Physical Sciences and Mathematics Commons^™

Learning The Structure Of Gene Regulatory Networks From Time Series Gene Expression Data, Haoni Li, Nan Wang, Ping Gong, Edward J. Perkins, Chaoyang Zhang

Faculty Publications

Background: Dynamic Bayesian Network (DBN) is an approach widely used for reconstruction of gene regulatory networks from time-series microarray data. Its performance in network reconstruction depends on a structure learning algorithm. REVEAL (REVerse Engineering ALgorithm) is one of the algorithms implemented for learning DBN structure and used to reconstruct gene regulatory networks (GRN). However, the two-stage temporal Bayes network (2TBN) structure of DBN that specifies correlation between time slices cannot be obtained by score metrics used in REVEAL.

Methods: In this paper, we study a more sophisticated score function for DBN first proposed by Nir Friedman for stationary …

Preparation Of Novel Hydrolyzing Urethane Modified Thiol-Ene Networks, Nicole M. Mackey, Bridget S. Confait, James Wynne, J. Paige Buchanan

Faculty Publications

Novel tetra-functional hydrolyzing monomers were prepared from the reaction of TEOS and select alkene-containing alcohols, ethylene glycol vinyl ether or 2-allyloxy ethanol, and combined with trimethylolpropane tris(3-mercaptopropionate) (tri-thiol) in a thiol-ene “click” polymerization reaction to produce clear, colorless thiol-ene networks using both radiation and thermal-cure techniques. These networks were characterized for various mechanical characteristics, and found to posses T_g’s (DSC), hardness, tack, and thermal stability (TGA) consistent with their molecular structures. A new ene-modified urethane oligomer was prepared based on the aliphatic polyisocyanate Desmodur^® N 3600 and added to the thiol-ene hydrolyzable network series in increasing amounts, …

A Modified Stokes-Einstein Equation For A Beta Aggregation, Srisairam Achuthan, Bong Jae Chung, Preetam Ghosh, Vijayaraghavan Rangachari, Ashwin Vaidya

Faculty Publications

Background: In all amyloid diseases, protein aggregates have been implicated fully or partly, in the etiology of the disease. Due to their significance in human pathologies, there have been unprecedented efforts towards physiochemical understanding of aggregation and amyloid formation over the last two decades. An important relation from which hydrodynamic radii of the aggregate is routinely measured is the classic Stokes-Einstein equation. Here, we report a modification in the classical Stokes-Einstein equation using a mixture theory approach, in order to accommodate the changes in viscosity of the solvent due to the changes in solute size and shape, to implement a …

The F5 Criterion Revised, Alberto Arri, John E. Perry

Faculty Publications

The purpose of this work is to generalize part of the theory behind Faugere's "F5" algorithm. This is one of the fastest known algorithms to compute a Gröbner basis of a polynomial ideal I generated by polynomials f₁,…,f_m. A major reason for this is what Faugere called the algorithm's "new" criterion, and we call "the F5 criterion": it provides a sufficient condition for a set of polynomialsGto be a Gröbner basis. However. the F5 algorithm is difficult to grasp, and there are unresolved questions regarding its termination. This paper introduces some new concepts that place the …

The Method Of Approximate Particular Solutions For Solving Elliptic Problems With Variable Coefficients, C.S. Chen, Chia-Ming Fan, Pihua Wen

Faculty Publications

A new version of the method of approximate particular solutions (MAPSs) using radial basis functions (RBFs) has been proposed for solving a general class of elliptic partial differential equations. In the solution process, the Laplacian is kept on the left-hand side as a main differential operator. The other terms are moved to the right-hand side and treated as part of the forcing term. In this way, the close-form particular solution is easy to obtain using various RBFs. The numerical scheme of the new MAPSs is simple to implement and yet very accurate. Three numerical examples are given and the results …

Thiolene-Based Microfluidic Flow Cells For Surface Plasmon Resonance Imaging, Gareth Sheppard, Takao Oseki, Akira Baba, Derek L. Patton, Futao Kaneko, Leidong Mao, Jason Locklin

Faculty Publications

Thiolene-based microfluidic devices have been coupled with surface plasmon resonance imaging (SPRI) to provide an integrated platform to study interfacial interactions in both aqueous and organic solutions. In this work, we develop a photolithographic method that interfaces commercially available thiolene resin to gold and glass substrates to generate microfluidic channels with excellent adhesion that leave the underlying sensor surface free from contamination and readily available for surface modification through self-assembly. These devices can sustain high flow rates and have excellent solvent compatibility even with several organic solvents. To demonstrate the versatility of these devices, we have conducted nanomolar detection of …

A Hybrid Background Error Covariance Model For Assimilating Glider Data Into A Coastal Ocean Model, Max Yaremchuk, Dmitri A. Nechaev, Chudong Pan

