Digital Commons Network^™

Mean Affect Moderates The Association Between Affect Variability And Mental Health, Brooke N. Jenkins, Lydia Q. Ong, Anthony D. Ong, Hee Youn (Helen) Lee, Julia K. Boehm

Psychology Faculty Articles and Research

Increasing evidence suggests that within-person variation in affect is a dimension distinct from mean levels along which individuals can be characterized. This study investigated affect variability’s association with concurrent and longitudinal mental health and how mean affect levels moderate these associations. The mental health outcomes of depression, panic disorder, self-rated mental health, and mental health professional visits from the second and third waves of the Midlife in the United States Study were used for cross-sectional (n = 1,676) and longitudinal outcomes (n = 1,271), respectively. These participants took part in the National Study of Daily Experiences (NSDE II), …

A Single-Center, Assessor-Blinded, Randomized Controlled Clinical Trial To Test The Safety And Efficacy Of A Novel Brain-Computer Interface Controlled Functional Electrical Stimulation (Bci-Fes) Intervention For Gait Rehabilitation In The Chronic Stroke Population, Piyashi Biswas, Lucy Dodakian, Po T. Wang, Christopher A. Johnson, Jill See, Vicky Chan, Cathy Chou, Wendy Lazouras, Alison L. Mckenzie, David J. Reinkensmeyer, Danh V. Nguyen, Steven C. Cramer, An H. Do, Zoran Nenadic

Physical Therapy Faculty Articles and Research

Background

In the United States, there are over seven million stroke survivors, with many facing gait impairments due to foot drop. This restricts their community ambulation and hinders functional independence, leading to several long-term health complications. Despite the best available physical therapy, gait function is incompletely recovered, and this occurs mainly during the acute phase post-stroke. Therapeutic options are limited currently. Novel therapies based on neurobiological principles have the potential to lead to long-term functional improvements. The Brain-Computer Interface (BCI) controlled Functional Electrical Stimulation (FES) system is one such strategy. It is based on Hebbian principles and has shown promise …

Mechanistic Study Of Antimicrobial Effectiveness Of Cyclic Amphipathic Peptide [R4W4] Against Methicillin-Resistant Staphylococcus Aureus Clinical Isolates, Ajayi David Akinwale, Keykavous Parang, Rakesh Kumar Tiwari, Jason Yamaki

Pharmacy Faculty Articles and Research

Antimicrobial peptides (AMPs) are being explored as a potential strategy to combat antibiotic resistance due to their ability to reduce susceptibility to antibiotics. This study explored whether the [R₄W₄] peptide mode of action is bacteriostatic or bactericidal using modified two-fold serial dilution and evaluating the synergism between gentamicin and [R₄W₄] against Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA) by a checkered board assay. [R₄W₄] exhibited bactericidal activity against bacterial isolates (MBC/MIC ≤ 4), with a synergistic effect with gentamicin against E. coli (FICI = 0.3) but …

Mechanistic Insight Into The Mode Of Inhibition Of Dietary Flavonoids; Targeting Macrophage Migration Inhibitory Factor, Ali Raza Siddiqui, Mamona Mushtaq, Madiha Sardar, Lubna Atta, Mohammad Nur-E-Alam, Aftab Ahmad, Zaheer Ul-Haq

Pharmacy Faculty Articles and Research

Introduction: The Macrophage Migration Inhibitory Factor (MIF), a key pro-inflammatory mediator, is responsible for modulating immune responses. An array of inflammatory and autoimmune diseases has been linked to the dysregulated activity of MIF. The significance in physiological as well as pathophysiological phenomena underscores the potential of MIF as an attractive target with pharmacological relevance. Extensive research in past has uncovered a number of inhibitors, while the ISO-1, or (S, R)-3-(4-hydroxyphenyl)-4,5-dihydro-5-isoxazole acetic acid methyl ester being recognized as a benchmark standard so far. Recent work by Yang and coworkers identified five promising dietary flavonoids, with superior activity compared to the standard …

Pediatric Obesity In The United States: Age–Period–Cohort Analysis, Ashley W. Kranjac, Dinko Kranjac, Roxanne I. Aguilera

