Digital Commons Network^™

Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu

Master's Theses

In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.

We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used …

Posture Affects Affordance Perception Of Reachability In Virtual Reality, Hannah Masoner

Master's Theses

Tasks such as standing and reaching require differing levels of postural stability. Postural equilibrium is necessary to perceive the location of objects (Lee, Pacheco, & Newell, 2018). Visual perception of whether an object is within reach was investigated while standing upright. Participants viewed a 3D virtual reality (VR) environment with a stimulus object (red ball) placed at different egocentric distances. Participants made affordance judgements while in a standard stance condition as well as two separate active balance conditions (yoga tree pose, and toe-to-heel pose). Feedback on accuracy was not provided, and participants were not allowed to attempt to reach. Response …

Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao

Master's Theses

Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik’s and Wang’s methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ancestor node …

Zika Message Analysis, Alexandria Phipps

Master's Theses

The following study employs the Extended Parallel Processing Model and Theory of Planned Behavior to understand how to create health messages with the greatest influence on individuals’ behavioral intent to adopt mosquito-borne virus protection behaviors. The study employs a 2 (susceptibility) x 2 (self-efficacy) factorial design, evenly distributing the participants between four messages (N=186). Although the selfefficacy manipulation was ultimately unsuccessful, the findings highlighted the significance of perceived susceptibility on one’s intent to adopt protective behaviors. The results exemplify the importance of the theoretical critical point of the EPPM, where danger control shifts to fear control, and the importance of …

A Linear Approach To John Adams' Recent Works, Olivia Maynard

Master's Theses

This paper presents and demonstrates a linear approach to works from John Adams’ most recent compositional period (1991–). Existing research into this period primarily focuses on specific surface-level events, with little examination of deeper large-scale structures within the works. Chapter 1 reviews the existing research, as well as relevant research into minimalist music and post-tonal analysis, and some existing approaches are then incorporated into the methodology presented in Chapter 2. The methodology is presented in three stages: identifying formal structure, identifying linear structures through salient pitches, and determining harmonic support for those salient pitches. The methodology is demonstrated in greater …

Exploring The Moderating Effects Of Aggression On The Relationship Between Negative Urgency And Suicidal Desire, Rachel L. Martin

Master's Theses

Suicide is a health concern with 44,965 deaths in 2016. Typical assessment of risk factors relies on self-report, which can be susceptible to underreporting. As such, non-face valid measures and innovative assessment approaches such as implicit association tests may help identify risk factors by eliminating conscious underreporting. The Interpersonal-Psychological Theory of Suicidal Behavior is an empirically supported theory hypothesizing why individuals die by suicide. The theory comprises three elements: thwarted belongingness, perceived burdensomeness, and capability for suicide. Thwarted belongingness and perceived burdensomeness have been found to be non-face valid measures and less susceptible to conscious underreporting. Objective measures, such as …

A Machine Learning Approach To Network Intrusion Detection System Using K Nearest Neighbor And Random Forest, Ilemona S. Atawodi

Master's Theses

The evolving area of cybersecurity presents a dynamic battlefield for cyber criminals and security experts. Intrusions have now become a major concern in the cyberspace. Different methods are employed in tackling these threats, but there has been a need now more than ever to updating the traditional methods from rudimentary approaches such as manually updated blacklists and whitelists. Another method involves manually creating rules, this is usually one of the most common methods to date.

A lot of similar research that involves incorporating machine learning and artificial intelligence into both host and network-based intrusion systems recently. Doing this originally presented …

Are You Happy? Local Economic Development In Northern Thailand, Katherine Sorensen

Master's Theses

Thailand has had a long history of economic development. In recent years, Thailand began to focus on economic development initiatives a local level. The implementation process has been slow, but the introduction of social enterprise programs has proven a promising strategy in local economic development. Successful examples of economic development can be found in Thailand wherein this paper argues through collaboration between government agencies and local communities lies the key to success.

