Digital Commons Network^™

Cellular And Molecular Mechanisms Of Lung Regeneration, Repair, And Fibrosis, Volume Ii, Yong Qiu, Xiao Xiao Tang, Shigeyuki Shichino, Prem Prakash Kushwaha, Yan Y. Sanders, Remo Castro Russo, Chunheng Mo

Department of Biomedical and Translational Sciences Faculty Publications

[Introduction] Organ fibrosis represents a substantial a major contributor to global disease burden, implicated in over 30% of cases leading to disability-associated and fatal conditions. Among these conditions, idiopathic pulmonary fibrosis (IPF) stands as a progressive and frequently fatal interstitial lung disease characterized by aberrant extracellular matrix deposition and parenchymal scarring. The prognosis for IPF patients is poor, with a median survival time of just 3–5 years (Bhattacharya and Ramachandran, 2023; Lederer and Martinez, 2018, Ma et al., 2024, Wei et al., 2024). Current FDA-approved therapeutics, Pirfenidone and Nintedanib, demonstrate capacity to attenuate functional decline in pulmonary fibrosis but remain …

Codon Composition In Human Oocyters Reveals Age-Associated Defects In Mrna Decay, Pavla Brachova, Lane K. Christenson, Nehemiah S. Alvarez

Department of Biomedical and Translational Sciences Faculty Publications

Oocytes from women of advanced reproductive age exhibit diminished developmental potential, but the underlying mechanisms remain incompletely defined. Oocyte maturation depends on translational control of maternal mRNA synthesized during growth. We performed a computational analysis on human oocytes from women < 30 versus ≥40 years and observed that mRNA GC content correlates negatively with half-life in oocytes from young (< 30 yr) but positively with oocytes from aged (>40 yr) women. In young oocytes, longer mRNA half-life is associated with lower protein abundance, whereas in aged oocytes GC content correlates positively with protein abundance. During the GV-to-MII transition, codon composition stratifies stability: codons that support rapid translation (optimal) stabilize mRNA, while slow-translating codons (non-optimal) promote decay. With reproductive aging, GC-containing codons become more optimal and align with increased …

Pediatric Cancer Incidence, Temporal Trends, And Mortality In The United States By Health Disparities Indicators, Seer (1973-2014), Prachi P. Chavan, Laurens Holmes Jr.

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Background: Pediatric cancer incidence has been increasing in the United States, despite improvement in pediatric cancer survival. This steady increase in incidence trends is not completely understood but maybe associated with social and environmental factors. In this study we aimed to assess the cumulative incidence, temporal trends, and mortality rates in pediatric cancer. Additionally, we examined sub-group variability in both incidence and mortality rates. Methods: Data from Surveillance, Epidemiology, and End Results (SEER) −18 from 1973–2014 were used for the purpose of analysis in this study. Age-adjusted incidence rates were used to assess temporal trends in cancer among children aged < 1–19 years. Univariable and multivariable binomial regression models were used to examine the association between race and cancer mortality while adjusting for potential confounders. Results: There were 92,594 cancer diagnoses during this period. White children comprised 74,758, (80.7%), black children 10,030, (10.8%), and other races 6648, (7.2%). Overall the age-adjusted cumulative incidence was slightly higher among white children (16.4%) than black children (12.4%) and other (13.0%). Children aged 15–19 years and those in metropolitan regions were more likely to be diagnosed with pediatric cancer. Relative to females, males were 16% more likely to die from the disease [adjusted Risk Ratio (aRR): 1.16, 95% Confidence Interval (CI): 1.09–1.22]. Additionally, compared to white children, black children had higher mortality rates [(aRR): 1.37, 99% CI: 1.23–1.52]. Conclusions: There is an increasing trend in pediatric cancer incidence; while white children have the highest incidence, black children and males indicated a survival disadvantage, indicative of racial and sex variability in overall pediatric cancer in the United States.

