Physical Sciences and Mathematics Commons^™

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.

Influence Of Irradiance And Iron On The Growth Of Colonial Phaeocystic Antarctica: Implications For Seasonal Bloom Dynamics In The Ross Sea, Antarctica, Nathan S. Garcia, Peter N. Sedwick, Giacomo R. Ditullio

OES Faculty Publications

Laboratory culture experiments were used to investigate the growth rate of colonial Phaeocystis anarctica as a function of irradiance and dissolved iron concentration. The experiments were conducted with a P. antarctica strain isolated from the southern Ross Sea, Antarctica, and made use of natural, low-iron (P. antarctica attained an average maximum cell-specific growth rate of 0.37 d^-1at an irradiance of 68 μE m^-2s^-1, above which growth rates decreased to 0.27 d^-1 at an irradiance of 314 μE m^-2s^-1. The dependence of growth rate on ambient dissolved iron concentration was …

Cross-Basin Comparison Of Phosphorus Stress And Nitrogen Fixation In Trichodesmium, Annette M. Hynes, P. Dreux Chappell, Sonya T. Dyhrman, Scott C. Doney, Eric A. Webb

OES Faculty Publications

We investigated the phosphorus (P) status and N₂ fixation rates of Trichodesmium populations from the North Pacific, western South Pacific, and western North Atlantic. Colonies of Trichodesmium were collected and analyzed for endogenous alkaline phosphatase (AP) activity using enzyme-labeled fluorescence ( ELF) and for nitrogenase activity using acetylene reduction. AP hydrolyzes dissolved inorganic phosphate (DIP) from dissolved organic phosphorus and is active in Trichodesmium colonies experiencing P stress. Across multiple stations in the subtropical North and South Pacific, there was low to moderate ELF labeling in Trichodesmium, although labeling was present in other taxa. In contrast, Trichodesmium ELF …

On The Interpretation Of Caribbean Paleo-Temperature Reconstructions During The Younger Dryas, Xiuquan Wan, Ping Chang, R. Saravanan, Rong Zhang, Matthew W. Schmidt

OES Faculty Publications

A conundrum exists regarding whether the sea-surface temperatures decreased or increased over the southern Caribbean and the western Tropical Atlantic region during the Younger Dryas when the North Atlantic cooled substantially and the Atlantic thermohaline circulation was weakened significantly. Despite the proximity of core locations, some proxy reconstructions record a surface cooling, while others indicate a warming. We suggest that this seemingly paradoxical finding may, at least partially, be attributed to the competing physical processes that result in opposing signs of temperature change in the region in response to weakened North Atlantic meridional overturning circulation. Our coupled ocean-atmosphere model experiments …

Cirene Air-Sea Interactions In The Seychelles-Chagos Thermocline Ridge Region, J. Vialard, J. P. Duvel, M. J. Mcphaden, P. Bouruet-Aubertot, B. Ward, E. Key, D. Bourras, R. Weller, P. Minnett, A. Weil

OES Faculty Publications

A field experiment in the southwestern Indian Ocean provides new insights into ocean-atmosphere interactions in a key climatic region.

Early Neoproterozoic Origin Of The Metazoan Clade Recorded In Carbonate Rock Texture: Reply, Fritz Neuweiler, Elizabeth C. Turner, David J. Burdige

OES Faculty Publications

We (Neuweiler et al., 2009) used scanning electron microscopic, fluorescence spectroscopic, fluorescence microscopic, and thin-section analytical work from modern, Cretaceous, Silurian, and early Neoproterozoic reefal material to make a geological case for an early Neoproterozoic origin of animals. In a modern analogue for ancient petrographic textures, degradative calcification of the extracellular collagenous matrix (ECM) of a modern siliceous sponge can be directly observed (Neuweiler et al., 2007).

