Physical Sciences and Mathematics Commons^™

Biomarkers Of Mild Cognitive Impairment And Alzheimer's Disease, Mark A. Lovell, Bert C. Lynn

Chemistry Faculty Patents

A method for quantifying a neurodegenerative disorder in a patient that includes obtaining a fluid sample from the subject; measuring a protein biomarker complex in said fluid sample and correlating the measurement with mild cognitive impairment or Alzheimer's disease status. The biomarkers include those that comprise at least one of a transthyretin protein and/or a prostaglandin-H2 D-isomerase protein, and at least one second, different protein selected from a transthyretin, prostaglandin-H2 D-isomerase, beta-2-microglobulin, cystatin C, superoxide dismutase [Cu—Zn], plasma retinol-binding protein, phosphatidylethanolamine-binding protein, carbonic anhydrase 2, prostaglandin-H2 D-isomerase, and/or serotransferrin protein.

Precatalysts Useful In Polyolefin Polymerization Reactions, Omofolami Tesileem Ladipo, Richard Eaves, Alexey Zazybin, Sean Parkin

Chemistry Faculty Patents

Compounds are provided that are useful as precatlysts in the polymerization of olefins such as ethylene and propylene. Other compounds are useful as intermediates in the production of such precatalysts.

Structure And Feedback In 30 Doradus. I. Observations, E. W. Pellegrini, J. A. Baldwin, Gary J. Ferland

Physics and Astronomy Faculty Publications

We have completed a new optical imaging and spectrophotometric survey of a 140 × 80 pc² region of 30 Doradus centered on R136, covering key optical diagnostic emission lines including Hα, Hβ, Hγ, [O III] λλ4363, 4959, 5007, [N II] λλ6548, 6584, [SII] λλ6717, 6731 [S III] λ6312, and in some locations [S III] λ9069. We present maps of fluxes and intensity ratios for these lines, and catalogs of isolated ionizing stars, elephant-trunk pillars, and edge-on ionization fronts. The final science-quality spectroscopic data products are available to the public. Our analysis of the new data finds that, while stellar …

Endothelial Cell Capture Of Heparin-Binding Growth Factors Under Flow, Bing Zhao, Changjiang Zhang, Kimberly Forsten-Williams, Jun Zhang, Michael Fannon

Ophthalmology and Visual Science Faculty Publications

Circulation is an important delivery method for both natural and synthetic molecules, but microenvironment interactions, regulated by endothelial cells and critical to the molecule's fate, are difficult to interpret using traditional approaches. In this work, we analyzed and predicted growth factor capture under flow using computer modeling and a three-dimensional experimental approach that includes pertinent circulation characteristics such as pulsatile flow, competing binding interactions, and limited bioavailability. An understanding of the controlling features of this process was desired. The experimental module consisted of a bioreactor with synthetic endothelial-lined hollow fibers under flow. The physical design of the system was incorporated …

Mapsplice: Accurate Mapping Of Rna-Seq Reads For Splice Junction Discovery, Kai Wang, Darshan Singh, Zheng Zeng, Stephen J. Coleman, Yan Huang, Gleb L. Savich, Xiaping He, Piotr Mieczkowski, Sara A. Grimm, Charles M. Perou, James N. Macleod, Derek Y. Chiang, Jan F. Prins, Jinze Liu

Computer Science Faculty Publications

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.

On The Disappearance Of The Broad-Line Region In Low-Luminosity Active Galactic Nuclei, Moshe Elitzur, Luis C. Ho

Physics and Astronomy Faculty Publications

The disk-wind scenario for the broad-line region (BLR) and toroidal obscuration in active galactic nuclei (AGNs) predicts the disappearance of the BLR at low luminosities. In accordance with the model predictions, data from a nearly complete sample of nearby AGNs show that the BLR disappears at luminosities lower than 5 × 10³⁹(M/10⁷ M_⊙)^2/3 erg s^-1, where M is the black hole mass. The radiative efficiency of accretion onto the black hole is ≲10^-3 for these sources, indicating that their accretion is advection-dominated.

