Digital Commons Network^™

Auprc: A Metric For Evaluating The Performance Of In-Silico Perturbation Methods In Identifying Differentially Expressed Genes, Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P Long

Faculty, Staff and Student Publications

In silico perturbation models, computational methods that can predict cellular responses to perturbations, present an opportunity to reduce the need for costly and time-intensive in vitro experiments. Many recently proposed models predict high-dimensional cellular responses, such as gene or protein expression to perturbations such as gene knockout or drugs. However, evaluating in silico performance has largely relied on metrics such as $R^{2}$, which assess overall prediction accuracy but fail to capture biologically significant outcomes like the identification of differentially expressed (DE) genes. In this study, we present a novel evaluation framework that introduces the AUPRC metric to assess the precision …

Braingenebot: A Framework For Variant Prioritization And Generative Pretrained Transformer-Informed Interpretation Across Polygenic Risk Score Studies, Gang Qu, Nitesh Enduru, Xinyi Liu, Xiaoqian Jiang, Zhongming Zhao

Faculty, Staff and Student Publications

Polygenic risk scores (PRS) are widely used to assess genetic susceptibility in Alzheimer's disease (AD) research. However, the rapid expansion of PRS studies has led to dataset-specific biases-stemming from factors like population makeup, genotyping methods, and analysis pipelines-that result in inconsistent variant prioritization and limit generalizability and reproducibility. To address these challenges, we propose a transductive learning framework that integrates multiple PRS datasets for more robust risk variant prioritization, incorporating genome-wide association study (GWAS) priority scores as biologically informed priors. Additionally, we introduce BrainGeneBot, an AI-driven tool leveraging generative pretrained transformers with retrieval-augmented generation technology to streamline genomic analyses in …

Reconstruction Of Water Storage Variability In The Aral Sea Region, Nikita Murzintcev, Sahibjamal Nietullaeva, Timur Berdimbetov, Buddhi Pushpawela, Asiya Tureniyazova, Sherly Shelton, Bakbergen Aytmuratov, Khusen Gafforov, Kanat Parakhatov, Alimjan Erdashov, Abdul-Aziz Makhamatdinov, Timur Allamuratov

Plants, Soils and Climate Student Research

The Gravity Recovery and Climate Experiment (GRACE) mission, operational from 2002 to 2017, provided critical measurements of Earth's gravity field anomalies which have been extensively used to study groundwater and terrestrial water storage (TWS) dynamics. In this research, we utilize GRACE data to identify, model, and analyze potential climate parameters contributing to the reconstruction of TWS variability in the Aral Sea Basin region (ASB). We assess the impact of climate change and anthropogenic nature management on TWS change using a quantitative method. Our analysis reveals a significant decline in the TWS at a rate of 0.44 cm year^-1 during …

Impact Of Temperature On Larval Mortality And Performance Of The Acorn Barnacle Chthamalus Fissus In San Diego, Ca, Alberto Rivera

Theses

Rising ocean temperatures and increasingly frequent marine heatwaves threaten the physiological performance and survival of marine larvae. This study quantifies the thermal tolerance, respiration, and swimming behavior of Chthamalus fissus cyprid larvae to establish a baseline for understanding their vulnerability under future climate scenarios. Larvae were collected from the Scripps Pier in La Jolla, CA and exposed to a range of temperatures (12–50°C, dependent on the experiment) to assess oxygen consumption, mortality, and swimming speeds. Oxygen consumption rates increased significantly with temperature, peaking at 30°C, with cyprids exposed to temperatures above 26°C showing significantly higher respiration rates than those below …

Low Economic Level And The Risk Of Overweight Among Indonesian Junior And Senior High School Students, Ariyanto Nugroho, Purwo Setiyo Nugroho, Amarin Yudhana, Sri Sunarti

Kesmas

Overweight and obesity among Indonesian adolescents have emerged as a pressing public health issue, reflecting global trends. This study examines the relationship between economic status and overweight prevalence among junior and senior high school students in Indonesia, using secondary data from the Global School-based Health Survey (GSHS). This study analyzed data from 9,977 students aged 11–18 years through a cross-sectional design and binary logistic regression, adjusting for dietary habits, physical activity, and sedentary behavior. Overall, 14.7% of students were overweight; the prevalence was notably higher among low-income students (27.4%) compared to high-income groups (14.2%). Students from lower economic backgrounds were …

