Medicine and Health Sciences Commons^™

Attention-Based Multi-Omics Fusion For Drug Synergy Prediction, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug combination therapy in disease management gained popularity in the last few decades. Computational modeling of such combinations is an active area of research in the drug discovery domain. While earlier approaches solely emphasized on the structural features of participating drugs for designing synergistic models, they lack other crucial factors directly linked with drug administration - omics expressions. As differential omics expression is a downstream consequence of the administered drug combinations, utilizing such expressions while designing synergistic models promises robust and dynamic modeling. In this work, we propose SynergyLM that fuses multi-omics features with drug embeddings to build an omics-aware …

Fumigant Toxicity Of Essential Oils From Chemotypes Of Curry Tree (Murraya Koenigii) Against Adult African Malaria Mosquito (Anopheles Gambiae Sensu Stricto), Clarence M. Mang’Era, Fathiya M. Khamis, Ahmed Hassanali, Paul O. Mireji

All Peer-Reviewed Publications

The toxicity of fumigant formulations of essential oils (EOs) from curry tree (Murraya koenigii (L.) Spreng (Rutaceae)) against African malaria adult mosquito (Anopheles gambiae sensu stricto (Giles, 1902) (Diptera: Culicidae: Culicini)) was evaluated to identify most effective chemotype of the curry tree against the mosquitoes. Ninety-two compounds (91.78%–96.47% coverage) in the EO profiles were identified, among which EO isolated from curry tree chemotype from Kibwezi was most toxic. This chemotype had a median lethal dose (LD50) of 3.6 × 10⁻³ mg/cm³ (95% CI: 2.70–4.58) and a lethal time (Ti50) of 1.91 ± 0.086 h (p < 0.001). The equivalent LD50 of EOs of chemotypes from Mombasa, Makindu, and Malindi in Kenya was 4.9 × 10⁻³, 6.6 …

Near Real-Time Adaptive Isotropic And Anisotropic Image-To-Mesh Conversion For Cerebral Aneurysm Simulations, Kevin Garner, Chander Sadasivan, Nikos Chrisochoides

Computer Science Faculty Publications

This paper presents two performance optimization techniques for a mesh adaptation method that is designed to help streamline the discretization of complex vascular geometries within the numerical modeling process. This method is integrated into a pipeline with an image-to-mesh conversion tool to generate adaptive anisotropic meshes from segmented medical images. The pipeline is shown to satisfy quality, fidelity, smoothness, and robustness requirements while providing near real-time performance for medical image-to-mesh conversion. Tested with two brain aneurysm cases and utilizing up to 96 CPU cores within a single, multicore node on Purdue University’s Anvil supercomputer, the parallel adaptive anisotropic meshing method …

Adaptive Self-Attention For Enhanced Segmentation Of Adult Gliomas In Multi-Modal Mri, Evan P. Savaria, Jiangwen Sun

Computer Science Faculty Publications

Every year there are an estimated 80,000–90,000 new glioma cases, highlighting the need for reliable imaging-based decision support. Although deep learning has improved tumor sub-region segmentation, many state-of-the-art models fail to fully capture complementary information across T1, T1Gd, T2, and FLAIR MRI modalities and often operate as “black boxes,” limiting physician trust when precise delineation is critical for surgical planning, radiation targeting, and treatment monitoring. To address these limitations, we propose AIMS, an Adaptive Integrated Multi-Modal Segmentation framework that maintains modality-specific feature streams and employs adaptive self-attention within a hierarchical CNN-Transformer architecture to prioritize and fuse multi-modal MRI features. We …

Sage: Spatially Aware Gene Selection And Dual-View Embedding Fusion For Domain Identification In Spatial Transcriptomics, Yi He, Yunpei Xu, Liqing Ding, Hong-Dong Li, Yaohang Li, Shaokai Wang

