Physical Sciences and Mathematics Commons^™

Acrb Trimer Stability And Efflux Activity, Insight From Mutagenesis Studies, Linliang Yu, Wei Lu, Yinan Wei

Chemistry Faculty Publications

The multidrug transporter AcrB in Escherichia coli exists and functions as a homo-trimer. The assembly process of obligate membrane protein oligomers, including AcrB, remains poorly understood. In a previous study, we have shown that individual AcrB subunit is capable of folding independently, suggesting that trimerization of AcrB follows a three-stage pathway in which monomers first fold, and then assemble. Here we destabilized the AcrB trimer through mutating a single Pro (P223) in the protruding loop of AcrB, which drastically reduced the protein activity. We replaced P223 separately with five residues, including Ala, Val, Tyr, Asn, and Gly, and found that …

Exploration And Comparison Of Methods For Combining Population- And Family-Based Genetic Association Using The Genetic Analysis Workshop 17 Mini-Exome, David W. Fardo, Anthony R. Druen, Jinze Liu, Lucia Mirea, Claire Infante-Rivard, Patrick Breheny

Biostatistics Faculty Publications

We examine the performance of various methods for combining family- and population-based genetic association data. Several approaches have been proposed for situations in which information is collected from both a subset of unrelated subjects and a subset of family members. Analyzing these samples separately is known to be inefficient, and it is important to determine the scenarios for which differing methods perform well. Others have investigated this question; however, no extensive simulations have been conducted, nor have these methods been applied to mini-exome-style data such as that provided by Genetic Analysis Workshop 17. We quantify the empirical power and false-positive …

Critical Differences And Clues In Eta Car's 2009 Event, Andrea Mehner, Kris Davidson, John C. Martin, Roberta M. Humphreys, Kazunori Ishibashi, Gary J. Ferland

Physics and Astronomy Faculty Publications

We monitored Eta Carinae with the Hubble Space Telescope WFPC2 and Gemini GMOS throughout the 2009 spectroscopic event, which was expected to differ from its predecessor in 2003. Here we report major observed differences between events and their implications. Some of these results were quite unexpected. (1) The UV brightness minimum was much deeper in 2009. This suggests that physical conditions in the early stages of an event depend on different parameters than the "normal" inter-event wind. Extra mass ejection from the primary star is one possible cause. (2) The expected He II λ4687 brightness maximum was followed several weeks …

Bankfull Hydraulic Geometry Relationships For The Inner And Outer Bluegrass Regions Of Kentucky, Carmen Agouridis, Ruth Roseann Brockman, Stephen R. Workman, Lindell E. Ormsbee, Alex Fogle

Biosystems and Agricultural Engineering Faculty Publications

Bankfull hydraulic geometry relationships relate bankfull stream dimensions, such as cross-sectional area, width, mean depth, mean velocity, width to depth ratio, and slope to bankfull discharge. These relationships can assist in determining a design discharge for stream restoration and management projects. This study assessed 27 stable streams located in the Inner Bluegrass and Outer Bluegrass regions of Kentucky. Reaches were selected based on the presence of a U.S. Geological Survey gage, as well as other conditions such as presence of readily identifiable bankfull indicators, stability indices, and site accessibility. Bankfull channel dimensions and discharges were determined, and hydraulic geometry relationships …

Rna Oxidation Adducts 8-Ohg And 8-Oha Change With Aβ42 Levels In Late-Stage Alzheimer's Disease, Adam M. Weidner, Melissa A. Bradley, Tina L. Beckett, Dana M. Niedowicz, Amy L.S. Dowling, Sergey V. Matveev, Harry Levine, Mark A. Lovell, M. Paul Murphy

Sanders-Brown Center on Aging Faculty Publications

While research supports amyloid-β (Aβ) as the etiologic agent of Alzheimer's disease (AD), the mechanism of action remains unclear. Evidence indicates that adducts of RNA caused by oxidation also represent an early phenomenon in AD. It is currently unknown what type of influence these two observations have on each other, if any. We quantified five RNA adducts by gas chromatography/mass spectroscopy across five brain regions from AD cases and age-matched controls. We then used a reductive directed analysis to compare the RNA adducts to common indices of AD neuropathology and various pools of Aβ. Using data from four disease-affected brain …

Star Formation In Self-Gravitating Disks In Active Galactic Nuclei. I. Metallicity Gradients In Broad-Line Regions, Jian-Min Wang, Jun-Qiang Ge, Chen Hu, Jack A. Baldwin, Yan-Rong Li, Gary J. Ferland, Fei Xiang, Chang-Shuo Yan, Shu Zhang

