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Inverted Sequence Identification In Diploid Genomic Scaffold Assembly Via Weighted Max-Cut Reduction, Paul Mark Bodily Jun 2013

Inverted Sequence Identification In Diploid Genomic Scaffold Assembly Via Weighted Max-Cut Reduction, Paul Mark Bodily

Theses and Dissertations

Virtually all genome assemblers to date are designed for use with data from haploid or homozygous diploid genomes. Their use on heterozygous genomic datasets generally results in highly-fragmented, error-prone assemblies, owing to the violation of assumptions during both the contigging and scaffolding phases. Of the two phases, scaffolding is more particularly impacted and algorithms to facilitate the scaffolding of heterozygous data are lacking. We present a stand-alone scaffolding algorithm, ScaffoldScaffolder, designed specifically for scaffolding diploid genomes. A fundamental step in the scaffolding phase is the assignment of sequence orientations to contigs within scaffolds. Deciding such an assignment in the presence …

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Stability And Change In Women's Personality Across The Life Course, Carly D. Lebaron Jun 2013

Stability And Change In Women's Personality Across The Life Course, Carly D. Lebaron

Theses and Dissertations

The current study sought to examine change and stability of personality in a sample of women over the course of 35 years. Existing research is mixed regarding whether or not personality changes over time or whether it remains stable. Using a sample of 187 women tracked over four time points (approximately 10 years between each time point), change and stability in openness to experience, extraversion, and neuroticism was tested using a stacked multilevel growth curve analysis. Four life course events (transition to parenthood, change in marital status, wife entering or leaving the workforce, and husband retiring) were added as predictors …

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Experiments With Gmti Radar Using Micro-Doppler, Benjamin Walter Dilsaver Jun 2013

Experiments With Gmti Radar Using Micro-Doppler, Benjamin Walter Dilsaver

Theses and Dissertations

As objects move, their changing shape produces a signature that can be measured by a radar system. That signature is called the micro-Doppler signature. The micro-Doppler signature of an object is a distinguishing characteristic for certain classes of objects. In this thesis features are extracted from the micro-Doppler signature and are used to classify objects. The scope of the objects is limited to humans walking and traveling vehicles. The micro-Doppler features are able to distinguish the two classes of objects. With a sufficient amount of training data, the micro-Doppler features may be used with learning algorithms to predict unknown objects …

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All Animals Will Get Along In Heaven, Camila Nagata Jun 2013

All Animals Will Get Along In Heaven, Camila Nagata

Theses and Dissertations

My final thesis exhibition is directed towards children and parents. My goal is to create a connection between parent and child, and their past, present, and future through memory. Such a connection is accomplished through the implementation of these three different ideas in the artwork: 1) creating different layers of understanding, 2) producing everlasting memories, 3) connecting adult viewers to their past. In addition, I use principles as the foundation for each piece, such as the principles of kindness and learning. These principles are presented to the viewer through parables of current social and political issues, illustrated through my own …

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Improving Implicit Learning And Explicit Instruction Of Adult And Child Learners Of Chinese, Li-Hui Kuo Jun 2013

Improving Implicit Learning And Explicit Instruction Of Adult And Child Learners Of Chinese, Li-Hui Kuo

Theses and Dissertations

This study explored the main effects and interaction effects of implicit learning and explicit instructional approaches on the language acquisition of beginning adult and child learners of Chinese and analyzed the successful adult and child learners' learning styles in their information processing time, second language acquisition techniques, and cognitive strategies. Volunteers from Brigham Young University and Wasatch Elementary School were randomly assigned to either an Explicit Instruction Treatment (EIT) or an Implicit Learning Treatment (ILT). Following the treatment, the participants completed an online survey and a vocabulary application test. Results from a 2 x 2 factorial ANOVA indicated that adults …

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Screening Of Secondary Chemicals From Selected Species Of North American Lichens Against Various Pathologenic Bacteria, Jocelyn Raphael, Dr. Larry St. Clair Jun 2013

