Digital Commons Network^™

Bridging Physiology, Data Science, And Genomics To Illuminate Photosynthetic Variation In Sunflower, Rebekah E. Davis

Graduate Thesis and Dissertation post-2024

Photosynthesis is a critical metabolic process in plants involving ‘light reactions’ that capture solar energy to produce ATP and NADPH, and ‘dark reactions’ where these molecules power the enzyme Rubisco to synthesize sugars in the Calvin-Benson cycle. These processes serve as the primary energy source for plant growth and reproduction, displaying significant variation across species and environments. In Helianthus, distinct differences in photosynthetic traits are observed between annual and perennial species. Notably, carboxylation rates, photon capture, and maximum photosynthetic rates show strong phylogenetic signal (Pagel’s λ = 0.99) and are significantly higher in annuals. Photosynthesis is modeled here as a …

Skeletal Embodiment Of Structural Violence: Testing Application Of The Weathering Hypothesis In Analyses Of Identified Sex, Jasper K. Shaw

Graduate Thesis and Dissertation post-2024

Structural violence refers to the experiences of inequality faced by marginalized sex, gender, race, and socioeconomic groups. Unequal access to healthcare, housing, and education can cause poor health that may affect how a decedent is analyzed by forensic anthropologists. This research hypothesizes that, due to gender- and sex-based marginalization, females will display greater rates of stress and correlated accelerated aging (i.e., weathering), than males. Computed tomography scans from 100 males and 99 females aged 20-69 years old and white and middle class, were sampled from the New Mexico Decedent Image Database (NMDID). Stress was assessed via cranial porosities, antemortem tooth …

Change Point Monitoring In High-Dimensional Factor Models, Mahdi Mirhosseini

Graduate Thesis and Dissertation post-2024

This dissertation presents the Factor-Augmented Detection (FAD) algorithm, a robust methodological framework for online change point detection in high-dimensional data streams, grounded in classical factor model analysis. To tackle the challenges of monitoring large-scale datasets, the FAD algorithm decomposes data into a parsimonious set of common factors and sparsely changing idiosyncratic residuals, facilitating independent, targeted analysis of low-dimensional factor dynamics and sparse high- dimensional residual evolution.

Following decomposition, structural changes in the factor components are identified using established multivariate sequential monitoring techniques, specifically the Multivariate Cumulative Sum (mCUSUM) and Multivariate Exponentially Weighted Moving Average (mEWMA) procedures. Simultaneously, sparse alterations in …

Kinetic Model Of Glycolysis And Glutaminolysis Interplay Developed In Matlab Simbiology, Zohreh Mirveis, Hugh J. Byrne, Nitin Patil

Datasets

This dataset contains a kinetic model developed in MATLAB SimBiology to simulate the metabolic dynamics of glycolysis and glutaminolysis and their interconnection. The model was used in the study ‘Experimental and computational investigation of the kinetic evolution of the glutaminolysis pathway and its interplay with the glycolysis pathway’ (Mirveis et al., 2024). The dataset includes the original SimBiology project file together with the experimental data used for model training. These resources enable reproduction of the simulations reported in the publication and provide a reusable framework for further computational exploration of metabolic pathway kinetics.

Lowering The Barrier For Reading Primary Literature In Stem, Sebastian G. Alvarado, Maral Tajerian

Open Educational Resources

Building Bridges of Knowledge (BBK) is a cross‑CUNY initiative that integrates artificial intelligence (AI) and open educational resources to lower the barrier to primary literature and enhance research‑focused pedagogy. Recognizing that scientific papers are often dense and inaccessible to newcomers, we developed a suite of AI‑assisted instructional materials and activities to help students interpret complex data and methodology. A central component is the use of large language models (LLMs) and tools such as Scite.ai to provide citation‑context analytics and personalized research support. These tools allow students to filter literature by supportive, neutral, or contrasting citation statements and to troubleshoot laboratory …

Exploring Senescence For Improved Diagnosis And Treatment In Head And Neck Cancer, Md Tanjim Alam

Graduate Thesis and Dissertation post-2024

Head and Neck Squamous Cell Carcinoma (HNSCC) comprises a heterogeneous group of malignancies originating from the mucosal epithelium of the oral cavity, pharynx, and larynx. Accounting for approximately 4.5% of global cancer incidence and mortality, HNSCC poses a persistent public health concern. Major risk factors include tobacco use, alcohol consumption, and infection with high-risk Human Papillomavirus (HPV) strains. Although conventional treatments such as surgery, chemotherapy, and radiotherapy have improved patient outcomes, therapeutic resistance and tumor recurrence remain significant challenges. A growing body of evidence implicates therapy-induced cellular senescence as a key mechanism in treatment resistance. Senescence is a stable state …

