Digital Commons Network^™

Development Of A Python Pipeline For The Inference Of Selection In Human Genomes And Applications To Adh1b*2, Aine Macdermott

Honors Theses

Human evolutionary genomics provides an avenue to understand how genetic variation has been impacted by the environmental pressures of the past, revealing how selective pressures impacted past populations and contributed to present-day biological diversity. In this thesis, I describe the construction of a Python-based computational pipeline designed to automate and integrate multiple analyses of positive selection across worldwide population datasets, including derived allele frequency calculation, haplotype-based tests of selection, RELATE-based genealogical inference, and CLUES2-based temporal modeling. By automating file preparation, format conversion, job submission, result aggregation, model comparison, and visualization, this pipeline streamlines the data interpretation process, and shifts focus …

“What Are The Security Issues Surrounding Cislunar Space And Lunar Resources? How Do Theories Of International Politics And Territory Apply To Those Issues?”, Ina Loka

Honors Theses

In the recent decades, cislunar space has attracted significant interest among the biggest spacefaring nations, Russia, China, and the United States. Cislunar space is no longer a distant subject solely associated with scientific studies. It has become a crucial domain in the conduct of military operations and its importance has been increasingly emphasised in these states’ military doctrines. In an environment where the intentions of other actors are hard to determine and where there is a high degree of uncertainty, these three states are ramping up their (counter)space capabilities in order to protect themselves from any adversarial attacks, and to …

Rockyou2024: What’S Your Password?, Yixuan Zhang

Honors Theses

Passwords remain a critical part of almost every account security system. As a result, password guessing attacks remain one of the most widespread yet profitable attacks possible. Setting a password resistant to attacks is thus an important task for account holders. In this paper, we use the RockYou2024 database, a collection of approximately 10 billion real-world passwords collected from data breaches, to analyze the characteristics of passwords found in real life. We start with basic statistical property analysis, such as length, distribution of digits and symbols, and proceed onto more complicated properties such as frequencies of combinations of characters, entropy …

The Conscription Imperative: A Philosophical, Paternalist, And Egalitarian Case For Universal National Service, Timothy Wenhsiang Khoh

Honors Theses

Inspired by my experience as a conscript for two years prior to college, this three-chapter honors thesis presents a philosophical justification and proposal for an American implementation of a national service model. This thesis seeks to justify conscription (a) on moral/ethical grounds as a coercive measure, (b) as a paternalistic policy, and (c) on egalitarian grounds. More broadly, my national service proposal contributes to the debate on methods and measures the American government ought to pursue to increase equity and solidarity among an ever-polarized citizenry.

Mnes Vs. Local Firms’ Resilience To Global Shocks: Evidence From The 2008 Financial Crisis And Covid-19, Yijie Wang

Honors Theses

This thesis examines whether multinational enterprises (MNEs) are more resilient than domestic firms during major global shocks, using the 2008 Financial Crisis and COVID-19 as case studies. Although MNEs may benefit from diversification, internal capital markets, and foreign linkages, they may also face greater exposure to global demand shrinkage and supplychain disruption.

Using Compustat North America firm-level panel data from WRDS, this study analyzes publicly listed U.S. and Canadian firms across 2007–2013 and 2018–2024. Firm resilience is measured through net sales, net income, and gross profit using a two-way fixed effects panel model. Multinational status is identified through two different …

Exploring Phosphoregulation Of Myo3a Using Quantitative Fluorescence Image Analysis In Cos7 Cells, Vu Hao Minh Nguyen Phan

Honors Theses

Myosin 3A (MYO3A) is an unconventional myosin involved in the formation and maintenance of hair-cell stereocilia of the sensory epithelia in the inner ear. The kinase domain has been implicated in phosphoregulation of MYO3A activity through intermolecular autophosphorylation. Previous studies using mass spectrometry identified two potential phosphorylation sites in the motor domain. To investigate the regulatory roles of these sites, we generated glutamic acid point mutations in our mchr-MYO3AΔK construct to mimic phosphorylation and assayed the constructs for their ability to tip-localize and influence filopodial density via transfection into COS7 cells. The phosphomimic constructs were less able to generate filopodia …

Associations Between College Students' Belonging, Classroom-Based Relationships, And Mental Health Outcomes, Ella Grace Will

