Digital Commons Network^™

Methods To Improve Efficiency, Sensitivity, And Selectivity Of Sequence Similarity Search, Daniel Olson

Graduate Student Theses, Dissertations, & Professional Papers

The rapid growth of biological sequence data presents significant challenges for bioinformatic analysis. A cornerstone of this analysis, sequence similarity search, is hampered by three main obstacles: sensitivity in detecting distant evolutionary relationships, selectivity in distinguishing true homology from spurious similarity caused by features like tandem repeats, and scalability to handle massive databases. This dissertation introduces two novel computational tools, ULTRA and NEAR, that address these challenges to improve the efficiency, sensitivity, and selectivity of sequence similarity search. Part I of this dissertation addresses the problem of selectivity by focusing on tandem repeats, a common source of false-positive results in …

Advancing Wildfire Science Through The Application And Parametrization Of Process Based Fire Models, Anthony Albert Marcozzi

Graduate Student Theses, Dissertations, & Professional Papers

Computational models of wildfires are an important tool for fire managers and scientists. However, representing fuel inputs with sufficient detail for process-based fire models to accurately reflect observed fire phenomena while remaining computationally tractable is a major challenge. This dissertation advances wildland fire science by applying and parametrizing such models to investigate complex fire-fuel interactions across multiple scales.

A primary contribution addresses fine-scale fuel characterization through a novel voxel-based technique converting Terrestrial Laser Scan (TLS) point clouds into three-dimensional (3D) fuel representations. This method was evaluated by comparing simulated fire behavior in the Fire Dynamics Simulator (FDS), optimized using the …

Depth Distribution Of Liquid Water In Greenlands Firn Layer Based On L-Band Radiometry, A Snow Physics Model, And Machine Learning, Taylor D. Moon

Graduate Student Theses, Dissertations, & Professional Papers

The accurate estimation of the amount of meltwater retained by Greenland’s firn layer and its distribution over depth is essential for assessing both the current and future mass balance of the Greenland Ice Sheet. When meltwater infiltrates the firn, it exists as a quantifiable volume of liquid water, measurable as the one-dimensional liquid water amount, hereafter referred to as LWA. A promising new tool for estimating LWA is L-band passive microwave satellite radiometry, which can provide twice-daily estimates using empirical models of firn microwave emission. However, this method faces two primary limitations. First, retrievals are untested against field observations and …

America's Highest Stage: Utopians, Capitalists, And Trail Runners On Pikes Peak, Mitchell Morris

Graduate Student Theses, Dissertations, & Professional Papers

Since ancient times, Pikes Peak’s prominence on the land has endowed it with prominence in the minds of all who have lived around it. This ancient dynamic was reinforced in the nineteenth century by the famed expedition of Lieutenant Zebulon Pike in 1806 and the Pike’s Peak Gold Rush in 1858. Since then, the mountain has become a stage. Standing tall, visible from hundreds of miles around, and known from coast to coast, Pikes Peak is a platform that has attracted diverse historical actors to come and perform, elevate their endeavors to new heights, and demonstrate what they, and people …

Investigating Non-Invasive Survey Methods And Building A Predictive Occupancy Model For Harlequin Ducks (Histrionicus Histrionicus) In Western Montana And Northern Idaho, Holli Ann Holmes

Graduate Student Theses, Dissertations, & Professional Papers

Harlequin Ducks (Histrionicus histrionicus; HADU) are an imperiled sea duck that breeds along white-water mountain streams, but challenges in surveying them have made it difficult to understand population trends in their Northern Rocky Mountain breeding population. In this study we had two objectives: (1) evaluate non-invasive survey methods for detecting HADU on their breeding grounds in Western Montana and Northern Idaho, and (2) develop an occupancy model to predict potential breeding stream use for HADU across the region. First, we assessed the efficacy of ground-based foot surveys (GBS), environmental DNA (eDNA), and camera traps to detect breeding HADU during …

