …


False Narratives, Real Consequences, Russell W. Cantrell, Matt Campbell Mar 2025

False Narratives, Real Consequences, Russell W. Cantrell, Matt Campbell

Shelby Hall Graduate Research Forum Posters

Social media is an increasingly significant tool in modern cyber warfare, capable of rapidly shaping public opinion. The swift dissemination of information complicates efforts to distinguish fact from fiction [1]. During public health crises, healthcare professionals use these platforms to share updates, yet their credible content must contend with false or deliberately misleading narratives [2]. This environment creates an opportunity for cyberattacks through social media influence campaigns [3]. While disinformation's role in political interference has been widely studied, its potential to destabilize healthcare remains largely unexplored. Prior research primarily focuses on how vaccine misinformation affects the general public [4]. This …


Feasibility And Acceptability Of The Mazi Umntanakho Digital Tool In South African Settings: A Qualitative Evaluation, Catherine E. Draper, Caylee J. Cook, Elizabeth A. Ankrah, Jesus A. Beltran, Franceli L. Cibrian, Kimberley D. Lakes, Hanna Mofid, Lucretia Williams, Gillian R. Hayes Jan 2025

Feasibility And Acceptability Of The Mazi Umntanakho Digital Tool In South African Settings: A Qualitative Evaluation, Catherine E. Draper, Caylee J. Cook, Elizabeth A. Ankrah, Jesus A. Beltran, Franceli L. Cibrian, Kimberley D. Lakes, Hanna Mofid, Lucretia Williams, Gillian R. Hayes

Engineering Faculty Articles and Research

To address the need for interventions targeting social emotional development and mental health of young children in South Africa, the Mazi Umntanakho (‘know your child’) digital tool was co-designed, and piloted with caregivers and 3–5-year-old children involved in home visiting programmes promoting early childhood development. The aim of this study was to qualitatively evaluate the feasibility and acceptability of this tool in four urban and four rural low-income communities, from the perspective of home visitors and caregivers. Focus groups were conducted with home visitors (n = 117) and caregivers (n = 72). Issues relating to the feasibility of …


A Guideline For Open-Source Tools To Make Medical Imaging Data Ready For Artificial Intelligence Applications: A Society Of Imaging Informatics In Medicine (Siim) Survey, Sanaz Vahdati, Bardia Khosravi, Elham Mahmoudi, Kuan Zhang, Pouria Rouzrokh, Shahriar Faghani, Mana Moassefi, Aylin Tahmasebi, Katherine Andriole, Peter Chang, Keyvan Farahani, Mona Flores, Les Folio, Sina Houshmand, Maryellen Giger, Judy Gichoya, Bradley Erickson Oct 2024

A Guideline For Open-Source Tools To Make Medical Imaging Data Ready For Artificial Intelligence Applications: A Society Of Imaging Informatics In Medicine (Siim) Survey, Sanaz Vahdati, Bardia Khosravi, Elham Mahmoudi, Kuan Zhang, Pouria Rouzrokh, Shahriar Faghani, Mana Moassefi, Aylin Tahmasebi, Katherine Andriole, Peter Chang, Keyvan Farahani, Mona Flores, Les Folio, Sina Houshmand, Maryellen Giger, Judy Gichoya, Bradley Erickson

Department of Radiology Faculty Papers

In recent years, the role of Artificial Intelligence (AI) in medical imaging has become increasingly prominent, with the majority of AI applications approved by the FDA being in imaging and radiology in 2023. The surge in AI model development to tackle clinical challenges underscores the necessity for preparing high-quality medical imaging data. Proper data preparation is crucial as it fosters the creation of standardized and reproducible AI models while minimizing biases. Data curation transforms raw data into a valuable, organized, and dependable resource and is a fundamental process to the success of machine learning and analytical projects. Considering the plethora …


Advancing Endovascular Neurosurgery Training With Extended Reality: Opportunities And Obstacles For The Next Decade, Shray Patel, Michael Covell, Saarang Patel, Sandeep Kandregula, Sai Krishna Palepu, Avi Gajjar, Oleg Shekhtman, Georgios Sioutas, Ali Dhanaliwala, Terence Gade, Jan-Karl Burkhardt, Visish Srinivasan Aug 2024

Advancing Endovascular Neurosurgery Training With Extended Reality: Opportunities And Obstacles For The Next Decade, Shray Patel, Michael Covell, Saarang Patel, Sandeep Kandregula, Sai Krishna Palepu, Avi Gajjar, Oleg Shekhtman, Georgios Sioutas, Ali Dhanaliwala, Terence Gade, Jan-Karl Burkhardt, Visish Srinivasan