Occupational Exposure To Cooking Emissions And Evaluation Of Ventilation System In Restaurant Kitchens, Matthew Kaleb Hanvey

All ETDs from UAB

Background: In the restaurant environment, there are many harmful contaminants generated during the cooking process that kitchen workers are potentially exposed to. The purposes of this study were to evaluate the potential exposure to aldehydes and respirable particles among restaurant kitchen workers and to examine the ventilation performance of the kitchen exhaust hoods. Methods: There were three restaurants recruited for this study and they cooked seafood/poultry (Restaurant 1), farm style foods (Restaurant 2), and finger foods (Restaurant 3). The three restaurants had wall-mounted canopy hoods. Restaurant 1 had two hoods, Restaurant 2 had two hoods, and Restaurant 3 had one …

Understanding Women's Access To And Utilization Of Syringe Service Programs, Annelisa E. Swiersz

Honors Undergraduate Theses

As of 2020, 138 million Americans ages 12 and over reported illicit drug use in their lifetime, with over 3 million of those people injecting drugs. There are risks for all people who use drugs, but people who inject drugs (PWID) pose specific risks such as hepatitis B, hepatitis C, and human immunodeficiency virus (HIV), with women who inject drugs (WWID) facing even more risks. WWID involved in sex work have a higher risk of HIV transmission and lack access to sterile injection devices and sexual and reproductive health services. To address these risks, syringe service programs (SSPs) were developed …

Use Of Augmented Reality For Mosquito Breeding Sites Identification, Venant Niyonkuru, Sylla Sekou, Jimmy J. Sinzinkayo

Digital Journal of Clinical Medicine

An augmented reality app is used for detecting the possible breeding locations of mosquitoes in different settings precisely. With the aid of the advanced augmented vision technology, the AR system recognizes water-containing containers that are frequent breeding places for mosquitoes according to the visual information obtained through a head-mounted display. It then overlays visual highlights and labels directly onto these containers within the user's field of view, allowing one to instantly identify and spot breeding sites in real time. By combining state-of-the-art AR functionality with powerful computer vision algorithms, the method provides real-time visual feedback for identifying and tagging mosquito …

Place, Culture, And Care: A Socioecological Examination Of Type 2 Diabetes Among Hispanics In The U.S., Danielle Montoya

Theses and Dissertations

Introduction: Type 2 diabetes (T2D) disproportionately affects U.S. Hispanic populations. This dissertation examined whether structural determinants fundamentally drive T2D disparities among Hispanics, with attention to within-group racial heterogeneity.

Methods: Three studies utilized nationally representative data. Study 1 examined neighborhood segregation and ethnic enclave residence associations with T2D using restricted NHANES data (2011-2018, n=5,056). Study 2 investigated acculturation and T2D associations using restricted NHANES data (2011-2018, n=4,540). Study 3 analyzed patient-provider racial/ethnic concordance and adequate diabetes care using MEPS data (2008-2021, n=17,138).

Results: Structural factors demonstrated primacy across all studies. Neighborhood segregation (aOR=1.17, p>0.05) and ethnic enclave residence showed no …

Establishing A Microfiber Recovery Rate In Human Lung Tissue, Kylie Nicole Babin-Howard

Graduate Research Theses & Dissertations

Microplastics (plastic particles smaller than 5mm) are of increasing concern to environmental and human health as they have persistently been found in all areas of study—becoming a ubiquitous part of the planet. Microplastics have been found in a variety of human tissues (lungs, blood, brain matter, etc.) yet their health effects are poorly understood, with experimental exposure model studies indicating adverse health effects. Microfibers have been found to be more toxic when compared to other microplastic shapes and are also shed from a majority of everyday items, with environmental reports showing that fibers are more than twice as prevalent than …