Computer Science Faculty Publications

Despite enabling high-resolution mapping of gene expression within tissues, spatial transcriptomics (ST) still faces challenges in accurately segmenting spatial domains due to complex tissue architecture and limitations of current methods. Most approaches rely on local spatial priors, lack gene-level interpretability, and fall short in capturing structure-discriminative genes or long-range functional relationships, limiting their ability to resolve biologically meaningful architectures. We present Spatially Aware Gene selection and dual-view Embedding fusion (SAGE), a unified and reproducible framework for domain identification in spatial transcriptomics that combines topic-driven gene selection with dual-view embedding fusion to address these gaps. SAGE integrates non-negative matrix factorization (NMF)-based …

Analysis Theories On Artificial Intelligence, Chatgpt, Data Science, And Metaverse: The Case Of Digital Medicine, Yin Yang, Xingyun Liu, Jorge Luis Cuyubamba Dominguez, Yuan Fang, Wen Xie, Bairong Shen, Keng Siau

Research Collection School Of Computing and Information Systems

Healthcare organizations are increasingly adopting digital technologies, with Artificial Intelligence (AI), Data Science, and the metaverse driving significant advancements in smart healthcare. Al facilitates personalized medicine and efficient drug development, while Data Science enables predictive analytics and big data management, enhancing patient outcomes and healthcare quality. The metaverse introduces immersive training and telemedicine platforms, revolutionizing patient engagement and healthcare research. This study conducts' a scoping review of 6,171 articles, analyzing the transformational impact of AI, ChatGPT, Data Science, and the metaverse on healthcare. It highlights the benefits and risks of these technologies, identifies research gaps in their application within the …

Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du

Electronic Theses & Dissertations (2024 - present)

RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.

The first part of this dissertation focuses on establishing …

Error-Driven Density Control For Compact Gaussian Splatting Under Sparse Supervision, Abdelrhman Elrawy

Theses and Dissertations (Comprehensive)

This thesis studies efficiency and stability challenges in Gaussian-splatting-based reconstruction under sparse supervision. In few-shot novel view synthesis, standard 3D Gaussian Splatting (3DGS) can overfit the limited training views and grow an unnecessarily large number of primitives due to limitations in its Adaptive Density Control (ADC) mechanism. This thesis introduces an error-driven reformulation of ADC that triggers densification using opacity gradients as a lightweight proxy for rendering error, and shows that such aggressive densification must be paired with delayed and conservative pruning to prevent destructive create--destroy cycles. When combined with depth-based geometric regularization, the resulting framework produces substantially more compact …

Designing Narrative-Based Ai Assistance For Sensemaking In Collaborative Environments: Case Studies In Education And Dementia Care, Dylan Edward Moore

Dartmouth College Ph.D Dissertations

This thesis addresses a gap in the human-computer interaction literature regarding the design, development, and evaluation of narrative-based AI assistance for collaborative, complex problem solving. I explore this design space through three case studies across the domains of education and dementia care. This work encompasses multi-year industry partnerships and longitudinal fieldwork, user-centered design, dataset curation, model training, and system evaluation.

Specifically, the first case study considers a story-based web platform for teaching AI literacy through peer-generated, personalized narrative scaffolding. Learners on the platform showed significant knowledge gains and other learning-related outcomes. To describe the novel design of this system, I …

A Novel Mathematical Model Of Hiv Transmission Incorporating The Effects Of Treatment And Pre-Exposure Prophylaxis: Sensitivity Analysis And Numerical Simulations, Erick Manuel Delgado Moya

Mathematical Modelling and Numerical Simulation with Applications

Human immunodeficiency virus (HIV) continues to be a public health problem in many countries of the world, and Pre-exposure prophylaxis (PrEP) is a preventive method for HIV, which has shown great efficacy and is in use worldwide. This work presents a new mathematical model for HIV transmission incorporating PrEP use and evaluates the impact of PrEP along with its increasing use in a population. The construction of the model takes into account three forms of diagnosis: diagnosis of individuals in risky sexual contact, diagnosis after risky contact (diagnosis in the undiagnosed infected compartment), and diagnosis associated with attempting to enter …

Analysis And Numerical Investigation Of A Breast Cancer Treatment Model Incorporating Ketogenic Diet And Immune Boosters Via Optimal Control Theory, Kunnisai Muniroh, Ummu Habibah, Wuryansari Muharini Kusumawinahyu, Nur’Izzati Hamdan

