Digital Commons Network^™

Mirage: A Novel Multiple Protein Sequence Alignment Tool, Alex Nord

Graduate Student Theses, Dissertations, & Professional Papers

A fundamental problem in computational biology is the organization of many related sequences into a multiple sequence alignment (MSA) [2]. MSAs have a range of research applications, such as inferring phylogeny [22] and identifying regions of conserved sequence that indicate functional similarity [18]. In the case of protein isoforms, MSAs are valuable tools for transitively annotating post-translational modifications (PTMs) by enabling information transfer between known PTM sites and the sites that they align to [11].

For protein MSA tools, one challenging biological phenomenon is alternative splicing, wherein identical genomic sequence will differentially select from a subset of available coding regions …

Decolonization And Political Engagement For The Health And Wellbeing Of The Selish, Ksanka And Qlispe People, Anita Louise Dupuis

Graduate Student Theses, Dissertations, & Professional Papers

What would a contemporary cultural model for health and wellbeing look like for an Indigenous community and what domains would feature prominent today? How would this model be reflected in governance for the Confederated Salish and Kootenai Tribes (CSKT)?

This autoethnographic, interdisciplinary, action research study suggests ten cultural domains for inclusion in a contemporary cultural model for health and wellbeing for the Selish, Ksanka and Qlispe (SKQ), the Indigenous Nations of the CSKT. It then provides a revised, annotated draft of a culture-based constitutional governance structure, which integrates, synthesizes, and incorporates these ten domains.

The key purposes of the study …

Carrying The Seeds: Adaptations And Transitions Of Hmong American Food Producers In Missoula County, Montana, Rachel Cramer

Graduate Student Theses, Dissertations, & Professional Papers

Forty years after the initial resettlement of Hmong refugees in Missoula County, Montana, the Hmong American community has undergone significant agricultural and cultural adaptations. Today, there are about 200 Hmong Americans in the county, less than 2% of the population (US Census Bureau 2010), but they make up around 40% of the farmers’ market produce vendors. The thesis demonstrates that, while agriculture has played a central role in helping Hmong refugees adapt, its role is becoming more symbolic as the second generation develops an identity less connected to growing and selling food. Through a qualitative research approach using 19 in-depth …

Early 20th Century Xenophobic Perceptions Among American Security Rally Of Montana Participants In 2016, Christian S. Boyce

Graduate Student Theses, Dissertations, & Professional Papers

The goal of this research was to investigate immigration perceptions among participants in the American Security Rally of Montana using in-depth interviews and participant observation qualitative techniques. The thesis was guided by the following questions. What are the perceptions of participants among the American Security Rally of Montana with respect to immigration, where do they come from and why are they are created? The main theme highlighted by participants was one of xenophobia. This xenophobic rhetoric was predominantly directed towards potential Syrian refugee migrants to Montana but also encompassed a perspective pertaining to Hispanic/Latino undocumented migrants. Theodore Adorno’s notion of …

Social Justice In Social-Ecological Systems: Resilience Through Stakeholder Engagement, Frederick I. Lauer

Graduate Student Theses, Dissertations, & Professional Papers

Successful management of social-ecological systems (SES) is predicated on quality collaborative exchanges between project stakeholders and management. The Southwest Crown of the Continent Collaborative (SWCC) Collaborative Forest Landscape Restoration Program (CFLRP) provided an opportunity to explore landscape scale collaborative management and SES outcomes. Global change and future uncertainty of landscapes prompted the SWCC to employ restoration treatment alternatives throughout 1.4 million acres of forests, most of which are publicly held. The SWCC currently monitors environmental and economic variables, with plans to monitor social variables. This thesis formalizes a proposed framework to investigate SES resilience, and explores public engagement as an …

K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler

Graduate Student Theses, Dissertations, & Professional Papers

Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process …

Sharing Nature: Rival Visions Of Environmental Discourse, Charles B. Hayes

Graduate Student Theses, Dissertations, & Professional Papers

In this paper I compare and evaluate the work of Steven Vogel, Akeel Bilgrami, and Jedediah Purdy regarding the place of normative conceptions of nature in political discourse. I argue that it is not in principle undemocratic, nor is it theoretically illegitimate, nor domineering to hold and express ideas involving normative conceptions of nature. On the contrary, it is often exemplary political discourse, well suited for deeply questioning our impact on the world and for inspiring collective change.