Adults With Learning Disabilities Navigating The Transition From School To Work, Shatrece L. Jenkins

Doctoral Dissertations and Projects

The purpose of this qualitative case study was to explore the experiences of adults with learning disabilities when transitioning from academics to the workplace, with an emphasis on emotional intelligence. The two research questions asked how adults with learning disabilities described their lived experiences and experiences of emotions and emotional regulation in their transition from academic environments to the professional workplace. The theory guiding this study was the emotional intelligence theory developed by Salovey and Mayer, which was used as a determinant in building relationships and upholding social interactions. The sample consisted of 13 adults with learning disabilities working at …

An Antioxidant Approach To Ameliorate The Effects Of Radiation And Chemotherapy On Cognition, Raymond Anan Otoo

Theses and Dissertations

Acute Lymphoblastic Leukemia (ALL) is a hematologic malignancy that primarily affects children and young adults. While advancements in treatment—including chemotherapy and cranial irradiation—have significantly improved 5-year survival rates in children to nearly 90%, radiation-induced cognitive impairment (RICI) remains a persistent and debilitating side effect. The brain, particularly the hippocampus, is highly susceptible to radiation-induced oxidative stress and inflammation. In the treatment of ALL, the combined use of chemotherapy and radiotherapy contributes to a heightened oxidative burden, exacerbating the risk of cognitive dysfunction. Although previous studies have linked radiation exposure to neurocognitive decline, the molecular mechanisms underlying RICI and chemotherapy-induced cognitive …

An Economic Assessment Of Precision Conservation With On-Farm Precision Experiment Data, Karina A. Schoengold, Badri Khanal, Taro Mieno, David S. Bullock

Cornhusker Economics

Using a novel dataset that includes within field variation in productivity, we find that partial field retirement for a prairie strip can not only provide conservation benefits, but can also be economically beneficial. We note that these results are for a single field with one year of data, and that additional years of production and fields are essential to determine how much these results can be generalized. We also note that precision systems can be costly, and a comparison of outcomes with and without this information is essential to determine if investing in such systems is profitable. However, variable rate …

Adapting To Southwest Idaho's Shifting Wildfire Regime: Sustainable Collaboration As A Means To Socioecological Resilience, Olivia Awbrey

Dissertations and Theses

Community wildfire adaptation is happening at multiple scales across the western United States. A range of collaboratively formed groups have addressed compounding issues related to wildfire risk, forest health and land use. In Southwestern Idaho, place-based collaboratives emerging in the early 2000s have considered trade-offs between localized social and ecological needs as they approach wildfire adaptation from the bottom-up. More recently, regional partnerships have emerged that emphasize cross-boundary wildfire risk reduction to cover larger geographic areas for risk mitigation. In between these micro- and macro-scales of activity exist bridging agencies such as county and state-level programs that account for gaps …

Montserrat Developments Impacting Local Coral Reefs, Emma I. Bartholomew

2025 Symposium

Montserrat is a small island in the Caribbean, and over half of the island is in the exclusion zone because of the active volcano, Soufrière Hills. In that half was the old capital, Plymouth, which has since been abandoned, and its old port. The old port was getting less reliable and accessible, so they decided to build a new port in Little Bay, closer to the seat of government in Brades. This study explored how the addition of the new port impacted the corals in that area. We explored several different bays and recorded the diversity and health of the …

08.25.2025 Ored Connect, Liz Williamson

ORED Newsletter

• Research Security Required Training
• ORED Research Reception

A Comparison Of Diving Behavior Of Goose-Beaked And Dense-Beaked Whales From Tagging Studies In Multiple Ocean Basins, Jay Barlow, Robin W. Baird, Janelle Badger, Gregory S. Schorr, Erin A. Falcone, Shannon N. Coates, Peter L. Tyack, Andrew J. Read, Leigh S. Hickmott, John W. Durban, Diane Claridge, Natacha Aguilar De Soto, Daniel Miranda Gonzalez, Fleur Visser, Machiel G. Oudejans, Stacy L. De Ruiter, David A. Sweeney, Brenda K. Rone, Stephanie L. Watwood

