Digital Commons Network^™

Novel Implementation Of Conditional Co-Regulation By Graph Theory To Derive Co-Expressed Genes From Microarray Data, Arun Rawat, Georg J. Seifert, Youping Deng

Faculty Publications

Background

Most existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (similar pathways and biosynthetic cycles) based on correlation. These utilize conventional methods like Pearson correlation and Spearman rank correlation to calculate correlation among genes. However, not all are genes expressed in all the conditions and this leads to their exclusion in these transcriptional databases that consist of experiments performed in varied conditions. This leads to incomplete studies of co-regulation among groups of genes that might be linked to the same or related biosynthetic pathway.

Results …

Multijet Cross Sections In Charged Current E±P Scattering At Hera, S. Chekanov, M. Derrick, S. Magill, B. Musgrave, D. Nicholass, J. Repond, R. Yoshida, Margarita C. K. Mattingly, M. Jechow, N. Pavel, P. Antonioli, G. Bari, L. Bellagamba, D. Boscherini, A. Bruni, G. Bruni, F. Cindolo, M. Corradi, G. Iacobucci, A. Margotti, R. Nania, A. Polini, S. Antonelli, M. Basile, M. Bindi, L. Cifarelli, A. Contin, S. De Pasquale, G. Sartorelli, A. Zichichi, D. Bartsch

Faculty Publications

Jet cross sections were measured in charged-current deep inelastic e±p scattering at high boson virtualities Q2 with the ZEUS detector at HERA II using an integrated luminosity of 0.36fb-1. Differential cross sections are presented for inclusive-jet production as functions of Q2, Bjorken x and the jet transverse energy and pseudorapidity. The dijet invariant mass cross section is also presented. Observation of three- and four-jet events in charged-current e±p processes is reported for the first time. The predictions of next-to-leading-order (NLO) QCD calculations are compared to the measurements. The measured inclusive-jet cross sections are well described in shape and normalization by …

Search Of S3 Ligo Data For Gravitational Wave Signals From Spinning Black Hole And Neutron Star Binary Inspirals, B. Abbott, R. Abbott, R. Adhikari, J. Agresti, P. Ajith, B. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. Arain, M. Araya, H. Armandula, M. Ashley, S. Aston, P. Aufmuth, C. Aulbert, S. Babak, S. Ballmer, H. Bantilan, B. C. Barish, C. Barker, D. Barker, B. Barr, P. Barriga, M. A. Barton, K. Bayer, J. Betzwieser, P. T. Beyersdorf, B. Bhawal, I. A. Bilenko, G. Billingsley, R. Biswas, E. Black

Faculty Publications

We report on the methods and results of the first dedicated search for gravitational waves emitted during the inspiral of compact binaries with spinning component bodies. We analyze 788 hours of data collected during the third science run (S3) of the LIGO detectors. We searched for binary systems using a detection template family specially designed to capture the effects of the spin-induced precession of the orbital plane. We present details of the techniques developed to enable this search for spin-modulated gravitational waves, highlighting the differences between this and other recent searches for binaries with nonspinning components. The template bank we …

Search Of S3 Ligo Data For Gravitational Wave Signals From Spinning Black Hole And Neutron Star Binary Inspirals, B. Abbott, R. Abbott, R. Adhikari, J. Agresti, P. Ajith, B. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. Arain, M. Araya, H. Armandula, M. Ashley, S. Aston, P. Aufmuth, C. Aulbert, S. Babak, S. Ballmer, H. Bantilan, B. C. Barish, C. Barker, D. Barker, B. Barr, P. Barriga, M. A. Barton, K. Bayer, J. Betzwieser, P. T. Beyersdorf, B. Bhawal, I. A. Bilenko, G. Billingsley, Tiffany Z. Summerscales

Faculty Publications

We report on the methods and results of the first dedicated search for gravitational waves emitted during the inspiral of compact binaries with spinning component bodies. We analyze 788 hours of data collected during the third science run (S3) of the LIGO detectors. We searched for binary systems using a detection template family specially designed to capture the effects of the spin-induced precession of the orbital plane. We present details of the techniques developed to enable this search for spin-modulated gravitational waves, highlighting the differences between this and other recent searches for binaries with nonspinning components. The template bank we …

Effect Of Long-Range Hopping On Tc In A Two-Dimensional Hubbard-Holstein Model Of The Cuprates, Ehsan Khatami, A. Macridin, M. Jarrell