Qualitative techniques including a two months of fieldwork in Thailand, first hand observations, and appreciative inquiry interviews are used to analyze economic development initiatives in the communities of …

Exploring The Gamification Paradox: Why Does Improved Engagement Not Lead To Improved Performance?, Katarzyna Maria Sliwinska

Master's Theses

Gamification is the application of game elements to non-game environments (Deterding, 2012), and is often used to engage people and make their experiences more enjoyable in areas ranging from fitness and education to psychological research. Previous studies have shown that adding gamification to new environments can result in increased motivation (Hamari, Koivisto, & Sarsa, 2014). However, increased motivation from gamification does not seem to increase performance in terms of accuracy or response times (Hawkins et al., 2013). This research study examined this “gamification paradox” by testing the performance of 87 participants on a visual search task both with and without …

Magnesium-Rich Phyllosilicates In Creeping Faults: A Study Of The Maacama Fault Zone, Mendocino County, California, Brittany M. Martin

Master's Theses

The Maacama Fault Zone in Mendocino County, California consists of multiple fault gouges with varying mineralogy, making this an ideal location to study the potential relationship between the magnesium phyllosilicate content of a fault gouge and fault creep. This study uses the presence of magnesium-rich phyllosilicates to test the hypothesis that faults to the northeast of Little Lake Valley in Mendocino County are accommodating strain on the Maacama Fault Zone through creep. Analytical work expands the work of Schroeder (2010) to more completely address the relationship between fault creep and mineralogy by sampling three fault gouges in the Maacama Fault …

Effects Of Bio-Composites In Corrugated Sandwich Panels Under Edgewise Compression Loading, Jalen Christopher Mano

Master's Theses

Present day composite sandwich panels provide incredible strength. Their largest problem, however, is early bonding failure between the core and the skin. This is due to the low bonding surface area of present cores like honeycomb. Corrugated structures could provide a remedy for this with their much larger bonding surface area. Corrugated structures have extreme mechanical properties deeming them particularly useful in aerospace and automotive applications. However, previous research has shown that the stiffness of carbon fiber causes debonding and drastic failure when used as both a core and a skin. Bio-composites have properties that could strengthen the corrugated sandwich …

He's The Hero We Deserve: Batman As A Figure Of Dominant Masculinity, Karen Medrano

Master's Theses

For decades, comic books have been a prevalent media format through which cultural perceptions of masculinity are disseminated. Batman is an exemplary character who is expected to perform and behave in a manner that corresponds with social constructs of the American masculine identity: strong, dominant, and protective. These gendered traits, as represented through Batman’s body and relationships with various allies, are analyzed through the lens of R.W. Connell’s theory of dominant and subordinated masculinities (derived from her larger theory of hegemonic masculinity). As our cultural perception of masculinity has shifted, so has the visual representation of Batman over his eighty-year …

Creating A Cultural Context For Dong And Miao Folk Music Using An Orff-Inspired Methodology, Ke Guo

Master's Theses

As children grow up surrounded by various ethnicities, races, and religious beliefs, we teach them music and dance to cultivate respect and empathy for the diverse people in our multicultural society. On the other side of the globe, China is also a multi-ethnic country and is home to 56 ethnic minority groups that speak multiple different languages. “Chinese music” is thus a collective term for the many disparate styles and genres of music in the country, which is especially rich in the varieties of folk music heard and played. Although Chinese folk music frequently appears in music textbooks in elementary …

The Effect Of Precipitation On Copy Number Of Nitrogenase Gene Nifh In Soil Bacteria In The Mojave Desert, Christy Armstrong

Master's Theses

Animals, plants, and microbes all rely on nitrogen to be readily available to build amino acids. The earth’s atmosphere is made of 78% nitrogen gas, but this molecule has a strong triple bond that prevents many species from utilizing it directly. Nitrogen fixation must occur in order for individuals to incorporate this nitrogen into their genome. The Mojave Desert is the most arid region in North America, averaging 3.5 inches of rain annually at its lowest elevation. Despite the extreme arid conditions, many species are supported in the region, all of which must rely on some form of nitrogen. This …

Avocado Root Rot: Steep, Rocky Terrain And Biodiversity Help Protect Small Farmers In Post-Conflict Colombia, Morgan Frankel

Master's Theses

In recent years, small avocado producers in coastal Colombia returned to their farms after decades of war to discover they must battle the pathogen Phytophthora cinnamomi devastating their trees. While this disease is well-described in the U.S., Australia, and Europe, no previous research has examined environmental correlates of P. cinnamomi in avocado in the diverse tropical agroecosystem of the Colombian Montes de Maria. I used agroecosystem inventory, in-field diagnostics, and disease observations to describe avocado agroecosystem diversity and identify relationships among P. cinnamomi presence, root rot disease, slope, pH, soil compaction, elevation, and distance to the household in remote smallholder …