Faculty Publications

A hybrid background error covariance (BEC) model for three-dimensional variational data assimilation of glider data into the Navy Coastal Ocean Model (NCOM) is introduced. Similar to existing atmospheric hybrid BEC models, the proposed model combines low-rank ensemble covariances B(m) with the heuristic Gaussian-shaped covariances B(0) to estimate forecast error statistics. The distinctive features of the proposed BEC model are the following: (i) formulation in terms of inverse error covariances, (ii) adaptive determination of the rank m of B(m) with information criterion based on the innovation error statistics, (iii) restriction of the heuristic covariance operator B(0) to the null space of …

Non-Esterified Fatty Acids Generate Distinct Low-Molecular Weight Amyloid-Β (Aβ42) Oligomers Along Pathway Different From Fibril Formation, Amit Kumar, Rebekah L. Bullard, Pritesh Patel, Lea C. Paslay, Dipti Singh, Ewa A. Bienkiewicz, Sarah E. Morgan, Vijayaraghavan Rangachari

Faculty Publications

Amyloid-beta (A beta) peptide aggregation is known to play a central role in the etiology of Alzheimer's disease (AD). Among various aggregates, low-molecular weight soluble oligomers of A beta are increasingly believed to be the primary neurotoxic agents responsible for memory impairment. Anionic interfaces are known to influence the A beta aggregation process significantly. Here, we report the effects of interfaces formed by medium-chain (C9-C12), saturated non-esterified fatty acids (NEFAs) on A beta 42 aggregation. NEFAs uniquely affected A beta 42 aggregation rates that depended on both the ratio of A beta:NEFA as well the critical micelle concentration (CMC) of …

Soil Carbon And Material Fluxes Across The Eroding Alaska Beaufort Sea Coastline, Chien-Lu Ping, Gary J. Michaelson, Laodong Guo, M. Torre Jorgensen, Mikhail Z. Kanevskiy, Yuri L. Shur, Fugen Dou, Jingjing Liang

Faculty Publications

Carbon, nitrogen, and material fluxes were quantified at 48 sampling locations along the 1957 km coastline of the Beaufort Sea, Alaska. Landform characteristics, soil stratigraphy, cryogenic features, and ice contents were determined for each site. Erosion rates for the sites were quantified using satellite images and aerial photos, and the rates averaged across the coastline increased from 0.6 m yr^-1 during circa 1950-1980 to 1.2 m yr^-1 during circa 1980-2000. Soils were highly cryoturbated, and organic carbon (OC) stores ranged from 13 to 162 kg OC m^-2 in banks above sea level and averaged 63 kg OC …

Nuclear Pairing Reduction Due To Rotation And Blocking, X. Wu, Z.H. Zhang, J.Y. Zeng, Y.A. Lei

Faculty Publications

Nuclear pairing gaps of normally deformed and superdeformed nuclei are investigated using the particle-number-conserving (PNC) formalism for the cranked shell model, in which the blocking effects are treated exactly. Both rotational frequency omega dependence and seniority (number of unpaired particles) nu dependence of the pairing gap (Delta) over tilde are investigated. For the ground-state bands of even-even nuclei, PNC calculations show that, in general, (Delta) over tilde decreases with increasing omega, but the omega dependence is much weaker than that calculated by the number-projected Hartree-Fock-Bogolyubov approach. For the multiquasiparticle bands (seniority nu > 2), the pairing gaps stay almost omega independent. …

Circulation In The Philippine Archipelago Simulated By 1/12° And 1/25° Global Hycom And Eas Ncom, Harley E. Hurlbert, E. Joe Metzger, Janet Sprintall, Shelley Riedlinger, Robert A. Arnone, Toshiaki Shinoda, Xiaobiao Xu

Faculty Publications

Three ocean models, 1/25 degrees global HYbrid Coordinate Ocean Model (HYCOM), 1/12 degrees global HYCOM, and East Asian Seas Navy Coastal Ocean Model (EAS NCOM) nested in global NCOM, were used to provide a global context for simulation of the circulation within the Philippine Archipelago as part of the Philippine Straits Dynamics Experiment (PhilEx). The Philippine Archipelago provides two significant secondary routes for both the Indonesian throughflow and the western boundary current of the Pacific northern tropical gyre. The deeper route enters the archipelago from the north through Mindoro Strait, after passing through Luzon Strait and the South China Sea. …

Thiol-Yne 'Click' Chemistry As A Route To Functional Lipid Mimetics, Sandeep S. Naik, Justin W. Chan, Christopher Comer, Charles E. Hoyle, Daniel A. Savin

Faculty Publications

Thiol-alkyne 'click' chemistry is a modular, efficient mechanism to synthesize complex A₂B 3-arm star polymers. This general motif is similar to a phospholipid where the A blocks correspond to lypophilic chains and the B block represents the polar head group. In this communication we employ thiol-yne chemistry to produce polypeptide-based A₂B lipid mimetics. The utility of the thiol-yne reaction is demonstrated by using a divergent and a convergent approach in the synthesis. These polymers self-assemble in aqueous solution into spherical vesicles with a relatively narrow size distribution independent of block composition over the range studied. Using …