Mathematical Modelling and Numerical Simulation with Applications

This paper develops a mathematical model to investigate breast cancer dynamics by incorporating tumor–immune interactions, ketogenic diet effects, and medical treatment. The model is formulated as a system of nonlinear ordinary differential equations and analyzed within an optimal control framework. Time-dependent control variables are introduced to represent treatment strategies aimed at minimizing tumor progression while reducing therapeutic costs. The model’s well-posedness is established through positivity and boundedness analysis. The necessary conditions for optimality are derived using Pontryagin’s Minimum Principle, resulting in a coupled system of state and adjoint equations. Numerical solutions are obtained using the fourth-order Runge–Kutta method combined with …

Mathematical Analysis And Numerical Simulation Of A Fractional-Order Sir-Si Model For Malaria Transmission Dynamics, Gassan A. M. O. Farah, Abdulaziz Y. A. Mukhtar, Kailash C. Patidar

Mathematical Modelling and Numerical Simulation with Applications

This study investigates the complex transmission dynamics of malaria, a critical global health challenge, with a focus on the African continent. We introduce a novel approach that employs Fractional Differential Equations (FDEs) to advance the understanding of malaria spread and control. Specifically, we develop a new SIR-SI model using the Caputo fractional operator, which captures the memory effects and time-delay characteristics inherent in real-world epidemiological systems. A detailed analysis of the model's solvability and uniqueness is conducted using fixed-point theory. To obtain an analytical solution, the system is solved via the Laplace transform method, with solutions expressed in closed form …

Panda-Plus: Improved Dataset Of Prostate Whole Slide Images From Panda Challenge With Pixel-Level Expert Annotations, Spencer Hopson, Carson Mildon, Corbyn Kubalek, Joshua L. Ebbert, Ryan Vance, Lauren Laverty, Paul Urie, Dennis Della Corte

Faculty Publications

Artificial intelligence (AI)-based prostate cancer detection through whole slide images (WSIs) offers promising potential to address the global pathologist shortage while improving clinical consistency. Digital slides and improving image analysis methods encourage the creation of tools to aid in WSI classification. Despite promising advances, these tools are still limited by available training data. Current publicly available datasets, such as Kaggle's PANDA Challenge, while large in scale, rely on slide-level labels that may introduce noise and limit model reliability. Others contain detailed annotations, but are smaller in size due to manual processing efforts. In this work, we introduce PANDA-PLUS, a 546-image …

Physicochemical, Pharmacognostic Standardisation And Phytochemical Analyses Of The Homoeopathic Drug Justicia Adhatoda, Bibaswan Biswas, Satish Patel, Digvijay Verma, Satyajit Maity, Shilpi Singh, Paulami Majumdar, Narasimha Kumar Gv

Indian Journal of Research in Homoeopathy

Background: Justicia adhatoda (J. adhatoda), also well known as Vasaka in India is a medicinal plant chiefly used to treat respiratory ailments in traditional and alternative medical systems. Objective: This study aimed to establish the physicochemical, pharmacognostic, and phytochemical standardisation parameters of the drug. The study involved the measurement of physicochemical parameters and chemical profiling of the raw drug. The chemical characteristics of the in-house mother tincture (prepared from in-house raw drug) and commercial mother tinctures available in India were also evaluated to assess the quality of commercially available mother tinctures. Materials and Methods: The present study …

Perspectives On Implementing Environmentally Sustainable Practices In Cataract Surgeries: Interviews Of Administrative And Frontline Healthcare Workers, Daniel Parra, Brooke Sherry, Emma Pak, Lauren Taylor, Erin S. Rogers, Sarah E. Hochman, Maria De Los Angeles Ramos Cadena, Joel S. Schuman, Christina R. Prescott, Cassandra L. Thiel

Wills Eye Hospital Papers

BACKGROUND: Healthcare is responsible for 8.5% of greenhouse gas emission in the United States. Physicians are becoming increasingly concerned about the climate crisis, particularly in the field of ophthalmology where there is a growing body of literature related to sustainability. Although emissions of cataracts surgery, one of the most performed surgical procedures in the world, have been quantified, modifications to practice have yet to be made. This study aims to uplift the perspectives of a diverse set of healthcare workers on implementing environmentally sustainable practices in the cataract surgery setting.

