Physical Sciences and Mathematics Commons^™

Transport Of Nordic Seas Overflow Water Into And Within The Irminger Sea: An Eddy-Resolving Simulation And Observations, Xiaobiao Xu, W.J. Schmitz Jr., Harley E. Hulbert, Patrick J. Hogan, Eric P. Chassignet, H.M. Van Aken

Faculty Publications

Results from a climatologically forced, eddy-resolving (1/12 degrees) Atlantic simulation using the Hybrid Coordinate Ocean Model help clarify some presently unresolved connections between volume transports of Nordic Seas overflow water at key locations in the northernmost North Atlantic Ocean. The model results demonstrate that, in addition to the known westward flow through the Charlie Gibbs Fracture Zone (CGFZ), some Iceland Scotland overflow water (ISOW) flows westward through gaps in the Reykjanes Ridge north of the CGFZ into the Irminger Sea, and some flows southward along the eastern flank of the Mid-Atlantic Ridge into the West European Basin. These results provide …

F5c: A Variant Of Faugere's F5 Algorithm With Reduced Gröbner Bases, Christian Eder, John E. Perry

Faculty Publications

The F5 algorithm for computing Gröbner bases achieves a high level of efficiency through the careful analysis of signatures assigned to each computed polynomial. However, it computes and uses many polynomials that turn out to be redundant. Eliminating these redundant polynomials is a non-trivial task, because they correspond to signatures required for reduction. This paper revisits the theory underlying F5 and describes F5C, a new variant that prunes redundant polynomials, then re-computes signatures to preserve correctness. This strategy successfully reduces both overhead and execution time. (C) 2010 Elsevier Ltd. All rights reserved.

In Vitro Gene Regulatory Networks Predict In Vivo Function Of Liver, Youping Deng, David R. Johnson, Junmei Ai, Edward J. Perkins, Sharon A. Meyer

Faculty Publications

Background: Evolution of toxicity testing is predicated upon using in vitro cell based systems to rapidly screen and predict how a chemical might cause toxicity to an organ in vivo. However, the degree to which we can extend in vitro results to in vivo activity and possible mechanisms of action remains to be fully addressed.

Results: Here we use the nitroaromatic 2,4,6-trinitrotoluene (TNT) as a model chemical to compare and determine how we might extrapolate from in vitro data to in vivo effects. We found 341 transcripts differentially expressed in common among in vitro and in vivo assays …

Speckle Reducing Bilateral Filter For Cattle Follicle Segmentation, Jinshang Teng, Shengwen Guo, Qingling Sun, Youping Deng, Dongfeng Zhou

Faculty Publications

Background: Ultrasound imaging technology has wide applications in cattle reproduction and has been used to monitor individual follicles and determine the patterns of follicular development. However, the speckles in ultrasound images affect the post-processing, such as follicle segmentation and finally affect the measurement of the follicles. In order to reduce the effect of speckles, a bilateral filter is developed in this paper.

Results: We develop a new bilateral filter for speckle reduction in ultrasound images for follicle segmentation and measurement. Different from the previous bilateral filters, the proposed bilateral filter uses normalized difference in the computation of the …

Identification And Optimization Of Classifier Genes From Multi-Class Earthworm Microarray Dataset, Ying Li, Nan Wang, Chaoyang Zhang, Ping Gong

Faculty Publications

Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes and have used it to profile gene expression in 248 earthworms exposed to TNT, RDX or neither. We assembled a new machine learning pipeline consisting of several well-established feature filtering/selection and classification techniques to analyze the 248-array dataset in order to construct classifier models that …

Characterization Of Subsurface Polycyclic Aromatic Hydrocarbons At The Deepwater Horizon Site, Arne Diercks, Raymond C. Highsmith, Vernon L. Asper, Dongjoo Joung, Zhengzhen Zhou, Laodong Guo, Alan M. Shiller, Andreas P. Teske, Norman Guinasso, Terry L. Wade, Steven E. Lohrenz

Faculty Publications

Here, we report the initial observations of distributions of polycyclic aromatic hydrocarbons (PAH) in subsurface waters near the Deepwater Horizon oil well site (also referred to as the Macondo, Mississippi Canyon Block 252 or MC252 well). Profiles of in situ fluorescence and beam attenuation conducted during 9-16 May 2010 were characterized by distinct peaks at depths greater than 1000 m, with highest intensities close to the wellhead and decreasing intensities with increasing distance from the wellhead. Gas chromatography/mass spectrometry (GC/MS) analyses of water samples coinciding with the deep fluorescence and beam attenuation anomalies confirmed the presence of polycyclic aromatic hydrocarbons …

Seasonal Variability In Air-Sea Fluxes Of Co2 In A River-Influenced Coastal Margin, Steven E. Lohrenz, Wei-Jun Cai, Fengwei Cai, Xiaogang Chen, Merritt Tuel

