Digital Commons Network^™

Assessment Of Alignment Algorithms, Variant Discovery And Genotype Calling Strategies In Exome Sequencing Data, Anthony Corbett

Theses

Advances in next generation sequencing (NGS) technologies, in the past half decade, have enabled many novel genomic applications and have generated unprecedented amounts of new knowledge that is quickly changing how biomedical research is being conducted, as well as, how we view human diseases and diversity. As the methods, algorithms and software used to process NGS data are constantly being developed and improved, performing analysis and determining the validity of the results become complex. Moreover, as sequencing moves from being a research tool into a clinical diagnostic tool understanding the performance and limitations of bioinformatics pipelines and the results they …

Homology Based Motif Generation, Cameron Baker

Theses

Generating motifs from known active sites and matching those motifs to an uncharacterized protein is a classic way of determining protein function. Until now, the generation of motifs has been based purely on enzymatic function. This approach does not account for situations where highly different active sites can arrive at the same function by processes like convergent evolution. As such, a secondary metric on which to base the generation of motifs is necessary. This metric exists in the form of UniProt designation for homologous proteins on a global scale or PFam for designation of homologous proteins at the active site …

Experiential Metaphors: Create Anti-Negative Home Products, Hong Ying Guo

Theses

Experiential metaphor is a user-centered design approach and methodology that I developed for my thesis project. This approach can be applied to a design to influence a user's perception or design process to facilitate the designer's concept ideation. The intention of this approach is to create a pleasurable product experience and a positive emotional response through interaction with the product and interpretation of its meaning. Grounded in meaning association, which is correlated with non-linguistic cognitive metaphor and human emotional models, four different levels of experiential metaphor are formed by the synthesis of the metaphor structure and levels of emotional elicitation. …

Evaluation Of Reproductive Strategies In Captive California Yellowtail (Seriola Dorsalis) Using Genetic Parentage Analyses, Elizabeth K. Smith, Mark Drawbridge Ms, John Hyde Phd, Geoffrey Morse Phd

Theses

A good understanding of spawning dynamics of species in aquaculture is vital in order to maximize egg production and quality as well as efficient allocation of food and space resources. The breeding program of California yellowtail (CYT; Seriola dorsalis previously Seriola lalandi) at Hubbs-SeaWorld Research Institute (HSWRI) is set up such that up to 30 wild caught brood fish can broadcast spawn in a group setting, just as CYT reproduce in the wild. The population of brood fish were originally caught offshore from Southern California, and are maintained under ambient sea water and natural lighting conditions. The spawning season …

Automatic Localization Of Epileptic Spikes In Eegs Of Children With Infantile Spasms, Supachan Traitruengsakul

Theses

Infantile Spasms (ISS) characterized by electroencephalogram (EEG) recordings exhibiting hypsarrythmia (HYPS) are a severe form of epilepsy. Many clinicians have been trying to improve ISS outcomes; however, quantification of discharges from hypsarrythmic EEG readings remains challenging.

This thesis describes the development of a novel method that assists clinicians to successfully localize the epileptic discharges associated with ISS in HYPS. The approach includes: construct the time-frequency domain (TFD) of the EEG recording using matching pursuit TFD (MP-TFD), decompose the TFD matrix into two submatrices using nonnegative matrix factorizations (NMF), and employ the decomposed vectors to locate the spikes.

The proposed method …

A Secure Neuromemristive Primitive To Mitigate Correlation Power Analysis On Sha-3 Hash Function, James B. Thesing

Theses

Passing messages to soldiers on the battle field, conducting online banking, and downloading files on the internet are very different applications that all share one thing in common, concerns over security of the data being processed. Data security depends on the cryptographic systems that take into account both the algorithmic weakness and the weaknesses of the hardware devices they are implemented on. The current dominant hardware design medium is complementary metal-oxide-semi-conductor (CMOS). CMOS has been shown to leak more power as the technology node size decreases. The leaked power has a strong correlation with the bits being manipulated inside a …

Effect Of Endplate On The Blast Wave Profile In A Compressed Gas Shock Tube, Sudeepto Kahali

Theses

Blast related brain injuries are commonly encountered in the recent wars of Iraq and Afghanistan increased use of improvised explosive devices (IEDs). An estimated 20% of veterans returning from these operations have suffered traumatic brain injuries (TBI). The mechanisms and long-term effects of the injury are not fully understood, and extensive research effort is being focused toward identifying the mechanisms of primary blast injury. When a pure shock-blast wave encounters a subject, in the absence of shrapnel, casing or gaseous products, the loading is termed as primary blast loading, and its effects can be studied using shock tubes.

