Physical Sciences and Mathematics Commons^™

Regulation Of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity In The Model Rhizosphere-Dwelling Bacterium Pseudomonas Putida Kt2440, Ran An, Luke Moe

Plant and Soil Sciences Faculty Publications

Soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (gcd) and PQQ biosynthesis genes (pqq operon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts …

South Padre Island Beach Management: Assessment Of Dune Restoration, Shelby Rose Bessette

Theses and Dissertations

Dune restoration is a common method of increasing coastal resilience. A dune restoration program was initiated by the City of South Padre Island, TX in 2010 consisting primarily of plantings of Sea Oats, Uniola paniculata, and Bitter Panicum, Panicum amarum and has continued approximately annually thereafter. These restoration efforts were evaluated in this study by comparing dune ecological structure and function among reference sites and restoration plots ranging in age from 2 to 5 years. Plant and animal communities were examined using a combination of quadrat sampling, funnel traps, pit-falls and sweep nets. Soil organic content and soil electric …

Lie Symmetry To Second-Order Nonlinear Differential Equations And Its First Integrals, Pengfei Gu

Theses and Dissertations

There are many well-known techniques for obtaining exact solutions of differential equations, but most of them are merely special cases of a few powerful symmetry methods. In this paper, we focus our attention on a second-order nonlinear ordinary differential equation of special forms with arbitrary parameters, which is a combination of Liénard-type equation and equation with quadratic friction. With the help of Lie Symmetry methods, we identify several integrable cases of this equation. And for each case, we use the Lie Symmetry method to derive the associated determining system, and apply it further to find infinitesimal generators under …

A Comparative Study And Data Analysis For The Ultimate Fighting Championship, Victor Villalpando

Theses and Dissertations

Mixed Martial Arts is the fastest growing sport with many organizations worldwide. The biggest stage or biggest organization for Mixed Martial Arts is the Ultimate Fighting Championship (UFC). There are eight weight classes for men. The website: http://www.foxsports.com/ufc/stats provides data on fighters in all these categories. This data measures Striking Accuracy, Take downs, Reversals, Knockdowns, etc. in each category. It is interesting to understand and interpret all these numbers and study their relationships. Statistical tools like both parametric and nonparametric inference may give rise to such interpretations and provide explanations how the weight classes differ from one another. In this …

Analysis Of Artificial Neural Networks In The Diagnosing Of Breast Cancer Using Fine Needle Aspirates, Janette Vazquez

Theses and Dissertations

This thesis examines how Artificial Neural Networks can be used to classify a set of samples from a fine needle aspirate dataset. The dataset is composed of various different attributes, each of which are used to come to the conclusion as to whether a sample is benign or malignant. To automate the process of analyzing the various attributes and coming to a correct prediction, a neural network was implemented. First, a Feedforward Neural Network was trained with the dataset using a Backpropagation training method and an activation sigmoid function with one hidden layer in the architecture of the network. After …

Towards Building A Computer-Aided Accreditation System, Emmanuel Alejandro Santillana Fayett

Theses and Dissertations

Accreditation is a big subject. What is accreditation? Why should it matter to us? How many types of accreditation can an institution have? Is the government involved? What issues are present? How can we improve the accreditation process? All these questions will be covered in this paper. In addition, I will build towards a software that will apply the most important points in this paper, like applying the mission, objectives, and outcomes expected from the students in the form of a syllabus. This will help the faculty with the accreditation process and will help the students know what is expected …

Does Lowest Order Perturbation Of Λ Affect Ligo Detection?, Shuang Liang

Theses and Dissertations

Gravitational waves under the effect of a positive Cosmological Constant Λ has been a long time puzzle. To date, the full wave solution is still under construction, while attempts have been made to solve the linearized equations. We present a detailed derivative of the linearized Einstein’s Equations in a covariant manner, then solve for a lowest order perturbation in Λ. Results suggest that the Cosmological Constant has a large contribution to the phase of gravitational waves, which might be detectable.