How Should We Conceptualize Moral Disagreements About Animals?, Kristian Cantens

Graduate Student Theses, Dissertations, & Professional Papers

I intend this paper as a sort of philosophical reflection on my experiences as an animal activist. In my three years of doing outreach on college campuses, I came to an increasing appreciation for what Murdoch referred to as “the difficulty and complexity of the moral life and the opacity of persons” (Murdoch 1998d, 293). This appreciation came in turn at the cost of an increasing disappointment with many of the philosophers I admired at the time – namely, Peter Singer and Tom Regan. What I came to understand is that many of these contemporary moral theories were in fact …

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …

An Investigation Of The Relations Between Stress And Prospective Memory, Brandon T. Stewart

Graduate Student Theses, Dissertations, & Professional Papers

Prospective memory (PM) is a future-oriented memory system that entails “remembering to remember” intentions, or to perform actions in the future. People spend significant portions of their day-to-day lives forming and acting on intentions, and the ability to successfully generate, retain, and complete these intentions has important implications for one’s daily functioning and quality of life. Another common human experience is stress, whether that be short-term, acute stress, or long-term, chronic stress. Despite the significance and ubiquity of both PM and stress, the research base documenting the relations between them is sparse. This topic area necessitates additional research to delineate …

Lgbtq-Inclusive Sexuality Education In Montana Public High Schools: An Assessment Of The Needs Of Health Enhancement Teachers, Andrew G. Johnson

Graduate Student Theses, Dissertations, & Professional Papers

BACKGROUND

LGBTQ youth face many unique health challenges. Rates of depression and suicide are exponentially higher for LGBTQ youth than for their heterosexual, cisgender peers. Rates of HIV and STI infection are rising among this demographic. Comprehensive sexuality education has demonstrated the potential to address some of these health challenges. Specifically, it has been shown to delay the onset of sexual intercourse, and to reduce pregnancy and transmission rates of HIV and STIs among youth. Several studies have looked at LGBTQ-inclusive sexuality education from the perspective of LGBTQ students, but few have looked at this issue from the perspective of …

Coupling Biophysical Complexity And Forest Metabolism In A Floodplain Landscape, Peter Davis

Graduate Student Theses, Dissertations, & Professional Papers

Floodplains are biophysically complex systems that are considered among the most productive and biodiverse ecosystems on Earth. Until recently, quantitative assessment of the relationship between complexity and terrestrial production has been constrained by technological limitation. To address how floodplain biophysical complexity and ecosystem function are related, I employed remote sensing, GIS, and spatial analyses to quantify and couple metrics of complexity and terrestrial production, as well as explore the relationship among complexity, vegetation structural diversity, and terrestrial primary productivity. The study site is a 6.75-km by 1.75-km portion of the Bitterroot River floodplain near Carlton, MT upon which 551 sample …

Fertility And Reproduction's Niche: Human Sexual Diversity, Samuel W. Austin

Graduate Student Theses, Dissertations, & Professional Papers

Abstract: Biologically exploring the origins and forms of human sexuality is of paramount importance. Scientific research has indicated that homosexuality was linked to reproduction, fertility, and adaptive child caring strategies, traits that seem to display cross-cultural similarities. This suggests that sexual diversity may be one of human’s earliest adaptations. While most of the previous research has been on individuals of European descent, little research on Native American populations has been completed to test whether these patterns continue in their population.

