Digital Commons Network^™

A Statistical Analysis And Machine Learning Of Genomic Data, Jongyun Jung

All Graduate Theses, Dissertations, and Other Capstone Projects

Machine learning enables a computer to learn a relationship between two assumingly related types of information. One type of information could thus be used to predict any lack of informaion in the other using the learned relationship. During the last decades, it has become cheaper to collect biological information, which has resulted in increasingly large amounts of data. Biological information such as DNA is currently analyzed by a variety of tools. Although machine learning has already been used in various projects, a flexible tool for analyzing generic biological challenges has not yet been made. The recent advancements in the DNA …

Racial Microaggressions And Alienation Among Hmong American College Students, Bruce Yang

All Graduate Theses, Dissertations, and Other Capstone Projects

Students of color continue to experience racism within institutions of higher education across the United States. These experiences often include racial microaggressions, which are evolved forms of racism that are subtle, difficult to detect, and harmful. Racial microaggressions have been found to be associated with several consequences including mental health, emotional, and physical problems (Dahlia & Lieberman, 2010; Connolly, 2011; Cheng, Tran, Miyake, & Kim, 2017). Furthermore, studies have also alluded to the potential relationship between racial microaggressions and the dimensions of alienation for student populations of color (Fissori, 2010; James, 1988; Lambert, Herman, Bynum, & Ialongo, 2009; Sauceda, 2010; …

From Paris To Projects: Clarifying The Implications Of Canada’S Climate Change Mitigation Commitments For The Planning And Assessment Of Projects And Strategic Undertakings (Full Report), Robert B. Gibson, Karine Peloffy, Daniel Horen Greenford, Meinhard Doelle, H Damon Matthews, Christian Holz, Kiri Staples, Bradley Wiseman, Frédérique Grenier

Reports & Public Policy Documents

Canada has signed the Paris Agreement and made other international commitments to doing our fair share of what is needed to keep overall global warming to the Paris Agreement limit of well below 2ºC, and to aim for 1.5ºC, to avoid devastating climate change. However, we have not yet progressed far in translating these commitments into implications for decision making on proposed undertakings with significant implications for meeting those commitments.

Clarifying those implications and determining how best to incorporate them in deliberations and decision making is overdue and now imperative. The federal government’s new Impact Assessment Act, which is now …

Alfred Russel Wallace Notes 9: The South Asian Connection, Charles H. Smith, Sahotra Sarkar, Nirmali Wijegoonawardana

Faculty/Staff Personal Papers

Alfred Russel Wallace (1823−1913) is best known for his natural history explorations and theoretical biology, but he was also a potent social critic on subjects ranging from land tenure and colonial policy to antivaccinationism and poverty. Here, one of his emphases in the latter domain is spotlighted: his interest in South Asian affairs. This extended to a variety of subjects in the areas of politics, economics, health, literature, sociology, etc., and to a degree that may have had some influence on the development of thought of some major South Asian figures, including Mahatma Gandhi and Ananda K. Coomaraswamy.

Targeted Short-Term Nutrient Reduction To Manage Ventenata Dubia An Invasive Winter Annual Grass: Soil And Plant Responses, Jaren F. Lamm

EWU Masters Thesis Collection

Invasive winter annual grasses, IWAGs, have degraded extensive ecosystems around the world and continue to invade new ones yearly. IWAGs readily form large monocultures or near monocultures, thus management and restoration goals largely focus on maintaining or increasing plant diversity in impacted ecosystems. Unfortunately, common management methods also reduce native plant diversity and harm the soil microbiome. These effects require additional measures to be taken, like reseeding, and plant diversity is still usually well below remnant targets. Early season short-term nutrient reduction to manage IWAGs is largely unexplored and would potentially decrease IWAG abundance, active earlier than most plants, but …

Abolishing The Suicide Rule, Alex B. Long

Northwestern University Law Review

Suicide is increasingly recognized as a public health issue. There are over 40,000 suicides a year in the U.S., making suicide the tenth-leading cause of death in the country. But societal attitudes on the subject remain decidedly mixed. Suicide is often closely linked to mental illness, a condition that continues to involve stigma and often triggers irrational fears and misunderstanding. For many, suicide remains an immoral act that flies in the face of strongly held religious principles. In some ways, tort law’s treatment of suicide mirrors the conflicting societal views regarding suicide. Tort law has long been reluctant to permit …

The Impact Of Salient Naming Targets During Aphasia Therapy, Kathy Kay Molesh, Catherine Off Ph.D., Craig Mcfarland Ph.D., Jenna Griffin M.S.

