Medical Specialties Commons^™

Prevalence Of Electrocardiographic Changes And Risk Factors For Qtc Prolongation Among Steady State Sickle Cell Disease Patients: Cooperative Study Of Sickle Cell Disease, Mohammed B. Nawaiseh, Rund R. Haddadin, Yara B. Nawaiseh, Mohammad Z. Salameh, Abdallah A. Shurman, Osama Abu-Shawer, Asma I. Aljesrawi, Ibrahim A. Abuelbeh, Allaa Roto, Hadil Zureigat, Lana Mango, Munir Q. Zaqqa, Hanna K. Al-Makhamreh, Nakhleh Abu-Yaghi

Department of Medicine Faculty Publications

Objectives: Sickle cell disease (SCD) is associated with several cardiovascular adverse events. Corrected QT (QTc) interval prolongation is one of the potential life-threatening complications that predispose patients to sudden cardiac death. This study aims to assess the prevalence of electrocardiogram (ECG) changes and to investigate risk factors associated with increased propensity of QTc prolongation. Methods: This study utilized data from the Cooperative Study of Sickle Cell Disease Cardiac Ancillary Study. QT intervals were corrected using the Bazett formula, and prolongation was defined using sex-specific thresholds. The study population included African American patients with steady-state SCD across four clinical centers located …

Epicardial Cryoablation During Cardiopulmonary Bypass In A Pig Survival Model, Federica Serra, Jonathan M. Philpott, Anna Bulysheva, Christian W. Zemlin

Electrical & Computer Engineering Faculty Publications

Objective

Atrial cryolesions are usually created from the endocardium with the heart arrested. Some cardiac surgeons have used cryoablation epicardially during cardiopulmonary bypass, which is convenient because it does not require an incision into the atrial wall. Here, we analyzed the transmurality of epicardial cryoablations created during cardiopulmonary bypass in an arrested heart 30 days after ablation.

Methods

In Yucatan minipigs (n=5), hearts were exposed via sternotomy. Both caval veins were cannulated to collect blood for the cardiopulmonary bypass. Cryolesions were created applying a cryoprobe for 4 minutes per lesion. Hearts were harvested 30 days after the surgery. The transmurality …

Incorporating Insulin Into Alginate-Chitosan 3d-Printed Scaffolds: A Comprehensive Study On Structure, Mechanics, And Biocompatibility For Cartilage Tissue Engineering, Afsaneh Jahani, Mohammad Sagdegh Nourbakhsh, Ali Moradi, Marzieh Mohammadi, Lobat Tayebi

Electrical & Computer Engineering Faculty Publications

Osteoarthritis is a leading cause of disability worldwide, challenging current treatments to limited cartilage self-healing capacity. Cartilage tissue engineering (CTE) integrates cells, scaffolds, and signaling molecules, with Insulin being utilized as a differentiation biomolecule due to cost-effectiveness, dose-dependent influence on chondrogenesis, suitable biological activity, and ability to activate relevant receptors. Yet, administering differentiation biomolecules through conventional scaffolds poses a persistent challenge. Alginate (Alg) is commonly employed in CTE for its biocompatibility, though it lacks sufficient mechanical properties. Chitosan (Cs), while enhancing scaffold mechanical properties, but does not independently provide optimal support for chondrogenesis. While Alg-Cs scaffolds have garnered attention, challenges …

Obesity Prediction From Structural Mri Using Conformal Deep Learning With Uncertainty Quantification, W. Farzana, A. G. A. Temtam, B. Humud-Arboleda, L. Ma, M. Bean, F. Gerard Moeller, K. M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

Obesity arises from a neurobehavioral disorder in which the brain’s regulation of hunger and food intake is impaired, leading to an imbalance between energy consumption and expenditure. One key phenotype associated with obesity is body mass index (BMI). BMI is influenced by multiple causal pathways driven by behavioral, metabolic, and genetic factors. Traditional obesity prediction studies often rely on magnetic resonance imaging (MRI) voxel-based morphometry to correlate BMI with obesity-related clinical measurements and brain structure, predominantly gray matter volume (GMV). However, the altered brain regions are variable and widespread between studies, with some literature presenting contradictory results between BMI and …