University Faculty Publications and Creative Works

Studies of cetacean diving behavior in multiple locations in different ocean basins allow for an assessment of variability within and among populations. We examine foraging dive behaviors of goose-beaked whales (Ziphius cavirostris) and dense-beaked whales (Mesoplodon densirostris) using data from 132 tagged whales in seven locations in the Pacific and Atlantic Oceans and the Mediterranean Sea. Acoustic recording tags are used to identify foraging dives by the presence of echolocation. For other tag types, foraging dives are identified based on maximum dive depth. Five parameters are used to characterize foraging dives: maximum dive depth, foraging dive duration, dive cycle duration, …

Novel Nano-Composite Materials (Nncms) With The Designations J1, J2, And J3 For Removal Several Harmful Ions, Mohammed K. Al-Doseri, Safaa. R. Fouda, Mohamed Mossad, Mahmoud H. Mahmoud

Mansoura Engineering Journal

The most toxic material to the environment is heavy metals. remove heavy metals from wastewater is done by adsorption. Many papers have been done using different materials to take off toxic dangerous ions from wastewater. Noval Nano-composites material (NNCM)as designated as J1, J2, and J3 the most used adsorbents in this study. To conduct the experiments, synthetic wastewater was generated in the lab. Batch experiments were conducted to create the best conditions for removing these ions from the wastewater. The optimum conditions obtained were 90 min optimum contact time, and pH equal seven, optimal NNCM dose was 0.5 g/L achieving …

Performance Analysis Of Computational Methods For Predicting Protein Function In Rare Diseases, Aichetou Mohamed Sidiya, Hanin Alzaher, Razan Almahdi, Tayeb Brahimi

Effat Undergraduate Research Journal

Protein function prediction is crucial for understanding the underlying mechanisms of rare diseases. With the increasing availability of computational methods including machine learning-based approaches, network-based methods, and sequence-based methods, predicting protein functions has become more accessible. However, it is not clear which of these methods performs better or how they compare to each other in terms of accuracy, efficiency, and scalability. In this study, we evaluate several computational methods for predicting protein functions in rare diseases using key performance indicators (KPIs). We analyze the strengths and weaknesses of each method and provide recommendations for researchers and clinicians interested in using …

Advancing Rfid Systems: From Head Orientation To Robotic Localization Using Passive Tags, Guilherme Ricardo Mendes Da Silva Barreto De Figueiredo

Doctoral Dissertations

No abstract provided.

Centrosomal And Non-Centrosomal Microtubule Networks Coordinate To Drive Nuclear Dynamics In Developing Epithelium, Rashmi Budhathoki

Electronic Theses and Dissertations

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving …

Role Of Nucleic Acids As Chaperones In Protein Folding, Zijue Huang

Electronic Theses and Dissertations

Many proteins have slow folding times in vitro that are physiologically untenable. To combat this challenge, ATP-dependent chaperonins are thought to possess the unique ability to catalyze protein folding. Performing quantitative model selection using protein folding and unfolding data, we here show that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding. Performing the experiments as a function of temperature demonstrates that the G4 reshapes the underlying driving forces of protein folding. To understand the structural basis of this catalytic activity, we introduce NMR method to solve the structures, at base-level resolution, of a multiconformer G4 with …

Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops, Keith Skolnick M.D., Anu Valiaveedu

Mako: NSU Undergraduate Student Journal

Many preoperative and postoperative cataract patients struggle with comprehending the use of prescription medication as directed. Language barriers and low health literacy levels are major factors contributing to improper use of prescriptions. To increase patients comprehension, the Fort Lauderdale Eye Institute employed an educational intervention consisting of a live presentation and an instructional video. Results found that 44% of patients were hesitant to ask questions to clinical staff, 32% felt overwhelmed, and nearly 70% lacked confidence in using their prescribed eye drops. Following the intervention, 91% of patients reported increased confidence in their medications, and most indicated that the video …

From Infection To Restoration: A Case Study On Dental Extraction In The Maxilla Anterior, Melanie Ramirez

Mako: NSU Undergraduate Student Journal

A dental implant is a restorative surgical procedure that serves as a solution to replace missing teeth that imitate the function, sensation, and appearance of natural teeth. The objective of this dental case study is to examine the diagnosis, treatment, and post-operation of a patient with a history of tooth loss and infection in the anterior maxilla. This case follows a 55-year-old patient, Jorge Marquez, name changed for confidentiality, who presented a severe tooth abscess on tooth #10 on the anterior maxilla which had previously undergone root canal treatment (Figure 1B). Radiographic evaluations illustrated the severity of the abscess the …

