Digital Commons Network^™

Enhancing Llm Code Generation: A Systematic Evaluation Of Multi-Agent Collaboration And Runtime Debugging For Improving Accuracy, Reliability, And Latency, Nazmus Ashrafi

Theses

The use of large language models (LLMs) for automated code generation has emerged as a significant focus within AI research. As these pretrained models continue to evolve, their ability to understand and generate complex code structures has opened up new possibilities for automating intricate programming tasks with greater accuracy. Although contemporary foundational models demonstrate promising results, researchers continue to explore optimal post-training strategies to enhance code quality. These include supervised fine-tuning, retrieval-augmented generation (RAG), debugging, and many others. In this thesis, I combine two such widely used post training approaches—namely (1) multi agent collaboration and (2) runtime execution of information-based …

Illustrations For A Scientific Review Article Publication : Human Stem Cell-Derived Organoids, Sunghwan Bae

Theses

This thesis explores the role of scientific illustration in improving the comprehension of complex scientific concepts. It traces the historical development of illustrations in scientific literature and examines their functions in both research and review articles. The central contribution of this work is the development of twelve vector-based illustrations that elucidate the applications of human organoids within a review article context. These visuals transform intricate ideas into clear, engaging representations, supported by extensive research and verification to maintain scientific accuracy. The thesis concludes by addressing the future of scientific illustration, advocating for reader-oriented design approaches and the use of innovative …

Democratizing Community Discourse Analysis In Computational Social Science, Md Towhidul Absar Chowdhury

Theses

Community resource inequities and undetected infrastructure vulnerabilities cost municipalities billions annually, with disproportionate impacts on marginalized communities. Current computational approaches to community needs assessment suffer from two critical limitations: they rely on aggregate-level analysis that obscures granular community expressions, and they implement sophisticated computational tools that remain inaccessible to stakeholders without technical expertise. This creates what we term the Community-Computational Gap—a persistent divide where domain experts with vital contextual knowledge cannot access the analytical tools they need, while computational experts develop models without sufficient community context. This dissertation addresses these challenges through a novel methodological framework for fine-grained utterance-level classification …

Characterizing Fish Communities Using Traditional And Emerging Monitoring Approaches In San Diego County Estuaries, Natalie Katherine De Wet

Theses

Fish communities are essential to estuarine health, playing key roles in food webs, nutrient cycling, and ecosystem functioning. However, the persistence of native fish populations is increasingly threatened by the cumulative impacts of coastal development, pollution, and climate change. Rapid, effective monitoring of species distributions is a priority, enabling timely conservation and management. However, the study of any ecosystem is limited by time, resources, and the consideration that research of a system can damage the ecosystem under study.

This research aimed to characterize fish species richness and evaluate the benefits and limitations of different estuary monitoring approaches. Specifically, this study …

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 …

Post-Traumatic Stress Disorder Symptom Scale And Coping Mechanisms Among Internally Displaced Persons Of Typhoon Yolanda, Christian Paul S. Biluan

Theses

The study aimed to determine the Post-Traumatic Stress Disorder Symptom Scale and the Coping Mechanisms utilized by the Internally Displaced Persons of Typhoon Yolanda. It sought to identify the profile, risk factors of the respondents, the Post-Traumatic Stress Disorder (PTSD) symptoms manifested and coping mechanisms utilized. The study also distinguished the differences in PTSD and Coping mechanisms when respondents are grouped according to their profile and death of family members and examined the relationship of PTSD and Coping. The study adopted the PTSD Symptom Scale and Brief COPE Inventory questionnaires and were consequently translated to Visayan-Waray. These were then pilot-tested …

From Sim To 6dof: Deep Learning For Real-Time Satellite Pose Estimation From Resolved Ground-Based Imagery, Thomas W.N. Dickinson

Theses

This dissertation presents the first practical system for automated six degrees of freedom (6DOF) satellite pose estimation from resolved ground-based adaptive optics (AO) imagery. Addressing a key challenge in Space Domain Awareness (SDA), the proposed approach eliminates the need for human labeling by directly regressing satellite orientation and position from blurry, noisy, and deeply-shadowed imagery. The architecture consists of a multi-stage deep neural network pipeline that localizes the satellite, predicts pose, and optionally smooths predictions over time. Networks are trained exclusively on fully synthetic imagery generated from a 3D CAD model. Despite this, the model generalizes effectively, bridging the Sim2Real …

Degradation Of Anthropogenic Debris In Stormwater Infrastructure Of The Lake Ontario Watershed, Evan Batte

