bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of methods to measure yield stress of soft solids
Authors: Castro M. , Giles D. W. , Macosko C. W. , Moaddel T.
Published: January 2010

Many interesting industrial materials are highly viscous or paste-like, i.e., soft solids. Their complexity, proceeding from heterogeneous structures, often reveals interesting rheological properties. Their processing requires the determination of rheological parameters such as viscosity, modulus, and yield stress value. We compare three methods to measure the yield stress of one particular soft solid system, i.e., concentrated surfactant systems, models for bar soap. One method is based on orifice die extrusion and uses the Benbow–Bridgwater equation. Two methods used a rotational rheometer: in one, dynamic (small strain sinusoidal oscillation) experiments were performed as a function of increasing strain amplitude with serrated parallel plate geometry. The maximum in the elastic stress curve was used to estimate the yield stress. The other method using the rotational rheometer, which we call strand shearing, involves the use of a new fixture designed to grip these samples that were too stiff for serrated plates but too soft for traditional solids fixtures. In this method, the maximum of a plot of stress versus time at a constant shear rate is taken as the yield stress. The advantages and limitations of these techniques are discussed and applied to our particular soap model system.
Planar extensional flow resistance of a foaming plastic
Authors: Wang Jing , James David F. , Park Chul B.
Published: January 2010

The planar extensional flow resistance of a foaming-grade polystyrene, with and without a blowing agent, was characterized using two dies, each one consisting of a high-aspect-ratio straight rectangular channel followed by a hyperbolic convergent rectangular channel. With the hyperbolic geometry, the fluid near the centerline of the convergent channel was subjected to a constant rate of extension. The shear viscosity was found from the pressure drop along the straight channel, and the planar extensional viscosity was determined from the pressure drop in the convergent channel, taking into account the pressure drop due to shearing. Values of the planar extensional viscosity are compared with values of the uniaxial extensional viscosity measured with a shear-free fixture. Tests with a polystyrene and with a solution of 5% carbon dioxide in the polystyrene revealed that the gas caused significant reductions in both the shear and extensional viscosities.
Inclined plane rheometry of a dense granular suspension
Authors: Bonnoit C. , Darnige T. , Clement E. , Lindner A.
Published: January 2010

We present a new method to measure the viscosity of a dense model suspension using an inclined plane rheometer. The suspension is made of mono-disperse, spherical, non-Brownian polystyrene beads immersed in a density matched silicon oil. We show that with this simple set-up, the viscosity can be directly measured up to volume fractions of ϕ=61% and that particle migration can be neglected. The results are in excellent agreement with local viscosity measurements obtained by magnetic resonance imaging techniques by Ovarlez et al. [J. Rheol. 50(3), 259–292 (2006)]. In the high density regime, we show that the viscosity is within the tested range of parameters, independent of the shear rate and the confinement pressure. Finally, we discuss deviations from the viscous behavior of the suspensions.
Comparisons of modified effective medium theory with experimental data on shear thinning of concentrated latex dispersions
Authors: Takamura Koichi , van de Ven Theo G. M.
Published: January 2010

Measured viscosity vs shear rate relationships were analyzed for a wide variety of carboxylated latexes reported in the literature using a modified effective-medium theory proposed by one of the authors. The theory contains three main parameters, cm, ko, and δ, which are the maximum volume fraction, a particle interaction parameter, closely related to the secondary electroviscous effect, and the thickness of the stabilizing surface layer, respectively. It is assumed that sheared dispersions always approach close packing for high volume fractions, i.e., cm=0.74 (for monodisperse suspensions). In general, ko increases with the magnitude of the secondary electroviscous effect and its value varies typically between 2.46 and 4.0 for low Péclet numbers, Pe, and approaches 1.7 for very high Pe. For dispersions of highly charged particles at low electrolyte concentrations, the electroviscous effects become especially significant and experiments show that the viscosity can increase by more than three orders of magnitude when the electrolyte concentration is reduced from 10−1 to 10−3 M, an effect predicted by the modified effective medium theory. The viscosity of carboxylated latex is also influenced by a “hairy” surface layer, the thickness, δ, of which appears to be closely related to the amount and type of functional monomers, and the degree of dissociation of carboxylic acid groups on the latex surface. The theory also explains the shear thinning behavior of blends of latexes with different size.
Molecular Basis of the Death-Associated Protein Kinase–Calcium/Calmodulin Regulator Complex
Authors: de Diego Iñaki , Kuper Jochen , Bakalova Neda , Kursula Petri , Wilmanns Matthias
Published: January 2010

The structure of the death-associated protein kinase and calmodulin complex reveals how calmodulin binding leads to kinase activation.
Not Just a Cell Cycle Protein
Authors: Wong Wei
Published: January 2010

Cyclin D controls gene transcription during mouse retinal development.
Changing the Program
Authors: Foley John F.
Published: January 2010

Kaposi’s sarcoma–associated herpesvirus reprograms infected endothelial cells by producing microRNAs that target the transcription factor c-Maf.
Of Wnt, Prorenin Receptor, and V-ATPase
Authors: Ray L. Bryan
Published: January 2010

