Digital Commons Network^™

Interpretable Machine Learning Of Plasma Proteomics Reveals Stage-Specific Signatures Across The Alzheimer's Disease Continuum, Hemshankar Laugi

2026 Spring Honors Capstones Projects

Alzheimer’s pathology begins years before clinical symptoms, starting early with amyloid-β accumulation, followed by tau deposition and neurodegeneration. Although existing tools, such as cerebrospinal fluid (CSF) screening and PET/MRI imaging, can accurately track disease progression, they are invasive, expensive, and not scalable for population-level screening. So, there is a growing interest in using blood-based plasma biomarkers as a scalable alternative. While recent studies demonstrate strong predictive performance with plasma biomarkers, most rely on a small set of canonical blood-based protein biomarkers such as amyloid-β, p-tau, and neurofilament light. These biomarkers primarily reflect downstream brain pathology and may fail to capture …

How Do Different Food Influents Affect Biogas Production, Process And Operational Stability, And System Performance In The Armfield W8, A Bench-Scale Anaerobic Digester, Jarko Rumbaoa, Anahita Adhikari

Rose-Hulman Undergraduate Research Publications

No abstract provided.

Center Of Mass (Com) Shift In Electric Vertical Takeoff And Landing (Evtol) Aircraft, Irene Lema Madueno

Rose-Hulman Undergraduate Research Publications

No abstract provided.

Sustainable Extraction Of A New Diketopiperazine, Anthony Chapman

Rose-Hulman Undergraduate Research Publications

No abstract provided.

Native Plants For Green Roofs In Indiana, Alasdair Curts

Rose-Hulman Undergraduate Research Publications

No abstract provided.

Evaluation Of Loading, Release, And Bioavailability Of Resveratrol Encapsulated In Porous Starch, Yu-Yun Wang

Graduate Theses and Dissertations

Resveratrol (Res) is a polyphenolic compound found in grapes, red wine, and berries, with health benefits such as antioxidant, anti-inflammatory, and cardioprotective properties. The poor stability and bioaccessibility of Res after consumption by humans require the development of delivery systems. Among many delivery systems, porous starch (PS) is a safe, cost-effective, and high in adsorption capacity encapsulation material for drugs and bioactive compounds sensitive to environmental factors like light and heat. Porous rice, corn, and potato starch have different granule sizes, pore volumes, and surface areas. However, the impact of these encapsulation capabilities remains unclear among the three porous starches. …

Nitrogen Use Efficiency Of Rice Expressing Arabidopsis Thaliana Dreb1a Gene, Yanis Anetha Vasquez Valdes

Graduate Theses and Dissertations

Rice is a globally consumed crop and feeds more than half of the world’s population. Nitrogen (N) fertilization is required for increasing rice crop production and yield, but producers often overuse N fertilizers, exceeding plant uptake capacity. Around 40% of the applied N is lost through volatilization and denitrification to the environment, causing algal bloom formation, greenhouse gas emissions, and water pollution. Therefore, improving nitrogen use efficiency (NUE) in rice has become a principal objective to achieve sustainable agriculture. NUE is a complex trait in rice that coordinates three processes: nitrogen uptake, transport and assimilation, which together support photosynthesis, biomass …

Evaluation Of Thresholds For Adult Tarnished Plant Bug, Lygus Lineolaris (Beauvois), In Thryvon® Cotton, William Anderson Fletcher

Graduate Theses and Dissertations

Tarnished plant bug (TPB) is the most economically damaging insect pest of Mid-South cotton. TPB reduces yield is reduced by damaging squares, terminal growth, and small bolls, resulting in reduced yield. Currently, cotton grown in the Mid-South averages 1-6 insecticide applications per year for control of TPB. The introduction of ThryvOn® cotton technology provides a new management strategy for TPB control. ThryvOn® technology produces the Bacillus thuringiensis (Bt) protein Mpp51Aa2, which has insecticidal activity on TPB. A field study was conducted at five locations in 2024 and seven locations in 2025 across the Mid-South to evaluate different threshold levels for …

Cryptic Habits: The Hidden Lives Of Midsouth Entomologists. Interview With Dr. Jerome Goddard, Mississippi Public Health Entomologist And Fiction Novelist, C. J. Peterson, Jerome Goddard

Midsouth Entomologist

No abstract provided.