Screening Of Secondary Chemicals From Selected Species Of North American Lichens Against Various Pathologenic Bacteria, Jocelyn Raphael, Dr. Larry St. Clair

Journal of Undergraduate Research

Lichens consist of a fungus occurring symbiotically with a photosynthetic organism (such as an alga and/or cyanobacterium). Lichens are known to produce a high number of secondary metabolites. Studies have shown that these secondary compounds have various biological roles such as antibiotic, antiviral, anti-inflammatory, anti-proliferative, antioxidant, etc. (Huneck, 1999; Molnar & Farkas, 2010). There is a great need for new forms of antibiotics as bacterial infection is an ongoing problem and many bacteria have become resistant to available treatments. To develop new forms of antibiotics many different potential compounds need to be tested. The purpose of this project was to …

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Rescuing The Collagen 2a1 Gene In Mouse Model To Alleviate Stickler Syndrome Symptoms, Jamie Twiggs, Dr. Robert Seegmiller Jun 2013

Rescuing The Collagen 2a1 Gene In Mouse Model To Alleviate Stickler Syndrome Symptoms, Jamie Twiggs, Dr. Robert Seegmiller

Journal of Undergraduate Research

Stickler Syndrome is a severe disease with no cure that occurs in 1/7500 births resulting in extreme ocular, craniofacial, musculoskeletal and cardiovascular problems for those diagnosed. It is caused by mutations in the collagen genes, most often a premature stop codon in the collagen 2A1 gene, although in some cases it is caused by mutations in the collagen 11 A1 and A2 genes. The purpose of this research was to discover an effective method of gene therapy in mice models by reinserting a functional collagen gene into mice embryos using a viral vector and plasmids. I hypothesized that if the …

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From Plato To Ipads: Dialogical Opportunities In Twenty-First Century Secondary English Classrooms, Emily Ensign Jun 2013

From Plato To Ipads: Dialogical Opportunities In Twenty-First Century Secondary English Classrooms, Emily Ensign

Theses and Dissertations

Technology offers students and educators an uncharted digital landscape of possibilities. Some educators feel strongly that technology enhances the classroom; others feel that it doesn't necessarily improve traditional teaching methods, and some even feel that it is detrimental to students' ability to focus or engage in face-to-face conversations. My project focuses on critical dialogue as defined by various theorists, and explores whether or not secondary English classrooms that use iPads continue to use the dialogical methods as outlined by these theorists (most of which could not have foreseen today's technological advancements). By relying on these theorists and scholars to provide …

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The Effects Of Daidumene Lineata On The Intertidal Rock Pools, Preston Wilson, Russell Rader Jun 2013

The Effects Of Daidumene Lineata On The Intertidal Rock Pools, Preston Wilson, Russell Rader

Journal of Undergraduate Research

My experiment was to test the effect Diadumene lineata has on the marine life of the intertidal rock pools in the northwest.

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Brain Structures Associated With Temperament And Social Behavior In Rhesus Monkeys: An Mri Study, Andrew C. Chaffin Jun 2013

Brain Structures Associated With Temperament And Social Behavior In Rhesus Monkeys: An Mri Study, Andrew C. Chaffin

Theses and Dissertations

Temperament is thought to be the foundation for normative personality and subsequent behaviors later in life. To assess the relationship of early temperament with variation in structural brain development, this study examined rhesus macaque mother-infant behavior, and then three years later, used MRI to assess neurostructural differences. Individual differences in mother-infant interactions and emotionality were then linked to brain differences. Extensive behavioral data obtained over the first year of life under both resting and stressful conditions was used to assess the quality of mother-infant interactions and emotionality. The MRI focused on brain volume in areas thought to be related to …

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The Seed Ecology Of Rare And Endangered Gibbens' Beardtongue (Penstemon Gibbensii) And Blowout Penstemon (Penstemon Haydenii), Kassie Lorraine Tilini Jun 2013

The Seed Ecology Of Rare And Endangered Gibbens' Beardtongue (Penstemon Gibbensii) And Blowout Penstemon (Penstemon Haydenii), Kassie Lorraine Tilini

