Digital Commons Network^™

Bias, Structure, And Inference In Applied Network Analysis, Anna Vasenina

Dartmouth College Ph.D Dissertations

This dissertation develops mathematical and statistical methods for extracting reliable information from network data across biological applications, with an emphasis on understanding what observed network structure can and cannot resolve. The first study leverages protein–protein interaction network topology in the c-di-GMP signaling system of Pseudomonas fluorescens, showing that node centrality measures accurately classify protein domain types and that physical interaction structure contributes statistically significant predictive power for biofilm formation phenotypes across nearly 200 environments, while gene expression does not. The second study examines sampling bias in lemur-plant trophic interaction networks in Madagascar, demonstrating that differential detection of diurnal versus …

Determinants Of Cardiovascular And Metabolic Noncommunicable Diseases Among People Living With Hiv In Rwanda: Protocol For The Ncohirwa Prospective Cohort Study, Valentine Dushimiyimana, Marc Twagirumukiza, Madeleine Durand, Ntobeko Ntusi, Brenda Asiimwe Kateera, Noella Bigirimana, Ladislas Nshimiyimana, Pacifique Ndishimye, Vivianne Niyonkuru Umuhire, Prosper Karame, Valens Ndagijimana, Joseph Mucumbitsi, Alfred Dusabimana, Cecile Ingabire, Yvonne Delphine Nsaba Uwera, Km Monirul Islam, Celestin Hategeka, Sabin Nsanzimana, Ernst Rietzschel, Steven Callens, Clarisse Musanabaganwa, Jean Claude Semuto Ngabonziza, Eric Remera, Jean Pierre Musabyimana, Claude Mambo Muvunyi, Albert Tuyishime, Gallican Nshogoza Rwibasira, Gregorie Muhorakeye, Simeon Tuyishime, Francois Uwinkindi, Evarist Ntaganda, Simon Pierre Niyonsenga, Noel Gahamanyi, Kayigi Etienne, Fidel Umwanankabandi, Theogene Kubahoniyesu, Alphonse Mbarushiman, Muhammed Semakula, Leopold Bitunguhari, Jean Damascene Kabakambira, Annette Uwineza, Marcellin Musabende, Felix Babane, Vincent Karamuka, Fidens Dusabeyezu, Alyson Kelvin, Pacifique Mukashema, Augustin Murindabigwi, Steven Karera, Katia Giguère, Godfrey Katende, Jean Berchmans Tugirimana, Deo Mutambuka

School of Nursing & Midwifery, East Africa

Background: Noncommunicable diseases (NCDs), particularly cardiovascular diseases (CVDs), hypertension and diabetes, are major contributors to morbidity and mortality globally and in Rwanda, where the dual burden of HIV and NCDs is increasing. Evidence remains limited on how biological, behavioural, social, environmental and health-system determinants influence cardiovascular and metabolic outcomes among people living with HIV (PLHIV) in Rwanda. The NCOHIRWA cohort was established to prospectively investigate determinants associated with CVDs, hypertension, diabetes and related NCD outcomes among PLHIV, newly diagnosed PLHIV and people without HIV (PWoH). This manuscript presents the protocol for the NCOHIRWA cohort study.

Methods:  The NCOHIRWA study …

Prosocial Behaviors As A Protective Factor Against Suicide Risk: An Ecological Momentary Assessment Approach, Bradley A. Brown

USF Tampa Graduate Theses and Dissertations

Suicidal ideation (SI) fluctuates substantially over short timescales, and the Interpersonal Theory of Suicide proposes that suicidal thinking emerges through dynamic interpersonal states involving perceived burdensomeness (PB), thwarted belongingness (TB), and hopelessness regarding these interpersonal states (IH). Although ecological momentary assessment (EMA) research has demonstrated that these risk factors fluctuate meaningfully within individuals and are associated with short-term changes in SI, comparatively little research has examined interpersonal processes that may attenuate suicide risk in real time. Prosocial behavior — voluntary actions intended to benefit others — may represent one such process, yet no known EMA study has examined whether prosocial …

Fluorescence Cryotomography For Preclinical Validation: Applications In Gene Therapy And Fluorescence-Guided Surgery, Caleb Y. J. Kwon

