Digital Commons Network^™

A Data Analysis Study Of Temperature Based On California Cooperative Oceanic Fisheries Investigations (Calcofi) Data., Afsana Mimi

Dissertations, Theses, and Capstone Projects

This research presents an integrated analytical framework for predicting ocean temperatures using long-term observations from the California Cooperative Oceanic Fisheries Investigations (CalCOFI) data files. The study applies advanced data engineering and statistical modeling to assess how a variety of indicators, such as salinity, dissolved oxygen, key nutrients, and ocean depth shape oceanic temperature patterns along the California coastline. Using Microsoft SQL Server software for large-scale data integration and the R for statistical packages (R Core Team, 2025) for statistical computation, I developed and compared multiple regression models, including the ridge regression model, to evaluate the relative influence of physical and …

Theatrical Agency In The Constitution Of Logical Space, Esther Marveta Neff

Dissertations, Theses, and Capstone Projects

This dissertation takes advantage of our current moment of collapse and shifting episteme to move from resistance and critique into modes of position, prefiguration, and praxiocentricism, giving not only a critique of the colonial-modern logical space of Theatrum Mundi, but also aiming to configure the thetic consciousness that grounds “theatrical agency” in the logic of cognitive and social epistemological modelling.  In what ways do we “build our own worlds”? What does “theatricality” tell us about human agency, especially in the domain of “theoretical attitudes,” and “consciousness”? In what ways, and to what extent, are we responsible for constituting …

Immunomodulatory And Signaling Molecules From Plant-Associated Bacteria: Toll-Like Receptor 4 Agonist Adjuvants And Diketopiperazine-Mediated Communication, Marian Romaine

Dissertations, Theses, and Capstone Projects

Medicinal plants and their associated microbiomes constitute a rich source of bioactive natural products with applications in immunotherapy and microbial ecology. Herbal formulations have long been valued for safe immune enhancement, while bacterial signaling molecules govern community behaviors critical to pathogenesis, symbiosis, and environmental processes. Bacterial lipopolysaccharides (LPS) from plant-associated Gram-negative bacteria have emerged as potent TLR4 agonists, yet their endotoxic potential limits direct use, and diketopiperazines (DKPs) serve as versatile quorum-sensing mediators capable of modulating biofilms in mixed microbial systems.

The work in this thesis comprises two independent but complementary research strands. The first strand pursued the engineering of …

Profiling Nucleolin Phosphorylation During Dna Damage Response And Cell Cycle Arrest, Hanjun Jeon

Dissertations, Theses, and Capstone Projects

This dissertation examines site-specific and global phosphorylation dynamics of nucleolin (NCL) in response to DNA damage and cell-cycle perturbations. By combining phospho-specific immunoblotting with Phos-tag SDS-PAGE analysis, distinct phosphorylation patterns were identified across experimental conditions. The results define reproducible, condition-dependent phosphorylation states of NCL and provide a framework for studying its regulation under cellular stress.

Lethal Autonomous Weapons Systems And The Principles Of Distinction And Proportionality, Nicholas Cromie

Dissertations, Theses, and Capstone Projects

Lethal Autonomous Weapons Systems (LAWS) challenge the core principles of International Humanitarian Law (IHL), distinction and proportionality, by delegating life-and-death decisions to algorithms rather than human judgment.  This dissertation examines whether LAWS can conform to these principles and, if so, under what conditions.  Through process tracing, the study traces the historical integration of disruptive weapons technologies, including chemical, biological, nuclear, and armed drones, into IHL-compliant frameworks or their exclusion via prohibition.  Each case reveals distinct pathways: outright bans for indiscriminate or inherently inhumane systems (chemical and biological weapons), normative restraint and limited acceptance despite destructive power (nuclear weapons) and phased …

Identifying Textual Predictors Of Early Termination In Clinical Trials In Medicine: An Explainable Machine-Learning Study, Rohan Ramnarain

Dissertations, Theses, and Capstone Projects

About one in five clinical trials in medicine ends early, wasting valuable resources and reducing the evidence available for developing life-saving medical treatments. This project uses a method called Trial2Vec, which is a self-supervised machine-learning method that converts clinical trial documents into dense numerical representations that capture their key design and clinical characteristics, to turn each proposed clinical trial’s written protocol into a compact numerical profile (a process referred to as embedding). These profiles are then paired with a predictive machine learning models to identify the words and phrases in the trial documents that can signal a higher risk of …

Jurisdictional Waters, Jamison E. Colburn

Faculty Scholarship

No abstract provided.