Personalized Prediction Of Tumor Recurrence With Image-Guided Physics-Informed Computational Model In High-Grade Gliomas, Walia Farzana, Khan M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

High grade gliomas are infiltrating tumors characterized by their diffusive invasion and proliferative growth. Across and within patients heterogeneity of tumors makes it challenging to determine tumor spatial extent after surgical resection. Traditionally, tumor growth predictions after surgical resections rely on generalized models and population-based observations, which do not account for individual patient differences. To address this gap, we propose a personalized approach with image-guided computational model (digital twin) that incorporates physics-based modeling to predict tumor recurrence. Our digital twin involves an inverse modeling step, followed by a recurrence model that accounts for varying surgical effects. The physics-guided inverse model …

Key Brain Region Identification In Obesity Prediction With Structural Mri And Probabilistic Uncertainty Aware Model, Walia Farzana, Megan A. Witherow, Ahmed Temtam, Liangsuo Ma, Melanie Bean, F. Gerry Moeller, K. M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

Objectives/Goals: Predictive performance alone may not determine a model’s clinical utility. Neurobiological changes in obesity alter brain structures, but traditional voxel-based morphometry is limited to group-level analysis. We propose a probabilistic model with uncertainty heatmaps to improve interpretability and personalized prediction. Methods/Study Population: The data for this study are sourced from the Human Connectome Project (HCP), with approval from the Washington University in St. Louis Institutional Review Board. We preprocessed raw T1-weighted structural MRI scans from 525 patients using an automated pipeline. The dataset is divided into training (357 cases), calibration (63 cases), and testing (105 cases). Our probabilistic model …

A Fast Framework For Generating Radioactive Mixture Spectra And Its Application To Remote High-Performance Mixture Identification, Chiman Kwan, Bulent Ayhan, Adam Stavola, Kazi Aminul Islam, Hongfang Zhang, Jiang Li

Electrical & Computer Engineering Faculty Publications

Remote detection of radioactive materials in mixtures using handheld or portal detectors remains a challenge because of factors such as low concentration, environmental interference, sensor noise, and other complications. This work introduces a fast framework for generating realistic mixture spectra. Moreover, we present mixture isotope identification using data generated by the fast framework. Researchers have examined a range of conventional and recent algorithms within the fields of machine learning and deep learning. An application to uranium enrichment-level prediction has been included. Extensive simulation experiments validated the efficacy of the proposed framework.

A Method For Ultrasound Servo Tracking For Puncture Needle, Shitong Ye, Bo Yang, Hao Quan, Shan Liu, Minyu Tang, Jiawei Tian

Electrical & Computer Engineering Faculty Publications

Computer-aided surgical navigation technology helps and guides doctors to complete the operation smoothly, which simulates the whole surgical environment with computer technology, and then visualizes the whole operation link in three dimensions. At present, common image-guided surgical techniques such as computed tomography (CT) and X-ray imaging (X-ray) will cause radiation damage to the human body during the imaging process. To address this, we propose a novel Extended Kalman filter-based model that tracks the puncture needle-point using an ultrasound probe. To address the limitations of Kalman filtering methods based on position and velocity, our method of Kalman filtering uses the position …

A Customized Large Single-Piece Bifrontal Implant For Post-Craniectomy Defect Reconstruction: A Case Study, Omid Ghaderzadeh, Ehsan Amirbeyk, Seyed Roholah Ghodsi, Zahra Namazi, Lobat Tayebi

Electrical & Computer Engineering Faculty Publications

Background: Large bifrontal defects pose unique reconstruction challenges due to their complex curvature and mechanical requirements. This case demonstrated how computer-aided design/manufacturing (CAD/CAM) enabled precise single-piece polymethyl methacrylate (PMMA) implant fabrication, thereby overcoming traditional limitations. Case presentation: A 25-year-old male who had undergone bifrontal decompressive craniectomy suffered a severe traumatic brain injury. The autologous bone flap had been temporarily stored in a subcutaneous fat area of the abdomen for 3 months to preserve its viability. A secondary cranioplasty was then performed using titanium miniplates and self-tapping screws for final fixation. After 2 years, the patient developed empyema and a brain …

Novel Micro-And Nanoformulations Of Paclitaxel For Targeting Metastatic Breast, Non-Small Cell Lung, And Pancreatic Cancers, Lobat Tayebi, Mehran Alavi