Dartmouth College Ph.D Dissertations

Fluorescence imaging has become a powerful tool in biomedical research and clinical practice, offering molecular specificity and high sensitivity for visualizing biological processes in real time, However, the successful translation of novel fluorescent probes or medicines from preclinical development to clinical applications requires rigorous validation of their biodistribution and target specificity. Traditional methods for assessing performance, such as bulk excised organ analysis or two-dimensional histology, provide limited information as they cannot capture the complete, organism-wide distribution of these probes or medicines. This thesis aims to improve this analysis pipeline through the application and optimization of fluorescence cryotomography for quantitative, high-resolution …

Deciphering Small Sequence Differences In T Cell Receptor-Antigen Pairing, Yi Han, Yuqiu Yang, James Zhu, Farjana J Fattah, Mitchell S Von Itzstein, Minying Zhang, Casey Bermack, Peixin Jiang, Shailbala Singh, Yanhua Tian, Yifei Hu, Yafang Deng, Xiongbin Kang, Donghan M Yang, Jialiang Liu, Yaming Xue, Chaoying Liang, Indu Raman, Chengsong Zhu, Olivia Xiao, Jonathan E Dowell, Jade Homsi, Sawsan Rashdan, Ke Pan, Shengjie Yang, Mary E Gwin, David Hsiehchen, Yvonne Gloria-Mccutchen, Fangjiang Wu, John V Heymach, Don Gibbons, Junzhou Huang, Chao Cheng, Jianjun Zhang, Cassian Yee, Alexandre Reuben, David E Gerber, Tao Wang

Faculty, Staff and Students Publications

T cells have important functions in development and disease processes through T cell receptor (TCR)-dependent activities. Many tools were developed to predict the binding between TCRs and antigens. However, one of the uncertainties is whether such tools can decipher how small changes in the TCRs or antigenic peptides contribute to binding. We develop a deep learning model, pMTnet-omni, which not only predicts the binding vs. non-binding of TCRs towards pMHCs, but also distinguishes the stronger vs. weaker binding of TCRs similar in sequence. We leverage this capability to interpret the biological rules that govern TCR-antigen pairing. This also enables pMTnet-omni …

Semantic Directing: A Human-Ai Workflow For Interative Virtual Cinematography, Lejie Liu

Dartmouth College Master’s Theses

This thesis presents AI Director, a Unity-based prototype for semantic directing in virtual cinematography. The system enables creators to describe cinematic intent in natural language, receive editable shot-strategy plans generated by a large language model, and refine specific shots through text and visual references. By separating semantic planning from deterministic camera execution, the workflow keeps user authorship centered on shot intent while making the resulting camera plans inspectable, editable, and executable in real time. This work explores semantic directing as a human-AI workflow for iterative cinematic authoring in dynamic 3D scenes.

Constitutional Inferences On Emerging Technologies: Analyzing Government Overreach, The Fourth Amendment, And Democratic Process In The Age Of Artificial Intelligence, Alan To

McNair Research Journal SJSU

The rapid adoption of artificial intelligence (AI) and machine learning (ML)

technologies by federal agencies presents novel constitutional questions that

existing legal doctrine has not yet adequately addressed. This paper

examines the emerging constitutional dimensions of the 2026 conflict

between Anthropic and the Department of Defense (DOD), in which the

Pentagon demanded unrestricted use of Anthropic's AI model Claude for

domestic mass surveillance and autonomous weapons systems, ultimately

designating Anthropic a supply chain risk when the company refused.

Drawing on three salient constitutional frameworks, specifically the Fourth

Amendment doctrine established in Kyllo v. United States (2001) and

Carpenter v. United …

Words Can Hurt: A Review Of Racial Microaggressions And Their Effects On Cortisol Level, Edgar Perez-Lopez

McNair Research Journal SJSU

The study examines the impact of racial microaggressions on cortisol levels,

highlighting inconsistent findings across various research methodologies.

Microaggressions--subtle discriminatory actions--are linked to stress and

can raise cortisol levels, a hormone released in response to stress. Some

studies suggest that frequent microaggressions blunt cortisol response,

making it less available for future stressors, while others reported increased

cortisol levels. The divergence in results may be due to differences in

research designs, such as cross-sectional, interpersonal research, or

nomothetic, versus longitudinal, intrapersonal research, or idiographic

approaches. Combined, the results of each type of research proves chronic

and acute impact of microaggressions. The …

Platonic Affection, Philia, And Trans-Philosophy, Kai Parker

McNair Research Journal SJSU

In this article, I review the heteronormative social conventions of cisgender

men and women's abilities to build and maintain friendships vis-.vis

traditional Western gender roles. It divides the philosophical concept of

Plato’s “platonic love” as fully realized Eros from the basic social

interpretation of “platonic” relationships as connections devoid of sexual or

romantic feelings. Aristotle's definitions of friendship, divided into the three

categories of pleasure, utility, and virtue, are compared to friendships

cisgender men and women form with others of the same orientation. Men's

friendships are found to more often fall into friendships of utility and

pleasure, while women's friendships …

The Relationship Between Gender, Platonic Physical Affection, And Interpersonal Sensitivity, Mariam Malik