Targeting Il-6 Signaling And Release Pathways Modulates Inflammation And Restores Intestinal Epithelial Integrity And Function During Mycobacterium Avium Paratuberculosis Infection, Ala' Mahmoud Saleem Alhendi

Graduate Thesis and Dissertation post-2024

Like TNFα, IL-6 is upregulated in Crohn’s disease (CD) associated with Mycobacterium avium paratuberculosis (MAP) infection. Limited therapeutic response to anti-IL-6 therapy may be related to the dual role of IL-6. In this study, we investigated the effects and the signaling mechanism of IL-6 in intestinal epithelial integrity and function during MAP infection using an in vitro model that consists of THP-1, HT-29 and Caco-2 cell lines. Clinically, we determined that plasma samples from MAP-infected CD patients have higher IL-6 levels compared to controls (P-value < 0.001). In CD-like macrophages, MAP infection has significantly upregulated the secretion of IL-6 and the shedding of IL-6 receptor (IL-6R). Moreover, it resulted in significant upregulation of intestinal damage markers including CLDN2, NOX-1 and SERPINE1. Blocking IL-6 signaling exacerbated that damage and enhanced the levels of the damage markers. In HT-29 cells, MAP infection upregulated MUC2 expression, a protective response that was reversed when IL-6R was neutralized. More importantly, blocking IL-6 signaling during MAP infection rescued damaged Caco-2 cells from MAP-induced apoptosis. We also examined the role of monocarboxylate transporter 4 (MCT4), a proton-coupled lactate symporter, that facilitates the inflammatory shift in macrophages, and its impact on intestinal epithelial homeostasis during MAP infection. MAP infection increased lactate export and upregulated the expression of MCT4, TNFα, and IL-6 via TLR2. Inhibition of MCT4 during MAP infection using α-cyano-4-hydroxycinnamic acid (CHCα) significantly reduced TNFα and IL-6 and led to restoring baseline oxidative status, mucin level, and SERPINE1. It also enhanced tight junction protein TJP1 (ZO-1) expression. These findings emphasize the role of IL-6 in MAP-associated CD pathogenesis and explain the ineffective response to IL-6 therapies in CD patients. Moreover, our findings revealed the role of MCT4 in CD pathophysiology during MAP infection and highlighted MCT4 as a potential therapeutic target for effective CD treatment.

Wavefront Sensing Using Nonlocal Metasurfaces, Arturo Martin Jimenez

Graduate Thesis and Dissertation post-2024

Many laser applications require wavefront control to compensate for aberrations caused by system misalignment, component fabrication errors, and propagation through inhomogeneous atmospheres. Aberrations caused by atmospheric turbulence remain particularly challenging to measure due to the temporally fluctuating wavefront distortions and large transverse phase variations in the beam. Conventional wavefront sensors, like the Schack-Hartmann (SHWS) are effective at low turbulence levels, but require relatively bulky optical elements. This thesis investigates the use of metasurface optical elements for use in wavefront sensors both in the low-turbulence limit and in deep turbulence conditions. Such metasurface-based wavefront sensors can achieve the functionality of complex …

You And Me: Imagination As A Coping Mechanism For Childhood Trauma, Rachel B. Sacks

Graduate Thesis and Dissertation post-2024

You and Me is a two-dimensional (2D) animated short film about a young girl who suffers from an unknown illness. As she tries to rest, two otherworldly monsters transform her room into an unsettling nightmare. These monsters stem from her own distorted perceptions of the doctor and nurse caring for her. You and Me focuses on the difficulties that children navigating medical challenges face in communicating their fears with their caretakers. It is a film rooted staunchly in the subjective world of its protagonist. The art style deliberately combines conventionally appealing character design with surrealist imagery and evocative, unsettling lighting …

Digitally-Mediated Nature-Connectedness?: Listeners’ Emotional Responses To And Perception Of Digitized Nature Sounds, Marissa Salas

Graduate Thesis and Dissertation post-2024

• Faced with the potential closure or privatization of the U.S. National Park Service (NPS), it is important to reflect on the conservation efforts using soundscapes. This dissertation explores the gap between experts and lay listeners in listening to soundscapes through the digitally-mediated spaces (e.g. YouTube). In a pilot project conducted in 2024 that used facial emotional recognition software and a talk-aloud protocol, data on emotions was collected. Using NPS video recordings on its webpages, social media accounts and via other digital channels (YouTube, etc.) created by NPS experts, this project employed an innovative, interdisciplinary, mixed-methods experimental design to investigate …