Honors Theses

Humans have a fundamental need to belong (Baumeister & Leary, 1995). A lack of belonging is associated with negative mental health outcomes, making it important to study student belonging in higher education (Strayhorn, 2019). Classroom-based relationships with professors and peers positively impact students' belonging (Tinto, 1993). The purpose of this study was to evaluate: the relative contribution of professor trust and peer interactions to classroom and university belonging, and to assess the associations between student belonging and internalizing symptoms. Survey data were collected via Qualtrics in September 2025 (baseline) and December 2025 from students in 32 first-year seminars participating in …

Mosaics: An Artist’S Thesis Of Identity Through Memory And Belonging, Sofia I. Menco

Honors Theses

Conceptually, this thesis engages visually with Magical Realism as pioneered by Colombian writer, Gabriel Garcia Marquez, as well as the symbolic color fields of Colombian painter Alejandro Obregon, and the narrative portraiture of Spanish illustrator, David de las Heras, by situating my personal narratives within broader themes of memory, color symbolism and faith-based art. Having this visual research in mind, I drew a lot of inspiration from Colombian Artisan Practices such as Mochilas Wayuu and the folkloric colors of such. At the same time, I explored the sociological and religious lens coming from a theoretical approach of George Hebert Mead’s …

Paradise Lost And Character Motivation: Sinful Behavior Or Inferiority Complex?, Esperanza Barrios

Honors Theses

Sin is a concept that is always viewed through a religious perspective. But, through Paradise Lost, John Milton was able to bring further understanding towards human nature and one’s own sense of committing what’s perceived as sinful behavior without the veil of religion glazing over academics' understanding. In religious terms, sinful behavior is the idea of defying God’s commandments, but for this research, sinful behavior may be described as abnormal behavior that damages our best interests and relationships, usually for selfish gains. Each of Milton’s main characters, Satan, Adam, and Eve, fell from grace because all three damaged their relationship …

The Effects Of Vestibular Dysfunction On Cognition, Sai Puneeth Kothuru

Honors Theses

Virtual Reality (VR) systems are being used more in education, entertainment, and research, but can produce motion sickness that could temporarily disrupt cognitive functioning. This study examined whether exposure to a VR roller coaster experience leads to short-term changes in cognitive flexibility, attention, spatial orientation awareness, and anxiety compared to a control condition. Participants were randomly assigned to a VR condition or a computer-based 2D viewing condition with identical roller coaster visual content. Participants completed three testing blocks: baseline, after exposure, and after a 10-minute recovery period. Cognitive flexibility and attention were assessed using the Trail Making Test (TMT), and …

Microsolvation Effects Of 1,1-Dimethyl-Biguanide (Metformin), Jasmine L. Sanders

Honors Theses

The microsolvation of a 1,1-dimethyl-biguanide hydrochloride molecule in the presence of water molecules illustrates the initial interactions between the common drug metformin and water. This explicit water-solvation approach employs coupled-cluster theory with an explicit-correlation F12 correction and the cc-pVTZ-F12 basis set to determine the optimalgeometry of the molecule and to observe intermolecular interaction energies. 1,1-dimethyl-biguanide hydrochloride (an antidiabetic agent, metformin) is constantly in contact with water molecules in the human body, where it reduces intestinal glucose absorption, lowers hepatic glucose sensitivity, and improves overall insulin sensitivity to lower blood-glucose concentration. The B3LYP method with an aug-cc-pVTZ basis set is used …

Asymptotics Of Discrete Convolution Powers And Applications To Difference Schemes, Pedro Henrique Alves Silva Dos Santos

Honors Theses

In this thesis we provide Gaussian Estimates and Local Limit Theorems describing the asymptotic behavior of convolution powers of a class of complex-valued functions on $\mathbb{Z}^d$. Convolution powers arise naturally in the study of partial differential equations, as well as in random walks in probability theory. In particular, they are connected to the stability theory of difference schemes used to approximate solutions to partial differential equations. We take inspiration from the work of Vidar Thomée on stability theory to restrict our attention to convolution powers of functions whose Fourier Transforms satisfy certain local expansions. We then combine the Cauchy Integral …