McNair Research Journal SJSU

Interpersonal sensitivity (IS), also known as emotional maturity or empathy,

is characterized by recognizing emotions and displaying empathy, which

are important social skills. Understanding the factors that are associated

with interpersonal sensitivity can provide the foundation for research

revolving around improving interpersonal sensitivity, and in turn,

improving social skills. Platonic physical affection (PPA), such as holding

hands and hugging, is a social variable often associated with those close to

one another (e.g., friends and family). However, the exhibition and

receptivity to this social variable may differ across cultures and genders.

This study aimed to see if there is a relationship …

Front Matter, Maria Cruz

McNair Research Journal SJSU

No abstract provided.

Full Issue

McNair Research Journal SJSU

No abstract provided.

Bridging Interprofessional Gaps: A Pilot Study On Aac And Asl Training For Allied Health Profession Students, Angela M. Riccelli, Danielle Osmelak, Leslie Guca, Keith Werosh, Valerie Coolman, Rebecca Kvasnicka

Journal of Applied Disciplines

Interprofessional education (IPE) is recognized as a critical component of health professions training, equipping future clinicians with the skills necessary for collaborative practice and patient-centered care. However, students in speech-language pathology, occupational therapy, and physical therapy programs often have limited exposure to individuals who rely on Augmentative and Alternative Communication (AAC) or American Sign Language (ASL). This study evaluated the impact of a grant-funded, AAC- and ASL-focused IPE event at Governors State University on students’ self-reported interprofessional competencies. Using the Interprofessional Collaborative Competencies Attainment Survey (ICCAS-R) developed by Archibald, D., Trumpower, D., and MacDonald, C.J., in 2009 and revised in …

Refining A Flow Injection Analysis Method For Trace Concentrations Of Iron In Seawater, Brooke I. Stafford, Liam W. Hodgson, Noah S. Schuhmann, Elijah J. Vestal, Claire P. Till

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Iron is an essential micronutrient required for the growth of phytoplankton, the base of the oceanic food chain. Iron exists in the ocean in extremely low concentrations, limiting primary productivity in ~⅓ of the surface ocean, and can be affected by physical processes such as upwelling of water masses, and by biological and chemical processes within the water. In order to further our understanding of iron availability in the ocean, here we refine and improve our understanding of an analytical method to measure nanomolar iron in seawater. The method used is an adaptation of Lohan et al. (2006), a flow …

Interrogating Settler Narratives Of Erasure In The Schatz Tree Farm Archives, Sangeeta Sarkar

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

In 1987, L. W. Schatz donated a 385-acre parcel of land to Cal Poly Humboldt to be used as an experimental station, outdoor classroom, and demonstration area for forestry educators and students. Previous student research and other institutional narratives have extensively documented the history of this land from a settler perspective. However, this documentation contains few mentions of the Indigenous history of the landscape. Through literature review and archival research, this paper critically analyzes settler colonial narratives around the Schatz Tree Farm and the ways in which they contribute to Indigenous erasure. The predominant forms of narrative erasure in settler …

Exploring The Relationship Between Tree Dbh And Lichen Cover On Coast Redwood, Grace M. Personeus, Sierra Gittleman, Alisa A. Zarattini

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

We investigated the relationship between Diameter at Breast Height (DBH) and lichen cover on coast redwood (Sequoia sempervirens) to see if larger trees had higher percentages of cover. We measured cover using 10 cover classes on the southeastern and southwestern sides of trees in a secondary growth forest. We found a significant relationship between DBH and cover, yet no significant difference between the two sides measured. We suggest that further research with a larger sample size and more varied age classes will provide further insight into the relationship.