METHODS: 16 semi-structured interviews were conducted with professionals working in …

Quantitative Structure-Activity Relationship, Pharmacokinetics, Drug-Likeness, Toxicity, And Molecular Docking Studies Of 4-N-(Methyl)-4-Aminoquinoline Derivatives As Antimalarial Compounds, Muhamad Jalil Baari, Devi Hardiyanti

Makara Journal of Science

Antimalarial drug resistance has encouraged various innovations to develop novel drug compounds that are effective, feasible, and safe, adhering to health standards. One way to do that is by observing and predicting the biological activity of drug compounds using quantitative structure–activity relationship (QSAR) analysis. In this study, QSAR analysis was conducted on the 4-N-(methyl)-4-aminoquinoline derivatives, which effectively inhibit the growth of Plasmodium falciparum as a source of malaria. The research stages involved molecular structure modeling, molecular geometry optimization using the AM1 semi-empirical method, and QSAR descriptor calculations, including electronic (atomic charges (q), HOMO and LUMO energies, polarizability (α), …

Suitability Of Mobile Phase Recycling For Methylxanthine Quantification In Coffee Samples Using Hplc, Kaitlin O’Keeffe, Marcos Mariano, Brian Murphy

SURE Journal: Science Undergraduate Research Experience Journal

Caffeine, theobromine and theophylline fall under a drug class known as methylxanthines. These three compounds are of major interest in the food industry due to their presence in popular foods and beverages such as tea, coffee, and chocolate. As these compounds can cause physical and mental stress at high dosages, their quantification is essential to ensure product safety and quality. Here, we describe an eco-friendly HPLC method developed to quantify the amount of these analytes in coffee samples sourced across the SETU Waterford, Cork Road campus. Using an isocratic mixture of water and methanol, a mobile phase recycling approach was …

Developing A Tool To Measure Resistance To Sustainable Food Choices: A Pilot Study In Ireland And The Netherlands, Kate Flanagan, Bart Sinteur, Patricia J. Bulsing, John M. Kearney

SURE Journal: Science Undergraduate Research Experience Journal

Consumer uptake of a sustainable diet is critical for addressing environmental challenges and promoting public health. Understanding why consumers resist adopting sustainable eating habits can inform targeted interventions and policies. This pilot study examines whether a newly developed scale can effectively detect consumer resistance to a sustainable diet. Currently, there is a lack of research on a tool to measure consumer resistance to a sustainable diet, highlighting the need for a reliable instrument.

The aim of this study is to develop a scale, based on existing literature, to measure consumer resistance to a sustainable diet. Additionally, the study aims to …

Editorial-Sure Journal Volume 7, Issue 2, Geraldine M. Dowling, Eva Campion, Sinead Loughran, Ariane Perez-Gavilan, Josephine Treacy

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Assessment Of Polymeric Chloroquine Formulations For Targeted Therapy Of Ulcerative Colitis And Metastatic Colorectal Cancer, Neha Kumari

Theses & Dissertations

Effective targeted drug delivery is a critical unmet need in the management of both ulcerative colitis and metastatic colorectal cancer, where conventional systemic therapies may be hindered by suboptimal efficacy and significant side effects. This thesis explores the development and preclinical assessment of polymeric chloroquine (PCQ)-based nanotherapeutics, leveraging stimuli-responsive designs for disease-specific delivery and action.