Graduate Student Theses, Dissertations, & Professional Papers

Translational research has led to aphasia therapies that incorporate principles of experience dependent neuroplasticity. The neuroplasticity principle of salience has received less attention from speech language pathologists than other principles, such as dose and treatment intensity. Incorporating salience in aphasia therapies has the potential to increase functional outcomes by addressing multiple aspects of the World Health Organization’s International Classification of Functioning, Disability and Health. This study explored the impact of salient stimuli targets on picture naming acquisition and maintenance for two individuals with chronic aphasia, following cerebrovascular accident. Participants were enrolled in a five-week Intensive Comprehensive Aphasia Program (ICAP) at …

Dna Analysis On Ceramic Cooking Vessels, Britney J. Radford

Graduate Student Theses, Dissertations, & Professional Papers

Ceramic vessels are a durable material found in abundance throughout the archaeological record. Organic residue analysis has been used to study ceramic vessels utilizing lipid analysis and protein analysis. Lipids and proteins analysis provide limited information at the genus level, leaving out valuable information that species-specific results can tell us such as unique genetic and environmental information. Lipids and proteins analysis provide limited information at the genus and taxonomic levels leading to issues of misclassification of species. If only certain animals or plants of a genus are being used, then unique genetic and environmental information found only at the species …

New, Multi-Scale Approaches To Characterize Patterns In Vegetation, Fuels, And Wildfire, Christopher Jacob Moran

Graduate Student Theses, Dissertations, & Professional Papers

Pattern and scale are key to understanding ecological processes. My dissertation research aims for novel quantification of vegetation, fuel, and wildfire patterns at multiple scales and to leverage these data for insights into fire processes. Core to this motivation is the 3-dimensional (3-D) characterization of forest properties from light detection and ranging (LiDAR) and structure-from-motion (SfM) photogrammetry. Analytical methods for extracting useable information currently lag the ability to collect such 3-D data. The chapters that follow focus on this limitation blending interests in machine learning and data science, remote sensing, wildland fuels (vegetation), and wildfire. In Chapter 2, forest canopy …

Reconnecting Indigenous Knowledge To The Sunlight Basin: Integrating Traditional Ecological Knowledge And Archaeology, Liz Dolinar

Graduate Student Theses, Dissertations, & Professional Papers

Traditional ecological knowledge (TEK) specific to plants has been developed over long-term connections to the environment, diligent observations, and practical experience by Indigenous communities. The traditional ecological knowledge of Indigenous peoples is a vital source for the contextualization and further understanding of past human environmental relationships in the Sunlight Basin of northwestern Wyoming. The Eastern Shoshone people, among many other groups, traditionally occupied the Sunlight Basin of northwestern Wyoming, a region of the Greater Yellowstone Ecosystem. There is a growing necessity for collaboration with Indigenous populations within archaeological and anthropological research. The aim of this project is to develop a …

Protecting Natural Resources On Agricultural Lands: Producers' Perspectives On The Conservation Stewardship Program In Montana, Mary Ellis

Graduate Student Theses, Dissertations, & Professional Papers

Industrial agricultural production contributes to some of the most significant environmental problems in the United States today. Scientists have identified agricultural production as a primary cause for the decline of native species, soil degradation, and water pollution in the U.S. In response to this crisis, grassroot organizations crafted, and got Congress to pass, the Conservation Stewardship Program (CSP), a federal program aimed to incentivize producers to increase on-farm conservation practices. CSP is designed to serve as a space for producers to gain access to financial and technical support, test out new practices, and provide a platform to discuss best practices …

Shaping The Tools Of Battle : Sexual Selection, Contest Dynamics, And Weapon Divergence In The Asian Rhinoceros Beetle Trypoxylus Dichotomus, Jillian F. Del Sol