Allosteric And Uncompetitive Inhibition Of Yeast Alcohol Dehydrogenase Identified By Enzyme Kinetics, Dylan Jeremy Harrison, Jenny A. Cappuccio

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Enzyme kinetics is a powerful technique used to quantify the rate at which an enzyme converts a substrate into a product and to identify potential inhibitors. In this study, kinetic analysis was employed to assess the activity of yeast alcohol dehydrogenase (YADH) in the presence and absence of sweeteners commonly found in alcoholic beverages. YADH catalyzes the oxidation of ethanol to acetaldehyde using NAD⁺ as a cofactor; the reduction to NADH can be monitored spectrophotometrically at 340 nm. Based on structural similarities to the ribose moiety of NAD⁺, it was hypothesized that sucrose and sucralose could directly interact with the …

Full Issue, The Press At Cal Poly Humboldt

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

No abstract provided.

Narrative, Identity, And Liminality Of Player Development Personnel In Ncaa Power 4 Conferences: Supporting Athlete Identity Development And Navigating Role Evolution In The Nil Implementation Era, Joseph L. Herman Ii

Journal of Issues in Intercollegiate Athletics

Derived from a larger study, this article examines Player Development Personnel (PDPs) in NCAA Power 4 (P4) conferences as they support athlete identity development and navigate role evolution during the NIL implementation era. Although academic advisors and support staff have long contributed to athlete development, limited scholarship has examined how PDPs understand their professional identities, responsibilities, and institutional constraints in NIL-era athletics. Guided by the Narrative, Identity, and Liminality Model (NILM), MNF, and institutional logics, this study situates PDP work within an ecosystem shaped by commercialization, racialized narratives, and organizational expectations (McLean & Syed, 2015; Southall et al., 2008). Semi-structured …

Educating Ncaa Student-Athletes To Mitigate Social Media Risks: Results From An Intervention Pilot Program, Ksenia Power, Nataliya Bredikhina, Bomin Paek

Journal of Issues in Intercollegiate Athletics

With the introduction of the NCAA’s Name, Image, and Likeness (NIL) policy in July 2021, student-athletes have become increasingly reliant on social media for personal branding and monetization. However, prior research suggests that excessive social media use can negatively impact student-athletes’ well-being, highlighting the need for targeted digital literacy education. Addressing these concerns, this study designed and evaluated an online intervention, “Student-Athlete Training for Online Resilience Management” (STORM), aimed at improving student-athletes’ perceived knowledge and confidence in navigating social media-related risks. Using two waves of survey data (N = 117), the study assessed changes in perceived knowledge of social …

Online Harassment And Mental Health Among Collegiate Student-Athletes: Findings From An Ncaa Division I Conference Survey, M. Courtney Hughes, Michelle K. Demaray, Emily A. Skiba, Sarah E. Warriner

Journal of Issues in Intercollegiate Athletics

Social media is central to college athletics, yet public visibility can expose collegiate student-athletes to online harassment, a risk the NCAA has recently highlighted by documenting sizable volumes of abusive, discriminatory, and betting-related content directed at athletes and officials. This study surveyed 85 NCAA Division I student-athletes from ten universities across the Mid-American Conference and assessed social-media behaviors, online harassment exposure, depression, and anxiety. Most athletes used social media 1–3 hours/day, 78% enabled name-mention alerts, and platforms commonly used included Instagram (98.8%) and X (65.9%). Online harassment was reported via social posts (9.4%), direct messages (4.7%), and texts (3.5%), with …

“Where’S This Energy When They’Re Killing Us!?”: Black Sport Media, Disruptions Of Linked Fate, And The Plantation Politics Of Protection, Sayvon Jl Foster

Journal of Issues in Intercollegiate Athletics

Following the viral interaction between Nyck Harbor and the Texas State Trooper, Black sport media figures dominated the discourse surrounding the incident. By centering Black sport media figures as sources of discursive authority, this study illuminates the role of (Black) sport media in shaping the understanding and response to experiences of Black college athletes. Using Thompson’s (2022) abductive thematic content analysis, commentary from eight prominent Black sport media voices - Bomani Jones, Stephen A. Smith, Ryan Clark, Cam Newton, Von Miller, Marcellus Wiley, Jason Whitlock, and Etan Thomas - was analyzed. With Dawson's (1994) Linked Fate Theory (LFT) as the …

2nd National Research Day Lebanese Medical Schools

MEAMS Middle East Annals of Medical Sciences - Saint Joseph University of Beirut

No abstract provided.