Wayfindr: Investigating Feedback In Biological Pathways, Polina Bombina, Reginald L Mcgee Ii, Jake Reed, Zachary B Abrams, Lynne V Abruzzo, Kevin R Coombes

2020-Current year OA Pubs

Understanding biological pathways requires more than static diagrams. We present WayFindR, an R package that converts pathway data from WikiPathways and KEGG into graph structures using igraph, enabling computational analysis of regulatory features such as negative feedback loops. Rooted in control theory, negative feedback is essential for system stability, yet it is often underrepresented in curated pathway data. In this study, we systematically analyzed pathway information from both databases across multiple species and found that feedback loops-particularly negative ones-are rarely captured. This gap likely reflects both biological and technical challenges. Biologically, feedback mechanisms are inherently complex and often remain uncharted …

Artelon Graft Augmentation In Revision Anterior Cruciate Ligament Reconstruction: Surgical Technique Guide., Taylor Manes, Morgan Turnow, Trent Davis, Anthony Perugini, Michael Anderson, Benjamin Taylor

Surgery Articles

INTRODUCTION: Revision anterior cruciate ligament (ACL) procedures are becoming more prevalent. Variable grafts for ACL reconstruction are available, including autograft, allograft, and synthetic graft options. Various augmentation techniques are also available and typically consist of synthetic material such as Artelon graft. This type of synthetic material has been used and shown to produce safe and reliable augmentation in ligament injuries. The purpose of this study was to describe our unique revision ACL reconstruction technique utilizing Artelon graft augmentation and report our short-term results.

MATERIALS AND METHODS: We retrospectively reviewed patients undergoing revision ACL reconstruction with Artelon graft augmentation, a Flexband …

Neuroenvironmental Footprint: Integrating Air Quality Into Neuroarchitectural Research In Educational Spaces, María Beltrán Rodríguez, Ivette Caldelas

Congresos y Conferencias

Environmental quality is widely recognised as one of the most decisive factors in public health. Its relevance is particularly critical in the case of children, as it directly affects both their physical and cognitive development. Indeed, different researches showed how the exposure to inadequate environmental conditions during early life stages may compromise health outcomes, learning capacity, and overall well-being. Consequently, improving environmental quality in educational settings is not only a matter of comfort, but an essential public health priority. In this context, the International Symposium of Environmental Quality in Educational Spaces (inSiEqES) emerges as a necessary initiative to foster dialogue, …

Emerging Biomaterials For Next-Generation Wound Healing: From Infection Control To Tissue Regeneration, Unqa Mustafa, Aiman Kaleem, Syeda Zunaira Bukhari, Hamna Riaz, Maryam Iftikhar, Muhammad Usman Munir, Xianghao Xiao, Mingwu Shen, Xiangyang Shi, Mostafa Yazdi, Ayesha Ihsan

Chemical and Biochemical Engineering Faculty Research & Creative Works

Wound healing is a multifactorial biological process that regenerates damaged tissues through a series of molecular and cellular events in a coordinated manner. An interruption in this cascade can lead to impaired healing, especially in diabetic complications, where effective treatment is crucial for controlling infections and promoting tissue regeneration. Recent advances in bioengineering and digital health have catalyzed the development of next-generation wound therapies capable of actively modulating the wound microenvironment, promoting regeneration, and enabling real-time clinical assessment. This review summarizes the fundamentals of physiological wound healing and highlights the significant developments in biomaterial dressings and scaffolds, 3D bioprinting, as …

Fluency ≠ Literacy: Practical Strategies To Scaffold, Not Offload, Rachel Rupprecht, Heidi Keller, Vanessa Hörmann

Teaching & Learning with AI

This open-access resource kit helps faculty transition students from passive AI outsourcing to critical evaluation and essential skill cultivation. It includes 11 Assignment Templates & Rubrics, a Template Selector Gem, an AI Literacy Coach Gem, a Mindset Shifts & Expert Blind Spots visual guide, and student-facing resources.

