Digital Commons Network^™

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.

Ptp1b Inhibitors Of Marine Sponge-Derived Secondary Metabolites From Dysidea, Irvin B. Rondolo, G. A. Lasam, M. N. Aguila, A. J. De Jesus

Biology Faculty Publications

Diabetes is a chronic metabolic disease with high morbidity and mortality due to its complications. Recently, there has been growing interest in identifying new bioactive compounds, including marinederived secondary metabolites, for potential antidiabetic activities. This study focuses on secondary metabolites from marine sponges from the genus Dysidea that show strong inhibition of protein tyrosine phosphatase 1B (PTP1B), a key target in antidiabetic therapy. Thirteen out of the thirty-one compounds were identified to have promising in silico potentials vs PTP1B: avarol (1), avarone (2), furodysin (3), nakafuran 8 (4), haterumadysin A (5), pyrodysinoic acid (6), avinosol (7), puupehenone (8), α-santonin (9), …

Clerodendrum Kelli (Lamiaceae), A New Species From Carranglan, Nueva Ecija, Philippines, And Lectotypification Of Clerodendrum Mindorense, Adriane B. Tobias, D. J. Ples, J. Patykowski, L. C. Udasco

Biology Faculty Publications

Clerodendrum kelli R.Bustam., A.B.Tobias & Ples—a new species of the genus Clerodendrum L. (Lamiaceae) from the montane forests of Carranglan, Nueva Ecija, Luzon Island, Philippines—is described and illustrated. The species shares morphological features that are uncommon for the genus with both Clerodendrum quadriloculare (Blanco) Merr. (purple abaxial leaf surfaces) and C. mindorense Merr. (reduced fruiting calyx lobes), but differs from both in having lax (vs dense/compact) inflorescences bearing flowers with shorter corolla tubes and reddish-pink (vs green or purple) calyces with ovate (vs triangular or lanceolate) lobes. Additionally, a lectotype for C. mindorense is assigned. Preliminary assessment of its conservation …

New Record And Amended Description Of Bulbophyllum Placochilum (Orchidaceae) With A Key To Bulbophyllum Sect. Alticeptrum Of The Philippines, Adriane B. Tobias, K. E. Boco, J. P. Collantes, J. C. Altomonte

Biology Faculty Publications

Bulbophyllum placochilum J.J.Verm., endemic to Borneo, is newly recorded in the Philippines based on a specimen collected from Mt Malinao, Albay Province, Luzon Island. We provide a comprehensive account of the species, including a detailed morphological description, ecological observations, distribution range, phenology, and photographs. The species is assessed as Vulnerable under the IUCN Red List Categories and Criteria. A key to species of Bulbophyllum sect. Altisceptrum J.J.Sm. in the Philippines is also included.

Evaluation Of A Customer Development Simulator Using Large Language Model-Based Multi-Agent System And Synthetic Respondents, Lois Abigail To, Zachary Matthew C. Alabastro, Joseph Benjamin R. Ilagan

Quantitative Methods and Information Technology Faculty Publications

Customer development (CD) is a Lean Startup (LS) methodology for startups to validate their business hypotheses and refine their business model based on customer feedback. This paper proposes designing a large language model-based multi-agent system (LLM MAS) to enhance the customer development process by simulating customer feedback. Using LLMs’ natural language understanding (NLU) and synthetic multi-agent capabilities, startups can conduct faster validation while obtaining preliminary insights that may help refine their business model before engaging with the real market. The study presents a model in which the LLM MAS simulates customer discovery interactions between a startup founder and potential customers, …

Collaborative Product Innovation Model With Large Language Models And Agentic Systems, Zachary Matthew C. Alabastro, Stephen Daeniel Mansueto, Joseph Benjamin R. Ilagan