Graduate Student Theses, Dissertations, & Professional Papers

Exaggerated weapons of sexual selection often diverge more rapidly and dramatically than other body parts, suggesting that relevant agents of selection may be discernible in contemporary populations. I examined the ecology, reproductive behavior, and strength of sexual selection on horn length in five recently diverged beetle populations that differ in relative horn size. I show that mating system ecology differs between these locations and corresponds with the local strength of contemporary selection on horn length. Comparisons of ecological conditions and selection strength across populations offer a critical first step towards meaningfully linking mating system dynamics, selection patterns, and diversity in …

Zero-Knowledge De Novo Algorithms For Analyzing Small Molecules Using Mass Spectrometry, Patrick Anthony Kreitzberg

Graduate Student Theses, Dissertations, & Professional Papers

In the analysis of mass spectra, if a superset of the molecules thought to be in a sample is known a priori, then there are well established techniques for the identification of the molecules such as database search and spectral libraries. Linear molecules are chains of subunits. For example, a peptide is a linear molecule with an “alphabet” of 20 possible amino acid subunits. A peptide of length six will have 20⁶ = 64, 000, 000 different possible outcomes. Small molecules, such as sugars and metabolites, are not constrained to linear structures and may branch. These molecules are …

Blasting The Farm: Chemical High Explosives And The Rise Of Industrial Agriculture, 1867-1930, Patrick Benjamin Swart

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Adaptation To A Geothermal Soil Mosaic Shapes Genome-Wide Patterns Of Diversity And Differentiation In Yellowstone Monkeyflowers (M. Guttatus), Kory M. Kolis

Graduate Student Theses, Dissertations, & Professional Papers

Local adaptation across habitat mosaics can generate phenotypic divergence in the face of gene flow; however, adaptive divergence in reproductive traits may also create barriers to genetic exchange within and among distinct habitats. In plants, life-history, phenology, and mating system traits may lead to divergent selection over short (microgeographic) spatial scales. Changes to these traits are likely to directly affect patterns of gene flow and genomic diversity. In this study, we combined field, common garden, and population genomic approaches to investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) adapted to a complex geothermal soil mosaic in Yellowstone National …

Use Of Computer Software To Do Mathematics And The Mathematics Achievement Of Students In Puerto Rico Using Restricted 2015 Naep, Ricela Feliciano-Semidei

Graduate Student Theses, Dissertations, & Professional Papers

This quantitative study explored the relationship between the mathematics achievement patterns of eighth grade students in Puerto Rico and their use of computer software application programs for doing mathematics. The theoretical framework used is the educational production function, which allowed the use of a function to analyze this relationship. The researcher analyzed 2015 restricted National Assessment of Educational Progress (NAEP) mathematics data. Data analysis consisted of descriptive statistical analysis and multilevel modeling analysis. Control variables to measure socioeconomic status and absenteeism were included in the multilevel model. Results of this study showed that average scores on NAEP 2015 were higher …

Characterization Of Novel Cyp26b1-Inhibitor, Dx314, For The Treatment Of Keratinization Disorders, Joachim Gwenn-Stephan Veit

Graduate Student Theses, Dissertations, & Professional Papers

Our skin, particularly the barrier provided by the epidermis, functions as our primary protection from the harsh environment. It protects us from dangerous pathogens, allergens, ultraviolet radiation, and mechanical injury, as well as playing a major role in fluid and thermal regulation. Disruption of skin functions can lead to life-threatening consequences due to increased risk of infection, trans-epidermal water loss, and allergen sensitization. Many common skin disorders often result in a disrupted skin barrier placing patients at risk of complications.