Mosaic Loss Of Y Chromosome Associates With Lung Function, Emphysema, And Epigenetic Aging, Woei Yuh Saw, Kangjin Kim, Yichen Huang, Jeong H. Yun, Xiaolong Ma, Jason Bacon, Yash Pershad, Daniel Levy, George T. O’Connor, John Blangero

Human Genetics Publications

Rationale: As the global population ages, identifying risk factors for age-related diseases, such as COPD, is crucial for public health. Mosaic loss of Y chromosome (mLOY) in blood cells is an age-related somatic mosaicism event, but its relationship with pulmonary health remains undercharacterized. Objectives: To examine the association between mLOY and pulmonary outcomes in men. Methods: Leveraging mLOY assessment (cell fraction ≥ 5%) in over 12 000 men, including 5097 from the COPDGene Study and 7235 from six additional cohorts in the Trans-Omics for Precision Medicine program, we investigated mLOY associations with respiratory outcomes and epigenetic aging using multivariable cross-sectional, …

A Remarkable Diversity Of Syngnathid Fishes In A Highly Modified Large Coastal Embayment In The Southeastern Indian Ocean, Glenn I. Moore, Jenelle A. Ritchie, Georgia M. Nester, Glenn A. Hyndes, Alan J. Kendrick

Research outputs 2022 to 2026

Southern Australia supports a high diversity of fishes in the family Syngnathidae, which is recognised as globally threatened, facing threats from coastal development, over-exploitation and bycatch. In southwestern Australia, Cockburn Sound houses a large industrial port and naval defence assets with plans to substantially expand the port facilities but also sits within a recognised syngnathid ‘hotspot’. Using a broad array of data sources, including historical museum vouchers, published records, historical and contemporary observations from notebooks and diving surveys, historical and contemporary trawl surveys, citizen science observations and environmental DNA, we compiled 4839 records of syngnathid fishes from the embayment. Twenty-one …

Evaluation Of A High Protein Low Oligosaccharide Soybean Meal In Poultry Production, Kasey Matusik

Graduate Theses and Dissertations

The purpose of this study was to evaluate the influence of feeding a high protein, low oligosaccharide soybean meal to optimize poultry nutrition by the effects of feeding the soybean meal to roosters, broiler chickens, and turkeys. Two research objectives were evaluated to determine whether high protein, low oligosaccharide soybean meal would have increased nutritional value. The first objective assessed the metabolizable energy (ME) content of a high protein, low oligosaccharide soybean meal compared to a conventional soybean meal. Using roosters, broiler chickens, and turkey poults, three bioassays were conducted to evaluate the ME of the soybean meal. Results demonstrated …

Valorization Of Rice Bran For Functional Film Fabrication Using Cold Plasma For Food Packaging And Biomedical Applications, Saydul Md Safwa

Graduate Theses and Dissertations

Abstract Over the past few years, conventional plastic packaging materials have become increasingly concerned with their environmental impact. Therefore, the demand for bioplastics has been increasing significantly over the years. Rice milling, a process that modifies paddy rice into edible rice, generates by-products such as rice bran. Rice bran has cellulose, hemicellulose, lignin, and protein, which makes it a potential material for bioplastic fabrication. However, like most biodegradable films, rice bran films fall short when it comes to practical packaging applications. They often lack the strength, flexibility, moisture resistance, and barrier performance needed to compete with synthetic plastics. Most importantly, …

Identification Of Conditionally Essential Genes Required For Salmonella Enterica Serovar Typhimurium Adaptation To The Chicken Cecal Extract Through Ex Vivo Modeling And Transposon Insertion Sequencing, Deborah Bukola Olubanjo

Graduate Theses and Dissertations

Salmonella enterica serovar Typhimurium (S. Typhimurium) remains a major foodborne pathogen associated with chicken, where it can persist in the intestinal tract without overt disease and contribute to zoonotic transmission. The chicken cecum represents a complex ecological niche shaped by microbial competition, host-derived substrates, short-chain fatty acids, oxygen limitation, extracellular components, and diverse metabolic gradients. Although transposon insertion sequencing (Tn-seq) has been widely used to define bacterial fitness determinants, limited work has examined genome-wide adaptation of S. Typhimurium in chicken ceca-derived ex vivo systems that preserve key features of the avian cecal environment. This dissertation investigated conditionally essential genes required …