Trans-Excision-Splicing Ribozyme And Methods Of Use, Stephen M. Testa, Michael A. Bell

Chemistry Faculty Patents

A group I intron-derived ribozyme which binds RNA in trans, excises an internal segment from within the RNA, and splices the remaining 5′ and 3′ ends of the RNA back together (the trans-excision-splicing reaction) is disclosed. The excised segment can be as long as 28 nucleotides, or more, and as little as one nucleotide. The ribozymes of the invention are easily modified to alter their sequence specificity. Such ribozymes represent a new and potentially powerful class of generally adaptable genetic therapeutics.

Thinking Outside The Curve, Part Ii: Modeling Fetal-Infant Mortality, Richard Charnigo, Lorie W. Chesnut, Tony Lobianco, Russell S. Kirby

Statistics Faculty Publications

BACKGROUND: Greater epidemiologic understanding of the relationships among fetal-infant mortality and its prognostic factors, including birthweight, could have vast public health implications. A key step toward that understanding is a realistic and tractable framework for analyzing birthweight distributions and fetal-infant mortality. The present paper is the second of a two-part series that introduces such a framework.

METHODS: We propose estimating birthweight-specific mortality within each component of a normal mixture model representing a birthweight distribution, the number of components having been determined from the data rather than fixed a priori.

RESULTS: We address a number of methodological issues related to our …

Thinking Outside The Curve, Part I: Modeling Birthweight Distribution, Richard Charnigo, Lorie W. Chesnut, Tony Lobianco, Russell S. Kirby

Statistics Faculty Publications

BACKGROUND: Greater epidemiologic understanding of the relationships among fetal-infant mortality and its prognostic factors, including birthweight, could have vast public health implications. A key step toward that understanding is a realistic and tractable framework for analyzing birthweight distributions and fetal-infant mortality. The present paper is the first of a two-part series that introduces such a framework.

METHODS: We propose describing a birthweight distribution via a normal mixture model in which the number of components is determined from the data using a model selection criterion rather than fixed a priori.

RESULTS: We address a number of methodological issues, including how the …

White Matter Diffusion Alterations In Normal Women At Risk Of Alzheimer's Disease, Charles D. Smith, Himachandra Chebrolu, Anders H. Andersen, David A. Powell, Mark A. Lovell, Shuling Xiong, Brian T. Gold

Neurology Faculty Publications

Increased white matter mean diffusivity and decreased fractional anisotropy (FA) has been observed in subjects diagnosed with mild cognitive impairment (MCI) and Alzheimer's disease (AD). We sought to determine whether similar alterations of white matter occur in normal individuals at risk of AD. Diffusion tensor images were acquired in 42 cognitively normal right-handed women with both a family history of dementia and at least one apolipoprotein E4 allele. These were compared with images from 23 normal women without either AD risk factor. Group analyses were performed using tract-based spatial statistics. Reduced FA was observed in the fronto-occipital and inferior temporal …

A Sea Change In Eta Carinae, Andrea Mehner, Kris Davidson, Roberta M. Humphreys, John C. Martin, Kazunori Ishibashi, Gary J. Ferland, Nolan R. Walborn

Physics and Astronomy Faculty Publications

Major stellar-wind emission features in the spectrum of η Car have recently decreased by factors of order 2 relative to the continuum. This is unprecedented in the modern observational record. The simplest, but unproven, explanation is a rapid decrease in the wind density.

