Digital Commons Network^™

Deep5mc: Predicting 5-Methylcytosine (5mc) Methylation Status Using A Deep Learning Transformer Approach, Evan Kinnear, Houssemeddine Derbel, Zhongming Zhao, Qian Liu

Faculty, Staff and Student Publications

DNA methylations, such as 5-methylcytosine (5mC), are crucial in biological processes, and aberrant methylations are strongly linked to various human diseases. Genomic 5mC is not randomly distributed but exhibits a strong association with genomic sequences. Thus, various computational methods were developed to predict 5mC status based on DNA sequences. These methods generated promising achievements and overcome the limitations of experimental approaches. However, few studies have comprehensively investigated the dependency of 5mC on genomic sequences, and most existing methods focus on specific genomic regions. In this work, we introduce Deep5mC, a deep learning transformer-based method designed to predict 5mC methylations. Deep5mC …

Mmrt: Multimut Recursive Tree For Predicting Functional Effects Of High-Order Protein Variants From Low-Order Variants, Bryce Forrest, Houssemeddine Derbel, Zhongming Zhao, Qian Liu

Faculty, Staff and Student Publications

Protein sequences primarily determine their stability and functions. Mutations may occur at one, two, or three positions at the same time (low-order variants) or at multiple positions simultaneously (high-order variants), which affect protein functions. So far, low-order variants, such as single variants, double variants, and triple variants, have been well-studied through high-throughput experimental scanning techniques and computational prediction methods. However, research on high-order variants remains limited because of the difficulty of scanning an exponentially large number of potential variant combinations. Nonetheless, studying higher-order variants is crucial for understanding the pathogenesis of complex diseases, advancing protein engineering, and driving precision medicine. …

Enhancing The Utility Of Polygenic Scores In Alzheimer’S Disease Through Systematic Curation And Annotation, Savannah Mwesigwa, Yulin Dai, Nitesh Enduru, Zhongming Zhao

Faculty, Staff and Student Publications

Introduction: Polygenic Scores (PGSs) assess cumulative genetic risk variants that contribute to the association with complex diseases like Alzheimer's Disease (AD). The PGS Catalog is a valuable repository of PGSs of various complex diseases, but it lacks standardized annotations and harmonization, making the information difficult to integrate for a specific disease.

Methods: In this study, we curated 44 PGS datasets for AD from the PGS Catalog, categorized them into five methodological groups, and annotated 813,257 variants to nearby genes. We aligned the scores based on the "GWAS significant variants" (GWAS-SV) method with the GWAS Catalog and flagged redundant files and …

Lp-118 Is A Novel B-Cell Lymphoma 2 / Extra-Large Inhibitor That Demonstrates Efficacy In Models Of Venetoclaxresistant Chronic Lymphocytic Leukemia, Janani Ravikrishnan, Daisy Y Diaz-Rohena, Elizabeth Muhowski, Xiaokui Mo, Tzung-Huei Lai, Shrilekha Misra, Charmelle D Williams, John Sanchez, Andrew Mitchell, Suresh Satpati, Elizabeth Perry, Tierney Kaufman, Chaomei Liu, Arletta Lozanski, Gerard Lozanski, Kerrya Rogers, Adam S Kittai, Seema A Bhat, Mary C Collins, Matthew S Davids, Nitin Jain, William G Wierda, Rosa Lapalombella, John C Byrd, Fenlai Tan, Yi Chen, Yu Chen, Yue Shen, Stephen P Anthony, Jennifer A Woyach, Deepa Sampath

Faculty, Staff and Student Publications

Patients with chronic lymphocytic leukemia (CLL) respond well to initial treatment with the B-cell lymphoma 2 (BCL2) inhibitor venetoclax. Upon relapse, they often retain sensitivity to BCL2 targeting, but durability of response remains a concern. We hypothesize that targeting both BCL2 and B-cell lymphoma-extra large (BCLXL) will be a successful strategy to treat CLL, including for patients who relapse on venetoclax. To test this hypothesis, we conducted a pre-clinical investigation of LP-118, a highly potent inhibitor of BCL2 with moderate BCLXL inhibition to minimize platelet toxicity. This study demonstrated that LP-118 induces efficient BAK activation, cytochrome C release, and apoptosis …

Optimal Timing Of Organs-At-Risk-Sparing Adaptive Radiation Therapy For Head-And-Neck Cancer Under Re-Planning Resource Constraints, Fatemeh Nosrat, Cem Dede, Lucas B Mccullum, Raul Garcia, Abdallah S R Mohamed, Jacob G Scott, James E Bates, Brigid A Mcdonald, Kareem A Wahid, Mohamed A Naser, Renjie He, Aysenur Karagoz, Amy C Moreno, Lisanne V Van Dijk, Kristy K Brock, Jolien Heukelom, Seyedmohammadhossein Hosseinian, Mehdi Hemmati, Andrew J Schaefer, Clifton D Fuller

Faculty, Staff and Student Publications

Background and purpose: Prior work on adaptive organ-at-risk (OAR)-sparing radiation therapy has typically reported outcomes based on fixed-number or fixed-interval re-planning, which represent one-size-fits-all approaches and do not account for the variable progression of individual patients' toxicities. The purpose of this study was to determine the personalized optimal timing of re-planning in adaptive OAR-sparing radiation therapy, considering limited re-planning resources, for patients with head and neck cancer (HNC).