Inverse Modeling The Geo-Spread Of Covid-19 In Brazil, Cameron Keith Mills

ETDs from 2020-2029

In 2021 Fitzgibbon, Morgan, Webb, and Wu used a modified SEIR (susceptible, exposed, infected, and recovered) model to predict how COVID-19 spread through Brazil [12]. For their model, six constant coefficients were used that were fitted, referenced, or assumed. In this thesis, we geo-spatially modify their SEIR model and formulate an inverse problem to recover the now spatial coefficients of the model. We first show there exists a unique solution to the modified model. To solve the inverse problem, we modify an inverse method [17] that focused on minimizing convex functionals. These recovered spatial coefficients can be used with Matlab’s …

Neuroinflammation And Neuropathology In A Novel Tau, Amyloid-Beta And Alpha-Synuclein Co-Pathology Model, Jhodi Mickayla Webster

ETDs from 2020-2029

Neurodegenerative diseases including Alzheimer’s disease (AD) and Parkinson disease (PD) often present with overlapping proteinopathies rather than aggregated proteins in isolation. Amyloid-β (Aβ) and phosphorylated tau are found in a substantial proportion of idiopathic PD cases, while α-synuclein (α-syn) pathology is present in over half of AD cases. The presence of these co-pathologies is associated with accelerated cognitive decline and increase mortality in these patients. In parallel, neurodegenerative diseases are increasingly recognized as being shaped by interactions between central nervous system (CNS) pathology and the immune system. Despite this, most experimental animal models of neurodegenerative disease examine single pathologies in …

Biomedical Applications Of Structurally Defined Natural And Semi-Synthetic Saponins, Chaeeun Lim-Paik

ETDs from 2020-2029

Triterpenoid saponins are amphiphilic glycosides that exhibit a wide range of biological and pharmacological properties, including antifungal, antiviral, molluscicidal, hypoglycemic, and hypocholesterolemic effects. These biological and pharmacological properties make saponins attractive for diverse applications. In this work, we demonstrate three biological applications: (i) immunostimulant vaccine adjuvant, (ii) protein delivery enhancement, and (iii) gene transfection enhancement. In light of the strong structure dependence of saponin activity, expanding the structural diversity of available scaffolds is essential for establishing structure-activity relationships (SAR) across these applications. Here, we expanded our saponin collection through semi-synthetic derivatization and the isolation of new saponins from distinct natural …

With A Love So Hard And Filled With Defeat:' A Queer Reading Of Bruce Springsteen, Samuel Tucker Carden

ETDs from 2020-2029

Long an open, yet misinterpreted political artist, Bruce Springsteen has never shied away from calling out injustices through his songs. Over the course of his long career, he has used his platform to lyrically speak out against war, the brutality of American capitalism, and the struggles of marginalized people of all backgrounds. However, the potential queerness of his lyrics has remained an underdiscussed political aspect of his artistry for decades, especially in academic settings. Many of the themes that Springsteen returns to in his writing – the need to hide one’s true self, struggles with self-identity, the desperate desire to …

Phosphogypsum-Based Road Materials: A Review Of Practicality, Longevity, And Safety In The United States, Catesby Elisabeth Mallard

ETDs from 2020-2029

The development of the phosphate fertilizer industry, while integral to the success of modern-day agriculture, continues to produce staggering amounts of phosphogypsum (PG), an acidic and hazardous waste byproduct concentrated with heavy metals, technologically enhanced naturally occurring materials (TENORM), and other toxic elements. Due to the potentially harmful emission of radon from PG, the United States (US) Environmental Protection Agency (EPA) has regulated the disposal of PG in engineered stacks under the National Emission Standards for Hazardous Air Pollutants (NESHAP) for nearly four decades. However, with roughly five tons of PG produced per single ton of phosphoric acid, and a …

Dock7 Is A Novel Modifier Of Duchenne Muscular Dystrophy Pathology, Katherine English

ETDs from 2020-2029

Duchenne muscular dystrophy (DMD) is a progressive, x-linked neuromuscular disorder affecting 1/5000 male births every year. DMD results from mutations in DMD, a critical structural protein within the muscle. In the absence of Dystrophin, the muscle degrades, increasing inflammation, destabilizing the cell membrane and going through constant cycles of regeneration which depletes the stem cell population. Over time, muscle tissue is replaced by fibrosis and adipose tissue, leading to loss of ambulation, respiratory and cardiac failure leading to death by early 20s. The standard of care for DMD patients is corticosteroid treatment. However, gene therapies have recently emerged which present …

Finite Element Analysis Of Post Vs Threaded-Post Glenoid Baseplates In Reverse Total Shoulder Arthroplasty: A Comparative Study, Christopher Morgan

