Digital Commons Network^™

Book Review Of Philosophical Fragments As The Poetry Of Thinking: Romanticism And The Living Present By Luke Fischer, Michael Vater

Philosophy Faculty Research and Publications

No abstract provided.

Icu-Length Of Stay Prediction On Electronic Health Records Using Graph Neural Networks And Homogeneous Similarity Graphs, Ahmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman Iv, Rishabh Kapoor, Preetam Ghosh

Computer Science Faculty Publications

Predicting the length of stay (LoS) is important for hospital administration, as it helps allocate proper resources, such as bed management and hospital staffing. Patients' Electronic Health Records (EHRs) contain highly relevant data for LoS prediction; however, their integration and effective use in predictive modeling for accurately estimating LoS remain challenging. To address this, we propose a homogeneous Graph Neural Network (GNN)-based framework for predicting LoS. This method employs a comprehensive data fusion strategy based on the hospital Visit-based Similarity Graph (VSG), which integrates diverse multi-modal clinical features into a coherent, homogeneous graph representation. Next, this VSG is fed into …

Humans Vs. Llms On Open Domain Scientific Claim Verification: A Baseline Study, Benjamin Curtis, Stefania Dzhaman, Matthew Maisonave, Jian Wu

Computer Science Faculty Publications

Verifying scientific claims is challenging for the general public because most people lack domain knowledge. Manual verification by subject domain experts is accurate, but it is obviously not scalable to meet the rising number of scientific claims on the Web. Whether the emerging large language models and large reasoning models can be used for scientific claim verification, and how their performances compare to humans, are still research questions. To this end, we developed a new benchmark MSVEC2 that consists of 138 claims from credible fact verification websites and science news outlets. Two tasks were given to both human and LLM …

Foundation Models In Bioinformatics, Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang

Computer Science Faculty Publications

With the adoption of foundation models (FMs), artificial intelligence (AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges, such as pre-training frameworks, model evaluation and interpretability. FMs demonstrate notable proficiency in managing large-scale, unlabeled datasets, because experimental procedures are costly and labor intensive. In various downstream tasks, FMs have consistently achieved noteworthy results, demonstrating high levels of accuracy in representing biological entities. A new era in computational biology has been ushered in by the application of FMs, focusing on both general and specific biological issues. In this review, we introduce recent advancements in bioinformatics FMs …

Gramseq-Dta: A Grammar-Based Drug-Target Affinity Prediction Approach Fusing Gene Expression Information, Kasul Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug–target affinity (DTA) prediction is a critical aspect of drug discovery. The meaningful representation of drugs and targets is crucial for accurate prediction. Using 1D string-based representations for drugs and targets is a common approach that has demonstrated good results in drug–target affinity prediction. However, these approach lacks information on the relative position of the atoms and bonds. To address this limitation, graph-based representations have been used to some extent. However, solely considering the structural aspect of drugs and targets may be insufficient for accurate DTA prediction. Integrating the functional aspect of these drugs at the genetic level can enhance …

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. …

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 …

A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Conventional drug discovery is expensive, time-consuming, and prone to failure. Artificial intelligence has become a potent substitute over the last decade, providing strong answers to challenging biological issues in this field. Among these difficulties, drug-target binding (DTB) is a key component of drug discovery techniques. In this context, drug-target affinity and drug–target interaction are complementary and essential frameworks that work together to improve our comprehension of DTB dynamics. In this work, we thoroughly analyze the most recent deep learning models, popular benchmark datasets, and assessment metrics for DTB prediction. We look at the paradigm shift in the development of drug …

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 …

Parenteral Nutritional Support In Surgical Patients: Expert Consensus Statements Regarding Intravenous Lipid Emulsions Containing Omega-3 Fatty Acids., Robert G Martindale, David C Evans, Dan Waitzberg, Malissa Warren, Manpreet S Mundi, Stanislaw Klek, Paul E Wischmeyer, Martin D Rosenthal

Surgery Articles

OBJECTIVES: The International Lipids in Parenteral Nutrition (PN) Summit was convened to offer practical guidance and expert consensus opinion regarding the use of intravenous lipid emulsions (ILEs) in various clinical settings. Herein, we briefly review aspects from this summit that are of particular importance for surgical/hospitalized patients.