A dual-function protein acts as an adaptor in a major developmental signaling pathway.
Proline Promotes Virulence
Authors: Gough Nancy R.
Published: January 2010

Proline in insects triggers a change in bacteria from benign to pathogenic.
Late-Running Clock Components
Authors: Ray L. Bryan
Published: January 2010

Rhythmic activation of signaling occurs by core components of the biological clock mechanism.
Production of a Class II Two-Component Lantibiotic of
Streptococcus pneumoniae
Using the Class I Nisin Synthetic Machinery and Leader Sequence
Authors: Majchrzykiewicz Joanna A. , Lubelski Jacek , Moll Gert N. , Kuipers Anneke , Bijlsma Jetta J. E. , Kuipers Oscar P. , Rink Rick
Published: January 2010

Recent studies showed that the nisin modification machinery can successfully dehydrate serines and threonines and introduce lanthionine rings in small peptides that are fused to the nisin leader sequence. This opens up exciting possibilities to produce and engineer larger antimicrobial peptides
in vivo
. Here we demonstrate the exploitation of the class I nisin production machinery to generate, modify, and secrete biologically active, previously not-yet-isolated and -characterized class II two-component lantibiotics that have no sequence homology to nisin. The nisin synthesis machinery, composed of the modification enzymes NisB and NisC and the transporter NisT, was used to modify and secrete a putative two-component lantibiotic of
Streptococcus pneumoniae
. This was achieved by genetically fusing the propeptide-encoding sequences of the
spr1765
(
pneA1
) and
spr1766
(
pneA2
) genes to the nisin leader-encoding sequence. The chimeric prepeptides were secreted out of
Lactococcus lactis
, purified by cation exchange fast protein liquid chromatography, and further characterized. Mass spectrometry analyses demonstrated the presence and partial localization of multiple dehydrated serines and/or threonines and (methyl)lanthionines in both peptides. Moreover, after cleavage of the leader peptide from the prepeptides, both modified propeptides displayed antimicrobial activity against
Micrococcus flavus
. These results demonstrate that the nisin synthetase machinery can be successfully used to modify and produce otherwise difficult to obtain antimicrobially active lantibiotics.
Plasma Ribavirin Trough Concentrations at Week 4 Predict Hepatitis C Virus (HCV) Relapse in HIV-HCV-Coinfected Patients Treated for Chronic Hepatitis C
Authors: Morello Judit , Soriano Vincent , Barreiro Pablo , Medrano José , Madejón Antonio , González-Pardo Gema , Jiménez-Nácher Inmaculada , González-Lahoz Juan , Rodríguez-Novoa Sonia
Published: January 2010

The influence of ribavirin trough concentrations (RBVCtrough) on the risk of hepatitis C virus (HCV) relapse was retrospectively analyzed in 99 HIV-HCV-coinfected patients who achieved end-of-treatment response with pegylated alpha interferon plus weight-based RBV. The independent predictors (odds ratio [OR] [95% confidence interval (CI)]) of HCV relapse were RBV plasmaCtroughof <2.5 μg/ml (4.5 [1.3 to 15.5]), baseline serum HCV RNA (2.5 [1.2 to 5.1]), and HCV genotype 1 or 4 (13.3 [2.6 to 66.7]). Monitoring of RBVCtroughmay permit early adjustment of RBV dosage to avoid HCV relapse.
In Vitro
Activity of Ceftaroline against 623 Diverse Strains of Anaerobic Bacteria
Authors: Citron D. M. , Tyrrell K. L. , Merriam C. V. , Goldstein E. J. C.
Published: January 2010

The
in vitro
activities of ceftaroline, a novel, parenteral, broad-spectrum cephalosporin, and four comparator antimicrobials were determined against anaerobic bacteria. Against Gram-positive strains, the activity of ceftaroline was similar to that of amoxicillin-clavulanate and four to eight times greater than that of ceftriaxone. Against Gram-negative organisms, ceftaroline showed good activity against β-lactamase-negative strains but not against the members of the
Bacteroides fragilis
group. Ceftaroline showed potent activity against a broad spectrum of anaerobes encountered in respiratory, skin, and soft tissue infections.
Candida albicans
β-Glucan Exposure Is Controlled by the Fungal
CEK1
-Mediated Mitogen-Activated Protein Kinase Pathway That Modulates Immune Responses Triggered through Dectin-1
Authors: Galán-Díez Marta , Arana David M. , Serrano-Gómez Diego , Kremer Leonor , Casasnovas José M. , Ortega Mara , Cuesta-Domínguez Álvaro , Corbí Angel L. , Pla Jesús , Fernández-Ruiz Elena
Published: January 2010