Intestinal Oxygen Utilisation And Cellular Adaptation During Intestinal Ischaemia-Reperfusion Injury, Paraschos Archontakis-Barakakis, Theodoros Mavridis, David-Dimitris Chlorogiannis, Georgios Barakakis, Eleni Laou, Daniel I Sessler, George Gkiokas, Athanasios Chalkias

Faculty, Staff and Student Publications

The gastrointestinal tract can be deranged by ailments including sepsis, trauma and haemorrhage. Ischaemic injury provokes a common constellation of microscopic and macroscopic changes that, together with the paradoxical exacerbation of cellular dysfunction and death following restoration of blood flow, are collectively known as ischaemia-reperfusion injury (IRI). Although much of the gastrointestinal tract is normally hypoxemic, intestinal IRI results when there is inadequate oxygen availability due to poor supply (pathological hypoxia) or abnormal tissue oxygen use and metabolism (dysoxia). Intestinal oxygen uptake usually remains constant over a wide range of blood flows and pressures, with cellular function being substantively compromised …

Rbd Amplicon Sequencing And Evolutionary Analysis Of Sars-Cov-2 Variants From Wastewater Samples, Xingwen Chen, Chunfu Zheng, Fuqing Wu

Faculty, Staff and Student Publications

The surveillance of SARS-CoV-2 is significantly limited by the presence of numerous variants with distinct behaviors driven by rapid evolution. Although the conventional clinical genome sequencing method provides comprehensive data, it has limitations in capturing the epidemiological dynamics of the variants circulating in the community. In this chapter, we describe a protocol using RBD amplicon sequencing of wastewater samples. We present the detailed experimental procedure for wastewater sample processing, robust nested-PCR-based amplification of the target RBD sequence, and library preparation. Moreover, we describe a general pipeline of sequencing data processing and interpretation, showing the epidemiological and evolutionary trends of SARS-CoV-2 …

Effects Of High-Intensity Interval Training On Biomarkers And Inflammatory Factors In Patients With Heart Failure: A Meta-Analysis Of Randomized Controlled Trials, Wanting Zhang, Jooyeon Hwang, Beibei Lu, Xin Xu

Faculty, Staff and Student Publications

Background: There is still controversy about the effect of high-intensity interval training (HIIT) on the levels of cardiac and inflammatory biomarkers in patients with heart failure compared with moderate-intensity continuous training (MCT) and conventional healthcare activities. This article is to systematically investigate the effects of HIIT on the levels of cardiac and inflammatory biomarkers in patients with heart failure compared with MCT and conventional healthcare activities.

Methods: A computerized search of databases was conducted with the search year from the establishment of the database, and the screened results were subjected to quality assessment and data extraction, and the data was …

Community Engagement Studios To Improve Racial Diversity And Health Equity In Parkinson’S, Eunyoung Kang, Dominique Woodhouse, Kandace Davis, Jane Q Yap, Peter S Myers, Meghan C Campbell, Yvonne D Hughes, Joyce E Balls-Berry, Erin R Foster

Faculty, Staff and Student Publications

Background: Black or African Americans (AA) with Parkinson's disease (PD) are underrepresented in both care and research and experience significant health disparities. The existing literature provides limited guidance on how to enhance the engagement of AA individuals in PD care and research, particularly from the perspectives of AA patients, care partners, and healthcare providers. This project aimed to (1) describe the use of Community Engagement (CE) Studios as a community-engaged research approach to inform culturally appropriate and inclusive research and (2) examine factors influencing AA engagement in PD-related activities.

Methods: We conducted three CE Studios: one with AA with PD …

A Directed Content Analysis For Greatest Problems Among People With And Without Traumatic Brain Injury, Emily Dudek, Michael W Williams, Chung Lin Novelle Kew, Annalyn Demello, Brittany Wright, Alexandra B Holland, Alyssa Day-Gorman, Alexa S Gonzalez, Luis Leon Novelo, Xiangyi Liu, Shannon B Juengst

Faculty, Staff and Student Publications

Objective: To characterize the greatest problem or need among individuals with a history of traumatic brain injury (TBI), as compared with individuals with a history of other neurologic conditions, mental health conditions, and no history of neurologic or mental health conditions.