Macabre Therapeutics: An Exploration Into The Cathartic Nature Of Splatter Utilizing The Saw Franchise As Corpus, Rosalind E. Rohrbaugh

Graduate Thesis and Dissertation post-2024

This project positions splatter (a subgenre of horror films that centralizes gore) as applicable for sociopolitical critique and emotional catharsis, disrupting the narrative of splatter as a solely shock-based enterprise. The project utilizes the Saw franchise as a corpus, which reignited audience interest in extreme horror in 2004, rejuvenating splatter film releases since their stagnancy throughout the 1990s. This research seeks to answer why Saw captured the attention of audiences and returned the splatter subgenre to the 21st century, utilizing psychoanalytical film analysis, sociopolitical analysis, semiotics, content analysis, and archival research as methodology and drawing on Aristotle’s Catharsis and Rhetorical …

Multi-Objective Bike Routing Problem: A Survey And Comparative Evaluation, Dominic Peter Macisaac

EWU Masters Thesis Collection

Multi-objective routing has been studied for over forty years, yet its application to the bike routing problem is a relatively recent development. The Multi-Objective Bike Routing Problem (MOBRP) seeks to optimize a set of bike routes from a single source to a single destination, given multiple cost criteria. This paper makes two primary contributions. First, it consolidates existing research on the MOBRP, including the criteria chosen and associated cost functions, the search algorithms used, and the testing setups and metrics used for evaluation. Second, it implements the most promising search algorithms and evaluates these approaches through comprehensive cross-testing, a topic …

Principles Of Biomedical Research, Faina Linkov, Matthew C. Kostek

Open Education Materials

HLT 430/530

CC BY-NC-SA

Romantic Beliefs And Their Effect On Relationship Satisfaction, Psychological Well-Being, And Psychological Distress, John D. Pinsky

PCOM Psychology Dissertations

Relationship satisfaction has been shown to have a powerful effect on both individual psychological well-being and psychological distress. One factor that influences an individual’s relationship satisfaction is their endorsement of romantic beliefs. This finding has not been replicated in the U.S. in the past 20 years and the influence of romantic beliefs on relationship satisfaction, psychological well-being, and psychological distress has not been studied in depth. This study implemented a quasi-experimental design using online self-report measures to test whether level of endorsement of romantic beliefs can predict relationship satisfaction, psychological well-being, or psychological distress. It was hypothesized that romantic beliefs …

“Stay Afloat, Stay Alive”: Stories Of The Challenges And Perseverance Of Foster Care Alumni In Higher Education, Marshall S. Parrent

College of Graduate Studies: Theses & Dissertations

The purpose of this critical narrative inquiry was to collect the stories of foster care alumni (FCA) in higher education, and so that we may better understand how FCA describe their experiences and what colleges and universities can do to help FCA achieve their goal of degree completion. This study highlights the need for a culturally responsive and sustaining curriculum in order to create an environment supportive of FCA needs. Undergraduate FCA are considered one of the most underserved student populations in higher education (Johnson, 2021). While 70-84% of FCA wish to attend college and earn a two- or four-year …

Ease Of Product Disassembly Through A Systematic Structured Time-Based Design For Disassembly Methodology, Emeka S. Igwe

College of Graduate Studies: Theses & Dissertations

This research introduces a systematic time-based design for disassembly (DfD) framework aimed at optimizing product disassembly by addressing important features like liaisons between components in product, component accessibility and the overall modularity of the product. This study specifically covers electromechanical and mechatronic systems in both household and industrial setup, identifying their disassembly challenges and high value pointers for improvement. The methodology involves using a design for disassembly framework called LeanDfD in carrying out a holistic disassembly process and evaluating quantitative metrics like disassembly time and complexity and suggesting further redesign strategies to minimize disassembly time and cost. Adopting this systematic …

Stachys Matthewsii: Photo Essay Of A Rare Plant, W. John Hayden

Biology Faculty Publications

On the morning of June 14, 2021, while collecting bryophytes in Goochland County with my student, Mikayla Quinn, we stumbled upon a previously unknown population of stachys matthewsii, Yadkin's Hedge Nettle.