METHODS: Summit participants identified and discussed new evidence, data, and analyses, that potentially influence the benefits and risks of ILEs in PN or their use in clinical practice. The summit meeting consisted of expert presentations that assessed recent clinical data and best practice, followed by periodic panel discussions to formulate consensus statements. Consensus …

A Primer On Anatomy, Biophysics, Pathology, Imaging And Treatment Of The Intervertebral Disc And The Anterior Spinal Column: The Discogenic, Intervertebral, Spinal Column (Disc) Aspn Workgroup., Jay S Grider, Timothy R Deer, Douglas P Beall, Melissa Z Murphy, Jacob W Fleming, Steven M Falowski, Christopher J Mallard, Hamzah A Ramawad, Rosa Amelia Garcia, Usman Latif, Chau M Vu, Anne Christopher, Michael E Harned, Raj G Patel, Anuj J Shah, Iden M Cowan, Kristin Jarzombek, Jordan L Tate, Nasir Khatri, Mateusz J Graca, Marcin K Karcz, Timothy T Davis, Kaku Barkoh, Olivier Clerk-Lamalice, Brian Durkin, Mark N Malinowski, Dagmar K Gross, Thomas Hedman, Matthew Green, Michael J Dorsi, Kasra Amirdelfan, Dawood Sayed

Surgery Articles

OBJECTIVE: As therapeutic options are rapidly expanding to treat pain of discogenic and vertebrogenic origin, it is important for the clinician to have an evidence-based understanding of the latest information regarding the normal and pathological anatomy of the intervertebral disc as well as imaging characteristics and treatment strategies. The American Society of Pain and Neuroscience (ASPN) commissioned the DISC project to inform and update the interventional spine community about anterior column pain syndromes.

METHODS: Using established literature review methods a clinical oversight group was convened to create an outline covering topics that will be key to meeting the objectives delineated …

Basic Skills Of 21st Century Teachers, Ömer Cem Karacaoğlu

Australian Journal of Teacher Education

This study aims to determine the basic skills that 21st century teachers should have. The study is based on the opinions of 79 teachers working in different disciplines on four different campuses in Izmir. The qualitative study used storage technique and content analysis. The opinions of the participants were evaluated to clarify the skill expressions, create themes and determine data categories. The study found that teachers prioritized several core competencies, including creativity, empathy and communication, critical thinking, problem solving and crisis management, and collaboration, curiosity and digital literacy. Other skills were determined as reading comprehension, learning to learn, patience, emotional …

Analysis Of Pre-Service Teachers’ Personal Metaphors About Foreign Language Teaching, Juan Luis De La Montaña Conchiña, Guadalupe De La Maya Retamar, Magdalena López-Pérez

Australian Journal of Teacher Education

This study analyses the characterisation and evolution of the personal metaphors of a sample of 34 trainee foreign language teachers, through a questionnaire of open-ended questions that included asking the participants to make drawings representing the roles of the teacher. Four categories of metaphors were considered for the analysis: behaviourist/transmissive, cognitivist/constructivist, situated, and self-referential. The results indicate that most participants were able to conceptualise their image of the teacher in the form of metaphors. The pre-service teachers’ metaphors represented are mainly cognitivist/constructivist and behaviourist/transmissive. When comparing them before and after the internship in the primary schools, most of them did …

Teaching In Racially Diverse Schools: Towards A Racial Competency Framework, Tebeje Molla, Kerri Garrard, Tim Corcoran

Australian Journal of Teacher Education

Safe learning environments foster the wellbeing, engagement, and educational outcomes of students. To develop resources that enable schools to create safe learning environments, we conducted focus group discussions with teachers and African heritage students in selected public schools in an Australian state. This paper reports insights from our discussions with the school staff. The findings indicate that teachers face ‘relational uncertainty’ in dealing with racial issues impacting their engagement with these students. To address these challenges, we propose a racial competency framework, featuring distinctive dimensions, drivers, and domains. The framework emphasises the need for schools to support racial value awareness, …

Unveiling Raciolinguistic Ideologies: Pre-Service Teachers’ Insights On Refugee Integration In Schools, Tuba Yilmaz, Rosanna Ellis