The wave …

The Role Of Electronsensory Signals On The Locomotor Performance Of The Weakly Electric Fish Apteronotus Albifrons, Oswaldo Gil-Guevara

Theses

Animal locomotion performance responds to different ecological factors that shape relevant aspects of behavior. Conspecific signals is one of these factors and operates in a wide range of contexts. In schooling fish, coordinated movement is based on visual or mechanical cues and signals. In contrast, most gymnotiforms and mormyriforms are nocturnal or live in dark waters and use electric signals for social communication. However, the effect of conspecific electric signals on locomotion and group movement is largely unknown.

Apteronotus albifrons is a well-known model in neuroethological studies of signal processing and locomotion control that relies mostly on visual inputs but …

Doping Profile Measurements In Silicon Using Terahertz Domain Spectroscopy (Thz-Tds) Via Electrochemical Anodic Oxidation, Gaurav Tulsyan

Theses

Doping profiles are engineered to manipulate device properties and to determine electrical performances of microelectronic devices frequently. To support engineering studies afterward, essential information is usually required from physically characterized doping profiles.

Secondary Ion Mass Spectrometry (SIMS), Spreading Resistance Profiling (SRP) and Electrochemical Capacitance Voltage (ECV) profiling are standard techniques for now to map profile. SIMS yields a chemical doping profile via ion sputtering process and owns a better resolution, whereas ECV and SRP produce an electrical doping profile detecting free carriers in microelectronic devices. The major difference between electrical and chemical doping profiles is at heavily doped regions greater …

Factors Affecting Terrigenous Sedimentation In Coastal Bays With Coral Reefs: Implications For Monitoring The Effectiveness Of Watershed Restoration, Whitney Sears

Theses

In the Caribbean, sedimentation has been identified as a serious threat to coral reef communities. Although land-based sediment delivery to coastal waters harboring coral reefs occurs under natural conditions, human activities in the watersheds above reefs increases the erosion and delivery of terrigenous sediment to the reefs. Delivery of terrigenous sediment into marine areas below developed watersheds affects sedimentation rates, alters the composition and texture of sediments that are suspended in the water column, and/or sediments that are deposited on the sea floor and on corals.

St. John, U.S. Virgin Islands is an ideal location to study the effects of …

A Comparison Of Fish Communities In Southwestern Lake Ontario Tributaries From One Century Ago, Ben Carson

Theses

I evaluated a study performed by Albert Hazen Wright between 1902 and 1904, on the Tributaries of Lake Ontario in Monroe County, NY. I extracted data from Wright's original graphical analysis, and analyzed these data with Canonical Correspondence Analysis (CCA), to assess the value of these data for use as historical benchmarks for future studies on the same tributaries. Wright identified 52 species of fish within his distribution diagrams, eight of the species were rare species and were not analyzed with the CCA. Of the 44 remaining species analyzed, 37 matched very well between Wright's interpretations of his data, and …

Design Of A Neuromemristive Echo State Network Architecture, Qutaiba Mohammed Saleh

Theses

Echo state neural networks (ESNs) provide an efficient classification technique for spatiotemporal signals. The feedback connections in the ESN enable feature extraction in both spatial and temporal components in time series data. This property has been used in several application domains such as image and video analysis, anomaly detection, and speech recognition. The software implementations of the ESN demonstrated efficiency in processing such applications, and have low design cost and flexibility. However, hardware implementation is necessary for power constrained resources applications such as therapeutic and mobile devices. Moreover, software realization consumes an order or more power compared to the hardware …