Innate immunity to
Candida albicans
depends upon the recognition of molecular patterns on the fungal cell wall. However, the masking of major components such as β-glucan seems to be a mechanism that fungi have evolved to avoid immune cell recognition through the dectin-1 receptor. Although the role of
C. albicans
mitogen-activated protein kinase (MAPK) pathways as virulence determinants has been established previously with animal models, the mechanism involved in this behavior is largely unknown. In this study we demonstrate that a disruption of the
C. albicans
extracellular signal-regulated kinase (ERK)-like 1 (
CEK1
)-mediated MAPK pathway causes enhanced cell wall β-glucan exposure, triggering immune responses more efficiently than the wild type, as measured by dectin-1-mediated specific binding and human dendritic cell (hDC)- and macrophage-mediated phagocytosis, killing, and activation of intracellular signaling pathways. At the molecular level, the disruption of
CEK1
resulted in altered spleen tyrosine kinase (Syk), Raf-1, and ERK1/2 activations together with IκB degradation on hDCs and increased dectin-1-dependent activator protein 1 (AP-1) activation on transfected cells. In addition, concurring with these altered pathways, we detected increased reactive oxygen species production and cytokine secretion. In conclusion, the
CEK1
-mediated MAPK pathway is involved in β-glucan exposure in a fungal pathogen, hence influencing dectin-1-dependent immune cell recognition, thus establishing this fungal intracellular signaling route as a promising novel therapeutic target.
Characterization and Modulation of the Immunosuppressive Phase of Sepsis
Authors: Muenzer Jared T. , Davis Christopher G. , Chang Kathy , Schmidt Robert E. , Dunne W. Michael , Coopersmith Craig M. , Hotchkiss Richard S.
Published: January 2010

Sepsis continues to cause significant morbidity and mortality in critically ill patients. Studies of patients and animal models have revealed that changes in the immune response during sepsis play a decisive role in the outcome. Using a clinically relevant two-hit model of sepsis, i.e., cecal ligation and puncture (CLP) followed by the induction ofPseudomonas aeruginosapneumonia, we characterized the host immune response. Second, AS101 [ammonium trichloro(dioxoethylene-o,o′)tellurate], a compound that blocks interleukin 10 (IL-10), a key mediator of immunosuppression in sepsis, was tested for its ability to reverse immunoparalysis and improve survival. Mice subjected to pneumonia following CLP had different survival rates depending upon the timing of the secondary injury. Animals challenged withP. aeruginosaat 4 days post-CLP had ∼40% survival, whereas animals challenged at 7 days had 85% survival. This improvement in survival was associated with decreased lymphocyte apoptosis, restoration of innate cell populations, increased proinflammatory cytokines, and restoration of gamma interferon (IFN-γ) production by stimulated splenocytes. These animals also showed significantly lessP. aeruginosagrowth from blood and bronchoalveolar lavage fluid. Importantly, AS101 improved survival after secondary injury 4 days following CLP. This increased survival was associated with many of the same findings observed in the 7-day group, i.e., restoration of IFN-γ production, increased proinflammatory cytokines, and decreased bacterial growth. Collectively, these studies demonstrate that immunosuppression following initial septic insult increases susceptibility to secondary infection. However, by 7 days post-CLP, the host's immune system has recovered sufficiently to mount an effective immune response. Modulation of the immunosuppressive phase of sepsis may aid in the development of new therapeutic strategies.
Staphylococcus aureus
Fur Regulates the Expression of Virulence Factors That Contribute to the Pathogenesis of Pneumonia
Authors: Torres Victor J. , Attia Ahmed S. , Mason William J. , Hood M. Indriati , Corbin Brian D. , Beasley Federico C. , Anderson Kelsi L. , Stauff Devin L. , McDonald W. Hayes , Zimmerman Lisa J. , Friedman David B. , Heinrichs David E. , Dunman Paul M. , Skaar Eric P.
Published: January 2010

The tremendous success of
Staphylococcus aureus
as a pathogen is due to the controlled expression of a diverse array of virulence factors. The effects of host environments on the expression of virulence factors and the mechanisms by which
S. aureus
adapts to colonize distinct host tissues are largely unknown. Vertebrates have evolved to sequester nutrient iron from invading bacteria, and iron availability is a signal that alerts pathogenic microorganisms when they enter the hostile host environment. Consistent with this, we report here that
S. aureus
senses alterations in the iron status via the ferric uptake regulator (Fur) and alters the abundance of a large number of virulence factors. These Fur-mediated changes protect
S. aureus
against killing by neutrophils, and Fur is required for full staphylococcal virulence in a murine model of infection. A potential mechanistic explanation for the impact of Fur on virulence is provided by the observation that Fur coordinates the reciprocal expression of cytolysins and a subset of immunomodulatory proteins. More specifically,
S. aureus
lacking
fur
exhibits decreased expression of immunomodulatory proteins and increased expression of cytolysins. These findings reveal that Fur is involved in initiating a regulatory program that organizes the expression of virulence factors during the pathogenesis of
S. aureus
pneumonia.
Water content and reserve allocation patterns within the bulb of the perennial geophyte red squill (Liliaceae) in relation to the Mediterranean climate
Authors: Al-Tardeh Sharaf , Sawidis Thomas , Diannelidis Barbara-Evelin , Stylianos Delivopoulos
Published: January 2010