The research presented here tests the Sexually Antagonistic Hypothesis for Male Homosexuality, Fraternal Birth Order Effect, and childhood atypical gender …

Self Reported Knowledge Of Concussion Symptoms And Management By Middle And High School Club Lacrosse Coaches, Logan Ellis

Graduate Student Theses, Dissertations, & Professional Papers

TITLE: Self-reported knowledge of concussion symptoms and management by middle and high school club lacrosse coaches

AUTHORS: Logan Ellis

BACKGROUND: With an increase in sport participation across all levels, concussion prevalence has increased as well as reliance on coaches to recognize a concussed player. Little research has been done investigating how effective our current educational materials are with Lacrosse coaches of grades 6-12.

STUDY DESIGN: Cross- Sectional

LEVEL of EVIDENCE: Level 4

METHODS: Self-administered, online survey that included closed ended questions regarding recognition of signs and symptoms, consequences of inappropriate care, perception of own knowledge, …

A Quantitative Study On The Influence Of Persistence Factors On American Indian Graduate Students, Aislinn Rae Heavy Runner-Rioux

Graduate Student Theses, Dissertations, & Professional Papers

The underrepresentation of American Indian students continues to exist at the undergraduate and graduate levels of postsecondary education despite increases of American Indian student enrollment. The purpose of this quantitative survey study was to identify correlations between academic factors and graduate student persistence, as well as to understand how likely graduate degree completion is based on known academic factors for American Indian students. The analyses of the data included survey results, descriptive statistics, bivariate correlation, and multivariate regression. A sample of n=63 American Indian Graduate students represented 41 tribes and villages with over 32 unique tribal languages. The respondents indicated …

The Influence Of Tree Height On Lidar’S Ability To Accurately Characterize Forest Structure And Spatial Pattern Across Reference Landscapes, Haley L. Wiggins

Graduate Student Theses, Dissertations, & Professional Papers

Successful restoration of degraded forest landscapes requires reference models that adequately capture structural heterogeneity at multiple spatial scales. Field-based methods for assessing variation in forest structure are costly and inherently suffer from limited replication and spatial coverage. LiDAR is a more cost-effective approach for generating landscape-scale data, but it has a limited ability to detect understory trees. Increased understanding of appropriate height cut-offs for trees to be reliably included in LiDAR-based analysis could improve applications of LiDAR to assessments of landscape-scale forest structure. Toward that end, I investigated the effect of varying tree-height criterion (minimum height cutoffs of 6, 9, …

Visions Of Sovereignty: Tribal Sovereignty Through The Lenses Of Postcolonialism, Indigenous Film, And Visual Anthropology, Martin I. Lopez

Graduate Student Theses, Dissertations, & Professional Papers

Tribal sovereignty has been a topic of discussion since the beginning of colonization in America. Anthropological thought, especially postcolonialism theory, addresses how colonialism can be analyzed to gain a better understanding of Indigenous perspectives on sovereignty. Visual sovereignty, an example of Indigenous Film, is an interdisciplinary approach that can contextualize in specific histories and social interactions all while serving individual tribes, depending on which tribe the filmmaker represents. A film, for instance, can be edited in a way to convey Indigenous ideas of time and space and staged presentations of oral histories that are nearly impossible to display through written …

Lateral Heterogeneity And Architectural Analysis Of The Wall Creek Member Of The Upper Cretaceous (Turonian) Frontier Formation, John Zupanic

Graduate Student Theses, Dissertations, & Professional Papers

The Upper Turonian Wall Creek Member (WCM) of the Frontier Formation is part of a series of marine sandstones that were deposited on the western flank of the Cretaceous Western Interior Seaway (KWIS). The KWIS was a low accommodation shallow-marine foreland basin system that included many large deltaic complexes on its western margin. Deposition of WCM deltaic deposits was strongly influenced by fourthorder glacioeustatic cycles, oceanographic circulation patterns, and tectonics related to the active Sevier fold and thrust belt to the west. An in-depth field study of the WCM was performed on the western flank of the Powder River Basin …

Radical Dissonance And Haunted Gestures: Rupture And Reverence In The Artwork Of Aja Mujinga Sherrard, Aja M. Sherrard

Graduate Student Theses, Dissertations, & Professional Papers

This paper serves to establish the studio practice of Aja Mujinga Sherrard within the framework of conceptual art, touching on the flexible use of media, the subversive or political nature of the work, and its relationship to movements and disciplines such as Feminism and Poststructuralism.

