bluuebunny/crossref_metadata_2025 huggingface dataset:
Mycobacteria Exploit p38 Signaling To Affect CD1 Expression and Lipid Antigen Presentation by Human Dendritic Cells
Authors: Gagliardi Maria Cristina , Teloni Raffaela , Giannoni Federico , Mariotti Sabrina , Remoli Maria Elena , Sargentini Valeria , Videtta Melissa , Pardini Manuela , De Libero Gennaro , Coccia Eliana Marina , Nisini Roberto
Published: September 2009

Group I CD1 proteins are specialized antigen-presenting molecules that present both microbial and self lipid antigens to CD1-restricted α/β T lymphocytes. The production of high levels of gamma interferon and lysis of infected macrophages by lipid-specific T lymphocytes are believed to play pivotal roles mainly in the defense against mycobacterial infections. We previously demonstrated thatMycobacterium tuberculosisand bacillus Calmette-Guérin (Mycobacterium bovisBCG) induce human monocytes to differentiate into CD1−dendritic cells (DC), which cannot present lipid antigens to specific T cells. Here, we show that in human monocytes mycobacteria trigger phosphorylation of p38 mitogen-activated protein kinase to inhibit CD1 expression in DC derived from infected monocytes. Pretreatment with a specific p38 inhibitor renders monocytes insensitive to mycobacterial subversion and allows them to differentiate into CD1+DC, which are fully capable of presenting lipid antigens to specific T cells. We also report that one of the pathogen recognition receptors triggered by BCG to activate p38 is complement receptor 3 (CR3), as shown by reduced p38 phosphorylation and partial reestablishment of CD1 membrane expression obtained by CR3 blockade before infection. In conclusion, we propose that p38 signaling is a novel pathway exploited by mycobacteria to affect the expression of CD1 antigen-presenting cells and avoid immune recognition.
The Major Neutralizing Antibody Responses to Recombinant Anthrax Lethal and Edema Factors Are Directed to Non-Cross-Reactive Epitopes
Authors: Nguyen Melissa L. , Terzyan Simon , Ballard Jimmy D. , James Judith A. , Farris A. Darise
Published: September 2009

Anthrax lethal and edema toxins (LeTx and EdTx, respectively) form by binding of lethal factor (LF) or edema factor (EF) to the pore-forming moiety protective antigen (PA). Immunity to LF and EF protects animals from anthrax spore challenge and neutralizes anthrax toxins. The goal of the present study is to identify linear B-cell epitopes of EF and to determine the relative contributions of cross-reactive antibodies of EF and LF to LeTx and EdTx neutralization. A/J mice were immunized with recombinant LF (rLF) or rEF. Pools of LF or EF immune sera were tested for reactivity to rLF or rEF by enzyme-linked immunosorbent assays, in vitro neutralization of LeTx and EdTx, and binding to solid-phase LF and EF decapeptides. Cross-reactive antibodies were isolated by column absorption of EF-binding antibodies from LF immune sera and by column absorption of LF-binding antibodies from EF immune sera. The resulting fractions were subjected to the same assays. Major cross-reactive epitopes were identified as EF amino acids (aa) 257 to 268 and LF aa 265 to 274. Whole LF and EF immune sera neutralized LeTx and EdTx, respectively. However, LF sera did not neutralize EdTx, nor did EF sera neutralize LeTx. Purified cross-reactive immunoglobulin G also failed to cross-neutralize. Cross-reactive B-cell epitopes in the PA-binding domains of whole rLF and rEF occur and have been identified; however, the major anthrax toxin-neutralizing humoral responses to these antigens are constituted by non-cross-reactive epitopes. This work increases understanding of the immunogenicity of EF and LF and offers perspective for the development of new strategies for vaccination against anthrax.
Yersinia pseudotuberculosisVirulence Determinants Invasin, YopE, and YopT Modulate RhoG Activity and Localization
Authors: Mohammadi Sina , Isberg Ralph R.
Published: September 2009

TheYersinia pseudotuberculosissurface protein invasin binds to multiple β1 integrins with high affinity, leading to misregulation of Rac1 activity. Upon host cell binding, alteration of Rho GTPase activity results from the action of severalYersiniaouter proteins (Yops) that are translocated into the cytoplasm. We report here that three virulence determinants encoded byY. pseudotuberculosismanipulate the Rho GTPase RhoG.Y. pseudotuberculosisbinding to cells caused robust recruitment of RhoG to the site of attachment, which required high-affinity invasin-β1 integrin association. Furthermore, inactivation of RhoG significantly reduced the efficiency of invasin-mediated bacterial internalization. To investigate the activation state of RhoG, a fluorescence resonance energy transfer-based activation biosensor was developed and used to show distinct spatial activation of RhoG at the site of bacterial attachment. The biosensor was also used to show efficient RhoG inactivation byY. pseudotuberculosisYopE, a potent Rho GTPase activating protein. Additionally, RhoG mislocalization by the prenylcysteine endoprotease YopT was demonstrated by two independent assays. Functional bacterial uptake experiments demonstrated that RhoG activation can bypass a deficit in Rac1 activity. Interestingly, increasing the size of the particle gave results more consistent with a linear pathway, in which RhoG acts as an upstream activator of Rac1, indicating that increased surface area introduces constraints on the signaling pathways required for efficient internalization. Taken together, these data demonstrate the misregulation of RhoG by multipleY. pseudotuberculosisvirulence determinants. Since RhoG is imperative for proper neutrophil function, this misregulation may represent a unique mechanism by whichYersiniaspecies dampen the immune response.
Babesia divergens
Apical Membrane Antigen 1 and Its Interaction with the Human Red Blood Cell
Authors: Montero Estrella , Rodriguez Marilis , Oksov Yelena , Lobo Cheryl A.
Published: September 2009