Sociology Faculty Articles and Research

The rates of obesity among American children aged 2–5 years has reached a historic high. It is crucial to identify the putative sources of population-level increases in obesity prevalence among preschool-aged children because early childhood is a critical window for obesity prevention and thus reduction of future incidence. We used the National Health and Nutrition Examination Survey data and hierarchical age–period–cohort analysis to examine lifecycle (i.e., age), historical (i.e., period), and generational (i.e., cohort) distribution of age- and sex-specific body mass index z-scores (zBMI) among 2–5-year-olds in the U.S. from 1999 to 2018. Our current findings indicate that period effects, …

Effectiveness Of Empiric Carbapenem Versus Non-Carbapenem Therapy For Extended-Spectrum Β-Lactamase Producing Enterobacterales Infections In Non-Intensive Care Unit Patients: A Real-World Investigation In A Hospital With High-Prevalence Of Extended-Spectrum Β-Lactamase Producing Enterobacterales, Amy Y. Kang, Mary Elkomos, Danny Pham, Michelle Guerrero, Deborah Kupferwasser, Loren G. Miller

Pharmacy Faculty Articles and Research

Objective:

To investigate whether empiric carbapenem therapy, compared to empiric non-carbapenem therapy, was associated with improved clinical outcomes among hospitalized, non-intensive care unit (ICU) patients with extended-spectrum β-lactamase (ESBL)-producing Enterobacterales infections.

Methods:

We performed a retrospective cohort study of adult, non-ICU patients admitted with ESBL-producing Enterobacterales infections. Primary outcome was time to clinical stability from the first empiric antibiotic dose. Secondary outcomes were early clinical response and 30-day all-cause hospital readmission. We used multivariate regression methods to examine time to clinical stability.

Results:

Of the 142 patients, 59 (42%) received empiric carbapenems and 83 (58%) received empiric …

Individual Longitudinal Changes In Dna-Methylome Identify Signatures Of Early-Life Adversity And Correlate With Later Outcome, Annabel K. Short, Ryan Weber, Noriko Kamei, Christina Wilcox Thai, Hina Arora, Ali Mortazavi, Hal S. Stern, Laura M. Glynn, Tallie Z. Baram

Psychology Faculty Articles and Research

Adverse early-life experiences (ELA) affect a majority of the world's children. Whereas the enduring impact of ELA on cognitive and emotional health is established, there are no tools to predict vulnerability to ELA consequences in an individual child. Epigenetic markers including peripheral-cell DNA-methylation profiles may encode ELA and provide predictive outcome markers, yet the interindividual variance of the human genome and rapid changes in DNA methylation in childhood pose significant challenges. Hoping to mitigate these challenges we examined the relation of several ELA dimensions to DNA methylation changes and outcome using a within-subject longitudinal design and a high methylation-change threshold. …

Perceptions Of Metabolic Syndrome Management Utilization In Relation To Patient Experience And Health-Related Quality Of Life, Olajide Adekunle, Jon C. Schommer, Yun Wang, Ismaeel Yunusa, Marc L. Fleming, Enrique Seoane-Vazquez, Lawrence M. Brown

Pharmacy Faculty Articles and Research

Background

One factor for the poor health outcomes among adult people with metabolic syndrome (MetS) is poor utilization of disease management resources, which may be attributable to prior experience with pharmacists (PEwP) and perceptions of disease management resource utilization (PMU). Therefore, understanding patients' experience could be critical to improving their perceptions and promoting health outcomes.

Objectives

The study explored the influence of PEwP and PMU on the health-related quality of life (HRQoL) of people with MetS.

Methods

Data on perceptions of healthcare, medication, and pharmacy services utilization, PEwP, and HRQoL were collected using validated tools via an electronic survey. Chi-square …

Combined Use Of Donepezil And Memantine Increases The Probability Of Five-Year Survival Of Alzheimer’S Disease Patients, Ehsan Yaghmaei, Hongxia Lu, Louis Ehwerhemuepha, Jianwei Zheng, Sidy Danioko, Ahmad Rezaie, Seyed Ahmad Sajjadi, Cyril Rakovski

Mathematics, Physics, and Computer Science Faculty Articles and Research

Background

Alzheimer’s disease (AD) is the most common neurodegenerative disease. Studying the effects of drug treatments on multiple health outcomes related to AD could be beneficial in demonstrating which drugs reduce the disease burden and increase survival.