Afforestation Strategies In Semi-Arid Mediterranean Ecosystems: Experimental Evidence From Chmistar, Lebanon, Ahmad Saker, Mohammad Saleh, Wael Mostafa, Safaa Baydoun, Jamilah Borjac, Dalia El-Badan

BAU Journal - Science and Technology

The success rate of broadleaf tree growth in semi-arid Mediterranean environments is reduced in afforestation operations constrained by water scarcity, shallow soil depth, and intense competition from herbaceous vegetation. This study, conducted between 2022 and 2024 in Chmistar, East Lebanon, using a completely randomized block design, aimed to evaluate the impact of three planting broadleaf trees techniques (traditional digging pits , hoedad tools, and auger digging) and four effective vegetation control (herbicide application, mowing,  mulching, and no control) on the early growth of three native broadleaf tree species (Pistacia palaestina, Quercus calliprinos, and Quercus infectoria ).

The …

Lesson-3 On Mni Wiconi (Water Is Life): Analyzing Evidence And Communicating Solutions (Community Stewardship), Reycel Jugo, Madhav P. Nepal

iLEARN Teaching Resources

Students analyze the data collected from their filter tests, construct an evidence-based argument for their most effective design, and communicate their solution to a “community council” (the class), connecting their technological solution back to community well-being. In the final lesson, students will analyze their data, draw conclusions, and communicate their findings. They will present their improved water filter designs to the class, acting as consultants for the fictional community.

Problem-Based Learning (PBL) Scenario: Students are now ready to present their final water filter prototypes and a summary of their findings to a “community council” (the rest of the class). They …

The Development Of An In Silico Vaccine Design-Based E-Module To Improve Students' Biological Literacy, Qairinasherin Qwine Ferendi, Rusdi Rusdi, Hanum Isfaeni

Jurnal Pendidikan Sains

Low levels of biological literacy among students, particularly in biotechnology, highlight the need for innovative digital learning media that facilitate meaningful and contextual learning experiences. This study aimed to develop and evaluate an interactive biotechnology e-module based on in silico vaccine design to improve students’ biological literacy. The study employed Educational Design Research (EDR) using the Hannafin and Peck model, which consists of three phases: needs assessment, development, and implementation. The participants included 73 tenth-grade science students and one biology teacher from SMAN 68 Jakarta, Indonesia. The e-module was developed using Canva and Heyzine to create an interactive flipbook integrating …

Lesson-1 On Mni Wiconi (Water Is Life): Understanding The Problem Of Water Contamination, Reycel Jugo, Madhav P. Nepal

iLEARN Teaching Resources

Students investigate a scenario of water contamination in a fictional community. They define the engineering problem of dirty water and explore the cultural and ecological significance of water through the lens of indigenous principles. This lesson introduces students to the concept of water contamination and the need for purification, grounding the learning in a real-world problem and connecting to Indigenous knowledge about the land and water.

Problem-Based Learning (PBL) Scenario: Students receive a letter from a fictional community whose water source has become cloudy and is making people sick. They are tasked with becoming “Water Engineers” to investigate the …

Lesson-2 On Mni Wiconi (Water Is Life): Designing And Testing Solutions (Water Filtration), Reycel Jugo, Madhav P. Nepal

iLEARN Teaching Resources

Students apply the engineering design process to build, test, and refine a simple water filter prototype. This hands-on experiential learning activity focuses on the properties of filtering materials and iterative problem-solving.  In this lesson, students will apply the engineering design process to build and test their own simple water filters. They will use their newfound knowledge to begin developing a practical solution to the problem presented in Lesson 1 - Mni Wiconi: A Water Engineering Challenge for 4th Graders.

Problem-Based Learning (PBL) Scenario: Having identified the problem, students are now tasked with designing and building a prototype water filter …

Developing Biodegradable Packaging Films And Beads From Agricultural Residues, Sandeep Paudel, Santosh Rijal, Srinivas Janaswamy, Madhav P. Nepal

iLEARN Teaching Resources

Agricultural waste is produced in large amounts worldwide. These are often discarded despite being valuable sources of cellulose and renewable, biodegradable products. At the same time, rising environmental concerns about petroleum-based plastic packaging have created demand for sustainable alternatives. Introducing K-12 students to biodegradable packaging materials developed from agricultural waste can enhance understanding of sustainability, basic materials science, and circular bioeconomy concepts while encouraging interest in STEM fields. Another concern is the presence of microplastics and nanoplastics in drinking water, which can pose serious risks to human health. Traditional coagulation agents, such as ferric and aluminum salts, are less effective …