Physics and Astronomy Faculty Publications

It has been suggested that the high metallicity generally observed in active galactic nuclei (AGNs) and quasars originates from ongoing star formation in the self-gravitating part of accretion disks around supermassive black holes (SMBHs). We designate this region as the star-forming (SF) disk, in which metals are produced from supernova explosions (SNexp) while at the same time inflows are driven by SNexp-excited turbulent viscosity to accrete onto the SMBHs. In this paper, an equation of metallicity governed by SNexp and radial advection is established to describe the metal distribution and evolution in the SF disk. We find that the metal …

Galaxy Formation In Heavily Overdense Regions At Z ~ 10: The Prevalence Of Disks In Massive Halos, Emilio Romano-Díaz, Jun-Hwan Choi, Isaac Shlosman, Michele Trenti

Physics and Astronomy Faculty Publications

Using a high-resolution cosmological numerical simulation, we have analyzed the evolution of galaxies at z ~ 10 in a highly overdense region of the universe. These objects could represent the high-redshift galaxies recently observed by the Hubble's Wide Field Camera 3 and could as well be possible precursors of QSOs at z ~ 6-7. To overcome the sampling and resolution problems in cosmological simulations of these rare regions, we have used the constrained realizations method. Our main result for z ~ 10 shows the high-resolution central region of 3.5 h^–1 Mpc radius in comoving coordinates being completely dominated by …

Structure And Feedback In 30 Doradus. Ii. Structure And Chemical Abundances, E. W. Pellegrini, J. A. Baldwin, Gary J. Ferland

Physics and Astronomy Faculty Publications

We use our new optical-imaging and spectrophotometric survey of key diagnostic emission lines in 30 Doradus, together with CLOUDY photoionization models, to study the physical conditions and ionization mechanisms along over 4000 individual lines of sight at points spread across the face of the extended nebula, out to a projected radius 75 pc from R136 at the center of the ionizing cluster NGC 2070. We focus on the physical conditions, geometry, and importance of radiation pressure on a point-by-point basis, with the aim of setting observational constraints on important feedback processes. We find that the dynamics and large-scale structure of …

N Ii Λλ5668−5712: A New Class Of Spectral Features In Eta Carinae, Andrea Mehner, Kris Davidson, Gary J. Ferland

Physics and Astronomy Faculty Publications

We report on the N II λλ5668-5712 emission and absorption lines in the spectrum of η Carinae. Spectral lines of the stellar wind regions can be classified into four physically distinct categories: (1) low-excitation emission such as H I and Fe II, (2) higher-excitation He I features, (3) the N II lines discussed in this paper, and (4) He II emission. These categories have different combinations of radial velocity behavior, excitation processes, and dependences on the secondary star. The N II lines are the only known features that originate in "normal" undisturbed zones of the primary wind but depend primarily …

Torus And Active Galactic Nucleus Properties Of Nearby Seyfert Galaxies: Results From Fitting Infrared Spectral Energy Distributions And Spectroscopy, Almudena Alonso-Herrero, Almeida Cristina Ramos, Rachel Mason, Ramos Andrés Asensio, Patrick F. Roche, Nancy A. Levenson, Moshe Elitzur, Christopher Packham, José Miguel Rodríguez Espinosa, Stuart Young, Tanio Díaz-Santos, Ana M. Pérez-García

Physics and Astronomy Faculty Publications

We used the CLUMPY torus models and a Bayesian approach to fit the infrared spectral energy distributions and ground-based high angular resolution mid-infrared spectroscopy of 13 nearby Seyfert galaxies. This allowed us to put tight constraints on torus model parameters such as the viewing angle i, the radial thickness of the torus Y, the angular size of the cloud distribution σ_torus, and the average number of clouds along radial equatorial rays N₀. We found that the viewing angle i is not the only parameter controlling the classification of a galaxy into type 1 or …

The Dark Side Of Qso Formation At High Redshifts, Emilio Romano-Díaz, Isaac Shlosman, Michele Trenti, Yehuda Hoffman

Physics and Astronomy Faculty Publications

Observed high-redshift QSOs, at z ~ 6, may reside in massive dark matter (DM) halos of more than 10¹² M_☉ and are thus expected to be surrounded by overdense regions. In a series of 10 constrained simulations, we have tested the environment of such QSOs. The usage of constrained realizations has enabled us to address the issue of cosmic variance and to study the statistical properties of the QSO host halos. Comparing the computed overdensities with respect to the unconstrained simulations of regions empty of QSOs, assuming there is no bias between the DM and baryon distributions, and …