ETDs from 2020-2029

This study compared a standard‑post baseplate with a threaded‑post baseplate in reverse total shoulder arthroplasty (rTSA) to determine whether threaded central fixation improves micromotion and stress distribution. A finite element model of a left scapula with a commercially available rTSA system was created; the two designs differed only by the central post (standard press‑fit versus threaded). A 756 N physiological load was applied at 60°, 90°, and 120° of abduction. Outcomes included total and directional relative micromotion at the bone–implant interface and von Mises stress in the glenoid and baseplate. Total micromotion remained below the 150 µm osseointegration threshold for …

The Healthcare Transition Experiences Of Emerging Adults With Congenital Adrenal Hyperplasia, Leslie Noojin Pitts

ETDs from 2020-2029

Congenital adrenal hyperplasia (CAH) is a group of disorders characterized by enzyme deficiencies impairing adrenal hormone production and requiring lifelong management. Individuals with CAH experience increased morbidity and mortality due to the underlying condition, steroid exposure, and inadequate preventative care. Despite clinical guidelines recommending a structured healthcare transition (HCT), little is known about the HCT experiences of emerging adults with CAH. Understanding these experiences is critical for identifying practice gaps and developing interventions to improve health outcomes. This qualitative descriptive study explored the HCT experiences, challenges, and outcomes of emerging adults with CAH, as guided by the refined Social Ecological …

Thermodynamic Modeling Of Ph Impacts On Subsurface Microbial Consortia, Jackfin K C

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Underground hydrogen storage is affected by microbial consumption, and the different minerals present in the subsurface. However, most studies consider either biotic or abiotic factors in isolation and hence, the conditions that drive a self-sustaining storage remain poorly understood. This thesis uses a genome-informed thermodynamic model developed by Kharel et al. (2026) in which pH is the central variable coupling hydrogenotrophic microbial metabolism, inter-species competition, and carbonate mineral buffering. The model includes four hydrogen-consuming species: methanogen (Methanobacterium), acetogen (Acetoanaerobium), aerobic acetate oxidizer (Pseudomonas stutzeri), and sulfate reducer (Nitratidesulfovibrio) by conditioning each organism's …

Investigation Of Warfarin–Human Serum Albumin Binding By Ultrafast Affinity Extraction Using Single- And Dual-Column Affinity Microcolumn Systems, Samiul Alim

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation examined the interaction of warfarin with human serum albumin (HSA) by using affinity chromatography, with particular emphasis on ultrafast affinity extraction (UAE) and affinity microcolumns. HSA affinity supports were prepared by immobilizing HSA onto diol-bonded silica via Schiff base chemistry and used to prepare affinity microcolumns for chromatographic studies under physiological-like conditions at pH 7.4 and 37.0 °C. UAE studies were performed to investigate the effects of residence time, flow rate, and column configuration on the measured apparent free fraction of warfarin and on the calculated apparent binding parameters. The results showed that the measured apparent free fraction …

Traditional Ecological Knowledge And Ecosystem Resilience: Implementing A Native Plants Landscaping Policy In Santa Clara, Isabella 'Amne Gomez

Silicon Valley Power Sustainable Futures Program

The goal of this research project is to provide implementable suggestions and guidelines for the City of Santa Clara that will incentivize local cities, residents, businesses, and parks to embrace planting more native plants. Currently, native plant landscaping in Northern California is not yet in a mature policy environment, despite the vast ecological and drought-tolerant qualities of native plants. While lawn-rebate programs that promote native plants exist, progress in policy is still needed to ensure long-term planting of native plant species. The city of Santa Clara could take the opportunity to be a leader in the current premature policy state …

Pcb Design For Place Cells Vlsi Chip, Gavin Reaksecker, Alex Krier, Joshua Lin

Electrical Engineering

This project presents the design and implementation of a 2 layer test-bench printed circuit board (PCB) for evaluating the functionality of a custom 40-pin VLSI integrated circuit. The objective is to create a reliable and portable platform capable of supplying configurable bias voltages, generating variable input signals, and monitoring both analog and digital outputs. The board integrates adjustable bias networks using potentiometers, digital and analog buffering stages, and optional battery supply operation. The VLSI device under test is mounted in dual-in-line (DIP) sockets to enable rapid replacement and repeated characterization. Dedicated test points are incorporated throughout the PCB to facilitate …

Chemical And Sensory Consequences Of Oxidative And Reductive Handling Of White Wines, Amelia Pargellis

Master's Theses

In the 2024 and 2025 vintage four experiments were performed each with a different varietal, namely Albariño, Grenache blanc, Loureiro, and Vermentino. These experiments investigated the effects of hyperoxygenation, reductive winemaking techniques, while monitoring the oxidation-reduction potential.