Hegemonic Microtonality: Decolonizing The Soundscape Of Music Theory Pedagogy, Ash K. Wetty

Honors Theses

This thesis examines how Western music theory pedagogy—long organized around tonal and twelve-tone equal-temperament frameworks—structures both what is taught and how students are trained to listen. Through a literature review tracing the historical construction of tonal universality in undergraduate curricula, the project argues that dominant models of music theory reproduce broader epistemic hierarchies inherited from Western conservatory traditions. Situating these histories within my own experience as a student navigating institutional listening norms, the thesis combines critical self-reflection with ethnographic research conducted across five liberal arts institutions, including the CBB consortium and JanPlan research at Wesleyan University and Amherst College. Rather …

From Sorochyntsi To St. Petersburg: National Identity In The Works Of Nikolai Gogol, Gary Jay Kogoy Jr.

Honors Theses

Nikolai Gogol's extant works depict a man torn between his birthplace of Ukraine and the nineteenth-century milieu of Imperial Russia. Notably, he did not reveal his name for some time after publishing his first story collection Evenings on a Farm Near Dikanka; as a result, readers attributed the tales of Ukrainian life within not to Gogol, but to the charming "Ukrainian jester" persona of Rudy Panko. Even after revealing his identity and garnering respect in the St. Petersburg literary scene, his contemporaries often viewed him as sly and suspicious because of his ancestry. Perhaps due to external doubts regarding …

Climate Change And Species Interactions Jointly Shape Migration Timing And Growth At A Critical Ontogenetic Transition In Juvenile Sockeye Salmon, Margaret E. Veatch

Honors Theses

Climate change is shifting the timing of biological events globally, but the mechanisms linking environmental variation to phenological changes are poorly understood in many systems, particularly those where individuals undergo ontogenetic habitat shifts. Here, I examined the join influence of climate-driven environmental variability and species interactions migration timing and body size at migration in juvenile sockeye salmon (Oncorhynchus nerka) in Lake Aleknagik, Alaska, using a multi-decadal dataset (1967–2024). Migration timing varied widely among years and was best explained by a combination of ice-out phenology, epilimnetic temperature, and fish densities in littoral habitats. Juvenile sockeye salmon migrated earlier in …

"It's A Dance": Examining Midwives As Choreographers Of Reproduction In Maine, Annie Goldstein

Honors Theses

This thesis examines the contemporary work of community-based Maine midwives through the theoretical framework of choreography. In the context of this work, choreography can be understood as the well-thought-out, purposeful undertaking of a process during which negotiation, coordination, and improvisation are required to adapt to constantly changing circumstances. Using choreography, this thesis attempts to understand how Maine midwives navigate global market processes and practice under authoritative forms of biomedicine, ultimately linking them to other midwives across various global sites. Situated within Maine’s maternal health landscape that is characterized by the ongoing closure of labor and delivery units and rural hospitals, …

Racial Capitalism And Black Maritime Geography In 19th Century Portland, Maine, Jeremy Harrison

Honors Theses

Portland, Maine, is located on the rocky shores of the Atlantic Ocean and has served as home to a diverse population that has benefited from the economic and social aspects of the shipping and trading industry. This port city in one of the northernmost regions of the United States was one of the last stops for ships carrying goods before reaching the city centers of the Americas and Europe. As a result, during the late 18th and early to mid-19th centuries, skilled and unskilled Black laborers from somewhat fringe regions within the Atlantic migrated to Portland in search of not …

The Role Of Mscs In The Il23/17 Pathway And Their Response To Mechanical Stress, Norma Aileen Dominguez Jimenez

Honors Theses

Mechanical stress plays a central role in shaping cellular behavior within skeletal tissues. At the enthesis, where tendons and ligaments attach to bone, repeated mechanical loading is strongly associated with inflammation and the development of ankylosing spondylitis (AS). Although mesenchymal stem cells (MSCs) are known to contribute to tissue structure and repair at these sites, their potential role in inflammatory signaling, particularly within the I 23/IL 17 pathway, remains unclear. In this thesis I investigated whether MSCs are capable of expressing cytokines involved in this pathway and how mechanical stress and differentiation influence this expression. Using the mouse derived C3H/10T1/2 …

Near And Dear: How Proximity To Amenities Shapes Land Value In Maine, William Kopans

