bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical Interference Test in Wells With Downhole Water Sink Completions
Authors: Shirman Ephim , Wojtanowicz Andrew
Published: September 2009

Downhole water sink (DWS) well completions segregate production in the wellbore by producing water from the underlying aquifer and oil—from the oil zone of the reservoir. A pump drains water from the bottom completion to create a pressure drawdown that prevents water from coning up to the top, oil producing zone. Successful application of DWS technology in wells with water-coning problem requires effective isolation between the top and bottom completions of the well. Since DWS technology requires dual completion, the completion is configured for vertical interference testing. The problem is that such test involves flow of two fluids, water and oil. This paper presents a new mathematical model and analysis method for vertical interference testing using top completion (in the oil leg) for production and bottom completion (in the water leg) for observation. The model is analytical and accommodates partial penetration and permeability anisotropy. The analysis method employs a family of type-curves. Examples of possible applications of this new testing method are also shown in this paper.
Highly conformal film growth by chemical vapor deposition. I. A conformal zone diagram based on kinetics
Authors: Yanguas-Gil A. , Yang Y. , Kumar N. , Abelson J. R.
Published: September 2009

The authors present a unified description of conformal film growth in recessed features by low pressure chemical vapor deposition. Experimental data on step coverage and growth rate are interpreted in terms of a kinetic model for the elementary surface processes. This model is combined with the continuity equation for gas transport and consumption to predict the values of the precursor pressure and substrate temperature (p,T) that are necessary for conformal coverage to occur for a given precursor. They introduce a conformal zone diagram that considers the gas phase limitations (maximum precursor pressure and onset of secondary reactions), the surface limitations (minimum reaction temperature, precursor adsorption and desorption rates, and film growth rate), and the aspect ratio of the feature to be coated; the allowed intersection between the resulting boundaries defines the (p,T) zone for conformal growth. Sufficient precursor pressure is identified as a major requirement for conformal film growth, one that is not met by many commercially available molecules. Finally, they derive an approximate analytical solution to the inverse problem: what are the experimental conditions necessary to afford a desired degree of step coverage on a given aspect ratio feature at a desired growth rate. The solution depends on a set of rate constants in the kinetic model that can be extracted from measurements of the film growth rate as a function of precursor pressure and substrate temperature on trench or planar substrates.
LFA-1 Antagonists as Agents Limiting Human Immunodeficiency Virus Type 1 Infection and Transmission and Potentiating the Effect of the Fusion Inhibitor T-20
Authors: Tardif Mélanie R. , Gilbert Caroline , Thibault Sandra , Fortin Jean-François , Tremblay Michel J.
Published: September 2009

Adhesion molecules are known to play major roles in the initiation and stabilization of cell-to-cell contacts during the immunological response. Human immunodeficiency virus type 1 (HIV-1) exploits those interactions to facilitate infection and propagation processes. The primary objective of the present study was to investigate the ability of antagonists specific for lymphocyte function-associated antigen 1 (LFA-1) to diminish HIV-1 infection and transmission. We demonstrate here that LFA-1 antagonists can significantly reduce HIV-1 replication in primary human cells and virus propagation by affecting cell-to-cell interactions. Moreover, the inhibition of LFA-1-mediated adhesion events also potentiates the antiviral efficacy of the peptide fusion inhibitor T-20. Altogether, our data suggest that LFA-1 antagonists represent promising antiviral agents. Antiadhesion therapy could be considered a complementary strategy targeting cellular functions essential for HIV-1 spreading and against which the combined therapy currently used displays a limited efficacy.
Inhibition of Envelope-Mediated CD4+-T-Cell Depletion by Human Immunodeficiency Virus Attachment Inhibitors
Authors: Alexander Louis , Zhang Sharon , McAuliffe Brian , Connors David , Zhou Nannon , Wang Tao , Agler Michele , Kadow John , Lin Pin-Fang
Published: September 2009

Human immunodeficiency virus type 1 (HIV-1) envelope (Env) binding induces proapoptotic signals in CD4+T cells without a requirement of infection. Defective virus particles, which represent the majority of HIV-1, usually contain a functional Env and therefore represent a potentially significant cause of such CD4+-T-cell loss. We reasoned that an HIV-1 inhibitor that prohibits Env-host cell interactions could block the destructive effects of defective particles. HIV-1 attachment inhibitors (AIs), which potently inhibit Env-CD4 binding and subsequent downstream effects of Env, display low-nanomolar antiapoptotic potency and prevent CD4+-T-cell depletion from mixed lymphocyte cultures, also with low-nanomolar potency. Specific Env amino acid changes that confer resistance to AI antientry activity eliminate AI antiapoptotic effects. We observed that CD4+-T-cell destruction is specific for CXCR4-utilizing HIV-1 strains and that the fusion blocker enfuvirtide inhibits Env-mediated CD4+-T-cell killing but is substantially less potent than AIs. These observations, in conjunction with observed antiapoptotic activities of soluble CD4 and the CXCR4 blocker AMD3100, suggest that this AI activity functions through a mechanism common to AI antientry activity, e.g., prevention of Env conformation changes necessary for specific interactions with cellular factors that facilitate viral entry. Our study suggests that AIs, in addition to having potent antientry activity, could contribute to immune system homeostasis in individuals infected with HIV-1 that can engage CXCR4, thereby mitigating the increased risk of adverse clinical events observed in such individuals on current antiretroviral regimens.
Development of NS3/4A Protease-Based Reporter Assay Suitable for Efficiently Assessing Hepatitis C Virus Infection
Authors: Pan Kao-Lu , Lee Jin-Ching , Sung Hsing-Wen , Chang Teng-Yuang , Hsu John T.-A.
Published: September 2009