Thin Layer Formation During Runaway Stratification In The Tidally Dynamic San Francisco Estuary, Alexander B. Bochdansky, Stephen M. Bollens

OES Faculty Publications

During the course of a year, we repeatedly collected high-resolution vertical fluorometer data timed to coincide with a specific state during the tidal cycle. The time (end of the ebb during neap tide) and the location (a deep channel half-way between the Golden Gate and the point of tidally averaged bottom salinity of 2 psu) were chosen with the goal to observe runaway stratification. We consistently found at least one pronounced chlorophyll peak in the water column; however, the vertical location of these peaks varied within three types including surface, bottom and subsurface maxima. Our results showed that heterogeneity of …

A Robust, Multisite Holocene History Of Drift Ice Off Northern Iceland: Implications For North Atlantic Climate, John T. Andrews, Dennis A. Darby, Dennis Eberle, Anne E. Jennings, Matthias Moros, Astrid Ogilvie

OES Faculty Publications

An important indicator of Holocene climate change is provided by evidence for variations in the extent of drift ice. A proxy for drift ice in Iceland waters is provided by the presence of quartz. Quantitative xray diffraction analysis of the < 2 mm sediment fraction was undertaken on 16 cores from around Iceland. The quartz weight (wt.)% estimates from each core were integrated into 250-yr intervals between −0.05 and 11.7 cal. ka BP. Median quartz wt.% varied between 0.2 and 3.4 and maximum values ranged between 2.8 and 11.8 wt.%. High values were attained in the early Holocene and minimum values were reached 6–7 cal. ka BP. Quartz wt.% then rose steadily during the late Holocene. Our data exhibit no correlation with counts on haematite-stained quartz (HSQ) grains from VM129-191 west of Ireland casting doubt on the ice-transport origin. A pilot study on the provenance of Fe oxide grains in two cores that cover the last 1.3 and 6.1 cal. ka BP indicated a large fraction of the grains between 1 and 6 cal. ka BP were from either Icelandic or presently unsampled sources. However, there was a dramatic increase in Canadian and Russian sources from the Arctic Ocean ~1 cal. ka BP. These data may indicate the beginning of an Arctic Oscillation-like climate mode.

Superfluid Turbulence From Quantum Kelvin Wave To Classical Kolmogorov Cascades, Jeffrey Yepez, George Vahala, Linda L. Vahala, Min Soe

Electrical & Computer Engineering Faculty Publications

The main topological feature of a superfluid is a quantum vortex with an identifiable inner and outer radius. A novel unitary quantum lattice gas algorithm is used to simulate quantum turbulence of a Bose-Einstein condensate superfluid described by the Gross-Pitaevskii equation on grids up to 5760³. For the first time, an accurate power-law scaling for the quantum Kelvin wave cascade is determined: k^-3. The incompressible kinetic energy spectrum exhibits very distinct power-law spectra in 3 ranges of k space: a classical Kolmogorov k^-(5/3) spectrum at scales greater than the outer radius of individual quantum vortex …

Quantum Algorithm For Bose-Einstein Condensate Quantum Fluid Dynamics: Twisting Of Filamentary Vortex Solitons Demarcated By Fast Poincare Recursion, Jeffrey Yepez, George Vahala, Linda L. Vahala

Electrical & Computer Engineering Faculty Publications

The dynamics of vortex solitons is studied in a BEC superfluid. A quantum lattice-gas algorithm (measurementbased quantum computation) is employed to examine the dynamical behavior vortex soliton solutions of the Gross-Pitaevskii equation (ø⁴ interaction nonlinear Schroedinger equation). Quantum turbulence is studied in large grid numerical simulations: Kolmogorov spectrum associated with a Richardson energy cascade occurs on large flow scales. At intermediate scales, a new k^-6 power law emerges, due to vortex filamentary reconnections associated with Kelvin wave instabilities (vortex twisting) coupling to sound modes and the exchange of intermediate vortex rings. Finally, at very small spatial scales a …

Electronic And Structural Properties Of Molybdenum Thin Films As Determined By Real Time Spectroscopic Ellipsometry, J. D. Walker, H. Khatri, V. Ranjan, Jian Li, R. W. Collins, S. Marsillac

Electrical & Computer Engineering Faculty Publications

Walker, J.D., Khatri, H., Ranjan, V., Li, J., Collins, R.W., & Marsillac, S. (2009). Electronic and structural properties of molybdenum thin films as determined by real-time spectroscopic ellipsometry. Applied Physics Letters, 94(14). doi: 10.1063/1.3117222

Potential Export Of Unattached Benthic Macroalgae To The Deep Sea Through Wind Driven Langmuir Circulation, H. M. Dierssen, Richard C. Zimmerman, Lisa A. Drake, David J. Burdige