Quantitative Methods and Information Technology Faculty Publications

Product innovation is critical in strategizing business decisions in highly-competitive markets. For product enhancements, the entrepreneur must garner data from a target demographic through research. A solution to this involves qualitative customer feedback. The study proposes the viability of artificial intelligence (AI) as a co-pilot model to simulate synthetic customer feedback with agentic systems. Prompting with ChatGPT-4o’s homo silicus attribute can generate feedback on certain business contexts. Results show that large language models (LLM) can generate qualitative insights to utilize in product innovation. Results seem to generate human-like responses through few-shot techniques and Chain-of-Thought (CoT) prompting. Data was validated with …

Millennials And Generation Z Customers' Service Recovery Evaluation From A Self-Esteem Perspective, Megan Mcdade

Graduate Thesis and Dissertation post-2024

While a significant amount of research has been conducted to assess the effectiveness of service recovery based on various factors, there is limited research on emerging customer segments, specifically Generation Z and Millennials. Justice theory has been predominant in service recovery literature, however, recent studies suggest that self-esteem can provide valuable insight into understanding customers’ evaluations of service recovery. This research focuses on how Generation Z and Millennial customers evaluate service recovery efforts in the context of restaurants. The main objective of this study is to examine how these customers perceive economic (compensation) and psychological (apology) service recovery strategies, considering …

Understanding The Mechanism In Shaping Guest Acceptance Of Service Robots In Caribbean Hotels: The Moderating Role Of Cultural Familiarity In The Cac Model, Jamilia A. Lawrence

Graduate Thesis and Dissertation post-2024

Service robots continue to become increasingly popular in the hospitality and tourism industry. Understanding the cognitive and emotional processes is important in explaining the sequential processes of guests accepting new technologies. Especially in regions like the Caribbean, where human-to-human interaction and personalized services are highly valued.

This study investigates how cognitive evaluations of service robots, including utility, coolness, autonomy, courtesy, and interactivity, influence guests' emotional responses and their acceptance of the technology in Caribbean hotels. Additionally, the study explores the moderating role of cultural familiarity in the relationship between emotion and acceptance.

Using the cognitive-affective-conative (CAC) model, 415 responses were …

Transformation To Re-Engagement: A Temporal Analysis Of Tefl Tourism Experiences, Brianna Morman

Graduate Thesis and Dissertation post-2024

This study investigates the psychological and behavioral transformation resulting from long-term cultural immersion, using TEFL (Teaching English as a Foreign Language) tourism as a lens to examine how deep, lasting change unfolds. While prior literature has primarily classified TEFL as a niche form of tourism, its potential to facilitate enduring personal transformation has not been empirically assessed. This research addresses that gap by applying Transformative Learning Theory and the Model of Transformation within the Stimulus-Organism-Response (S-O-R) framework to explore how TEFL experiences lead to transformation, satisfaction, and long-term re-engagement. Uniquely, the study also examines two underexplored temporal moderators – duration …

Investing In Digital Solutions For Firm Value, Mahala Geronasso

Graduate Thesis and Dissertation post-2024

Digital investments have become integral to the strategies of hospitality firms, enabling data-driven decision-making, operational efficiency, and financial growth. This dissertation examines the impact of digital investments, specifically IT investment (CAPEX), research and development (R&D) intensity, and digital marketing intensity, on operational and financial performance within hospitality firms, guided by Innovation Diffusion Theory and Agency Theory. A comprehensive empirical analysis utilized financial data from publicly traded U.S. hospitality firms (2013–2023). Advanced econometric methods, including ARIMA, GARCH, and structured panel regressions, were rigorously assessed to evaluate performance dynamics. Findings reveal IT investments significantly enhance operational efficiency, profitability, and liquidity, despite causing …

Transformative Experience Design: Exploring The Supply-Side Perspective In The Theme Park Context, Juliana Rodrigues Vieira Tkatch

Graduate Thesis and Dissertation post-2024

This study investigates how hedonic tourism activities can facilitate personal transformation, particularly in the context of mass tourism. Focusing on theme parks, which draw millions of visitors annually, the research explores the design elements that can foster visitor transformation. The study aims to uncover the design elements embedded in the creation of these activities and the effects they intend to foster in visitors, answering the research question: How do theme park design practices contribute to transformative tourism experiences? This question is significant given the limited empirical work connecting experience design and transformative tourism from the supplier perspective. Using a qualitative …