What’S In A Name? Anapodophyllon? Podophyllum? It’S Still Mayapple, W. John Hayden

Biology Faculty Publications

No abstract provided.

Stress Affects Infectious Disease Outcomes In Canaries, Vansh Singhal, Erin Sauer, Salvador Barraza-Del Barco, Kamiah H. Turner, William H. Kirkpatrick, Weston Perrine, Sarah Heissenberger, Sarah E. Durant

2025 Research Poster Competition

Chronic stress is related to a decline in immune function in all living organisms and is known to increase the likelihood of developing or exacerbating chronic non-infectious diseases. However, the role of chronic stress in affecting outcomes of infection important to individual health and endpoints important for epidemic dynamics (e.g., likelihood of transmission) are not well understood. In this study we exposed canaries (Serinus canaria) to chronic stress or control conditions after which they were inoculated with Mycoplasma Gallisepticum, a bacterium that causes respiratory disease in birds.

Following the chronic stress protocol, the canaries were assessed every day for measures …

Effects Of Starter Cultures On The Metabolite Profile, Antioxidant Activities, And Anti-Aging Properties Of Tapuy Lees, Edward Kevin B. Bragais, Paul Mark B. Medina

Biology Faculty Publications

The Philippine rice wine (tapuy) and tapuy lees making process utilizes bubod, the traditional starter culture. The bubod contains variable number and species of microorganisms and influences the physical and chemical properties of tapuy and tapuy lees, resulting in inconsistent quality products. Hence, improvement and standardization of local starter culture are significant. Here, we examined the effects of well-defined starter cultures (Rhizopus oryzae (RO), Mucor indicus (MI), and Saccharomyces cerevisiae (SC)) and bubod on the metabolite profile, antioxidant, and anti-aging activities of tapuy lees. Our results showed the presence of polyphenols (102.36 ± 2.84 to 173.92 …

In Silico Screening And Identification Of Ctl And Htl Epitopes In The Secreted Virulence Factors Of Mycobacterium Tuberculosis, Edward Kevin B. Bragais, F. M. Heralde Iii, K. C. Fernandez, S. E. Caoili

Biology Faculty Publications

Background: Mycobacterium tuberculosis (MTb) is a highly infectious pathogen and a global health threat due to its resilient cell wall and immune evasion strategies. Despite the availability of the antituberculosis Bacille Calmette-Guérin (BCG) vaccine, its efficacy varies (0%–80%) and gradually decreases over time. This study aimed to identify cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes in MTb secretory proteins using immunoinformatics tools. Material and methods: The Protein Variability Server was used to identify highly conserved sequences, and epitope population coverage was estimated for the Southeast Asian (SEA) region. Selected epitopes were also docked to their major histocompatibility complex alleles. …

In Silico Prediction Of Cytotoxic T-Cell Epitopes From Helicobacter Pylori Virulence Factors Using An Immunoinformatics Approach, Demy Valerie Chacon, Kiana Alika Co, Daphne Noreen Enriquez, Aubrey Love Labarda

Biology Faculty Publications

Background: Helicobacter pylori infects approximately half of the global population, leading to gastric and duodenal ulcers. Despite the availability of antibiotics, challenges such as patient reluctance, high treatment costs, and antibiotic resistance limit their effectiveness, making vaccination a promising alternative. This study used immunoinformatics to identify candidate epitopes for a multiepitope vaccine construct against H. pylori. Material and methods: The protein variability server was utilized for conservation analysis. The epitopes were screened for antigenicity, allergenicity, toxicity, cross-reactivity, and population coverage. Selected epitopes were docked with their corresponding human leukocyte antigen (HLA) alleles, and thermodynamic quantities were determined. Five virulence factors …

Development And Pilot Of A Microgreens Project To Integrate Food Security In Grade 8 Science Using Systems Thinking, Iris Mae L. Caidic, C. K. Gonzales

Biology Faculty Publications

Among other countries, the Philippines faces the issue of food security, which must be addressed through education. However, the lack of coherence in teaching science content hinders Filipino junior high school students’ holistic understanding that science lessons are interconnected to food security. This study explores how systems thinking can be utilized to integrate food security into science topics. The pilot of the developed module on a microgreens project was implemented using systems thinking tools to tackle lessons on biodiversity, ecosystems, and the human digestive system within the context of food security. Data from end-of-scaffold check-ins, individual scaffold assessments, group performance …

A Concoction Pipeline For Generating Molecular Operational Taxonomic Units (Motus) Among Riparian And Aquatic Beetles, Emmanuel D. Delocado, Voltaire Rafael H. Banzon, Enrico Gerard S. Sanchez

Biology Faculty Publications

No abstract provided.