Theses and Dissertations

Penstemon gibbensii and Penstemon haydenii are two rare, perennial forbs inhabiting remote areas of the western United States. P. gibbensii is listed as a sensitive species by the Bureau of Land Management (BLM) in Colorado, Utah, and Wyoming (Heidel, 2009). P. haydenii was designated as Endangered by the U.S. Fish and Wildlife Service in 1987 (Heidel, 2012). This thesis research was geared toward helping land managers in their efforts to protect and rehabilitate these species by providing understanding on different aspects of their seed ecology. My first study was a laboratory experiment performed on P. gibbensii and P. haydenii seed …

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The Effect Of Male Dominance On Female Mate Choice In Poecilia Gillii, Michael Mcentire, Dr. Jerald Johnson Jun 2013

The Effect Of Male Dominance On Female Mate Choice In Poecilia Gillii, Michael Mcentire, Dr. Jerald Johnson

Journal of Undergraduate Research

Female mate choice (intersexual selection) and male dominance interactions (intrasexual selection) can each play important roles in sexual selection. These two mechanisms tend to be discussed in isolation. The goal of this study is to explore the interaction between these two forms of sexual selection. To test this idea, we focused on the livebearing tropical fish system Poecilia gillii (See Figure 1). We grouped males into similarly sized pairs and observed them for a week to determine which male was dominant. These pairs were then presented to females in mate choice trials to ascertain female preference. Our data appears to …

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What Fatty Acids In Dairy Cow Feces May Predict Resistance Or Susceptibility To Production-Related Metabolic Diseases, Brian Melville, Beverly Roeder Jun 2013

What Fatty Acids In Dairy Cow Feces May Predict Resistance Or Susceptibility To Production-Related Metabolic Diseases, Brian Melville, Beverly Roeder

Journal of Undergraduate Research

Dairy cows supply an important food source for humans, and any disease that hurts production threatens this source. Once a cow has a PRMD (production related metabolic disease) there are many signs and symptoms that are readily observed and tested for, but it would be useful to use diagnostic techniques to discover if an animal is at risk of a future disease when the cow is clinically normal. These diagnostic tools could be used with clinically normal healthy appearing cows, empowering producers to make more informed decisions about animal care to improve milk production. Other exciting possibilities exist, such as …

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Polyomavirus Phylogenetics In Relation To Host Switches, David Morris, Dr. Keith Crandall Jun 2013

Polyomavirus Phylogenetics In Relation To Host Switches, David Morris, Dr. Keith Crandall

Journal of Undergraduate Research

Evolutionary Biology is not a branch of biology that spends much time in the public eye. It just doesn’t have flashy results like cloning or evocative naturalist documentaries to captivate the imagination. However, this doesn’t mean that evolutionary biology is any less essential to our understanding of life and how it may eventually impact people in their daily lives.

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A Novel Role For Amp-Activated Protein Kinase As A Selective Inhibitor Of De Novo Ceramide Biosynthesis, Kate Erickson, Dr. Benjamin Bikman Jun 2013

A Novel Role For Amp-Activated Protein Kinase As A Selective Inhibitor Of De Novo Ceramide Biosynthesis, Kate Erickson, Dr. Benjamin Bikman

Journal of Undergraduate Research

The purpose of this project was to determine the cellular mechanisms that mediate AMPK-induced reductions in lipotoxicity. We predicted that AMPK activation inhibits lipotoxic ceramide biosynthesis via targeted reduction in transcription of a critical, rate-limiting enzyme involved in de novo ceramide synthesis.