Retinoic acid (RA) is a major component of the vitamin A pathway, which critically controls multiple skin functions including cell …

Bone Stress Injuries In Collegiate Distance Runners: Review Of Incidence, Distribution, And Risk Factors, Maryn E. Lowry

Graduate Student Theses, Dissertations, & Professional Papers

This literature review investigates the risk factors for bone stress injuries that apply to collegiate distance runners. Collegiate distance runners demonstrate high incidence rates of this type of injury and can suffer from a loss of training time. It is important to review the risk factors that apply to these athletes in order to mitigate the time lost to injury and optimize training. PubMed and Google Scholar were searched for original articles pertaining to risk factors associated with bone stress injuries and/or stress fractures. Results from these original articles demonstrate that this injury has many risk factors including biomechanical, biological, …

Probing Denatured State Conformational Bias In 3-Helix Bundles With Foldable Or Intrinsically Disordered Domains, Moses Joseph Leavens

Graduate Student Theses, Dissertations, & Professional Papers

Protein misfolding is associated with several life threatening diseases – Alzheimer’s, Parkinson’s, Cystic fibrosis, Sickle cell anemia, and the Transmissible spongiform encephalopathies, to include Chronic Wasting disease, Scrapie, and Creutzfeldt-Jakob disease. To provide insight into protein misfolding, it is beneficial to understand how an amino acid sequence encodes structure. Once thought to behave as random coil polymers under denaturing conditions, an abundance of recent evidence suggests denatured proteins retain ‘non-random’ or residual structure, which may bias a protein chain to fold efficiently to its native conformer. Probing energetics of residual structure in denatured proteins is challenging, given the shortage of …

Adaptation Under The Canopy: Coffee Cooperative And Certification Contributions To Smallholder Livelihood Sustainability In Santa Lucía Teotepec, Oaxaca, Meghan C. Montgomery

Graduate Student Theses, Dissertations, & Professional Papers

The collapse and reorganization of global coffee markets associated with the “coffee crisis” have had profound, negative impacts on smallholder producer livelihoods throughout the world. In Mexico, the collapse of the International Coffee Agreement (ICA) coincided with withdrawal of government support for agriculture, which devastated producers dependent on coffee for their livelihoods. Smallholders responded by shifting livelihood strategies to diversify income, migrating, and converting primary forest cover to subsistence crops and pasture to support household livelihood security. In some instances, producers also joined or formed cooperative organizations to access specialty certifications that offer higher priced markets, extension information, and other …

Modulation Of Cytochrome C’S Peroxidase Activity By Ω-Loops C And D In Monomers And Dimers, Haotian Lei

Graduate Student Theses, Dissertations, & Professional Papers

Mitochondrial cytochrome c is a heme containing protein with flexible heme ligation. Cytochrome c in its native state with Met80 bound to the heme is an electron shuttle in the electron transport chain. Under apoptotic stimuli, cytochrome c oxidizes the mitochondrial lipid cardiolipin, leading to the release of pro-apoptotic factors into the cytoplasm. To oxidize cardiolipin, Met80 in Ω-loop D must be dissociated from the heme iron, which allows cytochrome c to obtain access to alternative conformers. Two segments of cytochrome c, namely Ω-loops C and D, have been suggested to be important in regulating the dissociation of Met80. Unlike …

Pragmatist Ecological Economics: Focusing On Human-Nature Relationships And Social-Ecological Systems, Christopher Aden Armatas

Graduate Student Theses, Dissertations, & Professional Papers

I propose pragmatist philosophy as a companion for ecological economics, a research tradition with a focus on addressing sustainability issues and integrating ecological principles, economics, and the broader social sciences. Ecological economics laudable goals include balancing competing values, tradeoffs, and insights for more equitable decision-making. However, the field is built upon somewhat tenuous philosophical and theoretical foundations, which has resulted in a muddled body of literature, concerns about relativistic science, and questions about the future viability of the field. To address such concerns, I propose and articulate pragmatist ecological economics. Generally, joining pragmatism and ecological economics provides established beliefs about: …

Higher Dietary Diversity Scores And Protein-Rich Food Consumption Were Associated With Lower Risk Of All-Cause Mortality In The Oldest Old, Yuebin Lv, Virginia Byers Kraus, Xiang Gao, Zhaoxue Yin, Jinhui Zhou, Chen Mao, Jun Duan, Yi Zeng, Melanie S. Brasher, Wanying Shi, Xiaoming Shi

Human Development and Family Science Faculty Publications

Background & aims: Dietary diversity is widely advocated in national and international recommendations although whether the beneficial effects on survival or longevity still apply in the final phase of the lifespan remains understudied. We aimed to prospectively examine the association of dietary diversity, food items with all-cause mortality among the oldest old (80+) and determine whether dietary diversity recommendations were appropriate for this population.

