Physical Sciences and Mathematics Commons^™

Post-Translational Modification Of Hypoxia-Inducible Factor Proteins By O-Linked -N-Acetylglucosamine In Breast Cancer Cells, Sean Williamson

Honors Theses

One of the hallmarks of cancer is its ability to adapt its metabolism to survive and thrive despite needing to overcome significant energy barriers and low oxygen settings in order to do so. The hypoxia-inducible factor proteins (HIFs) play important roles in the processes in which cancer fulfills these requirements. The O-linked -N-acetylglucoseamine (O-GlcNAc) can be attached to cellular proteins through O-glycosylation, and is thus considered a potential target for anticancer mechanisms. HIFs are composed of (HIF-1 and HIF-2, respectively) and subunits. This research found that O-GlcNAc is able to attach to and modify the HIF proteins. This was accomplished …

Studying The Effects Of Hydrogen Bonding In 1h-1,2,3-Triazole And Its Derivatives, Leah Alexandra Wallace

Honors Theses

1,2,3-triazole is used as a building block in many pharmaceutical drugs. The molecule has several derivatives that are useful in other areas including treating fungal infections and in dealing with some environmental issues. One of its derivatives, benzotriazole, is commonly used as an inhibitor of corrosion through the formation of a copper-benzotriazole complex. One area of particular interest in studying triazoles is the ability of these molecules to tautomerize. The hydrogen atom can move from the 1H position to the 2H position and this transfer is thought to be affected by solvent interactions. Here, we study the effects of hydrogen …

Clustered Networks Protect Cooperation Against Catastrophic Collapse, Gwen Spencer

Mathematics Sciences: Faculty Publications

Assuming a society of conditional cooperators (or moody conditional cooperators), this computational study proposes a new perspective on the structural advantage of social network clustering. Previous work focused on how clustered structure might encourage initial outbreaks of cooperation or defend against invasion by a few defectors. Instead, we explore the ability of a societal structure to retain cooperative norms in the face of widespread disturbances. Such disturbances may abstractly describe hardships like famine and economic recession, or the random spatial placement of a substantial numbers of pure defectors (or round-1 defectors) among a spatially-structured population of players in a laboratory …

The Fivethirtyeight R Package: ‘Tame Data’ Principles For Introductory Statistics And Data Science Courses, Albert Y. Kim, Chester Ismay, Jennifer Chunn

Mathematics Sciences: Faculty Publications

As statistics and data science instructors, we often seek to use data in our courses that are rich, real, realistic, and relevant. To this end we created the fivethirtyeight R package of data and code behind the stories and interactives at the data journalism website FiveThirtyEight.com. After a discussion on the conflicting pedagogical goals of "minimizing prerequisites to research" (Cobb 2015) while at the same time presenting students with a realistic view of data as it exists "in the wild," we articulate how a desired balance between these two goals informed the design of the package. The details behind this …

How Often Does The Best Team Win? A Unified Approach To Understanding Randomness In North American Sport, Michael J. Lopez, Gregory J. Matthews, Benjamin Baumer

Mathematics Sciences: Faculty Publications

Statistical applications in sports have long centered on how to best separate signal (e.g. team talent) from random noise. However, most of this work has concentrated on a single sport, and the development of meaningful cross-sport comparisons has been impeded by the difficulty of translating luck from one sport to another. In this manuscript, we develop Bayesian state-space models using betting market data that can be uniformly applied across sporting organizations to better understand the role of randomness in game outcomes. These models can be used to extract estimates of team strength, the between-season, within-season, and game-to-game variability of team …

The Dihedral Genus Of A Knot, Patricia Cahn, Alexandra Kjuchukova

Mathematics Sciences: Faculty Publications

Let K ⊂ S³ be a Fox p-colored knot and assume K bounds a locally flat surface S ⊂ B⁴ over which the given p-coloring extends. This coloring of S induces a dihedral branched cover X → S⁴ . Its branching set is a closed surface embedded in S⁴ locally flatly away from one singularity whose link is K. When S is homotopy ribbon and X a definite four-manifold, a condition relating the signature of X and the Murasugi signature of K guarantees that S in fact realizes the four-genus of K. We exhibit an infinite …

Action Of The Symmetric Group On The Free Lanke: A Catalanke Theorem, Tamar Friedmann, Philip Hanlon, Richard P. Stanley, Michelle L. Wachs

