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Development Of An Analysis And Simulation Package For Protein Molecules & Improving The Graphics Of Their Conformational Transition, Hima N. Khoshreza

Master's Theses

Proteins are the building blocks of many living organisms and to study them is to discover many of nature’s processes. Abnormalities of these superb molecules make them also accountable for a wide range of human diseases. Every sixty seconds an American will be diagnosed with Alzheimer’s disease. The mystery behind this disease and many others might well be revealed by novel protein prediction techniques. This thesis investigates developments of two tools to benefit such techniques.

First, a user-friendly graphical interface (GUI) was developed based on a previously perfected program named ProtoFold. ProtoFold is a protein simulation software that examines the …

A Method For Network Clustering And Cluster Based Routing, Jonathan Adelson

Master's Theses

Social networks and sensor networks are two very different types of networks that have been made possible by modern technology. Portable wireless devices, including laptops and cell phones, have made social networks part of our daily lives. Similarly, cheap, fast, portable devices are ideal for sensor networks. The common thread is the underlying graph structure, which is decentralized and can naturally form groups. However, human groups are messy, and can best be modeled by graph clusters that can be allowed to overlap with each other. We apply this idea to the identification of pre-existing groups as well as discovering a …

Pbzrtio3 And Bifeo3 Ferroelectric Domains, Domain Boundaries, And Switching Investigated With Piezo Force Microscopy, Linghan Ye

Master's Theses

The domain structure of ferroelectric and multiferroic materials can have a significant effect on piezoelectric, dielectric, and thermal transport properties. Piezo Force Microscopy is an ideal tool based on Atomic Force Microscopy that allows unique investigations of such nanoscale effects, and can further be implemented to monitor domain switching dynamics.

A new method for polarization orientation mapping and statistical analysis is first employed to determine the domain variants present in a range of BiFeO₃ epitaxial (001) thin films with specifically engineered domain distributions. This allows domain wall densities to also be calculated, along with interfacial polarization angles between adjacent …

Effect Of Positional Dependence In Recognizing Transcription Factor Binding Sites, Saad A. Quader

Master's Theses

Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC) and the positional dependence of nucleotides within an aligned set of TFBSs has not been well researched for modeling variable-length binding sites. In this paper, we propose ML-Consensus, a consensus model for variable-length binding sites which does not exclude any input binding sites. We consider Pairwise Score (PS) as a measure of positional dependence of …

Effects Of Herbivory As An Ecological Constraint Of Willow Growth At A Restored Riparian Corridor, Jacqueline A. Mccrory

Master's Theses

A critical component of nearly all riparian restoration projects is the rapid successful recovery of native vegetation. The dynamic conditions and diverse biotic community supported by riparian ecosystems can present numerous constraints to restoration efforts. This study investigated stunted growth of arroyo willow (Salix lasiolepis) cuttings planted along the banks of Redwood Creek as part of the National Park Service’s Muir Beach Restoration Project to restore habitat for special status species in California. Based on observations of deer browsing, as well as signs of extensive biomass removal, I designed a field experiment using exclusionary fencing to test the significance of …

Teacher-Efficacy For Using Hots Pedagogy In The Classroom, Lindsey K. Le

Master's Theses

When considering the educational context and expectations of our teachers today, an evaluation of teacher-efficacy in promoting higher-order thinking skills (HOTS) in the classroom is more important than ever. Promoting these skills as illustrated in Anderson and Krathwohl’s (2001) taxonomy of educational objectives, through pedagogical techniques, provides an opportunity for students to develop metacognitive skills for learning. The literature (Thomas & Walker, 1997) stresses that the confidence that teachers have in actually promoting these skills (also known as teacher-efficacy (Bandura, 1986)), is important to bridging the gap between pedagogy and development of student thinking skills. The aim of the study …