Assessment Of Bat Species (Mammalia: Chiroptera) In Canubas Cave, Kibawe, Bukidnon, Philippines, Jurriel Mari D. Alce, Jasmine Rouida M. Abenes, Leo Gabriel Cervantes, Matthew Eli K. Llacer, Von Zhyrus P. Oche, Ian Jay P. Saldo, Jhovel Roy D. Calo

Sinaya: A Philippine Journal for Senior High School Teachers and Students

Bats, flying mammals, are essential to ecosystems, playing vital roles in pollination, seed dispersal, and insect control. Despite their ecological importance, no prior bat research exists for Canubas Cave, Kibawe, Bukidnon. This study aimed to assess the bat species at the site, documenting their morphometric data, diversity and richness indices, and conservation statuses. A purposive sampling design was implemented by setting up mist nets inside and outside the cave. A total of 13 individuals were identified, comprising three species from two families: Rousettus amplexicaudatus and Eonycteris spelaea (family Pteropodidae, fruit bats), and Miniopterus schreibersii (family Miniopteridae, bent-winged bats). Based on …

Development, Validation, And Applicability Of A Race-Specific Insulin Sensitivity Estimator (Rise) In Youth And Young Adults, Wonhee Cho

Dissertations - ALL

Parallel to the escalating rate of overweight and obesity in the youth and young adult population, the incidence and prevalence of type 2 diabetes are also mounting, presenting significant public health problems. Among the various pathophysiological factors, insulin sensitivity has emerged as a critical risk factor for impaired glucose tolerance (IGT) and type 2 diabetes in youth. Despite the pivotal role of insulin sensitivity in the development and progression of these conditions, current methodologies for its assessment, such as the hyperinsulinemic-euglycemic clamp and intravenous glucose tolerance test, are limited by their invasive methods, high cost, and unsuitability for use in …

Reducing Residential Landscape Water Use In Utah: Technologies And Strategies, Maya Cottam, Kendall Becker, Katlyn Stemmler, Shital Poudyal, Wesley Crump, Lewis Kogan, Scott Hotaling

All Current Publications

Water conservation is a critical issue in Utah, and several actions are already underway to help lower residential landscape water use. Strategies include smart irrigation controllers, efficient sprinkler bodies and nozzles, drip irrigation systems, soil amendments that increase water-holding capacity, and drought-tolerant grass cultivars for lawns. While additional conservation efforts will be necessary to reach sustainable water management, statewide adoption of current programs can help reduce water use and loss.

Statistical Analysis Of Multi-Endpoint Phenotypic Screening Increases Sensitivity Of Planarian Neurotoxicity Testing, Danielle Ireland, L. J. Word, Eva-Maria S. Collins

Biology Faculty Works

There is an urgent need for high-throughput screening (HTS) models to replace, refine, and/or reduce (“3Rs”) vertebrate toxicity testing. Replacing in vivo animal studies is challenging for neurotoxicity and developmental neurotoxicity (DNT), where the functional relevancy of adverse outcomes needs to be assessed on the whole organism. We previously screened the NTP 87-compound library (NTP87), consisting of known and suspected developmental neurotoxicants, and showed that planarian HTS can identify known (developmental) neurotoxicants. Because analysis methods can impact screening results, and our original analysis used the lowest-observed-effect-level (LOEL) only, we hypothesized that the use of state-of-the-art statistical analysis would increase the …

Human Interpretable Grammar Encodes Multicellular Systems Biology Models To Democratize Virtual Cell Laboratories, Jeanette A I Johnson, Daniel R Bergman, Heber L Rocha, David L Zhou, Eric Cramer, Ian C Mclean, Yoseph W Dance, Max Booth, Zachary Nicholas, Tamara Lopez-Vidal, Atul Deshpande, Randy Heiland, Elmar Bucher, Fatemeh Shojaeian, Matthew Dunworth, André Forjaz, Michael Getz, Inês Godet, Furkan Kurtoglu, Melissa Lyman, John Metzcar, Jacob T Mitchell, Andrew Raddatz, Jacobo Solorzano, Aneequa Sundus, Yafei Wang, David G Denardo, Andrew J Ewald, Daniele M Gilkes, Luciane T Kagohara, Ashley L Kiemen, Elizabeth D Thompson, Denis Wirtz, Laura D Wood, Pei-Hsun Wu, Neeha Zaidi, Lei Zheng, Jacquelyn W Zimmerman, Jude M Phillip, Elizabeth M Jaffee, Joe W Gray, Lisa M Coussens, Young Hwan Chang, Laura M Heiser, Genevieve L Stein-O'Brien, Elana J Fertig, Paul Macklin