Multiple parasite ligand-erythrocyte receptor interactions must occur for successful
Babesia
and
Plasmodium
invasion of the human red cell. One such parasite ligand is the apical membrane antigen 1 (AMA1) which is a conserved apicomplexan protein present in the micronemes and then secreted onto the surface of the merozoite. Much evidence exists for a vital role for AMA1 in host cell invasion; however, its interaction with the host erythrocyte has remained controversial. In this paper, we present a detailed characterization of a
Babesia divergens
homolog of AMA1 (BdAMA1), and taking advantage of the relatively high amounts of native BdAMA1 available from the parasite culture system, show that proteolytic products of native BdAMA1 bind to a trypsin- and chymotrypsin-sensitive receptor on the red blood cell. Moreover, immuno-electron microscopic images of the
B. divergens
merozoite captured during invasion offer additional evidence of the presence of BdAMA1 on the red cell membrane. Given the importance of AMA1 in invasion and the central role invasion plays in pathogenesis, these studies have implications both for novel drug design and for the development of new vaccine approaches aimed at interfering with AMA1 function.
Restriction of
L
egionella pneumophila
Replication in Macrophages Requires Concerted Action of the Transcriptional Regulators Irf1 and Irf8 and Nod-Like Receptors Naip5 and Nlrc4
Authors: Fortier Anne , Doiron Karine , Saleh Maya , Grinstein Sergio , Gros Philippe
Published: September 2009

The unique permissiveness of A/J mouse macrophages for replication of
Legionella pneumophila
is caused by a deficiency in the Nod-like receptor (NLR) protein and intracellular sensor for
L. pneumophila
flagellin (
Naip5
). The signaling pathways and proteins activated by Naip5 sensing in macrophages were investigated. Transcript profiling of macrophages from susceptible A/J mice and from resistant A/J mice harboring a transgenic wild-type copy of
Naip5
at 4 h following
L. pneumophila
infection suggested that two members of the Irf transcriptional regulator family, Irf1 and Irf8, are regulated in response to Naip5 sensing of
L. pneumophila
. We show that macrophages having defective alleles of either
Irf1
(
Irf1
−
/
−
) or its heterodimerization partner gene
Irf8
(

Irf8
R294C

) become permissive for
L. pneumophila
replication, indicating that both the Irf1 and Irf8 proteins are essential for macrophage defense against
L. pneumophila
. Moreover, macrophages doubly heterozygous (

Naip5
AJ/WT
Irf8
R294C/WT

or
Nlrc4
−/+

Irf8
R294C/WT

) for combined loss-of-function mutations in
Irf8
and in either
Naip5
or
Nlrc4
are highly susceptible to
L. pneumophila
, indicating that there is a strong genetic interaction between
Irf8
and the NLR protein family in the macrophage response to
L. pneumophila. Legionella
-containing phagosomes (LCPs) formed in permissive
Irf1
−
/
−
or

Irf8
R294C

macrophages behave like LCPs formed in
Naip5
-insufficient and
Nlrc4
-deficient macrophages which fail to acidify. These results suggest that, in addition to
Naip5
and
Nlrc4
,
Irf1
and
Irf8
play a critical role in the early response of macrophages to infection with
L. pneumophila
, including antagonizing the ability of
L. pneumophila
to block phagosome acidification. They also suggest that flagellin sensing by the NLR proteins Naip5 and Nlrc4 may be coupled to Irf1-Irf8-mediated transcriptional activation of key effector genes essential for macrophage resistance to
L. pneumophila
infection.
A MODIFIED GENERALIZED LORENZ-TYPE SYSTEM AND ITS CANONICAL FORM
Authors: YANG QIGUI , ZHANG KANGMING , CHEN GUANRONG
Published: September 2009

In this paper, a modified generalized Lorenz-type system is introduced, which is state-equivalent to a simple and special form, and is parameterized by two parameters useful for chaos turning and system classification. More importantly, based on the parameterized form, two classes of new chaotic attractors are found for the first time in the literature, which are similar but nonequivalent in topological structure. To further understand the complex dynamics of the new system, some basic properties such as Lyapunov exponents, Hopf bifurcations and compound structure of the attractors are analyzed and demonstrated with careful numerical simulations.
CLASSIFICATION OF BIFURCATIONS AND CHAOS IN CHUA'S CIRCUIT WITH EFFECT OF DIFFERENT PERIODIC FORCES
Authors: SRINIVASAN K. , THAMILMARAN K. , VENKATESAN A.
Published: September 2009