Analysis And Mitigation Of The Cubesat Dynamic Environment, Steve M. Furger

Master's Theses

A vibration model was developed for CubeSats inside the Poly-Picosatellite Orbital Deployer (P-POD). CubeSats are fixed in the Z axis of deployers, and therefore resonate with deployer peaks. CubeSats generally start fixed in the X and Y axes, and then settle into an isolated position. CubeSats do not resonate with deployers after settling into an isolated position. Experimental data shows that the P-POD amplifies vibration loads when CubeSats are fixed in the deployer, and vibration loads are reduced when the CubeSats settle into an isolated position. A concept for a future deployer was proposed that isolates CubeSats from the deployer …

Thinking Through The Box: The Art Teacher's Role In Setting Ideationally Generative Assignment Parameters, And Expanding Students' Problem-Finding Strategies, Brad James Conklin

Master's Theses

This thesis explores the nature of generative parameters, and their present – as well as their much greater potential – function in visual art assignments. An effort of thoughtful self-study, it examines important questions that were revealed during the teaching of a fifth grade art unit. Collaboration and chance were used in that unit as productive constraints. Bringing together insights gathered from a number of sources and my own classroom action research, a theory of teaching for creative behavior is offered with suggestions for good practices in the art room. Promoting creative thinking in the art classroom does not require …

Automated Filtering And Attribution Of Archive Bathymetry Based On A Priori Knowledge, Rodney Wade Ladner

Master's Theses

Hydrographic offices hold large volumes of historical bathymetric data. Many of these valuable datasets were collected using older generation survey systems and contain little or no metadata. Current efforts to utilize these data require human intervention to remove outliers and assess quality. This thesis develops automated algorithms based on a priori knowledge of existing bathymetric topography to remove errant soundings and concurrently provide an estimate of uncertainty.

Comparison Of Liquid-Liquid Extraction And Solid Phase Extraction Of Mephedrone, Brittany Simone Love

Master's Theses

Legal high drugs are modified scheduled drugs. As with any new drug, researchers have to conduct studies to gather information about the drug. The problem with obtaining accurate information on new drugs is that by the time information is gathered, drug abusers and street chemists have developed new ones. Comparing designer drugs to their illegal counterparts is often helpful in that it can provide a starting point. Mephedrone is a new designer drug that has become a problem over the past few years. Often marketed as bath salts and plant food, mephedrone has become the knockoff replacement for amphetamines. This …

Primary Productivity Distributions Along The River-Dominated Shoreline Of The Bay Of St. Louis, Ms Estuary, Adam Douglas Boyette

Master's Theses

Potential primary production was measured for six consecutive months (July 2010 to December 201 0) at selected stations along the shoreline of the Bay of Saint Louis (BSL) estuary. Monthly surface and a series of subsurface (0.5 m) samples were taken to observe the temporal (monthly and short-term) and spatial variability in production relative to environmental variables that potentially could influence phytoplankton photosynthesis. Daily areal primary production, PP was modeled using photosynthesis-irradiance (P-E) parameters in conjunction with in situ irradiance measurements and biomass data collected during sampling. Although spatial variability was not observed, PP varied seasonally and ranged from 1.90 …

Solutions Of Matrix Equations, Thir Raj Dangal

Master's Theses

Two n x n matrices A and B can make many different matrix equations, e.g., AB = BA, AB = AA, ABA = BAB, and AAB = BAA. It is not always easy to describe solutions to these matrix equations. This thesis considers the problem of describing solutions to the matrix equations A² = B², AB = A² and AB = B². This problem is motivated by considering the properties of commutative matrices (i.e., AB = BA), as well as the matrix form of the Yang-Baxter equation, ABA = …

Growth And Carboxysome Composition Of The Csosia Pore Mutants Of Halothiobacillus Neapolitanus, Jenifer Milam

Master's Theses

Carboxysomes are specialized organelles that are filled with ribulose 1,5- bisphosphate carboxylase/oxygenase (RubisCO) needed for CO2 fixation. The major carboxysome shell proteins, CsoSl A, B, and C, form hexamers which tile together to form the facets of the thin shell. Each hexamer has a small central pore that may play a role in metabolite flux. Using predicted structural models, a specific amino acid within the conserved hexamer pore motif (Phe-Val-Gly-Gly-Gly-Tyr) was chosen to change the size and charge of the pore, respectively. Two mutants of Halothiobacillus neapolitanus were generated in which the wild type csoSJA gene was replaced with the …