A Review On Nanoparticles: Classification And Roles In Plant Systems, Muhammad Junaid Zafar, Muhammad Shafiq, Muhammad Azeem Rana

Journal of Bioresource Management

Nanotechnology has been a new paradigm of the twenty-first century with several good breakthroughs. These tiny particles, known for their outstanding qualities, are enjoying an increasing influence in many research fields concerning foodstuff, cosmetics, electronics, and pharmacology. Synthesis of nanoparticles includes utilizing chemical processes with reducing agents, alongside employing physical techniques such as top-down and bottom-up approaches for NP formation. The biological approach, known as green synthesis, utilizes plant extracts to ensure increased safety. Biological methods also involve bacteria and fungi, known as the major sources of nanoparticles. It is acknowledged as the most effective and environmentally conscious approach, attributed …

Crispr/Cas9-Based Genome Editing: Understanding Differences In Dna Repair Pathways, Profiles, And Outcomes, Samuel Effah, Shirley Barrera, Nahia Urturi Ortiz, Will Dampier, Michael Nonnemacher, Brian Wigdahl

Kimmel Cancer Center Faculty Papers

Over a decade of advances in Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9)-based technologies have culminated in the first-ever FDA-approved CRISPR/Cas-based therapy. Aside from this approved therapy for sickle cell anemia, several CRISPR/Cas-based therapies are currently under development or testing for a range of chronic diseases, including viral diseases like human immunodeficiency virus type 1 (HIV-1) infection, genetic diseases like familial hypercholesterolemia, and cancer. The success of these therapies hinges on the effective delivery of CRISPR/Cas9 components to target regions, efficient Cas endonuclease editing, repair profiles generated, and their resulting outcomes. Here, we discuss the …

Operational Risk Assessment Of Ship To Shore Petroleum Transfer Using Fuzzy Rule-Based Bayesian Networks, Ayman F. Alghanmi

Journal of King Abdulaziz University: Marine Science

Petroleum ports represent critical infrastructure in global energy supply chains, where operational risks during ship-to-shore transfer operations can lead to catastrophic consequences including environmental damage and human casualties. Despite rigorous safety protocols, these facilities remain vulnerable to operational hazards in dynamic maritime environments. This research aimed to develop and apply a hybrid Fuzzy Rule-Based Bayesian Reasoning (FRBBR) model to identify, evaluate, and prioritize operational hazards during crude oil transfer operations at petroleum port berths, with a case study conducted in Saudi Arabia, addressing the challenge of risk assessment where historical data is limited.
The research employed a mixed-methods approach combining …

Microalgae As Sustainable Biofactories For Bioplastic Production: Challenges And Future Perspectives: A Review, Zahraa Hussein Obaid, Noor S. Naji, Jasim M. Salman, Layla Mustafa A.A. Alkatrani

Journal of King Abdulaziz University: Marine Science

The widespread use of traditional plastics, combined with their slow breakdown, has exacerbated environmental and health problems. Therefore, it has become imperative to find alternatives. Due to their simplicity of cultivation, quick growth, tolerance to challenging growing conditions, and low cost, microalgae are being used more frequently as a bio-source for bioplastics lately. Additionally, a variety of biopolymers, including polyhydroxybutyrate, polylactic acid (PLA), starch, polyhydroxyalkanoates (PHA), protein, and cellulose, could be produced by microalgae. These polymers show promising qualities including biodegradability, biocompatibility, and non-toxicity under various cultivation conditions. The purpose of this study is to demonstrate the potential of microalgae …

Magnetically Treated Water: Enhancing Stocking Density, Water Quality, And Growth In Nile Tilapia (Oreochromis Niloticus), Mortada M. A. Hussein, Ayatollah A. H. Abd-El Said, Asmaa N. Mohammed, Fatma M. M. Korni

Journal of King Abdulaziz University: Marine Science

This study aimed to explore the potential of using magnetic treated water (MTW) to increase stocking densities of growing Nile tilapia, Oreochromis niloticus, in storage, productive, and/or rearing holding facilities with limited mortality and water loss. The experimental period was 12 weeks, with 1500 O. niloticus fingerlings acclimated with maintained water parameters. After acclimation, 1350 were randomly selected and used for experiment setting up, including its triplicates. For each replicate, 225 fingerlings were distributed in three experimental tanks of MTW units as group set A, B and C, each received 50, 75, and 100 fingerlings, respectively. Besides, 225 fingerlings …