Australian Journal of Teacher Education

This study investigates pre-service teachers' ideologies about refugee students' belonging and integration in Türkiye and examines how these ideologies shape their anticipated pedagogical practices. Using the framework of raciolinguistic ideologies, the study highlights how linguistic and cultural hierarchies influence educational practices, often perpetuating systemic exclusion. Data were collected through in-depth interviews with 13 pre-service teachers from various educational programs, utilizing a qualitative, phenomenological design. The findings reveal a predominant reliance on deficit-based perspectives, with refugee students framed as linguistically deficient and culturally "othered." While participants expressed professional commitments to inclusivity, their approaches often emphasized assimilation into Turkish norms, reflecting cultural …

An Evidence-Based Consensus For The Use Of Neurostimulation For The Treatment Of Non-Surgical Low Back Pain: The Neuron Group., Timothy Ray Deer, Jason E Pope, Erika A Petersen, Rany T Abdallah, Kasra Amirdelfan, Nomen Azeem, Vishal Bansal, Kaku Barkoh, Kenneth B Chapman, Daniel R Denis, Michael J Dorsi, Alexander Escobar, Steven Michael Falowski, Rosa Amelia Garcia, Jonathan M Hagedorn, Robert D Heros, Whitney S James, Hemant Kalia, Todd Lansford, Mark N Malinowski, Suzanne Marie Manzi, Pankaj Mehta, Robert Z Moghim, Gregory Anthony Moore, Soriaya Lizette Motivala, Yeshvant A Navalgund, Raj G Patel, Julie G Pilitsis, Michael E Schatman, Philip Michael Shumsky, Natalie Holmes Strand, Nestor D Tomycz, James J Yue, Dawood Sayed

Neuroscience Articles

INTRODUCTION: The use of electrical neuromodulation has often been limited to those with previous back surgery, peripheral neuropathy, and complex regional pain syndrome. Many patients with severe intractable low back pain were thought to be candidates for spinal cord stimulation (SCS), dorsal root ganglion stimulation, or peripheral nerve stimulation but did not meet the criteria. Recently, additional high-level data has supported the use of SCS in non-surgical low back pain (NSLBP), and United States Food and Drug Administration approval has been granted. The American Society of Pain and Neuroscience (ASPN) executive committee realized an unmet need to develop criteria for …

Real-World Clinical Utility Of A Multi-Protein, Blood-Based Biomarker Assay For Disease Activity Assessments In Multiple Sclerosis., Angela Sanchez, Elisa Sheng, Sarah Eagleman, James L Eubanks, Patricia Izbicki, Shannon Mccurdy, Matt Burril, Ferhan Qureshi, Ati Ghoreyshi, Mitzi Joi Williams, Megan Weigel, William Kilgo, Jacqueline Nicholas, Annette Okai, Martin Belkin, Julie Burnham, Yasir Jassam, Michael Sy, Taylor Gonyou

Neuroscience Articles

BACKGROUND: Blood-based biomarkers have emerged as promising tools to optimize treatment decisions in multiple sclerosis (MS) including initiation, switch, or cessation of disease modifying therapies.

OBJECTIVES: The clinically validated MS disease activity (MSDA) test measures 18 proteins to derive a disease activity score. This study tests the clinical utility of MSDA in real-world practice.

METHODS: Twenty clinicians from 14 clinics conducted a chart review utilizing a retrospective, longitudinal design, with a pre-post component. Chart reviews captured clinician decision-making before and after receipt of each MSDA result, while separate clinician assessments also captured the perceived impact of MSDA on MS management. …

Psychosocial Behavioral Phenotypes Of Racially/Ethnically Minoritized Older Adults Enrolled In Habs-Hd Differ On Neuroimaging Measures Of Brain Age Gap, Hippocampal Volume, And Cortical Thickness, Alexandra L Clark, Makenna B Mcgill, Alexandra J Weigand, Julie K Wisch, Kalen Petersen, Beau Ances, Meredith N Braskie, Sid O'Bryant, Kelsey R Thomas, Habs‐Hd Study Team

2020-Current year OA Pubs

INTRODUCTION: This study examined whether previously identified psychosocial behavioral phenotypes differed on structural neuroimaging markers.