The section entitled “Race and Incoherence” addresses the practice of Radical Dissonance—or the creation of ruptures within commonly accepted concepts and social constructions—through the Costuming Kinship Series, 13≠12≠12.2 (Genetics Project), and Body Double. The section entitled ”Art, Loss, and the Unspeakable” traces an emotional shift in her work and speaks directly to the pieces …

Predicting Habitat Distribution For Five Rare Plant Species Within The Blackfoot Swan Landscape Restoration Project, Annalisa Suzan Ingegno

Graduate Student Theses, Dissertations, & Professional Papers

This study predicted rare-plant habitat at the landscape scale. Using the Maximum Entropy (MaxEnt) algorithm, relationships to and between each environmental variable were quantified for five species in the Blackfoot Swan Landscape Restoration Project (BSLRP) study area in western Montana. This project is part of a greater vegetation assessment for BSLRP that utilizes remotely sensed products for planning and management purposes. The five rare plant species studied in this analysis were common camas (Camassia quamash), clustered lady’sslipper (Cypripedium fasciculatum), western pearlflower (Heterocodon rariflorum), Howell’s gumweed (Grindelia howellii), and crested shieldfern (Dryopteris cristata). Rare plant models typically do not address dispersal …

Dispersal, Genetic Structure, Network Connectivity And Conservation Of An At-Risk, Large-Landscape Species, Todd Bartholomew Cross

Graduate Student Theses, Dissertations, & Professional Papers

Wide-ranging species face many threats to genetic connectivity. In light of these threats, one major challenge is the efficient use of scarce resources for the conservation of these species. Setting conservation priorities for landscapes and connectivity can be informed using molecular genetics, and can ensure the efficient use of scare resources to maximize returns in biodiversity conservation.

The greater sage-grouse (Centrocercus urophasianus; hereafter sage grouse) is a species of conservation concern that spans eleven state boundaries, land managed by multiple agencies, and one international boundary. Across the species’ distribution, the threats to the genetic connectivity range from agricultural conversion to …

Ecological Momentary Assessment Of Daily Microaggressions And Stigma-Based Substance Use Among Lesbian, Gay, And Bisexual Individuals, Nicholas Alexander Livingston

Graduate Student Theses, Dissertations, & Professional Papers

Background: People who identify as LGBTQ experience elevated rates of minority stress, which has been linked to higher rates of substance use. Unfortunately, most extant research on this disparity is predicated on cross-sectional or longitudinal research methods that are insensitive to the effects of daily microaggression experiences, or their possible relation to daily substance use risk. The aim of this study was to address this knowledge gap using ecological momentary assessment (EMA). Method: LGBTQ individuals (N = 50) were recruited from the University of Montana, attended a 90-minute orientation to complete baseline measures, and received instruction regarding the proper use …

Linking Landscape Pattern To Population Processes For A Carnivorous Mammal, Keith Michael Slauson

Graduate Student Theses, Dissertations, & Professional Papers

As a taxonomic group, carnivores are amongst those with the highest conservation concern due to the combination of wide-ranging behavior, typically slow reproductive rates, and low density. The Pacific marten (Martes caurina) is a carnivore species of conservation concern throughout much of its southern range in the U. S. The Pacific marten (marten hereafter) is considered a habitat-specialist, due to its association with late-successional forest habitat which provide specific elements, such as cavities in large-diameter trees for denning, to meet a variety of its life history needs. Across its range, threats to marten persistence range from timber harvest, wildfire and …