Untangling Mining, Past And Present: An Analysis Of Key Informant Interviews On The Prospects Of Renewed Mining Activity Near Cañon City, Colorado, Lauren E. Nelson, Brian C. Chaffin

Graduate Student Theses, Dissertations, & Professional Papers

The Rocky Mountain West represents a distinct social-ecological region in a time of transition. As a subregion of the American West, it is defined by aridity, topography, and the physical, cultural, and economic impacts of mining across the landscape. Contemporarily, the region is increasingly shaped by an influx of tourism as well as seasonal and permanent residents who value the landscape for its recreational opportunities and aesthetic values. Most of the communities in the region owe their start to the mining booms of the 19th century, and many are still grappling with contamination left behind by mining. The transition between …

Changes In Efficiency And Magnitude Of Recharge Due To Climate Change For Headwater Catchments In The Mountain West, Harrison Mcgillen

Graduate Student Theses, Dissertations, & Professional Papers

Changes to groundwater recharge and stream flow were simulated from downscaled CMIP6 global climate models in a headwater catchment of the Blackfoot River, MT. A calibrated, 3-D, coupled surface and groundwater GSFLOW model, forced with minimum and maximum temperature, and precipitation from a downscaled CMIP6 simulation was used to quantify groundwater recharge and stream flow. The model was calibrated against measured groundwater head and stream flow using observed temperature and precipitation boundary conditions. The calibrated model was then forced with downscaled temperature and precipitation from the CANESM5 model for the SSP245, 370 and 585 scenarios, as well as a manual …

Occupational Therapy Assistant Education: Exploring The Relationship Between Student Factors And Nbcot Examination Pass Rates, Micahela Parker

Graduate Student Theses, Dissertations, & Professional Papers

The purpose of this retrospective quantitative study was to examine the predictive ability of gender, age, GPA, attendance and both Level II fieldwork scores (Fieldwork One and Fieldwork Two) on first attempt NBCOT exam success. To practice as an occupational therapy assistant, an individual must complete an accredited occupational therapy assistant (OTA) program and pass the National Board for Certification in Occupational Therapy (NBCOT) exam. The NBCOT exam was developed to ensure entry-level occupational therapy assistants have the necessary knowledge to make safe and competent decisions.

The overarching research focus was to understand the extent of one or more of …

Identity Construction Of Post-2000s Class Monitors In The Public University Of China, Guoming Li

Graduate Student Theses, Dissertations, & Professional Papers

The identity construction experiences of a key group of student leaders in China’s public universities, class monitors born after the year 2000, were explored through a descriptive phenomenological approach guided by Giorgi’s (2019) framework. From the in-depth interviews with 14 participants, how these student leaders interpret and make meaning of their experiences within the unique context of China’s student cadre system was investigated. Three central dimensions of identity construction were showed: (1) alignment with servant leadership discourses that emphasize responsibility, care, and moral commitment to peers; (2) navigation of a complex followership process involving compliance and responsiveness to institutional supervisors; …

Impacts Of Fire-Driven Vegetation Changes On Evapotranspiration In North American Boreal Forests, Tyler Glen Albrethsen

Graduate Student Theses, Dissertations, & Professional Papers

A growing body of evidence suggests that land cover change could be impacting evapotranspiration (ET) trends more than the direct impacts of climate change (Dashti et al., 2022; Zhang et al., 2015). In boreal forests, one of the Earth’s most important carbon sinks (Kang et al., 2006), climate and disturbance-driven land cover change is progressing rapidly, threatening the resilience of conifer-dominated forests (Baltzer et al., 2021; Massey et al., 2023). The spread of deciduous trees and the changing structure of boreal forests likely have large implications for the magnitude and seasonality of ecosystem water fluxes (Young-Robertson et al., 2016). This …

Mapping Mesic Resilience In Western Rangelands: Productivity Trends, Predictors, And Targeting Frameworks, Kristopher Robert Mueller