A Low-Cost Production Method For Bst Dna Polymerase (Large Fragment), Crisanto M. Lopez, M. V. San Pedro, V. A. Cañas, J. R. Garcia

Biology Faculty Publications

BstLF, the large fragment of Bst DNA polymerase, is a recombinant strand-displacing DNA polymerase derived from Geobacillus stearothermophilus and serves as the primary enzyme utilized in loopmediated isothermal amplification (LAMP). Recently, the application of LAMP as a convenient and accessible diagnostic tool has gained considerable attention. However, the high cost of reagents presents a significant barrier to the development of LAMP diagnostic kits, limiting accessibility for laboratories in low-resource settings. In this study, we report a low-cost production method for BstLF utilizing more readily available alternative reagents coupled with a simplified purification process. The resulting homebrewed BstLF demonstrated comparable amplification …

Assessment Of Validity And Reliability Of Survey Tool For Good Aquaculture Practices Of Philippine Shellfish Farmers, Crisanto M. Lopez, A. Rustia, E. Barrios, D. Tanay

Biology Faculty Publications

Food safety farm-to-fork model compliance to good aquaculture practices (GAqP) of Filipino shellfish farmers placed a special consideration in the validation and reliability of the developed survey tool that consisted of 11 sections of GAqP provisions based on Philippine National Standards 207:2017 and CXS 52-2003 standards. Validation [content validity index (CVI) and impact factor (IF)] and reliability (Cronbach’s alpha) included pre-testing (item difficulty and discrimination index) (n = 7 shellfish farmers; n = 7 technical personnel on fisheries), validation (n = 30 shellfish farmers and five experts), and pilot testing (n = 30 shellfish farmers) to measure the reliability. Pre-testing …

Dr. Wolfram Mey’S Stonefly (Insecta: Plecoptera) Collection From Luzon, Philippines: Part Ii. Leuctridae, Arthien Lovell P. Pelingen

Biology Faculty Publications

Leuctrid specimens were examined from a collection expedition conducted over 20 years ago by Dr. Wolfram Mey. Rhopalopsole luzonensis sp. nov., R. absentia sp. nov., and R. rotundus sp. nov. are described based on male specimens. Additionally, a distribution hypothesis, discussion of female specimens, and an updated checklist are briefly provided.

The Use Of Synthesized Stabilized Nanoparticles Of Selenium As A Feed Additive In Shrimp Litopenaeus Vannamei Diets: Performance, Antibacterial Activity, Gut Microbiota And Immune-Related Genes Expression, Janice A. Ragaza, F. Mustafa, S. Hassan, O. Ashary

Biology Faculty Publications

The shrimp aquaculture industry faces challenges that hinder production, including pathogens and infections from bacteria-causing diseases. The present study aimed to examine the impact of dietary synthesized chitosan stabilized selenium nanoparticles (CSSeNPs) on the growth performance of gut microbiota and immuneassociated genes for shrimp L. vannamei aquaculture. The experiments were accomplished for 12 weeks in triplicate fiberglass circular tanks (200 L). A 300 shrimp post-larvae (PL) weighing an average of 0.14 ± 0.001 g was utilized. Four experimental groups were assigned to 12 tanks. Each tank contained 25 PL. Each group fed with one of the following diets: control (C), …

Native No More? The Catfish Dilemma In The Philippines, Janice A. Ragaza, Alexis Faye A. Olarte, James Darren R. Pelaez

Biology Faculty Publications

The shrimp aquaculture industry faces challenges that hinder production, including pathogens and infections from bacteria-causing diseases. The present study aimed to examine the impact of dietary synthesized chitosan stabilized selenium nanoparticles (CSSeNPs) on the growth performance of gut microbiota and immuneassociated genes for shrimp L. vannamei aquaculture. The experiments were accomplished for 12 weeks in triplicate fiberglass circular tanks (200 L). A 300 shrimp post-larvae (PL) weighing an average of 0.14 ± 0.001 g was utilized. Four experimental groups were assigned to 12 tanks. Each tank contained 25 PL. Each group fed with one of the following diets: control (C), …

From Bait To Breakthrough: How Polychaetes Are Revolutionizing Philippine Aquaculture, Janice A. Ragaza, Irnes Rebien H. Bailon, Rochelle A. Jabines

Biology Faculty Publications

No abstract provided.