A cell culture system for the production of hepatitis C virus (HCV) whole virions has greatly accelerated studies of the virus life cycle and the discovery of anti-HCV agents. However, the quantification of the HCV titers in a whole-virus infection/replication system currently relies mostly on reverse transcription-PCR or immunofluorescence assay, which would be cumbersome for high-throughput drug screening. To overcome this problem, this study has generated a novel cell line, Huh7.5-EG(Δ4B5A)SEAP, that carries a dual reporter, EG(Δ4B5A)SEAP. The EG(Δ4B5A)SEAP reporter is a viral protease-cleavable fusion protein in which the enhanced green fluorescence protein is linked to secreted alkaline phosphatase (SEAP) in frame via Δ4B5A, a short peptide cleavage substrate for NS3/4A viral protease. This study demonstrates that virus replication/infection in the Huh7.5-EG(Δ4B5A)SEAP cells can be quantitatively indicated by measuring the SEAP activity in cell culture medium. The levels of SEAP released from HCV-infected Huh7.5-EG(Δ4B5A)SEAP cells correlated closely with the amounts of HCV in the inocula. The Huh7.5-EG(Δ4B5A)SEAP cells were also shown to be a suitable host for the discovery of anti-HCV inhibitors by using known compounds that target multiple stages of the HCV life cycle. The Z′-factor of this assay ranged from 0.64 to 0.74 in 96-well plates, indicating that this reporter system is suitable for high-throughput screening of prospective anti-HCV agents.
Salmonella entericaSerovar Typhimurium Exploits Toll-Like Receptor Signaling during the Host-Pathogen Interaction
Authors: Wong Christine E. , Sad Subash , Coombes Brian K.
Published: September 2009

Salmonellasurvives and replicates in host cells by using a type III secretion system to evade host immune defenses. The innate immune system plays an important role as a first line of defense against pathogens and is mediated in part by Toll-like receptors (TLRs); however, the infection dynamics ofSalmonella entericaserovar Typhimurium within macrophages stimulated with TLR ligands is poorly understood. We studied the infection dynamics ofSalmonellain murine macrophages previously exposed to TLR ligands and report that treatment of macrophages with four different TLR agonists resulted in their increased phagocytic capacity towardSalmonellabut not fluorescent microspheres. Further analysis revealed that the intracellular replication ofSalmonellawas enhanced in TLR-stimulated macrophages in a manner requiring a functional type III secretion system and enhanced transcriptional activity of thesseAvirulence gene operon. Studies of mice that normally resolve an acute primary infection withSalmonellarevealed that pretreatment of animals with CpG DNA had a detrimental effect on disease outcome. CpG-treated mice infected withSalmonellaall succumbed to infection and had higher bacterial loads in the spleen than did control animals. These data suggest thatSalmonellacan exploit macrophages activated via the innate immune system for increased intracellular survival.
Binding and Internalization ofClostridium botulinumC2 Toxin
Authors: Nagahama Masahiro , Hagiyama Tohko , Kojima Takashi , Aoyanagi Kouhei , Takahashi Chihiro , Oda Masataka , Sakaguchi Yoshihiko , Oguma Keiji , Sakurai Jun
Published: September 2009

Clostridium botulinumC2 toxin is a binary toxin composed of an enzymatic component (C2I) and a binding component (C2II). The activated binding component (C2IIa) forms heptamers, and the oligomer with C2I is taken up by receptor-mediated endocytosis. We investigated the binding and internalization of C2IIa in cells. The C2IIa monomer formed oligomers on lipid rafts in membranes of MDCK cells. Methyl-beta-cyclodextrin inhibited the binding of C2IIa and the rounding of the cells induced by C2I plus C2IIa. C2I was localized to the rafts in the presence, but not the absence, of C2IIa. Surface plasmon resonance analysis revealed that C2I bound to the oligomer of C2IIa, but not the monomer of C2IIa. C2I and C2IIa were rapidly internalized in the cells. LY294002, a phosphatidylinositol 3-kinase (PI3K) inhibitor, inhibited the internalization of C2IIa in the cells and the rounding activity in the presence of C2I plus C2IIa. Incubation of the cells with C2I plus C2IIa resulted in the activation of PI3K and in phosphorylation of phosphoinositide-dependent kinase 1 and protein kinase B/Akt (Akt), but that with C2IIa alone did not. Akt inhibitor X, an Akt phosphorylation inhibitor, inhibited the rounding activity but not the internalization of C2IIa. The results suggest that the binding of C2I to the oligomer of C2IIa on rafts triggers the activation of the PI3K-Akt signaling pathway and, in turn, the initiation of endocytosis.
Werner syndrome as a possible cause of non-alcoholic steatohepatitis
Authors: Hashizume H , Sato K , Takagi H , Kanda D , Kashihara T , Kiso S , Mori M
Published: September 2009