Faculty Publications

We study the effect of long-range hoppings on Tc for the two-dimensional (2D) Hubbard model with and without Holstein phonons using parameters evaluated from band-structure calculations for cuprates. Employing the dynamical cluster approximation (DCA) with a quantum Monte Carlo (QMC) cluster solver for a 4-site cluster, we observe that without phonons, the long-range hoppings, t′ and t′′, generally suppress Tc. We argue that this trend remains valid for larger clusters. In the presence of the Holstein phonons, a finite t′ enhances Tc in the under-doped region for the hole-doped system, consistent with local-density approximation (LDA) calculations and experiment. This is …

The Complexity Of Recognizing Linear Systems With Certain Integrality Properties, Guoli Ding, Li Feng, Wenan Zang

Faculty Publications

Let A be a 0 - 1 matrix with precisely two 1's in each column and let 1 be the all-one vector. We show that the problems of deciding whether the linear system Ax ≥ 1,x ≥ 0 (1) defines an integral polyhedron, (2) is totally dual integral (TDI), and (3) box-totally dual integral (box-TDI) are all co-NP-complete, thereby confirming the conjecture on NP-hardness of recognizing TDI systems made by Edmonds and Giles in 1984. © 2007 Springer-Verlag.

On Atkin And Swinnerton-Dyer Congruence Relations (3), Ling Long

Faculty Publications

It is now well known that Hecke operators defined classically act trivially on genuine cuspforms for noncongruence subgroups of SL2 (Z). Atkin and Swinnerton-Dyer speculated the existence of p-adic Hecke operators so that the Fourier coefficients of their eigenfunctions satisfy three-term congruence recursions. In the previous two papers with the same title ([W.C. Li, L. Long, Z. Yang, On Atkin and Swinnerton-Dyer congruence relations, J. Number Theory 113 (1) (2005) 117-148] by W.C. Li, L. Long, Z. Yang and [A.O.L. Atkin, W.C. Li, L. Long, On Atkin and Swinnerton-Dyer congruence relations (2), Math. Ann. 340 (2) (2008) 335-358] by A.O.L. …

Morse Theory And Conjugacy Classes Of Finite Subgroups, Noel Brady, Matt Clay, Pallavi Dani

Faculty Publications

We construct a CAT(0) group containing a finitely presented subgroup with infinitely many conjugacy classes of finite-order elements. Unlike previous examples (which were based on right-angled Artin groups) our ambient CAT(0) group does not contain any rank 3 free abelian subgroups. We also construct examples of groups of type Fn inside mapping class groups, Aut(double-struck Fk), and Out(double-struck Fk) which have infinitely many conjugacy classes of finite-order elements. © 2008 Springer Science+Business Media B.V.

Effective Single-Particle Order-N Scheme For The Dynamics Of Open Noninteracting Many-Body Systems, Yuriy V. Pershin Dr, Y. Dubi, M. Di Ventra

Faculty Publications

Quantum master equations are common tools to describe the dynamics of many-body systems open to an environment. Due to the interaction with the latter, even for the case of noninteracting electrons, the computational cost to solve these equations increases exponentially with the partical number. We propose a simple scheme, which allows to study the dynamics of N noninteracting electrons taking into account both dissipation effects and Fermi statistics, with a computational cost that scales linearly with N. Our method is based on a mapping of the many-body system to a specific set of effective single-particle systems. We provide detailed …

Watertight Trimmed Nurbs, Thomas W. Sederberg, Xin Li, Hongwei Lin, Heather Ipson

Faculty Publications

This paper addresses the long-standing problem of the unavoidable gaps that arise when expressing the intersection of two NURBS surfaces using conventional trimmed-NURBS representation. The solution converts each trimmed NURBS into an untrimmed T-Spline, and then merges the untrimmed T-Splines into a single, watertight model. The solution enables watertight fillets of NURBS models, as well as arbitrary feature curves that do not have to follow isoparameter curves. The resulting T-Spline representation can be exported without error as a collection of NURBS surfaces.

Community Detection In Complex Networks By Dynamical Simplex Evolution, Vladimir Gudkov, V. Montealegre, S. Nussinov, Z. Nussinov

Faculty Publications

We benchmark the dynamical simplex evolution (DSE) method with several of the currently available algorithms to detect communities in complex networks by comparing correctly identified nodes for different levels of "fuzziness" of random networks composed of well-defined communities. The potential benefits of the DSE method to detect hierarchical substructures in complex networks are discussed.