Graduate Student Theses, Dissertations, & Professional Papers

Mesic ecosystems in riparian areas and wetlands make up only 2% of western U.S. rangelands but support 80% of wildlife during dry periods, providing vital late-season forage and refuge when surrounding uplands dry out. Yet, mesic habitats are often overlooked in landscape-scale conservation planning. This thesis addresses two key gaps: understanding how mesic productivity responds to environmental change and developing frameworks to incorporate these habitats into current conservation strategies. Using 40 years of Landsat imagery (1984–2024), we examined long-term trends in late-season mesic vegetation productivity and its relationship with drought across the sagebrush biome. From 1984 to 2004, mesic productivity …

Challenged: A Practice-Based Analysis Of Simulating The Realities Of Teaching Through Play, Shanel Lara Locke

Graduate Student Theses, Dissertations, & Professional Papers

ChallengED is a classroom simulation game designed to explore the emotional and procedural realities of teaching through interactive play. Rather than attempting to manufacture empathy, the project focuses on conveying the unpredictability, humor, and fatigue that shape daily classroom life. Drawing from my own teaching experience, the game uses experiential realism and embodied interaction to communicate how educators navigate constant interruptions, shifting demands, and limited control. The development process also became a therapeutic practice, offering a way to reinterpret professional challenges through creative experimentation. Situated within practice-based research, ChallengED demonstrates how game design can function as both artistic inquiry and …

A Retrospective Assessment Of Post-Fire Planting In The Us: Aligning Actual And Optimal Planting Sites To Address The Reforestation Gap, Lewis Faller

Graduate Student Theses, Dissertations, & Professional Papers

The natural regeneration processes that maintain semi-arid North American conifer forests are being disrupted. Increasingly, large wildfires burn core areas beyond the typical seed dispersal range of surviving adult trees and even when seeds are present, climate conditions increasingly are unsuitable for conifer recruitment, establishment, and survival. The USDA Forest Service (USFS), mandated to maintain forest cover in response to harvest or disturbance, now faces a planting backlog of over 3.8 million acres. Here, we conduct a retrospective assessment (1986–2023) of USFS post-fire reforestation to evaluate (1) whether historical planting patterns align with the goal to close the national reforestation …

Re-Establishing People And Industry: A Study Of The Historical Context Of The Winters Decision (1908) Involving Indian Agent William R. Logan, The Plantiffs In Winters, And Sugar Beet Agriculture On The Fort Belknap Reservation, Montana, 1856-1910, Kellen R. Neighbors

Graduate Student Theses, Dissertations, & Professional Papers

In 1905, Indian Agent William R. Logan filed an injunction to stop upriver irrigators from diverting Milk River water before it reached the Fort Belknap reservation. This culminated in Winters v. U.S. (1908) and became known as the Winters decision, the Winters Doctrine, or Indian Reserved Water Rights. This case is the foundation for Native American water rights cases today. This study explores the historical context of the case, specifically focusing on Fort Belknap Indian Agent William Logan’s role. William Logan was a devout Montana entrepreneur who carried his entrepreneurial spirit into his tenure as Fort Belknap Agent. This fact …

Human-Bear Conflicts In Western Montana: Mapping Attractants And Prevention Efforts, Jessica Nichole Reyes

Graduate Student Theses, Dissertations, & Professional Papers

Human-bear conflicts (conflicts) are rising across North America, largely due to the expansion of the wildland-urban interface into bear habitat. These conflicts are driven by ecological and human factors, including habitat fragmentation, loss of natural food sources and the widespread availability of human-related attractants such as garbage, fruit trees, and bird feeders. While studies increasingly examine the ecological and spatial predictors of conflicts, fewer have explored how attractant types, land cover changes, and local geography shape conflict trends. Montana communities have long managed bear conflicts, but recent increases in incidents and human-caused bear mortalities—alongside expanding grizzly bear populations—have prompted growing …