The patterns of water content and reserve allocation in the bulb parts of red squill ( Urginea maritima (L.) Baker) and the plant’s adaptive strategy to Mediterranean climate (Crete, Greece) were investigated. The different bulb parts serve varying ecological functions in terms of their resources and their importance for these functions. The basal plate is the active centre, developing one or two apical meristems and roots in autumn, as well as the flowering bud in late summer. The middle of the bulb (approximately the third bulb scale) stores the resources and the tunics (the outer covering structures) that provide mechanical defense. The water content and reserve allocation patterns synchronize the plant’s phenological development with the seasonality of the Mediterranean climate. The adaptive strategies are based on the development of a deciduous semisubterranean life form primarily for the avoidance of drought, herbivores, and other environmental hazards, as well as nutrient shortage. The presence of cells containing lipids, polysaccharides, raphides, water, mucilage, bufadienolides, the presence of sclerenchyma, the tightly packed epidermis, and the presence of the tunics facilitate this.
Genetic diversity ofFrankiastrains in root nodules fromHippophae¨ rhamnoidesL.
Authors: Chen Li-hong , Liu Jian , Yao Gui-min , Yan Wei
Published: January 2010

The Hippophae¨ rhamnoides L. – Frankia symbiosis is of ecological and practical importance, but very little is known about H. rhamnoides-infective Frankia strains. To address this problem, we have used PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of nifD–nifK intergenic spacer (IGS) to estimate their genetic diversity at 19 sites in Northern China. Restriction analysis indicated that H. rhamnoides-infective Frankia had a high genetic diversity; the samples were divided into nine RFLP patterns (A–I). Elevation and precipitation likely affect the distribution of different Frankia patterns in root nodules. The patterns A and D were present in relatively large areas, which were located at various elevations; however, the distribution of patterns B, C, E, F, G, H, and I generally followed a geographic range. The richness of Frankia diversity was influenced by plant cover and geographic factors such as elevation and precipitation. H. rhamnoides cover had a higher diversity than that of natural vegetation cover. The center part of the geographical range, with intermediate elevation and precipitation, had a higher level of Frankia diversity than that of the west part and east part with high or low elevations and precipitations, respectively. The nifD–nifK IGS regions were sequenced from 28 nodule samples. Phylogenetic analysis showed that H. rhamnoides-infective Frankia strains were all clustered with the Elaeagnus group, and the diversity of this group was quite extensive. Phylogenetic relationships between Hippophae¨ and Elaeagnus-infective Frankia strains were relatively close to each other. Although not very close to either Hippophae¨- or Elaeagnus-infective Frankia strains, Shepherdia -infective strain SCN10a was closer to Hippophae¨-infective strains than to Elaeagnus- infective strains. This is the first detailed report on the genetic diversity and phylogenetic analysis of H. rhamnoides-infective Frankia.
Interactions between mitochondrial electron transport, reactive oxygen species, and the susceptibility of Nicotiana tabacum cells to programmed cell death
Authors: Robson Christine A. , Zhao Dorothy Y. , Vanlerberghe Greg C.
Published: January 2010

We investigated the impact of steady-state cellular reactive oxygen species (ROS) level on subsequent susceptibility to cell death induction by signaling molecules or respiratory inhibitors. We utilized Nicotiana tabacum L. (‘Petit Havana SR1’) suspension cell lines differing in steady-state ROS level owing to either genetic manipulation of the mitochondrial electron transport chain or manipulation of growth conditions. In either case, higher steady-state ROS level increased susceptibility to the signaling molecules salicylic acid and nitric oxide, suggesting that these molecules can engage a “steady-state ROS-primed cell death pathway”. We found that susceptibility to the complex III inhibitor antimycin A (AA) was also dependent upon steady-state ROS level and that this susceptibility was independent of that afforded by the inhibition of energy metabolism by AA. AA was unique in this respect, since susceptibility to two other electron transport chain inhibitors appeared strictly dependent upon their ability to inhibit energy metabolism. The results indicate that complex III may have a particular capacity to engage the steady-state ROS-primed cell death pathway (similarly to salicylic acid and nitric oxide) and may relate to the ability of this complex to generate superoxide. We also examined changes in cellular ROS post-treatment with the signaling molecules and respiratory inhibitors. In this case, the more susceptible cells (i.e., those that had experienced higher steady-state ROS levels) exhibited post-treatment declines in cellular ROS level, whereas the less susceptible cells were able to better maintain or increase their ROS post-treatment. This differential response may be an important determinant of cell fate.
Leaf variegation is associated with reduced herbivore damage in Hydrophyllum virginianum
Authors: Campitelli Brandon E. , Stehlik Ivana , Stinchcombe John R.
Published: January 2010

Leaf variegation refers to local regions of the upper surface of a leaf having reduced or obstructed chlorophyll, which results in whitish spots. These lighter spots may compromise the photosynthetic efficiency of a leaf, and many competing hypotheses have been put forward to explain why this patterning may be adaptive. It has been suggested that variegation is either an adaptive response to environmental conditions or a defence mechanism against herbivore damage. To test whether leaf variegation reduces herbivore damage, we first assessed the frequency of variegated and nonvariegated leaves in natural populations of the plant Hydrophyllum virginianum L., and second, measured herbivore damage to both variegated and nonvariegated leaves. We found that variegated leaves were present at high frequencies within natural populations (6%–31%) and that nonvariegated leaves sustained nearly twice the amount of damage by comparison with variegated leaves. Therefore, leaf variegation appears to be beneficial by reducing herbivore damage to leaves. These data are consistent with the fundamental prediction of the herbivory hypothesis for the benefits of leaf variegation.
In the Virtual Extension
Authors: CACM Staff
Published: January 2010