Synthesis And Characterization Of Imidazolo 3,1- Tetrakis (N-Phenylacetamidato) Dirhodium (Ii) And A Crystallographic Study Of A Copper And Two Molybdenum Model Cofactors, Gabriel I.G. Thompson

Electronic Theses and Dissertations

Imidazole was reacted with 3,1-tetrakis (N-phenlyacetamidato) dirhodium (II) to explore the chemistry of asymmetric dirhodium catalysts. The imidazolo 3,1-tetrakis (Nphenlyacetamidato) dirhodium (II) complex was synthesized and then characterized by Nuclear Magnetic Resonance and Ultraviolet-Visible spectroscopies as well as by single crystal X-ray Diffraction. Additionally, one copper and two molybdenum model cofactors were characterized by XRD to better understand their structure/function relationships. NMR results gave evidence of the formation of the 3,1-imidazole complex, and UV-Vis indicated that even in large excess imidazole was coordinated only to one axial site. The structure of the 3,1-imidazole complex was confirmed by XRD with the …

Pore Characterizations And Distributions Within Niagaran – Lower Salina Reef Complex Reservoirs In The Silurian Northern Niagaran Pinnacle Reef Trend, Michigan Basin, Agam Arief Suhaimi

Masters Theses

The Northern Niagaran Pinnacle Reef Trend (NNPRT) has generated significant oil and gas production in Michigan. The best reservoir rock in the Reef Trend reservoirs are from porous and permeable dolomite of the Guelph Dolomite. Low-to-non reservoir limestone occurs interstratified with reservoir dolomite in many locations. This study utilizes available cores data, thin section Petrographic Image Analysis (PIA), Mercury Injection Capillary Pressure (MICP) and a newly developed Niagaran Reef depositional model (Rine, 2015) to characterize the distribution of pore geometry within each dolomitized Niagaran Reef Complex (Brown Niagaran – Lower Salina Group) reservoir facies and lithofacies. This study shows that …

The Precarious Health Of Young Mexican American Men In South Texas, Cameron County Hispanic Cohort, 2004–2015, Gordon P. Watt, Kristina Vatcheva, Derek M. Griffith, Belinda M. Reininger, Laura Beretta, Michael Fallon, Joseph B. Mccormick, Susan P. Fisher-Hoch

School of Mathematical & Statistical Sciences Faculty Publications

Introduction

Hispanic men have higher rates of illness and death from various chronic conditions than do non-Hispanic men. We aimed to characterize the health of Mexican American men living on the US–Mexico border in South Texas and elucidate indications of chronic disease in young men.

Methods

We sampled all male participants from the Cameron County Hispanic Cohort, an ongoing population-based cohort of Mexican Americans in Brownsville, Texas. We calculated descriptive statistics and stratified the sample into 3 age groups to estimate the prevalence of sociodemographic, behavioral, and clinical factors by age group and evaluated differences between age groups.

Results

Obesity …

Cytoplasmic Dynein Binding, Run Length, And Velocity Are Guided By Long-Range Electrostatic Interactions, Lin Li, Joshua Alper, Emil Alexov

Publications

Dyneins are important molecular motors involved in many essential biological processes, including cargo transport along microtubules, mitosis, and in cilia. Dynein motility involves the coupling of microtubule binding and unbinding to a change in the configuration of the linker domain induced by ATP hydrolysis, which occur some 25 nm apart. This leaves the accuracy of dynein stepping relatively inaccurate and susceptible to thermal noise. Using multi-scale modeling with a computational focusing technique, we demonstrate that the microtubule forms an electrostatic funnel that guides the dynein’s microtubule binding domain (MTBD) as it finally docks to the precise, keyed binding location on …

Accelerating Object Extraction And Detection Using A Hierarchical Approach With Shape Descriptors, Bassam Syed Arshad

Theses and Dissertations

Automatic object recognition is a fundamental problem in the fields of computer vision and machine learning, that has received a lot of research attention lately. Miniaturization and affordability, of both, high resolution digital cameras and advanced computing hardware, have further advanced the scope and applications of object recognition methods. While there are different methods, that build upon various low level features to construct object models, this work explores and implements the use of closed-contours as formidable object features. A hierarchical technique is employed to extract the contours, exploiting the inherent spatial relationships between the parent and child contours of an …

Stratigraphy Of The Upper Devonian-Lower Mississippian Michigan Basin: Review And Revision With An Emphasis On The Ellsworth Petroleum System, Bryan J. Currie

Masters Theses

Compression associated with the formation of the Transcontinental Arch and the Acadian Mountains initiated subsidence in the Michigan Basin and lead to a depositional switch in the Michigan Basin from an oxic shallow-water carbonate platform (Traverse Group and Squaw Bay Limestone) to a deep anaerobic sea floor and the beginning of Upper Devonian Antrim Shale. The vertical distribution of the different Upper Devonian-Lower Mississippian formations and members demonstrates large scale cycles of anaerobic-dysaerobic transitions attributed fluctuations in sea-level, different rates of subsidence and sediment influx triggered by different orogenic events to.