Non-alcoholic steatohepatitis (NASH) is characterised by steatosis, liver cell injuries, the presence of a mixed inflammatory lobular infiltrate, and variable degrees of fibrosis. Werner syndrome (WS) is a rare autosomal recessive disease characterised by the premature onset of multiple age-related disorders. Central obesity and insulin resistance are common symptoms of both NASH and WS. Three cases were studied to evaluate the association between WS and NASH. NASH was diagnosed by liver biopsies and imaging studies following the exclusion of alcohol consumption, viral disease or autoimmune liver disease. Liver histology was compatible with NASH in all cases. Liver dysfunction, hyperlipidaemia, insulin resistance and regional increase of intra-abdominal fat even though the body mass indices were all normal or low, were observed. Metabolic disorders due to WS may complicate and cause NASH. Hence, the observed clinical association between WS and NASH suggests that patients with WS should also be screened for NASH.
ON A CLASS OF SINGULAR NONLINEAR TRAVELING WAVE EQUATIONS (II): AN EXAMPLE OF GCKdV EQUATIONS
Authors: LI JIBIN , ZHANG YI , ZHAO XIAOHUA
Published: September 2009

By using the method of dynamical systems, we continuously study the dynamical behavior for the first class of singular nonlinear traveling wave systems. As an example, the traveling wave solutions for a generalized coupled KdV equations are discussed. Exact explicit parametric representations of solitary wave solutions, periodic wave solutions and kink wave solutions are given.
A SCALAR SIGN FUNCTION APPROACH TO DIGITAL CONTROL OF CONTINUOUS-TIME CHAOTIC SYSTEMS WITH STATE CONSTRAINTS
Authors: WU JIAN , SHIEH LEANG S. , TSAI JASON S. H.
Published: September 2009

In this paper, a scalar sign function-based digital design methodology is presented to develop a digital tracking controller for the continuous-time chaotic systems with absolute value state constraints. A scalar sign function, which is the counterpart of the well-known matrix sign function, is utilized to approximately represent the absolute value state term by a rational function. As a result, the original state constrained nonsmooth nonlinear system becomes a smooth nonlinear system having rational nonlinear terms. Then, an optimal linearization technique is applied to the afore-mentioned nonlinear system for finding an optimal linearization model, which has the exact dynamics of the original nonlinear system at any operating point of interest with minimal modeling error in the vicinity of the operating point on the trajectory. To overcome the effect of modeling errors and to quickly track the desired reference signals, a high-gain optimal analog tracker is designed for the obtained linear model. For practical implementation of the high-gain analog tracker, the prediction-based digital redesign technique is utilized to obtain a low-gain digital tracker for digital control of the sampled-data nonlinear system with constrained states. Chua's chaotic circuits are used to demonstrate the effectiveness of the proposed approach.
LIMIT CYCLES FOR A CLASS OF QUINTIC NEAR-HAMILTONIAN SYSTEMS NEAR A NILPOTENT CENTER
Authors: JIANG JIAO , ZHANG JIZHOU , HAN MAOAN
Published: September 2009

In this paper we deal with a centrally symmetric quintic near-Hamiltonian system whose unperturbed system is a simple cubic Hamiltonian system having a nilpotent center. We prove that the system can have ten limit cycles by using a homoclinic bifurcation method based on stability-change.
ALTERNATED JULIA SETS AND CONNECTIVITY PROPERTIES
Authors: DANCA MARIUS-F. , ROMERA M. , PASTOR G.
Published: September 2009

In this work we present the alternated Julia sets, obtained by alternated iteration of two maps of the quadratic family [Formula: see text] and prove analytically and computationally that these sets can be connected, disconnected or totally disconnected verifying the known Fatou–Julia theorem in the case of polynomials of degree greater than two. Some examples are presented.
A NONLINEAR DYNAMICS PERSPECTIVE OF WOLFRAM'S NEW KIND OF SCIENCE PART XI: PERIOD-2 RULES
Authors: CHUA LEON O. , PAZIENZA GIOVANNI E. , SHIN JINWOOK
Published: September 2009

The 11th part of our tour through one-dimensional binary Cellular Automata concerns period-2 rules, which form the second group in our classification of the 88 globally-independent CA rules according to the properties of their periodic orbits. In this article, we display the basin tree diagrams of all period-2 rules along with their time-2 characteristic functions, and then we prove that all rules belonging to group 2 have robust period-2 ω-limit orbits for any finite, and infinite, bit string length. This rigorous result, which pairs with the one about period-1 rules given in the tenth installment of our chronicle, confirms what we stated about period-2 rules on the basis of empirical evidence. In the second part of this tutorial, we introduce the notion of quasi global-equivalence and prove that there are only 82 quasi globally-independent CA rules. For the first time, we show that the space-time patterns of globally-independent local rules can depend on each other, and we present an example of quasi-global transformation. We also define the super string 𝄞, and its unique decimal representation x𝄞, dubbed the super decimal, which provides a completely transparent yet rigorous proof that rule [Formula: see text] is chaotic when L → ∞. Moreover, we present the basin tree generation formulas, which uncover the analytical relationships between basin trees of globally-equivalent rules. Last but not least, for pedagogical and epistemological reasons, we conclude this paper with the selection of rule[Formula: see text], instead of rule [Formula: see text], as the prototypic universal Turing machine for our future discourse.
DARK MATTER ANNIHILATION IN THE GRAVITATIONAL FIELD OF A BLACK HOLE
Authors: BAUSHEV ANTON
Published: September 2009