Topological Network Alignment Based On Graphlet Degree Signature, Shengai Jin

Master's Theses

A large number of experimental biological network data of different types are becoming available due to advanced experimental techniques. Network alignment is considered to be one of the most common methods to analyze and compare biological networks to understand evolution, biological mechanisms, and the complexity of diseases. Kuchaiev, Milenkovic, Memisevic, Hayes, & Przulj (2010) recently proposed a topological method of network alignment based on graphlet degree signatures, called GRAAL, which can be used to align any kind of networks not just biological ones. Several global network alignment algorithms also have been designed based on GRAAL, such as MI-GRAAL, H-GRAAL, and …

Direct Chain-End Functionalization Of Living Polyisobutylene With Phenoxyalkyl(Meth)Acrylates, Conor Patrick Roche

Master's Theses

This volume describes efforts toward the synthesis and employment of phenoxyalkyl (meth)acrylates, which were used to end-quench 1sobutylene polymers m1tiated from 2-chloro-2,4,4-tnmethylpentane (TMPCl), and 5-tert-butyl-1 ,3-d1(1-chlorol- methylethyl)benzene (bDCC), respectively, at -70 °C in 40/60 (v/v) hexane/methyl chlonde. The quencher/cham end molar rat10s typically ranged from 2.5-4, while the ratio of Lewis ac1d/cham end was vaned from approximately 3 5-6 In all cases, alkylation occurred exclusively at the para position of the quencher and no cham degradat10n was observed, even at high concentrations of TiC14 and long reaction times. Prellmmary qualitative studies mvolved the reaction of quenchers of varymg alkyl tether …

Determinants Of Food Insecurity Among Vulnerable White And Latino Households: Contextualizing The Impact Of Sociodemographic And Household-Level Factors, Alexandra Lund

Master's Theses

Household-level characteristics have been shown to be associated with food insecurity but studies among vulnerable populations are sparse. A food security assessment was developed to determine food security and collect sociodemographic and household level data across San Luis Obispo County. The assessments were administered to vulnerable groups through interviews at multiple sites across the County. Three household characteristics (marital status, number of children in the household and number of workers in the household) were examined in this analysis. A total of 808 surveys were collected, 69% in English and 31% in Spanish. Through ethnicity-stratified sequentially adjusted logistic regression models, the …

Transient Small Wind Turbine Tower Structural Analysis With Coupled Rotor Dynamic Interaction, George R. Katsanis

Master's Theses

Structural dynamics is at the center of wind turbine tower design - excessive vibrations can be caused by a wide range of environmental and mechanical sources and can lead to reduced component life due to fatigue, noise, and impaired public perception of system integrity. Furthermore, periodic turbulent wind conditions can cause system resonance resulting in significantly increased structural loads. Structural vibration issues may become exacerbated in small wind applications where the analytical and experimental resources for system verification and optimization are scarce. This study combines several structural analysis techniques and packages them into a novel and integrated form that can …

Modeling And Analysis Of A Pv Grid-Tied Smart Inverter's Support Functions, Benjamin Anders Johnson

Master's Theses

The general trends in the past decade of increasing solar cell efficiency, decreasing PV system costs, increasing government incentive programs, and several other factors have all combined synergistically to reduce the barriers of entry for PV systems to enter the market and expand their contribution to the global energy portfolio. The shortcomings of current inverter functions which link PV systems to the utility network are becoming transparent as PV penetration levels continue to increase. The solution this thesis proposes is an approach to control the inverters real and reactive power output to help eliminate the problems associated with PV systems …

Cretaceous And Paelogene Stratigraphy Of Forrest County, Mississippi, Joel Kenneth Loeffler