Materials and methods: A novel Markov decision process (MDP) model was developed to determine optimal timing of re-planning based on the patient's expected toxicity, characterized by normal tissue complication probability (NTCP), for …

Intersecting Inequities: How Rurality And Socioeconomic Disadvantage Amplify Cancer Disparities In Ohio, Jessica Zittel, Jason Chen

Student Scholarship

No abstract provided.

Local Food Systems And Sustainability: A Granville Cookbook, Jocelyn Rafter

Student Scholarship

No abstract provided.

Exploring The State Of Homelessness In Franklin And Licking County, Justice Ofosuhene Jr.

Student Scholarship

No abstract provided.

The Creation Of An Andean Body: Early Andean State Reliance On A Gendered Division Of Labor, Emma Showalter

Student Scholarship

No abstract provided.

How Equitas Health Strives To Heal The Lgbtq+ And Hiv/Aids Community In 2024 And 2025, Virginia Lawrence

Student Scholarship

No abstract provided.

Efforts Towards The Total Synthesis Of Teredinibactin A, Duncan Curry

Student Scholarship

No abstract provided.

Strawberry Season Settles, The Crimson Nestles, Tra Huong Vo

Student Scholarship

No abstract provided.

Assessing The Effects Of Low Polyunsaturated Fatty Acids (Pufas) Diets On Priming Immunity In Drosophila Melanogaster, Minh B. Tran Ha

Student Scholarship

No abstract provided.

Zika Virus Modulates Arthropod Histone Methylation For Its Survival In Mosquito Cells, Telvin Harrell

Biological Sciences Faculty Publications

Zika virus (ZIKV) is a mosquito-borne human pathogen that causes mild febrile illness in adults and severe neurological complications and microcephaly in newborns. Studies have reported that ZIKV modulates methylation of human and viral RNA critical for its replication in vertebrate cells. In this study, we show that ZIKV modulates mosquito S-adenosyl methionine (SAMe)-synthase, an enzyme involved in the production of SAMe (methyl donor), and histone methylation for its survival in mosquito cells. Reverse transcription quantitative PCR followed by immunoblotting analysis showed increased amounts of SAMe synthase at both RNA and protein levels, respectively, in C6/36 mosquito cells infected with …

Addressing The Productivity-Susceptibility Analysis In Data-Limited Fisheries For Understudied Fish In The Marine Aquarium Trade, Alice Wynn, Jemelyn Baldisimo, Gabrielle Baillargeon, Michael Tlusty, Andrew Rhyne

Biological Sciences Faculty Publications

The marine aquarium trade (MAT) harvests millions of coral reef fishes from the wild yearly. While the MAT supports fishers, hobbyists and marine education, harvested fishes are crucial in maintaining coral reef health and balanced marine cycles within their native habitats. Understanding the impact of the MAT on fish populations is critical for sustaining the trade in the long-term. Productivity-susceptibility analyses (PSAs) offer semiquantitative methods of analyzing the productive capacity of each fish stock, as well as its susceptibility to overfishing. The present study revises and expands upon a PSA conducted by Baillargeon et al. (2020) that focused on 32 …

Divergent Floral And Vegetative Trait Responses To Abiotic Factors Drive Phenotypic Diversity In Platanthera Dilatata (Orchidaceae) Across Alaska, Marlin L. Bowles, Lisa E. Wallace

Biological Sciences Faculty Publications

Multiple traits make up an integrated phenotype, but traits may be shaped by differing drivers. It is often assumed that selection by biotic agents drives floral variation, but abiotic factors are also known to influence floral traits. Understanding trait covariations and their association with diverse environmental factors is a central question in evolution and ecology. Here, we studied covariation in floral and vegetative traits in relation to climate and topo-edaphic variation in the orchid Platanthera dilatata. In Platanthera, nectar spur length is associated with pollinator tongue length, but much variation exists in other traits too, likely to be …

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 …

Squid Paralarvae Turn With High Agility Using Jets Near The Reynolds Number Threshold For Viscous Domination, Ian K. Bartol, Alissa M. Ganley, Paul S. Krueger, Joseph T. Thompson