In this paper we consider dark matter particle annihilation in the gravitational field of black holes. We obtain the exact distribution function of the infalling dark matter particles, and compute the resulting flux and spectra of gamma rays coming from the objects. It is shown that the dark matter density significantly increases near a black hole. Particle collision energy becomes very high, affecting relative cross-sections of various annihilation channels. We also discuss possible experimental consequences of these effects.
EQUATION OF STATE FOR DENSE SUPERNOVA MATTER
Authors: MOUSTAKIDIS C. C.
Published: September 2009

We provide an equation of state for high density supernova matter by applying a momentum-dependent effective interaction. We focus on the study of the equation of state of high density and high temperature nuclear matter containing leptons (electrons and neutrinos) under the chemical equilibrium condition. The conditions of charge neutrality and equilibrium under the β-decay process lead first to the evaluation of the lepton fractions and afterward to the evaluation of internal energy, pressure, entropy and, in total to the equation of state of hot nuclear matter for various isothermal cases. Thermal effects on the properties and equation of state of nuclear matter are evaluated and analyzed in the framework of the proposed effective interaction model. Since supernova matter is characterized by a constant entropy, we also present the thermodynamic properties for the isentropic case. Special attention is devoted to the study of the contribution of the components of β-stable nuclear matter to the entropy per particle, a quantity of great interest for the study of structure and collapse of supernovas.
TIME VARIATION OF THE GRAVITATIONAL CONSTANT AND SECULAR EVOLUTION OF THE ORBIT OF BINARY STARS
Authors: LI LIN-SEN
Published: September 2009

The author of this paper examines the influence of time variation of the gravitational constant on the evolution of the orbital elements of binary stars. The theoretical results show that the semimajor axis, eccentricity and mean longitude exhibit periodic, secular and mixed periodic variation, but the longitude of the periastron exists in periodic and mixed periodic variation, but not secular variation. The inclination and ascending node exhibit no variation. In addition, the limits of the secular evolution of the orbit of six binary stars due to time variation of the gravitational constant are estimated. The numerical results are given. The theoretical results are discussed and conclusions drawn.
VISCOUS CARDASSIAN UNIVERSE
Authors: SUN CHANG-BO , WANG JIA-LING , LI XIN-ZHOU
Published: September 2009

The viscous Cardassian cosmology is discussed, assuming that there is a bulk viscosity in the cosmic fluid. The dynamical analysis indicates that there exists a singular curve in the phase diagram of the viscous Cardassian model. In the viscous PL model, the equation-of-state parameter wk is no longer a constant and it can cross the cosmological constant divide wΛ = -1, in contrast with the same problem of the ordinary PL model. Other models possess similar characteristics. For MP and exp models, wk evolves more near -1 than the case without viscosity. The bulk viscosity also affects the virialization process of a collapse system in the universe: R vir /R ta is increasingly large when the bulk viscosity is increasing. In other words, the bulk viscosity retards the progress of the collapse system. In addition, we fit the viscous Cardassian models to current type Ia supernova data and give the best fit value of the model parameters, including the bulk viscosity coefficient τ.
WILL IT BE POSSIBLE TO MEASURE INTRINSIC GRAVITOMAGNETISM WITH LUNAR LASER RANGING?
Authors: IORIO LORENZO
Published: September 2009

In this paper we mainly explore the possibility of measuring the action of the intrinsic gravitomagnetic field of the rotating Earth on the orbital motion of the Moon with the lunar laser ranging (LLR) technique. Expected improvements in it should push the precision in measuring the Earth–Moon range to the mm level; the present-day root mean square (RMS) accuracy in reconstructing the radial component of the lunar orbit is about 2 cm; its harmonic terms can be determined at the mm level. The current uncertainty in measuring the lunar precession rates is about 10-1 milliarcseconds per year. The Lense–Thirring secular — i.e. averaged over one orbital period — precessions of the node and the perigee of the Moon induced by the Earth's spin angular momentum amount to 10-3 milliarcseconds per year, yielding transverse and normal shifts of 10-1-10-2 cm yr-1. In the radial direction there is only a short-period — i.e. nonaveraged over one orbital revolution — oscillation with an amplitude of 10-5 m. Major limitations come also from some systematic errors induced by orbital perturbations of classical origin, such as the secular precessions induced by the Sun and the oblateness of the Moon, whose mismodeled parts are several times larger than the Lense–Thirring signal. The present analysis holds also for the Lue–Starkman perigee precession due to the multidimensional braneworld model by Dvali, Gabadadze and Porrati (DGP); indeed, it amounts to about 5 × 10-3 milliarcseconds per year.
A ROUTING AND WAVELENGTH ASSIGNMENT STRATEGY FOR SUCCESSFUL TRANSMISSION IN OPTICAL NETWORKS
Authors: AGUSTÍ-TORRA ANNA , CERVELLÓ-PASTOR CRISTINA , FIOL MIQUEL A.
Published: September 2009