Mathematics Sciences: Faculty Publications

We initiate a study of the representation of the symmetric group on the multilinear component of an n-ary generalization of the free Lie algebra, which we call a free LAnKe. Our central result is that the representation of the symmetric group S_2n−1 on the multilinear component of the free LAnKe with S_2n−1 generators is given by an irreducible representation whose dimension is the nth Catalan number. This leads to a more general result on eigenspaces of a certain linear operator. A decomposition, into irreducibles, of the representation of S_3n−2 on the multilinear component the free LAnKe …

Strong Comparison Principle For P-Harmonic Functions In Carnot-Caratheodory Spaces, Luca Capogna, Xiaodan Zhou

Mathematics Sciences: Faculty Publications

We extend Bony’s propagation of support argument to C1 solutions of the nonhomogeneous subelliptic p-Laplacian associated to a system of smooth vector fields satisfying Hörmander’s finite rank condition. As a consequence we prove a strong maximum principle and strong comparison principle that generalize results of Tolksdorf.

Enabling Quantification Of Protein Concentration In Human Serum Biopsies Using Attenuated Total Reflectance – Fourier Transform Infrared (Atr-Ftir) Spectroscopy, Kate Spalding, Franck Bonnier, Clément Bruno, Hélène Blasco, Ruth E. Board, Isabelle Benz-De-Bretagne, Hugh Byrne, Holly J. Butler, Igor Chourpa, Pretheepan Radhakrishnan, Matthew J. Baker

Articles

Changes in protein concentrations within human blood are used as an indicator for nutritional state, hydration and underlying illnesses. They are often measured at regular clinical appointments and the current analytical process can result in long waiting times for results and the need for return patient visits. Attenuated total reflectance – Fourier transform infrared (ATR-FTIR) spectroscopy has the ability to detect minor molecular differences, qualitatively and quantitatively, in biofluid samples, without extensive sample preparation. ATR-FTIR can return an analytical measurement almost instantaneously and therefore could be deemed as an ideal technique for monitoring molecular alterations in blood within the clinic. …

Inverse Function: Pre-Service Teachers’ Techniques And Meanings, Teo Paoletti, Irma E. Stevens, Natalie L.F. Hobson, Kevin C. Moore, Kevin R. Laforest

Department of Mathematics Faculty Scholarship and Creative Works

Researchers have argued teachers and students are not developing connected meanings for function inverse, thus calling for a closer examination of teachers’ and students’ inverse function meanings. Responding to this call, we characterize 25 pre-service teachers’ inverse function meanings as inferred from our analysis of clinical interviews. After summarizing relevant research, we describe the methodology and theoretical framework we used to interpret the pre-service teachers’ activities. We then present data highlighting the techniques the pre-service teachers used when responding to tasks that involved analytical and graphical representations of functions and inverse functions in both decontextualized and contextualized situations and discuss …

A Covariational Understanding Of Function: Putting A Horse Before The Cart, Teo Paoletti, Kevin C. Moore

Department of Mathematics Faculty Scholarship and Creative Works

Supporting students developing understandings of function has been a notoriously elusive task in mathematics education. We present Thompson and Carlson’s (2017) description of a covariational meaning of function and provide an example of a student who maintains meanings compatible with this description. We use this student’s activity to illustrate nuances in a covariational meaning of function and to highlight how such meanings can be powerful for students. In doing so, we argue that a student who has develop meanings compatible with the covariational meaning of function presented by Thompson and Carlson has the foundational meanings needed to understand a formal …

Interlace Polynomials Of Friendship Graphs, Christina Eubanks-Turner, Aihua Li

Department of Mathematics Faculty Scholarship and Creative Works

In this paper, we study the interlace polynomials of friendship graphs, that is, graphs that satisfy the Friendship Theorem given by Erdös, Rényi and Sos. Explicit formulas, special values, and behaviour of coefficients of these polynomials are provided. We also give the interlace polynomials of other similar graphs, such as, the butterfly graph.

Tissue Mimicking Materials For Multi-Modality Breast Phantoms, G. Fiaschetti, Jacinta Browne, M. Cavagnaro, L. Farina, G. Ruvio

Conference Papers

The paper proposes two different Tissue Mimicking Material (TMM) techniques for the development of breast phantoms which are suitable for multi-modality imaging. In particular, the focus is on the behavior of dielectric and acoustic properties when fat, sodium chloride and sugar are added to the mixtures.