Biological Sciences Faculty Publications

Turning is critical for survival in the ocean, as marine animals need to maneuver to capture prey, elude predators, and navigate complex environments. While prior research has focused on turning performance of adult swimmers, less is known about early ontogenetic stages that locomote within lower Reynolds number (Re) regimes, especially young jetters. To evaluate squid paralarval turning proficiency and the role of the pulsed jet in maneuvers, recently hatched longfin squid Doryteuthis pealeii swimming in a viewing chamber were studied using digital particle image velocimetry and kinematic motion analyses. Paralarvae exhibited a wide repertoire of turning behaviors, including those performed …

High Temporal Resolution Gene Expression Analysis Of Acute Heat Stress Response In Acropora Cervicornis And Porites Astreoides, Katherine Parker, Nicolas Evensen, Iliana Baums, Daniel Barshis

Biological Sciences Faculty Publications

Widespread coral bleaching and mortality events are becoming increasingly frequent due to rising ocean temperatures, though certain coral species and populations have displayed higher tolerance to elevated emperatures than others. As such, it is of high research priority to identify thermally tolerant coral populations for research and conservation and assess the biological mechanisms allowing these populations to survive exposure to higher temperatures. This research utilized the Coral Bleaching Automated Stress System (CBASS), a portable experimental aquaria system with precise temperature manipulation, to assess the thermal thresholds and heat stress response of two coral species from Summerland Key, FL, USA. Seven …

Genome-Wide Snp Analyses Reveal High Gene Flow Of Endemic Smallscale Croaker (Boesemania Microlepsis) In The Lower Mekong Basin, Quyen Dang Ha Vu, Christopher E. Bird, Oanh Thi Truong, Sang Quang Tran, Ellen E. Biesack, Amanda S. Ackiss, Kent E. Carpenter, Binh Truy Dang

Biological Sciences Faculty Publications

The Smallscale Croaker, Boesemania microlepis, is a valuable fishery resource in the Mekong River basin that lacks clear biological data to understand its basic ecology and conservation management priorities. This species is common in the southernmost floodplain of the Mekong which extends from Tonlé Sap in Cambodia to the Mekong Delta in Vietnam. This floodplain is of particular biodiversity conservation concern because of the many upstream dams that restrict water flow in an ecology that relies heavily on a flood-pulse cycle. The literature regarding the biology B. microlepis in this region contains conflicting ideas that populations are both highly …

Endocrine Responses To Two Distinct Foraging Contexts In The Bonobo (Pan Paniscus), Lauren Mitchell

Master's Theses

In gregarious animals, a social structure characterized by female dominance is relatively rare. However, bonobos (Pan paniscus), one of the two species most closely related to humans, are characterized by partial female dominance, with females forming close social bonds. In contrast, chimpanzees (Pan troglodytes), a close relative of the bonobo, are characterized by strong male-male bonding and social dominance with female chimpanzees lacking close social bonds. There is a lack of consensus concerning the reasons for these behavioral differences in Pan, specifically, the physiological processes responsible for female dominance in bonobos. The role of hormones …

A New G Family: Properties, Characterizations, Different Estimation Methods And Port-Var Analysis For U.K. Insurance Claims And U.S. House Prices Data Sets, Ahmad M. Aboalkhair, Gholamhossein Hamedani, Nazar Ali Ahmed, Mohamed Ibrahim, Mohammad A. Zayed, Haitham M. Yousof

Mathematical and Statistical Science Faculty Research and Publications

This paper introduces a new class of probability distributions, termed the generated log exponentiated polynomial (GLEP) family, designed to enhance flexibility in modeling complex real financial data. The proposed family is constructed through a novel cumulative distribution function that combines logarithmic and exponentiated polynomial structures, allowing for rich distributional shapes and tail behaviors. We present comprehensive mathematical properties, including useful series expansions for the density, cumulative, and quantile functions, which facilitate the derivation of moments, generating functions, and order statistics. Characterization results based on the reverse hazard function and conditional expectations are established. The model parameters are estimated using various …

Path Nets: Concurrence And Recurrence In The Dynamics Of Organizing, Brian T. Pentland, Waldemar Kremser, Kenneth T. Goh

Research Collection Lee Kong Chian School Of Business

This article proposes a link between temporal structuring and the dynamics of organizing that is manifest in a fabric of concurrent paths that we call a path net. Path nets are shaped by mechanisms of temporal structuring, such as entrainment, planning, agency, and chance. Path nets materialize the effects of temporal structuring “here” and “now” in the comings and goings of actors and resources, thereby setting the stage for doings and sayings of situated practice and shaping the dynamics of organizing. Path nets offer a parsimonious system of picturing the complexity of organizing that is built on a processual ontology …