OES Faculty Publications

Carbon export to the deep sea is conventionally attributed to the sinking of open ocean phytoplankton. Here, we report a Langmuir supercell event driven by high winds across the shallow Great Bahama Bank that organized benthic non-attached macroalgae, Colpomenia sp., into visible windrows on the seafloor. Ocean color satellite imagery obtained before and after the windrows revealed a 588 km² patch that rapidly shifted from highly productive macroalgae to bare sand. We assess a number of possible fates for this macroalgae and contend that this event potentially transported negatively buoyant macroalgae to the deep Tongue of the Ocean …

Anthropogenic Osmium In Rain And Snow Reveals Global-Scale Atmospheric Contamination, Cynthia Chen, Peter N. Sedwick, Mukul Sharma

OES Faculty Publications

Osmium is one of the rarer elements in seawater, with typical concentration of ≈10 x 10^-15 g g^-1 ( 5.3 x 10^-14 mol kg^-1. The osmium isotope composition (¹⁸⁷Os/¹⁸⁸Os ratio) of deep oceans is 1.05, reflecting a balance between inputs from continental crust (≈ 1.3) and mantle/cosmic dust (≈ 0.13). Here, we show that the ¹⁸⁷Os/¹⁸⁸Os ratios measured in rain and snow collected around the world range from 0.16 to 0.48, much lower than expected (>1), but similar to the isotope composition of ores (approximate to 0.2) …

Peptide Hydrolysis And The Uptake Of Dipeptides By Phytoplankton, Margaret R. Mulholland, Cindy Lee

OES Faculty Publications

Rates of peptide hydrolysis (using the fluorescent substrate, lucifer yellow anhydride-labeled tetra-alanine) and dipeptide uptake (using dually labeled, ¹⁵N and ¹³C, dialanine) were measured in phytoplankton cultures and in natural populations during algal blooms dominated by one or two taxa. During most sampling events, both peptide hydrolysis and dipeptide uptake were greatest in the size fraction containing the dominant phytoplankter, suggesting that phytoplankton contribute substantially to or may even dominate observed extracellular peptide hydrolysis and dipeptide uptake in the environment. These are the first data suggesting that dipeptides may be taken up directly by phytoplankton and this may …

Spatial Variation In Otolith Chemistry Of Atlantic Croaker Larvae In The Mid-Atlantic Bight, Jason J. Schaffler, Christian S. Reiss, Cynthia M. Jones

OES Faculty Publications

Larval Atlantic croaker Micropogonias undulatus (1 to 7 mm in standard length) were collected on the east coast of the United States from North Carolina to Delaware during 2000. We defined 3 water-mass boundaries for potential groups of spawning Atlantic croaker using temperature and salinity measured at each sampling station. We tested the hypothesis that distinct otolith chemistries existed among 3 groups of larval Atlantic croaker collected from these water masses using solution-based inductively coupled plasma-mass spectrometry. Multivariate analysis of variance indicated that otolith chemistry differed significantly among water masses. Using a quadratic discriminant function, we were able to correctly …

Geobiology: Evidence For Early Life On Earth And The Search For Life On Other Planets, Sherry L. Cady, Nora Noffke

OES Faculty Publications

Extensive research efforts in the subdisciplinary field of geobiology have focused on the interactions between Earth and life through time. As a consequence, gaps in our knowledge of Earth’s history are closing, and the search for life beyond Earth is expanding. A few examples of geobiology studies designed to advance our understanding of life on early Earth and to improve the chances of finding life on other planets are provided to highlight recent developments and research areas that are on the verge of new discoveries.

Predicting The Effect Of Wetland Restoration On Phosphorus Retention, Northwest Minnesota, Ryan J. Whittaker

Theses and Dissertations

Water quality in the Red River Valley and downstream in Lake Winnipeg has been diminishing due to excess nutrients from agriculture. One method to reduce nutrient loading to surface water is to create or restore wetlands in agricultural areas that drain cropped fields. It is commonly believed that wetlands improve water quality, but research has shown that restoring wetlands can actually release phosphorus (P) into solution. Reducing conditions caused by soil flooding can release Fe-bound P, since ferrous Fe is more soluble than ferric Fe. Little is known concerning how the soils in the Red River Valley will be affected …

Carbon Dioxide Flooding Induced Geochemical Changes In A Saline Carbonate Aquifer, Alyssa Boock