Theses

The accumulation of anthropogenic debris (AD) in the Great Lakes is a growing issue with largely unknown consequences for ecological and human health. To better constrain estimates of debris loading into Lake Ontario and elucidate the fate of AD accumulating upstream, an incubation experiment of the most commonly identified littered products was conducted in different stormwater infrastructure within the Lake Ontario Watershed. Chip bags, cigarette filters, and shopping bags were placed into storm drains, stormwater retention ponds, and along riparian zones of tributaries in December of 2022 and July of 2023 to test the spatial (type of stormwater infrastructure [SWI]) …

Enhancing Adversarial Robustness In Convolutional Neural Networks By Integrating Human Viewing Strategies, Diana Velychko

Theses

Adversarial examples pose a serious threat to the reliability of deep neural networks by subtly manipulating inputs to induce incorrect outputs. Despite progress in the field, convolutional neural networks (CNNs) remain vulnerable to such perturbations. This research proposes a novel approach to improve adversarial robustness of CNNs by incorporating human viewing behavior into both training and testing processes. To establish a baseline for comparison with models trained from scratch, an eye-tracking dataset—collected during experiments involving novel objects from the Greeble dataset—was used to capture how humans learn to classify previously unseen object categories. This study compares model saliency with human …

Pd Chlorin-Based Molecμlar Imaging Probes For Breast Cancer, Yoonjung Cho

Theses

Breast cancer (BrCa) is the second most common cancer and the second leading cause of cancer death among women in the U.S. This highlights the necessity of developing effective therapeutic agents to aid in the treatment of BrCa. A promising new method of treatment is photodynamic therapy (PDT), a clinically approved therapeutic procedure that uses a porphyrin-based photosensitizer (PS) dye to kill cancer cells upon excitation with a light source. It has been observed that chelation of a metal ion into the porphyrin increases the therapeutic efficacy. We have developed a synthetic route incorporating the palladized analogue of the PS …

Digital Biophilia In Web Interface Design For Accessibility And User Well-Being, Bryana Michelle Peifer

Theses

This interdisciplinary study explores the intersection between horticultural therapy and web design, focusing on the impact of biophilic design principles in shaping contemporary practices within digital interface design. This exploration addresses the multifaceted relationship between humanity and the natural world, particularly how this connection serves as a source for the emergence of nature-inspired elements in digital expressions and their subsequent integration into modern web design for accessibility and well-being. As digital environments increasingly dominate daily experiences, the need for digital wellness through nature integration has become critical, especially for individuals who have physical disabilities, limited mobility, or limited access to …

Advancing The Utility Of Unmanned Aerial Systems (Uas)-Based Imaging Techniques In Broadacre Agriculture: A Multimodal Case Study On Table Beets, Mohammad Shahriar Saif

Theses

Efficient and sustainable food production and management are growing concerns in the context of an ever-increasing global population. It is in this context that the integration of remote sensing with advanced imaging technologies presents transformative opportunities for data-driven decision-making in agriculture. This study therefore explores the use of unmanned aerial systems (UAS) equipped with multispectral, hyperspectral, and LiDAR sensors for the non-destructive monitoring of table beet (Beta vulgaris) crop traits, with a specific focus on root yield estimation and foliar disease assessment. Table beet, a subterranean crop of increasing commercial and nutritional importance, poses unique challenges for above-canopy sensing due …

Engineering Tunable Collagen Fiber Alignment Gradients To Quantify Contact Guidance Effects On Cell Migration, Indranil Mandar Joshi

Theses

Directional migration of cells is one of the most important physiological processes, necessary for tissue and organ development. It also plays a crucial role in pathological conditions such as cancer metastasis. This directed migration is influenced by various factors present in the native environment, which guide cells to migrate steadily in a specific direction. Due to its importance, over the years, a lot of emphasis has been placed on understanding and exploring the biochemical and biophysical factors that direct cell migration. In addition to the commonly studied biochemical and biophysical cues, contact guidance from collagen fibers, in the native matrix, …

Comparative Phylogeography Of Three Widely Distributed Amazonian Poison Frogs, Sofia Del Milagro Granados Martinez

Theses

Amazonia has gone through extensive changes in its climates, geology, hydrology and drainage systems over the past 10 mya; these processes have been postulated as key drivers of diversification. Contrary to the trend where species once broadly distributed are subdivided into several species with restricted distributions, many taxa span the Amazon basin without noticeable genetic differentiation. In my thesis, I studied the phylogenetic and phylogeographic patterns of three widely distributed Amazonian poison frogs: Ameerega hahneli, Ameerega trivittata and Ranitomeya variabilis. I examined phylogenetic relationships based on two different types of genomic data—nuclear and mitochondrial—and I carried out population structure analyses. …