Methods

We conducted a comprehensive causal inference study implementing doubly robust estimators and using one of the largest high-quality medical databases, the Oracle Electronic Health Records (EHR) Real-World Data. Our work was focused on the estimation of the effects of the two common Alzheimer’s disease drugs, Donepezil and Memantine, and their combined use on the five-year survival since initial diagnosis of AD patients. …

Proteomic Characterization And Cytotoxic Potential Of Proteins From Cuscuta (Cuscuta Epithymum (L.) Crude Herbal Product Against Mcf-7 Human Breast Cancer Cell Line, Umaima Akhtar, Yamna Khurshid, Bishoy El-Aarag, Basir Syed, Ishtiaq A. Khan, Keykavous Parang, Aftab Ahmed

Pharmacy Faculty Articles and Research

Background

The burden of breast cancer, the second leading cause of death worldwide, is increasing at an alarming rate. Cuscuta, used in traditional medicine for different ailments, including cancer, is known for containing phytochemicals that exhibit anticancer activity; however, the bioactivities of proteins from this plant remain unexplored. This study aimed to screen the cytotoxic potential of proteins from the crude herbal product of Cuscuta epithymum(L.) (CE) harvested from the host plants Alhagi maurorum and Medicago sativa.

Methods

The proteins from CE were extracted using a salting-out method, followed by fractionation with a gel filtration chromatography column. Gel-free shotgun …

Highlighting Health And Diversity: Curating Digital Exhibits To Promote Online Resources Across Cultural Months, Ivan Portillo, David Carson

Library Presentations, Posters, and Audiovisual Materials

This poster presentation demonstrates how digital exhibits can be leveraged to promote health literacy and enhance health education by creating awareness of resources to benefit diverse cultural and ethnic groups. It showcases examples of online exhibits that highlight health-related information, history, and resources to address health disparities and promote health equity among different populations.

Making The Most Of Artificial Intelligence And Large Language Models: A Novel Approach For Book Recommendation And Discovery In Medical Libraries, Ivan Portillo, David Carson

Library Presentations, Posters, and Audiovisual Materials

This poster presentation evaluates the use of Artificial Intelligence and large language models (LLMs) to assist health science libraries in recommending and discovering book titles as part of their collection development. Using pre-determined prompts, the researchers evaluated ChatGPT 4.0, Bing Chat, and Google Bard as recommender systems for book discovery and ranking existing titles.

Co-Designing Situated Displays For Family Co-Regulation With Adhd Children, Lucas M. Silva, Franceli L. Cibrian, Clarisse Bonang, Arpita Bhattacharya, Aehong Min, Elissa M. Monteiro, Jesus A. Beltran, Sabrina E. B. Schuck, Kimberley D. Lakes, Gillian R. Hayes, Daniel A. Epstein

Engineering Faculty Articles and Research

Family informatics often uses shared data dashboards to promote awareness of each other’s health-related behaviors. However, these interfaces often stop short of providing families with needed guidance around how to improve family functioning and health behaviors. We consider the needs of family co-regulation with ADHD children to understand how in-home displays can support family well-being. We conducted three co-design sessions with each of eight families with ADHD children who had used a smartwatch for self-tracking. Results indicate that situated displays could nudge families to jointly use their data for learning and skill-building. Accommodating individual needs and preferences when family members …

Short-Term Benefits From Manual Therapy As An Adjunct Treatment For Persistent Postural-Perceptual Dizziness Symptoms: A Preliminary Prospective Case Series, Brent A. Harper, Larry Steinbeck

Physical Therapy Faculty Articles and Research

Persistent dizziness and balance deficits are common, often with unknown etiology. Persistent Postural-Perceptual Dizziness (3PD) is a relatively new diagnosis with symptoms that may include dizziness, unsteadiness, or non-vertiginous dizziness and be persistent the majority of time over a minimum of 90 days. The purpose of this case series was to investigate short-term outcomes of reducing dizziness symptoms using a manual therapy intervention focused on restoring mobility in the fascia using a pragmatically applied biomechanical approach, the Fascial Manipulation^® method (FM^®), in patients with 3PD. The preliminary prospective case series consisted of twelve (n = 12) patients …