Herschel Photometry Of Brightest Cluster Galaxies In Cooling Flow Clusters, A. C. Edge, J. B. R. Oonk, R. Mittal, S. W. Allen, S. A. Baum, H. Böhringer, J. N. Bregman, M. N. Bremer, F. Combes, C. S. Crawford, M. Donahue, E. Egami, A. C. Fabian, Gary J. Ferland, S. L. Hamer, N. A. Hatch, W. Jaffe, R. M. Johnstone, B. R. Mcnamara, C. P. O'Dea, P. Popesso, A. C. Quillen, P. Salomé, C. L. Sarazin, G. M. Voit, R. J. Wilman, M. W. Wise

Physics and Astronomy Faculty Publications

The dust destruction timescales in the cores of clusters of galaxies are relatively short given their high central gas densities. However, substantial mid-infrared and sub-mm emission has been detected in many brightest cluster galaxies. In this letter we present Herschel PACS and SPIRE photometry of the brightest cluster galaxy in three strong cooling flow clusters, A1068, A2597 and Zw3146. This photometry indicates that a substantial mass of cold dust is present (> 3×10⁷ M⊙) at temperatures significantly lower (20–28 K) than previously thought based on limited MIR and/or sub-mm results. The mass and temperature of the dust appear …

Herschel Observations Of Fir Emission Lines In Brightest Cluster Galaxies, A. C. Edge, J. B. R. Oonk, R. Mittal, S. W. Allen, S. A. Baum, H. Böhringer, J. N. Bregman, M. N. Bremer, F. Combes, C. S. Crawford, M. Donahue, E. Egami, A. C. Fabian, Gary J. Ferland, S. L. Hamer, N. A. Hatch, W. Jaffe, R. M. Johnstone, B. R. Mcnamara, C. P. O'Dea, P. Popesso, A. C. Quillen, P. Salomé, C. L. Sarazin, G. M. Voit, R. J. Wilman, M. W. Wise

Physics and Astronomy Faculty Publications

The question of how much gas cools in the cores of clusters of galaxies has been the focus of many, multiwavelength studies in the past 30 years. In this letter we present the first detections of the strongest atomic cooling lines, [Cii], [Oi] and [Nii] in two strong cooling flow clusters, A1068 and A2597, using Herschel-PACS. These spectra indicate that the substantial mass of cold molecular gas (> 10⁹ M_⊙) known to be present in these systems is being irradiated by intense UV radiation, most probably from young stars. The line widths of these FIR lines …

Herschel Images Of Ngc 6720: H2 Formation On Dust Grain, P. A. M. Van Hoof, G. C. Van De Steene, M. J. Barlow, K. M. Exter, B. Sibthorpe, T. Ueta, V. Peris, M. A. T. Groenewegen, J. A. D. L. Blommaert, M. Cohen, W. De Meester, Gary J. Ferland, W. K. Gear, H. L. Gomez, P. C. Hargrave, E. Huygen, R. J. Ivison, C. Jean, S. J. Leeks, T. L. Lim, G. Olofsson, E. T. Polehampton, S. Regibo, P. Royer, B. M. Swinyard, B. Vandenbussche, H. Van Winckel, C. Waelkens, H. J. Walker, R. Wesson

Physics and Astronomy Faculty Publications

Herschel PACS and SPIRE images have been obtained of NGC 6720 (the Ring nebula). This is an evolved planetary nebula with a central star that is currently on the cooling track, due to which the outer parts of the nebula are recombining. From the PACS and SPIRE images we conclude that there is a striking resemblance between the dust distribution and the H₂ emission, which appears to be observational evidence that H₂ forms on grain surfaces. We have developed a photoionization model of the nebula with the Cloudy code which we used to determine the physical conditions of …

A Bright Molecular Core In A Crab Nebula Filament, E. D. Loh, J. A. Baldwin, Gary J. Ferland

Physics and Astronomy Faculty Publications

In a sub-arcsec near-infrared survey of the Crab Nebula using the new Spartan Infrared Camera, we have found several knots with high surface brightness in the H2 2.12 μm line and a very large H₂ 2.12 μm to Brγ ratio. The brightest of these knots has an intensity ratio I(H₂ 2.12 μm)/I(Brγ) = 18 ± 9, which we show sets a lower limit on the ratio of masses in the molecular and recombination (i.e., ionized) zones M _mol/M _rec ≥ 0.9, and a total molecular mass within this single knot M _mol ≥ …