Faculty Publications

Recent studies in the northern Gulf of Mexico and elsewhere have demonstrated that enhanced biological production in large river plumes may contribute to a net surface influx of atmospheric CO2. However, large rivers also deliver significant amounts of terrestrial carbon into continental margin waters; hence, the potential for large and variable signals in carbon flux exist in these regions. Here, we used a combination of satellite and ship-based observations to examine variability in surface pCO(2) and air-sea flux of carbon dioxide in relation to variations in river discharge and seasonal environmental conditions. Underway surface pCO(2) showed large seasonal differences based …

Wave Heights During Hurricane Katrina: An Evaluation Of Ppp And Ppk Measurements Of The Vertical Displacement Of The Gps Antenna, Stephan D. Howden, David Dodd, Leslie C. Bender Iii, Norman Guinasso, Josh Kohut

Faculty Publications

In August 2005 the eye of Hurricane Katrina passed 49 n mi to the west of a 3-m discus buoy operated by the Central Gulf of Mexico Ocean Observing System (CenGOOS). Buoy motions were measured with a strapped-down 6 degrees of freedom accelerometer, a three-axis magnetometer, and a survey-grade GPS receiver. The significant wave heights were computed from the buoy's accelerometer record and from the dual-frequency GPS measurements that were processed in two different ways. The first method was postprocessed kinematic (PPK) GPS, which requires another GPS receiver at a fixed known location, and the other was precise point positioning …

Biofunctionalization And Immobilization Of A Membrane Via Peptide Binding (Cr3-1, S2) By A Monte Carlo Simulation, Ras B. Pandey, Hendrik Heinz, Jie Feng, Barry L. Farmer

Faculty Publications

A coarse-grained computer simulation model is used to study the immobilization of a dynamic tethered membrane (representation of a clay platelet) in a matrix of mobile peptide chains CR3-1:(1)Trp-(2)Pro-(3)Ser-(4)Ser-(5)Tyr-(6)Leu-(7)Ser-(8)Pro-(9)Ile-(10)Pro-(11)Tyr-(12)Ser and S2:(1)His-(2)Gly-(3)Ile-(4)Asn-(5)Thr-(6)Thr-(7)Lys-(8)Pro-(9)Phe-(10)Lys-(11)Ser-(12)Val on a cubic lattice. Each residue interacts with the membrane nodes with appropriate interaction and executes their stochastic motion with the Metropolis algorithm. Density profiles, binding energy of each residue, mobility, and targeted structural profile are analyzed as a function of peptide concentration. We find that the binding of peptides S2 is anchored by lysine residues ((7)Lys,(10)Lys) while peptides CR3-1 do not bind to membrane. The membrane slows down …

Reconstruction And Analysis Of The Chukchi Sea Circulation In 1990-1991, Gleb Panteleev, Dmitri A. Nechaev, Andrey Proshutinsky, R. Woodgate, J. Zhang

Faculty Publications

The Chukchi Sea (CS) circulation reconstructed for September 1990 to October 1991 from sea ice and ocean data is presented and analyzed. The core of the observational data used in this study comprises the records from 12 moorings deployed in 1990 and 1991 in U. S. and Russian waters and two hydrographic surveys conducted in the region in the fall of 1990 and 1991. The observations are processed by a two-step data assimilation procedure involving the Pan-Arctic Ice-Ocean Modeling and Assimilation System (employing a nudging algorithm for sea ice data assimilation) and the Semi-implicit Ocean Model [utilizing a conventional four-dimensional …

Non-Convexity Of The Dimension Function For Sierpinski Pedal Triangles, Jiu Ding, Yifa Tang

Faculty Publications

We disprove the conjecture of the paper by Zhang et al.(1) on the Schur-convexity of the dimension function for the family of Sierpinski pedal triangles. We also show that this function is not convex and the related area-ratio function is not concave in their respective domain.

A Comparison Of Methods For Determining Significant Wave Heights-Applied To A 3-M Discus Buoy During Hurricane Katrina, Leslie C. Bender Iii, Norman Guinasso, John N. Walpert, Stephan D. Howden

Faculty Publications

In August 2005, the eye of Hurricane Katrina passed 90 km to the west of a 3-m discus buoy deployed in the Mississippi Sound and operated by the Central Gulf of Mexico Ocean Observing System (CenGOOS). The buoy motions were measured with a strapped-down, 6 degrees of freedom accelerometer, a three-axis magnetometer, and from the displacement of a GPS antenna measured by postprocessed-kinematic GPS. Recognizing that an accelerometer experiences a large offset due to gravity, the authors investigated four different means of computing wave heights. In the most widely used method for a buoy with a strapped-down, 1D accelerometer, wave …

Numerical Gram-Schmidt Orthonormalization, Charles M. Werneth, Mallika Dhar, Khin Maung Maung, Christopher J. Sirola, John W. Norbury

Faculty Publications

A numerical Gram-Schmidt orthonormalization procedure is presented for constructing an orthonormal basis function set from a non-orthonormal set, when the number of basis functions is large. This method will provide a pedagogical illustration of the Gram-Schmidt procedure and can be presented in classes on numerical methods or computational physics.