We study the effect of different periodic excitations like sine, square, triangle and sawtooth waves on Chua's circuit and show that the circuit can undergo distinctly modified bifurcation structure, generation of new periodic regimes, induction of crises and so on. In particular, we point out that under the influence of different periodic excitations, a rich variety of bifurcation phenomena, including the familiar period-doubling sequence, intermittent route to chaos and period-adding sequences, reverse bifurcations, remerging chaotic band attractors, a large number of coexisting periodic attractors exist in the system. The analysis is carried out numerically using phase portraits, two-parameter phase diagrams in the forcing amplitude-frequency plane and one-parameter bifurcation diagrams. The chaotic dynamics of this circuit is also realized experimentally.
PERIODIC MOTIONS AND CHAOS WITH IMPACTING CHATTER AND STICK IN A GEAR TRANSMISSION SYSTEM
Authors: LUO ALBERT C. J. , O'CONNOR DENNIS
Published: September 2009

This paper focuses on periodic motions and chaos relative to the impacting chatter and stick in order to find the origin of noise and vibration in such a gear transmission system. Such periodic motions are predicted analytically through mapping structures, and the corresponding local stability and bifurcation analysis are carried out. The grazing and stick conditions presented in [Luo & O'Connor, 2007] are adopted to determine the existence of periodic motions, which cannot be achieved from the local stability analysis. Numerical simulations are performed to illustrate periodic motions and stick motion criteria. Such an investigation may provide some clues to reduce the noise in gear transmission systems.
ROBUST CONTROL OF SPATIOTEMPORAL CHAOS IN COUPLED MAP LATTICES
Authors: RAHMANI Z. , MOTLAGH M. R. JAHED , DITTO WILLIAM
Published: September 2009

In this paper, a new method for controlling spatiotemporal chaos in discrete-time spatially extended systems modeled by coupled map lattices is proposed. This method is based on quasi-sliding mode using a Lyapunov function. This method enables the system to drive the chaotic motion toward any desired trajectory via a sliding surface in the error space. The controller also guarantees finite time convergence of the state trajectory. The main advantage of this method is its robustness with respect to additive uncertainties and its applicability for all types of coupled map lattices. A diffusively coupled map lattice is used as an example to demonstrate the method. Simulation results reveal the robustness and the effectiveness of the method in controlling spatiotemporal chaos in coupled map lattices.
STABILIZING A TWO-CELL DC-DC BUCK CONVERTER BY FIXED POINT INDUCED CONTROL
Authors: EL AROUDI A. , ANGULO F. , OLIVAR G. , ROBERT B. G. M. , FEKI M.
Published: September 2009

In this paper, we study nonlinear and bifurcation behavior of a two-cell DC-DC buck power electronic converter. The system shows nonsmooth period doubling bifurcation and chaotic phenomena in a certain zone of parameter space. This zone is located both analytically and from numerical simulations. One-dimensional, two-dimensional bifurcation diagrams and Lyapunov exponent spectrum are used to detect the different dynamic behaviors of the system. The Fixed Point Induced Control (FPIC) technique is applied to the system in order to widen the stability zone. The performance of the FPIC technique applied to the stabilization of a two-cell DC-DC buck converter is analyzed. With this technique, stabilization is achieved without changing the fixed point. The robustness in the presence of a noisy environment is checked by numerical simulations by considering different noise levels.
GLOBAL ANALYSIS AND FOCAL POINTS IN A MODEL WITH BOUNDEDLY RATIONAL CONSUMERS
Authors: NAIMZADA AHMAD K. , TRAMONTANA FABIO
Published: September 2009

In this paper we present a contribution toward a dynamic theory of the consumer. Canonical economic theory assumes a perfectly rational agent that acts according to optimization principles of a utility function subject to budget constraints. Here we propose a two-dimensional discrete dynamical system that describes the choice problem of a consumer under the assumption of bounded rationality. The map representing this adaptive process is characterized by the presence of a denominator that can vanish. We use recent results on the global bifurcations of this kind of maps in order to explain the coexistence of different attractors and the structure of the corresponding basins of attraction. The stationary equilibria of the map represent the rational choices of the consumer in the static setting, i.e. solutions of the utility maximization problem under budget constraints. We use geometric and numerical methods to study the problem of coexistence of different attractors and the related problem of the basins of attraction and their global bifurcations.
A QUALITATIVE ANALYSIS OF DECIPHERING ERRORS IN CHAOS SHIFT KEYING
Authors: MANJUNATH G. , FOURNIER-PRUNARET D.
Published: September 2009

This article gives a topological and measure-dynamics based analysis on the deciphering of cipher texts encoded by the basic chaos shift keying scheme. Our analysis gives a proof of the ambiguity involved in deciphering and also shows that the deciphering error is a source of practical concern.
MECHANISM OF IMPACTING CHATTER WITH STICK IN A GEAR TRANSMISSION SYSTEM
Authors: LUO ALBERT C. J. , O'CONNOR DENNIS
Published: September 2009

In this paper, an investigation on nonlinear dynamical behaviors of a transmission system with a gear pair is conducted. The transmission system is described through an impact model with a possible stick between the two gears. From the theory of discontinuous dynamical systems, the motion mechanism of impacting chatter with stick is investigated. The onset and vanishing conditions of stick motions are developed, and the condition for maintaining the stick motion is achieved as well. The corresponding physics interpretation is given for a better understanding of nonlinear behaviors of gear transmission systems. Furthermore, such an understanding may be very helpful to improve the efficiency of gear transmission systems.
ON DE SITTER RADIATION VIA QUANTUM TUNNELING
Authors: VOLOVIK G. E.
Published: September 2009