Communications'
Virtual Extension brings more quality articles to ACM members. These articles are now available in the ACM Digital Library.
Open access to scientific publications
Authors: Beaudouin-Lafon Michel
Published: January 2010

The good, the bad, and the ugly.
Managing contention for shared resources on multicore processors
Authors: Fedorova Alexandra , Blagodurov Sergey , Zhuravlev Sergey
Published: January 2010

Contention for caches, memory controllers, and interconnects can be eased by contention-aware scheduling algorithms.
A few billion lines of code later
Authors: Bessey Al , Block Ken , Chelf Ben , Chou Andy , Fulton Bryan , Hallem Seth , Henri-Gros Charles , Kamsky Asya , McPeak Scott , Engler Dawson
Published: January 2010

How Coverity built a bug-finding tool, and a business, around the unlimited supply of bugs in software systems.
Recent progress in quantum algorithms
Authors: Bacon Dave , van Dam Wim
Published: January 2010

What quantum algorithms outperform classical computation and how do they do it?
Understanding transportation modes based on GPS data for web applications
Authors: Zheng Yu , Chen Yukun , Li Quannan , Xie Xing , Ma Wei-Ying
Published: January 2010

User mobility has given rise to a variety of Web applications, in which the global positioning system (GPS) plays many important roles in bridging between these applications and end users. As a kind of human behavior, transportation modes, such as walking and driving, can provide pervasive computing systems with more contextual information and enrich a user's mobility with informative knowledge. In this article, we report on an approach based on supervised learning to automatically infer users' transportation modes, including driving, walking, taking a bus and riding a bike, from raw GPS logs. Our approach consists of three parts: a change point-based segmentation method, an inference model and a graph-based post-processing algorithm. First, we propose a change point-based segmentation method to partition each GPS trajectory into separate segments of different transportation modes. Second, from each segment, we identify a set of sophisticated features, which are not affected by differing traffic conditions (e.g., a person's direction when in a car is constrained more by the road than any change in traffic conditions). Later, these features are fed to a generative inference model to classify the segments of different modes. Third, we conduct graph-based postprocessing to further improve the inference performance. This postprocessing algorithm considers both the commonsense constraints of the real world and typical user behaviors based on locations in a probabilistic manner. The advantages of our method over the related works include three aspects. (1) Our approach can effectively segment trajectories containing multiple transportation modes. (2) Our work mined the location constraints from user-generated GPS logs, while being independent of additional sensor data and map information like road networks and bus stops. (3) The model learned from the dataset of some users can be applied to infer GPS data from others. Using the GPS logs collected by 65 people over a period of 10 months, we evaluated our approach via a set of experiments. As a result, based on the change-point-based segmentation method and Decision Tree-based inference model, we achieved prediction accuracy greater than 71 percent. Further, using the graph-based post-processing algorithm, the performance attained a 4-percent enhancement.
Declarative specification and verification of service choreographiess
Authors: Montali Marco , Pesic Maja , Aalst Wil M. P. van der , Chesani Federico , Mello Paola , Storari Sergio
Published: January 2010

Service-oriented computing, an emerging paradigm for architecting and implementing business collaborations within and across organizational boundaries, is currently of interest to both software vendors and scientists. While the technologies for implementing and interconnecting basic services are reaching a good level of maturity, modeling service interaction from a global viewpoint, that is, representing service choreographies, is still an open challenge. The main problem is that, although declarativeness has been identified as a key feature, several proposed approaches specify choreographies by focusing on procedural aspects, leading to over-constrained and over-specified models.

To overcome these limits, we propose to adopt DecSerFlow, a truly declarative language, to model choreographies. Thanks to its declarative nature, DecSerFlow semantics can be given in terms of logic-based languages. In particular, we present how DecSerFlow can be mapped ontoLinear Temporal Logicand ontoAbductive Logic Programming. We show how the mappings onto both formalisms can be concretely exploited to address the enactment of DecSerFlow models, to enrich its expressiveness and to perform a variety of different verification tasks. We illustrate the advantages of using a declarative language in conjunction with logic-based semantics by applying our approach to a running example.
A High Throughput FPGA-Based Floating Point Conjugate Gradient Implementation for Dense Matrices
Authors: Roldao Antonio , Constantinides George A.
Published: January 2010

