Digital Commons Network^™

The Aggregation Of Microplastics By Enhancing Extracellular Polymeric Substance Production In Pseudoalteromonas Sp. Ncimb 2021 To Improve Removal Efficiencies In Environmental Matrices, Janelle L. Mercer

All Theses

Microplastics (MP) are ubiquitous in the natural environment and are a growing threat due to their small size and durability. Plastics are released into the environment through improper waste management, wastewater treatment outfalls, industrial spills, agricultural runoff, and landfills. These particles breakdown into secondary MP through degradation pathways. MP, less than 5 mm, require intricate removal techniques from water systems. Filtration techniques, though viable and effective, have implementation constraints due to high cost, maintenance demands, and filter fouling. By integrating coagulation and flocculation processes prior to filtration, MP removal efficiencies can increase, while minimizing operational challenges during filtration. Extracellular polymeric …

Can Kinematics Specify Tool Use Affordances?, Tyler Duffrin

All Dissertations

Object properties such as length, shape, and heaviness, as well as affordance-based properties such as strike-with-ability and poke-with-ability, can be perceived via dynamic touch as functions of inertia tensor invariants. The primary question addressed here was whether people can perceive these same power and precision properties for purely virtual objects, which lack dynamic physical forces. The Kinematic Specification of Dynamics (KSD) principle asserts that missing dynamics are lawfully specified by kinematic (visual) motion patterns, such that kinematic information alone may support successful interactions with virtual objects. In three experiments, we investigated (1) whether virtual reality (VR) users could calibrate to …

Lizards In The Trees: Structural, Functional, And Behavioral Specializations To A High-Risk Environment, Victor D. Munteanu

All Dissertations

Animals must contend with unexpected changes in their habitat and environment to thrive. Arboreal habitats can consist of a wide variety of environmental features, and failure to adequately contend with these features can result in high risk of injury or death upon falling. Despite these strong selective pressures, many vertebrate lineages have successfully invaded arboreal habitats. Using lizard taxa as a model system, I investigated how morphology and behavior have evolved within this specific habitat transition. I pursued these investigations through complementary analyses including: 1) evaluating the effect of stance height and tail prehensility on perturbation recovery, 2) assessing behavior …

The Past, Present, And Future Of Climate Adaptation In A Widespread Lizard Species, Matthew R. Mcternan

All Dissertations

Climate, as a selective force, shapes patterns of biodiversity globally. However, how species adapt to climate remains a central question of biology. The need to understand climate adaptation is paramount, as global climate change threatens a large portion of global diversity. Climate can impose selection on life by either controlling rates of energy intake and expenditure through effects on body temperature and activity, or by exposing organisms to conditions beyond their physiological limits. Studies of climate adaptation have identified a wide-range of putatively adaptive phenotypic patterns, but genomic evidence is increasingly being used to investigate these patterns and better understand …

Why Technical Readiness Is Not Enough: Institutional Barriers To Full Harvest Strategy Adoption In The International Pacific Halibut Commission, Evelyn Roozee, Owen Temby, Gordon M. Hickey

School of Earth, Environmental, & Marine Sciences Faculty Publications

Harvest strategies are increasingly promoted as a mechanism to reduce political discretion and align fisheries management with pre-agreed scientific objectives. While substantial progress has been made in tuna regional fisheries management organizations (RFMOs), non-tuna RFMOs have lagged behind. Existing research has focused primarily on technical modeling challenges, with comparatively limited attention to the governance dynamics shaping adoption. Using the International Pacific Halibut Commission (IPHC) as an instrumental case study, we examine the progress and delays in the development of a harvest strategy policy (HSP) through semi-structured interviews and participant observation. We find that the IPHC successfully addressed commonly cited barriers, …

Quaking Aspen On Cedar Mountain, Utah: Status And Update, Jaycee Cappaert, Larissa L. Yocom, Paul C. Rogers, Darren J. Mcavoy, R. Justin Derose