Gene Set Analysis For Longitudinal Gene Expression Data, Ke Zhang, Haiyan Wang, Arne C. Bathke, Solomon W. Harrar, Hans-Peter Piepho, Youping Deng

Statistics Faculty Publications

BACKGROUND: Gene set analysis (GSA) has become a successful tool to interpret gene expression profiles in terms of biological functions, molecular pathways, or genomic locations. GSA performs statistical tests for independent microarray samples at the level of gene sets rather than individual genes. Nowadays, an increasing number of microarray studies are conducted to explore the dynamic changes of gene expression in a variety of species and biological scenarios. In these longitudinal studies, gene expression is repeatedly measured over time such that a GSA needs to take into account the within-gene correlations in addition to possible between-gene correlations.

RESULTS: We provide …

Biofilter Media Characterization Using Water Sorption Isotherms, Guilherme Del Nero Maia, George B. Day, Richard S. Gates, Joseph L. Taraba

Biosystems and Agricultural Engineering Faculty Publications

Compost material has been used extensively as a gas‐phase biofilter media for contaminant gas treatment in recent years. One of the biggest challenges in the use of this type of material is adequate control of compost moisture content and understanding its effect on the biofiltration process. The present work provides a methodology for characterization of biofilter media under low moisture conditions. Results indicated that low levels of equilibrium moisture content (EMC) were obtained for high levels of equilibrium relative humidity (ERH), i.e., 99% ERH produced EMC of approximately 20% (dry basis) at 25° C. Most bacteria struggle to survive in …

Numerical Modeling Of The Cn Spectral Emission Of The Stardust Re-Entry Vehicle, Alexandre Martin, Erin D. Farbar, Iain D. Boyd

Mechanical Engineering Faculty Publications

Re-entry vehicles designed for space exploration are usually equipped with thermal protection systems made of ablative material. In order to properly model and predict the aerothermal environment of the vehicle, it is imperative to account for the gases produced by ablation processes. In the case of charring ablators, where an inner resin is pyrolyzed at a relatively low temperature, the composition of the gas expelled into the boundary layer is complex and may lead to thermal chemical reactions that cannot be captured with simple ow chemistry models. In order to obtain better predictions, an appropriate gas ow chemistry model needs …

A Survey Of Molecular Hydrogen In The Crab Nebula, E. D. Loh, J. A. Baldwin, Z. K. Curtis, Gary J. Ferland, C. R. O'Dell, A. C. Fabian, Philippe Salomé

Physics and Astronomy Faculty Publications

We have carried out a near-infrared, narrowband imaging survey of the Crab Nebula, in the H₂ 2.12 μm and Brγ 2.17 μm lines, using the Spartan Infrared camera on the SOAR Telescope. Over a 2.8 × 5'.1 area that encompasses about 2/3 of the full visible extent of the Crab, we detect 55 knots that emit strongly in the H₂ line. We catalog the observed properties of these knots. We show that they are in or next to the filaments that are seen in optical-passband emission lines. Comparison to Hubble Space Telescope [S …

Physical Conditions In Barnard's Loop, Components Of The Orion-Eridanus Bubble, And Implications For The Warm Ionized Medium Component Of The Interstellar Medium, C. R. O'Dell, Gary J. Ferland, R. L. Porter, P. A. M. Vanhoof

Physics and Astronomy Faculty Publications

We have supplemented existing spectra of Barnard's Loop with high accuracy spectrophotometry of one new position. Cloudy photoionization models were calculated for a variety of ionization parameters and stellar temperatures and compared with the observations. After testing the procedure with recent observations of M43, we establish that Barnard's Loop is photoionized by four candidate ionizing stars, but agreement between the models and observations is only possible if Barnard's Loop is enhanced in heavy elements by about a factor of 1.4. Barnard's Loop is very similar in properties to the brightest components of the Orion-Eridanus Bubble and the warm ionized medium …

Emission From Hot Dust In The Infrared Spectra Of Gamma-Ray Bright Blazars, Michael P. Malmrose, Alan P. Marscher, Svetlana G. Jorstad, Robert Nikutta, Moshe Elitzur

Physics and Astronomy Faculty Publications

A possible source of γ-ray photons observed from the jets of blazars is inverse Compton scattering by relativistic electrons of infrared seed photons from a hot, dusty torus in the nucleus. We use observations from the Spitzer Space Telescope to search for signatures of such dust in the infrared spectra of four γ-ray bright blazars, the quasars 4C 21.35, CTA102, and PKS 1510-089, and the BL Lacertae object ON231. The spectral energy distribution (SED) of 4C 21.35 contains a prominent infrared excess indicative of dust emission. After subtracting a non-thermal component with a power-law spectrum, we fit a …