Neuromuscular Responses During Vigorous Intensity Heart Rate-Clamp Cycling Exercise, Clara J. Mitchinson, Pasquale J. Succi, Brian Benitez, Djadmann Gustave, Minyoung Kwak, Erik Snell, Haley C. Bergstrom

Journal for Sports Neuroscience

Introduction: Electromyography (EMG) and mechanomyography (MMG) provide non-invasive assessments of neuromuscular function and fatigue during dynamic exercise. This study examined neuromuscular fatigue and cycling performance through changes in power output (PO), total work (TW), EMG and MMG, amplitude (AMP) and mean power frequency (MPF) during three, heart rate (HR)-Clamp trials in the vigorous range (77-95% HR_max). Methods: Ten men (mean±SD, 25.9±5.0yr, 74.9±15.0kg, HR_max=178±12b×min^-1) performed a cycle ergometer graded exercise test, followed by three separate HR-Clamp trials at 77%HR_max (HR_L, time to exhaustion [T_Lim]=58.5±4.6 min, range=45.3-60.0min), 86%HR_max (HR_{M …}

A Professional Development Course On Data-Driven Dynamical Systems At A Primarily Undergraduate Institution: Part A - Scientific Content, Alessandro M. Selvitella, Jeffrey R. Anderson

CODEE Journal

In the age of data-driven decision making, ordinary differential equations (ODEs) remain a powerful and interpretable framework for modeling dynamic processes, especially when integrated with modern tools from statistical learning and data-driven dynamical systems. Yet, general undergraduate and graduate curricula do not typically address key opportunities in data-driven dynamical systems.

This first paper in a series focuses on the mathematical and methodological core of a professional development course first developed in the academic year 2025-2026 at a Primarily Undergraduate Institution, Purdue University Fort Wayne. The curriculum developed in this course emphasized how regression, regularization, and sparse identification can be used …

Socioeconomic And Cultural Factors In Shared Book Reading Interactions, Jessica Wood Folsom

Theses and Dissertations

This study examined socioeconomic and language factors influencing the implementation of shared book reading behaviors following participation in caregiver-trained shared book reading workshops. While shared book reading is known to support language and literacy outcomes of children, less is known about how socioeconomic and language differences affect its implementation. Eighteen participants were recruited from a local preschool and completed a 34-question pre-survey prior to attending a 2-week shared book reading workshop, followed by a 27-question post-survey. Parents reported on literacy practices, confidence level, and shared book reading behaviors. Results indicated increased positive shared book reading behaviors and caregiver confidence following …

Escaping Quarantine: Marine Hospitals, The Constitution Act, 1867 And Canada’S First Federal Health Care Program, Dan Dwyre

Dalhousie Journal of Legal Studies

Previous scholarship has argued that the enumeration of marine hospitals as a federal head of power in the Constitution Act, 1867 reflected a national concern over immigration and quarantine. This article disputes that. Using primary sources, this paper demonstrates that Canadian marine hospitals were established in port communities to provide for the general health of itinerant merchant sailors, who would otherwise be a burden on local hospitals and charitable organizations. The article concludes that marine hospitals can be viewed in retrospect as one of Canada’s first federal health care programs.

One Step Further: An Overview Of Canada’S Past And Present Responses To Homelessness And The Argument For Alternative Conceptions Of Property Ownership, Logan Billard

Dalhousie Journal of Legal Studies

Homelessness in Canada continues to worsen year after year. Despite the shift from punitive, neoliberal policies to a human rights-based model, homelessness remains a national crisis. Federal initiatives like the National Housing Strategy Act and the Housing First Model aim to provide stable housing, but their impact remains limited. This paper explores the structural factors contributing to homelessness, including poverty, housing financialization, and systemic discrimination, particularly against Indigenous communities. It also highlights the limitations of the current human rights-based approach, focussing on the lack of enforceability and failure to create substantial, sustainable change due to systemic reliance on the financialization …

A Theoretical And Empirical Framework To Estimate The Impact Of Conflict On The Economic Resilience Of Clustered Firms In Ukraine, Alexander D. Ginn

Electronic Theses and Dissertations

In this thesis, I develop a theoretical and empirical framework to estimate whether participation in industrial clusters contributes to firm-level economic resilience to conflict-based shocks. Focusing on Ukraine following the full-scale Russian invasion in February 2022, the study situates industrial organization and firms’ resilience to conflict within a dynamic environment characterized by spatially heterogeneous exposure to conflict events and persistent institutional constraints. I document how Ukraine’s contemporary economic geography reflects the interaction of Soviet-era industrial path dependence, uneven post-transition institutional development, and conflict-induced reconfiguration, evaluating how these dynamics generate systematic variation in both firms’ baseline vulnerability and their exposure to …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …