Digital Commons Network^™

Computational Design Of 3-Phosphoinositide Dependent Kinase-1 Inhibitors As Potential Anti-Cancer Agents, Mohamed Diwan Mohideen Abdulhameed

University of Kentucky Doctoral Dissertations

Computational drug design methods have great potential in drug discovery particularly in lead identification and lead optimization. 3-Phosphoinositide dependent kinase-1 (PDK1) is a protein kinase and a well validated anti-cancer target. Inhibitors of PDK1 have the potential to be developed as anti-cancer drugs. In this work, we have applied various novel computational drug design strategies to design and identify new PDK1 inhibitors with potential anti-cancer activity. We have pursued novel structure-based drug design strategies and identified a new binding mode for celecoxib and its derivatives binding with PDK1. This new binding mode provides a valuable basis for rational design of …

Eigenvalue Inequalities For A Family Of Spherically Symmetric Riemannian Manifolds, Julie Miker

University of Kentucky Doctoral Dissertations

This thesis considers two isoperimetric inequalities for the eigenvalues of the Laplacian on a family of spherically symmetric Riemannian manifolds. The Payne-Pólya-Weinberger Conjecture (PPW) states that for a bounded domain Ω in Euclidean space Rⁿ, the ratio λ1(Ω)/λ0(Ω) of the first two eigenvalues of the Dirichlet Laplacian is bounded by the corresponding eigenvalue ratio for the Dirichlet Laplacian on the ball B_Ωof equal volume. The Szegö-Weinberger inequality states that for a bounded domain Ω in Euclidean space Rⁿ, the first nonzero eigenvalue of the Neumann Laplacian μ1(Ω) is maximized on the ball B_{Ω …}

Visualization And Characterization Of Ultrasonic Cavitating Atomizer And Other Automotive Paint Sprayers Using Infrared Thermography, Nelson Kudzo Akafuah

University of Kentucky Doctoral Dissertations

The disintegration of a liquid jet emerging from a nozzle has been under investigation for several decades. A direct consequence of the liquid jet disintegration process is droplet formation. The breakup of a liquid jet into discrete droplets can be brought about by the use of a diverse forcing mechanism. Cavitation has been thought to assist the atomization process. Previous experimental studies, however, have dealt with cavitation as a secondary phenomenon assisting the primary atomization mechanism. In this dissertation, the role of the energy created by the collapse of cavitation bubbles, together with the liquid pressure perturbation is explicitly configured …

Statistical Methods In Microarray Data Analysis, Liping Huang

University of Kentucky Doctoral Dissertations

This dissertation includes three topics. First topic: Regularized estimation in the AFT model with high dimensional covariates. Second topic: A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data. Third topic: Normalization and analysis of cDNA microarray using linear contrasts.

Specific Heat Measurements On Strongly Correlated Electron Systems, Vijayalakshmi Varadarajan

University of Kentucky Doctoral Dissertations

Studies on strongly correlated electron systems over decades have allowed physicists to discover unusual properties such as spin density waves, ferromagnetic and antiferromagnetic states with unusual ordering of spins and orbitals, and Mott insulating states, to name a few.

In this thesis, the focus will be on the specific heat property of these materials exhibiting novel electronic ground states in the presence and absence of a field. The purpose of these measurements is to characterize the phase transitions into these states and the low energy excitations in these states. From measurements at the phase transitions, one can learn about the …

Rotational Quenching Rate Coefficients For H2 In Collisions With H2 From 2 To 10,000 K, T.-G. Lee, N. Balakrishnan, R. C. Forrey, P. C. Stancil, G. Shaw, D. R. Schultz, Gary J. Ferland