Whole Genome Sequencing From Snowshoe Hare Fecal Samples, Jessica J. Powell

Graduate Student Theses, Dissertations, & Professional Papers

Genomic analyses can provide powerful insights into important issues in conservation biology, including rapid estimates of overall genetic diversity and related population genetic parameters. Noninvasive DNA sampling from fecal samples is an affordable, efficient, and broadly applicable sampling method that has been used in many targeted genetic analyses. However, the efficacy of whole genome sequencing from fecal samples remains relatively unexplored in most taxa. Here, we present results from two experiments designed to test the quantity and quality of whole genome resequencing data obtained from snowshoe hare (Lepus americanus) fecal pellets. Extensive previous research has used genetic analyses …

Climate Change And Behavioral Plasticity: Migration, Parturition, And Phenological Mismatch In Northern Rockies Elk, Tara Kelly Meyer

Graduate Student Theses, Dissertations, & Professional Papers

The survival and reproduction of large herbivores depend on the synchronization of life-history events with ephemeral resource availability. Migratory ungulates have navigated this seasonality by relying on environmental cues (e.g., snowmelt or green-up) to predict when to migrate to distant foraging areas. However, anthropogenic climate change is rapidly altering environmental baselines. This dissertation investigates the intersection of climate change, behavioral plasticity, and reproductive ecology in a partially migratory elk (Cervus canadensis) population in Alberta, Canada. Integrating 22 years of longitudinal monitoring data (2002–2024) of individual elk with remotely sensed NDVI and statistical modeling, I examine how three coexisting migratory tactics …

Enhancing School Counselor Preparedness: The Effect Of Emotional Regulation Training On Outcomes Of Emotional Regulation, Self-Efficacy, And Wellness Measures, Allison Lynn Bristow

Graduate Student Theses, Dissertations, & Professional Papers

School Counselors in Training (SCITs) face distinctive challenges while developing their clinical skills and managing the complexities of school counseling. These challenges can lead to emotional strain and burnout, making it essential for SCITs to cultivate strong emotional regulation skills. Counseling and education researchers have discussed various strategies to assist counselors in enhancing emotional regulation skills. However, limited research has assessed the effectiveness of specific trainings on emotion regulation, especially for SCITs. This quantitative study investigates the effectiveness of an emotional regulation (ER) training program offered to SCITs during their field placements in schools. The central research question is whether …

Armed By Design: Posters And Publications Of Cuba's Organization Of Solidarity Of The Peoples Of Asia, Africa, And Latin America (Ospaaal), Jen Hoyer, Lani Hanna, Josh Macphee, Vero Ordaz, Sarah Seidman

Publications and Research

This book reflects on the intersection of graphic design and political solidarity work of OSPAAAL, the Organization of Solidarity of the Peoples of Africa, Asia, and Latin America. Based in Havana, Cuba, OSPAAAL produced nearly 500 posters, magazines, and books beginning in the late sixties. Their output provides one of the most robust examples of political design ever seen; it offers a wealth of opportunities for thinking about how design is—and could be—deployed today in the search for more egalitarian social transformation.

Armed By Design brings together artists and thinkers from around the world whose work has been impacted by …

Certificate Of Need Laws' Effect On Provisions Of Uncompensated Care, Connor Anthony Mostek

Graduate Student Theses, Dissertations, & Professional Papers

Certificate of need (CON) laws are regulations that require healthcare facilities to seek permission from a state government board to enter a market or expand/modify their established business. Proponents of CON laws claim that, among other things, CON laws protect hospitals and other healthcare providers from competition, allowing them to charge private or fully insured patients more in order to use the profits to “cross-subsidize” free care for low-income and uninsured patients. By employing an unbalanced panel dataset on hospital cost reports for the years 2012, 2014, 2016, and 2019, this study finds that there is no strong evidence that …