SKMC Student Presentations and Publications

Background: Extended reality (XR) includes augmented reality (AR), virtual reality (VR), and mixed reality (MR). Endovascular neurosurgery is uniquely positioned to benefit from XR due to the complexity of cerebrovascular imaging. Given the different XR modalities available, as well as unclear clinical utility and technical capabilities, we clarify opportunities and obstacles for XR in training vascular neurosurgeons. Methods: A systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. Studies were critically appraised using ROBINS-I. Results: 19 studies were identified. 13 studies used VR, while 3 studies used MR, and 3 studies used AR. …


Interpretation Models For Prostate Lesion: Detecting, Explaining, And Understanding., Mehmet Akif Gulum Aug 2024

Interpretation Models For Prostate Lesion: Detecting, Explaining, And Understanding., Mehmet Akif Gulum

Electronic Theses and Dissertations

Prostate cancer is a major public health concern, affecting millions of men worldwide. While early detection and treatment of prostate cancer is critical for improving patient outcomes, the detection of prostate lesions is even more important for timely intervention and management of the disease. Prostate lesions are abnormal growths or lumps within the prostate gland, which may or may not be cancerous. The timely detection and accurate diagnosis of prostate lesions is crucial for effective treatment and management of the disease. In recent years, deep learning models have shown promise in accurately detecting and characterizing prostate lesions using advanced imaging …


Mixed Uncertainty Analysis On Pumping By Peristaltic Hearts Using Dempster-Shafer Theory, Yanyan He, Nicholas A. Battista, Lindsay D. Waldrop Jun 2024

Mixed Uncertainty Analysis On Pumping By Peristaltic Hearts Using Dempster-Shafer Theory, Yanyan He, Nicholas A. Battista, Lindsay D. Waldrop

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this paper, we introduce the numerical strategy for mixed uncertainty propagation based on probability and Dempster–Shafer theories, and apply it to the computational model of peristalsis in a heart-pumping system. Specifically, the stochastic uncertainty in the system is represented with random variables while epistemic uncertainty is represented using non-probabilistic uncertain variables with belief functions. The mixed uncertainty is propagated through the system, resulting in the uncertainty in the chosen quantities of interest (QoI, such as flow volume, cost of transport and work). With the introduced numerical method, the uncertainty in the statistics of QoIs will be represented using belief …


Exploring Binding Pockets In The Conformational States Of The Sars-Cov-2 Spike Trimers For The Screening Of Allosteric Inhibitors Using Molecular Simulations And Ensemble-Based Ligand Docking, Grace Gupta, Gennady M. Verkhivker May 2024

Exploring Binding Pockets In The Conformational States Of The Sars-Cov-2 Spike Trimers For The Screening Of Allosteric Inhibitors Using Molecular Simulations And Ensemble-Based Ligand Docking, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and …


Predicting Ffar4 Agonists Using Structure-Based Machine Learning Approach Based On Molecular Fingerprints, Zaid Anis Sherwani, Syeda Sumayya Tariq, Mamona Mushtaq, Ali Raza Siddiqui, Mohammad Nur-E-Alam, Aftab Ahmed, Zaheer Ul-Haq Apr 2024

Predicting Ffar4 Agonists Using Structure-Based Machine Learning Approach Based On Molecular Fingerprints, Zaid Anis Sherwani, Syeda Sumayya Tariq, Mamona Mushtaq, Ali Raza Siddiqui, Mohammad Nur-E-Alam, Aftab Ahmed, Zaheer Ul-Haq

Pharmacy Faculty Articles and Research

Free Fatty Acid Receptor 4 (FFAR4), a G-protein-coupled receptor, is responsible for triggering intracellular signaling pathways that regulate various physiological processes. FFAR4 agonists are associated with enhancing insulin release and mitigating the atherogenic, obesogenic, pro-carcinogenic, and pro-diabetogenic effects, normally associated with the free fatty acids bound to FFAR4. In this research, molecular structure-based machine-learning techniques were employed to evaluate compounds as potential agonists for FFAR4. Molecular structures were encoded into bit arrays, serving as molecular fingerprints, which were subsequently analyzed using the Bayesian network algorithm to identify patterns for screening the data. The shortlisted hits obtained via machine learning protocols …