For ulcerative colitis, a reactive oxygen species (ROS)-responsive nanogel system was engineered to release PCQ, a macromolecular derivative of hydroxychloroquine, specifically in the inflamed areas within the colon. Nanogels with well-defined size and positive surface charge were synthesized via reversible fragmentation chain transfer (RAFT) polymerization …

Validating Pharmacogenomics Generative Artificial Intelligence Query Prompts Using Retrieval-Augmented Generation (Rag), Ashley Rector, Beth Breeden, Jay Dorris

Student Scholar Symposium

This study evaluated the performance of Sherpa Rx, an artificial intelligence platform leveraging large language models and retrieval-augmented generation (RAG) for pharmacogenomics, by validating its performance across key response metrics. Sherpa Rx integrated Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines with Pharmacogenomics Knowledgebase (PharmGKB) data to generate contextually relevant responses. A dataset (N=260 queries) spanning 26 CPIC guidelines was used to evaluate drug-gene interactions, dosing recommendations, and therapeutic implications. In Phase 1, only CPIC data was embedded; Phase 2 additionally incorporated PharmGKB. Responses were scored on accuracy, relevance, clarity, completeness (5-point Likert scale), and recall. Wilcoxon signed-rank tests compared accuracy between …

Spilling The Tea: Effects Of Uv Disinfection On Bioactive Compounds In South African Rooibos Tea, Sora Ghanem, Leah Ankiah, Yusra Ahmed

Student Scholar Symposium

This study investigated the effects of ultraviolet (UV) light disinfection on key bioactive flavonoid compounds in rooibos tea (Aspalathus linearis). There is an interest in non-thermal food preservation technologies, and UV treatment offers potential advantages for beverage processing. However, concerns exist regarding possible degradation of health-promoting compounds during treatment. Rooibos tea samples were subjected to five UV exposure intensities (0, 25, 50, 75, and 100 mJ/cm²), and concentrations of four major flavonoids (aspalathin, orientin, vitexin, and rutin) were measured using high performance liquid chromatography (HPLC). Surprisingly, most flavonoids showed stability or slight concentration increases at higher UV doses. Aspalathin concentrations …

Exploration Of Euclidean Distances In Five-Dimensional Color Space As Proof-Of-Concept For Identification Of Promising Alternatives To Platinum-Based Cancer Drug Candidates, Kiomi Tanakura, Elena G. Harvey

Student Scholar Symposium

Cisplatin, cis-Pt(NH₃)₂Cl₂, is one of the most successful anticancer drugs of all time. However, it has some negative aspects, including toxicity to healthy cells, side effects, and cost. Our goal in this project is to design metal-based anticancer drugs that would be less expensive, less toxic, and more efficient for cancer patients than cisplatin. To begin this research we calculated Euclidean distances - as used by computerized recognition systems - to compare the properties of colors within seasonal palettes that are proven and visible to the eye. These Euclidean distances were then used …

Unveiling Hidden Hazards: A Complementary Approach To Affordable Non-Destructive Heavy Metal Detection, Mario Faragalla, Gulsin Barwari, Makenzie Brinkoeter, Eimy Lozano-Fuentes, Isabelle Riera

Student Scholar Symposium

History has bestowed upon us vast treasures, with the Victorian Era offering a wealth of gifts, such as vibrant art and even secrets preserved in books of this period. However, concealed within the pigments that bring these works to life lie heavy metals. Not only do they pose significant health risks, but they can also be found within these pieces centuries later. Intrigued by the Winterthur project, Beaman librarians, Jan Cohu and Kayla Rutledge, discovered that our library housed some of these Victorian Era books. From there, the Beaman staff sent an inquiry to the chemistry department and Dr. Weinstein-Webb …

Importance Of Sustainability Within Children’S Hospitals, Ashley Newby

Student Scholar Symposium

Author: Ashley Newby

Presentation Type: Poster

Faculty Mentor: G. Dodd Galbreath

Discipline: Sustainability and Pediatric Nursing

Importance of Sustainability within Children’s Hospitals

Sustainability is an important aspect of every environment that one encounters. For pediatric patients entering a children’s hospital, it is probably not something that is important and at the top of their list when looking for healthcare. However, sustainable children’s hospitals have not only their patients as their first priority, but they also take the earth into account. Some might not realize that they are walking into a sustainable children’s hospital unless someone tells them.