Albariño grapes were made following two juice protocols, control/reductive (Reductive Control) and oxidative (HyOx). Reductive Control received antioxidants (50 ppm SO₂, 160 mg/L ascorbic acid) and CO₂ blanketing, and HyOx underwent hyperoxygenation at approximately 700 mL/L/h of air for two hours through a stainless-steel sparging stone with 10-µm pores. Juice was cold-settled and racked. Reductive Control juice was split into …

The Effects Of Bone Health And Variation On Saw Mark Signatures, Lily Ambrose

PCOM Biomedical Studies Student Scholarship

Bone health and structural variation are multifactorial. Population, environment, age, diet, and health influence the overall functional morphology of bone and its response to stressors. Reduced cortical porosity, trabecular thinning, and low bone mass are common indicators of age-related and pathological changes, affecting a significant portion of the population. Because of this, bones encountered in medicolegal investigations often differ from what is considered “normal.” The structural integrity of bone needs to be considered because density influences mechanical strength and response to external forces. In criminal dismemberment cases, forensic scientists analyze saw marks to identify tool class and reconstruct events. While …

2026 Cyber-Resilient Health Care Workshop Report, Malcolm Schongalla, Sergey Bratus

Computer Science Technical Reports

The ISTS and the Dartmouth College Cybersecurity Cluster hosted the successful, inaugural Cyber-Resilient Health Care (CRHC) Workshop, March 5th & 6th, 2026. The event theme was "Innovation and Implementation," in response to the need to shift from reactive to proactive resiliency measures in the healthcare sector. Approximately 30 experts in clinical health care, cybersecurity, medical technology, policy, and innovation met to discuss solution-focused innovations addressing hard, cyber-related problems in health care. The agenda featured keynotes, an expert panel, innovation pitches, small group discussions, and a tabletop infrastructure disaster exercise. Participants gained insights into the obstacles and solutions involved in supporting …

Predicting Clinical Outcomes Of Non-Specific Low Back Pain By Studying The Interaction Of Clinical And Demographic Factors Of A Retrospective Data Set, Erica Michelle Fernandes

Dissertations

The purpose of this research is to investigate demographic factors, including age, gender, body mass index (BMI), race, marital status, insurance type, severity of disease (initial pain level), and clinical factors such as number of visits (no. of visits) at physical therapy (PT), length of time at PT and the type of clinician either physical therapist versus physical therapy assistant (PTA), that most predict PT clinical outcomes in patients with nonspecific low back pain (NSLBP) and see if there is an interaction between demographic and clinical variables.

Methods

The current study is a retrospective, cross-sectional, observational study using secondary electronic …

Mapping The Tar Vrna Interaction With Hiv-1 Integrase, Jian Sun, Rahul Yadav, Tolga Catmakas, Luke Fisher, Nicholas C. Fitzkee, Jacques J. Kessl

Faculty Publications

A series of critical interactions within the viral core between viral RNA (vRNA) and HIV-1 Integrase (IN) has previously been reported. In these studies, contact points between vRNA and IN were identified using RNA-seq and MS-based protein foot-printing approaches. Several IN amino acids located in its C-terminal domain (CTD) were found to be essential for vRNA binding, and their alanine substitution severely impacted the correct morphogenesis of the mature viral core. Here, we have used the TAR element to extend these studies by performing a comprehensive mapping of the interaction by deploying RNA crosslinking and NMR methodologies. Together, these approaches …

One Assay To Rule Them All: Development Of A Global Environmental Dna Tool To Support Range-Wide Surveys Of An Imperiled Sawfish And Its Application In The Eastern Tropical Pacific, Juan C. Cubillos-M, Annmarie Fearing, Demian D. Chapman, Peter M. Kyne, P. Joana Dias, Cindy Gonzalez, Ryan N. Lehman, Yaliana Chichaco, Bryan L. Huerta-Beltrán, Kayla L. Mcculloch, Sarah M. Toepfer, John K. Carlson, Nicole M. Phillips

Faculty Publications

Environmental DNA (eDNA) has emerged as a powerful tool to support the conservation of threatened species. The sawfishes are one of the most imperiled vertebrate groups, with all five species classified as Critically Endangered on the IUCN Red List of Threatened Species. Owing to their toothy rostra, sawfishes are easily entangled in a wide range of fishing gear, with mortalities in fisheries and loss of habitat driving global declines. The Largetooth Sawfish, Pristis pristis, historically had a circumtropical range, but has experienced severe declines in geographic range and abundance. Viable populations are thought to be confined to northern Australia, but …