Impacts Of Permafrost Thaw And Methane Cycling In A Northern Peatland, Hannah Defelice

Theses

Climate change is disproportionately impacting high latitude regions, resulting in thawing permafrost, changes in vegetation, hydrology and greenhouse gas emissions. As permafrost thaws in peatlands, ground subsidence occurs, resulting in a transition from elevated palsa to lower, wetter bogs and fens. Changes in vegetation and hydrology with thaw result in increased methane (CH4) fluxes and distinctive shifts in the carbon isotope signature of porewater and emitted CH4. Previous research has established the differences between these landcover classes; however, we know little about how CH4 cycling processes change during land class transitions. To address this gap, we compared recently formed bogs …

Zoo Visitors Learn By Observing Olive Baboons (Papio Anubis) Participate In Cognitive Research Or Engage In Natural Behaviors, Anna Sofia Hege

Theses

I conducted two experiments at the baboon exhibit at the Seneca Park Zoo in Rochester, New York to measure attitudes and actual knowledge in children and adults, as well as perceived learning in adults. I also recorded caregiver-child conversations in the presence and absence of live research. Experiment 1 included 150 adult participants, and Experiment 2 included 18 caregiver-child dyads. In each experiment, the research on-scientist present and research on-scientist absent group watched the baboons engage with live cognitive research while the research off-scientist present and research off-scientist absent group watched the baboons carry out their natural behaviors. A scientist …

Effects Of Self-Monitoring On Teachers’ Behavior-Specific Praise And Students’ Behavior In A Center-Based Classroom, Samantha Walsh

Theses

The current study explores the effects of self-monitoring on teachers' use of behavior-specific praise (BSP) and its impact on student behavior in a center-based classroom. Self-monitoring, a cost-effective and time-efficient intervention, has been proven effective in previous research for enhancing educator performance. However, previous studies have often combined self-monitoring with other interventions, leaving a gap in understanding its effects in isolation. This study aims to replicate the work of Justus et al. (2023) by examining the impact of self-monitoring on paraprofessionals in a center-based classroom with students aged 6-10. Using a multiple baseline design across participants, three paraprofessionals were trained …

Protein Language Models-Based Representation For Post-Translational Modification Prediction, Suresh Pokharel

Theses

Post-translational modifications (PTMs) are chemical changes that occur after translation and play a key role in regulating protein function and cellular processes. Their dysregulation is associated with various diseases, making accurate prediction of PTM sites essential for understanding cellular mechanisms and informing therapeutic strategies. This work focuses on the computational prediction of two biologically significant PTMs, namely succinylation and O-GlcNAcylation, utilizing recent advances in protein language models (pLMs). Drawing an analogy to natural languages, amino acids are treated as words and sequences as sentences, allowing pLMs to capture contextual dependencies within protein sequences. One of the earliest contributions of this …

Benedictine Art And Design: How Color Psychology Can Positively Influence Department Enrollment, Claire Pauline Fink

Theses

This thesis examines how design strategies informed by color psychology and experimental aesthetics can be used to strengthen the visual identity and recruitment efforts of the Benedictine College Art & Design Department (BCAD). Following the recent addition of Graphic Design as a major and the department’s name change in 2021, there has been a noticeable gap in public awareness and printed promotional materials tailored to prospective students. Grounded in theoretical frameworks, such as D. E. Berlyne’s optimal arousal theory, and supported by survey responses from current Art & Design students, this project identifies key needs in marketing to prospective students. …

Through A Mother's Eyes: The Psychology Of Color, Katie Kutz

Theses

This project investigates the intersection of color psychology, maternal experience, and visual perception through a series of five artworks. Using a qualitative methodology, this project draws upon interdisciplinary research such as neuroscience, marketing, art history, and personal experiences as a mother. This work explores how sensory changes during pregnancy and postpartum influence the emotional perception of color, and how this can be represented in art. Inspired by artists that have explored the theme of motherhood such as Mary Cassatt, Käthe Kollwitz, Paula Modersohn-Becker, Jenny Saville, and Alice Neel, this project uses an emotionally charged approach to depicting motherhood. Color changing …

Elisabetta Sirani’S Timoclea: Baroque Agency And The Aesthetics Of Feminine Rage, Shaylen Grace Gardner