Refining Population-Level Measures Of Early Childhood Vaccination Coverage Using National Immunization Survey-Child Data, Alexandria Nicole Albers

Graduate Student Theses, Dissertations, & Professional Papers

Background: From 2011-2021, the U.S. Advisory Committee on Immunization Practices (ACIP) recommended 10 vaccine series by age 24 months, with guidelines for minimum vaccination age, maximum age for rotavirus vaccination, minimum dose intervals, and a catch-up schedule for delayed series initiation. National vaccination surveillance evaluates series completion based on whether children received the recommended number of doses, including a combined 7-vaccine metric (completed seven series collectively). However, this approach overlooks: 1) vaccinations given too early, too late, or too close together, 2) catch-up schedule vaccinations, and 3) completion of all 10 recommended vaccines.

Purpose: To refine national childhood vaccination coverage …

Mountain Pine Beetle Host Tree Selection And Climate-Growth Dynamics In Whitebark Pine, Hannah Rose Alverson

Graduate Student Theses, Dissertations, & Professional Papers

Recent climate-driven outbreaks of mountain pine beetles (Dendroctonus ponderosae) in whitebark pine (Pinus albicaulis) have raised fears of increasing whitebark pine mortality with increased warming and drought due to climate change. However, little is known about how whitebark pine responds to climate, what characteristics may predict whitebark pine susceptibility to mountain pine beetle outbreaks, or how these may interact. This information is critical in understanding how whitebark pine might persist in a changing climate. My research investigated how whitebark pine growth responds to various climate variables and how these responses may be predictive of attack by …

Examining Pathways For Front-Country Camping Access In The Rural American West: An Application Of Access Theory, Hayley Ann Johnson

Graduate Student Theses, Dissertations, & Professional Papers

Access to front-country camping on North American public lands has historically been preferential to those who are White, relatively wealthy, and highly educated. In theory, however, all activities on public lands are available to all people, and everyone has equal right to enjoy the benefits from recreational activities like camping in these spaces. Since the 1960s, research on access has focused on the barriers, or constraints, that influence overall participation in leisure activities; however, few studies have examined access specific to front-country camping.

As a complement and extension of traditional leisure constraints theory, this study presents a unique application of …

Binoculars To Bytes: Development And Field Validation Of An Ai-Driven System For Avian Monitoring, Christian J. Dupree

Graduate Student Theses, Dissertations, & Professional Papers

Autonomous camera-trap arrays coupled with artificial-intelligence (AI) vision can lift bird monitoring beyond the spatial, temporal, and labor limits of traditional field surveys. We present Binoculars to Bytes (B2B), an open-source pipeline that turns 180–360° time-lapse imagery into analysis-ready avian data. At Freezout Lake Wildlife Management Area (Montana, USA) the system ran four-hour morning deployments during spring and fall migrations (2023–2024). A YOLO-NAS detector, incrementally refined with a “Specialized Localized Iterative Model” workflow, quadrupled local accuracy and, after confidence-based species-binning, cut false-positive rates in half. Daily AI species lists were benchmarked against contemporaneous eBird citizen-science checklists and recovered ≥ …

"I'Ve Never Felt A Pain Like This" A Dialogic Analysis Of Parent-Child Estrangement Narratives On Reddit, Grant W. Lane

Graduate Student Theses, Dissertations, & Professional Papers

How do adult children estranged from their parent(s) create meaning and make sense of their estrangement in Reddit posts on the subreddit r/EstrangedAdultChild? This study analyzed Reddit posts written by estranged adult children for a presumed audience of other estranged adult children. Using relational dialectics theory (RDT) as a lens for analysis, this research examined the competing discourses that influence the meaning-making and sense-making processes of estranged adult children in their posts when the intended audience is fellow estranged adult children. Seventy-four posts from r/EstrangedAdultChild, authored by adult children who self-identified as estranged from at least one parent, were collected …