Recent developments in the capacity of modern Field Programmable Gate Arrays (FPGAs) have significantly expanded their applications. One such field is the acceleration of scientific computation and one type of calculation that is commonplace in scientific computation is the solution of systems of linear equations. A method that has proven in software to be very efficient and robust for finding such solutions is the Conjugate Gradient (CG) algorithm. In this article we present a widely parallel and deeply pipelined hardware CG implementation, targeted at modern FPGA architectures. This implementation is particularly suited for accelerating multiple small-to-medium-sized dense systems of linear equations and can be used as a stand-alone solver or as building block to solve higher-order systems. In this article it is shown that through parallelization it is possible to convert the computation time per iteration for an order
n
matrix from
Θ
(
n
2
) clock cycles on a microprocessor to
Θ
(
n
) on a FPGA. Through deep pipelining it is also possible to solve several problems in parallel and maximize both performance and efficiency. I/O requirements are shown to be scalable and convergent to a constant value with the increase of matrix order. Post place-and-route results on a readily available VirtexII-6000 demonstrate sustained performance of 5 GFlops, and results on a Virtex5-330 indicate sustained performance of 35 GFlops. A comparison with an optimized software implementation running on a high-end CPU demonstrate that this FPGA implementation represents a significant speedup of at least an order of magnitude.
Tag based feedback for programming courses
Authors: Cummins Stephen , Burd Liz , Hatch Andrew
Published: January 2010

This paper reports the findings of a preliminary investigation into whether feedback generated by annotating source code with tags is considered useful by undergraduate students. These types of annotations facilitate a new approach to presenting assessment feedback to students in the form of a Web 2.0 tagging environment. This paper highlights the benefits and limitations of this approach as well as details of student reaction and behavior. This investigation focuses on assessment and feedback for an undergraduate Software Engineering Group Project. The preliminary results collected encourage further investigation of this approach.
Engaging computer science students through cooperative education
Authors: Huggins James K.
Published: January 2010

Computer science educators continuously seek creative and effective ways of engaging students. The model of cooperative education, in which students systematically combine academic learning with practical work experiences, provides opportunities to deepen student learning, promote student retention, and prepare students for professional life. We discuss ways in which cooperative learning can engage students in the broader discipline of computer science.
An evaluation of object oriented example programs in introductory programming textbooks
Authors: Börstler Jürgen , Hall Mark S. , Nordström Marie , Paterson James H. , Sanders Kate , Schulte Carsten , Thomas Lynda
Published: January 2010

Research shows that examples play an important role for cognitive skill acquisition. Students as well as teachers rank examples as important resources for learning to program. Therefore examples must be consistent with the principles and rules of the topics we are teaching.

However, educators often struggle to find or develop objectoriented example programs of high quality. Common examples are often perceived as not fully faithful to all principles and guidelines of the object-oriented paradigm, or as not following general pedagogical principles and practices. Unless students are able to engage with good examples, they will not be able to tell desirable from undesirable properties in their own and others' programs.

In this paper we report on a study in which experienced educators reviewed a wide range of object-oriented examples for novices from popular textbooks. This review was accomplished using an on-line checklist that elicited responses on 10 quality factors. Results show that the evaluation instrument provides a sufficiently consistent set of responses to distinguish examples.

The paper then goes on to examine some of the characteristics of good and bad examples and how this study will influence the evolution of the evaluating instrument.
Naturally occurring data as research instrument
Authors: Lister Raymond , Clear Tony , Simon  , Bouvier Dennis J. , Carter Paul , Eckerdal Anna , Jacková Jana , Lopez Mike , McCartney Robert , Robbins Phil , Seppälä Otto , Thompson Errol
Published: January 2010

In New Zealand and Australia, the BRACElet project has been investigating students' acquisition of programming skills in introductory programming courses. The project has explored students' skills in basic syntax, tracing code, understanding code, and writing code, seeking to establish the relationships between these skills. This ITiCSE working group report presents the most recent step in the BRACElet project, which includes replication of earlier analysis using a far broader pool of naturally occurring data, refinement of the SOLO taxonomy in code-explaining questions, extension of the taxonomy to code-writing questions, extension of some earlier studies on students' 'doodling' while answering exam questions, and exploration of a further theoretical basis for work that until now has been primarily empirical.
(Re)defining computing curricula by (re)defining computing
Authors: Isbell Charles L. , Stein Lynn Andrea , Cutler Robb , Forbes Jeffrey , Fraser Linda , Impagliazzo John , Proulx Viera , Russ Steve , Thomas Richard , Xu Yan
Published: January 2010

What is the core of Computing? This paper defines the discipline of computing as centered around the notion of modeling, especially those models that are automatable and automatically manipulable. We argue that this central idea crucially connects models with languages and machines rather than focusing on and around computational artifacts, and that it admits a very broad set of fields while still distinguishing the discipline from mathematics, engineering and science. The resulting computational curriculum focuses on modeling, scales and limits, simulation, abstraction, and automation as key components of a computationalist mindset.
On the design and development of a domain based integrated knowledge repository
Authors: Lubliner David , Widmeyer George , Deek Fadi P.
Published: January 2010