Design: A directed content analysis of open-text responses to a single online survey question using a framework guided by the Mayo-Portland Adaptability Inventory-4.

Setting: Community.

Participants: A total of 2861 community-dwelling adults (n=274 with TBI; n=289 with other neurologic conditions besides TBI; n=454 with mental health conditions but no neurologic conditions; and n=1844 controls).

Interventions: Not applicable.

Main outcome …

Risk And Prognosis Of Hepatocellular Carcinoma In Mexican Americans With Type 2 Diabetes Mellitus, Rikita I Hatia, Lu-Yu Hwang, Ruosha Li, Catherine Troisi, Prasun K Jalal, Christopher I Amos, Henry F Gomez, Yun Shin Chun, Asif Rashid, Ahmed O Kaseb, Paul A Scheet, Manal M Hassan

Faculty, Staff and Student Publications

INTRODUCTION: Hepatocellular carcinoma (HCC) disproportionately affects Hispanic persons with higher age-specific incidence and increased mortality rates compared to non-Hispanic Whites. These high rates of incidence and mortality may be explained by the variation in risk factors. Given the high prevalence of type 2 diabetes mellitus (DM) among the Hispanic population, we aimed to assess the risk and prognosis of HCC in Mexican Americans with type 2 DM with consideration of treatment for DM.

METHODS: A case-control study of 241 Mexican American HCC patients and 500 healthy controls in Texas was conducted. Multivariable logistic regression analysis was performed to determine the …

Clarification Of Public Health Pathways Toward Clinical Careers: A Pilot Study Describing A Benchmark Analysis Project, Elizabeth A. Brown, Melissa Feliciano, Daniel Martinez

Health Behavior, Policy & Management Faculty Publications

Introduction: Undergraduate public health programs have adapted the required basic sciences based on medical and technological advances and the needs of the public health workforce. We aim to demonstrate how a benchmark analysis project was used to improve curriculum and develop a model where basic sciences in public health can be used to build pathways to clinical graduate programs like medicine, pharmacy, physician assistant, etc.

Methods: Authors conducted a benchmark analysis of Bachelor of Science in Public Health (BSPH) Degrees (or public health-related degrees) in the southern region of the United States (US) to explore required basic sciences. Authors searched …

Enhancing Malaria Prevention: Barriers To Expanding Vaccine Access In Sub-Saharan Africa, Nenrot Gopep, Patra Chisom Ezeamii, Ho-Jui Tung

Eagles Talking About the Public’s Health

No abstract provided.

Psychometric Evaluation Of A Novel Measure Of Trauma-Related Cannabis Use To Cope, Sage E. Hawn, Terrell A. Hicks, Christopher Latourrette, Anita Thomas, Daniela Chaname, Sarah Ehlke, Abigail Powers Lott

Psychology Faculty Publications

Background: Posttraumatic stress disorder (PTSD) and cannabis use disorder (CUD) are commonly comorbid and are associated with many negative public health outcomes. One plausible explanation for this comorbidity comes from a self-medication framework, which suggests people use cannabis to cope with PTSD symptoms. Despite theoretical and empirical evidence for PTSD-related cannabis use to cope, no measure of this construct exists.

Objective: We sought to address this gap by developing and validating a novel measure of PTSD-specific cannabis self-medication, which we have termed the Trauma-Related Cannabis Use to Cope (TRCU) questionnaire.