Optical Burst and Packet Switching (OBS/OPS) are techniques designed to serve higher-layer packet-based communication protocols by allowing statistical multiplexing. Since OBS and OPS networks provide connectionless transport, they both suffer from contention, which occurs when multiple communications want to use simultaneously the same wavelength in a link. This paper proposes a Routing and Wavelength Assignment (RWA) strategy based on the concept of (rooted) collision-free digraph, which represents all paths assigned by the routing to those communications sharing a wavelength. Using the proposed RWA strategy, the contention problem can be successfully solved by using simple mechanisms based on adding a suitable additional delay to burst/packet transmissions. Here we define and characterize the routing-antipodal networks, in which we can define [n/2] pairs of arc-disjoint collision-free digraphs (with n being the number of nodes) that altogether include all arcs of the network. This implies that, using [n/2] wavelengths, we can achieve connectivity between any pair of nodes under the wavelength-continuity constraint. Solutions with fewer wavelengths are also feasible. In particular, if the routing-antipodal network has a trail that passes through all vertices at least once, one wavelength is enough to ensure connectivity between each pair of nodes. We also show that the line digraph technique provides us with a simple tool for obtaining proper collision-free digraphs. The proposed method works in either a synchronous or an asynchronous transmission environment. Also, the arriving and length burst/packet distributions can be of any type, provided that the maximum theoretical offered load is not exceeded.
GENERALIZING AND FINE TUNING TRIPLE-LOOP NETWORKS
Authors: LIN BEY-CHI , HWANG F. K.
Published: September 2009

Several triple-loop networks have been recently proposed and their efficiency studied. However, the number of cases for which one of these networks exists is sparse. We extend these networks to larger classes to enhance their realizability. We also give a heuristic method to optimize the network parameters to increase their efficiency. Finally, we determine their wide diameters to understand their fault-tolerance performance.
AN ANALYTICAL COMPARISON OF THE SPIDERGON AND RECTANGULAR MESH NoCs
Authors: MOADELI MAHMOUD , SHAHRABI ALI , VANDERBAUWHEDE WIM , OULD-KHAOUA MOHAMED
Published: September 2009

Networks on chip (NoC) emerged as a structured and scalable communication medium for development of future Systems-on-Chip (SoC). Due to its unique features in terms of scalability and ease of synthesis, the (rectangular) mesh topology is regarded as an appropriate candidate for on-chip network development. On the other hand, the Spidergon NoC has been proposed as an alternative topology to realize cost effective multi-processor SoC (MPSoC) development. This paper presents analytical models of the average message latency and network throughput for both rectangular mesh and the Spidergon NoC employing wormhole switching. For each model, the validity of the analysis is verified by comparing the analytical model against the results produced by a discrete event simulator. Using the developed models, we then compare these topologies from different perspectives including manufacturing issues, message latency and network throughput.
SAWTOOTH BEHAVIOUR OF NATURAL BIO-MACROMOLECULES AND SYNTHETIC POLYMERS
Authors: WANG YING , CHEN YOUPING
Published: September 2009

In this paper, we present molecular dynamic simulation of natural and synthetic polymers, including tropocollagen (TC), Lustrin A and poly-acrylic acid (PAA), located inside the bone, abalone shells and bio-mimetic materials, respectively. The objective of these simulations is to investigate the well-known `sawtooth' behaviour observed in atomic force microscopy (AFM) experiments of bio-minerals. We have observed the sawtooth behaviour in the force-extension curves of Lustrin A and PAA only when their interactions with calcareous minerals are considered. On the other hand, the TC does not show the sawtooth behaviour even in the presence of calcareous minerals. We have also simulated a NC1 α-helix and a β-sheet domain to investigate the structural effect on the sawtooth behaviour. Based on these simulation results, we propose a new toughening mechanism that the electrostatic force in the organic–inorganic interface plays a critical role in the sawtooth behaviour. These simulated phenomena can explain some of the AFM experiment observation and provide insight into the molecular mechanism of the super toughness of bio-minerals.
A MULTI-SCALE NONEQUILIBRIUM MOLECULAR DYNAMICS ALGORITHM AND ITS APPLICATIONS
Authors: SHENG NI , LI SHAOFAN
Published: September 2009

In this paper, we introduce a multi-scale nonequilibrium molecular dynamics (MS-NEMD) model that is capable of simulating nano-scale thermal–mechanical interactions. Recent simulation results using the MS-NEMD model are presented. The MS-NEMD simulation generalises the nonequilibrium molecular dynamics (NEMD) simulation to the setting of concurrent multi-scale simulation. This multi-scale framework is based on a novel concept of multi-scale canonical ensemble. Under this concept, each coarse scale finite element (FE) node acts as a thermostat, while the atoms associated with each node are assumed to be in a local equilibrium state within one coarse scale time step. The coarse scale mean field is solved by the FE method based on a coarse-grained thermodynamics model; whereas in the fine scale the NEMD simulation is driven by the random force that is regulated by the inhomogeneous continuum filed through a distributed Nośe–Hoover thermostat network. It is shown that the fine scale distribution function is canonical in the sense that it obeys a drifted local Boltzmann distribution.
STRUCTURAL PHASE TRANSITIONS IN A DISCRETE ONE-DIMENSIONAL CHAIN
Authors: VEDANTAM SRIKANTH , MOHANRAJ S.
Published: September 2009