U.S. Geological Survey (Usgs) Topographic Map Collection, Kentucky Library Research Collections

Research Collections

This is a listing of the Topo maps housed in the KLRC; 7.5, 15 and 30 minute Kentucky and Boundary State Maps. These maps are helpful in genealogy to show how the landscape may have changed and they may have the locations of lost towns and cemeteries and indicate houses, barns, and other structures and how place names, roads, and streams changed over time.

Estimating The Optimal Cutoff Point For Logistic Regression, Zheng Zhang

Open Access Theses & Dissertations

Binary classification is one of the main themes of supervised learning. This research is concerned about determining the optimal cutoff point for the continuous-scaled outcomes (e.g., predicted probabilities) resulting from a classifier such as logistic regression. We make note of the fact that the cutoff point obtained from various methods is a statistic, which can be unstable with substantial variation. Nevertheless, due partly to complexity involved in estimating the cutpoint, there has been no formal study on the variance or standard error of the estimated cutoff point.

In this Thesis, a bootstrap aggregation method is put forward to estimate the …

Geophysical Investigations Of Southcentral Alaska, Felix Dziedzorm Ziwu

Open Access Theses & Dissertations

The Castle Mountain Fault (CMF) is the closest (<50 km) active fault to Anchorage, Alaska and is known to be capable of producing earthquakes of magnitude 7.0 â?? 7.1. While several mapping and trenching studies have been conducted along the CMF, geophysical investigations along the fault zone have been limited. We use over 700 recently collected, closely spaced gravity observations, in addition to existing regional gravity, aeromagnetic, seismic reflection, well log data, and geologic information, to develop new 2D models of the deeper structure of the CMF system. We developed four 2D integrated forward models across the Castle Mountain Fault. These models indicate differences between the western and eastern segments of the Castle Mountain Fault. The models show a thick sequence of Tertiary to Mesozoic sediments overlying the Peninsular terrane basement at varying depths within the area. We identified two main intrusive granitic rocks based on the varying susceptibilities. These granitic rocks share a possible fault contact with the Mesozoic sedimentary rocks. The model also shows that the CMF cuts through the Mesozoic sediments at depth. These rocks can create strong coupling along the fault and with the decreasing eastward angle of subduction, it is highly for fluid migration to the eastern edge of the subducting Yakutat microplate. Seismic events plotted along the profiles supports the Holocene motion along the western CMF (WCMF) and indicates a deeper extent of the CMF into the crust. The eastern CMF shows high rate of deformation based on the structures associated with the Mesozoic rocks.

Estimating Exploitation Rates In The Alabama Red Snapper Fishery Using A High-Reward Tag–Recapture Approach, Dana K. Sackett, Mattgew Catalano, J. Marcus Drymon, Sean P. Powers, Mark Albins

University Faculty and Staff Publications

Accurate estimates of exploitation are essential to managing an exploited fishery. However, these estimates are often dependent on the area and vulnerable sizes of fish considered in a study. High-reward tagging studies offer a simple and direct approach to estimating exploitation rates at these various scales and in examining how model parameters impact exploitation rate estimates. These methods can ultimately provide a better understanding of the spatial dynamics of exploitation at smaller local and regional scales within a fishery—a measure often needed for more site-attached species, such as the Red Snapper Lutjanus campechanus. We used this approach to tag 724 …

Walls And Wilderness: Analyzing The Impacts Of Border Barriers On U.S. Government Lands Of The United States - Mexico Border, Bryce Garrett Fugate

Open Access Theses & Dissertations

This paper seeks to describe the impacts of physical structures (fences, walls, barricades, etc.) on five selected areas of federally-protected U.S. lands along the U.S.-Mexico border that fall under the jurisdiction of the U.S. Department of the Interior. The five selected areas are: Santa Ana National Wildlife Refuge, Big Bend National Park, Organ Mountains - Desert Peaks National Monument, the Tohono O'odham Nation Reservation, and Organ Pipe Cactus National Monument. The research looks into the historical development of structures put in place on the U.S. - Mexico border, how they have become ever more ubiquitous in the region, and what …

Effects Of Increasing Deciduous Shrub Litter On Ecosystem Functioning In Alpine Tundra, Alejandro Emmanuel Benhumea

Open Access Theses & Dissertations

Rising temperatures due to global warming have resulted in rapid environmental changes in northern environments, resulting in an increase in deciduous shrub growth which has the potential to alter soil ecosystem properties and processes. In order to address some potential mechanisms by which shrubs alter ecosystem properties and processes, we designed an experiment which separated the effects of physical shrub presence and the effects of litter quantity in a fully factorial experiment on a north facing alpine plateau in the southwest Yukon, Canada. Specifically, we asked the following questions: What are effects of shrub litter, independent of shrub presence, on …