Influencing Sustainability: The Impact Of Digital Influencers On Sustainable Tourism Behaviors, Karen C. N. Tavares

Graduate Thesis and Dissertation post-2024

This dissertation investigates how digital influencers shape sustainable tourism communication and behavioral intentions through a multi-method research approach. As influencer marketing increasingly drives destination visibility and traveler decision-making, understanding its role in advancing sustainability is essential for aligning economic growth with environmental and social responsibility. To address this gap, two complementary studies were conducted.

Study 1 applied social media content analysis to examine sustainable tourism discourse, identifying trends in topics, message framing and content. The analysis revealed a largely positive and gain-framed conversation, emphasizing lifestyle identity, collective values, and all three pillars of sustainability. Influencer analysis showed that while institutional …

Inhibition Of Activin A Signaling Slows The Progression Of Barrett's Esophagus Induced Esophageal Adenocarcinoma, Lily A. Giardino

Graduate Thesis and Dissertation post-2024

In 2020, approximately 1.03 billion cases of Gastro-esophageal Reflux Disease (GERD) were reported worldwide, representing a significant global health burden. Chronic GERD is a potent initiator of Barrett’s Esophagus (BE), a precancerous condition in which the squamous epithelium is converted into columnar-like epithelium in the distal esophagus in response to reflux injury. Barrett’s Esophagus is the only known precursor to Esophageal Adenocarcinoma (EAC), a disease with a five-year survival rate of 21%. First line treatments focus on acid suppression and endoscopic mucosal resection but did not result in a decrease of EAC incidence highlighting the importance of new therapeutics. Previous …

Multi-Omics Analysis Of Streptococcus Pneumoniae Serotype 3 Using A Murine Infection Model, Jash Kamlesh Trivedi

Graduate Thesis and Dissertation post-2024

Streptococcus pneumoniae (SPN), a gram-positive encapsulated pathogen, inhabits the human nasopharynx asymptomatically but can cause severe infections, including invasive pneumococcal diseases (IPD). Although targeted by vaccines, serotype 3 (ST3) remains highly prevalent within the United States and globally. Sequence type 180 lineage within Clonal Complex (CC)180 is the predominant lineage of serotype 3 globally. Genetically, Clonal Complex 180 is divided into clade I and II, with clade II recently surpassing clade I in prevalence. However, the molecular mechanisms driving this shift remain poorly understood. Here, we employ a multi-omics approach, combining pangenome analysis and dual-RNA sequencing, to investigate genetic factors …

Comparing Inter-Rater Reliability For Two Coding Methodologies In Meta-Analysis Data Extraction, Christine D. Destefano

Graduate Thesis and Dissertation post-2024

Meta-analyses are critical tools for evidence-based policymaking, but their validity depends heavily on accurate data extraction from primary studies. While previous research has focused on procedural aspects of coding and reliability of effect size extraction, there remains a significant gap in understanding how to improve inter-rater reliability (IRR) for moderator variables that provide crucial context for meta-analytic findings. This study compared two methodological approaches for coding moderator variables: traditional low-inference coding and a novel drill-down questioning technique adapted from database development principles. Using a comparative analysis design, two independent coders extracted data from 18 primary studies included in a published …

The Representation Of Racially And Ethnically Diverse Students Identified With Giftedness In Third Grade In Florida, Ioanna Katsavria

Graduate Thesis and Dissertation post-2024

This study examines the proportional representation of Black, Hispanic, White, and Asian third-grade gifted students across urban and rural school districts in the U.S. state of Florida. It incorporates secondary quantitative datasets for the Fall 2023 and Spring 2024 school terms from the Florida Department of Education (FLDOE, n.d.), collected in the Fall 2024, along with qualitative data gathered in Spring 2025 from the websites of sixty-seven county-based school districts. Significant disparities among all groups of racially and ethnically diverse students were exposed through the quantitative data analysis. Notably, Black, Hispanic, and Asian students, especially in rural areas, were shown …