Honors Theses

Residential land values reflect the benefits of accessibility to amenities as well as the costs associated with commercial activity. This trade-off is particularly important in Maine, a predominantly rural state where most households rely on automobiles to access employment, retail, and civic amenities. Drawing on hedonic theory, I analyze how households value proximity to public and private amenities located within downtowns and shopping centers. Using parcel-level transaction data from ATTOM combined with amenity data from OpenStreetMap, I construct a novel approach that differentiates downtown and shopping center clusters across the state. The findings demonstrate that properties located immediately adjacent to …

Metamorphosed Components In Cv Chondrites Camel Donga 003 And Camel Donga 040 As Evidence For Varying Degrees Of Metamorphism Within The Parent Body, Kathryn E. Stone

Honors Theses

The CV carbonaceous chondrites are a group of primitive stony meteorites that record early solar-system evolution processes. They are typically of low metamorphic grade, though some metamorphosed CVs have recently been found. Two CV chondrite breccias, Camel Donga 003 (CD 003) and Camel Donga 040 (CD 040) consist of multiple lithologies. CD 003 consists of three lithologies, one of which – Lithology C – has been metamorphosed to petrologic type ~3.7 (Alevy et al. 2025). CD 040 consists of two lithologies, one of which is metamorphosed to petrologic type 3.7 (Dunn and Alevy, 2024; Dunn et al. unpublished). Both samples …

The Prestige Paradox: Can Venture Capital Prestige Lead To Lower Startup Exit Rates?, Charlie Fenollosa

Honors Theses

This project investigates how the prestige of VC firms investing in early-stage startups affects the likelihood of successful exits, defined as IPOs or acquisitions. Using Crunchbase data on companies, funding rounds, and investments, I construct six measures of prior VC success to proxy for prestige. Contrary to conventional expectations, VC prestige is not associated with increased exit probability, a finding robust to composite, LASSO-selected, and PCA-based indices. Further analysis suggests this relationship is driven by mechanisms through which high VC prestige paired with large syndicates and high funding may create frictions, while prestigious VCs help smaller companies grow more effectively.

A Regime Of Fear: Barriers To Healthcare Access In Times Of Intensifying Anti-Immigrant Rhetoric And Immigration Enforcement, Kathryn F. Masetti

Honors Theses

The U.S. immigration regime produces the conditions that deny immigrants equitable access to healthcare. The Trump administration’s second term, characterized by aggressive immigration enforcement and anti-immigrant rhetoric, continued to intensify these conditions, contributing to a widespread decline in healthcare utilization by immigrant patients throughout the United States. This thesis investigates how policies and rhetoric from the Trump Administration, including immigration enforcement, shape the barriers that immigrants with and without status encounter when accessing healthcare services in Maine, and how the fear of surveillance, detention, or deportation influences how immigrant communities perceive and utilize healthcare services. Two in-depth semi-structured qualitative interviews …

Ultra-Processed Or Ultra-Addictive? A Demand-Based Redefinition Of Ultra-Processed Foods, Braden Jondro

Honors Theses

Ultra-processed foods now comprise the majority of the U.S. food supply and have been directly associated with 32 chronic diseases including obesity, cardiovascular disease, cancer, and diabetes. Current classification systems such as NOVA provide a useful framework for identifying food processing, but rely on broad and subjective categorizations that may not capture the mechanisms most closely associated with promoting persistent overconsumption. In particular, existing classification systems remain limited in their ability to evaluate addiction-like behaviors associated with highly processed foods, including persistent purchasing patterns, reinforcement effects, and substitution responses. This paper introduces the Ultra-Processed Food Intensity (UPFI) index, an objective, …

Three-Photon Rydberg Eit Lineshape Analysis In Rubidium, Jackson Lake

Honors Theses

Electromagnetically Induced Transparency detection of high-lying Rydberg states in room-temperature rubidium vapor was investigated using a four state ladder-type excitation scheme with light provided by three External Cavity Diode Lasers (ECDLs) at 780 nm, 776 nm, and 1266 nm. This detection technique was studied by characterizing the lineshape parameters of the EIT transmission peak, specifically the height, width and area of the transparency window as functions of the dressing and coupling laser powers. With the goal of characterizing the linewidth of the transmission signal, a confocal etalon was built and implemented in the optical setup to perform frequency calibration of …