Cardiogpt: An Ecg Interpretation Generation Model, Guohua Fu, Jianwei Zheng, Islam Abudayyeh, Chizobam Ani, Cyril Rakovski, Louis Ehwerhemuepha, Hongxia Lu, Yongjuan Guo, Shenglin Liu, Huimin Chu, Bing Yang Apr 2024

Cardiogpt: An Ecg Interpretation Generation Model, Guohua Fu, Jianwei Zheng, Islam Abudayyeh, Chizobam Ani, Cyril Rakovski, Louis Ehwerhemuepha, Hongxia Lu, Yongjuan Guo, Shenglin Liu, Huimin Chu, Bing Yang

Mathematics, Physics, and Computer Science Faculty Articles and Research

Numerous supervised learning models aimed at classifying 12-lead electrocardiograms into different groups have shown impressive performance by utilizing deep learning algorithms. However, few studies are dedicated to applying the Generative Pre-trained Transformer (GPT) model in interpreting electrocardiogram (ECG) using natural language. Thus, we are pioneering the exploration of this uncharted territory by employing the CardioGPT model to tackle this challenge. We used a dataset of ECGs (standard 10s, 12-channel format) from adult patients, with 60 distinct rhythms or conduction abnormalities annotated by board-certified, actively practicing cardiologists. The ECGs were collected from The First Affiliated Hospital of Ningbo University and Shanghai …


Understanding Social Dynamics In Toxic Conversations And Public Health Intervention Acceptance On Social Media, Ana Aleksandric Jan 2024

Understanding Social Dynamics In Toxic Conversations And Public Health Intervention Acceptance On Social Media, Ana Aleksandric

Computer Science and Engineering Dissertations - Archive

Social media is now central to daily life, offering users a space to share content and opinions. However, these platforms also facilitate the spread of hate speech and misinformation, which can negatively impact public health. This dissertation develops methodologies to analyze social media data for insights that could inform health interventions. The research first examines user responses to toxic content, focusing on behavioral and emotional reactions, as well as group dynamics and bystander effects in toxic interactions. Another key focus is public opinion toward health interventions, particularly COVID-19 vaccination, using geolocated posts and analyzing factors such as race, ethnicity, and …


The Impact Of Dissolved Organic Matter On Photodegradation Rates, Byproduct Formations, And Degradation Pathways For Two Neonicotinoid Insecticides In Simulated River Waters, Josephus F. Borsuah, Tiffany L. Messer, Daniel D. Snow, Steven D. Comfort, Shannon Bartelt-Hunt Jan 2024

The Impact Of Dissolved Organic Matter On Photodegradation Rates, Byproduct Formations, And Degradation Pathways For Two Neonicotinoid Insecticides In Simulated River Waters, Josephus F. Borsuah, Tiffany L. Messer, Daniel D. Snow, Steven D. Comfort, Shannon Bartelt-Hunt

UK CARES Faculty Publications

The influences of dissolved organic matter (DOM) on neonicotinoid photochemical degradation and product formation in natural waters remain unclear, potentially impacting the sustainability of river systems. Therefore, our overall objective was to investigate the photodegradation mechanisms and phototransformation byproducts of two neonicotinoid pesticides, imidacloprid and thiamethoxam, under simulated sunlight at the microcosm scale, to assess the implications of DOM for insecticide degradation in rivers. Direct and indirect photolysis were investigated using twelve water matrices to identify possible reaction pathways with two DOM sources and three quenching agents. Imidacloprid, thiamethoxam, and potential degradants were measured, and reaction pathways identified. The photodegradation …


Machine-Learning-Assisted Design Of Deep Eutectic Solvents Based On Uncovered Hydrogen Bond Patterns, Usman Lame Abbas, Yuxuan Zhang, Joseph Tapia, Md Selim, Jin Chen, Jian Shi, Qing Shao Jan 2024

Machine-Learning-Assisted Design Of Deep Eutectic Solvents Based On Uncovered Hydrogen Bond Patterns, Usman Lame Abbas, Yuxuan Zhang, Joseph Tapia, Md Selim, Jin Chen, Jian Shi, Qing Shao

Markey Cancer Center Faculty Publications

Non-ionic deep eutectic solvents (DESs) are non-ionic designer solvents with various applications in catalysis, extraction, carbon capture, and pharmaceuticals. However, discovering new DES candidates is challenging due to a lack of efficient tools that accurately predict DES formation. The search for DES relies heavily on intuition or trial-and-error processes, leading to low success rates or missed opportuni- ties. Recognizing that hydrogen bonds (HBs) play a central role in DES formation, we aim to identify HB features that distinguish DES from non-DES systems and use them to develop machine learning (ML) models to discover new DES systems. We first analyze the …