Parallel Algorithms For Large Scale Dynamic Graph Analysis, Arindam Khanda

Doctoral Dissertations

A complex system of interacting entities in contemporary scenarios, be it biological, technological, or social, can be represented using graphs. Dynamic graphs, unlike their static counterparts, are ones in which the underlying topology changes over time. These networks act as a model for numerous systems, from transportation to social interactions, capturing the ever-evolving nature of real-world phenomena. However, the inherent temporality of these networks presents a unique set of challenges and the traditional static graph algorithms often fall short in efficiency and applicability. In our research, we delve into the complexities presented by large dynamic networks and suggest various methodologies …

Implication And Applications Of Machine Learning On Biomedical Images, Jason Hagerty

Doctoral Dissertations

Medical imaging ranges in modality including computer tomography imaging, x-ray imaging, digital microscopy, and macro-focus dermoscopy images. The latter two modalities are the focus of the presented work.

To perform a diagnostic evaluation on the captured dermoscopy image, it begins with what is usually a labor-intensive operation that requires an expert to perform the initial segmentation for localizing a region of interest (ROI). Once that ROI is obtained, a physician with years of training and experience will observe biological markers that can be used to visually differentiate whether a lesion is benign or malignant. A similar process is used for …

Perceptions Of Mental Health School-Based Team Members On Addressing Suicidal And Non-Suicidal Self-Injurious Behaviors: A Qualitative Inquiry Into Policy Implementation And Practice In School Settings, Ashlande Smith

Theses and Dissertations

The purpose of this study was to explore the perceptions of mental health school-based team members regarding the effectiveness of current prevention and intervention practices for addressing suicidal and non-suicidal self-harming behaviors among school-age children in a large suburban school district in the southern United States. Despite the alarming increase in self-injurious behaviors, with crisis calls rising from 144 incidents in the 2022 school year to 736 incidents in the 2025 school year, the district lacked comprehensive prevention and intervention strategies to effectively address this critical issue.

The researcher used a qualitative phenomenological approach to capture the lived experiences and …

Perceptions Of Victims On The Influence Of Domestic Violence Programs On The Decision To Leave, Tiffany Kleiman-Bourdeau

Theses and Dissertations

Dating back to earlier times, domestic violence was referred to as marital disputes and was not even considered a crime by law enforcement. However, that has since changed and now individuals are convicted for such crimes against another person. There are several treatment plans and options for these abusive individuals to take to receive the help they need to refrain from being abusive towards others, but what of the victims? What programs and/or services are available to them? Do these services even help the victims? This Idea Paper will examine the effectiveness of the programs and services available to domestic …

Foster Care Placement And Law Enforcement Contact, Tranika Guerrero De Los Reyes

Theses and Dissertations

Interaction with law enforcement and delinquency are higher among youth in foster care, and they are likely to experience higher incarceration rates and be involved in criminality, which limits their access to education and employment. The problem addressed in this study was the elevated risk of law enforcement contact outcome (LEO) among adolescents and young adults with a history of foster care placement. The purpose of this quantitative research was to investigate differences in the number of LEO contacts and LEO arrests based on foster care placement type among youth in California’s foster care system.

Guided by the social control …

The Impact Of The Annapolis Police Athletic League On Youth Crime Prevention And Police-Youth Relationships, Talia Carol Lisko

Theses and Dissertations

The Annapolis Police Athletic League (PAL) was established as an initiative to prevent juvenile delinquency by fostering positive relationships between at-risk youth and law enforcement. The study explored the effectiveness of the PAL program using a generic qualitative research approach informed by the CIPP evaluation model. Semi-structured interviews with police officers and volunteer mentors involved in the program provided insight into the program’s implementation, outcomes, and its influence on youth crime prevention in the Annapolis community. The findings from this study contribute to a deeper understanding of community-based crime prevention and the role of law enforcement in promoting pro-social attitudes …

Mini-Maps, Crucial Or Controversial: Assessing The Influence Of Perceived Spatial Orientation And Cognitive Mapping Performance On Video Game User Experience, Angela Le

Doctoral Dissertations and Master's Theses

Decades of game studies, also known as video games research, have revealed frequent video gameplay is positively correlated with enhanced cognition. An area of study that is limited, however, is the relationship between spatial cognition, specifically the domains of spatial orientation and cognitive mapping and their effects on video game user experience for games employing visual navigational aids. Video game user experience is influenced by many factors such as graphics and audio, gameplay mechanics, user interface design, etc. The present study aims to explore whether spatial abilities influence and are significantly correlated with user experience for games using heads-up displays …