Golden Spirals Everywhere? Solutions For Fermi Questions, January 2025, John Adam

Mathematics & Statistics Faculty Publications

The article discusses different types of spirals, including Archimedean, hyperbolic, and logarithmic spirals, with a focus on the golden ratio and golden spirals. It addresses the misconception that golden rectangles and spirals can be found in various natural and man-made structures, emphasizing the importance of understanding the properties of logarithmic spirals. The article provides mathematical explanations and solutions for questions related to pitch angles and self-similarity in logarithmic spirals, using examples like the nautilus shell and an ammonite-like stone. It concludes by referencing additional sources for further exploration of the golden ratio and golden spiral myths.

Enhancing The Accuracy Of Image Classification For Degenerative Brain Diseases With Cnn Ensemble Models Using Mel-Spectrograms, Sang-Ha Sung, Michael Pokojovy, Do-Young Kang, Woo-Yong Bae, Yeon-Jae Hong, Sangjin Kim

Mathematics & Statistics Faculty Publications

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are prevalent neurodegenerative disorders among the elderly, leading to cognitive decline and motor impairments. As the population ages, the prevalence of these neurodegenerative disorders is increasing, providing motivation for active research in this area. However, most studies are conducted using brain imaging, with relatively few studies utilizing voice data. Using voice data offers advantages in accessibility compared to brain imaging analysis. This study introduces a novel ensemble-based classification model that utilizes Mel spectrograms and Convolutional Neural Networks (CNNs) to distinguish between healthy individuals (NM), AD, and PD patients. A total of 700 voice …

A Time-Domain Boundary Integral Equation For Moving Acoustic Sources In Uniform Flow And Its Solution By An Advanced Time Propagation Approach, Fang Q. Hu, Douglas M. Nark

Mathematics & Statistics Faculty Publications

This paper presents a time-domain boundary integral equation (TDBIE) formulation for predicting acoustic scattering from moving sources in a uniform mean flow. This work is motivated by the increasing need for accurate aeroacoustic modeling of modern aircraft configurations, including VTOL and eVTOL systems with rotating components. A key challenge in time-domain scattering simulations with moving sources is the determination of retarded time for a given observer time, which involves solving an implicit equation at each time step. This can be computationally costly, particularly for numerical solution of the TDBIE where every surface element on the scattering body acts as an …

Covariate Selection For Rna-Seq Differential Expression Analysis With Hidden Factor Adjustment, Farzana Noorzahan, Hyeongseon Jeon, Yet Nguyen

Mathematics & Statistics Faculty Publications

In RNA-seq data analysis, a primary objective is the identification of differentially expressed genes, which are genes that exhibit varying expression levels across different conditions of interest. It is widely known that hidden factors, such as batch effects, can substantially influence the differential expression analysis. Furthermore, apart from the primary factor of interest and unforeseen artifacts, an RNA-seq experiment typically contains multiple measured covariates, some of which may significantly affect gene expression levels, while others may not. Existing methods either address the covariate selection or the unknown artifacts separately. In this study, we investigate two integrated strategies, FSR_sva and SVAall_FSR, …

In Search Of The Rational Voter In The 2020 Presidential Election: Understanding The Impact Of Voter Costs And Benefits On Turnout, Norou Diawara, Tiffany Henley, Samuel L. Brown, Md Iqbal Hossain

Mathematics & Statistics Faculty Publications

The ability to vote is one of the most valuable rights and privileges afforded by the Constitution of the United States to its citizens. For many, voting is not just a civic duty; it is also a choice. Voting is crucial to our democracy, and any changes to it may affect the efficiency of the democratic process. The bigger question is whether voters behave rationally by engaging in a cost-benefit calculus in deciding whether or not to vote. Using data science, this paper will examine the probability of voting and investigate its impact via cost and benefit among other variables …