Trace Level Benzoylecgonine Detections In Equine Plasma/Serum – A Proposed Interim Plasma Level Regulatory “Cut-Off“, Andreas F. Lehner, Kimberly Brewer, Levent Dirikolu, Abelardo Morales Briceñod, Robert Holland, George Maylin, Clara Fenger, Thomas Tobin

Maxwell H. Gluck Equine Research Center Faculty Publications

Cocaine is a widely used human recreational substance routinely transferring at pharmacologically irrelevant trace level amounts to non-user humans and horses. Horses and humans rapidly demethylate cocaine to benzoylecgonine which is excreted in urine at concentrations approaching two thousand times higher than the corresponding plasma cocaine concentrations. In human workplace drug testing, these usually pharmacologically irrelevant trace level urinary detections of benzoylecgonine are handled by application of a 100 ng/ml urinary “cut-off“, as presented by the Substance Abuse and Mental Health Services Administration (SAMHSA). In horse racing several American states have long used published urinary “cut-offs“ for benzoylecgonine of from …

Formication With Destruction Of The Nasal Septum: A Rare Case Report, Michele White, Dwayne Evans, Gary Frey, Cleverick Cd Johnson, Ben F Warner

Faculty, Staff and Student Publications

Delusions of parasitosis are known by several names, one of which is formication. It is an uncommon psychiatric disorder listed in the DSM V under the classification of delusional disorders. Patients experience an established, incorrect belief that they have an infection of living organisms such as parasites. There are two types of delusions of parasitosis, primary and secondary. In the primary form, the symptom is the delusion of a parasitic infection without secondary cause. The secondary form includes this symptom as well as additional psychiatric disorder, drug abuse, or medical illness. Patients often seek consultation with dental providers for dental …

To Be Soft Again: A Phenomenological Study Of Uncertainty And Resilience In Childbearing During The Covid-19 Pandemic, Marcianna Nosek

Nursing and Health Professions Faculty Research and Publications

Background:

During the COVID-19 pandemic, uncertainty was exacerbated in experiences of pregnancy and childbirth as people navigated through uncharted territory. Building resilience may be one effective way to cope. However, for those who carry a heavier burden in upholding others, a societal expectation of “toughness” and the ability to endure may lead to an appearance of resilience, while on the inside, well-being may be compromised.

Objectives:

This study is part of a larger phenomenological study that explored the broad research question: What is the lived experience of childbearing during the COVID-19 pandemic? Specific themes of uncertainty and resilience are reported …

Church Ministers' Perceptions On Burnout And How It Shapes Their Leadership Practices., Jason Young

Dissertations

This qualitative phenomenological study explored how large church ministry leaders experienced burnout and how that burnout shaped their leadership practices. The study was motivated by a research gap concerning the lived experiences of ministers in large churches. Framed by the job demands-resources theory and the conservation of resources theory, the study sought to understand how the demands of ministry leadership and the availability of personal and organizational resources influenced the experience of burnout. The research employed a qualitative phenomenological design, utilizing semi-structured interviews. A purposive and snowball sampling approach was used to recruit 13 large US church ministry leaders. The …

Dental Management Of A Talon Cusp On A Permanent Incisor In Traumatic Occlusion, Bret Lesavoy Dmd, Richard Yoon D.D.S.

The New York State Dental Journal

The purpose of this paper is to report the case of an 8-year-old female with occlusal interferences involving the permanent maxillary right central incisor (PMRCI) due to a Type 1 dens evaginatus, also known as a talon cusp (TC), causing displacement of the affected tooth. Clinical concerns related to TCs include occlusal interferences and increased risk for dental injury, displacement of the affected tooth, caries, tongue irritation and esthetic concerns. The TC in this report was reduced periodically over two months. Following each reduction, 5% topical sodium fluoride varnish was applied as a desensitizing agent. Upon completion and removal of …