Physical Sciences and Mathematics Commons^™

Software Jimenae Allows Efficient Dynamic Simulations Of Boolean Networks, Centrality And System State Analysis, Martin Kaltdorf, Tim Breitenbach, Stefan Karl, Maximilian Fuchs, David Komla Kessie, Eric Psota, Martina Prelog, Edita Sarukhanyan, Regina Ebert, Franz Jakob, Gudrun Dandekar, Muhammad Naseem, Chunguang Liang, Thomas Dandekar

All Works

The signal modelling framework JimenaE simulates dynamically Boolean networks. In contrast to SQUAD, there is systematic and not just heuristic calculation of all system states. These specific features are not present in CellNetAnalyzer and BoolNet. JimenaE is an expert extension of Jimena, with new optimized code, network conversion into different formats, rapid convergence both for system state calculation as well as for all three network centralities. It allows higher accuracy in determining network states and allows to dissect networks and identification of network control type and amount for each protein with high accuracy. Biological examples demonstrate this: (i) High plasticity …

Design And Synthesis Of N-Succinyl-L,L-2.6-Diaminopimelic Acid Desuccinylase Inhibitors As Potential Novel Antibiotics, Thomas Dipuma

Master's Theses

N-Succinyl-L,L-2,6-Diaminopimelic Acid Desuccinylase (DapE) is a bacterial enzyme located in the lysine biosynthetic pathway of all Gram-negative and most Gram-positive species of bacteria including the notorious ESKAPE pathogens, or pathogenic strains of bacteria that have developed significant levels of resistance to currently available antibiotics. As a means to combat this challenge of growing antimicrobial resistance, we have identified the bacterial enzyme DapE as a conserved, novel enzymate target within these resistant bacterial strains,as DapE is responsible for the production of m-DAP and lysine which are ultimately employed in bacterial cell wall synthesis. The overall aim of this research is to …

A Review On Antibacterial Activity Of Nanoparticles, Badr-Edine Sadoq, Mohammed Reda Britel, Adel Bouajaj, Ramzi Maâlej, Ahmed Touhami, Marwa Abid, Hanen Douiri, Fakhita Touhami, Amal Maurady

Physics and Astronomy Faculty Publications and Presentations

The increasing resistance of bacteria to antibiotic agents is a main global public health problem. The use of nanoparticles is one of the promising ways to overcome microbial resistance to antimicrobial agents. Metal nanoparticles are increasingly used to target bacterial strains. Advances in nanotechnology, in particular the ability to synthesize nanoparticles of specific size and shape, are likely to lead to the development of new antibacterial agents. The antibacterial activities of nanoparticles are largely influenced by their sizes and large surface area/mass ratio. The antibacterial mechanisms of nanoparticles are poorly understood, but the currently accepted mechanisms include oxidative stress induction, …

Meet Me In The Middle: A Scoping Review On Understanding Adolescent Needs In Climate Communication, Gwendolyn Monica Hoff Anderson

Master's Projects and Capstones

The greatest effects of climate change are likely to be felt by youth. Young people are disproportionately affected by climate change due to their critical developmental stage and lack of power, and they experience both higher severity and prevalence of mental health issues related to climate change. Strong emotions have long been recognized as potential catalysts for action, or they may lead to paralyzing feelings of being overwhelmed. Climate communication is a critical tool to spark climate concern and encourage action. Activism, in turn, may help youth manage their anxiety about climate change. This scoping review examines emerging evidence on …

What Is The Mathematics In Mathematics Education?, Eva Thanheiser

Mathematics and Statistics Faculty Publications and Presentations

In this paper I tackle the question What is the mathematics in mathematics education? By providing three different frames for the word mathematics.

1.

Frame 1: Mathematics as an abstract body of knowledge/ideas, the organization of that into systems and structures, and a set of methods for reaching conclusions.

2.

Frame 2: Mathematics as contextual, ever present, as a lens or language to make sense of the world.

3.

Frame 3: Mathematics as a verb (not a noun), a human activity, part of one’s identity.

After introducing the frames and examining their distinction and their overlap, I discuss their implication …

The Loneliest Galaxies In The Universe: A Gama And Galaxy Zoo Study On Void Galaxy Morphology., Lori E. Porter

College of Arts & Sciences Senior Honors Theses

The large-scale structure (LSS) of the Universe is comprised of galaxy filaments, tendrils, and voids. The majority of the Universe’s volume is taken up by these voids, which exist as underdense, but not empty, regions. The galaxies found inside voids are void galaxies and expected to be some of the most isolated objects in the Universe. However, their standard morphology remains poorly studied. This study, using the Galaxy and Mass Assembly (GAMA) data and Galaxy Zoo survey, aims to remedy this. For completeness purposes, we use void galaxies identified by Alpaslan et al. (2014) with stellar masses (M*) of 10 …

The Novel Chlorination Of Zirconium Metal And Its Application To A Recycling Protocol For Zircaloy Cladding From Spent Nuclear Fuel Rods, Breanna K. Vestal

Doctoral Dissertations

A novel protocol has been developed for the chemical removal of zirconium alloy (Zircaloy) cladding from spent nuclear fuel rods and subsequent isolation and purification of nuclear-grade zirconium chloride derived therefrom. This protocol is based on the chemistry developed from two new scientific findings.