A Bare Molecular Cloud At Z ~ 0.45*, Therese M. Jones, Toru Misawa, Jane C. Charlton, Andrew C. Mshar, Gary J. Ferland

Physics and Astronomy Faculty Publications

Several neutral species (Mg I, Si I, Ca I, Fe I) have been detected in a weak Mg II absorption line system (W_r (2796) ~ 0.15 Å) at z ~ 0.45 along the sightline toward HE0001-2340. These observations require extreme physical conditions, as noted in D'Odorico. We place further constraints on the properties of this system by running a wide grid of photoionization models, determining that the absorbing cloud that produces the neutral absorption is extremely dense (~100-1000 cm^-3), cold (< 100 K), and has significant molecular content (~72%-94%). Structures of this size and temperature have been detected in Milky Way CO surveys and have been predicted in hydrodynamic simulations of turbulent gas. In order to explain the observed line profiles in all neutral and singly ionized chemical transitions, the lines must suffer from unresolved saturation and/or the absorber must partially cover the broad emission line region of the background quasar. In addition to this highly unusual cloud, three other ordinary weak Mg II clouds (within densities of ~0.005 cm^-3 and temperatures of ~10, 000 K) lie within 500 km s^-1 along the …

Luminosity-Variation Independent Location Of The Circum-Nuclear, Hot Dust In Ngc 4151, Jorg-Uwe Pott, Matt A. Malkan, Moshe Elitzur, Andrea M. Ghez, Tom M. Herbst, Rainer Schödel, Julien Woillez

Physics and Astronomy Faculty Publications

After recent sensitivity upgrades at the Keck Interferometer (KI), systematic interferometric 2 μm studies of the innermost dust in nearby Seyfert nuclei are within observational reach. Here, we present the analysis of new interferometric data of NGC 4151, discussed in context of the results from recent dust reverberation, spectro-photometric, and interferometric campaigns. The complete data set gives a complex picture, in particular the measured visibilities from now three different nights appear to be rather insensitive to the variation of the nuclear luminosity. KI data alone indicate two scenarios: the K-band emission is either dominated to ~90% by size …

Scalable Object Recognition Using Hierarchical Quantization With A Vocabulary Tree, David Nistér, Henrik Stewénius

Center for Visualization and Virtual Environments Faculty Patents

An image retrieval technique employing a novel hierarchical feature/descriptor vector quantizer tool—‘vocabulary tree’, of sorts comprising hierarchically organized sets of feature vectors—that effectively partitions feature space in a hierarchical manner, creating a quantized space that is mapped to integer encoding. The computerized implementation of the new technique(s) employs subroutine components, such as: A trainer component of the tool generates a hierarchical quantizer, Q, for application/use in novel image-insertion and image-query stages. The hierarchical quantizer, Q, tool is generated by running k-means on the feature (a/k/a descriptor) space, recursively, on each of a plurality of nodes of a resulting quantization level …

Effects Of Uvb-Induced Oxidative Stress On Protein Expression And Specific Protein Oxidation In Normal Human Epithelial Keratinocytes: A Proteomic Approach, Marzia Perluigi, Fabio Di Domenico, Carla Blarzino, Cesira Foppoli, Chiara Cini, Alessandra Giorgi, Caterina Grillo, Federico De Marco, D. Allan Butterfield, Maria E. Schininà, Raffaella Coccia

Chemistry Faculty Publications

BACKGROUND: The UVB component of solar ultraviolet irradiation is one of the major risk factors for the development of skin cancer in humans. UVB exposure elicits an increased generation of reactive oxygen species (ROS), which are responsible for oxidative damage to proteins, DNA, RNA and lipids. In order to examine the biological impact of UVB irradiation on skin cells, we used a parallel proteomics approach to analyze the protein expression profile and to identify oxidatively modified proteins in normal human epithelial keratinocytes.