Method: The psychometric properties of the TRCU and how it …

Assessing The Relationship Between Perceived Psychological And Physical Pain In Adults With Orthopedic Pain, Daniel C. Karimi Dehkordi

Honors Undergraduate Theses

Suicide remains a public health concern in the U.S., particularly among individuals experiencing chronic pain and psychological distress. This cross-sectional study investigated the relationship between perceived physical and psychological pain in 41 adults with chronic orthopedic conditions. The relationship between other risk and protective factors and perceived levels of pain distress was also examined. Results showed a significant positive correlation between psychological distress and physical pain (r(39) = 0.388, p < .05) and psychological distress and depressive/anxiety symptoms (r (39) = 0.477, p < .01). Psychological distress was moderately associated with feelings of hopelessness (r (39) = 0.403, p < .01), however, the relationship between physical pain and hopelessness was weak and nonsignificant (r (39) = -0.06, p = .71). Contrary to expectations, emotional support did not buffer the effects of psychological distress (r (39) = 0.07, p = 0.66). Mediational analysis confirmed that emotional support did not influence the relationship between physical pain and psychological distress (Beta (β) = -0.969, p = 0.572; Sobel Z = 0.5598, p = 0.575). Age was not correlated with psychological distress (r (39) = -0.24, p = 0.13) or mental health symptoms (r (39) = -0.05, p = .77). While there was no significant difference across sex, males reported higher mental health symptomatology and psychological distress scores than female counterparts. These findings underscore the direct impact of physical pain on psychological distress and challenge assumptions about the protective role of social support. The study highlights the need for integrated, multidisciplinary interventions targeting both physical and psychological pain to mitigate suicide risk among individuals with chronic orthopedic conditions. Future research should iii explore alternative support mechanisms and resilience-building strategies to address the complex interplay of pain, distress, and suicidality.

Physical Activity And Hypertension Outcomes Around Menopause In Adult Women—A Secondary Analysis Of The All Of Us Research Program, Meriam F. Naguib

Honors Undergraduate Theses

Hypertension significantly impacts menopausal women due to a decrease in estrogen levels. That is due to estrogen level changes, causing many metabolic alterations, one of which is increased vascular resistance, leading to hypertension. Advanced treatments are made available to help alleviate the condition; however, lifestyle modifications—especially physical activity—show a critical role in hypertension control. This thesis explored the effect of physical activity as a non-pharmacological, lifestyle intervention on hypertension in women by menopausal status (pre-, peri-, and post-menopausal). This study used a secondary analysis with a retrospective design. Physical activity was defined using the American Heart Association's (AHA) guidelines (i.e., …

Generation Z’S Perception Of Skin Cancer And How It Relates To Climate Change, Piercen Bogolea

Honors Undergraduate Theses

Skin cancer is the most common cancer worldwide, and climate change has been identified as a significant contributor. Preventative action early on can help reduce occurrence, but it is unknown if Generation Z is aware of this and is taking the necessary action now to protect themselves. This research aims to gauge the perception of Generation Z on the severity of skin cancer, the relationship between climate change and skin cancer, and the prevalence of preventative measures being taken. A survey was distributed to students aged 18 to 27 enrolled at the University of Central Florida through mixed sampling. The …

Weighted Family History Density Of Substance Use: Influence On Participant Substance Use Onset, Escalation, And Duration, Carleigh A. Litteral

Theses and Dissertations--Psychology

Substance use disorders impose a staggering toll on the United States (U.S.), straining healthcare systems, destabilizing communities, and profoundly impacting both individuals and families. Approximately one in six Americans aged 12 and older had a past-year substance use disorder in 2022 (Key Substance Use, 2022), and nearly one-third of adults experience a substance use disorder in their lifetime (Wu, 2010), contributing to an economic burden exceeding $400 billion annually (National Drug Threat Assessment, 2011). Family history of substance use disorders is a key predictor of vulnerability, with individuals who have affected relatives being 2–8 times more …

A Scoping Review Of Population Diversity In The Common Genomic Aberrations Of Clear Cell Renal Cell Carcinoma, Sean S. Kumar, Ninad Khandekar, Komal Dani, Saina R. Bhatt, Vinay Duddalwar, Anishka D' Souza