METHODS: Latent profile analysis (LPA) employed in a sample of 1820 community-dwelling older adults (1118 Hispanic and 702 Black) replicated previous Low Resource/Low Distress, High Resource/Low Distress, and Low Resource/High Distress phenotype classifications. Analyses of covariance (ANCOVAs) adjusting for relevant factors examined phenotype differences on neuroimaging outcomes of predicted brain age gap (BAG) (DeepBrainNet

RESULTS: The Low Resource/Low Distress and Low Resource/High Distress phenotypes had significantly higher predicted BAGs relative to the High Resource/Low Distress phenotype, and the Low Resource/High Distress group displayed significantly lower …

Data‐Driven Approach To Dynamic Resting State Functional Connectivity In Post‐Traumatic Stress Disorder: An Enigma‐Pgc Ptsd Study, Jacklynn M. Fitzgerald

Psychology Faculty Research and Publications

Using functional magnetic resonance imaging (fMRI), symptoms of posttraumatic stress disorder (PTSD) have been associated with aberrations in brain networks in the absence of a given cognitive demand or task, called resting-state networks. Prior work has focused on disruption in the static functional connectivity (FC) among specific regions constrained by a priori hypotheses. However, dynamic FC, an approach that examines brain network characteristics over time, may provide a more sensitive measure to understand the network properties underlying dysfunction in PTSD. Further, using a data-driven analytic approach may reveal the contribution of other larger network disturbances beyond those revealed by hypothesis-driven …

Pseudoachondroplasia, A Case Report (Preprint), Alec J. Pupo, Connor J. Stinson, Autumn Dye

Internal Medicine Resident Research

No abstract available.

Wearable-Derived Heart Rate Variability Reveals Autonomic Dysfunction In Schizophrenia (Preprint), Alec J. Pupo, Stephanie H. Felgoise

Internal Medicine Resident Research

Autonomic dysfunction has long been implicated in schizophrenia, yet objective physiological markers remain underutilized in psychiatric research. Heart rate variability (HRV), a noninvasive measure of autonomic regulation, is conventionally derived from short electrocardiographic recordings. In this study, we tested whether continuous, wearable-derived HRV can identify physiologic alterations in schizophrenia-spectrum disorders. Using the NIH All of Us database, we analyzed second-level Fitbit heart rate data from 26 individuals with schizophrenia-spectrum diagnoses and 26 matched controls. Frequency-domain analyses focused on ultra-low frequency (ULF), very low frequency (VLF), and truncated low frequency (tLF) bands, given sampling constraints. Schizophrenia participants showed significantly reduced power …

Elevated Neutrophil-To-Lymphocyte Ratios In Schizophrenia: Insights From A Precision Medicine Cohort (Preprint), Alec J. Pupo, Connor J. Stinson, Chinwendu Madukwe, Stephanie H. Felgoise

Internal Medicine Resident Research

Systemic inflammation has been increasingly implicated in the pathophysiology of schizophrenia. The neutrophil-to-lymphocyte ratio (NLR), a readily available marker of systemic inflammation, has not been thoroughly investigated in large, demographically-matched schizophrenia cohorts. Using data from the All of Us Research Program, we analyzed participants with schizophrenia (n = 396) matched to controls (n = 396) by sex, race, and age. NLR was calculated as the ratio of each participant’s median neutrophil count to median lymphocyte count across all available measurements, excluding extreme values (NLR > 7). Distribution normality was assessed using the Shapiro–Wilk test, and group differences were evaluated with the …

The Correlation Between First-Dollar Promise Programs And Student Enrollment, Retention, And Completion, Jennifer Kotowski

Dissertations of Practice

Promise Programs gained popularity during the Great Recession to increase access to postsecondary education amid growing concerns regarding student loan debt. Promise Programs provide tuition-free scholarships to eligible students, typically based on non-merit criteria. Two common types of Promise Programs scholarships are first-dollar scholarships, which are awarded before any other grants, financial aid, or scholarships, and last-dollar scholarships, which are applied after all other grants, financial aid, or scholarships. Both models have been shown to positively impact student outcomes such as enrollment, semester-to-semester retention, and degree completion. This quantitative study determined whether student outcomes improved when a Promise Program scholarship …

The Beautiful Struggle: A Counter-Narrative Study Of African American Male School Leaders, Jamie Crosen Mr

Dissertations of Practice

This qualitative dissertation explores the lived experiences of African American male high school principals in urban and suburban schools across the Chicagoland area. Using critical race theory (CRT) and counter-narrative methodology, the study centers the voices of ten African American male principals to examine how race, systemic inequities, and social justice shape their leadership practices, professional identities, and navigation of racially charged educational environments. These leaders consistently confront institutionalized biases and racialized expectations that limit their professional advancement while reinforcing deficit narratives about African American leadership. Through semi-structured interviews and thematic analysis, three primary research questions guided this study: (1) …