Is Loop Quantization In Cosmology Unique?, Alejandro Corichi, Parampreet Singh

Faculty Publications

We reexamine the process of loop quantization for flat isotropic models in cosmology. In particular, we contrast different inequivalent "loop quantizations" of these simple models through their respective successes and limitations and assess whether they can lead to any viable physical description. We propose three simple requirements which any such admissible quantum model should satisfy: (i) independence from any auxiliary structure, such as a fiducial interval/cell introduced to define the phase space when integrating over noncompact manifolds; (ii) existence of a well defined classical limit, and (iii) a sensible "Planck scale" where quantum gravitational effects become manifest. We show that …

Modeling Phase Transitions Of Nanoemulsion For Ultrasonic Gene Delivery, Ghaleb A. Husseini, William G. Pitt, Ram Singh

Faculty Publications

A computer model was written that simulates the transformation of a nanoemulsion droplet to a gas bubble by the application of ultrasound. Experimentally such a technique could be used to enhance non-viral gene transfection beyond the boundary of the endothelial lining of the circulatory system, particularly in tumors exhibiting enhanced permeation and retention of nanoparticles.

Scaling Ant Colony Optimization With Hierarchical Reinforcement Learning Partitioning, Erik J. Dries, Gilbert L. Peterson

Faculty Publications

This paper merges hierarchical reinforcement learning (HRL) with ant colony optimization (ACO) to produce a HRL ACO algorithm capable of generating solutions for large domains. This paper describes two specific implementations of the new algorithm: the first a modification to Dietterich’s MAXQ-Q HRL algorithm, the second a hierarchical ant colony system algorithm. These implementations generate faster results, with little to no significant change in the quality of solutions for the tested problem domains. The application of ACO to the MAXQ-Q algorithm replaces the reinforcement learning, Q-learning, with the modified ant colony optimization method, Ant-Q. This algorithm, MAXQ-AntQ, converges to solutions …

Leaf Area Index Simulation In Soybean Grown Under Near-Optimal Conditions, T. D. Setiyono, A. Weiss, J. E. Specht, K. G. Cassman, A. Dobermann

Faculty Publications

Different approaches have been used to simulate leaf area index (LAI) in soybean (Glycine max L. Merr). Many of these approaches require genotype-specific calibration procedures. Studies modeling LAI dynamics under optimal growth conditions with yields close to the yield potential of soybean have remained scarce. A sink-driven approach was developed and evaluated for LAI simulation in soybean under near-optimal environments. The rate of change in expanding leaf area was simulated using the first derivative of a logistic function accounting for plant population density, air temperature, and water deficit. The rate of change in senescing leaf area was also simulated using …

An Ultrahigh Stability, Low-Noise Laser Current Driver With Digital Control, Christopher J. Erickson, Marshall Van Zijll, Greg Doermann, Dallin S. Durfee

Faculty Publications

We present a low-noise, high modulation-bandwidth design for a laser current driver with excellent long-term stability. The driver improves upon the commonly used Hall–Libbrecht design. The current driver can be operated remotely by way of a microprocessing unit, which controls the current set point digitally. This allows precise repeatability and improved accuracy and stability. It also allows the driver to be placed near the laser for reduced noise and for lower phase lag when using the modulation input. We present the theory of operation for our driver in detail, and give a thorough characterization of its stability, noise, set-point accuracy …

Stable Long-Time Semiclassical Description Of Zero-Point Energy In High-Dimensional Molecular Systems, Sophya Garashchuk, Vitaly A. Rassolov

Faculty Publications

Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys. 120, 1181 (2004)] is further developed to give a stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The method is based on a numerically cheap linearized quantum force approach; stabilizing terms compensating for the linearization errors are added into the time-evolution equations for the classical and nonclassical components of the momentum operator. The wave function normalization and energy are rigorously conserved. Numerical tests are performed for model systems of up to 40 degrees of freedom.