We present a lattice dynamics model for describing structural phase transitions in a one-dimensional setting. The model comprises of a chain of discrete masses interacting with nearest neighbours. In order to drive a temperature dependent exchange of stability between two phases, we allow the interatomic potential to be dependent on the temperature. The system exhibits thermal phase transitions accompanied by latent heat.
An Object-Oriented Design for Two-Dimensional Vortex Particle Methods
Authors: Ramachandran Prabhu , Ramakrishna M.
Published: September 2009

Vortex methods offer a grid-free alternative to simulating incompressible, viscous, fluid flows. They require the use of fairly sophisticated algorithms and can be complicated to implement for general flows. This article describes an object-oriented design used to implement a vortex particle based flow solver in two dimensions. We provide an overview of the various abstractions that arose as a result of this design. Several of the algorithms have common components that may be abstracted and reused. We demonstrate how the design allowed us to derive the traditional benefits of OOD. In addition, we show how the design directly suggested elegant generalizations of existing algorithms. Finally, we show the benefits of using software testing techniques and building a powerful scripting layer for the library.
pyMDO
Authors: Martins Joaquim R. R. A. , Marriage Christopher , Tedford Nathan
Published: September 2009

We present pyMDO, an object-oriented framework that facilitates the usage and development of algorithms for multidisciplinary optimization (MDO). The resulting implementation of the MDO methods is efficient and portable. The main advantage of the proposed framework is that it is flexible, with a strong emphasis on object-oriented classes and operator overloading, and it is therefore useful for the rapid development and evaluation of new MDO methods. The top layer interface is programmed in Python and it allows for the layers below the interface to be programmed in C, C++, Fortran, and other languages. We describe an implementation of pyMDO and demonstrate that we can take advantage of object-oriented programming to obtain intuitive, easy-to-read, and easy-to-develop codes that are at the same time efficient. This allows developers to focus on the new algorithms they are developing and testing, rather than on implementation details. Examples demonstrate the user interface and the corresponding results show that the various MDO methods yield the correct solutions.
Accurate Numerical Integration of Perturbed Oscillatory Systems in Two Frequencies
Authors: García-Alonso Fernando , Reyes José A. , Ferrándiz José M. , Vigo-Aguiar Jesús
Published: September 2009

Highly accurate long-term numerical integration of nearly oscillatory systems of ordinary differential equations (ODEs) is a common problem in astrodynamics. Scheifele’s algorithm is one of the excellent integrators developed in the past years to take advantage of special transformations of variables such as the K-S set. It is based on using expansions in series of the so-called
G
-functions, and generalizes the Taylor series integrators but with the remarkable property of integrating without truncation error oscillations in one basic known frequency. A generalization of Scheifele’s method capable of integrating exactly harmonic oscillations in two known frequencies is developed here, after introducing a two parametric family of analytical
φ
-functions. Moreover, the local error contains the perturbation parameter as a factor when the algorithm is applied to perturbed problems. The good behavior and the long-term accuracy of the new method are shown through several examples, including systems with low- and high-frequency constituents and a perturbed satellite orbit. The new methods provide significantly higher accuracy and efficiency than a selection of well-reputed general-purpose integrators and even recent symplectic or symmetric integrators, whose good behavior in the long-term integration of the Kepler problem and the other oscillatory systems is well stated in recent literature.
Processing spatial skyline queries in both vector spaces and spatial network databases
Authors: Sharifzadeh Mehdi , Shahabi Cyrus , Kazemi Leyla
Published: September 2009

In this article, we first introduce the concept of Spatial Skyline Queries (SSQ). Given a set of data points
P
and a set of query points
Q
, each data point has a number of
derived spatial
attributes each of which is the point's distance to a query point. An SSQ retrieves those points of
P
which are not dominated by any other point in
P
considering their derived spatial attributes. The main difference with the regular skyline query is that this
spatial domination
depends on the location of the query points
Q
. SSQ has application in several domains such as emergency response and online maps. The main intuition and novelty behind our approaches is that we exploit the geometric properties of the SSQ problem space to avoid the exhaustive examination of all the point pairs in
P
and
Q
. Consequently, we reduce the complexity of SSQ search from
O
(|
P
|
2
|
Q
|) to
O
(|
S
|
2
|
C
| + √|
P
|), where |
S
| and |
C
| are the solution size and the number of vertices of the convex hull of
Q
, respectively.