Beyond Grit: Structural Determinants Of Resilience Among College Women With Children In The U.S., Juliana Kahrs

Dissertations of Practice

This critical quantitative analysis explores how social determinants of health, including basic needs security, caregiving and work responsibilities, healthcare access, discrimination experiences, and institutional support predict resilience among U.S. college women with dependents. Using data from the Spring 2021 ACHA-NCHA III survey (n = 4,417), this study integrated the Health Equity Framework with the Social Ecological Theory of Resilience to examine multilevel influences on resilience. Descriptive analyses highlighted disproportionate burdens among single, first-generation, and racially minoritized groups. Bivariate chi-square tests revealed significant associations between resilience and sense of belonging, basic needs security, employment, healthcare utilization, and self-assessed overall health. Multinomial …

Stephen J. Lippard: Chemistry Meets Medicine, Radwa Elrouby

Natural Sciences Student Research Presentations

Key Study

In "DNA Sequence Context Modulates the Impact of a Cisplatin 1,2-GpG Intrastrand Cross-Link", Pilch, Todd, and Lippard found that the DNA sequence around the binding site influences how tightly cisplatin binds (Pilch, Todd, and Lippard).

Biophysical techniques like melting temperature and circular dichroism showed that some sequences stabilize DNA more strongly after drug binding (Pilch, Todd, and Lippard).

This explains why cisplatin is more effective in some tumor genomes (Todd and Lippard).

Infant Health Equity In Oklahoma: A Mixed-Methods Exploration Of Personal, Organizational, Environmental, And Policy Factors Contributing To Black Infant Mortality, Ayesha M. Lampkins

West Chester University Doctoral Projects

Black women experience higher rates of adverse birth outcomes, including infant mortality. There is a gap in the literature on multilevel strategies to achieve infant health equity and engage Black women. This study is unique in that no others have looked at the views of Oklahoma Black women to inform and address infant health equity strategies and utilize these views to provide context to existing infant mortality data. The study research questions are: 1) What views on infant health equity and infant mortality are held by Black women in Oklahoma? 2) What differences exist between Black and White mothers in …

Flags As Symbols Of Place: Unpacking Geographic Meaning And Identity In Student Flag Designs, Carlos A. Morales-Ramirez

West Chester University Doctoral Projects

Flags have been around for centuries; however, vexillology, the study of flags, was not officially coined until the 1960s. Despite this, there is still a need for more scientific and empirical research. Using qualitative arts-based research (ABR) methodology, this study investigates the creative journey of students in an undergraduate geography course as they design a flag for a place of their choosing. Students were asked to interpret the concept of ‘place’ through their flag designs while also incorporating flag design principles. The results showed that participants selected places tied to themes such as hometown, family, love, memories, and culture often …

Distinguishing Symptoms Of Racial Trauma From Conventional Trauma, Michelle Yoong

West Chester University Doctoral Projects

Trauma research in psychology has traditionally been shaped by a White-centric framework, leading to the underrepresentation of racial and ethnic minority experiences. This study aims to establish racial discrimination as a distinct traumatic stressor with significant psychological consequences by exploring the distinction between racial and conventionally recognized traumatic stressors and posttraumatic stress symptoms (PTSS). It also aims to address inconsistent and exclusionary assessment methodology involving underrepresented racial minority (URM) populations, including the neglect of racial trauma and discrimination measures in trauma research. Participants consisted of URMs who sought enrollment in a clinical trial for opioid use disorder at a community …

Virginia Commonwealth University: Program Profile, Christy Tyndall, Jacqueline Smith-Mason

National Collegiate Honors Council Monographs: Chapters

Virginia Commonwealth University (VCU) is an urban, public research university located in Richmond, Virginia. VCU is among only eighty-four R1 universities with a Carnegie Community Engagement classification, which is a testament to VCU’s strong commitment to integrating community engagement through teaching, research, and service to address societal challenges and improve the quality of life for all. The university enrolls more than 28,000 students, representing over one hundred countries. Eighty-five percent of students are Virginia residents, and more than half of all students represent ethnically diverse populations. Thirty-seven percent of all fall 2024 freshmen were first-generation college students. More than two …