First, two new oxidative chlorination reactions have been discovered for zirconium metal. In both solvents, zirconium can be quantitatively chlorinated at temperatures less than 150°C, with the operative equations seen below. In sulfur monochloride, the reaction is completed in 2 – 4 hours via surface etching, exhibiting 0^th order kinetic behavior. The elemental sulfur byproduct …

Leveraging Aruco Fiducial Marker System For Bridge Displacement Estimation Using Unmanned Aerial Vehicles, Mohamed Aly

Computer Science and Engineering: Theses, Dissertations, and Student Research

The use of unmanned aerial vehicles (UAVs) in construction sites has been widely growing for surveying and inspection purposes. Their mobility and agility have enabled engineers to use UAVs in Structural Health Monitoring (SHM) applications to overcome the limitations of traditional approaches that require labor-intensive installation, extended time, and long-term maintenance. One of the critical applications of SHM is measuring bridge deflections during the bridge operation period. Due to the complex remote sites of bridges, remote sensing techniques, such as camera-equipped drones, can facilitate measuring bridge deflections. This work takes a step to build a pipeline using the state-of-the-art computer …

Subterraneans: A Regional Earth Dwelling For Comfort And Beauty, Isaak Benchoff

Architecture Undergraduate Honors Theses

Subterraneans is a study of an affordable, self-sufficient, sustainable, and dignified housing prototype for the region of Northwest Arkansas. It is a design process investigation based on the ideas of turning a local, sustainable material into affordable homes that can be built within a community of people sharing land and resources. The homes would utilize as many natural materials as possible to minimize the impact on the Earth and the cost to the owners.

Research looked at many different vernacular building precedents as well as the work done by contemporary design firms in the area of economical, low-impact, and passively …

The Safe And Effective Clinical Deployment Of Artificial Intelligence Tools, Kelly Nealon

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

18 million new cancer cases are diagnosed each year. Roughly half of these patients will be treated with radiation therapy, a complex technique that requires an interdisciplinary team of clinical staff and expensive equipment to be delivered safely. Cancer centers in Low- and Middle-Income Countries (LMIC) have an especially difficult time meeting the demands of radiation therapy as the complexity of treatment techniques increase, with only 37% of patients in these regions having access to the care they need. Artificial Intelligence (AI) based tools are being developed to simplify the treatment planning and quality assurance processes to increase the number …

Enestr¨Om-Kakeya Type Results For Complex And Quaternionic Polynomials, Matthew Gladin

Electronic Theses and Dissertations

The well known Eneström-Kakeya Theorem states that: for P(z)=∑_i=0ⁿ a_i zⁱ, a polynomial of degree n with real coefficients satisfying 0 ≤ a₀ ≤ a₁ ≤ ⋯≤ a_n, all zeros of P(z) lie in |z|≤1 in the complex plane. In this thesis, we will find inner and outer bounds in which the zeros of complex and quaternionic polynomials lie. We will do this by imposing restrictions on the real and imaginary parts, and on the moduli, of the complex and quaternionic coefficients. We also apply similar restrictions on complex polynomials with …

Design And Synthesis Of Novel Peptide-Metal Organic Frameworks, Moustafa Mahmoud Abdel Wahid Hamaad

Theses and Dissertations

Metal-organic frameworks (MOFs) are a class of crystalline porous materials with extended network structures formed through the reticular assembly of inorganic and organic molecular building blocks through strong coordination bonds. Compared to other porous materials, MOFs offer a high degree of structural diversity as their shape and pore size as well as functionality can tuned by the precise selection and design of their metal centers and organic struts. Due to their high surface areas, pore volumes, and the possibility of introduction of a myriad of chemical functionalities in their structures, MOFs have gained popularity for applications in many fields such …

Cross-Boundary Stewardship In Protected Area Centered Ecosystems: Perceptions Of Success And Characteristics Of Cooperative Engagement, Ryan D. Tarver

All Graduate Theses and Dissertations

The legal boundaries of protected areas, such as national parks are established and enforced by humans. Therefore, jurisdictional boundaries are ultimately have human meaning but not necessarily ecological relevance as natural phenomena such as watersheds and wildlife habitat often extend beyond a jurisdictional boundary. When considering the extent of natural system, we find that protected areas only make up part of a given ecosystem. The result is a large expanse of lands that fall under a various ownership types that include both publicly and privately designated tracts of land. This presents a management challenge when attempting to manage at the …

Rational Design, Synthesis And Biology Of Immunostimulatory Peptides, Nelson Casanova