Deficiency Of Acute-Phase Serum Amyloid A Exacerbates Sepsis-Induced Mortality And Lung Injury In Mice, Ailing Ji, Andrea C. Trumbauer, Victoria P. Noffsinger, Luke W. Meredith, Brittany Dong, Qian Wang, Ling Guo, Xiangan Li, Frederick C. De Beer, Nancy R. Webb, Lisa R. Tannock, Marlene E. Starr, Christopher M. Waters, Preetha Shridas Dec 2023

Deficiency Of Acute-Phase Serum Amyloid A Exacerbates Sepsis-Induced Mortality And Lung Injury In Mice, Ailing Ji, Andrea C. Trumbauer, Victoria P. Noffsinger, Luke W. Meredith, Brittany Dong, Qian Wang, Ling Guo, Xiangan Li, Frederick C. De Beer, Nancy R. Webb, Lisa R. Tannock, Marlene E. Starr, Christopher M. Waters, Preetha Shridas

Saha Cardiovascular Research Center Faculty Publications

Serum amyloid A (SAA) is a family of proteins, the plasma levels of which may increase >1000-fold in acute inflammatory states. We investigated the role of SAA in sepsis using mice deficient in all three acute-phase SAA isoforms (SAA-TKO). SAA deficiency significantly increased mortality rates in the three experimental sepsis mouse models: cecal ligation and puncture (CLP), cecal slurry (CS) injection, and lipopolysaccharide (LPS) treatments. SAA-TKO mice had exacerbated lung pathology compared to wild-type (WT) mice after CLP. A bulk RNA sequencing performed on lung tissues excised 24 h after CLP indicated significant enrichment in the expression of genes associated …


Heterochiral Dna Nanotechnology For Biomedical Applications, Tracy L. Mallette Aug 2023

Heterochiral Dna Nanotechnology For Biomedical Applications, Tracy L. Mallette

Biomedical Engineering ETDs

In the past 30 years, there have been major advancements on how to treat and diagnose disease because of the improvement and increase in accessibility of sequencing technology. Nucleic acid-based therapeutics can manipulate protein expression. Likewise, pathogens can be identified and detected with single nucleotide specificity. However, the underlying oligonucleotide technology requires protection against natural defense systems that have evolved to destroy foreign nucleic acids. Many chemical modifications that can protect nucleotides also have significant cytotoxic side effects and must be carefully designed into the strands. A novel way to protect against nuclease-mediated degradation is through the use of mirror-image, …


Epileptic Seizure Classification Using Image-Based Data Representation, Amber Surles Aug 2023

Epileptic Seizure Classification Using Image-Based Data Representation, Amber Surles

Graduate Theses and Dissertations (2019 - present)

Epilepsy is a recurrence of seizures caused by a disorder of the brain in over 3.4 million people nationwide. Some people are able to predict their seizures based off prodrome, which is an early sign or symptom that usually resembles mood changes or a euphoric feeling even days to an hour before occurrence. Consequently, the natural instincts of the body to react to an upcoming attack lends credence to the existence of a pre-ictal state that precedes seizure episodes. Physicians and researchers have thus sought for an automated approach for predicting or detecting seizures.

In this research, we evaluate the …


Algorithmic Bias: Causes And Effects On Marginalized Communities, Katrina M. Baha May 2023

Algorithmic Bias: Causes And Effects On Marginalized Communities, Katrina M. Baha

Undergraduate Honors Theses

Individuals from marginalized backgrounds face different healthcare outcomes due to algorithmic bias in the technological healthcare industry. Algorithmic biases, which are the biases that arise from the set of steps used to solve or analyze a problem, are evident when people from marginalized communities use healthcare technology. For example, many pulse oximeters, which are the medical devices used to measure oxygen saturation in the blood, are not able to accurately read people who have darker skin tones. Thus, people with darker skin tones are not able to receive proper health care due to their pulse oximetry data being inaccurate. This …


Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols May 2023

Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols

DU Undergraduate Research Journal Archive

DU Undergraduate Showcase: Research, Scholarship, and Creative Works


From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao Apr 2023

From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …


Chatgpt As Metamorphosis Designer For The Future Of Artificial Intelligence (Ai): A Conceptual Investigation, Amarjit Kumar Singh (Library Assistant), Dr. Pankaj Mathur (Deputy Librarian) Mar 2023