Xic Clustering By Baseyian Network, Kyle J. Handy

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Does Shape Matter? Breeding Habitat Use And Reproductive Performance Of Gray Catbirds (Dumetella Carolinensis) In Two Western Woodland Habitats, Sharon Fuller

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

The Inflammatory Effects Of Natural And Engineered Airborne Particulate Matter In The Lung, And Related Cellular Mechanisms Of Immunity, Sophia Tracy Carvalho

Graduate Student Theses, Dissertations, & Professional Papers

Asthma, defined as a complex, chronic inflammatory disease of the airways, affects approximately 300 million individuals worldwide and is the single most common chronic disease among children. Airway inflammation is the defining characteristic of asthmatic pathophysiology; and as asthma increases in severity, the airways become more susceptible to environmental insults, including air pollutants. Wildfires and prescribed burns are significant sources of airborne particles, as well as gaseous pollution, which can temporarily increase the overall levels of air pollution over hundreds or thousands of square miles. Multi-walled carbon nanotubes (MWCNT) are increasingly used in a broad range of applications, including medical …

¬Multilocus Phylogeny Of The Lichen Family Megasporaceae, Tim B. Wheeler

Graduate Student Theses, Dissertations, & Professional Papers

The lichen symbiosis is one of the oldest studied mutualisms; in fact, Frank and De Bary coined the term "symbiosis" while studying lichens (Frank, 1877; De Bary 1879). The widespread, stable association between the mycobiont and photobiont in lichens offers an ideal system for the study of co-evolution. The recent application of molecular data to lichens has begun to unveil the complexities involved in these associations (Upreti et al. 2015, Spribille et al. 2016). Lichenized fungi make up a huge fraction of fungal diversity (Nash 2008), yet very little is known of their genetic diversity. Fungal taxonomy is notoriously difficult …

An Outlay Equivalence Analysis Of South African Households, Samuel Peevey

Graduate Student Theses, Dissertations, & Professional Papers

A significant amount of evidence suggests that gender inequality in the developing world negatively impacts women and girls’ health, education and future wage potential. This thesis investigates whether households in South Africa discriminated against their girl children, in favor of their boy children. Additionally, I will investigate whether household heads favored children matching their own sex. Using the 1^st wave of the National Income Dynamics Study and Angus Deaton’s outlay-equivalence ratio method, I will estimate the impact, 8 age and sex categories have on their household’s adult goods expenditure. I found statistically significant but practically insignificant evidence, from a …

Violence, Catastrophe, And Agency In Nepal: A Deeper Understanding Of The 2015 Earthquakes And Border Blockade, Kassandra D. Viers

Graduate Student Theses, Dissertations, & Professional Papers

In 2015, Nepal was struck by two catastrophes. First, on April 25, a 7.8 magnitude earthquake, followed by hundreds of aftershocks, struck in Gorkha. Then, in September, a blockade was formed that prevented goods from passing through trade checkpoints between India and Nepal. Both of these events highlight social suffering, a form of suffering that refers to the systems of oppression, unequal distribution of resources, and broad social structures that serve to keep certain people impoverished and subjugate. The earthquake caused the most damage to vulnerable people, people already suffering the effects of structural violence. The blockade was created by …

Enhancing Conservation With High Resolution Productivity Datasets For The Conterminous United States, Nathaniel Paul Robinson

Graduate Student Theses, Dissertations, & Professional Papers

Human driven alteration of the earth’s terrestrial surface is accelerating through land use changes, intensification of human activity, climate change, and other anthropogenic pressures. These changes occur at broad spatio-temporal scales, challenging our ability to effectively monitor and assess the impacts and subsequent conservation strategies. While satellite remote sensing (SRS) products enable monitoring of the earth’s terrestrial surface continuously across space and time, the practical applications for conservation and management of these products are limited. Often the processes driving ecological change occur at fine spatial resolutions and are undetectable given the resolution of available datasets. Additionally, the links between SRS …