Electrical & Computer Engineering Faculty Publications

Nonlinear pharmacokinetics resulting from high lipophilic and low oral bioavailability, and hypersensitivity reactions and hyperlipidemia caused by formulation by Cremophor EL have limited clinical effectiveness of paclitaxel (Taxol). In this way, there is the critical necessity of innovative drug delivery systems (DDSs) to mitigate severe side effects and overcome clinical limitations of paclitaxel. In recent years, various micro- and nanoformulations, specifically polymeric nanoparticles (NPs) and lipid NPs, have been presented and approved by the Food and Drug Administration (FDA). In addition, other nanoformulations, such as polymeric nanoparticles (NPs), micelles, liposomes, and mesoporous silica nanoparticles, have shown promising results in vitro …

Comparative Effectiveness Of High-Intensity Interval Training And Moderate-Intensity Continuous Training On Cardiometabolic Health In Patients With Diabesity: A Systematic Review And Meta-Analysis Of Randomized Controlled Trials, Sameer Badri Al-Mhanna, Eric Tsz-Chun Poon, Barry A. Franklin, Mark A. Tarnopolsky, John A. Hawley, John M. Jakicic, Emmanuel Stamatakis, Jonathan P. Little, Linda S. Pescatello, Deborah Riebe, Walter R. Thompon, James S. Skinner, Sheri R. Colberg, Jonathan K. Ehrman, George S. Metsios, Helen T. Douda, Norsuhana Omar, Abdullah F. Alghannam, Alexios Batrakoulis

Human Movement Studies & Special Education Faculty Publications

Objective

To evaluate the effects of high-intensity interval training (HIIT) on cardiometabolic health-related outcomes in patients with type 2 diabetes mellitus and concurrent overweight/obesity (diabesity).

Design

Systematic review and meta-analysis of randomized controlled trials (RCTs).

Data sources

PubMed, Web of Science, Scopus, Science Direct, Cochrane Library, and Google Scholar databases were searched from inception up to January 31, 2025.

Eligibility criteria for selected studies

RCTs comparing HIIT alone ≥ 2 weeks in duration with moderate-intensity continuous training (MICT). Participants were adults with diabesity.

Results

A total of 26 RCTs qualified, involving 790 patients (50/50 female/male ratio; age: 59.8 ± 12.9 …

The Efficacy Of Physical Activity Or Exercise Among Individuals With Cerebral Palsy: An Umbrella Review Of Systematic Reviews, Majed M. Alhumaid, Faris Yahya I. Asiri, Mohamed A. Said, Justin A. Haegele

Human Movement Studies & Special Education Faculty Publications

Introduction

Cerebral palsy (CP) is the most common childhood disability, affecting 1.5-3 per 1000 live births. Physical exercises have been shown to improve muscle and limb outcomes in CP. This systematic review critically appraises existing systematic reviews on the effects of physical activity and exercise on physical, functional, and psychosocial outcomes in individuals with CP compared to those without.

Methods

Using a PICO framework, the question was: In patients with CP, do physical activity and exercise improve muscle- and limb-related outcomes compared to no intervention or usual care? PubMed, Cochrane, ISI Web of Science, and Embase were searched for systematic …

Impact Of Aerobic Exercise On Cardiometabolic Health In Patients With Diabesity: A Systematic Review And Meta-Analysis Of Randomized Controlled Trials, Sameer Badri Al-Mhanna, Barry A. Franklin, John M. Jakicic, Emmanuel Stamatakis, Linda S. Pescatello, Deborah Riebe, Walter R. Thompson, James S. Skinner, Sheri R. Colberg, Jonathan K. Ehrman, George S. Metsios, Norsuhana Omar, Nouf H. Alkhamees, Bodor Bin Sheeha, Abdullah F. Alghannam, Alexios Batrakoulis

Human Movement Studies & Special Education Faculty Publications

Purpose

This systematic review and meta-analysis of randomized controlled trials (RCTs) aimed to evaluate the effects of aerobic exercise on cardiometabolic health-related indices in patients with type 2 diabetes and concurrent overweight/obesity (diabesity).