We discuss why the tunneling picture does not necessarily lead to Hawking radiation from the de Sitter horizon. The experience with the condensed matter analogs of the event horizon suggests that the de Sitter vacuum is stable against Hawking radiation. On the other hand, the detector immersed in the de Sitter background will detect the radiation, which looks thermal, with the effective temperature twice as large as the Hawking temperature associated with the cosmological horizon.
PERTURBATIONS OF DARK MATTER GRAVITY
Authors: MAIA M. D. , CAPISTRANO A. J. S. , MULLER D.
Published: September 2009

Until recently the study of the gravitational field of dark matter was primarily concerned with its local effects on the motion of stars in galaxies and galaxy clusters. On the other hand, the WMAP experiment has shown that the gravitational field produced by dark matter amplifies the higher acoustic modes of the CMBR power spectrum, more intensely than the gravitational field of baryons. Such a wide range of experimental evidences from cosmology to local gravity suggests the necessity of a comprehensive analysis of the dark matter gravitational field per se, regardless of any other attributes that dark matter may eventually possess.

In this paper we introduce and apply Nash's theory of perturbative geometry to the study of the dark matter gravitational field alone, in a higher-dimensional framework. It is shown that the dark matter gravitational perturbations in the early universe can be explained by the extrinsic curvature of the standard cosmology. Together with the estimated presence of massive neutrinos, such geometric perturbation is compatible not only with the observed power spectrum in the WMAP experiment but also with the most recent data on the accelerated expansion of the universe.

It is possible that the same structure formation exists locally, such as in the cases of young galaxies or in cluster collisions. In most other cases it seems to have ceased when the extrinsic curvature becomes negligible, leading to Einstein's equations in four dimensions. The slow motion of stars in galaxies and the motion of plasma substructures in nearly colliding clusters are calculated with the geodesic equation for a slowly moving object in a gravitational field of arbitrary strength.
RECONSTRUCTING A STRING-INSPIRED NONMINIMALLY COUPLED QUINTOM MODEL
Authors: SETARE M. R. , SADEGHI J. , AMANI A. R.
Published: September 2009

Motivated by the recent work of Zhang and Chen,1we generalize their work to the nonminimally coupled case. We consider a quintom model of dark energy with a single scalar field T given by a Lagrangian inspired by a tachyonic Lagrangian in string theory. We consider nonminimal coupling of the tachyon field to the scalar curvature, and then we reconstruct this model in the light of three forms of parametrization for dynamical dark energy.
HYBRID CONTENTION RESOLUTION SCHEMES FOR OPTICAL BURST SWITCHED HIGH-SPEED NETWORKS
Authors: GARG AMIT KUMAR , KALER R. S.
Published: September 2009

Optical burst switching (OBS) has attracted interest as a transport network architecture for the future optical Internet. However, many challenging issues have to be solved in order to pave the way for an effective implementation of OBS. Contention, which may occur when two or more bursts compete for the same wavelength on the same link, is a critical issue. This paper compares the basic and hybrid contention resolution strategies with respect to burst loss probability and end-to-end transfer delay. The simulation results show that hybrid techniques lead an effective reduction of the burst average loss rate compared to existing techniques. It is also observed that a significant differentiation with regard to burst loss has been achieved, when burst priorities are considered.
A NEW ISOMORPHIC DEFINITION OF THE CROSSED CUBE AND ITS SPANNING CONNECTIVITY
Authors: LIN CHENG-KUAN , CHANG CHIEN-PING , HO TUNG-YANG , TAN JIMMY J. M. , HSU LIH-HSING
Published: September 2009

In this paper, we propose a slightly different definition of the crossed cube. The interconnection network obtained form our new definition is exactly isomorphic to the one obtained from the original definition proposed by Efe. It is known that the crossed cube is not node symmetric. However, using our new definition, it reveals some relative symmetric properties of the crossed cube. We can take advantage of the symmetry to study the spanning connectivity of the crossed cube.
SIMULATIONS OF COLLISION CASCADES IN Cu–Nb LAYERED COMPOSITES USING AN EAM INTERATOMIC POTENTIAL
Authors: DEMKOWICZ M. J. , HOAGLAND R. G.
Published: September 2009

The embedded atom method (EAM) is used to construct an interatomic potential for modelling interfaces in Cu – Nb nanocomposites. Implementation of the Ziegler–Biersack–Littmark (ZBL) model for short-range interatomic interactions enables studies of response to ion bombardment. Collision cascades are modelled in fcc Cu , bcc Nb , and in Cu – Nb layered composites in the experimentally-observed Kurdjumov–Sachs (KS) orientation relation. The interfaces in these composites reduce the number of vacancies and interstitials created per keV of the primary knock-on atom (PKA) by 50–70% compared to fcc Cu or bcc Nb .
AB INITIO STUDY OF SIZE AND STRAIN EFFECTS ON THE ELECTRONIC PROPERTIES OF Si NANOWIRES
Authors: PENG X.-H. , ALIZADEH A. , KUMAR S. K. , NAYAK S. K.
Published: September 2009