Enumerating Matrices Of A Given Order Over Finite Fields, Thor Richard Gabrielsen

Honors Theses

This thesis derives a generating function that describes the matrices of a given multiplicative order over finite fields of a given order assuming that the order of a field is not a divisor of the desired order of the matrix. This is done by using the power series known as the cycle index derived from the rational canonical form. This index can be factored, and using the fact that the minimal polynomial divides some polynomial of the form x^k − 1 we can show that the minimal polynomial is squarefree. This sufficiently restricts the form of the rational canonical form …

Brewing Resilience: Cooperatives, Micro-Mills, And The Quest For Survival In Costa Rica's Changing Coffee Landscape, Leila N. Iredell

Honors Theses

This thesis examines how different organizational models in Costa Rica's coffee sector shape producers’ ability to capture value, build resilience, and sustain rural livelihoods in a rapidly changing global market. In comparing traditional cooperatives and new micro-mills, I examine specifically how control over the value chain, access to markets, and social infrastructure differ across models and what these differences mean for the farmers who depend on them. This project analyzes how the collapse of international price agreements and decades of market volatility drove producers toward new strategies, from independent processing and direct trade to coffee tourism. Costa Rica stands as …

Blood And Belonging: Remembering Massacres Of The American West In The Twentieth Century, Mountain Meadows And Sand Creek, Kenzie Burns

Honors Theses

The late nineteenth and early twentieth centuries marked a turning point in mainstream America’s sense of national identity. A wave of nostalgia for the American Frontier enshrined the region’s idealized nineteenth-century past as myth. A key part of the story is romanticized violence—often depicted through cultural imagery of cowboys, gunfights, and battles with American Indians. This project seeks to understand more about how violence is represented in the cultural memory of the American Western past. Within the past twenty years, scholars of the American West have begun to incorporate the study of memory into their scholarship, frequently with how cultural …

Borrowed Mantles: Neoclassicism, Theology, And The Construction Of Authority In Phillis Wheatley-Peters, Zoe N. Lament

Honors Theses

This thesis examines how Phillis Wheatley-Peters established literary and intellectual authority within an eighteenth-century world that questioned both her authorship and her intellectual capability as an enslaved Black woman. Rather than focusing on the external validation provided by the prefatory materials to Poems on Various Subjects, Religious and Moral (1773), this study argues that Wheatley-Peters constructs authority through the poetry itself. Specifically, it explores how her use of neoclassical poetic conventions alongside Christian theological language functions to establish credibility and strengthen her moral and intellectual arguments.

Through close readings of poems including "On Being Brought from Africa to America" and …

Evaluating Quahog (Mercenaria Mercenaria) Nursery Methods And Production Costs To Support Diversification Of Maine’S Fisheries And Aquaculture Sector, Hannah G. Wolf

Honors Theses

Populations of wild and farmed quahogs in Maine are expanding, driven by warming waters, declining soft-shell clam populations, and the need to diversify fisheries. The Northern quahog (Mercenaria mercenaria) is a potential species to diversify Maine’s marine sector, as its geographical range is expanding, and they appear more resistant to green crab predation. Enhancing wild quahog stock provides economic and social advantages for both the aquaculture and wild harvest industries. However, there is limited understanding about the commercial viability of producing quahog seed on existing farms for wild shellfish enhancement in Maine. This research, part of a larger NOAA …

Analyzing Rydberg Atoms Of Rubidium At Room Temperature: Applying Electromagnetically Induced Transparency, Bridger Stiles

Honors Theses

This thesis describes an experimental exploration of electromagnetically induced transparency (EIT) in atoms of 85Rb using a new MOGLabs external cavity diode laser. A two-step ladder technique of EIT was applied using a 5S_1/2→5P_3/2 probe transition and 5P_3/2→nD_5/2 coupling transitions. Significant apparatus tuning was done, including developing a reliable procedure of regulating frequency and scanning the coupling laser over a sufficient mode-hop free range. A Doppler-reduced technique was applied by counter-propagating the probe and coupling beams through the Rb vapor cell. EIT signals were collected at various probe and coupling laser powers to analyze changes in signal size and linewidth. …