Methods

PubMed, Web of Science, Scopus, Science Direct, Cochrane Library, and Google Scholar databases were searched from inception to October 2024. The search strategy included the following keywords: diabetes, aerobic exercise, and endurance training. RCTs comparing aerobic exercise training ≥2 weeks in duration to standard treatment were considered eligible. Participants were adults with diabesity.

Results

A total of 1391 middle-aged/older adult patients (55 % females) were included …

Impact Of High-Intensity Interval Training On Cardiometabolic Health In Patients With Diabesity: A Systematic Review And Meta-Analysis Of Randomized Controlled Trials, Sameer Badri Al-Mhanna, Barry A. Franklin, Mark A. Tarnopolsky, John A. Hawley, John M. Jakicic, Emmanuel Stamatakis, Jonathan P. Little, Linda S. Pescatello, Deborah Riebe, Walter R. Thompson, James S. Skinner, Sheri R. Colberg, Jonathan K. Ehrman, George S. Metsios, Helen T. Douda, Norsuhana Omar, Abdullah F. Alghannam, Alexios Batrakoulis

Human Movement Studies & Special Education Faculty Publications

Aims This systematic review and meta-analysis aimed to evaluate the effects of high-intensity interval training (HIIT) on cardiometabolic health-related outcomes in patients with type 2 diabetes and obesity (diabesity).

Methods PubMed, Web of Science, Scopus, Science Direct, Cochrane Library, and Google Scholar databases were searched from inception up to November 2024. The search strategy encompassed the following keywords: diabetes, obesity, and HIIT. Randomized controlled trials (RCTs) recruiting adult participants with diabesity and comparing HIIT per se for ≥ 2 weeks in duration with non-exercise standard treatment were included.

Results A total of 18 RCTs qualified involving 504 patients (52/48 women/men …

The Role Of Tgf-Beta Superfamily Members In Immune Homeostasis And Disease, Natalie Eva Nieuwenhuizen, Ioannis Eleftherianos, Piotr Jan Kraj, Maria Semitekolou

Biological Sciences Faculty Publications

[Introduction] The Transforming Growth Factor beta (TGF-beta) superfamily, encompassing molecules such as TGFs, activins, Bone Morphogenetic Proteins (BMPs), Growth/Differentiation Factor (GDFs) and Nodals, represents the largest family of growth and differentiation factors, playing crucial roles in developmental and physiological processes across animal species (1). These molecules are integral to tissue homeostasis and cell fate determination. Among them, TGF-beta is particularly noted for its regulatory influence on immune responses and tissue fibrosis (2, 3). Recent research has expanded our understanding of the immune functions of other superfamily members, including activin A and BMPs (4). These molecules signal through receptor complexes composed …

Long-Term Safety And Effectiveness Of The Treo Stent Graft For The Endovascular Treatment Of Infrarenal Abdominal Aortic Aneurysms, Matthew J. Eagleton, Michael C. Stoner, John Henretta, Maciej Dryjski, Jean M. Panneton, Apostolos Tassiopoulos, Manish Mehta, Benjamin Pearce, Mel J. Sharafuddin, Treo Investigators

Department Surgery Faculty Publications

Objective

Report on the long-term safety and effectiveness of the TREO stent graft in endovascular repair of AAA from a US investigational device clinical study.

Methods

Data from a multicenter, nonrandomized, prospective, US investigational device exemption pivotal study (NCT02009644) were used. From November 2013 to February 2016, 150 patients were enrolled at 29 US centers. Safety endpoints were defined as major adverse events (i.e., all-cause mortality, myocardial infarction, stroke, renal failure requiring renal replacement therapy, respiratory failure, paraplegia, bowel ischemia, and procedural blood loss of 1,000cc or greater). Effectiveness endpoints were defined as no aneurysm rupture, absence of sac increase …

Effect Of Family-Centered Care Interventions On Motor And Neurobehavior Development Of Very Preterm Infants: A Systematic Review And Meta-Analysis, Manasa Kolibylu Raghupathy, Shradha S. Parsekar, Shubha R. Nayak, Kalesh M. Karun, Sonia Khurana, Alicia J. Spittle, Leslie Edward S. Lewis, Bhamini Krishna Rao

Rehabilitation Sciences Faculty Publications

Aim

To assess the effectiveness of family-centered care (FCC) interventions on motor and neurobehavior development of very preterm infants.