Classification Of Hyperspectral Colon Cancer Images Using Convolutional Neural Networks, Sean Joseph Mobilia

Master's Theses

Hyperspectral images are 3-D images, which contain data in hundreds of spectral bands as opposed to 2-D images, which contain data in at most 3 bands (red, green, and blue). Hyperspectral imagery was initially developed for remote sensing; however, recently, researchers have started to see its potential in medical diagnosis and cancer detection. Hyperspectral images provide massive amounts of data about the objects they are studying, and this causes challenges during information processing. Machine learning tools, such as convolutional neural networks (CNNs), are known to be successful in extracting features and classifying traditional 2-D images. This thesis proposes CNN architectures …

Combining Blockchain And Swarm Robotics To Deploy Surveillance Missions, Ardalan Razavi

Master's Theses

Current swarm robotics systems are not utilized as frequently in surveillance missions due to the limitations of the existing distributed systems' designs. The main limitation of swarm robotics is the absence of a framework for robots to be self-governing, secure, and scalable. As of today, a swarm of robots is not able to communicate and perform tasks in transparent and autonomous ways. Many believe blockchain is the imminent future of distributed autonomous systems. A blockchain is a system of computers that stores and distributes data among all participants. Every single participant is a validator and protector of the data in …

A Systematic Theoretical Study Of Topological Insulator Bi₂Se₃, Thomas Reid

Master's Theses

No abstract provided.

Non-Destructive Evaluation Of Thermal Barrier Coatings Using Direct Heat Flux Method, Amadeusz Adam Nasuta

Master's Theses

Thermal barrier coatings are essential for reliable and efficient turbine engines. The coatings allow the engine to operate at higher temperatures and protect the super alloy components within the hot section. Turbine hot section components have complex geometries. Complex geometries can lead to inconsistent coatings. It is critical to determine which components have defective coatings because engine manufacturers warranty these parts and under life parts have large costs associated with them. Non-destructive detection of damage progression is useful for accurate part lifetime prediction and also in root cause analysis. The present thesis describes a new, non-destructive approach to test thermal …

Onshore Habitat Use As A Driver Of Diet, Contaminant Exposure, And Immune Function Of Southern Beaufort Sea Polar Bears (Ursus Maritimus), Jennifer Bourque

Master's Theses

No abstract provided.

Reanalysis Of The Usher Syndrome Type 2 Carrier As “Phenotype-Free”, Peter Perrino

Master's Theses

No abstract provided.

Topology Optimization Of Space Frames Via Geometry Projection, Manal Tahhan

Master's Theses

There is growing interest in space agencies to design lunar habitats for different stages of habitation. In this work, we present a topology optimization method to design a class of these structures consisting of rigid space frames with elements transported from earth and assembled in situ. Since the space frame must be made of stock material for ease of transportation and assembly, this work employs the geometry projection method, which is a topology optimization technique that render designs made exclusively of geometric primitives. This work makes three contributions to the geometry projection method that are necessary for the design of …

Indoor Air Monitoring Of Ethanol And Benzene In A Pilot Winery Using Active Sampling, Andrew I. Kaneda

Master's Theses

Acute indoor concentrations of benzene and ethanol were evaluated in the California Polytechnic State University San Luis Obispo’s pilot winery workroom. Air samples were collected during four different wine-making activities: fermentation, fermentation with Brix content testing, post-alcoholic fermentation pressing, and storage/finishing. Average workroom benzene concentrations ranged from 0.05 to 0.12 mg/m³. Ethanol concentrations in the winery workroom varied with the activity, ranging from 0.9 to 12 mg/m³. Pressing and fermentation with Brix content testing both led to higher indoor ethanol concentrations than fermentation without Brix content testing and storage/finishing.