The regional understanding and the distribution of the different …

A Library Of Coumarin-Enaminone Chemodosimeters For The Detection Of Analytes, Aaron Berrell Davis

Dissertations

Many anions and metal ions are of biological and environmental importance. This work describes our attempts to synthesize molecular probes to specifically target cyanide, zinc, cadmium and mercury as these species can often result in negative effects to the environment and the human body.

The work in this dissertation, describes the synthesis of a family of coumarin-enamine chemodosimeters, in a straightforward synthetic procedure, the reaction between 7-(diethylamino)-4-hydroxycoumarin and a primary amine. The work presented in this dissertation demonstrates that these molecules can play dual roles and therefore the work is split into two distinct parts: Part 1 describes one role …

Analysis Of The Intricacies Of Substrate Recognition Of High Mobility Group Proteins And Aminoacyl-Trna Synthetases Using Non-Cognate Substrates, Douglas Van Iverson Ii

Dissertations

The studies presented in section 1 (Chapters I-IV) focus on the design and development of nucleic acid four-way junctions (4WJs) to target a member of the high mobility group (HMG) proteins, the proinflammatory cytokine high mobility group box 1 protein (HMGB1). In the present study, hybrid PNA-DNA 4WJs based on a model DNA 4WJ were constructed to improve the thermal stability of 4WJs while maintaining strong binding affinity toward HMGB1. An electrophoretic mobility shift assay (EMSA) was used to examine the binding affinity of an isolated DNA binding domain of HMGB1, the HMGB1 b-box (HMGB1b), toward a set of PNA-DNA …

Active Calculus 1.0, Matthew Boelkins, David Austin, Steven Schlicker

Open Textbooks

Active Calculus is different from most existing calculus texts in at least the following ways: the text is free for download by students and instructors in .pdf format; in the electronic format, graphics are in full color and there are live html links to java applets; the text is open source, and interested instructors can gain access to the original source files upon request; the style of the text requires students to be active learners — there are very few worked examples in the text, with there instead being 3-4 activities per section that engage students in connecting ideas, solving …

Monte Carlo Convergence Analysis For Anisotropic Sampling Power Spectra, Gurprit Singh, Wojciech Jarosz

Computer Science Technical Reports

Traditional Monte Carlo (MC) integration methods use point samples to numerically approximate the underlying integral. This approximation introduces variance in the integrated result, and this error can depend critically on the sampling patterns used during integration. Most of the well known samplers used for MC integration in graphics, e.g. jitter, Latin hypercube (n-rooks), multi-jitter, are anisotropic in nature. However, there are currently no tools available to analyze the impact of such anisotropic samplers on the variance convergence behavior of Monte Carlo integration. In this work, we propose a mathematical tool in the Fourier domain that allows analyzing the variance, and …

Utilizing Computed To Mography Image Features To Advance Prediction Of Radiation Pneumonitis, Shane P. Krafft

Dissertations and Theses (Open Access)

Improving outcomes for non-small-cell lung cancer patients treated with radiation therapy (RT) requires optimizing the balance between local tumor control and risk of normal tissue toxicity. In approximately 20% of patients, severe acute symptomatic lung toxicity, termed radiation pneumonitis (RP), still occurs. Identifying the individuals at risk of RP prior to or early during treatment offers tremendous potential to improve RT by providing the physician with information to assist in making clinical decisions that enhance therapy. Our central goal for this work was to demonstrate the potential gain in predictive accuracy of normal tissue complication probability models for RP by …

An Automated Syringe Pump System For Improving The Reproducibility Of Dynamic Hyperpolarized Mri Phantoms, Harlee G. Harrison

Dissertations and Theses (Open Access)

AN AUTOMATED SYRINGE PUMP SYSTEM FOR IMPROVING THE REPRODUCIBILITY OF DYNAMIC HYPERPOLARIZED MRI PHANTOMS

Harlee Grace Harrison, B.S.

Advisory Professor: James Bankson, Ph.D.