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Cellular Mechanisms Behind Memory Formation In The Developing Brain, Spencer Bell, Dr. Jeffrey Edwards Jun 2013

Cellular Mechanisms Behind Memory Formation In The Developing Brain, Spencer Bell, Dr. Jeffrey Edwards

Journal of Undergraduate Research

Carrying out my research project with my mentor’s assistance has provided valuable experiences and important lessons. At the present time, however, my research has not produced the results we had anticipated. We had hoped to demonstrate that a certain receptor in the brain called transient receptor potential vanilloid 1 (TRPV1) modulated memory formation in the developing brain by influencing a process known as long-term depression, or the weakening of a chemical connection between two brain cells. Although we have not yet produced statistically significant results, our observations indicate that we may simply need to conduct more experiments to acquire enough …

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Comparisons Of Amantadine Analogues Against The Dominant Influenza A Virus M2 Proton Channel Mutant Via Circular Dichroism Spectroscopy And Tryptophan Fluorescence Anisotropy, Trevor Anderson, David Busath Jun 2013

Comparisons Of Amantadine Analogues Against The Dominant Influenza A Virus M2 Proton Channel Mutant Via Circular Dichroism Spectroscopy And Tryptophan Fluorescence Anisotropy, Trevor Anderson, David Busath

Journal of Undergraduate Research

The influenza A virus is a severe ongoing threat to public health, accounting for over 250,000 fatalities worldwide each year. In order to actuate the virus, it is necessary for the M2 proton channel to be activated upon fusion with an endosome.

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Exploring The Narrative-Oriented Qualities Of The Learner's Encounter With Unfamiliarity, Jonathan S. Spackman Jun 2013

Exploring The Narrative-Oriented Qualities Of The Learner's Encounter With Unfamiliarity, Jonathan S. Spackman

Theses and Dissertations

Learning, as embodied familiarization, is described as an embodied, non-representational, and non-mechanistic experience. Within this theoretical framework, a qualitative study is presented that offers a deeper understanding of the learner's encounter with unfamiliarity -- a key lived experience of embodied familiarization. Assertions related to encounters with unfamiliarity are made through a multiple case study analysis and a deeper understanding of the assertions is offered by way of a narrative-oriented framework. From this perspective, agentive, concernful, dispositional and meaningful aspects of learning are discernible.

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Premature Osteoarthritis In The Temporomandibular Joint Of Heterozygous Disporportionate Micromelia Mice, Jason Farrell, Dr. Robert Seegmiller Jun 2013

Premature Osteoarthritis In The Temporomandibular Joint Of Heterozygous Disporportionate Micromelia Mice, Jason Farrell, Dr. Robert Seegmiller

Journal of Undergraduate Research

The purpose of this study, as also summarized in the proposal for this research grant, was to analyze the temporomandibular joints (TMJs) of mice with a specific collagen defect, Disproportionate Micromelia. Examining these joints was done to provide an animal model to be used in Osteoarthritis research, and to propose a potential mechanism for osteoarthritis in this joint in humans. Better understanding of Osteoarthritis in this joint using an animal model can help lead to potential future treatments for a wide variety of TMJ disorders.

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Giving Birth To Empowerment: Motherhood And Autonomy In Greek Tragedy, Maggie Sharon Hoyt Jun 2013

Giving Birth To Empowerment: Motherhood And Autonomy In Greek Tragedy, Maggie Sharon Hoyt

Theses and Dissertations

The Greek tragedies of Classical Athens frequently portray mothers in central roles, but despite this significance, the relationship between mother and child has long been overshadowed in secondary scholarship by the relationship between husband and wife. This study demonstrates the direct relationship between a female character's active possession of her children and her autonomy, or her ability to act in her own interests, in three plays of Euripides: Electra, Medea, and Ion. In general, women who internalize their ownership of their children, expressed on stage both in word and action, have greater influence over the men around them and the …

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Kenneth Burke As Educator: What His Theories Of Aesthetic Form And (Non-Symbolic) Motion/(Symbolic) Action Suggest For Teachers In The Literature Classroom, Tara Brock Boyce Jun 2013

Kenneth Burke As Educator: What His Theories Of Aesthetic Form And (Non-Symbolic) Motion/(Symbolic) Action Suggest For Teachers In The Literature Classroom, Tara Brock Boyce