Implications For The Origin Of Grb 070201 From Ligo Observations, B. Abbott, R. Abbott, R. Adhikari, J. Agresti, P. Ajith, B. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. Arain, M. Araya, H. Armandula, M. Ashley, S. Aston, P. Aufmuth, C. Aulbert, S. Babak, S. Ballmer, H. Bantilan, B. C. Barish, C. Barker, D. Barker, B. Barr, P. Barriga, M. A. Barton, K. Bayer, J. Betzwieser, P. T. Beyersdorf, B. Bhawal, I. A. Bilenko, G. Billingsley, Tiffany Z. Summerscales

Faculty Publications

We analyzed the available LIGO data coincident with GRB 070201, a short-duration, hard-spectrum γ-ray burst (GRB) whose electromagnetically determined sky position is coincident with the spiral arms of the Andromeda galaxy (M31). Possible progenitors of such short, hard GRBs include mergers of neutron stars or a neutron star and a black hole, or soft γ-ray repeater (SGR) flares. These events can be accompanied by gravitational-wave emission. No plausible gravitational-wave candidates were found within a 180 s long window around the time of GRB 070201. This result implies that a compact binary progenitor of GRB 070201, with masses in the range …

Epigene And Hypogene Karst Manifestations Of The Castile Formation: Eddy County, New Mexico And Culberson County, Texas, Usa, Kevin W. Stafford, Raymond Nance, Laura Rosales-Lagarde, Penelope J. Boston

Faculty Publications

Permian evaporites of the Castile Formation crop out over ~1,800 km2 in the western Delaware Basin (Eddy County, New Mexico and Culberson County, Texas, USA) with abundant and diverse karst manifestations. Epigene karst occurs as well-developed karren on exposed bedrock, while sinkholes dominate the erosional landscape, including both solutional and collapse forms. Sinkhole analyses suggest that more than half of all sinks are the result of upward stoping of subsurface voids, while many solutional sinks are commonly the result of overprinting of collapsed forms. Epigene caves are laterally limited with rapid aperture decreases away from insurgence, with passages developed along …

Syzygies And The Rees Algebra, David Cox, J. William Hoffman, Haohao Wang

Faculty Publications

Let a, b, c be linearly independent homogeneous polynomials in the standard Z-graded ring R {colon equals} k [s, t] with the same degree d and no common divisors. This defines a morphism P1 → P2. The Rees algebra Rees (I) = R ⊕ I ⊕ I2 ⊕ ⋯ of the ideal I = 〈 a, b, c 〉 is the graded R-algebra which can be described as the image of an R-algebra homomorphism h: R [x, y, z] → Rees (I). This paper discusses one result concerning the structure of the kernel of the map h and its relation …

On Modular Forms For Some Noncongruence Subgroups Of Sl2 (Z), Chris A. Kurth, Ling Long

Faculty Publications

In this paper, we consider modular forms for finite index subgroups of the modular group whose Fourier coefficients are algebraic. It is well known that the Fourier coefficients of any holomorphic modular form for a congruence subgroup (with algebraic coefficients) have bounded denominators. It was observed by Atkin and Swinnerton-Dyer that this is no longer true for modular forms for noncongruence subgroups and they pointed out that unbounded denominator property is a clear distinction between modular forms for noncongruence and congruence modular forms. It is an open question whether genuine noncongruence modular forms (with algebraic coefficients) always satisfy the unbounded …

The Structure Of Crossing Separations In Matroids, Jeremy Aikin, James Oxley

Faculty Publications

Oxley, Semple and Whittle described a tree decomposition for a 3-connected matroid M that displays, up to a natural equivalence, all non-trivial 3-separations of M. Crossing 3-separations gave rise to fundamental structures known as flowers. In this paper, we define a generalized flower structure called a k-flower, with no assumptions on the connectivity of M. We completely classify k-flowers in terms of the local connectivity between pairs of petals. © 2007 Elsevier Inc. All rights reserved.

Maintaining 3-Connectivity Relative To A Fixed Basis, James Oxley, Charles Semple, Geoff Whittle

Faculty Publications

A standard matrix representation A of a matroid M represents M relative to a fixed basis B. Deleting rows and columns of A correspond to contracting elements of B and deleting elements of E (M) - B. If M is 3-connected, it is often desirable to perform such an element removal from M while maintaining 3-connectivity. This paper proves that this is always possible provided M has no 4-element fans. We also show that, subject to a mild essential restriction, this element removal can be done so as to retain a copy of a specified 3-connected minor of M. © …

A Review Of Fibroblast Populated Collagen Lattices, J. C. Dallon, Paul H. Ehrlich

Faculty Publications

Bellaes introduction of the fibroblast populated collagen lattice (FPCL) (1) has facilitated the study of collagen-cell interactions. As a result of the numerous modifications of the casting of FPCL's, the in vivo applications of these in vitro findings has been confusing. Here experimental FPCL contraction findings are viewed in regard to three proposed mechanisms responsible for lattice contraction. The cellular mechanisms responsible for generating FPCL contraction are: cell contraction, cell tractional forces related to cell locomotion, and initial cell elongation and spreading.