Seton Hall University Dissertations and Theses (ETDs)

This dissertation reports the design, synthesis, characterization, and biological studies of three uniquely structured peptides, derived from ubiquitinated multiple myeloma proteins and ubiquitinated B7H6 ligand. The peptides were made into linear or branched shapes, with the branched peptides containing both major histocompatibility complex (MHC) class two and NKp30 binding motifs properties in one peptide. This results in an immunocytotoxic response (via cytokines and chemokines) of both natural killer cells and cytotoxic T lymphocytes (CTLs). These shapes were determined for data comparison but also to increase cytokine proliferation, the shapes help with healthy cell aviation. Thus, the linear monomer (contains a …

Deephtlv: A Deep Learning Framework For Detecting Human T-Lymphotrophic Virus 1 Integration Sites, Johnathan Jia, Johnathan Jia

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

In the 1980s, researchers found the first human oncogenic retrovirus called human T-lymphotrophic virus type 1 (HTLV-1). Since then, HTLV-1 has been identified as the causative agent behind several diseases such as adult T-cell leukemia/lymphoma (ATL) and a HTLV-1 associated myelopathy or tropical spastic paraparesis (HAM/TSP). As part of its normal replication cycle, the genome is converted into DNA and integrated into the genome. With several hundreds to thousands of unique viral integration sites (VISs) distributed with indeterminate preference throughout the genome, detection of HTLV-1 VISs is a challenging task. Experimental studies typically use molecular biology …

Soil Health And Remediation For Urban Gardens In Utah, Melissa Chilinski

All Graduate Plan B and other Reports

Urban environments are at an increased risk of soil contamination and poor soil health due to anthropogenic causes. As healthy farmland is developed, new urban farmers and gardeners are often left growing food on unwanted land with unknown histories of previous use. Varied research and methods for obtaining healthy soils can cause new growers to make decisions that negatively impact soil health and fertility, or on the other hand, conflicting information can cause individuals to become unnecessarily fearful of common soil contaminants and their effect on human health. Common soil contaminants, like trace metals (often referred to as heavy metals) …

Methods For Preparing And Characterizing Granular Materials For Electron Yield Measurements, Tom Keaton

All Graduate Plan B and other Reports

This work presents a systematic study on sample preparation methods and accuracy of electron yield (EY) measurements of highly insulating, granular materials. EY measurements of highly insulating materials, especially those with high EY, are challenging due to the effects of sample charging even for very low fluence electron probe beams. EY measurements of particulates are complicated by: (i) roughness effects from particulate size, shape, coverage, and compactness; (ii) particle adhesion; (iii) substrate contributions; and (iv) electrostatic repulsion and potential barriers from charged particles and substrates. Numerous methods were explored to rigidly affix particles on conducting substrates at varying coverages for …

Opportunities And Challenges For Cooperative Extension Becoming A Major Actor In Climate Change Mitigation And Adaptation, Dakoeta R. Pinto

All Graduate Theses and Dissertations

Addressing climate change in the United States is an increasingly complex issue that requires social and technological changes throughout the country, which the Cooperative Extension System (Extension) can influence. Based at land-grant universities, their goals are to bring relevant science and innovation to the people of the United States. For a successful low-carbon transition, there are certain elements of society that must be influenced by innovators like Extension. Extension’s historical roots in agriculture prevail today with most of their programming focusing on this sector. However, there is a movement within Extension to expand their programmatic efforts to address more contemporary …

A Generative Neural Network For Discovering Near Optimaldynamic Inductive Power Transfer Systems, Md Shain Shahid Chowdhury Oni

All Graduate Theses and Dissertations

An urgent need is to electrify transportation to lower carbon emissions into the atmosphere. Wireless charging makes electrical vehicles (EVs) more convenient and cheaper because energy is transferred to the vehicle without the need to plug it in. Dynamic wireless charging is particularly interesting, where the vehicle does not need to stop to receive the energy. This technology requires the EV and the roadway to include coils of wire, where the roadway coil is energized as the vehicle passes over it to induce an electrical current in the EV coil through electromagnetic induction. However, the problem of designing the two …

Rethinking Integrated Computer Science Instruction: A Cross-Context And Expansive Approach In Elementary Classrooms, Umar Shehzad, Jody E. Clarke-Midura, Kimberly Beck, Jessica F. Shumway, Mimi M. Recker

Publications

This study examines how a rural-serving school district aimed to provide elementary level computer science (CS) by offering instruction during students’ computer lab, a class taught by paraprofessional educators with limited background in computing. As part of a research practice partnership, cross-context mathematics and CS lessons were co-designed to expansively frame and highlight connections across – as opposed to integration within – the two subjects. Findings indicate that the paraprofessionals teaching the lessons generally reported positive experiences and understanding of content; however, those less comfortable with the content reported lower student interest. Further, most students who engaged with the lessons …