Wildland Resources Student Research

Quaking aspen forests are important communities in the western United States where they provide preferential food and habitat for animals, limit wildfires from spreading, and have favorable aesthetics, among other things. Their putative decline is an issue for ecology and management. We remeasured the aspen population on Cedar Mountain, Utah, to assess changes to its condition since it was originally measured in 2008 and laid the groundwork for continued aspen monitoring on Cedar Mountain. Our objectives were to compare current metrics of stand structure and composition, mortality, crown dieback, bole damage, regeneration, and recruitment, to those of the original inventory. …

Agent-Based Modeling Of Cellular Dynamics In Adoptive Cell Therapies, Yujia Wang

Dissertations and Theses (Open Access)

Adoptive cell therapies (ACT) have shown promising progress in combating cancer, but clinical responses remain heterogeneous. Key determinants, including the functional states of infused cells, tumor–immune interactions, and dosing strategies, are difficult to resolve experimentally in the dynamic and heterogeneous tumor microenvironment, limiting optimization of ACT products and treatment regimens. To address the gap, we developed ABMACT (Agent-Based Model for Adoptive Cell Therapies), a computational framework that reconstruct key cellular functions, interactions, and molecular signatures to recapitulate cell population dynamics associated with differential treatment responses. ABMACT encodes autonomous “virtual cells” using literature-informed rules calibrated with experimental data, enabling simulation of …

Oxidative Stress Mediated Glutamate Release And Nmda Receptor-Dependent Synaptic Remodeling In Radiation-Induced Cognitive Dysfunction, Thanh Lam

Dissertations and Theses (Open Access)

In children younger than 14 years old, the brain and other parts of the central nervous system are the most common sites for solid tumors. Radiotherapy is an effective treatment for central nervous system (CNS) tumors. However, it often causes a progressive decline in cognitive functions, which is especially devastating for pediatric patients. Although post-mitotic neurons are generally considered resistant to radiation-induced immediate cell death, ionizing radiation causes complex neurochemical and structural changes that damage synaptic integrity. In this study, we examined the molecular cascades following a 10 Gy radiation dose applied to mouse cortical neurons. We found that radiation-induced …

From Geometry To Recognition: A Quantitative Framework For Tcr-Pmhc Structural Analysis In The Age Of Predicted Structures, Kun Hee Kim

Dissertations and Theses (Open Access)

Recognition of antigen by a T cell begins with a single physical event, the engagement of the T cell receptor (TCR) with a peptide-major histocompatibility complex (pMHC), and this interaction is encoded in the geometry with which the receptor docks onto the composite pMHC surface. Whether that docking geometry is biologically organized, and whether the structures now produced at scale by prediction preserve recognition or only reproduce that organization, are the two questions this thesis addresses. Two gaps stand in the way. The first is a gap of measurement, because docking geometry has never been made quantitatively comparable across many …

Antigen Discovery In Multiple Myeloma Using Integrated Long-Read Transcriptomics And Immunopeptidomics, Aya Albittar

Dissertations and Theses (Open Access)

Multiple myeloma (MM) remains an incurable plasma cell malignancy, with relapse driven by persistent chemotherapy-resistant cells and residual disease following treatment. Although immunotherapies have transformed MM care, their success depends on identifying tumor-specific antigens that can be safely targeted. While aberrant genomic structural variation and transcriptional dysregulation are increasingly recognized as sources of novel antigens in MM, the HLA-presented antigenic landscape of MM remains incompletely characterized, particularly for non-canonical, structurally-derived peptides, and long-read transcriptome-informed immunopeptidomic data specific to MM remain scarce.

We established an integrated antigen discovery platform combining long-read RNA sequencing (Iso-Seq) with mass spectrometry-based HLA immunoprecipitation and immunopeptidomics …

Alfred Russel Wallace Notes 42: How Accurate Are The Transcriptions Presented At The Alfred Russel Wallace Page Website?, Charles H. Smith

Faculty/Staff Personal Papers

A look is taken at the level of accuracy displayed by the transcriptions of Wallace writings offered at the Alfred Russel Wallace Page website, as determined by a ChatGPT analysis.