Non-Alcoholic Fatty Liver Disease: Role Of Pnpla3 And Its Association With Environmental Chemicals, Shakil A. Saghir, Ata Abbas, Saleh Alfuraih, Ajay Sharma, Jean Latimer, Yadollah Omidi, Rais Ansari

Pharmacy Faculty Articles and Research

Globally, non-alcoholic fatty liver disease (NAFLD) is on the rise with 30-32%, 27-33%, 35-48%, 36%, 9-20%, and 36-38% prevalence in Asia, Europe, North America, South America, Africa, and Australia, respectively. Approximately, 5-10% of NAFLD proceeds to hepatitis called non-alcoholic steatohepatitis (NASH). NASH often progresses to liver fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Precise mechanism(s) for the development of HCC is not fully understood in NAFLD and NASH patients. Higher insulin levels in type 2 diabetes (T2D) can result in lipolysis of adipose tissue activating lipid synthesizing enzymes such as fatty acid synthase and stearoyl-CoA desaturase-1, resulting in lipid accumulation in …

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 …

Sufferance For Snuff Puffs: The Acceptability And Behavior Of Smoking Marijuana And Tobacco Inside The House, Eusabeia Silfanus, Oliver Lopez, Vincent Berardi

Student Scholar Symposium Abstracts and Posters

Secondhand smoke (SHS) released from indoor smoking contributes to household air pollution, releasing large quantities of fine particulate matter which can pose negative health outcomes, especially for developing children who spend most of their time at home. The increased legalization of marijuana increases its recreational and medicinal use along with its acceptability. With tobacco use remaining prevalent, the use of marijuana and/or tobacco remains common and may occur inside the home. Project Fresh Air conducted in San Diego County studies the air quality in households (n = 298) with at least one adult smoking tobacco and/or marijuana living with at …

Postural Control In Young Adults With And Without Recurrent Back Pain: Influence Of Symptom Characteristics, Rachel Berns

Student Scholar Symposium Abstracts and Posters

Many individuals with low back pain (LBP) experience episodic symptoms. During symptomatic episodes, individuals with LBP have delayed trunk muscle activation during anticipated postural perturbations, though it's unclear if these postural control changes persist between symptomatic episodes. This study examined anticipatory postural muscle activation in adults with and without recurrent LBP to determine the influence of muscle fatigue and typical symptom characteristics on trunk muscle activation. 55 young adults with a greater than one-year history of recurrent LBP and 30 young adults with no history of LBP were recruited. Electromyography electrodes were placed on their thoracic and lumbar paraspinals, external …

Augmenting Hand And Arm Function For Persons With Hemiparesis, Brooke Stein, Susan Duff, Alison Mckenzie, Bailey Advincula, Isaac An, Annie Jeon, Casey Mcwilliam, Will Potter, Virginia Ruano, Paulina Vokulich, Audrey Howell, Rahul Soangra

Student Scholar Symposium Abstracts and Posters

Background. Hand and arm dysfunction due to neural disorders significantly influences quality of life. Activity-based training has been found to improve function. These improvements could be augmented with transcutaneous spinal cord stimulation (tSCS) due to the modulatory effect it has on spinal and supraspinal networks. Objective. The primary aim is to determine if a 4-week training program will improve hand and arm function. The secondary aim is to determine if the addition of tSCS to a second 4-week training session will further improve function. Design. This is a pre-posttest, controlled trial for persons 10-75 years of age, >6 months post …

Structural Sensorimotor Adaptations In Young Adults With Low Back Pain, Isaac Chrisman, Jo Armour Smith, Rongwen Tain, Kelli G. Sharp, Laura M. Glynn, Linda R. Van Dillen, Jesse V. Jacobs, Steven C. Cramer