Measuring The Terahertz Refractive Index Of Boron-Doped Silicon Using A Photoconducting Antenna Terahertz Generator, Brendan P. Mcnamara

Theses

The frequency range commonly referred to as the terahertz gap occurs between the infrared and microwave regions of the electromagnetic spectrum. This range of frequencies is highly suited to investigating the free carrier interactions of materials, as the range is particularly sensitive to these interactions. Using terahertz time-domain spectroscopy (THz-TDS), it is possible to measure the effect these interactions have on a terahertz pulse and, using classical optical techniques, determine the terahertz refractive index of a given material, which is directly related to the free carrier spectrum of said material. Knowing the refractive index of a material in the THz …

Controlling The Transient Interface Shape And Deposition Profile Left By Desiccation Of Colloidal Droplets On Multiple Polymer Surfaces, Peter David Dunning

Theses

A colloidal suspension is a small constituent of insoluble solid particles suspended in a liquid medium. Control over the wetting, evaporation, and deposition patterns left by colloidal suspensions is valuable in many biological, medical, industrial, and agricultural applications. Understanding the governing principles of wetting and evaporative phenomena of these colloidal suspensions may lead to greater control over resultant deposition patterns. Perhaps the most familiar pattern forms when an initially heterogeneous colloidal suspension leaves a dark ring pattern at the edge of a drop. This pattern is referred to as a coffee-stain and it can be seen from dried droplets of …

A Switched System Identification Approach To Spindle Modeling, Mohsin Farooq

Theses

Due to new advances in convex optimization, in particular, semidefinite programming, previously infeasible problems are now in the realm of possibility. Mainly, there have been new breakthroughs in the model- ing of signals as the output of switched dynamical systems where the switching indicates underlying events of interest. This method is known as hybrid system identification. These problems can be formulated as polynomial optimization problems by which, through algebraic refor- mulations, convex optimization approaches now exist.

In this work, we explore the application of these new approaches, which lay at the intersection of systems and control with machine learning, for …

Emergence Patterns Of Common Waterhemp And Palmer Amaranth In Southern Illinois, Lucas Xavier Franca

Theses

The continued spread of glyphosate-resistant common waterhemp [Amaranthus tuberculatus (Moq.) Sauer (syn. rudis)] and Palmer amaranth [Amaranthus palmeri (S. Wats.)] have complicated weed control efforts in soybean and corn production in Illinois. A thorough understanding of the weed biology of these species is fundamental in developing effective weed management strategies. The determination of emergence patterns as well as the influence of tillage practices on soil microclimate and soil seed bank will allow control strategies to be implemented at the most effective timing. Field experiments were conducted in southern Illinois throughout the growing season of 2013 and 2014 on two separate …

Influence Of Tio2 Engineered Nanoparticles On Photosynthetic Efficiency And Contaminant Uptake, Scott Jared Bradfield

Theses

The production of engineered nanoparticles (ENPs) is growing at an incredibly fast rate and will soon become a trillion dollar industry. At this rate of production, there is a great potential for engineered nanomaterials to be released into the environment, both intentionally and unintentionally. TiO2 ENPs are one of the most widely produced nanoparticles with a broad range of applications in paints, inks, sunscreens, cosmetics, astronautics, and air/water purification. TiO2 ENPs have been proposed for their use in agricultural settings as a UV protectant, a defense against harmful bacteria and fungi, or a catalyst for the degradation of pesticides and …

Using Stochastic Differential Equations To Model Gap-Junction Gating Dynamics In Cardiac Myocytes, Will Consagra

Theses

The cell-to-cell propagation of the cardiac action potential allows for the electro-mechanical coupling of cells, which promotes the coordinated contraction of cardiac tissue, often referred to as the heartbeat. The main structures that promote electrical coupling between adjacent cardiac cells are pore-like proteins called gap junctions that line the membranes of such cells, allowing a channel for electrically charged ions to travel between cells. It is known that the conformational, and hence conducting, properties of gap-junction channels change as a function of local gap-junctional voltage and local ionic concentrations and are stochastic in nature. Many previous models of gap junctions …

Forest Structure From Terrestrial Laser Scanning – In Support Of Remote Sensing Calibration/Validation And Operational Inventory, David Kelbe

Theses

Forests are an important part of the natural ecosystem, providing resources such as timber and fuel, performing services such as energy exchange and carbon storage, and presenting risks, such as fire damage and invasive species impacts. Improved characterization of forest structural attributes is desirable, as it could improve our understanding and management of these natural resources.