Optimizing Urban Forestry Through Green Infrastructure: Tree Health And Water Retention In Ciudad Juarez Rain Gardens, Tomas Rogelio Lizarraga Ruiz

Open Access Theses & Dissertations

Urban green spaces (UGS) in arid regions face significant challenges due to water scarcity and extreme thermal demand. This study evaluates the efficacy of Nature Based Solutions (NBS), rain gardens and median strips, in enhancing the physiological resilience of urban trees in Ciudad Juárez, Mexico. Using a comparative framework, the research monitored a native evergreen (Dermatophyllum secundiflorum) and an introduced deciduous species (Morus sp.) across six planting treatments. Statistical analysis reveals that green infrastructure (GI) acts as a critical physiological accelerant. Trees situated within rain gardens and medians significantly outperformed those in restricted pot and sidewalk settings, maintaining higher stomatal …

The Rpm-1/Phr Signaling Hub Modulates Tau-Induced Neurodegeneration Through Regulation Of Microtubule Stability And Mapk Pathways In C. Elegans, Xinxing Ding

Theses and Dissertations

Neurodegenerative diseases, including Alzheimer's disease and frontotemporal dementia, are characterized by the accumulation of pathological tau proteins and progressive neuronal loss. Although research regarding tau-mediated toxicity is extensive, the specific pathology that determine whether neurons maintain homeostasis or succumb to collapse under tau-induced stress remain incompletely elucidated. A central, yet still insufficiently understood, feature of these diseases is the disruption of the microtubule (MT) cytoskeleton . The PHR protein family is evolutionarily highly conserved; within this family, RPM-1 in C. elegans functions as an intracellular signaling hub that regulates axon development, synapse formation, axon termination, and various microtubule-associated processes. This …

The Effect Of Cerebellar Transcranial Direct Current Stimulation On Anxiety, Shivangi Bhardwaj

All-Inclusive List of Electronic Theses and Dissertations

Anxiety is one of the most prevalent mental health disorders in the U.S. Individuals of all ages are affected by anxiety. Therefore, research into anxiety and its potential treatment has constantly been an area of interest. Newer approaches to managing anxiety include non-invasive stimulation techniques, such as Transcranial Direct Current Stimulation (tDCS), because of its accessibility and effectiveness. Past tDCS work typically focused on regions in the frontal lobe. However, tDCS over the cerebellum has not received as much attention compared to the cerebrum, despite recent work demonstrating cerebellar involvement in emotion processing. Thus, a better understanding of how cerebellar …

Machine Learning In Flow Cytometry For Acute Myeloid Leukemia Diagnosis: A Scoping Review, Katrina Jezzela M. Dela Pena Md, Mls (Ascp)

Other Specialties

Manuscript version:

Introduction: Flow cytometry is essential for the diagnosis of acute myeloid leukemia (AML), but conventional analysis is labor-intensive, operator-dependent, and increasingly complex. Machine learning (ML) may support automated analysis; however, its readiness for clinical implementation remains unclear. This scoping review mapped ML approaches applied to flow cytometry for AML-related diagnosis.

Methods: PubMed was searched for English-language primary studies applying artificial intelligence, ML, or deep learning to human flow cytometry data for AML diagnosis or classification. Eligible studies reported diagnostic performance metrics. Study characteristics, preprocessing, data representation, model architecture, validation strategy, performance metrics, interpretability, and implementation considerations were descriptively …

An Evaluation Of Peer Mentoring In A Pre-Veterinary Science Program Within A College Of Forestry And Agriculture, Amy Neal

Electronic Theses and Dissertations

Mentoring is a tool utilized to improve the retention of college students and can serve as an effort to increase their willingness to persist despite challenges. Establishing mentoring relationships amongst first-year students and more-experienced students can create a sense of belonging. Mentorship programs may be developed within a particular major or program. Within this study, an online survey was formed to analyze the perceptions of first-year pre-veterinary students in Fall 2024 and Fall 2025. A peer-mentorship program was implemented amongst pre-veterinary students in Fall 2025. First-year students who completed the survey in Fall 2024 were not mentored. Many of the …

Forest Cover Effects On Canopy Interception Loss, Evapotranspiration, And Soil Infiltration On Stormwater Detention Basins, Alexandria N. C. Perez