We have applied density-functional theory (DFT) based calculations to investigate the size and strain effects on the electronic properties, such as band structures, energy gaps and effective masses of the electron and the hole, in Si nanowires along the 〈110〉 direction with diameters up to 5 nm. Under uniaxial strain, we find that the band gap varies with strain and this variation is size dependent. For the 1–2 nm wire, the band gap is a linear function of strain, while for the 2–4 nm wire the gap variation with strain shows nearly parabolic behaviour. This size dependence of the gap variation with strain is explained on the basis of orbital characters of the band edges. In addition we find that the expansive strain increases the effective mass of the hole, while compressive strain increases the effective mass of the electron. The study of size and strain effects on effective masses shows that effective masses of the electron and the hole can be reduced by tuning the diameter of the wire and applying appropriate strain.
AN APPROXIMATE FORMULATION OF THE EFFECTIVE INDENTATION MODULUS OF ELASTICALLY ANISOTROPIC FILM-ON-SUBSTRATE SYSTEMS
Authors: LI T. L. , LEE J. H. , GAO Y. F.
Published: September 2009

Frictionless contact between an arbitrarily-shaped rigid indenter and an elastically anisotropic film-on-substrate system can be regarded as being superposed incrementally by a flat-ended punch contact, the shape and size of which are determined by the indenter shape, indentation depth (or applied load) and elastic properties of film and substrate. For typical nanoindentation applications, the indentation modulus can thus be approximated from the response of a circular contact with pressure of the form of [1 - (r/a)2]-1/2, where r is the radial coordinate and a is the contact radius. The surface-displacement Green's function for elastically anisotropic film-on-substrate system is derived in closed-form by using the Stroh formalism and the two-dimensional Fourier transform. The predicted dependence of the effective modulus on the ratio of film thickness to contact radius agrees well with detailed finite element simulations. Implications in evaluating film modulus by nanoindentation technique are also discussed.
EQUILIBRIUM AND METASTABLE PHASE DIAGRAMS FOR ISLAND SELF-ORGANIZATION IN SELECTIVE AREA EPITAXY
Authors: MACHTAY NOAH D. , KUKTA ROBERT V.
Published: September 2009

An energetic model is used to understand the mechanics of Stranski–Krastanow epitaxial systems constrained to grow on a finite area of a substrate. The model is representative of physical systems that include selective area epitaxy and growth on patterned substrate features such as raised mesas and etched pits. By considering only strain energy, isotropic surface energy, wetting layer potential energy and the geometric constraints of the system, equilibrium configurations consisting of a single island, multiple islands or no islands can be obtained depending on the dimensions of the growth area. These results are in contrast to growth on a substrate of infinite dimensions where the minimum energy configuration of systems with deposited volumes beyond the wetting layer transition thickness is a single large island on top of the wetting layer. It is therefore concluded that growth on a finite area can suppress island coarsening and result in minimum energy configurations consisting of multiple self-organized islands of uniform size and shape. Qualitative comparisons are made to experimental results from literature, and are shown to have good agreement.
ACTION-DERIVED AB INITIO MOLECULAR DYNAMICS
Authors: JUN S. , PENDURTI S. , LEE I.-H. , KIM S. Y. , PARK H. S. , KIM Y.-H.
Published: September 2009

Action-derived molecular dynamics (ADMD) is a numerical method to search for minimum-energy dynamic pathways on the potential-energy surface of an atomic system. The method is based on Hamilton's least-action principle and has been developed for problems of activated processes, rare events, and long-time simulations. In this paper, ADMD is further extended to incorporate ab initio total-energy calculations, which enables the detailed electronic analysis of transition states as well as the exploration of energy landscapes. Three numerical examples are solved to demonstrate the capability of this action-derived ab initio molecular dynamics (MD). The proposed approach is expected to circumvent the severe time-scale limitation of conventional ab intio MD simulations.
Using NFFT 3---A Software Library for Various Nonequispaced Fast Fourier Transforms
Authors: Keiner Jens , Kunis Stefan , Potts Daniel
Published: September 2009

NFFT 3 is a software library that implements the nonequispaced fast Fourier transform (NFFT) and a number of related algorithms, for example, nonequispaced fast Fourier transforms on the sphere and iterative schemes for inversion. This article provides a survey on the mathematical concepts behind the NFFT and its variants, as well as a general guideline for using the library. Numerical examples for a number of applications are given.
C++ Bindings to External Software Libraries with Examples from BLAS, LAPACK, UMFPACK, and MUMPS
Authors: Meerbergen Karl , Fresl Krešimir , Knapen Toon
Published: September 2009

FORTRAN and C software packages are often used in generic C++ software. Calling nongeneric functions in generic code is not straightforward. The bindings in this article help the C++ programmer using external software with a small effort. The bindings provide a mechanism to keep external software interfaces and specific vector and matrix containers orthogonal. We show examples using BLAS, LAPACK, UMFPACK, and MUMPS functions and subroutines.
Small synopses for group-by query verification on outsourced data streams
Authors: Yi Ke , Li Feifei , Cormode Graham , Hadjieleftheriou Marios , Kollios George , Srivastava Divesh
Published: September 2009

Due to the overwhelming flow of information in many data stream applications, data outsourcing is a natural and effective paradigm for individual businesses to address the issue of scale. In the standard data outsourcing model, the data owner outsources streaming data to one or more third-party servers, which answer queries posed by a potentially large number of clients on the data owner's behalf. Data outsourcing intrinsically raises issues of trust, making outsourced query assurance on data streams a problem with important practical implications. Existing solutions proposed in this model all build upon cryptographic primitives such as signatures and collision-resistant hash functions, which only work for certain types of queries, for example, simple selection/aggregation queries.