Magnetic Resonance Imaging (MRI) is a powerful tool in the diagnosis of cancer due to its ability to provide good soft tissue contrast and image resolution without the use of ionizing radiation. The use of hyperpolarized pyruvate as a contrast agent for tumor metabolism during MR scans has the potential to provide information about tumor metabolism in vivo that is not available from traditional imaging measurements or any other method. Hyperpolarization is achieved through dynamic nuclear polarization. …

Measurement Of The Electron Return Effect Using Presage Dosimeter, Gye Won Choi

Dissertations and Theses (Open Access)

MR-guided radiation therapy (MRgRT) provides benefits such as superior soft tissue contrast, no imaging dose, and functional imaging capacities, but it also has concerns to be addressed. The electron return effect (ERE) refers to dose enhancement at the interface between different media, caused when radiation is delivered in the magnetic field. The ERE poses clinical concerns in MRgRT because it significantly enhances the dose at interfaces, and the intensity and pattern of the dose enhancement depends on many factors. The ERE results in a complex pattern of dose enhancement over a three-dimensional (3D) volume around tissue interfaces inside the patient …

Transitions Between Explosive And Effusive Phases During The Cataclysmic 2010 Eruption Of Merapi Volcano, Java, Indonesia, Katie Preece, Ralf Gertisser, Jenni Barclay, Sylvain J. Charbonnier, Jean-Christophe Komorowski, Richard A. Herd

School of Geosciences Faculty and Staff Publications

Transitions between explosive and effusive activity are commonly observed during dome-forming eruptions and may be linked to factors such as magma influx, ascent rate and degassing. However, the interplay between these factors is complex and the resulting eruptive behaviour often unpredictable. This paper focuses on the driving forces behind the explosive and effusive activity during the well-documented 2010 eruption of Merapi, the volcano’s largest eruption since 1872. Time-controlled samples were collected from the 2010 deposits, linked to eruption stage and style of activity. These include scoria and pumice from the initial explosions, dense and scoriaceous dome samples formed via effusive …

Water-Assisted Oxygen Activation During Selective Oxidation Reactions, Hung-Vu Tran, Hieu A. Doan, Bert D. Chandler, Lars C. Grabow

Chemistry Faculty Research

The selective functionalization of hydrocarbons with oxygen to produce valuable commodity chemicals is inherently challenging, because of the thermodynamic stability of the complete combustion products. Emerging green synthesis routes and sustainable energy production also rely on the success of selective oxidation reactions. As one of the unselective by-products, water is always present under reaction conditions and numerous studies indicate that the catalytic activity and selectivity of selective oxidation reactions may be tuned by judiciously controlling the water content during the reaction. Some experimentally verified examples include the preferential oxidation of carbon monoxide, direct hydrogen peroxide synthesis, propene epoxidation and alcohol …

Efficient Method For Calculations Of Ro-Vibrational States In Triatomic Molecules Near Dissociation Threshold: Application To Ozone, Alexander Teplukhin, Dmitri Babikov

Chemistry Faculty Research and Publications

A method for calculations of rotational-vibrational states of triatomic molecules up to dissociation threshold (and scattering resonances above it) is devised, that combines hyper-spherical coordinates, sequential diagonalization-truncation procedure, optimized grid DVR, and complex absorbing potential. Efficiency and accuracy of the method and new code are tested by computing the spectrum of ozone up to dissociation threshold, using two different potential energy surfaces. In both cases good agreement with results of previous studies is obtained for the lower energy states localized in the deep (∼10 000 cm−1) covalent well. Upper part of the bound state spectrum, within 600 cm−1 below dissociation …

Analysis Of Heme Iron Coordination In Dgcr8: The Heme-Binding Component Of The Microprocessor Complex, Hazel M. Girvan, Justin M. Bradley, Myles R. Cheesman, James R. Kincaid, Yilin Liu, Kazimierz Czarnecki, Karl Fisher, David Leys, Stephen E. J. Rigby, Andrew W. Munro

Chemistry Faculty Research and Publications

DGCR8 is the RNA-binding partner of the nuclease Drosha. Their complex (the “Microprocessor”) is essential for processing of long, primary microRNAs (pri-miRNAs) in the nucleus. Binding of heme to DGCR8 is essential for pri-miRNA processing. On the basis of the split Soret ultraviolet–visible (UV–vis) spectrum of ferric DGCR8, bis-thiolate sulfur (cysteinate, Cys^–) heme iron coordination of DGCR8 heme iron was proposed. We have characterized DGCR8 heme ligation using the Δ276 DGCR8 variant and combined electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), electron nuclear double resonance, resonance Raman, and electronic absorption spectroscopy. These studies indicate DGCR8 bis-Cys heme …