Environmental Assessment Of The Shatt Al-Basra Canal: Petroleum Hydrocarbons, Heavy Metals And Water Quality, Mohammed A. Jasim Aldoghachi, Bassam A. B. Alabdul Aziz, Shurooq Al-Mosawi

Journal of King Abdulaziz University: Marine Science

The environmental assessment of the Shatt al-Basra Canal in the area of the regulatory was studied. Petroleum hydrocarbons and heavy elements (cobalt (Co), zinc (Zn), lead (Pb), cadmium (Cd), and chromium (Cr)) in the waters of this area were analyzed. In addition, some water quality characteristics were evaluated (salinity, total dissolved solids (TDS), pH, oxygen, biological oxygen demand (BOD₅), chemical oxygen demand (COD), nitrate (NO_3^-), nitrite (NO_2^-), phosphate (PO₄ ^-3), and ammonia (NH₃). Petroleum hydrocarbons had been recorded in studied area and dominated with medium-chain alkanes, namely decane …

Impacts Of Coastal Development And Tourism On Fisheries And Aquatic Biodiversity Of The Red Sea: A Review, Lafi S. Al Solami

Journal of King Abdulaziz University: Marine Science

The Red Sea boasts a diverse coastal environment, unique coral reef biodiversity, and fisheries that support rapidly growing marine tourism. Its excellent tourism facilities make it a popular destination. However, intensive tourist activities such as swimming, boating, diving, and fishing have a negative impact on the coastal and marine ecosystem. Additionally, in line with Vision 2030, Saudi Arabia has launched mega projects along the Red Sea coast, increasing tourist activity and leading to human intrusion into critical yet vulnerable marine ecosystems like coral reefs, fish, sea grass beds, and mangrove stands. With the rise in tourism activities and disruptions to …

Coastal Landforms Analysis Of Al-Kharrar Lagoon And Rabigh Coast Using Aster (Ast_L1t) Imagery, Western Saudi Arabia, Omar A. Alharbi

Journal of King Abdulaziz University: Marine Science

The current study sought to examine the coastal geomorphology throughout the entire length of the Al-Kharrar Lagoon, in addition to the coastal region of Rabigh City, situated on the western coast of Saudi Arabia. The mechanisms underlying the formation of the wide variety of natural land features were also studied. These include sandy, pebble and rocky beaches and sand dunes; intertidal areas; salt flats (sabkhas) and marshes; elevated, terraced or fringing coral reefs; water inlets; and the deposition of terrigenous or alluvial materials, all reflecting the swift transformation that has impacted the region. Evaluation of the ASTER (AST_L1T) data enabled …

Multi-Label Seabed Image Classification: A Comparative Study Of Deep Learning And Machine Learning Models, Anis Bel Hadj Hassin, Elyes Omri

Journal of King Abdulaziz University: Marine Science

This study evaluates the effectiveness of deep learning and machine learning models for classifying seabed images into three ecologically significant categories: algae, rocks, and sand. We investigated five models: ResNet50, VGG16, a custom-designed convolutional neural network (CNN), support vector machines (SVM), and random forests (RF). Deep learning models were fine-tuned on 1259 seabed images, with the custom CNN architecture optimized using depthwise separable convolutions and global average pooling. For SVM and RF, features were extracted using a pre-trained VGG16 network. Class weighting was applied to address potential imbalances in the dataset. The custom CNN achieved the highest validation accuracy (82.01%), …

Dynamical Behavior, Extinction And Persistence In A Stochastic Delayed Two-Strain Epidemic Model With A Generalized Crowley-Martin Incidence Rate, Amina Allali, Dounia Bentaleb, Saida Amine

Mathematical Modelling and Numerical Simulation with Applications

This paper develops and analyzes a novel delayed stochastic SIR epidemic model with two interacting strains and general incidence functions. By establishing the existence and uniqueness of a positive global solution, the well-posedness of the model under stochastic perturbations is ensured. Extinction occurs when the stochastic reproduction number falls below unity, as demonstrated through Itô calculus and martingale convergence theorems, while persistence is guaranteed under the Crowley–Martin incidence when it exceeds one. Numerical experiments based on the Positive Preserving Truncated Euler–Maruyama (PPTEM) scheme confirm the analytical predictions and highlight the influence of time delay and noise intensity on the long-term …