Chatgpt As Metamorphosis Designer For The Future Of Artificial Intelligence (Ai): A Conceptual Investigation, Amarjit Kumar Singh (Library Assistant), Dr. Pankaj Mathur (Deputy Librarian)

Library Philosophy and Practice (e-journal)

Abstract

Purpose: The purpose of this research paper is to explore ChatGPT’s potential as an innovative designer tool for the future development of artificial intelligence. Specifically, this conceptual investigation aims to analyze ChatGPT’s capabilities as a tool for designing and developing near about human intelligent systems for futuristic used and developed in the field of Artificial Intelligence (AI). Also with the helps of this paper, researchers are analyzed the strengths and weaknesses of ChatGPT as a tool, and identify possible areas for improvement in its development and implementation. This investigation focused on the various features and functions of ChatGPT that …


Machine Learning And Protein Allostery, Sian Xiao, Gennady M. Verkhivker, Peng Tao Dec 2022

Machine Learning And Protein Allostery, Sian Xiao, Gennady M. Verkhivker, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The fundamental biological importance and complexity of allosterically regulated proteins stem from their central role in signal transduction and cellular processes. Recently, machine-learning approaches have been developed and actively deployed to facilitate theoretical and experimental studies of protein dynamics and allosteric mechanisms. In this review, we survey recent developments in applications of machine-learning methods for studies of allosteric mechanisms, prediction of allosteric effects and allostery-related physicochemical properties, and allosteric protein engineering. We also review the applications of machine-learning strategies for characterization of allosteric mechanisms and drug design targeting SARS-CoV-2. Continuous development and task-specific adaptation of machine-learning methods for protein allosteric …


Lens: A Novel Image Processing-Based Approach For Low-Cost Segmentation Of Computed Tomography Scans Of Lungs, Monica Hinga Dec 2022

Lens: A Novel Image Processing-Based Approach For Low-Cost Segmentation Of Computed Tomography Scans Of Lungs, Monica Hinga

Computer Science ETDs

A staggering amount of data has been collected and analyzed since the beginning of the COVID-19 pandemic. Some of that data, however, particularly computed tomography (CT) scans of lungs, are difficult to analyze computationally. Segmentation of COVID-19 lesions provides researchers with insights into where lesions form, their volume, and in the case of time course data, how lesions grow as disease progresses. Spatial information, which has received little attention in the literature, has the potential to provide valuable insight to within-host viral and immune dynamics. Unfortunately, state-of-the-art supervised deep learning methods require labeled data, which can be prohibitively expensive to …


Cov-Inception: Covid-19 Detection Tool Using Chest X-Ray, Aswini Thota, Ololade Awodipe, Rashmi Patel Sep 2022

Cov-Inception: Covid-19 Detection Tool Using Chest X-Ray, Aswini Thota, Ololade Awodipe, Rashmi Patel

SMU Data Science Review

Since the pandemic started, researchers have been trying to find a way to detect COVID-19 which is a cost-effective, fast, and reliable way to keep the economy viable and running. This research details how chest X-ray radiography can be utilized to detect the infection. This can be for implementation in Airports, Schools, and places of business. Currently, Chest imaging is not a first-line test for COVID-19 due to low diagnostic accuracy and confounding with other viral pneumonia. Different pre-trained algorithms were fine-tuned and applied to the images to train the model and the best model obtained was fine-tuned InceptionV3 model …


Classifying Toe Walking Gait Patterns Among Children Diagnosed With Idiopathic Toe Walking Using Wearable Sensors And Machine Learning Algorithms, Rahul Soangra, Yuxin Wen, Hualin Yang, Marybeth Grant-Beuttler Jul 2022

Classifying Toe Walking Gait Patterns Among Children Diagnosed With Idiopathic Toe Walking Using Wearable Sensors And Machine Learning Algorithms, Rahul Soangra, Yuxin Wen, Hualin Yang, Marybeth Grant-Beuttler

Physical Therapy Faculty Articles and Research

Idiopathic toe walking (ITW) is a gait abnormality in which children’s toes touch at initial contact and demonstrate limited or no heel contact throughout the gait cycle. Toe walking results in poor balance, increased risk of falling, and developmental delays among children. Identifying toe walking steps during walking can facilitate targeted intervention among children diagnosed with ITW. With recent advances in wearable sensing, communication technologies, and machine learning, new avenues of managing toe walking behavior among children are feasible. In this study, we investigate the capabilities of Machine Learning (ML) algorithms in identifying initial foot contact (heel strike versus toe …