Theses and Dissertations

Carbon dioxide (CO2) has been injected into depleted oil reservoirs for enhanced oil recovery for several decades. Injection of CO2 into geologic formations in the Williston Basin is currently under consideration for long-term CO2 storage to reduce anthropogenic CO2 emissions to the atmosphere. The Madison Group in the North Dakota Williston Basin provides the greatest potential for geologic sequestration in either deep saline aquifers or depleted oil reservoirs. Little is known about the geochemical reactions that take place when supercritical carbon dioxide is injected into deep saline aquifers at geologic conditions similar to those found in potential sequestration units of …

Tailoring Local Conductivity By The Formation Of Ag Nanoclusters In Sio2 Xerogel Films, Ricky Caperton

Theses and Dissertations

Porous silicon dioxide thin films were produced via dip-coating and doped with Ag+ by adding AgNO3 to the dipping solution. Nanoparticles were formed within the pores of these films by UV exposure. Nanoparticle formation was confirmed by UV-visible spectroscopy and Transmission Electron Microscopy (TEM). Conductive Atomic Force Microscopy (CAFM) showed that the conductivity of the films decreased upon exposure to UV. This decrease in the conductivity is most likely due to the clustering of charge carriers. Initially, Ag+ ions are attached to negatively charged pore walls in a dense packing network. Upon UV exposure (125 mW @ 266 nm), the …

Noncovalent Interaction Of Platinum Planar Amine Compounds With Tryptophan: A Strategy To Interfere With P53-Mdm2 Interactions And Targeting Retroviral Zn Finger-Dna Interaction (Hiv Ncp7), Aaron Bate

Theses and Dissertations

Non-covalent interactions involving π-π stacking play an essential role in self-assembly and molecular recognition processes such as protein folding and DNA/RNA-protein selective recognition. The knowledge gained from these studies could provide insight into possible site recognition complexes, inhibiting or mimicking protein-protein or protein-DNA interactions. Based on molecular modeling as well as HOMO and LUMO energies, several chromophores were selected with a variety of ∆ε values (∆ε= |εHOMO,NAcTrp – εLUMO,chromophores|), high and low, to establish a correlating trend with the modeling and experimental data. The corresponding Pt(dien) compounds were synthesized and their ability to stack to N-acetyl tryptophan was evaluated by …

The Malina Oceanographic Expedition: How Do Changes In Ice Cover, Permafrost And Uv Radiation Impact On Biodiversity And Biogeochemical Fluxes In The Arctic Ocean?, Phillippe Massicotte, Rainer Amon, David Antoine, Philippe Archambault, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Malik, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Et. Al.

Faculty Publications

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables was measured across seven shelf–basin transects (south-north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll-a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a barge …

An Investigation Of Training In Creative Problem Solving And Its Relationship To Affective And Effective Idea Generation Of Entrepreneurial Learners, Charles Edward Leach

CCAC Theses and Dissertations

A significant proportion of the population engages in entrepreneurial behavior but many ventures do not survive beyond startup thus decreasing the pool of entrepreneurs available to contribute to the economy. Opportunity recognition is central to entrepreneurial success and the improper delineation of opportunities is cited as a leading cause of venture failure. There is a logical link between creativity, innovation and entrepreneurship. The goal of the researcher in this study was to explore the relationships between CPS training and the generation of entrepreneurial ideas.

The investigation studied the relationship of training in creative problem solving (CPS) to the opportunity identification …

Administrative Support For Online Teaching Faculty, John David Meyer

CCAC Theses and Dissertations

When administrators make decisions about the infrastructure support needs of a current or planned online teaching program, these decisions are often based on external expert advice rather than on the advice of experienced ground level faculty who are living with the dynamic nature of the technology and support needed to develop and maintain an effective online teaching program. Online teaching faculty are the best source of advice and information on what works and what does not.

Faculty at the Medical College of Georgia (MCG) were surveyed to find out what elements are important to the development of an effective online …

Section 508 Adherence By Industry Professionals: Improving Universal Design Through Training, Antonio Rincon

CCAC Theses and Dissertations

Section 508 of the Rehabilitation Act Amendments of 1998 took effect in 2001 and provides encouragement for universal design and compliance requirements to the federal sector for purchases that are accessible by people with disabilities. A division of General Dynamics Advanced Information Systems (GDAIS) is located in Pittsfield, Massachusetts and provides electronic and information technology solutions to federal customers in the defense, intelligence, and homeland security communities.