Tracer gas decay air exchange tests were …

Perturbation Based Decomposition Of Semg Signals, Rachel Huettinger

Master's Theses

Surface electromyography records the motor unit action potential signals in the vicinity of the electrode to reveal information on muscle activation. Decomposition of sEMG signals for characterization of constituent motor unit action potentials in terms of amplitude and firing times is useful for clinical research as well as diagnosis of neurological disorders. Successful decomposition of sEMG signals would allow for pertinent motor unit action potential information to be acquired without discomfort to the subject or the need for a well-trained operator (compared with intramuscular EMG). To determine amplitudes and firing times for motor unit action potentials in an sEMG recording, …

Suitability Of Cultivated Forms Of Native Shrubs To Support Pollinators, Jacob Gordon Ricker

Master's Theses

There is increased interest in native plants for landscaping to support pollinators. The majority of native plants sold by nurseries are cultivars. Some consumer and conservation groups question the suitability of native cultivars to support pollinators. This work evaluated insect pollinator visitation for six native shrub species, and one or more cultivars of each species. The following species were installed in a full sun field behind the University of Connecticut Floriculture Greenhouse Facility in a randomized complete block design with three replicates: Aronia melanocarpa, A. melanocarpa ‘UCONNAM012’ Ground Hog®, A. melanocarpa ‘UCONNAM165’ Low Scape Mound®, Clethra alnifolia, C. …

Conflict Management Training In Video-Based Teams, Alexis Ward

Master's Theses

In the wake of an emerging economy that demands organizational agility, globalization and an increasing number of independent contractors, corporations have exponentially incorporated virtual teams in their organizations. However, despite their financial and geographical convenience, research has indicated that virtual teams have consistently experienced more conflict and lowered performance and satisfaction levels than that of their traditional counterparts. The present study sought to examine whether conflict management training could help video based virtual teams demonstrate more positive conflict handling techniques and less negative techniques, which would result in higher group process and group outcome satisfaction. This study did not find …

Pro Or Bust: Career Aspirations Of Division I And Community College Basketball Players, Alexander Shahriar Engel

Master's Theses

ABSTRACT

Pro or Bust: Career Aspirations of Division I and Community College Basketball Players

Alexander Shahriar Engel

The purpose of this study was to determine the difference, if any, between Division I and community college basketball players career aspirations. Interviews were held with eleven athletes from the Cal Poly Men’s Basketball team, and ten athletes from the Cuesta College Men’s Basketball team. The interviews were used to determine the impact of different variables on the athletes career aspirations, and to explore themes in the data. To look for themes, both axial and open coding was used. Division I athletes were …

Infection Control In Total Knee Replacement Prosthesis Using Nitric Oxide Releasing Biomaterials, Ashley Widing

Master's Theses

Replacing a weight-bearing joint is accompanied by long procedures, even longer recovery times, and intensive monitoring. This burden increases after infection; a complication requiring revision surgeries and therefore extensive additional recovery time. Infection can present itself at any time during the process, making it hard to predict. Currently, a two-part revision surgery is completed by removing all infected tissue and implanting an antibiotic spacer. The spacer fills the joint gap and is removed prior to the revision total knee replacement. A revision total knee replacement follows the same procedure as the initial surgery. Not only is this detrimental to patient …

From The Technology Gap To The Graduation Gap: Implications Of Technology Access And Postsecondary Success, Abigail Evans

Master's Theses

The gap in technology access in the United States is indicative of the larger inequalities that continue to plague our modern society. This research project focuses on the relationship between technology access and postsecondary success. Previous studies have established there is a connection between technology access and academic success, but many questions about how and when students access technology remain unanswered. in this thesis, I gather information from disparate sources to try and draw conclusions about the current state of technology in postsecondary education. This included research on technology use patterns among numerous demographic groups, information of the social behaviors …

Pilot Study Of Teacher Preparedness For Mandated Civics Education In Illinois, Zoe Michelle Prevatt

Master's Theses

Zoe M. Prevatt Loyola University Chicago PILOT STUDY OF TEACHER PREPAREDNESS FOR MANDATED CIVICS EDUCATION IN ILLINOIS Following thirty-nine states, Illinois became the 40th state to make Civic Education a mandatory class for students to graduate high school in 2015. The mandated class is a semester long and usually occurs in the students Junior or Senior year of high school. The Illinois General Assembly then passed a separate bill that indicated that the 2016-17 school year would be when the mandated class would be fully implemented. Throughout my piece I look to this implementation plan as well as the original …