In this article, we consider another common type of queries, namely, “GROUP BY, SUM” queries, which previous techniques fail to support. Our new solutions are not based on cryptographic primitives, but instead use algebraic and probabilistic techniques to compute a small synopsis on the true query result, which is then communicated to the client so as to verify the correctness of the query result returned by the server. The synopsis uses a constant amount of space irrespective of the result size, has an extremely small probability of failure, and can be maintained using no extra space when the query result changes as elements stream by. We then generalize our synopsis to allow some tolerance on the number of erroneous groups, in order to support semantic load shedding on the server. When the number of erroneous groups is indeed tolerable, the synopsis can be strengthened so that we can locate and even correct these errors. Finally, we implement our techniques and perform an empirical evaluation using live network traffic.
Incorporating constraints in probabilistic XML
Authors: Cohen Sara , Kimelfeld Benny , Sagiv Yehoshua
Published: September 2009

Constraints are important, not only for maintaining data integrity, but also because they capture natural probabilistic dependencies among data items. A
probabilistic XML database
(PXDB) is the probability subspace comprising the instances of a
p-document
that satisfy a set of constraints. In contrast to existing models that can express probabilistic dependencies, it is shown that query evaluation is tractable in PXDBs. The problems of sampling and determining well-definedness (i.e., whether the aforesaid subspace is nonempty) are also tractable. Furthermore, queries and constraints can include the aggregate functions
count, max, min,
and
ratio.
Finally, this approach can be easily extended to allow a probabilistic interpretation of constraints.
COVER STORYCitizen-centered design (slowly) revolutionizes the media and experience of U.S. elections
Authors: Hewitt Jessica Friedman
Published: September 2009

Editor's Note: This month's cover story describes how designers and policy makers alike developed a voting system that is useful, useable, and---above all else---fair. We are pleased to offer not only the following article by Jessica Friedman Hewitt, but also an accompanying sidebar by
interactions
advisory board member Richard Grefé, who founded AIGA Design for Democracy. Together, these pieces point to a new trend of design in, for, and with government.
TIMELINESReflections on the future of iSchools from inspired junior faculty
Authors: Wobbrock Jacob O. , Ko Amy J. , Kientz Julie A.
Published: September 2009

Editor's Note: New fields, such as computer science, cognitive science, neuroscience, human-computer interaction, and now information, have multidisciplinary origins. To overcome communication difficulties as they worked to define the field and set priorities, pioneers developed a pidgin language. Soon came a generation of scholars, who staked their careers on the new field, creolizing the language and shaping a coherent framework relatively free of the legacy disciplines. In this article three research faculty members from the Information School of the University of Washington, discuss the tensions and opportunities in this 21st-century discipline that could become the most influential of all. ---Jonathan Grudin
Investigating the role of body shape on the perception of emotion
Authors: McDonnell Rachel , Jörg Sophie , McHugh Joanna , Newell Fiona N. , O'Sullivan Carol
Published: September 2009

In order to analyze the emotional content of motions portrayed by different characters, we created real and virtual replicas of an actor exhibiting six basic emotions: sadness, happiness, surprise, fear, anger, and disgust. In addition to the video of the real actor, his actions were applied to five virtual body shapes: a low- and high-resolution virtual counterpart, a cartoon-like character, a wooden mannequin, and a zombie-like character (Figures 1 and 2). In a point light condition, we also tested whether the absence of a body affected the perceived emotion of the movements. Participants were asked to rate the actions based on a list of 41 more complex emotions. We found that the perception of emotional actions is highly robust and to the most part independent of the character's body, so long as form is present. When motion alone is present, emotions were generally perceived as less intense than in the cases where form was present.
FixTag: An algorithm for identifying and tagging fixations to simplify the analysis of data collected by portable eye trackers
Authors: Munn Susan M. , Pelz Jeff B.
Published: September 2009