A knowledge repository design artifact, the Constructivist Unifying Baccalaureate Epistemology (CUBE), incorporating conceptual mapping features and a semantic ontology structure was developed and evaluated. The aim is to achieve quantifiable improvement in learning outcomes by integrating course materials in a field of study. The CUBE knowledge repository was modeled as an organic structure with the ability to evolve over time by incorporating a ranking/voting feature that enables learners and instructors to add further content to the knowledge base and collectively evaluate the relative weights of conceptual threads. The goal of this research was to provide the means, models and tools that would allow learners, from their earliest studies, to develop and explore these conceptual threads that tie a discipline together. Although this paper focuses on the technological details of the design and implementation of the artifacts, it also describes the knowledge integration theoretical models used as the basis for tool design and presents the results of a qualitative and quantitative evaluation carried out to assess the effectiveness of the artifacts.
Ganesha
Authors: Pan Xinghao , Tan Jiaqi , Kavulya Soila , Gandhi Rajeev , Narasimhan Priya
Published: January 2010

Ganesha aims to diagnose faults transparently (in a black-box manner) in MapReduce systems, by analyzing OS-level metrics. Ganesha's approach is based on peer-symmetry under fault-free conditions, and can diagnose faults that manifest asymmetrically at nodes within a MapReduce system. We evaluate Ganesha by diagnosing Hadoop problems for the Gridmix Hadoop benchmark on 10-node and 50-node MapReduce clusters on Amazon's EC2. We also candidly highlight faults that escape Ganesha's diagnosis.
Feasibility regions
Authors: Riska Alma , Mi Ningfang , Smirni Evgenia , Casale Giuliano
Published: January 2010

Low utilization immediately suggests that placing the system into a low power mode during idle times may considerably decrease power consumption. As future workload remains largely unknown, "when" to initiate a power saving mode and for "how long" to stay in this mode remains a challenging open problem, given that performance degradation of future jobs should not be compromised. We present a model and an algorithm that manages to successfully explore feasible regions of power and performance, and expose the system limitations according to both measures. Extensive analysis on a set of enterprise storage traces shows the algorithm's robustness for successfully identifying "when" and for "how long" one should activate a power saving mode given a set of power/performance targets that are provided by the user.
Research on online social networks
Authors: Willinger Walter , Rejaie Reza , Torkjazi Mojtaba , Valafar Masoud , Maggioni Mauro
Published: January 2010

Online Social Networks (OSNs) provide a unique opportunity for researchers to study how a combination of technological, economical, and social forces have been conspiring to provide a service that has attracted the largest user population in the history of the Internet. With more than half a billion of users and counting, OSNs have the potential to impact almost every aspect of networking, including measurement and performance modeling and analysis, network architecture and system design, and privacy and user behavior, to name just a few. However, much of the existing OSN research literature seems to have lost sight of this unique opportunity and has avoided dealing with the new challenges posed by OSNs. We argue in this position paper that it is high time for OSN researcher to exploit and face these challenges to provide a basic understanding of the OSN ecosystem as a whole. Such an understanding has to reflect the key role users play in this system and must focus on the system's dynamics, purpose and functionality when trying to illuminate the main technological, economic, and social forces at work in the current OSN revolution.
Modeling virtual machine performance
Authors: Tickoo Omesh , Iyer Ravi , Illikkal Ramesh , Newell Don
Published: January 2010

Data centers are increasingly employing virtualization and consolidation as a means to support a large number of disparate applications running simultaneously on server platforms. However, server platforms are still being designed and evaluated based on performance modeling of a single highly parallel application or a set of homogenous work-loads running simultaneously. Since most future datacenters are expected to employ server virtualization, this paper takes a look at the challenges of modeling virtual machine (VM) performance on a datacenter server. Based on vConsolidate (a server virtualization benchmark) and latest multi-core servers, we show that the VM modeling challenge requires addressing three key problems: (a) modeling the contention of visible resources (cores, memory capacity, I/O devices, etc), (b) modeling the contention of invisible resources (shared microarchitecture resources, shared cache, shared memory bandwidth, etc) and (c) modeling overheads of virtual machine monitor (or hypervisor) implementation. We take a first step to addressing this problem by describing a VM performance modeling approach and performing a detailed case study based on the vConsolidate benchmark. We conclude by outlining outstanding problems for future work.
Modeling workloads and devices for IO load balancing in virtualized environments
Authors: Gulati Ajay , Kumar Chethan , Ahmad Irfan
Published: January 2010

Virtualization has been effective in providing performance isolation and proportional allocation of resources, such as CPU and memory between VMs by using automated distributed resource schedulers and VM migration. Storage VMotion allows users to migrate virtual hard disks from one data store to another without stopping the virtual machine. There is a dire need for an automated tool to manage storage resources more effectively by doing virtual disk placement and load balancing of workloads across multiple data stores. Applicable beyond virtualization, this problem is challenging because it requires modeling both workloads and characterizing underlying devices. Furthermore, device characteristics such as number of disks backing a LUN, disk types etc. are hidden from the hosts by the virtualization layer at the array. In this paper, we propose a storage resource scheduler (SRS) to manage virtual disk placement and automatic load balancing using Storage VMotion. Our initial results lead us to believe that we can effectively model workloads and devices to improve overall storage resource utilization in practice.
Enabling rich mobile applications
Authors: Mukhopadhyay Shoubhik , Schurgers Curt , Dey Sujit
Published: January 2010