Dusty Tori Of Luminous Type 1 Quasars At Z ~ 2, Rajesh P. Deo, Gordon T. Richards, Robert Nikutta, Moshe Elitzur, Sarah C. Gallagher, Željko Ivezić, Dean Hines

Physics and Astronomy Faculty Publications

We present Spitzer infrared (IR) spectra and ultraviolet (UV) to mid-IR spectral energy distributions (SEDs) of 25 luminous type 1 quasars at z ~ 2. In general, the spectra show a bump peaking around 3 μm and the 10 μm silicate emission feature. The 3 μm emission is identified with hot dust emission at its sublimation temperature. We explore two approaches to modeling the SED: (1) using the CLUMPY model SED from Nenkova et al. and (2) the CLUMPY model SED and an additional blackbody component to represent the 3 μm emission. In the first case, …

Differential Gene Expression In Liver And Small Intestine From Lactating Rats Compared To Age-Matched Virgin Controls Detects Increased Mrna Of Cholesterol Biosynthetic Genes, Antony Athippozhy, Liping Huang, Clavia Ruth Wooton-Kee, Tianyong Zhao, Paiboon Jungsuwadee, Arnold J. Stromberg, Mary Vore

Statistics Faculty Publications

BACKGROUND: Lactation increases energy demands four- to five-fold, leading to a two- to three-fold increase in food consumption, requiring a proportional adjustment in the ability of the lactating dam to absorb nutrients and to synthesize critical biomolecules, such as cholesterol, to meet the dietary needs of both the offspring and the dam. The size and hydrophobicity of the bile acid pool increases during lactation, implying an increased absorption and disposition of lipids, sterols, nutrients, and xenobiotics. In order to investigate changes at the transcriptomics level, we utilized an exon array and calculated expression levels to investigate changes in gene expression …

Methods And Compositions For Treating Neurological Disorders, Tae H. Ji, Inhae Ji

Chemistry Faculty Patents

This disclosure relates to methods and compositions useful for the treatment of senile dementia. More particularly the disclosure relates to methods and compositions for the treatment of senile dementia related to diabetes.

A Computational Tool For Estimating Off-Target Application Areas In Agricultural Fields, Rodrigo S. Zandonadi, Joe D. Luck, Timothy S. Stombaugh, Michael P. Sama, Scott A. Shearer

Biosystems and Agricultural Engineering Faculty Publications

A computational method for estimating off-target application areas based on the machine-controlled section width and the field shape was developed and implemented in software with a graphical user interface written in the MatLab environment. The program, which is called the Field Coverage Analysis Tool (FieldCAT), includes three modules: data import, data preparation, and coverage analysis. Nine field boundaries were evaluated to test the software using controlled section widths from 0.5 to 27 m and various swath orientations. The estimated off-target application area from the widest section width varied from 9% to 24% depending on the shape and size of the …

A Deep Spectroscopic Study Of The Filamentary Nebulosity In Ngc 4696, The Brightest Cluster Galaxy In The Centaurus Cluster, R. E. A. Canning, A. C. Fabian, R. M. Johnstone, J. S. Sanders, C. S. Crawford, Gary J. Ferland, N. A. Hatch

Physics and Astronomy Faculty Publications

We present results of deep integral-field spectroscopy observations using high-resolution optical (4150–7200 Å) VLT VIsible MultiObject Spectrograph spectra of NGC 4696, the dominant galaxy in the Centaurus cluster (Abell 3526). After the Virgo cluster, this is the second nearest (z= 0.0104) example of a cool-core cluster. NGC 4696 is surrounded by a vast, luminous Hα emission-line nebula (L_Hα= 2.2 × 10⁴⁰ erg s⁻¹). We explore the origin and excitation of the emission-line filaments and find their origin consistent with being drawn out, under rising radio bubbles, into the intracluster medium as in …

Detection Of Optical Coronal Emission From 106-K Gas In The Core Of The Centaurus Cluster, R. E. A. Canning, A. C. Fabian, R. M. Johnstone, J. S. Sanders, C. S. Crawford, N. A. Hatch, Gary J. Ferland

Physics and Astronomy Faculty Publications

We report a detection (3.5 × 10³⁷± 5.6 × 10³⁶ erg s⁻¹) of the optical coronal emission line [Fe X] λ6374 and upper limits of four other coronal lines using high-resolution VIMOS spectra centred on NGC 4696, the brightest cluster galaxy in the Centaurus cluster. Emission from these lines is indicative of gas at temperatures between 1 × 10⁶−5 × 10⁶ K, so traces the interstellar gas in NGC 4696. The rate of cooling derived from the upper limits is consistent with the cooling rate from X-ray observations (∼10 M_⊙ yr …