Electronic Theses and Dissertations

Developing cities and increased impervious surfaces has resulted in more surface runoff and severe flooding. Harris County, Texas has experienced major flooding events, such as Hurricane Harvey in 2017 which was estimated to be a 9,000-year flood event. The Harris County Flood Control District (HCFCD) is dedicated to creating, maintaining, and finding new ways to reduce flooding damage such as the use of detention basins as green infrastructure. These basins are either populated by grass or are planted with various tree species. This study will identify the planted trees’ canopy interception loss, reference evapotranspiration, and enhanced soil infiltration effects within …

Examining Pain Catastrophizing, Mental Toughness, Self-Efficacy, And Perceived Pain In The Performance Of Female Athletes During Their Menstrual Cycle, Carissa R. Martinez

Electronic Theses and Dissertations

Pain is a universal unpleasant or negative experience influenced by physiological, psychological, and environmental factors. Disruption in the neural pathways of pain can affect athletic performance and lead to injury risks. Both negative attributes, such as stress, anxiety, and depression, and positive attributes, such as mental toughness and self-efficacy, contribute to pain perception and catastrophic thinking. The menstrual cycle also plays a critical role in pain catastrophizing, as hormonal fluctuations across different phases may hinder pain perception and performance in female athletes. However, research lacks the inclusion of how these factors impact female athletes. Using a non-experimental quantitative analysis, this …

Harnessing Kenyan Aquaculture Through Social Media: Impacts, Challenges And Strategic Directions, Domitila Kyule, Jonathan Munguti, Mavindu Muthoka, Esther Magondu, Menaga Meenakshisundaram, Chrysantus M. Tanga, Kevin Obiero, Cecilia Githukia

All Peer-Reviewed Publications

Aquaculture is increasingly important for food, nutrition and livelihoods in Kenya, but the sector still faces persistent constraints in extension delivery, farmer learning, input access, market coordination and information reliability. This review examines how social media and related digital communication tools are shaping aquaculture development in Kenya, with attention to impacts, challenges, governance needs and strategic directions. A systematic literature review of studies and institutional sources published between 2015 and 2025 was conducted. The search identified 388 records, of which 45 sources were included in the final synthesis after screening, eligibility assessment and quality appraisal. Because the evidence was heterogeneous, …

A Comparison Of Ahdrift And Pitfall Traps For Surveying Small Vertebrates, Gabrielle Risko

All-Inclusive List of Electronic Theses and Dissertations

Understanding species occupancy is necessary to inform wildlife management and conservation decisions. To minimize the invasiveness of occupancy studies, some wildlife researchers have deployed game cameras to detect the presence of small vertebrates instead of utilizing stressful traditional live-capture methods. The Adapted Hunt Drift Fence Technique (AHDriFT) is an increasingly popular method for modifying and deploying camera traps to detect small vertebrates; however, no studies have directly compared AHDriFT to traditional pitfall traps operating at the exact same time, even though both are deployed along drift fences to capture small vertebrates. I compared these two methods (pitfall trapping and AHDriFT …

Reconstruction Of Copepod Populations In Sierra Nevada Lakes Using The Diatom Fragilaria Cyclopum, Rorie Reisner

All-Inclusive List of Electronic Theses and Dissertations

Copepods are one of the most abundant types of zooplankton, and their populations are often a vital part of the food chain, but their past populations cannot be estimated from lake sediments because their exoskeleton usually does not fossilize. Gull Lake is a glacial lake located in the subalpine region of the Sierra Nevada, California, which stands out due to the presence of the diatom Fragilaria cyclopum, which is rarer in diatom assemblages. Fragilaria cyclopum exclusively grows on copepods in lakes. Diatoms have an opaline silica skeleton that often fossilizes in lake sediments, so we can use this relationship with …

Reconstructing Stand-Age Structure In A Wet Miombo Woodland Using Dendrochronology, Zambia, Clara Tiyembekeze Zulu