Topics include:

-Look …

Is Ai Replacing Human Mental Health Professionals?, Michiko Ueda

Population Health Research Brief Series

An increasing number of people are turning to generative artificial intelligence (AI) tools and AI-assisted chatbots to manage mental health concerns. This data slice presents findings from a national survey of U.S. adults aged 18-49 (N = 1,805) conducted in October 2025. Among respondents, 35.2% reported using AI tools more than once a week for mental health support. Among those who had ever seen a human mental health professional, 28.4% reported visiting human providers less often since beginning to use AI for the same purpose. The findings suggest that a subset of users may be using AI to replace, rather …

Analysis Of Leakage In Nearshore Pipelines Using Fitness For Service Method To Ensure Mechanical Integrity Based On Api-579 Level 3, Elriandri Elriandri, Dedi Priadi

Journal of Materials Exploration and Findings

The Fitness for Service (FFS) analysis is performed as a quantitative assessment to evaluate the integrity condition of a pipeline. Essentially, FFS assessment helps determine whether equipment components can operate safely despite existing deficiencies. This evaluation is carried out using the Finite Element Method (FEM). In the case of an underwater pipeline that experiences leak due to anchor pull at the flange connection, it undergoes plastic deformation and is lifted approximately 1 meter. As a mitigation step, inspection and repairs have been carried out by the company. Subsequently, modeling is performed to reconstruct the deformation process of the pipeline. Then, …

Assessment Of The Melt Quality Of A 30% Scrap Adc12 Aluminium Alloy Using The Inclusion And Fluidity Measurement Instrument (Ifmi) With Mullite Ceramic Filters, Gusti Ruri Ruri Lestari, Sandya Ananda Riswan, Muhammad Anis, Ahmad Ashari, Paramita Vidya Ayuningtyas, Bambang Suharno Prof, Donanta Dhaneswara

Journal of Materials Exploration and Findings

The increasing demand for sustainable practices in the metal casting industry has driven the use of recycled aluminum alloys such as ADC12. However, the addition of aluminum scrap tends to increase oxide inclusions, which reduce melt fluidity and compromise casting quality. This study utilizes the Inclusion and Fluidity Measurement Instrument (IFMI), equipped with mullite ceramic filters, to assess the melt quality of ADC12 aluminum alloy containing 30% scrap. Fluidity and inclusion characteristics were evaluated at five pouring temperatures (660°C, 680°C, 700°C, 720°C, and 740°C). The results show that fluidity increased with temperature, reaching a peak of 84.6 g·s⁻¹ at 740°C, …

Equipment Criticality Analysis To Determine Asset Integrity Management System Scheme In Supporting Production Optimization Scenarios In The Aeging Field, Donny Andryanto, Donanta Dhaneswara

Journal of Materials Exploration and Findings

This research investigates the production decline and cost increase in the X&Y oil and gas fields from 2022 to 2023. Production fell by 34%, while production costs per barrel rose by 79%. To address these issues, a series of optimization processes are proposed. These aim to restructure and enhance the production facilities to reduce current production costs. The optimizations include reducing pressure at the PPP Platform in 2024. Additional steps include shutting down CPP-ORF 14” pipelines and most processes at CPP 2 Platform by 2027 to convert it into an accommodation platform. Further, the plan involves optimizing the release of …

Morphological Test Of Areca Nut Fiber Ceramic Membrane Using Scanning Electron Microscopy Energy Dispersive X-Ray Mapping Spectroscopy, Amelia Marzain, Siti Umi Kalsum, Marhadi Marhadi, Ahmad Nabil Shahab

Journal of Materials Exploration and Findings

This study investigates the potential of ceramic membranes derived from areca nut fiber as a cost-effective and environmentally sustainable material for the removal of iron (Fe) and manganese (Mn) from groundwater. Two types of membranes were fabricated: one without activation and one chemically activated using 10% sodium hydroxide (NaOH). The morphological and elemental characteristics of both membranes were analyzed using Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray (EDX) mapping. The concentrations of Fe and Mn before and after treatment were measured using Atomic Absorption Spectroscopy (AAS). The NaOH-activated membrane exhibited a more porous surface structure and higher oxygen content, …