Deep Learning Models For Scoring Protein-Ligand Interaction Energies, Md Mahmudulla Hassan

Open Access Theses & Dissertations

In recent years, the cheminformatics community has seen an increased success with machine learning-based scoring functions for estimating binding affinities. The prediction of protein-ligand binding affinities is crucial for drug discovery research. Many physics-based scoring functions have been developed over the years. Lately, machine learning approaches are proven to boost the performance of traditional scoring functions. In this study, two scoring functions were developed; one is based on the Convolutional Neural Networks and the other one, called DLSCORE, is based on an ensemble of fully connected neural networks. Both the models were trained on the refined PDBbind (v.2016) dataset using …

Development Of A Dna Aptamer That Specifically Inhibits Human Carbonic Anhydrase Ii, Afroz Karim

Open Access Theses & Dissertations

Carbonic anhydrases (CA) are a family of enzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate. Carbonic anhydrase II is the most abundant protein in the cytosol. CA II inhibitors are emergent therapeutic targets for the development of antiglaucoma agents. Glaucoma is a disease affecting large number of people and characterized by an elevated intraocular pressure due to excessive secretion of aqueous humor. The enzyme CA II is responsible for the secretion of aqueous humor. Isoforms of CA II such as CA IV and CA I are present in many tissues and organs other than the …

Gravitational Analysis And Fault Identification Within An Active Rift Basin: The Mesilla Valley Bolson In Western Texas - Southern New Mexico, Jose Pablo Cervantes

Open Access Theses & Dissertations

The metropolitan region of El Paso Texas and Ciudad Juárez, Chihuahua, located within the northern Chihuahua Desert, contains approximately two million inhabitants. The two main aquifers that supply groundwater to this region are the Mesilla and Hueco Bolsons. Both bolsons have been tapped for decades without sustainable recharge. This study's purpose is to use geophysical methods coupled with published geochemical analyses to determine the structural and stratigraphic controls on the quality and quantity of groundwater in the southern Mesilla Bolson.

The Mesilla Bolson is one of many fault-controlled basins within the Rio Grande Rift - southern Basin and Range. Faults …

Variety-Dependent Physiologic And Biochemical Effects Of Copper Nano Particles On Rosie And Green Bok Choy (Brassica Rapa) Phenotypes, Chaoyi Deng

Open Access Theses & Dissertations

The effects of Cu-based nanoparticles (NPs) in bok choy (Brassica rapa subsp. chinensis) are unknown. In this study, Rosie and Green, two varieties of bok choy, with different anthocyanin content, were cultivated for 70 days in soil amended with copper oxide nanoparticles (nano CuO), bulk copper oxide (bulk CuO) and copper chloride (CuCl2) at 75, 150, 300 and 600 mg Cu/kg soil. Cu and essential elements in tissues, and relative chlorophyll content, were determined. In both varieties, nano CuO treatments caused significantly more Cu uptake in roots and shoots, compared with bulk CuO and ion CuCl2 (p ≤ 0.05). Additionally, …

Backward Elimination Algorithm For High Dimensional Variable Screening, Sophia Korkor Foli

Open Access Theses & Dissertations

In recent times, variable selection in high-dimensional data has become a challenging prob- lem. We investigate here a popular but classical variable screening method, the Back- ward Elimination (BE) in a high dimensional setup (small-n-large P). The BE method as a variable screening method reduces the dimension of small-n-large P data into a lower dimensional data and then established shrinkage methods such as: LASSO, SCAD and MCP can be applied directly. To overcome the problems in high dimensional data, Chen and Chen (2008) recently developed a family of Extended Bayesian Information Criterion (EBIC) which is consistent with finite sample properties …

Attributes Of The Fisher Valley Megaflap And Comparison To The Gypsum Valley Megaflap, Paradox Basin, Utah And Colorado: Implications For Controls On Megaflap Formation, Kate Grisi

Open Access Theses & Dissertations

Megaflaps are panels of steeply dipping to overturned strata that extend kilometers up the side of a salt diapir or equivalent weld. They often form important components of salt-diapir related hydrocarbon systems, though little is known about their geologic characteristics or how they form. In this study, I collected structural, stratigraphic, and sedimentologic data of the Fisher Valley megaflap and compared these attributes to the previous studied Gypsum Valley megaflap to test the differential sediment loading model proposed for initiation of megaflap formation. This model predicts that the sediment source proximal megaflap of Fisher Valley should have started rotation earlier, …