Method

Randomized and quasi-randomized trials assessing the effect of FCC on motor and neurobehavioral outcomes in very preterm infants (28–32 wk gestation) were included. Five electronic databases and grey literature were searched from January 2010 to August 2022. Two reviewers independently screened the titles/abstracts and full texts, assessed the risk of bias, and extracted data. The Cochrane Risk of Bias 2.0 Tool and GRADE were used for risk and evidence certainty assessments. Meta-analysis or narrative synthesis was performed based on data …

Association Of Maternity Care Deserts With Maternal And Pregnancy-Related Mortality, Rula Atwani, Lindsay Robbins, George Saade

Department of Obstetrics & Gynecology Faculty Publications

OBJECTIVE:

To evaluate the association between the level of maternity care access and maternal and pregnancy-related mortality.

METHODS:

This was a cross-sectional analysis of county-level data in the United States from January 2018 to December 2021. Using the level of maternity care access, we categorized counties into desert, low access, moderate access, and full access. The primary outcome of interest was maternal mortality rate per 100,000 live births. A secondary outcome was pregnancy-related mortality rate per 100,000 live births. Absolute risk differences and adjusted incidence rate ratios were calculated for maternal mortality and pregnancy-related mortality with multivariable negative binomial mixed-effects …

Association Between The Intensity Of Exercise In The First Trimester And Early Second Trimester And The Risk Of Gestational Diabetes, Takaki Tanamoto, Misa Hayasaka, Tetsuya Kawakita

Department of Obstetrics & Gynecology Faculty Publications

Objective

Although some studies show that exercise decreases the incidence of gestational diabetes mellitus (GDM), the optimal exercise intensity during pregnancy remains unclear. We examined GDM risk according to exercise intensity in pregnant individuals.

Methods

We analyzed data from the Nulliparous Pregnancy Outcomes Study: Monitoring Mothers‐to‐Be (nuMoM2b), a prospective study enrolling nulliparous individuals in the first trimester. Participants with pregestational diabetes or delivery before 20 weeks were excluded. Exercise intensity during the first (6–13 weeks’ gestation) and early second (16–21 weeks’ gestation) trimesters was categorized by metabolic equivalent of task hours per week (MET‐hr/week) as none, low intensity (< 7.5), moderate intensity (7.5–14.9), or high intensity (≥ 15). The primary outcome was GDM; secondary outcomes included preeclampsia, gestational hypertension, preterm birth, small‐for‐gestational‐age birth, and stillbirth. Adjusted relative risks (aRRs) with 95% confidence intervals (CIs) were calculated using a generalized linear mixed‐effects model with a Poisson distribution and robust error variance, controlling for the random effects of individuals and potential confounders.

Results …

Association Of Mean Arterial, Systolic, And Diastolic Blood Pressure Trends In Early Pregnancy With Superimposed Preeclampsia With Severe Features In Pregnancies Complicated By Chronic Hypertension, Tetsuya Kawakita, Justin M. Leach, George R. Saade, Kim Boggess, Lorraine Dugoff, Brenna L. Hughes, Joseph Bell, Kjersti Aagaard, Rodney K. Edwards, Kelly Gibson, David M. Haas, Lauren Plante, Torri Metz, Brian Casey, Sherri Longo, Matthew K. Hoffman, Kara K. Hoppe, Methodius Tuuli, Michelle Y. Owens, Heather Frey, Todd Rosen, Uma M. Reddy, Wendy Kinzler, Emily Su, Iris Krishna, Mary E. Norton, Daniel Skupski, Yasser Y. El-Sayed, Ronald Librizzi, Mounira Habli, Shauna Williams, Gabriella Pridjian, David S. Mckenna, Sarah Osmundson, Joanne Quinones, Zorina Galis, Lorie Harper, Namasivayam Ambalavanan, Jeff M. Szychowski, Alan T.N. Tita

Department of Obstetrics & Gynecology Faculty Publications

OBJECTIVE: To evaluate the association of longitudinal systolic blood pressure (SBP), diastolic blood pressure (DBP), and mean arterial pressure (MAP) in early pregnancy with later development of superimposed preeclampsia with severe features in pregnancies complicated by mild chronic hypertension.