Physics and Astronomy Faculty Publications

Rate coefficients for rotational transitions in H₂ induced by H₂ impact are presented. Extensive quantum mechanical coupled-channel calculations based on a recently published (H₂)₂ potential energy surface were performed. The potential energy surface used here has been demonstrated to be more reliable than surfaces used in previous work. Rotational transition cross sections with initial levels of J≤8 were computed for collision energies ranging between 10^-4 and 2.5 eV, and the corresponding rate coefficients were calculated for the temperature range 2≤T≤10,000 K. In general, agreement with earlier calculations, which were limited to 100-6000 K, …

Differential Gene Expression Associated With Postnatal Equine Articular Cartilage Maturation, Michael J. Mienaltowski, Liping Huang, Arnold J. Stromberg, James N. Macleod

Veterinary Science Faculty Publications

BACKGROUND: Articular cartilage undergoes an important maturation process from neonate to adult that is reflected by alterations in matrix protein organization and increased heterogeneity of chondrocyte morphology. In the horse, these changes are influenced by exercise during the first five months of postnatal life. Transcriptional profiling was used to evaluate changes in articular chondrocyte gene expression during postnatal growth and development.

METHODS: Total RNA was isolated from the articular cartilage of neonatal (0-10 days) and adult (4-5 years) horses, subjected to one round of linear RNA amplification, and then applied to a 9,367-element equine-specific cDNA microarray. Comparisons were made with …

Focus On Rna Isolation: Obtaining Rna For Microrna (Mirna) Expression Profiling Analyses Of Neural Tissue, Wang-Xia Wang, Bernard R. Wilfred, Donald A. Baldwin, R. Benjamin Isett, Na Ren, Arnold J. Stromberg, Peter T. Nelson

Sanders-Brown Center on Aging Faculty Publications

MicroRNAs (miRNAs) are present in all known plant and animal tissues and appear to be somewhat concentrated in the mammalian nervous system. Many different miRNA expression profiling platforms have been described. However, relatively little research has been published to establish the importance of 'upstream' variables in RNA isolation for neural miRNA expression profiling. We tested whether apparent changes in miRNA expression profiles may be associated with tissue processing, RNA isolation techniques, or different cell types in the sample. RNA isolation was performed on a single brain sample using eight different RNA isolation methods, and results were correlated using a conventional …

Forage Spokesman Information, Clayton Geralds, Brady Jarvis

Kentucky Grazing Conference

No abstract provided.

Supplementing Cattle On Pasture: When, What And How Much?, Roy Burris

Kentucky Grazing Conference

The biggest advantage of maintaining cattle in the southeast is our ability to grow forages. It is generally an economic advantage to make maximum use of our forage and then supplement only when needed to meet our production goals. Judicious use of extra nutrition to grazing cattle can allow us to meet an objective which was best stated by Hoveland in 1986:

“Our objective is to maintain pasture at the highest quality that the environment will allow and efficiently convert as much of the pasture as possible into saleable animal product.”

Fencing And Watering Systems: Simpler Is Better, Ralph Quillin

Kentucky Grazing Conference

Sustainability and Grazing Management have taken on a new importance in the Americana farm community. The key components of the sustainable approach, profitability, agronomic, social and ecological responsibility and quality of life are becoming obtainable goals for this and future farming generations.

Practical Grazing Management And Feed Strategies To Alleviate Fescue Toxicosis, Glen Aiken

Kentucky Grazing Conference

Tall fescue grown in Kentucky is productive and persistent and that is why the state has 5 million acres of the stuff! Fescue has tolerances to drought, low fertility, and overgrazing that are attributed to a fungal endophyte which infects most tall fescue plants. Unfortunately, these advantages of tall fescue that livestock producers appreciate are offset by reduced calving percentages and calf weight gains caused by consumption of ergot alkaloids produced by the endophyte. Ergot alkaloids affect the physiology of cattle to cause elevation in body temperature, reduced sweating, retention of winter hair coats and uncontrollable growth of summer hair …

Herbicide Options For Pasture Weed Control, Jonathan D. Green

Kentucky Grazing Conference

Weeds have become more evident and problematic in grazed pastures as forage and livestock production systems have intensified. As animals consume the more desirable and palatable plant species in pastures, weedy plants become more abundant. In particular, animals tend to avoid grazing plants which contain thorns, prickly spines, or are unpalatable making some pastures less productive. In fact, many of the more problematic plants observed in Kentucky’s grazed pastures possess these characteristics including thistles, spiny amaranth (spiny pigweed), horsenettle, common cocklebur, tall ironweed, and buttercups.