Theses and Dissertations

Burke scholars oftentimes overlook Burke's fundamental role as educator and how his work can and should be applied to the classroom. This paper explores Burke's theoretical works and centers on two concepts important to developing rhetorical skills necessary for functioning and participating in a democratic society: his theory of aesthetic form and his distinction between motion and action. Specifically, this paper (1) clarifies these concepts and explains how they relate to each other and the emotional experience of literature, and (2) demonstrates how these concepts work together to imply a new method of practicing rhetorical criticism in the literature classroom …

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The Effectiveness Of Using Electropalatography To Remediate A Developmental Speech Sound Disorder In A School-Aged Child With Hearing Impairment, Kristina Lynne Pickett Jun 2013

The Effectiveness Of Using Electropalatography To Remediate A Developmental Speech Sound Disorder In A School-Aged Child With Hearing Impairment, Kristina Lynne Pickett

Theses and Dissertations

Advances in instrumentation and computer technology such as electropalatography (EPG) have offered additional types of feedback to more traditional therapy for individuals with speech disorders, specifically those with hearing impairment. The purpose of this study was to document whether therapeutic integration of EPG visual feedback in combination with traditional articulation therapy for a school-aged child with an articulation disorder secondary to hearing impairment was more effective than traditional therapy alone. One participant received five sessions of each therapy approach. Six adult listeners rated the quality of the participant's production of /r/ in words recorded during the therapy sessions. The EPG …

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Evaluating A Social And Emotional Learning Curriculum, Strong Kids, Implemented School-Wide, Thomas Jonathan Kramer Jun 2013

Evaluating A Social And Emotional Learning Curriculum, Strong Kids, Implemented School-Wide, Thomas Jonathan Kramer

Theses and Dissertations

The goal of this study was to explore whether Strong Kids could result in improved social and emotional competence when implemented as a school-wide universal intervention. No prior studies have examined this question. This study also evaluated whether teachers could implement Strong Kids as it was designed and whether they viewed it as socially valid. It used a non-equivalent control group design. The treatment school in the study involved 348 students and 17 teachers from a Title I school. School demographics indicated that 61% of students were Hispanic, 37% White, and 2% of other ethnicities. Approximately 82% of the students …

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Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy, Joshua Christopher Vert Jun 2013

Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy, Joshua Christopher Vert

Theses and Dissertations

From acid seeps and deep-sea thermal vents to glacial ice and hypersaline lakes, extreme environments contain relatively simplified communities consisting of extremophiles that have evolved to survive and thrive under adverse abiotic conditions. In more neutral environments, microorganisms use dormancy as a common life history strategy to weather temporal fluctuations of resources or stresses until more 'optimal' conditions are present. It is unclear if dormancy is an essential survival mechanism for microorganisms in extreme environments; however, recent studies suggest that extreme environments may create stable conditions for extremophiles to the extent that dormancy is of less ecological importance. Using lake …

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Identification And Differentiation Of Tier 1 Bacterial Agents Using Gas Chromatography-Mass Spectrometry, Dan Li Jun 2013

Identification And Differentiation Of Tier 1 Bacterial Agents Using Gas Chromatography-Mass Spectrometry, Dan Li

Theses and Dissertations

A simple method was developed for detection and differentiation of five Tier 1 bacterial agents, including Bacillus anthracis, Francisella tularensis, Yersinia pestis, Burkholderia pseudomallei and Burkholderia mallei as well as their closely related near neighbors by gas chromatography-mass spectrometry (GC-MS). Generally, different classes of compounds can be used as biomarkers for biowarfare agent detection, including nucleic acids (i.e., DNA or RNA), proteins (i.e., antibodies), carbohydrates (i.e., sugars), lipopolysaccharides, lipids (i.e., fatty acids) and small molecules. One-step thermochemolysis (TCM) was developed to provide GC-MS detectable biomarker signatures, including sugars, fatty acids and small molecules. Solid phase micro-extraction (SPME) was used for …

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Thymidine Kinase 1: Diagnostic And Prognostic Significance In Malignancy, Melissa Marie Alegre Jun 2013