METHODS: This secondary analysis used data from the CHAP (Chronic Hypertension and Pregnancy) trial, a multicenter randomized controlled trial that involved pregnant individuals with chronic hypertension. Participants were categorized based on the development of superimposed preeclampsia with severe features. Longitudinal blood pressure measurements from enrollment to the development of superimposed preeclampsia with severe features or delivery were assessed using regression models. …

Longitudinal Assessment Of Fetal Myocardial Performance Index In Normal Pregnancy Using Spectral Tissue Doppler, R. Horgan, E. Sinkovskaya, E. Kalafat, G. Saade, A. Abuhamad

Department of Obstetrics & Gynecology Faculty Publications

Objective

Although spectral tissue Doppler imaging is recognized as the optimal method for assessing the fetal myocardial performance index (MPI), longitudinal reference ranges for fetal MPI measured using spectral tissue Doppler have not been established. Our objective was to use spectral tissue Doppler data to establish gestational-age-specific reference ranges from 12–33 weeks for left and right ventricular fetal MPI.

Methods

This was a prospective longitudinal study of women aged 18–35 years, with a body mass index below 30 kg/m² and a singleton pregnancy conceived spontaneously. Fetal MPI measurements were obtained in the first, second and third trimesters and MPI was …

Interobserver Variability Regarding Adequacy Of Oropharyngeal Exposure For Transoral Robotic Surgery May Necessitate Staging Endoscopy: Evaluating Tors Exposure, Colleen Schinderle, Kevin J. Carlson, Reem Sharaf Alddin, Jeffery J. Houlton, Matthew J. Bak, Daniel W. Karakla, Jonathan R. Mark

Department of Otolaryngology (ENT) Faculty Publications

[First paragraph] Transoral robotic surgery (TORS) for the treatment of oropharyngeal cancer has become centered at tertiary referral centers. To avoid treatment delays or multiple anesthetics, the need for repeat operative endoscopy may be questioned when the diagnosis has been made at an outside institution. However, inadequate visualization of relevant anatomy can preclude TORS candidacy and may lead to procedure abortion or conversion to an open technique.²,³ To evaluate this dilemma, we explored the ability to assess oropharyngeal exposure for TORS candidacy via operative endoscopic photo-documentation.

Major Adverse Cardiovascular Events Are Less Frequent In Psoriasis Patients Starting Glp-1ra Compared To Controls: An Observable Retrospective Cohort Study, Ana Ormaza Vera, Marla F. Osorlo, Madison Olexson, June Choi, Chunghwan Ro, Clinton Enos

Department Dermatology Faculty Publications

Background: Psoriasis is an independent risk factor for major adverse cardiovascular events (MACE). We have previously shown that psoriasis patients with dyslipidemia have an increased incidence of MACE despite treatment with a biologic and a statin. Glucagon-like peptide-1 receptor agonists (GLP-1RA) have shown to reduce MACE in patients with type 2 diabetes and obesity, comorbidities that commonly co-occur with psoriasis. However, the association between GLP-1RA and the incidence of MACE among patients with psoriasis remains unknown.

Methods: We conducted a retrospective cohort study from 2014-2024 using a large, multi-center, electronic health record network (TriNetX). Patients aged 18-90 who started GLP-1RA …

Irritable Bowel Syndrome Risk In Acne Patients: Implications For Dermatologic Care, Alex Y. Liu, Ana Ormaza Vera, Clinton W. Enos

Department Dermatology Faculty Publications

[Practice points]

• Clinicians should consider monitoring for early signs of irritable bowel syndrome (IBS) in adult patients with acne to facilitate prompt diagnosis and intervention.
• Clinicians should remain judicious when prescribing antibiotics for acne management to minimize potential disruptions to the gut microbiota and the risk for IBS.
• Isotretinoin may serve as a safer alternative to antibiotics in patients with acne, particularly those with gastrointestinal concerns.

Educational Case: Disseminated Intravascular Coagulation In A Patient With Cancer, Kripa Ahuja, Richard M. Conran

Department of Biomedical and Translational Sciences Faculty Publications

The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see https://www.sciencedirect.com/journal/academic-pathology/about/pathology-competencies-for-medical-education-pcme.