Master's Theses

Extensive investigation has been done on the subsurface geology and structure of Maxie and Pistol Ridge fields of Forrest and Pearl River Counties, Mississippi. However, a comprehensive study has not been done on the whole of Forrest County as, aside from two minor fields, oil and gas plays do not exist elsewhere in the county. This thesis expands on the work done Vellora Foster (1941) to describe the subsurface geology of the county. Electrical logs from 289 wells drilled in Covington, Forrest, Jones, Lamar, Pearl River, Perry, and Stone counties were used to correlate stratigraphic horizons. Detailed Stratigraphic descriptions of …

Enabling Rapid Conceptual Design Using Geometry-Based Multi-Fidelity Models In Vsp, Joel Brian Belben

Master's Theses

The purpose of this work is to help bridge the gap between aircraft conceptual design and analysis. Much work is needed, but distilling essential characteristics from a design and collecting them in an easily accessible format that is amenable to use by inexpensive analysis tools is a significant contribution to this goal. Toward that end, four types of reduced-fidelity or degenerate geometric representations have been defined and implemented in VSP, a parametric geometry modeler. The four types are degenerate surface, degenerate plate, degenerate stick, and degenerate point, corresponding to three-, two-, one-, and zero- dimensional representations of underlying geometry, respectively. …

Novel Approach To Junctional Bleeding: Tourniquet Device Proposal For Battlefield Hemorrhage Control, Kyle W. Cabaniss

Master's Theses

This study investigated possible solutions to the current wartime problem of junctional hemorrhaging, or massive traumatic hemorrhaging in non-tourinquetable areas such as the neck, groin, or armpit. Junctional hemorrhaging has been identified as a major contributor to potentially survivable deaths seen on the battlefield today and therefore is a priority for the U.S. armed and coalition forces (Kragh et al., 2011a; Bozeman, 2011). Common tourniquets today are standard issue and carried by soldiers in the military, but are limited to distal extremity trauma. As the battlefield has changes however, trauma has transformed from commonly seen gunshot wounds to more extreme …

Improving Webide Through Delightful Design And Gamification, Michael Hilton

Master's Theses

WebIDE is a web-based online learning environment. WebIDE has been used

successfully to teach CS0 and CS1 students Java and C concepts and software

engineering best practices, specically Test Driven Development. Previous Web-

IDE development has concentrated on developing functionality. The main goal

of this eort is to improve two non-functional aspects of WebIDE. The rst is to

design a more delightful user interface. The second is to add a scoring mecha-

nism that encourages students to develop best practices. The scoring mechanism

rewards students who answer the question correctly on the rst attempt, dis-

couraging them from spamming the …

Spoons: Netflix Outage Detection Using Microtext Classification, Eriq A. Augusitne

Master's Theses

Every week there are over a billion new posts to Twitter services and many of those messages contain feedback to companies about their services. One company that recognizes this unused source of information is Netflix. That is why Netflix initiated the development of a system that lets them respond to the millions of Twitter and Netflix users that are acting as sensors and reporting all types of user visible outages. This system enhances the feedback loop between Netflix and its customers by increasing the amount of customer feedback that Netflix receives and reducing the time it takes for Netflix to …

Rfid Technology Selection And Economic Justification For Healthcare Asset Tracking, Tyler Robert Peabody, Tali Freed

Master's Theses

Although Radio Frequency Identification (RFID) and Real-Time Location System (RTLS) technologies for inventory tracking have been growing in popularity, the healthcare industry has been reluctant to adopt these technologies. One of the primary reasons for this lack of enthusiasm has been the risk associated with electromagnetic interference between RFID/RTLS systems and medical equipment functionality. The other reason has been the substantial cost and complexity of implementing RFID/RTLS in healthcare organizations. In this study, we show that there are several ways to safely install RFID/RTLS systems to improve the inventory management processes of hospitals and clinics. We then analyze the inventory …

Consumer Evaluation Of Low Sodium Mozzarella Cheese And Development Of A Novel Method For Evaluating Emotions, Lauren Alyse Collinsworth