All-Inclusive List of Electronic Theses and Dissertations

Dendrochronological research in tropical Africa has remained limited, leaving critical gaps in stand-age structure and climate-growth relationships in seasonally dry tropical woodlands. This study reconstructed stand-age structure and assessed climate sensitivity in the wet Miombo woodland of African Explosives Limited (AEL) forest, Copperbelt Province, Zambia. Field sampling was conducted during four African Dendrochronology Fieldschools (2021-2024) using a Modified Variable Area Transect (MVAT) design across nine plots. The series intercorrelation was 0.351; the average mean sensitivity was 0.423. The oldest tree was 170 years old, and more than 70% of the sampled species showed potential for dendrochronology. Markhamia obtusifolia was the …

Performance Of The Denitrification-Decomposition Model In Simulating Agronomic Properties And N2o Emissions Under Smallholder Climate-Smart Farming Systems, Esphorn Kibet, Collins M. Musafiri, Milka Kiboi, Onesmus K. Ng'etich, David K. Kosgei, Abdirahman Zeila, Franklin Mairura, Felix K. Ngetich

All Peer-Reviewed Publications

The DeNitrification-DeComposition (DNDC) model is a crucial tool for estimating soil greenhouse gas fluxes and understanding soil-plant interactions. This study evaluates the performance of the DNDC model in simulating soil temperature, moisture, crop yield, and nitrous oxide (N2O) fluxes across different land utilization types in Western Kenya. The land utilization types included: i) agroforestry M (agroforestry with Markhamia lutea, ii) sole sorghum, iii) agroforestry L (agroforestry with Leucaena leucocephala), iv) sole maize, and v) grazing Land, each replicated thrice. Fertilizer and manure were applied as part of the management practices, with manure applied at 2t ha⁻¹. Soil greenhouse …

The Relationship Between Depression And Cognitive Proficiency Index Across Biological Sex, Angela N. Ferdinardo

Dissertations

Depression is a widely studied mood disorder, and understanding its effect on cognitive functioning has become an important area of research. While research has examined relationships among depression, working memory, and cognitive deficits, limited research has explored depressive symptoms and cognitive proficiency across biological sex. Depression manifests similarly in men and women, though men are more likely to experience irritability, impulsivity, and anger, while women tend to experience sadness, stress, and sleep disturbances (Johns Hopkins Medicine, 2023). Women are also more likely to seek treatment and cope differently than men. This study examined the relationship between depression and cognitive proficiency …

Physiological, Cognitive, Behavioral, And Perceptual Contributors To Falls Risk Across Middle And Older Adulthood, Jacquelyn Moxey

Rehabilitation Sciences Theses & Dissertations

Falls are multifactorial events influenced by physiological, cognitive, behavioral, and perceptual factors. Although falls prevention research has traditionally focused on older adults and objectively measured physical impairments, less is known about how cognitive performance, physical activity, and perceptions of ability collectively contribute to falls risk vulnerability across middle and older adulthood. This dissertation examined these relationships through three complementary studies.

Study 1 examined associations between cognitive screening performance and physiological falls risk in 315 community-dwelling older adults. Lower global cognitive performance was associated with greater physiological falls risk. Performance on items reflecting attention and visuospatial/executive function demonstrated the strongest domain-level …

High Biochar Rate Improves Water Retention In Some Environmentally Sensitive Soils, Samundra Sigdel

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Improving water retention and other hydraulic properties is key to managing soil water and sustaining crop production under fluctuating and extreme weather events. We assessed how wood biochar (836 g C kg^-1) applied at 0, 6.25, 12.5, 25, and 50 Mg ha^-1 affected: i) soil hydraulic properties after 5 years and ii) corn and soybean yield, and biomass production of cereal rye cover crop (CC) and CC mix (cereal rye, radish, and winter pea) in sandy, sloping, and semi-arid soils in the central U.S. Great Plains over 6 years. Biochar affected field saturated hydraulic conductivity (K_{sat …}

An Analysis Of Mating Strategies In Rotifers Inhabiting Temporary Habitats, Ariel Bollinger