Remaining Resources Of The Herrin Coal, Gerald A. Weisenfluh

Map and Chart--KGS

The Herrin coal bed (W. Ky. No. 11) is one of the most important coal resources in the Illinois Basin. To 2009, the Herrin coal had an estimated 10 million tons of production in Kentucky, and remained the second largest producer in the Western Kentucky Coal Field. The Herrin is known for its regionally extensive "blue band" rock parting, and, in Kentucky, its close association with the overlying Providence Limestone Member and Paradise coal (W. Ky. No. 11) (see, for example, Greb and others, 1992). To fact, the Herrin and Paradise coal beds were so closely spaced in some areas …

Mapped Karst Groundwater Basins In The Somerset 30 X 60 Minute Quadrangle, James C. Currens, Randall L. Paylor, Joseph A. Ray, Robert J. Blair

Map and Chart--KGS

No abstract provided.

Methionine-35 Of Aβ(1-42): Importance For Oxidative Stress In Alzheimer Disease, D. Allan Butterfield, Rukhsana Sultana

Chemistry Faculty Publications

Alzheimer disease (AD) is an age-related progressive neurodegenerative disorder. This devastating disease is characterized by the presence of senile plaques (SP), neurofibrillary tangles (NFTs), and loss of synapses. Amyloid beta-peptide 1–42 (Aβ(1–42)) is the main component of SP and is pivotal to AD pathogenesis. Brain of subjects with AD and arguably its earliest manifestation, mild cognitive impairment (MCI), demonstrate increased levels of oxidative stress markers. Our laboratory combined these two aspects of AD and MCI and proposed the Aβ(1–42)-associated free radical oxidative stress hypothesis to explain oxidative stress under which the MCI and AD brain exist …

Geology Of Cumberland Gap National Historical Park, Matthew M. Crawford, Hanna Hunsberger

Map and Chart--KGS

Cumberland Gap National Historical Park is located in parts of Kentucky, Virginia, and Tennessee. The park was authorized by President Franklin Roosevelt on June 11, 1940, and is now the largest historical park in the National Park System. It contains 24,000 acres along Cumberland Mountain near Ewing, Va., proceeding southwest toward Fern Lake in Tennessee, a distance of approximately 20 miles. The average width of the park is only 1.6 miles.

The park hosts a distinctive range of geologic processes and features. Unique structural geology, caves and karst, surface and groundwater erosion, and mass wasting are just a few of …

Kentucky Landscapes Through Geologic Time, Daniel I. Carey

Map and Chart--KGS

We now understand that the earth’s crust is broken up into a number of plates, some of continental size, and that these plates have been moving— centimeters a year—throughout geologic history, driven by the internal heat of the earth. This movement creates our mountain chains, earthquakes, geologic faults, and volcanoes. The theory of plate tectonics (from the Greek, tektonikos: pertaining to building) attempts to describe the process and helps explain the geology of Kentucky.

The geologic story of the rocks that form Kentucky’s landscape began a half billion years ago when the area was covered by water. Deposits of sand, …

Summary Of Kentucky River Watershed Watch 2011 Water Sampling Results, Kentucky Water Resources Research Institute

Kentucky River Watershed Watch

No abstract provided.

Herschel Observations Of The Centaurus Oluster - The Dynamics Of Cold Gas In A Cool Core, R. Mittal, C. P. O'Dea, Gary J. Ferland, J. B. R. Oonk, A. C. Edge, R. E. A. Canning, H. Russell, S. A. Baum, H. Böhringer, F. Combes, M. Donahue, A. C. Fabian, N. A. Hatch, A. Hoffer, R. Johnstone, B. R. Mcnamara, P. Salomé, G. Tremblay

Physics and Astronomy Faculty Publications

Brightest cluster galaxies (BCGs) in the cores of galaxy clusters have distinctly different properties from other low-redshift massive ellipticals. The majority of the BCGs in cool-core clusters show signs of active star formation. We present observations of NGC 4696, the BCG of the Centaurus galaxy cluster, at far-infrared (FIR) wavelengths with theHerschel space telescope. Using the PACS spectrometer, we detect the two strongest coolants of the interstellar medium, [C II] at 157.74 μm and [O I] at 63.18 μm, and in addition [N II] at 121.90 μm. The [C II] emission is extended over a region of 7 kpc …