Video-based eye trackers produce an output video showing where a subject is looking, the subject's Point-of-Regard (POR), for each frame of a video of the scene. This information can be extremely valuable, but its analysis can be overwhelming. Analysis of eye-tracked data from portable (wearable) eye trackers is especially daunting, as the scene video may be constantly changing, rendering automatic analysis more difficult. A common way to begin analysis of POR data is to group these data into fixations. In a previous article, we compared the fixations identified (i.e., start and end marked) automatically by an algorithm to those identified manually by users (i.e., manual coders). Here, we extend this automatic identification of fixations to tagging each fixation to a Region-of-Interest (ROI). Our fixation tagging algorithm, FixTag, requires the relative 3D positions of the vertices of ROIs and calibration of the scene camera. Fixation tagging is performed by first calculating the camera projection matrices for keyframes of the scene video (captured by the eye tracker) via an iterative structure and motion recovery algorithm. These matrices are then used to project 3D ROI vertices into the keyframes. A POR for each fixation is matched to a point in the closest keyframe, which is then checked against the 2D projected ROI vertices for tagging. Our fixation tags were compared to those produced by three manual coders tagging the automatically identified fixations for two different scenarios. For each scenario, eight ROIs were defined along with the 3D positions of eight calibration points. Therefore, 17 tags were available for each fixation: 8 for ROIs, 8 for calibration points, and 1 for “other.” For the first scenario, a subject was tracked looking through products on four store shelves, resulting in 182 automatically identified fixations. Our automatic tagging algorithm produced tags that matched those produced by at least one manual coder for 181 out of the 182 fixations (99.5% agreement). For the second scenario, a subject was tracked looking at two posters on adjoining walls of a room. Our algorithm matched at least one manual coder's tag for 169 fixations out of 172 automatically identified (98.3% agreement).
Search task performance using subtle gaze direction with the presence of distractions
Authors: McNamara Ann , Bailey Reynold , Grimm Cindy
Published: September 2009

A new experiment is presented that demonstrates the usefulness of an image space modulation technique called subtle gaze direction (SGD) for guiding the user in a simple searching task. SGD uses image space modulations in the luminance channel to guide a viewer's gaze about a scene without interrupting their visual experience. The goal of SGD is to direct a viewer's gaze to certain regions of a scene without introducing noticeable changes in the image. Using a simple searching task, we compared performance using no modulation, using subtle modulation, and using obvious modulation. Results from the experiments show improved performance when using subtle gaze direction, without affecting the user's perception of the image. We then extend the experiment to evaluate performance with the presence of distractors. The distractors took the form of extra modulations, which do not correspond to a target in the image. Experimentation shows, that, even in the presence of distractors, more accurate results are returned on a simple search task using SGD, as compared to results returned when no modulation at all is used. Results establish the potential of the method for a wide range of applications including gaming, perceptually based rendering, navigation in virtual environments, and medical search tasks.
ROSE
Authors: Meneely Andrew , Williams Laurie , Gehringer Edward F.
Published: September 2009

Open-source project artifacts can be used to inject realism into software engineering courses or lessons on open-source software development. However, the use of open-source projects presents challenges for both educators and for students. Educators must search for projects that meet the constraints of their classes, and often must negotiate the scope and terms of the project with project managers. For students, many available open-source projects have a steep learning curve that inhibits them from making significant contributions to the project and benefiting from a "realistic" experience. To alleviate these problems and to encourage cross-institution collaboration, we have created the Repository for Open Software Education (ROSE) and have contributed three open-source projects intended for an undergraduate computer science or software engineering course. The projects in ROSE are education-friendly in terms of a manageable size and scope, and are intended to be evolved over many semesters. All projects have a set of artifacts covering all aspects of the development process, from requirements, design, code, and test. We invite other educators to contribute to ROSE and to use projects found on ROSE in their own courses.
Question answering from lecture videos based on an automatic semantic annotation
Authors: Repp Stephan , Linckels Serge , Meinel Christoph
Published: September 2009

The number of digital lecture video recordings has increased dramatically. The accessibility, usability and the traceability of their content for students-use is limited. Therefore retrieval of audiovisual lecture recordings is a complex task. Speech recognition is applied to create a tentative and deficient transcription of the video recordings. The imperfect transcription is sufficient to generate semantic metadata serialized in an OWL file. A question answering system based on the automatically generated semantic annotations and a semantic search engine are presented. The annotation process is discussed, evaluated and compared to a perfectly annotated OWL file and, further, to a corrected transcript of the lecture.
Databases, non-majors and collaborative learning
Authors: Goelman Don
Published: September 2009

In data modeling, a ternary relationship is sometimes necessary to express semantics richer than the union of the pairwise binary ones. So too, this paper describes a ternary relationship among three "entity types" in computer science education: databases as the subject, non-computer science majors as the target population, and collaborative learning as the pedagogical approach. While there is extensive research and experience in each binary link, the three-way investigation is new.
Evaluating OO example programs for CS1
Authors: Börstler Jürgen , Christensen Henrik B. , Bennedsen Jens , Nordström Marie , Kallin Westin Lena , Moström Jan Erik , Caspersen Michael E.
Published: September 2009

Example programs play an important role in learning to program. They work as templates, guidelines, and inspiration for learners when developing their own programs. It is therefore important to provide learners with high quality examples. In this paper, we discuss properties of example programs that might affect the teaching and learning of object-oriented programming. Furthermore, we present an evaluation instrument for example programs and report on initial experiences of its application to a selection of examples from popular introductory programming textbooks.
Jenuity
Authors: van Tonder Martin , Naude Kevin , Cilliers Charmain
Published: September 2009

The complexity and resource requirements of professional IDEs mean that they are unsuitable for use in intermediate level programming courses. Jenuity is an efficient development environment for the Java programming language. Efficiency is essential as students often have outdated hardware unable to run mainstream development environments. This is of particular relevance in the context of a developing country. Jenuity provides advanced features usually associated with more resource intensive tools. It provides a simple and intuitive interface, which is well suited to intermediate level programming courses. Jenuity has been used successfully in the teaching of these courses at the authors' institution since 2004. The requirements, development and optimisation of this tool are discussed. Techniques used to optimise Jenuity for low specification student hardware, some of which are novel, are presented. Experiences using Jenuity in a university environment are also reported. The efficiency of Jenuity is also demonstrated by means of a comparison to mainstream development environments.
Student use of the PeerWise system
Authors: Denny Paul , Luxton-Reilly Andrew , Hamer John
Published: September 2009

PeerWise is a web-based system that supports the creation of student-generated test banks of multiple choice questions. Students contribute question stems and answers, provide explanations, answer questions contributed by other students, rate questions for difficulty and quality, and participate in on-line discussions of all these activities.