RESULTS: The expression levels of fifteen proteins - involved in maintaining the cytoskeleton integrity, removal of damaged proteins …

Kentucky River Watershed Watch: A Summary Of Volunteer Water Quality Sampling Efforts In The Kentucky River Basin From 1999 To 2009, Malissa Mcalister, Madhu Akasapu, Ben Albritton, Lindell Ormsbee, Dan Carey

Kentucky River Watershed Watch

No abstract provided.

High-Excitation Emission Lines Near Eta Carinae, And Its Likely Companion Star, Andrea Mehner, Kris Davidson, Gary J. Ferland, Roberta M. Humphreys

Physics and Astronomy Faculty Publications

In order to study the distribution of gas and ionizing radiation around η Car and their implications for its likely companion star, we have examined high-excitation emission lines of [Ne III], [Fe III], etc., in spectra obtained with the Hubble Space Telescope/Space Telescope Imaging Spectrograph instrument during 1998-2004. Our principal results, some of them unexpected, are as follows. (1) The high-excitation fluxes varied systematically and non-trivially throughout η Car's 5.5 year spectroscopic cycle. Instead of rising to a plateau after the 1998 ''event,'' they changed continuously with a maximum in mid-cycle. (2) At one significant location a brief, strong …

Methods And Kit For Determination Of Prostacyclin In Plasma, Sylvia Daunert, Michael Poon, Urvee Desai, Sapna K. Deo

Chemistry Faculty Patents

A solid-phase immunoassay for 6-keto-Prostaglandin F_1α, the stable hydrolysis product of prostacyclin (Prostaglandin I₂) is disclosed. Prostacyclin, a potent vasodilator with anti-platelet and anti-proliferative properties is an effective treatment for primary pulmonary hypertension and pulmonary arterial hypertension associated with scleroderma and scleroderma-like syndrome. Levels of 6-keto-Prostaglandin F_1α can be directly correlated with levels of prostacyclin. Therefore, 6-keto-Prostaglandin F_1α has become the indicator of choice to measure prostacyclin levels. The single step immunoassay for 6-keto-Prostaglandin F_1α uses the bioluminescent protein, aequorin as a label. Analyte-label conjugates were constructed by linking the carboxyl group of …

Soil- And Groundwater-Quality Data For An Abandoned Cattle And Hog Feedlot In Henderson County, Kentucky, E. Glynn Beck, James S. Dinger, Eugenia Pena-Yewtukhiw, John H. Grove

Information Circular--KGS

Groundwater samples collected from a livestock well in southwestern Henderson County, Ky., contained nitrate-N concentrations greater than 20 mg/L, two times the U.S. Environmental Protection Agency’s maximum contaminant level. The well is located in an abandoned cattle and hog feedlot. The feedlot is located in an upland bedrock setting with Pleistocene loess overlying Pennsylvanian bedrock. One hundred twenty-one soil cores were collected to better define the areal extent of organic-rich soil believed to be the source of the elevated nitrate-N in the groundwater. Cores were collected on 25-ft centers to a depth of 4 ft below the land surface. Soil …

Assessment Of Row Crop, Alfalfa, And Pasture Field Practices On Groundwater Quality In An Upland Bedrock Setting, Henderson County, Kentucky: Report Of Soil- And Water-Quality Data, E. Glynn Beck, James S. Dinger, John H. Grove, Eugenia Pena-Yewtukhiw

Information Circular--KGS

An assessment of how present agricultural practices have influenced shallow groundwater and soil quality was conducted on a 540-acre farm in north-central Henderson County. Groundwater- and soil-quality data were collected from row crop (corn and soybean), alfalfa, and pasture fields. In addition to the field settings, groundwater and soil data were collected from the existing farmyard and an abandoned feedlot. Groundwater samples were analyzed for pH, specific conductance, temperature, oxidation-reduction potential, metals, anions, nutrients, herbicides, and various isotopes. Soil samples were analyzed for pH, bioavailable phosphorus, potassium, calcium, magnesium, zinc, organic matter, total nitrogen, and inorganic nitrogen (nitrate-N). Soil- and …