Theses

This thesis examines Timoclea Kills the Captain of Alexander the Great (1659) by Elisabetta Sirani as a foundational example of feminine rage within the Baroque period. By framing Timoclea’s violent act not as an outlier or solely reactive gesture, but as a deliberate, composed assertion of power, Sirani constructs a model of feminine agency that defies patriarchal expectations of female submission and passivity. Through interdisciplinary analysis grounded in feminist theory, formal visual analysis, and retrospective cultural studies, this research argues that Sirani’s Timoclea exemplifies the Baroque’s strategic use of socially acceptable iconography to veil explicit challenges to gendered expectations. This …

Consumer Behavior Of Gen Z In Kosovo: Purchasing Preferences And Brand Engagement, Sara Dumani

Theses

This capstone project examines the consumer behavior of Generation Z in Kosovo by analyzing their purchasing preferences and brand engagement. The Generation Z demographic, which includes individuals born between 1996 and 2010, is the focus of this study. This generation is characterized by digital savviness and a significant influence from social media platforms, shaping their purchasing decisions and brand engagement. Generation Z’s behavior is often marked by a preference for online shopping, collaborative marketing approaches, and sustainability, making it essential to understand these factors in the context of Kosovo. The data for analyzing Generation Z’s consumer behavior were collected through …

Development Of Nanopocket Membranes For The Isolation And Purification Of Extracellular Vesicles, Munther Alsudais

Theses

Extracellular vesicles (EVs) play a crucial role in intercellular communication and serve as significant biomarkers for various diseases. EVs carry biomolecules such as lipids, proteins, DNA, and RNA, which reflect the physiological state of their cells of origin, making them promising tools for non-invasive diagnostics and therapeutic applications. Effective isolation of EVs is essential for advancing scientific understanding of their biological roles and unlocking their clinical potential. Porous membranes have been widely used for the purification of various biological species from biological fluids. While membranes have prove highly effective for general size-based separation, recent innovations have focused on structurally refined …

Online And Offline Multi-Variate Time Series Forecasting With Neuroevolution Based Neural Architecture Search, Zimeng Lyu

Theses

Time series forecasting plays a crucial role in various fields, ranging from financial markets and predictive maintenance in industrial settings to healthcare analytics. Traditionally, statistical approaches were employed primarily for univariate forecasting tasks, but modern applications often require robust solutions capable of handling complex, multivariate, noisy, and non-stationary data. Current state-of-the-art solutions predominantly utilize transformer-based models, which demand significant computational resources, limiting their practicality, especially in resource-constrained environments. This dissertation introduces novel and efficient approaches to multivariate time series forecasting, leveraging NeuroEvolution-based Neural Architecture Search (NAS) methodologies. Specifically, two robust algorithms---Evolutionary eXploration of Augmenting Memory Models (EXAMM) for offline forecasting …

Network And Tree-Based Approaches To Data-Driven Modeling Of Complex Climate Systems, Adam M. Giammarese

Theses

The guiding thread throughout this thesis work is data-driven modeling of Earth's climate. We investigate a variety of settings within the field of complex climate systems, such as gridded, high-resolution reanalysis data, lower-resolution climate indices, and incomplete paleoclimate records with missing values. We begin with reanalysis data of high spatial and temporal resolution, and use climate network analysis to uncover hidden trends in the data in regards to the Amazon rainforest and its changing role in the global climate system. We introduce a novel formulation of k-nearest neighbors climate networks to study changing trends at a local level, and apply …

Advancements In Fabry-Pérot Cavity Fabrication And Its Applications In Photothermal Spectroscopy For Trace Gas Sensing., Giulia Malvicini

Theses

The detection of trace gases is essential in various applications, from environmental monitoring and industrial process control to medical diagnostics. The need for high-sensitivity, compact, and costeffective gas sensing systems drives continuous advancements in sensor technology. Among optical sensors, photothermal spectroscopy (PTS) offers distinct advantages, detecting the indirect effects of thermal waves induced in the sample by exciting the molecules with a laser. More particularly, photothermal interferometry (PTI) uses interferometric methods, such as the Fabry-Pérot (FP) interferometer for the read-out.