Horse Pasture Monitoring Program: Results After Three Years, Tom Keene, S. Ray Smith

Kentucky Grazing Conference

Since 2001-2002 and the outbreak of Mare Reproductive Loss Syndrome (MLRS) the University of Kentucky has been developing stronger ties with the state’s equine industry. Approximately 30% of the foal crop was lost in the Central Bluegrass region during this period with a devastating impact on the industry. Traditionally, many Thoroughbred farms have functioned as independent entities, but MLRS helped them to realize that the University of Kentucky had tremendous amount of expertise that they could provide in the areas of animal health, forage management, and other areas. Initially, there were many theories as to the cause of MLRS with …

Forage Legumes Vs. Fertilizer Nitrogen, Garry D. Lacefield

Kentucky Grazing Conference

A few weeks after I started to work as a Forage Extension Specialist at the University of Kentucky, I heard my mentor and forage idol, Mr. Warren Thompson, speak on forage legumes. Warren, along with Dr’s. Tim Taylor and W.C. Templeton had pioneered the “Pasture Renovation Program” in Kentucky. In addition, Mr. Ed Smith had joined the team and collectively they developed the “Power-til Pasture Renovator.” Warren began his presentation by talking about Kentucky Forages pointing out we were so fortunate to have a good grass base and the opportunity to grow lots of legumes. He also talked about all …

Growth Of Grasses And Legumes: Impact On Grazing, S. Ray Smith

Kentucky Grazing Conference

The primary, cool season, perennial pasture grasses used in Kentucky are orchardgrass, bluegrass, and tall fescue. When not grazed or harvested, each of these passes through successive stages of growth in the spring: 1) leafy vegetative; 2) boot with seed heads enclosed in leaf sheath; 3) heading when the seed heads begin to show and, 4) bloom when pollination has occurred ( Figure 2). Since fiber and lignin contents increase steadily beyond the vegetative stage, while percent protein and digestibility decrease, a major goal in grazing management is to maintain these grasses in the leafy, vegetative stage at all times. …

Foreword And Kfgc Award Winners [2008], Garry D. Lacefield, Christi L. Forsythe

Kentucky Grazing Conference

No abstract provided.

Sensitivity Of Pdr Calculations To Microphysical Details, N. P. Abel, P. A. M. Van Hoof, G. Shaw, Gary J. Ferland, T. Elwert

Physics and Astronomy Faculty Publications

Our understanding of physical processes in photodissociation regions or photon-dominated regions (PDRs) largely depends on the ability of spectral synthesis codes to reproduce the observed infrared emission-line spectrum. In this paper, we explore the sensitivity of a single PDR model to microphysical details. Our calculations use the Cloudy spectral synthesis code, recently modified to include a wealth of PDR physical processes. We show how the chemical/thermal structure of a PDR, along with the calculated spectrum, changes when the treatment of physical processes such as grain physics and atomic/molecular rates are varied. We find a significant variation in the intensities of …

Agn Dusty Tori. I. Handling Of Clumpy Media, Maia Nenkova, Matthew M. Sirocky, Željko Ivezić, Moshe Elitzur

Physics and Astronomy Faculty Publications

According to unified schemes of active galactic nuclei (AGNs), the central engine is surrounded by dusty, optically thick clouds in a toroidal structure. We have recently developed a formalism that for the first time takes proper account of the clumpy nature of the AGN torus. We now provide a detailed report of our findings in a two-paper series. Here we present our general formalism for radiative transfer in clumpy media and construct its building blocks for the AGN problem-the source functions of individual dusty clouds heated by the AGN radiation field. We show that a fundamental difference from smooth density …

Use Of Boron Compounds To Precipitate Uranium From Water, David A. Atwood

Chemistry Faculty Patents

A method is provided for removing uranium from water. The method includes the mixing of a boron reagent with water contaminated with uranyl dication ions, leading to removal of the uranium from that water.