Methods: The study included 28,790 participants aged 80+ (9957 octogenarians, 9925 nonagenarians, and 8908 centenarians). A baseline dietary diversity score (DDS) was constructed based on nine food items of a food frequency questionnaire. Cox models with …

Biological Membranes In Ev Biogenesis, Stability, Uptake, And Cargo Transfer: An Isev Position Paper Arising From The Isev Membranes And Evs Workshop, Ashley E. Russell, Alexandra Sneider, Kenneth W. Witwer, Paola Bergese, Suvendra N. Bhattacharyya, Alexander Cocks, Emanuele Cocucci, Uta Erdbrugger, Juan M. Falcon-Perez, David W. Freeman, Thomas M. Gallagher, Shuaishuai Hu, Yiyao Huang, Steven M. Jay, Shin-Ichi Kano, Gregory Lavieu, Aleksandra Leszczynska, Alicia M. Llorente, Quan Lu, Vasiliki Mahairaki, Dillon C. Muth, Nicole Noren Hooten, Matias Ostrowski, Ilaria Prada, Susmita Sahoo, Tine Hiroth Schoyen, Lifu Sheng, Deanna Tesch, Guillaume Van Niel, Roosmarijn E. Vandenbroucke, Frederik J. Verweij, Ana V. Villar, Marca Wauben, Hang Yin, David Raul Francisco Carter, Pieter Vader

Articles

Paracrine and endocrine roles have increasingly been ascribed to extracellular vesicles (EVs) generated by multicellular organisms. Central to the biogenesis, content, and function of EVs are their delimiting lipid bilayer membranes. To evaluate research progress on membranes and EVs, the International Society for Extracellular Vesicles (ISEV) conducted a workshop in March 2018 in Baltimore, Maryland, USA, bringing together key opinion leaders and hands-on researchers who were selected on the basis of submitted applications. The workshop was accompanied by two scientific surveys and covered four broad topics: EV biogenesis and release; EV uptake and fusion; technologies and strategies used to study …

Five-Year Follow Up Of A Low Glycaemic Index Dietary Randomised Controlled Trial In Pregnancy—No Long-Term Maternal Effects Of A Dietary Intervention, E.C. O'Brien, Aisling A. Geraghty, Elizabeth O'Sullivan, J.A. Riordan, Mary K. Horan, Elizabeth Larkin, John Mehegan, P.J. Twomey, Fionnuala M. Mcauliffe

Articles

Objective: To determine whether a dietary intervention in pregnancy had a lasting effect on maternal outcomes of diet, HbA1c and weight retention 5 years post-intervention; and to establish whether modifiable maternal behaviours were associated with these outcomes. Design: Randomised control trial of low glycaemic index (GI) diet in pregnancy with longitudinal follow up to 5 years post-intervention. Setting: Dublin, Ireland (2007–2016). Population: In all, 403 women of 759 (53.1%) were followed up at 5 years. A total of 370 (intervention n = 188; control n = 182) were included in this analysis. Methods: Fasting glucose was measured at 13 and …

Measuring The Impact Of Oesophagectomy On Physical Functioning And Physical Activity Participation: A Prospective Study, E.M. Guinan, A.E. Bennett, Suzanne Doyle, Luke O'Neill, J. Gannon, G. Foley, J.A. Elliott, J. O'Sullivan, J.V. Reynolds, J. Hussey

Articles

Background: Oesophagectomy remains the only curative intervention for oesophageal cancer, with defined nutritional and health-related quality of life (HR-QOL) consequences. It follows therefore that there is a significant risk of decline in physical wellbeing with oesophagectomy however this has been inadequately quantified. This study prospectively examines change in physical functioning and habitual physical activity participation, from presurgery through 6-months post-oesophagectomy. Methods: Patients scheduled for oesophagectomy with curative intent were recruited. Key domains of physical functioning including exercise tolerance (six-minute walk test (6MWT)) and muscle strength (hand-grip strength), and habitual physical activity participation, including sedentary behaviour (accelerometry) were measured presurgery (T0) …