Faculty, Staff and Student Publications

Cells interact as dynamically evolving ecosystems. While recent single-cell and spatial multi-omics technologies quantify individual cell characteristics, predicting their evolution requires mathematical modeling. We propose a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This enables systematic integration of biological knowledge and multi-omics data to generate in silico models, enabling virtual "thought experiments" that test and expand our understanding of multicellular systems and generate new testable hypotheses. This paper motivates and describes the grammar, offers a reference implementation, and demonstrates its use in developing both de novo mechanistic models and those informed …

The Future Of The Arab Media Industry In Utilizing Artificial Intelligence Technologies: A Foresight Study (2024 To 2034), Mohammedwesam Amer, Abdullah Mohammed Atbiqa

Middle East Journal of Communication Studies

This study explores the future of the Arab media industry from 2024 to 2034 in light of the increasing integration of artificial intelligence (AI) technologies. It identifies key media sectors likely to be affected by AI—such as content creation, news production, editing, and audience engagement—and proposes strategies for effective implementation. The study employs a descriptive survey methodology grounded in the Unified Theory of Acceptance and Use of Technology (UTAUT). Data were collected via an electronic questionnaire from a purposive sample of 264 respondents across 18 Arab countries, including academic elites and media professionals working with Arab media institutions. Findings reveal …

Exposure To Zinc Oxide Nanoparticles Reveals A Death Resistance Mechanism In Dictyostelium Discoideum, Zoya Nadeem Faruqui

Theses and Dissertations

Zinc oxide nanoparticles (ZnO NPs) are very versatile due to their multifunctional properties including unique physicochemical and antimicrobial characteristics. They are widely utilized across various fields such as biomedical, industrial fields, environmental remediation, and agriculture. Therefore, their cytotoxic effects on biological systems necessitate a deeper understanding of the cellular responses to nanoparticle exposure. This project primarily investigates the impact of ZnO NPs on the model organism Dictyostelium discoideum AX4 (social amoeba) which has not been examined before unlike a vast variety of organisms in the literature. The cytotoxic effects of ZnO NPs on Dictyostelium discoideum AX4 cells are compared with …

Collaborative Research: Bocp-Implementation: Us-China: Multi-Scale, Multi- Proxy, Integrative Investigation Of Functional Biodiversity On A Changing Proterozoic Planet, Carol Dehler

Funded Research Records

No abstract provided.

08.18.2025 Ored Connect, Liz Williamson

ORED Newsletter

ORED on-demand training, Tableau training, Research Reception 2025

Fabrication Of Protein-Based Nanomicelle Against Inflamed Synoviocytes In Rheumatoid Arthritis, Madhumithra Thangadurai

Theses and Dissertations

Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by persistent synovial inflammation, progressive cartilage and bone destruction, and systemic complications. 1% of the global population are affected by RA, when their immune system targets synovial tissues, leading to joint pain, swelling, and functional disability. Standard treatments, such as disease-modifying antirheumatic drugs (DMARDs) like methotrexate (MTX), are limited by systemic toxicity and inconsistent patient responses, highlighting the need for improved therapies. This research work explores protein-glycosaminoglycan nanomicelles engineered using Zein with Chondroitin or carboxymethylated Dextran Sulfate as targeted drug delivery vehicles for RA.

MTX was encapsulated within these nanomicelles to …

Facilitating Farmer-To-Farmer Elearning: An Evaluation Of Climate And Wildfires Online Courses In California, Natalia Pinzon, Caitlin Brimm

Journal of Extension

This study assesses the effectiveness of two online courses tailored for farmers and ranchers in California, with a particular focus on the role of farmer-to-farmer pedagogies. Utilizing live sessions, a social-learning platform, and multimedia content, we draw insights from engagement metrics, lesson and end-of-course survey evaluations, and course outcomes. Key findings highlight the pivotal role of peer interactions, featuring farmers and completion incentives. Based on the findings, we advocate for the integration of farmer-to-farmer education methods within online learning environments to cultivate regional learning networks, and promote the timely exchange and co-creation of agricultural knowledge amid environmental change.