Student Scholar Symposium Abstracts and Posters

Chronic low back pain (CLBP) is the largest cause of disability worldwide. There is evidence for regional structural brain adaptation in CLBP. Most studies have investigated middle-aged adults and show decreased grey matter density in pain processing regions. It is not clear if these adaptations are evident early in the lifespan of individuals with CLBP. The purpose of the study was to compare sensorimotor gray matter density in young adults with a history of CLBP with back-healthy controls. 53 young adults with a greater than 1-year history of CLBP and 29 young adults with no history of LBP participated. Clinical …

The Moderating Effect Of Socioeconomic Status And Walkability On The Efficacy Of Physical Activity Interventions, Analisa Vavoso, Vincent Berardi, Marc A. Adams

Student Scholar Symposium Abstracts and Posters

To enable physical activity (PA) interventions to better tailor procedures to participant characteristics, we investigated the role of neighborhood socioeconomic status (SES) and walkability on the differential effectiveness of adaptive versus static activity goals (AG vs. SG) and immediate versus delayed (IR vs. DR) reinforcement in a PA trial.

Data was collected as a part of the WalkIT Arizona study, where healthy, inactive adults (n = 512) were instructed to wear an accelerometer daily for one year and were provided with daily goals for moderate-to-vigorous PA (MVPA). The intersection of goal types (adaptive and static) as well as reinforcement types …

Synthesis Of Thermoresponsive Poly(N-Isopropyl Acrylamide) Based Core-Shell And Hollow Shell Nanogel With Tunable Core And Shell Thickness, Mohamad Hijazi, Molla R. Islam

Student Scholar Symposium Abstracts and Posters

Nanogels have emerged as a notably safer and more effective means for drug delivery, primarily due to their adjustable drug-loading capabilities. Hollow-core nanoparticles offer some unique properties that are desirable for drug delivery applications. Initially, silica core nanoparticles were synthesized using the Stöber process at different temperatures where Tetraethoxysilane (TEOS) undergoes hydrolysis in the presence of ethanol and then a condensation reaction to form silica nanoparticles. Scanning Electron Microscopy (SEM) and Optical Microscopy (OM) analysis revealed that the size of silica core particles varied with the synthesis temperature (300 nm at 30°C to 150 at 60°C). The core silica particles …

Spatiotemporal Gait Parameter Consistency Across Two Days Of Treadmill Walking In Stroke Survivors, Alejandro Aguirre Ramirez, Samantha N. Jeffcoat, Natalia Sanchez, Andrian Kuch

Student Scholar Symposium Abstracts and Posters

Retraining impaired gait is essential in post-stroke recovery. This project aims to determine between day variability of spatiotemporal gait measures in treadmill walking post-stroke to differentiate between changes due to the intervention and measurement errors due to between day test-retest variability. Six individuals post-stroke performed a two-minute walk test at a self-selected speed (SSS) for two consecutive days. SSS was assessed through the six-minute walk test. Reflective markers were placed on anatomical landmarks (van den Bogert et al. 2013). The heel markers were used for step detection. We calculated spatiotemporal parameters: stride length, stride time, step length, stance time, and …

“Pro-Woman, Pro-Life”: Framing Of The Anti-Abortion Movement, Olivia Rivet

Student Scholar Symposium Abstracts and Posters

This project on the “Pro-Woman, Pro-Life" framing of the Anti-Abortion Movement uses James Paul Gee's theoretical lens on discourse analysis. My research corpus is comprised of historical, legislative, news, editorial, and film data. This project focuses on when the term "Pro-Woman" first appeared in the anti-abortion discourse and how it has been used to reinforce the Pro-Life stance. I argue that the phrase -- "Pro-Woman" -- is a discoursal strategy to appeal to women who are ideologically aligned with the Pro-Choice movement. According to the Pro-Woman, Pro-Life framework, no "feminist" would want to support a practice, such as abortion, that …