Department of Medicine Faculty Publications

Introduction: Previous literature has shown that clear cell renal cell carcinoma (ccRCC) is becoming a more prevalent diagnosis and that the incidence and mortality differ both regionally and racially. While the molecular profiles for ccRCC are studied regionally through biopsy and sequencing techniques, the genomic landscape and ccRCC diversity data are not well studied. We conducted a review of the known genomic data on 6 of the most clinically relevant DNA biomarkers in ccRCC: von Hippel-Lindau (vHL), Polybromo-1 (PBRM1), Breast Cancer Gene 1-Associated Protein 1 (BAP1), Histone-Lysine N-Methyltransferase Domain-Containing 2 (SETD2), Mammalian Target of Rapamycin (mTOR), and Lysine-Specific Demethylase 5C …

Association Between Neighborhood-Level Social Vulnerability And Hypertension Outcomes, John E. Brush Jr., Chungsoo Kim, Yuntian Liu, Xin Xin, Chenxi Huang, Iris J. Lundy, Jordan R. Asher, Mitsuaki Sawano, Patrick Young, Jacob Mcpadden, Mark Anderson, John S. Burrows, Harlan M. Krumholz, Yuan Lu

Department of Medicine Faculty Publications

Background

Neighborhood-level social vulnerability is associated with hypertension prevalence and severity and with cardiovascular complications in conditions other than hypertension, but its association with cardiovascular complications in patients with hypertension is understudied.

Objectives

The aim of the study was to examine how the neighborhood-level social vulnerability index (SVI) influences cardiovascular outcomes in a large, diverse cohort of patients with hypertension.

Methods

We used electronic health data to examine the association between census tract-level rankings for the SVI with a composite endpoint of incident myocardial infarction, congestive heart failure, or stroke.

Results

In a longitudinal cohort of 330,972 patients with hypertension …

Micro/Nanoplastics And Cancer: Focus On Gastrointestinal Malignancies - A Narrative Review, Sana Rabeeah, Priyata Dutta, Ahmad Mahdi, Alejandra Vargas, Edward C. Oldfield, David A. Johnson

Department of Medicine Faculty Publications

Micro- and nanoplastics (MNPs) are plastic particles smaller than 5 mm and 1 μm, respectively, and are emerging environmental pollutants with growing implications for human health. These particles stem from either 'primary sources', such as intentionally manufactured microbeads and industrial abrasives, or 'secondary sources', where larger plastic items break down into smaller fragments over time. Human exposure primarily occurs through ingestion and inhalation, with contaminated seafood and plastic-laden food packaging representing key routes of entry. Once ingested, MNPs can cross the intestinal barrier, accumulate in gastrointestinal (GI) tissues, and trigger biological responses. Mechanistic studies reveal that MNPs induce oxidative stress, …

How Do Young Adults With Drug Use Disorder (Dud) Utilize Treatment? Exploring And Examining Lived Experiences Towards Treatment Completion In Indonesia, Dewi Kartikawatiningsih

Electronic Theses & Dissertations (2024 - present)

In Indonesia which has the highest rate of drug addiction in Southeast Asia, there is currently little knowledge about how young adults perceive the barriers faced when completing treatment or how treatment providers' perspectives influence their treatment completion. Understanding and identifying barriers to treatment completion is essential to making drug treatment more effective. The purpose of this study is to explore the perspectives and live experiences of young adults with DUD and their addiction counselors to develop a deeper understanding of treatment needs. This study interviewed 33 clients and 15 counselors from the rehabilitation center of the Badan Nasional Narkotika …

Comparing Patency Of Pulmonary Stent Implantation And Balloon Angioplasty In Pulmonary Vein Stenosis: A Systematic Review And Meta-Analysis, Izza Batool, Muhammad K. Khan, Muhammad Zohaib, Ibrahim A. Khan, Syed A. A. Bukhari, Shreeja Shah, Khaled Harmouch, Hussam Al Hennawi, Bruce D. Klugherz