Considering Euclidean distance, we propose two algorithms, B
2
S
2
and VS
2
, for static query points and one algorithm, VCS
2
, for streaming
Q
whose points change location over time (e.g., are mobile). VCS
2
exploits the pattern of change in
Q
to avoid unnecessary recomputation of the skyline and hence efficiently perform updates. We also propose two algorithms, SNS
2
and VSNS
2
, that compute the spatial skyline with respect to the network distance in a spatial network database. Our extensive experiments using real-world datasets verify that both R-tree-based B
2
S
2
and Voronoi-based VS
2
outperform the best competitor approach in terms of both processing time and I/O cost. Furthermore, their output computed based on Euclidean distance is a good approximation of the spatial skyline in network space. For accurate computation of spatial skylines in network space, our experiments showed the superiority of VSNS
2
over SNS
2
.
Semantics and complexity of SPARQL
Authors: Pérez Jorge , Arenas Marcelo , Gutierrez Claudio
Published: September 2009

SPARQL is the standard language for querying RDF data. In this article, we address systematically the formal study of the database aspects of SPARQL, concentrating in its graph pattern matching facility. We provide a compositional semantics for the core part of SPARQL, and study the complexity of the evaluation of several fragments of the language. Among other complexity results, we show that the evaluation of general SPARQL patterns is PSPACE-complete. We identify a large class of SPARQL patterns, defined by imposing a simple and natural syntactic restriction, where the query evaluation problem can be solved more efficiently. This restriction gives rise to the class of well-designed patterns. We show that the evaluation problem is coNP-complete for well-designed patterns. Moreover, we provide several rewriting rules for well-designed patterns whose application may have a considerable impact in the cost of evaluating SPARQL queries.
Keyword search over relational tables and streams
Authors: Markowetz Alexander , Yang Yin , Papadias Dimitris
Published: September 2009

Relational Keyword Search
(R-KWS) provides an intuitive way to query relational data without requiring SQL, or knowledge of the underlying schema. In this article we describe a comprehensive framework for R-KWS covering snapshot queries on conventional tables and continuous queries on relational streams. Our contributions are summarized as follows: (i) We provide formal semantics, addressing the temporal validity and order of results, spanning uniformly over tables and streams; (ii) we investigate two general methodologies for query processing,
graph based
and
operator based
, that resolve several problems of previous approaches; and (iii) we develop a range of algorithms and optimizations covering both methodologies. We demonstrate the effectiveness of R-KWS, as well as the significant performance benefits of the proposed techniques, through extensive experiments with static and streaming datasets.
Using Short Dependency Relations from Auto-Parsed Data for Chinese Dependency Parsing
Authors: Chen Wenliang , Kawahara Daisuke , Uchimoto Kiyotaka , Zhang Yujie , Isahara Hitoshi
Published: September 2009

Dependency parsing has become increasingly popular for a surge of interest lately for applications such as machine translation and question answering. Currently, several supervised learning methods can be used for training high-performance dependency parsers if sufficient labeled data are available.

However, currently used statistical dependency parsers provide poor results for words separated by long distances. In order to solve this problem, this article presents an effective dependency parsing approach of incorporating short dependency information from unlabeled data. The unlabeled data is automatically parsed by using a deterministic dependency parser, which exhibits a relatively high performance for short dependencies between words. We then train another parser that uses the information on short dependency relations extracted from the output of the first parser. The proposed approach achieves an unlabeled attachment score of 86.52%, an absolute 1.24% improvement over the baseline system on the Chinese Treebank data set. The results indicate that the proposed approach improves the parsing performance for longer distance words.
Word-Wise Thai and Roman Script Identification
Authors: Chanda Sukalpa , Pal Umapada , Terrades Oriol Ramos
Published: September 2009

In some Thai documents, a single text line of a printed document page may contain words of both Thai and Roman scripts. For the Optical Character Recognition (OCR) of such a document page it is better to identify, at first, Thai and Roman script portions and then to use individual OCR systems of the respective scripts on these identified portions. In this article, an SVM-based method is proposed for identification of word-wise printed Roman and Thai scripts from a single line of a document page. Here, at first, the document is segmented into lines and then lines are segmented into character groups (words). In the proposed scheme, we identify the script of a character group combining different character features obtained from structural shape, profile behavior, component overlapping information, topological properties, and water reservoir concept, etc. Based on the experiment on 10,000 data (words) we obtained 99.62% script identification accuracy from the proposed scheme.
Web Search Clustering and Labeling with Hidden Topics
Authors: Nguyen Cam-Tu , Phan Xuan-Hieu , Horiguchi Susumu , Nguyen Thu-Trang , Ha Quang-Thuy
Published: September 2009

Web search clustering is a solution to reorganize search results (also called “snippets”) in a more convenient way for browsing. There are three key requirements for such post-retrieval clustering systems: (1) the clustering algorithm should group similar documents together; (2) clusters should be labeled with descriptive phrases; and (3) the clustering system should provide high-quality clustering without downloading the whole Web page.