Tetrahymena Thermophila And Candida Albicans Group I Intron-Derived Ribozymes Can Catalyze The Trans-Excision-Splicing Reaction, P. Patrick Dotson Ii, Ashley K. Johnson, Stephen M. Testa

Chemistry Faculty Publications

Group I intron-derived ribozymes can catalyze a variety of non-native reactions. For the trans-excision-splicing (TES) reaction, an intron-derived ribozyme from the opportunistic pathogen Pneumocystis carinii catalyzes the excision of a predefined region from within an RNA substrate with subsequent ligation of the flanking regions. To establish TES as a general ribozyme-mediated reaction, intron-derived ribozymes from Tetrahymena thermophila and Candida albicans, which are similar to but not the same as that from Pneumocystis, were investigated for their propensity to catalyze the TES reaction. We now report that the Tetrahymena and Candida ribozymes can catalyze the excision of a …

Inversion Symmetry And Local Vs. Dispersive Interactions In The Nucleation Of Hydrogen Bonded Cyclic N-Mer And Tape Of Imidazolecarboxamidines, Sihui Long, Venkatraj Muthusamy, Peter G. Willis, Sean Parkin, Arthur Cammers

Chemistry Faculty Publications

Substitutional changes to imidazolecarboxamidine that preserved intermolecular hydrogen bonding in the solid state were used to study the relationship between packing and the hydrogen bond motif. Various motifs competed, but the most common imidazolecarboxamidine crystalline phase was a C_i symmetric dimer that established inversion centers by associating enantiomeric tautomers. Counter to intuition, the calculated gas-phase energies per molecule of the solid state atomic coordinates of the C_i dimer motifs were higher than those of the C₁ dimer, trimer, tetramer and tape motifs, while the packing densities of C_i dimers were found to be higher. This result …

Silylethynylated Heteroacenes And Electronic Devices Made Therewith, John E. Anthony, Marcia M. Payne, Susan A. Odom, Sean Parkin

Chemistry Faculty Patents

Novel silylethynylated heteroacenes and electronic devices made with those compounds are disclosed.

Adaptation And Mal-Adaptation To Ambient Hypoxia; Andean, Ethiopian And Himalayan Patterns, Guoqiang Xing, Clifford Qualls, Luis Huicho, Maria Rivera-Ch, Tsering Stobdan, Marat Slessarev, Eitan Prisman, Shoji Ito, Hong Wu, Angchuk Norboo, Diskit Dolma, Moses Kunzang, Tsering Norboo, Jorge L Gamboa, Victoria E. Claydon, Joseph Fisher, Guta Zenebe, Amha Gebremedhin, Roger Hainsworth, Ajay Verma, Otto Appenzeller

Physiology Faculty Publications

The study of the biology of evolution has been confined to laboratories and model organisms. However, controlled laboratory conditions are unlikely to model variations in environments that influence selection in wild populations. Thus, the study of "fitness" for survival and the genetics that influence this are best carried out in the field and in matching environments.

Therefore, we studied highland populations in their native environments, to learn how they cope with ambient hypoxia. The Andeans, African highlanders and Himalayans have adapted differently to their hostile environment.

Chronic mountain sickness (CMS), a loss of adaptation to altitude, is common in the …

Seismic Evaluation And Ranking Of Embankments For Bridges On And Over The Parkways In Western Kentucky, Han Shan Ding, Issam E. Harik, Ching Chiaw Choo

Kentucky Transportation Center Research Report

This study represents one of the Seismic Evaluation of Bridges on and over the Parkways in Western Kentucky investigative series. The effort is focused on the seismic vulnerability of bridge embankments against slope instability and liquefaction potential. An evaluation and rating procedure is presented to assist in identifying and prioritizing bridge embankments that are susceptible to failure due to projected seismic events.