Protein Marker-Dependent Drug Discovery Targeting Breast Cancer Stem Cells, Ashley V. Huang, Yali Kong, Kan Wang, Milton L. Brown, David Mu

Department of Biomedical and Translational Sciences Faculty Publications

Breast cancer is one of the most common cancers globally. Unfortunately, many patients with breast cancer develop resistance to chemotherapy and tumor recurrence, which is primarily driven by breast cancer stem cells (BCSCs). BCSCs behave like stem cells and can self-renew and differentiate into mature tumor cells, enabling the cancer to regrow and metastasize. Key markers like CD44 and aldehyde dehydrogenase-1 (ALDH1), along with pathways like Wingless-related integration site (Wnt), Notch, and Hedgehog, are critical to regulating this stem-like behavior of BCSCs and, thus, are being investigated as targets for various new therapies. This review summarizes marker-dependent strategies for targeting …

Heterogeneous Clustering Of Multiomics Data For Breast Cancer Subgroup Classification And Detection, Joseph Pateras, Musaddiq Lodi, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

The rapid growth of diverse -omics datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation–maximization routine for the joint latent variable modeling of multiomics patient profiles. By combining this approach with traditional biological feature selection methods, this study optimizes latent distribution, enabling efficient patient clustering from well-studied cancer types with reduced computational expense. The proposed optimization subroutines enhance survival analysis and improve runtime performance. This article presents a framework for distinguishing cancer subtypes and identifying potential biomarkers for breast cancer. Key insights into individual subtype expression and function were obtained through differentially expressed gene …

Benchmarking Batch-Effect Correction Methods Towards The Construction Of A Triple-Negative Breast Cancer Cell Atlas, Peter Scheible, Amy H. Tang, Jing He, Jiangwen Sun

Computer Science Faculty Publications

Triple-negative breast cancer (TNBC) requires detailed cellular mapping given its aggressive nature, immense tumor heterogeneity and genetic diversity. We integrated 156,794 cells from six scRNA-seq datasets—including tumors, metastases, and cell lines—to build a TNBC scRNA cell atlas, focusing on batch effect mitigation while maintaining biological and molecular details. Preprocessing f ilters noise, normalizes data, and leverages PCA for integration readiness. We utilized scANVI, a semi-supervised tool, to align datasets, preserving TNBC’s complex tumor heterogeneity via marker annotations [1]. UMAPs demonstrate biological clustering in integrated data, contrasted with datasetdriven unintegrated patterns. Assessments verifying effective batch correction. This method aligns with NASA’s …

Multi-Modal Mri Based Segmentation Of Brain Metastases Using Adaptive Self-Attention, Evan Savaria

Computer Science Faculty Publications

Brain metastases (BMs) are the most common adult central nervous system malignancy, affecting 20–40% of cancer patients. Accurate segmentation of metastatic lesions in multi-modal MRI is essential for treatment planning and prognosis however, manual delineation is time consuming and prone to variability. Traditional deep learning models such as U-Net, have improved segmentation accuracy but capture limited long-range dependencies and struggle with variations in metastasis size, shape, and distribution. This study introduces the Adaptive Integrated Multi-modal Segmentation (AIMS) model, an adaptive self-attention framework within a hybrid U-Net and Transformer architecture to enhance BM segmentation by leveraging multi-modal MRI integration. The proposed …

Coldstartcpi: Induced-Fit Theory-Guided Dti Predictive Model With Improved Generalization Performance, Qichang Zhao, Haochen Zhao, Linyuan Gao, Kai Zheng, Yajie Li, Qiao Ling, Jing Tang, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Predicting compound-protein interactions (CPIs) plays a crucial role in drug discovery. Traditional methods, based on the key-lock theory and rigid docking, often fail with novel compounds and proteins due to their inability to account for molecular flexibility and the high sparsity of CPI data. Here, we introduce ColdstartCPI, a framework inspired by induced-fit theory, which leverages unsupervised pre-training features and a Transformer module to learn both compound and protein characteristics. ColdstartCPI treats proteins and compounds as flexible molecules during inference, aligning with biological insights. It outperforms state-of-the-art sequence-based models, particularly for unseen compounds and proteins, and shows strong generalization capability …