Master's Theses

Mozzarella cheese is currently the highest consumed cheese in the United States. The popularity of mozzarella cheese is typically attributed to the high consumption rates of pizza cheese and string cheese; both of which are low moisture part skim (LMPS) mozzarella cheese. A single serving of LMPS mozzarella cheese contains approximately 8% of the daily value (DV) for sodium, a mineral which is currently consumed in excess among most Americans. On average, one in three Americans has hypertension. This condition is strongly associated with excessive sodium intake, and it is a leading risk factor for cardiovascular disease and stroke in …

Structural Health Monitoring For In-Service Highway Bridges Using Smart Sensors, Sushil Dahal

Master's Theses

With the rapid development of electrical circuits, Microelectromechanical system (MEMS) and network technology, wireless smart sensor networks (WSSN) have shown significant potential for replacing existing wired Structural health monitoring (SHM) systems due to their cost effectiveness and versatility. A few structural systems have been monitored using WSSN measuring acceleration, temperature, wind speed, humidity; however, a multi-scale sensing device which has the capability to measure the displacement has not been yet developed. In this research, a new high accuracy displacement sensing system has been developed combining a high resolution analog displacement sensor and MEMS-based wireless microprocessor platform. The developed multi-scale sensing …

Automated Point-Of-Care Image Processing Methodology For The Diagnosis Of Malaria, Michael B. Jorgensen

Master's Theses

Malaria has profoundly influenced human history for over four thousand years and despite numerous attempts at eradication, the prevention, diagnosis, and treatment of malaria have been largely ineffective. More than five hundred million people are affected by malaria every year resulting in over one million deaths. Drug resistance development by the parasite has diminished the effectiveness of numerous treatment options due, in part, to overtreatment of negative patients based on insufficient clinical algorithms and diagnostic methods. The goal of this research was to develop an image analysis algorithm to diagnose malaria with a high degree of sensitivity and specificity in …

Preparation Of Organofluorine Compounds: Exploring Mono-, Di-, And Tri-Fluorination, Diandra M. Rudzinski

Master's Theses

Organofluorine compounds exhibit biological activity and have advantageous properties for drug design. Natural occurring fluorinated molecules are rare, demanding new synthetic methods for their preparation. A novel route to access trifluoromethyl ketones from Weinreb amide precursors is discussed. This is the first documented method for the use of the Ruppert-Prakash reagent, (trifluoromethyl)trimethylsilane, for the production of trifluoromethyl ketones from amide starting materials. This method is tolerant of aryl and alkyl substrates exhibited by their moderate to excellent yields. A discussion of the unusual reactivity of these amides, their selectivity for mono-trifluoromethylation, and other mono-, and di-fluorination attempts are reported.

Perceptions Of Psychology Among Seminary And Biology Students At Andrews University, Sandro Moraes

Master's Theses

Problem. Both pastors and biologists frequently interact with individuals. These contacts often involve conversations that deal with an individual’s feelings, behaviors, and the relationship between mind and body. Thus, how seminarians and biologists perceive psychology will greatly affect such interactions. Therefore it is important to know how both professionals perceive psychology. This is not all that different from the research biologists perform as they learn about the brain. Because of the interrelatedness between these two professions, what are the perceptions of psychology among seminary and biology students at Andrews University? -- Method. The data gathered from the responses of biology …

The Comparative Morphology Of The Pectoral Free Rays In Scorpaenoid Fishes (Perciformes: Scorpaenoidea)), Jeremy Peter Harris

Master's Theses

The pectoral fins of many benthic taxa have evolved many unique features used to interact with the substrate. In one such group, the searobins (Triglidae: Scorpaenoidea), three of the pectoral fin rays have become separated from the fin as a whole, allowing them to operate as a separate appendage from the fin as a whole. The anatomical structure of these "free rays" was investigated and several previously unreported muscle and bone variations were found. This method was extended to include members of four other scorpaenoid families which possess free rays, which revealed important differences in the muscle, bone, and nervous …