The Inverse And Direct Hofmeister Series Of Hen Egg White Lysozyme At Ph Below The Isoelectric Point (Pi) As Seen By Small Angle X-Ray Scattering(Saxs), Pawan Koirala

Open Access Theses & Dissertations

The structural changes of Hen Egg White Lysozyme (HEWL) in the intermediate stages leading up to Hofmeister anion-induced aggregation were measured using small-angle x-ray Scattering (SAXS). We used three concentrations of HEWL: 10mg/ml, 60mg/ml and 200mg/ml and two concentrations of salts: 0.1M and 1.0M, mostly in a Tris-buffer solution with a pH of 9.0. For 200mg/ml in Di-water solution, the scattering signal was best fit using an ellipsoidal form factor with equatorial radius of 28.4±0.1 Å and polar radius of 11.3±0.1 Å, and a screened Coulomb repulsive structure factor with an effective radius of 19.9±0.1 Å and protein surface charge …

Magnetic And Catalytic Properties Of Transition Metal Doped Mos2 Nanocrystals, Luis Martinez

Open Access Theses & Dissertations

Magnetism and catalytic activity of nanoscale layered two-dimensional (2D) transition metal dichalcogenides (TMDs) have gained an increasing research interest in the recent past. To broaden the current knowledge and understanding on this subject, in this work, together with my collaborators, I study the magnetic and electrocatalytic properties of hydrothermally grown pristine and transition metal doped (10% of Co, Ni, Fe and Mn) 2H-MoS2 nanosheets/nanocrystals (NCs), with the particle size of 25-30 nm. A broad range of experimental measurements such as x-ray diffraction, transmission electron microscopy, x-ray photo absorption spectroscopy, Raman spectroscopy, magnetic, catalytic and electron spin resonance have been employed …

Assessing The Hydrologic Impacts Of Extreme Rainfall And Land Use Change On A Semiarid Watershed, Tahneen Jahan Neelam

Open Access Theses & Dissertations

Abstract: Intense precipitation events increase the risk of flash floods in the New Mexico-Texas-Mexico border region. Compounding effects of changing land use and precipitation pattern can influence rainfall-runoff processes that govern flash flooding. Paradoxically, this southwestern semiarid watershed has substantial water conflict that may get worse by 2025 due to changing climate and increasingly competitive demands for over-appropriated water resources. Using Soil and Water Assessment Tool (SWAT), we investigate the impact of changes in precipitation intensity and land use on runoff and arroyo flows in the dry, mountainous terrains. The baseline watershed simulation model shows that for a statistically insignificant …

Exploring The Effects Of Zinc Nanoparticle Concentration, Antioxidant, And Media On Cilantro (Coriandrum Sativum), And Radish (Raphanus Sativus) Plants Growth, Venkata Laxma Reddy Pullagurala

Open Access Theses & Dissertations

Engineered nanomaterials (ENMs) have proven to be one of the emerging chemicals of concern in the contemporary times. Soil acts as one of the major sinks of these ENMs. Reports have shown that ENMs have varied effects on soil biota. Particularly, their effects on plants are inconsistent. Amongst these ENMs, ZnO nanoparticles (nZnO) are the fourth largest raw materials in the nanotechnology industry. Globally, it is estimated that around 34,000 tons of n ZnO are utilized per year. The nZnO exposure on terrestrial plants yielded both beneficial as well as detrimental effects. Recently, there is an emerging evidence about the …

Solvent And Concentration Effects Governing The Hierarchical Organization Of Asphaltenes: A Small-Angle X-Ray Scattering Study, Hasan Rejoanur Rahman

Open Access Theses & Dissertations

Asphaltenes are a group of planar molecules found in crude oil and are prone to aggregation which often causes blockage of pipes along the oil production stream resulting a huge economic downside. In an effort to understand the hierarchical organization of asphaltene in different solvents and concentrations, the solution structure of various asphaltene solutions were studied using small-angle x-ray scattering (SAXS). Solvents were chosen based on miscibility maps. Such maps are generated on the critical value of the solubility parameter difference between asphaltenes or asphaltene components, and a range of solvents. The critical factors that affect asphaltene and asphaltene component …