However, the traditional, systematic collection of forest information – dubbed “forest inventory” – is time-consuming, expensive, and coarse when compared to novel 3-D measurement technologies. Remote sensing estimates, on the other hand, provide synoptic coverage, but often fail to capture the fine- scale structural …

The Role Of Philornis Downsi In Avian Disease Transmission In The Galápagos Islands, Courtney Lauren Pike

Theses

Philornis downsi is a dipteran fly species known to parasitize passerine birds in the Neotropics. P. downsi is speculated to be a recently introduced species in Galápagos Islands, so it is important to understand its effects on the archipelago’s native and endemic avian species. Avian parasites and pathogens have been previously reported in the Galápagos, leading the Galápagos National Park and the Charles Darwin Foundation to focus efforts on the study and management of potential avian disease vectors. The main goal of this study was to determine whether P. downsi is a host for avian parasites and pathogens found in …

Testing And Evaluating Dye Color: A Study Using Spectrophotometry On Technicolor And Eastman Color Motion Picture Film, Melissa Sagen

Theses

The history of color motion picture film is linked to two companies: Technicolor and Eastman Kodak. Technicolor was formed in 1915 by Herbert Kalmus, Daniel Comstock, and W. Burton Wescott, who realized that color film could enhance motion picture entertainment. Introduced in 1932, it was a three-color process that was widely used into the late 1950s. The three-color process utilized a camera with one lens that exposed three black and white negatives simultaneously by splitting the incoming visible light through a prism. The prism would create two beams of light which would then expose one film negative to green light …

An Empirical Analysis Of Predictive Machine Learning Algorithms On High-Dimensional Microarray Cancer Data, Jo A. Bill

Theses

This research evaluates pattern recognition techniques on a subclass of big data where the dimensionality of the input space p is much larger than the number of observations n. Seven gene-expression microarray cancer datasets, where the ratio κ = n/p is less than one, were chosen for evaluation. The statistical and computational challenges inherent with this type of high-dimensional low sample size (HDLSS) data were explored. The capability and performance of a diverse set of machine learning algorithms is presented and compared. The sparsity and collinearity of the data being employed, in conjunction with the complexity of the algorithms studied, …

Seasonal Variation In Chronic Stress And Energetic Condition In Three Species Of Migratory Birds, Meghan Oberkircher

Theses

Neotropical migrants face multiple challenges throughout their annual cycle. During migration, birds must avoid predation, face adverse weather, and find stopover sites with food adequate to support their needs. Upon return to the breeding grounds following migration, males must find and defend territory from other males. Females incubate eggs and both males and females may participate in feeding young leaving less time to feed themselves. After the breeding season birds undergo the energy intensive process of molt. Declines in populations of Neotropical migrants have been reported over the past several decades. In order to prevent further population declines of Neotropical …

Computational Identification Of Conserved Haustorial-Expressed Genes In The Grapevine Powdery Mildew Fungus Erysiphe Necator, Miriam E. Barnett

Theses

Erysiphe necator, commonly known as grape powdery mildew, is an obligately biotophic fungus that devastates the grape crops worldwide. Little is known as to how the fungus circumvents a plant’s basal defense, but it is believed that small effector proteins are secreted by fungal haustoria (feeding structures) into the cytoplasm of plant epidermal cells. Thus, the effector proteins and the host processes with which they interact likely determine whether powdery mildew infects successfully or not. The goal of this study was to use bioinformatics tools to identify candidate effector proteins that are specific to haustoria. A de novo reference transcriptome …

Factors Influencing Asiatic Oak Weevil Interactions With Native Ecosystem Engineers Over Time, Daniel Rothschild O'Brien