In 2007, the system was used in four computing classes that varied in level, instructors, and student reward. We present results that show common patterns of response from students, and outline some initial investigations into the impact of the system on student performance. Our main findings are: external motivators are needed only for question generation; exam performance is correlated with participation in on-line discussions; and, despite student enthusiasm, drill-and-practice use does not contribute to exam success.
A tablet-based paper exam grading system
Authors: Bloomfield Aaron , Groves James F.
Published: September 2009

We present the design and implementation of a system which allows a standard paper-based exam to be graded via tablet computers. The paper exam is given normally in a course, with a specialized footer that allows for automated recognition of each exam page. The exam pages are then scanned in via a high-speed scanner, graded by one or more people using tablet computers, and returned electronically to the students. The system provides many advantages over regular paper-based exam grading, and boasts a faster grading experience than traditional grading methods.
Electronic voting on-the-fly with mobile devices
Authors: Esponda Margarita
Published: September 2009

This paper describes a system for electronic voting in the classroom based on mobile devices. There is no need for special hardware. Cellular telephones or iPods with access to the Internet can be used for electronic polling. The system is so flexible, that the questions can be handwritten on the blackboard, on the spot, then generating automatically a web address which can be accessed with the voting device. Electronic voting can be started spontaneously without tedious preparations. This approach can be seamlessly integrated in E-Chalk, our electronic classroom software.
A graphics-based approach to data structures
Authors: Matzko Sarah , Davis Timothy A.
Published: September 2009

The Ä­Ç½· project was designed to educate students in undergra-duate computer science courses through the study of and solution to large-scale problems in computer graphics. Our ultimate aim is that this approach would be applied to all computer science courses in the B.A. curriculum. In the first years of this project, we have been working on the foundational sequence, which includes CS1, CS2, and CS3 (data structures and advanced programming). For this last course, which also includes the study of algorithms in our curriculum, we present an approach to teaching data structure concepts using advanced graphics algorithms. The results thus far have been promising, and we are continuing to evaluate and en-hance the approach.
Hypertextbooks and a Hypertextbook authoring environment
Authors: Ross Rockford J.
Published: September 2009

An ITiCSE 2006 working group explored the prospect of deploying educational visualizations (e.g., algorithm visualizations) in hypertextbooks [10]. In this paper we present our continuing work on a hypertextbook project that demonstrates the viability of many of the issues raised in that workshop. The project has two thrusts: (1) the authoring of hypertextbooks for specific academic subjects, and (2) the creation of an authoring environment for prospective hypertextbook authors. The status of both is discussed in detail. It is anticipated that the success of the project as well as access to the authoring environment will inspire the creation of more active-learning hypertextbooks covering many academic subjects.
VDE
Authors: Goldweber Michael , Davoli Renzo
Published: September 2009

Emulators have long been a valuable tool in teaching. Particularly in the OS course, emulators have allowed students to experiment meaningfully with different machine architectures. Furthermore, many such tools run in user-mode, allowing students to operate as system administrators without the concomitant security risks. Virtual Distributed Ethernet (VDE) is a system which emulates, in user-mode, all aspects of an internet, including switches, routers, communication lines, etc, in a completely realistic manner, consistent with the operation of such artifacts in the real world.

VDE's can be implemented on a single computer, spread over several machines on the same LAN or scattered across the Internet. A VDE can interoperate with both real systems (via standard virtual interface/connectivity tools) and several virtual machine environments, support encryption, and actually run fast enough to support real applications. Furthermore, a VDE can interface/interoperate with real networks. VDN's have proven highly effective in supporting both undergraduate and graduate networking courses, and a wide range of student experiments and projects.
Spamulator
Authors: Aycock John , Crawford Heather , deGraaf Rennie
Published: September 2009

We have developed an Internet simulator - the "Spamulator" - for a course on spam and spyware, a simulator that allows us to simulate the network services provided by a million domains. The Spamulator is lightweight in its resource usage, running on a single computer, and we currently have implementations for two different platforms.

Students interact with the Spamulator using unmodified client software, like web browsers. Alternatively, students can write their own software to use the simulated Internet using any programming language, without contrived constraints or special libraries. Furthermore, the Spamulator is extensible, making it useful as a research tool. It could easily be used for assignments on networking, peer-to-peer networks, distributed systems, and its lightweight nature allows large-scale experiments to be conducted even by underequipped institutions.

We discuss the motivation, design, and implementation of the Spamulator, and our experience with it in the spam and spyware class.