This article introduces a novel framework for clustering Web search results in Vietnamese which targets the three above issues. The main motivation is that by enriching short snippets with hidden topics from huge resources of documents on the Internet, it is able to cluster and label such snippets effectively in a topic-oriented manner without concerning whole Web pages. Our approach is based on recent successful topic analysis models, such as Probabilistic-Latent Semantic Analysis, or Latent Dirichlet Allocation. The underlying idea of the framework is that we collect a very large external data collection called “universal dataset,” and then build a clustering system on both the original snippets and a rich set of hidden topics discovered from the universal data collection. This can be seen as a richer representation of snippets to be clustered. We carry out careful evaluation of our method and show that our method can yield impressive clustering quality.
On uniform resampling and gaze analysis of bidirectional texture functions
Authors: Filip Jiří , Chantler Michael J. , Haindl Michal
Published: September 2009

The use of illumination and view-dependent texture information is recently the best way to capture the appearance of real-world materials accurately. One example is the Bidirectional Texture Function. The main disadvantage of these data is their massive size. In this article, we employ perceptually-based methods to allow more efficient handling of these data. In the first step, we analyse different uniform resampling by means of a psychophysical study with 11 subjects, comparing original data with rendering of a uniformly resampled version over the hemisphere of illumination and view-dependent textural measurements. We have found that down-sampling in view and illumination azimuthal angles is less apparent than in elevation angles and that illumination directions can be down-sampled more than view directions without loss of visual accuracy. In the second step, we analyzed subjects gaze fixation during the experiment. The gaze analysis confirmed results from the experiment and revealed that subjects were fixating at locations aligned with direction of main gradient in rendered stimuli. As this gradient was mostly aligned with illumination gradient, we conclude that subjects were observing materials mainly in direction of illumination gradient. Our results provide interesting insights in human perception of real materials and show promising consequences for development of more efficient compression and rendering algorithms using these kind of massive data.
Auditory self-motion simulation is facilitated by haptic and vibrational cues suggesting the possibility of actual motion
Authors: Riecke Bernhard E. , Feuereissen Daniel , Rieser John J.
Published: September 2009

Sound fields rotating around stationary blindfolded listeners sometimes elicit auditory circular vection, the illusion that the listener is physically rotating. Experiment 1 investigated whether auditory circular vection depends on participants' situational awareness of “movability,” that is, whether they sense/know that actual motion is possible or not. While previous studies often seated participants on movable chairs to suspend the disbelief of self-motion, it has never been investigated whether this does, in fact, facilitate auditory vection. To this end, 23 blindfolded participants were seated on a hammock chair with their feet either on solid ground (“movement impossible”) or suspended (“movement possible”) while listening to individualized binaural recordings of two sound sources rotating synchronously at 60°/s. Although participants never physically moved, situational awareness of movability facilitated auditory vection. Moreover, adding slight vibrations like the ones resulting from actual chair rotation increased the frequency and intensity of vection. Experiment 2 extended these findings and showed that nonindividualized binaural recordings were as effective in inducing auditory circular vection as individualized recordings. These results have important implications both for our theoretical understanding of self-motion perception and for the applied field of self-motion simulations, where vibrations, nonindividualized binaural sound, and the cognitive/perceptual framework of movability can typically be provided at minimal cost and effort.
Scalable apprenticeships
Authors: Long Philip D.
Published: September 2009

Today's students are typically over scheduled and hyper-connected, yet increasingly disconnected with their education. The classroom into which they step for core science, technology and engineering subjects is often removed from both the practice of the disciplines being taught and the technology tools which pervade other aspects of their life. A significant challenge is to reconnect the excitement and discovery that drew faculty into their disciplines back to the learning environments of STEM and CSE students they teach. Peer Instruction (inserting discussion and formative assessment into lecture) and project-based learning are two promising attempts at recapturing the process of science and engineering in introductory coursers.

Recent experiments in freshman project-based seminars such as nanoscale engineering and a major redesign of the introductory Course 6 (Computer Science and Electrical Engineering) at MIT are exploring ways to bring apprenticeship back to both small and large classes. Through Python-based tutoring tools, layered mentoring that includes just-in-time "guest laboratory assistants" to achieve 1:4 instructor-student ratios in large courses, and careful attention to learning space design new strategies for scaled apprenticeships are being forged.
Neither rocket science nor washing machine science, but computer science
Authors: Boyle Roger D.
Published: September 2009

Greyer haired computer scientists can easily remember the glory days, but waves of recent publications and opinion seem to have seen clouds on our horizon.

But maybe we worry too much and too soon. Every fairytale heroine goes through a glum patch before living happily ever after, and perhaps Prince Charming is just around the academic corner.

How did we get into the glum patch? What will Prince Charming look like when he sweeps us off our feet? What will life be like for us back at his place? We'll talk a bit about how we got to where we are in an effort to put ourselves into perspective, then think about the opportunities the Prince might bring.

But it's always possible that fickle Prince Charming has found another {boy, girl} and we will wait in vain: so we'll look closely at these clouds, and think about how real they are.

And thence well have a go at "you are here" for CS in universities, and that might help us in moving towards Prince Charming, wherever he may be, and not towards the cloudy horizon. Knowing where we are and where we are trying to head should then have some relevance for how and what we teach our students: they don't like (or need) history lessons, but they are unlikely to be able to head for tomorrow without knowing where yesterday was; they need a comprehension of the grand challenges that face us (but maybe not the "Grand Challenges"). They should know they aren't going to be building rockets, but they aren't going to be mending washing machines either.

But we probably also need to think about where they have come from, because they certainly aren't grey haired computer scientists.