Assessment Of Groundwater Quality In An Abandoned Feedlot, Henderson County, Kentucky: Data Report, E. Glynn Beck, James S. Dinger, John Grove, Eugenia Pena-Yewtukhiw

Information Circular--KGS

A three-phase project investigated the influence of past and present agricultural practices on groundwater resources in the Western Kentucky Coal Field. Phase II concentrated on past practices, specifically those associated with an abandoned dairy feedlot and an old homestead. Results of phase II analyses are presented in this report.

Sources And Occurrences Of Nonpoint-Source Chemicals In Groundwater, Jackson Purchase Region, Kentucky: Data Report, E. Glynn Beck

Information Circular--KGS

Groundwater from the Jackson Purchase Region was sampled to investigate possible contamination by nonpoint-source chemicals. Conclusions drawn from the resulting data and methodology can be found in “Sources and Occurrences of Nonpoint-Source Chemicals in Groundwater, Jackson Purchase Region, Kentucky,” Kentucky Geological Survey Report of Investigations 22 (series 12), by R.S. Fisher and E.G. Beck.

Remaining Resources Of The Springfield Coal, Gerald A. Weisenfluh

Map and Chart--KGS

Historically, the Springfield (W. Ky. No. 9) opal bed has been the leading source of coal production in the Western Kentucky Coal Field. With 2009 production more than 21 million tons and another 8 million tons of idle capacity, it is also the most important resource in the state of Kentucky. The Springfield coal is known for its lateral continuity in terms of both thickness and quality. It is a medium-sulfur product, desirable for power plants with sulfur-reduction capability, and has higher Btu values and lower chlorine contents compared to other Illinois Basin areas north of Kentucky. It is estimated …

Assessment Of Groundwater Quality In A Remediated Abandoned Feedlot, Henderson County, Kentucky: Data Report, E. Glynn Beck, James S. Dinger, John Grove, Eugenia Pena-Yewtukhiw

Information Circular--KGS

A three-phase project investigated the influence of past and present agricultural practices on groundwater resources in the Western Kentucky Coal Field. Phase III concentrated on an abandoned dairy feedlot that had been remediated. Results of phase III analyses are presented in this report.

Sources And Occurrences Of Nonpoint-Source Chemicals In Groundwater, Jackson Purchase Region, Kentucky, R. Stephen Fisher, E. Glynn Beck

Report of Investigations--KGS

Nitrate concentrations that exceed U.S. Environmental Protection Agency drinking-water standards have been reported in Jackson Purchase Region groundwater since the 1960's. More recently, other nonpoint-source chemicals such as pesticides and volatile organic compounds have also been found. The sources of these chemicals and the pathways by which they reach domestic groundwater supplies must be determined to protect human health and to design effective land-management practices.

To investigate the occurrence of nonpoint-source chemicals in Jackson Purchase groundwater, 60 wells were selected on the basis of geographic location, hydrostratigraphic unit penetrated, and well type (bored or drilled); distances to row crops, known …

Ground Motion For The Maximum Credible Earthquake In Kentucky, Zhenming Wang

Report of Investigations--KGS

Although they are not frequent, earthquakes occur in and around Kentucky and pose certain hazards. Assessing seismic hazards is challenging, however, because of a lack of observations. The best estimates of ground motions that could be expected if the maximum credible earthquake occurs in or around Kentucky are depicted in maps showing peak ground acceleration and short-period (0.2 second) and long-period (1.0 second) response accelerations with 5 percent critical damping on hard rock. Another consideration for seismic safety is that the maximum credible earthquake has a long recurrenece interval, from 500 to 1,000 years in the New Madrid Seismic Zone …