Graduate Training In Sociological Theory And Theory Construction, Barry N. Markovsky

Faculty Publications

Nearly all of sociology's top graduate training programs require their students to complete one or two courses on sociological theory. The instructors for these courses have an extraordinary opportunity to affect the perspectives and practices of future generations of scholars. This study assesses the backgrounds, attitudes, beliefs, and practices of those instructors regarding different approaches to theorizing, with particular attention paid to topics related to science and to theory construction. Sociologists who teach required theory courses in the discipline's top fifty graduate training programs were asked a series of questions pertaining to their own training and to the courses they …

Understanding (Dis)Abilities Through Children's Literature, Stephanie A. Kurtts, Karen W. Gavigan

Faculty Publications

The authors of this article examined how pre-service teachers can use children's and young adult literature about disabilities to enhance understanding of individual differences through a bibliotherapeutic approach. An introduction to bibliotherapy is provided along with related literature from the field. Strategies for using children's and young adult literature to enhance the understanding of issues associated with disabilities are presented along with one teacher candidate's application of the literature in her classroom. The authors have also included a selected bibliography of children's literature on disabilities as well as relevant websites

A Satisficing Approach To Aircraft Conflict Resolution, Wynn C. Stirling, James K. Archibald, Nicholas A. Jepsen, Richard L. Frost, Jared C. Hill

Faculty Publications

Future generations of air traffic management systems may give appropriately equipped aircraft the freedom to change flight paths in real time. This would require a conflict avoidance and resolution scheme that is both decentralized and cooperative. We describe a multiagent solution to aircraft conflict resolution based on satisficing game theory. A key feature of the theory is that satisficing decision makers form their preferences by taking into consideration the preferences of others, unlike conventional game theory that models agents that maximize self-interest metrics. This makes possible situational altruism, a sophisticated form of unselfish behavior in which the preferences of another …

Data-Driven Programming And Behavior For Autonomous Virtual Characters, Jonathan Dinerstein, Parris K. Egbert, Michael A. Goodrich, Dan A. Ventura

Faculty Publications

In the creation of autonomous virtual characters, two levels of autonomy are common. They are often called motion synthesis (low-level autonomy) and behavior synthesis (high-level autonomy), where an action (i.e. motion) achieves a short-term goal and a behavior is a sequence of actions that achieves a long-term goal. There exists a rich literature addressing many aspects of this general problem (and it is discussed in the full paper). In this paper we present a novel technique for behavior (high-level) autonomy and utilize existing motion synthesis techniques. Creating an autonomous virtual character with behavior synthesis abilities frequently includes three stages: forming …

Manipulating The Cavity Of A Porous Material Changes The Photoreactivity Of Included Guests, Mahender B. Dewal, Yuewen Xu, Jun Yang, Fiaz Mohammed, Mark D. Smith, Linda S. Shimizu

Faculty Publications

Changing an ether to a ketone within the framework of a bis-urea macrocycle has little effect on the supramolecular assembly of this building block into porous crystals but introduces a triplet sensitizer into the framework that dramatically alters the photochemical reactions of included guests.

A High Resolution Neutrino Experiment In A Magnetic Field For Project-X At Fermilab, Sanjib R. Mishra, Roberto Petti, Carl Rosenfeld

Faculty Publications

We propose a new high-resolution neutrino experiment within a dipole magnetic field, HiResMν. This experiment will run along with long-baseline neutrino oscillation experiments (LBLν) such as NOνA, a large-cavity detector at DUSEL, or a Liquid-Argon detector in the Medium-Energy (ME) configuration of the NuMI-beam. Assuming the 120 GeV Main Injector proton intensities we anticipate 140(50) million ν_μ (⊽μ) Charged-Current (CC) events in the fiducial volume, for 3(4)-year run with the ME (anti)neutrino beam. Alternatively, the same statistics could be collected in just 1(1.5) year with the High Energy (HE) beam configuration. …