Associations Between Maternal Physical Activity In Early And Late Pregnancy And Offspring Birth Size: Remote Federated Individual Level Meta‐Analysis From Eight Cohort Studies, S. Pastorino, T. Bishop, S. Crozier, C. Granstrom, K. Kordas, L. Kupers, E. O'Brien, K. Polanska, K. Sauder, M. Zafarmand, R. Wilson, C. Agyemang, P. Burton, C. Cooper, E. Corpeleijn, D. Dabelea, W. Hanke, H. Inskip, F. Mcauliffe, S. Olsen, T. Vrijkotte, S. Brage, A. Kennedy, D. O'Gorman, P. Scherer, K. Wijndaele, N. Wareham, G. Desoye, K. K. Ong

Articles

Objective

Evidence on the impact of leisure time physical activity (LTPA) in pregnancy on birth size is inconsistent. We aimed to examine the association between LTPA during early and late pregnancy and newborn anthropometric outcomes.

Design

Individual level meta‐analysis, which reduces heterogeneity across studies.

Setting

A consortium of eight population‐based studies (seven European and one US) comprising 72 694 participants.

Methods

Generalised linear models with consistent inclusion of confounders (gestational age, sex, parity, maternal age, education, ethnicity, BMI, smoking, and alcohol intake) were used to test associations between self‐reported LTPA at either early (8–18 weeks gestation) or late pregnancy (30+ …

Randomised Study Demonstrates Sustained Benefits Of A Pre-School Intervention Designed To Improve Nutrition And Physical Activity Practices, Diewerke De Zwarte, John Kearney, Clare A. Corish, Corina Glennon, Lorraine Maher, Charlotte Johnston Molloy

Articles

Background: Health-promoting programmes must demonstrate sustained efficacy in order to make a true impact on public health. This study aimed to determine the effect of the Healthy Incentive for Pre-schools project on health-promoting practices in full-day-care pre-schools 18 months after a training intervention.

Methods: Thirty-seven pre-schools completed the initial study and were included in this follow-up study. The intervention consisted of one training session with either the pre-school 'manager-only' or 'manager and staff' using a specifically developed needs-based training resource pack comprised of written educational material and a validated health-promoting practice evaluation tool. Direct observation data of health-promoting practices were …

Subjective And Objective Assessment Of Taste And Smell Sensation In Advanced Cancer, Niamh Mcgettigan, Pauline Uí Dhuibhir, Michelle Barrett, Jessica Sui, Lucy Balding, Stephen Higgins, Norma O'Leary, Aileen Kennedy, Declan Walsh

Articles

Context: Taste and smell abnormalities (TSA) occur throughout the cancer trajectory regardless of cancer primary site and contribute to cancer-associated malnutrition. TSA etiology is poorly understood. Tumor-related inflammation is a possible cause. Objective: This study examined the prevalence, characteristics, and severity of TSA in advanced cancer and explored the relationship between TSA and nutritional status. No previous study combined subjective and objective measures for both taste and smell assessment in this population. Method: Consecutive advanced cancer hospice patients were recruited. A modified version of the “Taste and Smell Survey” assessed subjective TSA. Validated taste strips and “Sniffin’ …

Maternal Sociodemographic And Health Behaviours Associated With Adiposity In Infants As Measured By Air Displacement Plethysmography., A. Bennett

Articles

BACKGROUND:

Identifying modifiable factors associated with body fat in infancy may improve health outcomes. Few studies have examined factors associated with percentage body fat calculated using air displacement plethysmography, a gold standard technique.

AIMS:

To investigate maternal sociodemographic and health behaviour characteristics associated with percentage body fat in offspring at birth.

STUDY DESIGN:

Observational cross-sectional study in which the body composition of term infants was measured by air displacement plethysmography during the hospital stay after birth.

SUBJECTS:

One-hundred-and-ninety-six women and their term (37-42 weeks) infants.

OUTCOME MEASURES:

Associations between infant body composition and maternal sociodemographic and health characteristics.

RESULTS:

One-hundred-and-ninety-six …