Open Access Theses & Dissertations

Reproduction is critical for organisms inhabiting ephemeral aquatic habitats where desiccation risk favors rapid and successful mating. Monogonont rotifers rely on sexual reproduction to produce diapausing eggs that withstand harsh conditions. I investigated how mating behaviors vary among populations of five rotifer species based on the hydroperiod of their habitat: Epiphanes brachionus and E. chihuahuaensis were sampled from habitats with short (SH) and long (LH) hydroperiods; Euchlanis dilatata was collected from a short (SH) and a permanent habitat; and Plationus patulus and Sinantherina socialis were collected from a long (LH) and a permanent (Perm) habitat. I hypothesized that SH populations …

Biomolecular Corona Of Extracellular Vesicles: Report On Isev Workshop, Lucia Paolini, Selene Tassoni, Khuloud T. Al-Jamal, Xavier Banquy, Tamás Beke-Somfai, Paolo Bergese, Fanni Annamária Boros, Massimo Bottini, Ben Boyd, Sara Busatto, Benedetta Bussolati, Ester Canepa, Valentina Castagnola, Aled Clayton, Kenneth Dawson, Samir El-Andaloussi, András Försönits, Orazio Fortunato, Roberto Frigerio, Martina Gabrielli, Cristina Grange, Michele Guescini, Yuya Hayashi, Jonas Klejs Hemmingsen, Seungmin Kim, Ilyes Kinga, Heikki Kyykallio, Metka Lenassi, Luize Goncalves Lima, Mỹ G. Mahoney, Camille Menaceur Vandenbroucke, Andreas Möller, Angelo Musicò, Inge Nelissen, Lucas Fabrício Bahia Nogueira, Christa Nöhammer, Pietro Parisse, Charles Ramassamy, Kelly Cristine Santos Roballo, Anna Salvati, María Sancho-Albero, Ganesh Shelke, Paniz Shirmast, Tasvilla Sonallya, Imola Csilla Szigyártó, Monique A. J. Van Eijndhoven, Tapani Viitala, Shan Wang, Yan Yan, Andrea Zendrini, Edit Buzás, Annalisa Radeghieri

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

The concept of the "biomolecular corona" (BC) was first introduced to describe the spontaneous absorption of molecules, mainly proteins, onto the surface of synthetic nanoparticles upon exposure to biological fluids. More recently, the same term has been used to describe biomolecules that dynamically interact with the surface of extracellular vesicles (EVs) during their biogenesis, secretion, or upon exposure to intracellular or extracellular milieus, including biological fluids. The EV biomolecular corona is a key determinant of EV identity, shaping their cellular uptake, biodistribution, and functional outcomes in both physiological and pathological contexts. EVs, in contrast to synthetic nanoparticles, introduce distinct challenges …

Building Bridges: Connecting Biomechanics And Lived Experience In Bertolotti's Syndrome, Andrea Morgan Muffly

Rehabilitation Sciences Theses & Dissertations

Bertolotti’s Syndrome (BSy), characterized by the presence of a lumbosacral transitional vertebra (LSTV), represents a complex clinical entity that affects not only the physical health of the individual, but the quality of their daily life. Prior research on BSy focused on epidemiology, not lived experience, revealing inconsistencies in diagnostic inconsistencies of LSTV morphology. A three-tiered diagnostic system is proposed to streamline the reporting of LSTV subtypes. We examined how BSy is diagnosed, its symptoms, presentation, and how this impacts individuals’ ability to participate in activities of daily living (ADLs) and instrumental activities of daily living (IADLs). We conducted a multi …

Modulation Of Electrophysiology And Plaque Aggregation In Huntington’S Disease Patient-Derived Cells By Picosecond Pulsed Electric Fields, Mackenzie A. Tardif-Kunk

Biomedical Sciences Theses & Dissertations

Huntington’s Disease (HD) is a fatal, autosomal dominant neurodegenerative disorder characterized by progressive motor and cognitive decline. Unstable expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats in the huntingtin gene, often exceeding 35–40 repeats, results in an extended polyglutamine (PolyQ) tract in the translated protein. Abnormal folding of the mutant huntingtin (mHTT) protein leads to accumulation and aggregation within the cell, dysregulating various cellular processes through molecular sequestration. While several therapeutic strategies have been proposed, this disease remains incurable with treatments limited to symptom management.

Pulsed electric fields (PEF), primarily in the microsecond and nanosecond ranges, have been studied extensively for the …