Potential Of Blood-Based Assays To Enhance The Diagnosis, Risk Stratification And Monitoring Of Multiple Myeloma Patients, Aisling O Brien

Theses

Multiple Myeloma (MM) remains an incurable haematological malignancy; however, continuous advancements in treatment strategies have significantly improved patient survival. There is now a pressing need for enhanced detection methods to ensure optimal patient outcomes. This includes rapid diagnosis, early detection of relapses, and identification of high-risk patients. Diagnosis: For optimal patient results, initiating early MM diagnosis at the primary care level is essential. Delays in diagnosis can result from nonspecific presenting symptoms such as anaemia and bone pain. A retrospective observational study identified calculated globulin as a promising clinical biomarker to indicate MM in primary care. Subsequent implementation of calculated …

Crispr-Dcas9 Genomic Engineering For Boosting The Therapeutic Potential Of Extracellular Vesicles, Iker Martinez Zalbidea

Theses

Degenerative disc disease is a major contributor to low back pain, characterized by inflammation of the intervertebral disc (IVD), degradation of the extracellular matrix, loss of hydration, and cell death. Current therapies fail to address these underlying mechanisms, underscoring the need for regenerative strategies. Mesenchymal stem cells (MSCs) exhibit immunomodulatory and regenerative potential, but their efficacy is hampered by the harsh microenvironment of the degenerated IVD. Acellular MSC-derived extracellular vesicles (EVs) have shown therapeutic potential and offer a promising alternative for IVD regeneration. Here, we explore CRISPR-dCas9 mediated activation of TSG6 and STEAP3 to boost the therapeutic potency and biogenesis …

Linking The Spatial, Temporal, And Compositional Variability Of Microplastics In The Nearshore Region Of Lake Ontario, Sophie Routenberg

Theses

Microplastic (MP) pollution is one of the most significant environmental issues of the modern era, driven by the persistence of plastic and its rapid accumulation in aquatic environments. MPs (5 mm -1 µm) are now pervasive across global ecosystems, including the Laurentian Great Lakes, which receives an estimated 11,000 tons of plastic debris annually. Despite their prevalence, critical gaps remain in understanding MP input sources, polymer composition, morphological diversity, and spatial and temporal distribution. This study addresses those gaps by quantifying and characterizing the spatial, temporal, and compositional variability of MPs in the nearshore region of Lake Ontario’s Rochester Embayment …

Associations Between Vitamin D Deficiency And Sociodemographic Factors, Lifestyle Behaviors, And Metabolic Conditions: A Cross-Sectional Study From The Hnnhs In Greece, Asmae Mohamad Sadek

Theses

Vitamin D deficiency (VDD) is a widespread global health concern associated with various sociodemographic, lifestyle, dietary, and metabolic factors. While previous studies examined VDD in Greece, few provided a comprehensive analysis across multiple determinants using representative national data. This study aimed to assess the prevalence and predictors of VDD among Greek adults and to examine its associations with sociodemographic, dietary, behavioral, and metabolic variables using data from the Hellenic National Nutrition and Health Survey (HNNHS). A cross-sectional analysis was conducted among 978 adults (≥19 years) from the HNNHS. Serum 25-hydroxyvitamin D [25(OH)D] concentrations < 20 ng/mL were defined as deficient and ≥20 ng/mL as normal. The median age of participants was 40.2 years, and 62.0% were female. The overall prevalence of VDD was 46.0%, with the highest rate observed among adults aged ≥60 years (62.2%). VDD was significantly associated with older age (p < 0.001), retirement status (62.9% among retired; p < 0.001), low and sedentary physical activity (32.7% and 32.6% vs. 50.8% among highly active; p < 0.001), higher HDL (median 52.0 vs. 49.0 mg/dL among VDD vs Normal; p = 0.001), elevated serum calcium (median 9.4 vs. 9.2 mg/dL among VDD vs Normal; p = 0.020), and lower insulin levels (median 7.5 vs. 8.0 μIU/mL among VDD vs Normal; p = 0.044). Dietary intake (total energy and macronutrients) and body composition were not significantly associated with VDD. In the multivariate model, significant independent predictors of VDD included being retired (AOR = 2.383; 95% CI: 1.596–3.558; p < 0.001), having higher serum calcium levels (AOR = 1.563; 95% CI: 1.078–2.266; p = 0.019), and higher HDL levels (AOR = 1.016; 95% CI: 1.005–1.027; p = 0.001). Physical activity level was also a key determinant; participants classified as sedentary or low active had significantly higher odds of deficiency compared to highly active individuals (AOR = 0.468; 95% CI: 0.319–0.690; p < 0.001). This counterintuitive result may be influenced by factors such as increased indoor physical activity, and warrants further investigation. Dietary intake and body composition were not significantly associated with VDD. The findings underscore the importance of incorporating sociodemographic and lifestyle factors into prevention strategies. Interventions should particularly focus on older adults, retired individuals, even if they have higher HDL and calcium levels, and are physically active.