With the universal adoption of mobile communication devices for many common computing applications like email and web access, there is a growing demand to use these devices for richer applications that require high computing power. This paper looks at a way of enabling thin wireless clients to support powerful applications by using processing and networking infrastructure that are available in our surroundings. One of the major challenges is in determining how to schedule both the wireless communication and computing resources together to support a broad set of client nodes. This scheduling has to take into account the resource limitations and locations of the processing elements, as well as the constraints on wireless communication, in terms of available channels and the capacity of each channel. Additionally, the scheduling needs to be completed in a short time, in order to minimize the delay in initiating the applications after the clients request the resources. We present this in the form of a joint-scheduling problem, and present a fast algorithm that can perform this scheduling efficiently. Our approach can achieve a scheduling performance close to the optimal exhaustive solution, but with an execution time that is reduced by three or more orders of magnitude (from hours to seconds).
Guest column
Authors: Dvir Z.
Published: January 2010

The finite field Kakeya problem deals with the way lines in different directions can overlap in a vector space over a finite field. This problem came up in the study of certain Euclidean problems and, independently, in the search for explicit randomness extractors. We survey recent progress on this problem and describe several of its applications.
BFTW
3
Authors: Kuznetsov Petr , Rodrigues Rodrigo
Published: January 2010

The first BFTW3 workshop took place in Elche, Spain, on the 22nd of September, just before the 23rd International Symposium on Distributed Computing (DISC).

The workshop gathered researchers from both the theory and systems communities and aimed at discussing recent advances and understanding why the impressive research activity in the area of Byzantine fault-tolerance is not yet instantiated in practice. Has the moment for a wide deployment of BFT systems arrived, and if so, where BFT systems should be deployed in the first place?
A Brain-Based Endophenotype for Major Depressive Disorder
Authors: Peterson Bradley S. , Weissman Myrna M.
Published: January 2010

We have identified a brain-based endophenotype for major depressive disorder (MDD) that includes thinning of the cortex of the lateral aspect of the right hemisphere and the medial aspect of the left, as well as bilateral hypoplasia of frontal and parietal white matter. The endophenotype status of these abnormalities is supported by their presence in a multigenerational cohort of persons who themselves do not have MDD but who are at increased familial risk for developing the illness. Those who have the endophenotype but who are not ill nevertheless still suffer from inattention and poor visual memory for social stimuli in direct proportion to the magnitude of cortical thinning and white matter hypoplasia within the endophenotype. Identification of this endophenotype and its cognitive correlates provides targets for devising new preventive and therapeutic interventions for MDD.
Interactions Between Gut Microbiota and Host Metabolism Predisposing to Obesity and Diabetes
Authors: Musso Giovanni , Gambino Roberto , Cassader Maurizio
Published: January 2010

Novel, culture-independent, molecular and metagenomic techniques have provided new insight into the complex interactions between the mammalian host and gut microbial species. It is increasingly evident that gut microbes may shape the host metabolic and immune network activity and ultimately influence the development of obesity and diabetes. We discuss the evidence connecting gut microflora to obesity and to type 1 and type 2 diabetes, and we present recent insights into potential mechanisms underlying this relationship: increased nutrient absorption from the diet, prolonged intestinal transit time, altered bile acid entero-hepatic cycle, increased cellular uptake of circulating triglycerides, enhanced de novo lipogenesis, reduced free fatty acid oxidation, altered tissue composition of biologically active polyunsaturated fatty acid, chronic low-grade inflammation triggered by the endotoxin toll-like receptor 4 axis, and altered intestinal barrier function.
Imaging of Atherosclerosis
Authors: Owen D.R.J. , Lindsay A.C. , Choudhury R.P. , Fayad Z.A.
Published: January 2010

It is now well recognized that the atherosclerotic plaques responsible for thrombus formation are not necessarily those that impinge most on the lumen of the vessel. Nevertheless, clinical investigations for atherosclerosis still focus on quantifying the degree of stenosis caused by plaques. Many of the features associated with a high-risk plaque, including a thin fibrous cap, large necrotic core, macrophage infiltration, neovascularization, and intraplaque hemorrhage, can now be probed by novel imaging techniques. Each technique has its own strengths and drawbacks. In this article, we review the various imaging modalities used for the evaluation and quantification of atherosclerosis.
Alpha-1-Antitrypsin Deficiency: Importance of Proteasomal and Autophagic Degradative Pathways in Disposal of Liver Disease–Associated Protein Aggregates
Authors: Perlmutter David H.
Published: January 2010

Alpha-1-antitrypsin (AT) deficiency is the most common genetic cause of liver disease in children. The primary pathological issue is a point mutation that renders an abundant hepatic secretory glycoprotein prone to altered folding and a tendency to polymerize and aggregate. However, the expression of serious liver damage among homozygotes is dependent on genetic and/or environmental modifiers. Several studies have validated the concept that endogenous hepatic pathways for disposal of aggregation-prone proteins, including the proteasomal and autophagic degradative pathways, could play a key role in the variation in hepatic damage and be the target of the modifiers. Exciting recent results have shown that a drug that enhances autophagy can reduce the hepatic load of aggregated protein and reverse fibrosis in a mouse model of this disease.