Theses

I sought to build a model to predict current and future abundance of Asiatic oak weevil (Coleoptera: Curculionidae: Cyrtepistomus castaneus) by using the relative abundance of leaf tying and leaf rolling caterpillars. The Asiatic oak weevil is an exotic species that has been observed inside leaf ties and leaf rolls made by native Lepidoptera caterpillars. Chapter one is a review of the known relationships between animal constructs and exotic species. Within this review I transition from natural structures, to animal architects, and to ecosystem engineers and how they have a population dynamic impact on the invasive species. I also discuss …

Phylogeographic Study Of Ctenosaura Similis, Hasret Ozturk

Theses

The genus Ctenosaura (spiny-tailed iguanas) represents the most diverse group of iguanas with 18 currently recognized species. Ctenosaura similis has the most widespread ranges of all the Ctenosaura species, and extends from southern Mexico to Panama including many coastal islands. The purpose of this study is to explore the genetic diversity within C. similis and look for correlations between genetic relationships and biogeographic patterns related to the spread of the species. This study sequenced and aligned 1140 bp from the cytochrome b (cytb) locus for 159 individuals and 847-878 bp from the rhodopsin locus for 127 individuals. A total of …

The Apnaase/Mrna Decapping Nudix Hydrolases From M. Tuberculosis And M. Leprae, Peipei Zhu

Theses

Throughout history, Mycobacterium tuberculosis (MTB) has killed more people than any other infectious agent, while Mycobacterium leprae is an ancient human pathogen that still causes disease today. Each has developed drug resistance, thus the discovery of potential novel antibiotic targets is essential. The diadenosine polyphosphatases (ApnAases) / mRNA decapping enzymes of the Nudix hydrolase superfamily have been found to be essential for a number of pathogens (Bartonella bacilliformis, Legionella pneumophila) to invade human host cells, a process often essential for pathogenesis, and thus potential novel drug targets. There are two ApnAases in MTB: Rv2985 and Rv3908 and two corresponding orthologs …

Design And Analysis Of A Reconfigurable Hierarchical Temporal Memory Architecture, Abdullah M. Zyarah

Theses

Self-learning hardware systems, with high-degree of plasticity, are critical in performing spatio-temporal tasks in next-generation computing systems. To this end, hierarchical temporal memory (HTM) offers time-based online-learning algorithms that store and recall temporal and spatial patterns. In this work, a reconfigurable and scalable HTM architecture is designed with unique pooling realizations. Virtual synapse design is proposed to address the dynamic interconnections occurring in the learning process. The architecture is interweaved with parallel cells and columns that enable high processing speed for the cortical learning algorithm.

HTM has two core operations, spatial and temporal pooling. These operations are verified for two …

Forma Naturalis, Patrick Kana

Theses

Mankind’s fascination with natural form is undeniably long-lived. From collecting and preserving specimens for evolutionary research, to documenting and expressing natural form through artistic practice, Mankind continues to embrace for scientific and aesthetic benefit that which surrounds us. I believe that botany, marine biology, and environmental phenomena—all areas of influence and study from my childhood—are sources that illustrate perfection in form and utility. The sheer beauty evident in these scientific forms continues to inspire me, and I will celebrate them and explore my relationship with them through an experimental making process in wood.

Carved objects, form studies, and functional furniture …

Biological Significance Of Dual Oriented P6 From Nontypeable Haemophilus Influenzae: Assessing Surface P6 Levels In Different Strains Of Nthi, Cultured Under Various Physiologically Relevant Environmental Conditions, Casey Reulbach

Theses

Nontypeable Haemophilus influenzae (NTHi) or nonencapsulated Haemophilus influenzae has been connected to such diseases as pneumonia, bacteremia, meningitis and sepsis in adults. NTHi is also linked to 25-35% of the roughly 25 million annual cases (within The United States) of acute otitis media (ear infections) in children. Vaccines against encapsulated strains of Haemophilus influenzae have been proven effective; yet, no vaccines have been produced to protect against NTHi infection. The 16-kDa outer membrane lipoprotein P6 has been shown to be nearly homologous between NTHi strains, making it one of the leading vaccine candidates for NTHi. However, it was recently demonstrated, …