The general lack of training is a major factor for low compliance to Section 508. Improving awareness is important at GDAIS in order to increase its federal sales market share, develop new products …

A Model For The Evaluation Of Is/It Investments, Paul M. Tuten

CCAC Theses and Dissertations

Evaluation is a vital--yet challenging--part of IS/IT management and governance. The benefits (or lack therefore) associated with IS/IT investments have been widely debated within academic and industrial communities alike. Investments in information technology may or may not result in desirable outcomes. Yet, organizations must rely on information systems to remain competitive. Effective evaluation serves as one pathway to ensuring success. However, despite a growing multitude of measures and methods, practitioners continue to struggle with this intractable problem.

Responding to the limited success of existing methods, scholars have argued that academicians should first develop a better understanding of the process of …

An Investigation Of The Contributions Of Gender, Shopping Orientation, Online Experience, And Website's Interactive Features To Consumers' Intentions To Engage In Apparel E-Commerce Shopping, Amanda Wynn

CCAC Theses and Dissertations

E-commerce has experienced exponential growth within the last few years. The rapid growth of e-commerce has created a need to improve consumer acceptance and the consumer's intention to engage in e-commerce. Female consumers have yet to embrace e-commerce as readily as male consumers. Differences between male and female consumer shopping behavior were examined.

This study developed and empirically tested a model to predict the consumer's intention to engage in apparel e-commerce shopping based on the constructs of gender, shopping orientation, online experience, and Website's interactive features. Male and female U.S. consumers age 18 and older were surveyed to determine their …

Measurement And Simulation Of Laser-Induced Fluorescence From Nonequilibrium Ultracold Neutral Plasmas, A. Denning, Scott D. Bergeson, F. Robicheaux

Faculty Publications

We report measurements and simulations of laser-induced fluorescence in ultracold neutral plasmas. We focus on the earliest times, when the plasma equilibrium is evolving and before the plasma expands. In the simulation, the ions interact via the Yukawa potential in a small cell with wrapped boundary conditions. We solve the optical Bloch equation for each ion in the simulation as a function of time. Both the simulation and experiment show the initial increase in ion fluorescence, disorder-induced heating, and coherent oscillation of the rms ion velocity. Detailed modeling of the fluorescence signal makes it possible to use fluorescence spectroscopy to …

Author Entropy Vs. File Size In The Gnome Suite Of Applications, Jason R. Casebolt, Daniel P. Delorey, Charles D. Knutson, Jonathan Krein, Alexander C. Maclean

Faculty Publications

We present the results of a study in which author entropy was used to characterize author contributions per file. Our analysis reveals three patterns: banding in the data, uneven distribution of data across bands, and file size dependent distributions within bands. Our re- sults suggest that when two authors contribute to a file, large files are more likely to have a dominant author than smaller files.

Psoda: Open Source Phylogenetic Search And Dna Analysis, Mark J. Clement, Quinn O. Snell, Kenneth Sundberg

Faculty Publications

PSODA is an open source (GPL v2) sequence analysis package that implements sequence alignment using biochemical properties, phylogeny search with parsimony or maximum likelihood criteria and selection detection using biochemical properties (TreeSAAP ). PSODA is compatible with PAUP and the search algorithms are competitive with those in PAUP. PSODA also adds a basic scripting language to the PAUP block, making it possible to easily create advanced meta-searches. Because PSODA is open-source, we have also been able to easily add in advanced search techniques and characterize the benefits of various optimizations. PSODA is available for Macintosh OS X, Windows, and Linux.

Computer-Aided Reasoning About Knowledge And Justifications, Natalia Novak

Dissertations, Theses, and Capstone Projects

In the first Chapter we compare two well-known type-based computer frameworks for computer aided logical reasoning and verification: MetaPRL and Coq. In particular, we implement in MetaPRL the Calculus of Inductive Constructions which is the theoretical base for Coq. This work has shown the common points of MetaPRL and Coq, and revealed their principal methodological differences. A possible application of this work is a possibility to perform re-validation in MetaPRL of the existing library of Coq proofs which could help to build more trust in the latter.

Chapter 2 is the main contribution of the dissertation. It contains the description …