Abington Jefferson Health Papers

Pulmonary vein stenosis (PVS) is an insidious diagnosis associated with morbidity and mortality. Pharmacologic therapy may suffice initially, but advanced stages demand mechanical intervention. Pulmonary stent implantation (PSI) and pulmonary balloon angioplasty (PBA) are common strategies, both carrying restenosis risks. This meta‐analysis compares PSI and PBA to determine the superior revascularization strategy. We systematically searched databases until November 2023, identifying 11 studies with 780 patients. Studies, including those involving patients undergoing balloon angioplasty (BA) or stent angioplasty (SA) for PVS, were selected. Case reports, editorials, and cross‐sectional studies were omitted. Primary outcomes included restenosis requiring reintervention, 5‐year freedom from restenosis, …

Stigma Of Obesity And Healthcare Utilization, Moya A. O'Leary

Antioch University Dissertations & Theses

The impact of personal factors on healthcare utilization is an essential area of research to improve overall health outcomes among the population. This study explored the relationship between perceived stigma and healthcare avoidance among men and evaluated the relationship between self-reported body mass index (BMI) and avoidance of healthcare appointments due to weight-related stigma and other reasons. This study found no significant relationship between BMI and avoidance of preventive medical appointments due to perceived stigma. However, men from all weight categories endorsed avoiding preventive healthcare appointments due to weight-related reasons and for other reasons. This study explored the reported reasons …

Disparities In Maternal Healthcare: Examining The Impact Of Social Determinants Of Health On Provider Care Quality, Rishita Anumukonda

Honors Undergraduate Theses

Poor maternal health outcomes among racially and socioeconomically marginalized populations are a major public health concern in the United States. Effective clinician discussions during prenatal and postpartum care play an essential role in promoting maternal and infant well-being. However, the content of provider-patient discussions in maternal care and how it varies for patients exposed to different social determinants of health has not yet been well explored. This study aims to examine whether healthcare provider discussions about key maternal health topics, including preventative health tips, risk factors, and available resources, differ based on social factors such as income level and race. …

A Data-Driven Sliding-Window Pairwise Comparative Approach For The Estimation Of Transmission Fitness Of Sars-Cov-2 Variants And The Construction Of The Evolution Fitness Landscape, Md Jubair Pantho, Richard Annan, Landen Alexander Bauder, Sophia Huang, Letu Qingge, Hong Qin

Computer Science Faculty Publications

Estimating the transmission fitness of SARS-CoV-2 variants and understanding their evolutionary fitness trends are important for epidemiological forecasting. Existing methods are often constrained by their parametric natures and do not satisfactorily align with the observations during COVID-19. Here, we introduce a sliding-window data-driven pairwise comparison method, the differential population growth rate (DPGR) that uses viral strains as internal controls to mitigate sampling biases. DPGR is applicable in time windows in which the logarithmic ratio of two variant subpopulations is approximately linear. We apply DPGR to genomic surveillance data and focus on variants of concern (VOCs) in multiple countries and regions. …

Cath-Ddg: Towards Robust Mutation Effect Prediction On Protein-Protein Interactions Out Of Cath Homologous Superfamily, Guanglei Yu, Xuehua Bi, Teng Ma, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Protein-protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mutations on PPIs remains a critical requirement for drug design and disease mechanistic studies. Recently, deep learning models using protein 3D structures have become predominant for predicting mutation effects. However, significant challenges remain in practical applications, in part due to the considerable disparity in generalization capabilities between easy and hard mutations. Specifically, a hard mutation is defined as one with its maximum TM-score < 0.6 when compared to the training set. Additionally, compared to physics-based approaches, deep learning models may overestimate performance due to potential data leakage.

Results: We propose new training/test splits that mitigate data leakage according to the CATH homologous superfamily. Under the constraints of physical …