Alcohol Use Disorder: Behaviors And Comorbidities In Recovery, Ryann Schochet

Student Scholar Symposium Abstracts and Posters

The purpose of this study was to determine the connection between length of sobriety, for people with alcohol use disorder, and their experience with related disorders and traits. Impulsivity, compulsions, obsessions, generalized anxiety, panic attacks, and neuroticism have all been researched in relation with the development of alcohol use disorder and drinking behaviors. This study strived to determine the presence of these symptoms and behaviors within one’s recovery, and their effect on one’s overall sobriety. This study compared self-reported symptoms of Alcoholics Anonymous members to their current length of sobriety and past relapses. Symptoms of Attention- deficit/hyperactivity disorder, Obsessive Compulsive …

Assessing Brain Processing Deficits Using Neuropsychological And Vision-Specific Tests For Concussion, Brent A. Harper, Rahul Soangra

Physical Therapy Faculty Articles and Research

Introduction: Since verbal memory and visual processing transpire within analogous cerebral regions, this study assessed (i) if a visual function can predict verbal memory performance. It also hypothesized whether neurocognitive (e.g., ImPACT) tests focusing on the Visual Memory and Cognitive Efficacy Index will predict Verbal Memory scores and (ii) if vision metrics and age can identify individuals with a history of concussion. Finally, it also hypothesized that King–Devick and near point of convergence scores alongside age considerations will identify candidates with a prior reported history of concussion. Materials and methods: This observational cohort assessed 25 collegiate ice hockey players prior …

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 …

Broad-Spectrum Activity Of Membranolytic Cationic Macrocyclic Peptides Against Multi-Drug Resistant Bacteria And Fungi, Sandeep Lohan, Anastasia G. Konshina, Rakesh K. Tiwari, Roman G. Efremov, Innokentiy Maslennikov, Keykavous Parang

Pharmacy Faculty Articles and Research

The emergence of multidrug-resistant (MDR) strains causes severe problems in the treatment of microbial infections owing to limited treatment options. Antimicrobial peptides (AMPs) are drawing considerable attention as promising antibiotic alternative candidates to combat MDR bacterial and fungal infections. Herein, we present a series of small amphiphilic membrane-active cyclic peptides composed, in part, of various nongenetically encoded hydrophilic and hydrophobic amino acids. Notably, lead cyclic peptides 3b and 4b showed broad-spectrum activity against drug-resistant Gram-positive (MIC = 1.5–6.2 µg/mL) and Gram-negative (MIC = 12.5–25 µg/mL) bacteria, and fungi (MIC = 3.1–12.5 µg/mL). Furthermore, lead peptides displayed substantial antibiofilm action comparable …

Advancing Brain Tumor Segmentation With Spectral–Spatial Graph Neural Networks, Sina Mohammadi, Mohamed Allali

Engineering Faculty Articles and Research

In the field of brain tumor segmentation, accurately capturing the complexities of tumor sub-regions poses significant challenges. Traditional segmentation methods usually fail to accurately segment tumor subregions. This research introduces a novel solution employing Graph Neural Networks (GNNs), enriched with spectral and spatial insight. In the supervoxel creation phase, we explored methods like VCCS, SLIC, Watershed, Meanshift, and Felzenszwalb–Huttenlocher, evaluating their performance based on homogeneity, moment of inertia, and uniformity in shape and size. After creating supervoxels, we represented 3D MRI images as a graph structure. In this study, we combined Spatial and Spectral GNNs to capture both local and …

Ensemble-Based Mutational Profiling And Network Analysis Of The Sars-Cov-2 Spike Omicron Xbb Lineages For Interactions With The Ace2 Receptor And Antibodies: Cooperation Of Binding Hotspots In Mediating Epistatic Couplings Underlies Binding Mechanism And Immune Escape, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we performed a computational study of binding mechanisms for the SARS-CoV-2 spike Omicron XBB lineages with the host cell receptor ACE2 and a panel of diverse class one antibodies. The central objective of this investigation was to examine the molecular factors underlying epistatic couplings among convergent evolution hotspots that enable optimal balancing of ACE2 binding and antibody evasion for Omicron variants BA.1, BA2, BA.3, BA.4/BA.5, BQ.1.1, XBB.1, XBB.1.5, and XBB.1.5 + L455F/F456L. By combining evolutionary analysis, molecular dynamics simulations, and ensemble-based mutational scanning of spike protein residues in complexes with ACE2, we identified structural stability and binding …