Modeling Internet Traffic Generations Based On Users And Activities For Telecommunication Applications, Sara Stoudt, Pamela Badian-Pessot, Blanche Ngo Mahop, Erika Earley, Jordan Menter, Yadira Flores, Danielle Williams, Weijia Zhang, Liza Maharjan, Yixin Bao, Laura Rosenbauer, Van Nguyen, Veena Mendiratta, Nessy Tania

Mathematics Sciences: Faculty Publications

A traffic generation model is a stochastic model of the data flow in a communication network. These models are useful during the development of telecommunication technologies and for analyzing the performance and capacity of various protocols, algorithms, and network topologies. We present here two modeling approaches for simulating internet traffic. In our models, we simulate the length and interarrival times of individual packets, the discrete unit of data transfer over the internet. Our first modeling approach is based on fitting data to known theoretical distributions. The second method utilizes empirical copulae and is completely data driven. Our models were based …

Environmental And Economic Implications Of Alternative Cruise Ship Pathways In Bermuda, Sarah E. Lester, Crow White, Kevin Mayall, Ryan K. Walter

Physics

As the cruise ship industry moves towards ever larger vessels, many tourist destinations are faced with dilemmas about how to accommodate the latest generation of ships, which require deeper and wider shipping pathways. The location of nearshore shipping channels traveled by cruise ships has important environmental and economic implications, as dredging larger lanes damages habitat, ship traffic produces sediment plumes that can smother adjacent sensitive habitats (e.g., coral reefs, seagrass beds), and dredging costs vary spatially. These environmental and economic costs should ideally be evaluated in the context of projected benefits from increased tourism. To inform decision-making on cruise ship …

Metrics Dashboard Services: A Framework For Analyzing Free/Open Source Team Repositories, Shilpika Shilpika, George K. Thiruvathukal, Nicholas Hayward, Konstantin Läufer

Computer Science: Faculty Publications and Other Works

No abstract provided.

Detector Characterization For Advanced Ligo, Thomas James Massinger

Dissertations - ALL

The first observing run of Advanced LIGO spanned 4 months, from September

12, 2015 to January 19, 2016, during which gravitational waves were directly detected

from two binary black hole systems, namely GW150914 and GW151226. Confident

detection of gravitational waves requires an understanding of instrumental noise transients

and artifacts that can reduce the sensitivity of a search for gravitational waves.

Studies of the quality of the detector data yield insights into the cause of instrumental

artifacts and data quality vetoes specific to a search are produced to mitigate the

effects of problematic data.

This dissertation provides an overview of the …

The Sluggs Survey: The Mass Distribution In Early-Type Galaxies Within Five Effective Radii And Beyond, Adebusola Alabi, Duncan Forbes, Aaron Romanowsky, Jean Brodie, Jay Strader, Joachim Janz, Vincenzo Pota, Nicola Pastorello, Christopher Usher, Lee Spitler, Caroline Foster, Zachary Jennings, Alexa Villaume, Sreeja Kartha

Faculty Publications

We study mass distributions within and beyond 5 effective radii (Re) in 23 early-type galaxies from the SAGES Legacy Unifying Globulars and Galaxies Survey, using their globular cluster (GC) kinematic data. The data are obtained with Keck/DEep Imaging Multi-Object Spectrograph, and consist of line-of-sight velocities for ∼3500 GCs, measured with a high precision of ∼15 km s−1 per GC and extending out to ∼13 Re. We obtain the mass distribution in each galaxy using the tracer mass estimator of Watkins et al. and account for kinematic substructures, rotation of the GC systems and galaxy flattening in our mass estimates. The …

Cufa: A More Formal Definition For Digital Forensic Artifacts, Vikram S. Harichandran, Daniel Walnycky, Ibrahim Baggili, Frank Breitinger

Electrical & Computer Engineering and Computer Science Faculty Publications

The term “artifact” currently does not have a formal definition within the domain of cyber/ digital forensics, resulting in a lack of standardized reporting, linguistic understanding between professionals, and efficiency. In this paper we propose a new definition based on a survey we conducted, literature usage, prior definitions of the word itself, and similarities with archival science. This definition includes required fields that all artifacts must have and encompasses the notion of curation. Thus, we propose using a new term e curated forensic artifact (CuFA) e to address items which have been cleared for entry into a CuFA database (one …