Thymidine Kinase 1: Diagnostic And Prognostic Significance In Malignancy, Melissa Marie Alegre

Theses and Dissertations

Thymidine kinase 1 (TK1) is a cancer biomarker which has diagnostic and prognostic potential in a variety of malignancies. TK1 is significantly elevated in the serum and tumor tissue of most malignancies. This increase in TK1 can be detected in the very early stages of malignancy, including in pre-malignant disease with an increased risk for progression. Several studies have demonstrated that elevated TK1 is found in serum months before any clinical symptoms of malignancy. It has also been demonstrated that TK1 is elevated months before clinical recurrence of malignancy. This work first sought to demonstrate the early nature of TK1 …

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Resource Legacies And Priming Regulate Microbial Communities In Antarctica's Dry Valleys, Sabrina Deni Saurey Jun 2013

Resource Legacies And Priming Regulate Microbial Communities In Antarctica's Dry Valleys, Sabrina Deni Saurey

Theses and Dissertations

Multiple mechanisms control bacterial community structure but two in particular, the "legacy" of past environmental conditions, and the "priming" of bacteria to respond to seasonal or reoccurring fluctuations in resources, have the potential to determine both bacterial communities, as well as, temporal shifts in active bacterial taxa. To begin to evaluate the legacy effects of resources on microbial communities, we added four limiting resources annually (i.e., water only; C-mannitol + water; N-NH4NO3 + water; and C, N + water) and measured shifts in bacterial community composition after seven years in a cold desert ecosystem in the McMurdo Dry Valleys, Antarctica. …

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Ethical Metafiction In Dickens's Christmas Hauntings, Mark Brian Sabey Jun 2013

Ethical Metafiction In Dickens's Christmas Hauntings, Mark Brian Sabey

Theses and Dissertations

Many critics have examined metanarrative aspects of Dickens's writing, and many have studied Dickens's ethics. None, however, has yet assessed the ways in which Dickens's directly interrogates the ethics of fiction. Surprisingly philosophical treatments of the ethics of fiction take place in A Christmas Carol and A House to Let, both of which turn the ghost story of the traditional winter's tale to metafictional purposes. No one has yet dealt with Dickens's own meta-commentary on the ethics of fiction with the degree of philosophical nuance it deserves. Writings about the ethics of Dickens's fiction (and of fiction generally) often involves …

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Carla Kelly, Ed. On The Upper Missouri: The Journal Of Rudolph Friederich Kurz, 1851-1852, Victoria M. Breting-Garcia Jun 2013

Carla Kelly, Ed. On The Upper Missouri: The Journal Of Rudolph Friederich Kurz, 1851-1852, Victoria M. Breting-Garcia

Swiss American Historical Society Review

Rudolph Friederich Kurz (January 8, 1818-October 16, 1871) was born in Langnau im Emmental located in the Bern Canton of Switzerland. His talents as an artist were cultivated from an early age, including an extended period of study in Paris where he met the brilliant scholar and explorer, Baron Alexander von Humboldt, and the renowned artist Karl Bodmer. On retrospect, no great effort is required to understand the influence of these early foundations on Kurz's deep attraction for the sublime aspects of the American frontier. Of note is the influence of the American wilderness on the minds and imaginations of …

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Educational Services For Tibetan Students With Disabilities In India: A Case Study, Britany Anne Barnes May 2013

Educational Services For Tibetan Students With Disabilities In India: A Case Study, Britany Anne Barnes

Theses and Dissertations

This case study describes services for students with disabilities at Karuna Home in Bylakuppe, Karnataka, India. Karuna Home is a residential rehabilitation center for students with cognitive or physical disabilities whose parents are Tibetan refugees. The study triangulated data from interviews, observations, and school documents to describe educational policies and procedures, and cultural attitudes toward disability. Results show that the Karuna Home program is undergirded by Buddhist thought and theology regarding care and concern for those in difficult circumstances. The school serves students with a range of mild to severe disabilities and is fully staffed, but teachers and other service …

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