Globular Structure Of A Human Immunodeficiency Virus-1 Protease (1difa Dimer) In An Effective Solvent Medium By A Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer

Faculty Publications

A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg(41) and Arg(140) (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by …

Organization, Structure, And Assembly Of Alpha-Carboxysomes Determined By Electron Cryotomography Of Intact Cells, Cristina V. Iancu, Dylan M. Morris, Zhicheng Dou, Sabine Heinhorst, Gordon C. Cannon, Grant J. Jensen

Faculty Publications

Carboxysomes are polyhedral inclusion bodies that play a key role in autotrophic metabolism in many bacteria. Using electron cryotomography, we examined carboxysomes in their native states within intact cells of three chemolithoautotrophic bacteria. We found that carboxysomes generally cluster into distinct groups within the cytoplasm, often in the immediate vicinity of polyphosphate granules, and a regular lattice of density frequently connects granules to nearby carboxysomes. Small granular bodies were also seen within carboxysomes. These observations suggest a functional relationship between carboxysomes and polyphosphate granules. Carboxysomes exhibited greater size, shape, and compositional variability in cells than in purified preparations. Finally, we …

Carboxysomal Carbonic Anhydrases: Structure And Role In Microbial Co2 Fixation, Gordon C. Cannon, Sabine Heinhorst, Cheryl A. Kerfeld

Faculty Publications

Cyanobacteria and some chemoautotrophic bacteria are able to grow in environments with limiting CO₂ concentrations by employing a CO₂-concentrating mechanism (CCM) that allows them to accumulate inorganic carbon in their cytoplasm to concentrations several orders of magnitude higher than that on the outside. The final step of this process takes place in polyhedral protein microcompartments known as carboxysomes, which contain the majority of the CO₂-fixing enzyme, RubisCO. The efficiency of CO₂ fixation by the sequestered RubisCO is enhanced by co-localization with a specialized carbonic anhydrase that catalyzes dehydration of the …

Effects Of Metal Compounds With Distinct Physicochemical Properties On Iron Homeostasis And Antibacterial Activity In The Lungs: Chromium And Vanadium, Mitchell D. Cohen, Maureen Sisco, Colleen Prophete, Kotaro Yoshida, Lung-Chi Chen, Judith T. Zelikoff, Jason Smee, Alvin A. Holder, Jacqueline Stormhuerner, Debbie C. Crans, Andrew J. Ghio

Faculty Publications

In situ reactions of metal ions or their compounds are important mechanisms by which particles alter lung immune responses. The authors hypothesized that major determinants of the immunomodulatory effect of any metal include its redox behavior/properties, oxidation state, and/or solubility, and that the toxicities arising from differences in physicochemical parameters are manifest, in part, via differential shifts in lung iron (Fe) homeostasis. To test the hypotheses, immunomodulatory potentials for both pentavalent vanadium (V(V); as soluble metavanadate or insoluble vanadium pentoxide) and hexavalent chromium (Cr(VI); as soluble sodium chromate or insoluble calcium chromate) were quantified in rats after inhalation (5 h/day …

A Lanthanide-Based Chemosensor For Bioavailable Fe3+ Using A Fluorescent Siderophore: An Assay Displacement Approach, Karen M. Orcutt, William Scott Jones, Andrea Mcdonald, David Schrock, Karl J. Wallace

Faculty Publications

The measurement of trace analytes in aqueous systems has become increasingly important for understanding ocean primary productivity. In oceanography, iron (Fe) is a key element in regulating ocean productivity, microplankton assemblages and has been identified as a causative element in the development of some harmful algal blooms. The chemosenor developed in this study is based on an indicator displacement approach that utilizes time-resolved fluorescence and fluorescence resonance energy transfer as the sensing mechanism to achieve detection of Fe3+ ions as low as 5 nM. This novel approach holds promise for the development of photoactive chemosensors for ocean deployment.

An F4-Style Involutive Basis Algorithm, Miao Yu

Mathematics Student Presentations

This paper introduces a new algorithm for computing Gröbner bases. To avoid as much ambiguity as possible, this algorithm combines the F4 algorithm and basic algorithm of involutive bases and it replaces the symbolic precomputation of S-polynomials and ordinary division in F4 by a new symbolic precomputation of non-multiplicative prolongations and involutive division. This innovation makes the sparse matrix of F4 in a deterministic way. As an example the Cyclic-4 problem is presented.