To expedite the process, the algorithm titled Seismic Assessment System for Bridges (SASB) was programmed. Three hundred and eight-nine (389) bridge embankments (parallel bridges included) along the five western Kentucky parkways – Audubon, Pennyrile, Purchase, Western Kentucky, and …

Multi-Barge Flotilla Impact Forces On Bridges, Peng Yuan, Issam E. Harik, Michael T. Davidson

Kentucky Transportation Center Research Report

The current AASHTO equations for barge impact loads are based on scale models of barges, and may not accurately predict impact loads on bridge piers. The results of this study produce more realistic flotilla impact design loads, potentially leading to a reduction in construction costs of bridges over navigable waterways. The objectives of this study are: (1) To conduct theoretical finite element analysis on various types of flotillas impacting bridge piers. The flotillas and the respective barges will be of the type commonly traversing Kentucky’s waterways; and (2) To generate design equations for barge/flotilla impact loads. The study concludes the …

Agn Dusty Tori. Ii. Observational Implications Of Clumpiness, Maia Nenkova, Matthew M. Sirocky, Robert Nikutta, Željko Ivezić, Moshe Elitzur

Physics and Astronomy Faculty Publications

Clumpy torus models with N₀ ~ 5–15 dusty clouds along radial equatorial rays successfully explain AGN infrared observations. The dust has standard Galactic composition, with individual cloud optical depth τ_V ~ 30–100 at visual. The models naturally explain the observed behavior of the 10 μm silicate feature, in particular the lack of deep absorption features in AGNs of any type, and can reproduce the weak emission feature tentatively detected in type 2 QSOs. The clouds' angular distribution must have a soft edge, e.g., Gaussian, and the radial distribution should decrease as 1/r or 1/r^{2 …}

Caffeine Use: Association With Nicotine Use, Aggression, And Other Psychopathology In Psychiatric And Pediatric Outpatient Adolescents, Catherine A. Martin, Circe Cook, John H. Woodring, Gretchen Burkhardt, Greg Guenthner, Hatim A. Omar, Tom H. Kelly

Psychiatry Faculty Publications

The objective of this study was to evaluate the relationship between caffeine use, other drug use, and psychopathology in adolescents, using self-report measures. The study group consisted of 132 adolescents (average age 14.01 ± 2.06 years, 52% female, 19% African American, 5% other categories, 76% Caucasian). Most (47%) were recruited from a child psychiatry clinic with emphasis on youth with disruptive disorders, with 35% from an adolescent pediatric clinic with emphasis on prevention of risk-taking behavior and 18% from a pediatric clinic for families with limited resources. Subjects were consecutively recruited before or after regular clinic visits. Consent was obtained …

Silicates In Ultraluminous Infrared Galaxies, M. M. Sirocky, N. A. Levenson, Moshe Elitzur, H. W. W. Spoon, L. Armus

Physics and Astronomy Faculty Publications

We analyze the mid-infrared (MIR) spectra of ultraluminous infrared galaxies (ULIRGs) observed with the Spitzer Space Telescope's Infrared Spectrograph. Dust emission dominates the MIR spectra of ULIRGs, and the reprocessed radiation that emerges is independent of the underlying heating spectrum. Instead, the resulting emission depends sensitively on the geometric distribution of the dust, which we diagnose with comparisons of numerical simulations of radiative transfer. Quantifying the silicate emission and absorption features that appear near 10 and 18 μm requires a reliable determination of the continuum, and we demonstrate that including …

On The Optimality Of The Neighbor-Joining Algorithm, Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida

Statistics Faculty Publications

The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is "optimal" when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion. We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps R(n2)+ to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n ≤ 8. This requires the measurement of volumes of …