bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytolethal Distending Toxin fromAggregatibacter actinomycetemcomitansInduces DNA Damage, S/G2Cell Cycle Arrest, and Caspase- Independent Death in aSaccharomyces cerevisiaeModel
Authors: Matangkasombut Oranart , Wattanawaraporn Roongtiwa , Tsuruda Keiko , Ohara Masaru , Sugai Motoyuki , Mongkolsuk Skorn 
Published: December 2009

ABSTRACTCytolethal distending toxin (CDT) is a bacterial toxin that induces G2/M cell cycle arrest, cell distension, and/or apoptosis in mammalian cells. It is produced by several Gram-negative species and may contribute to their pathogenicity. The catalytic subunit CdtB has homology with DNase I and may act as a genotoxin. However, the mechanism by which CdtB leads to cell death is not yet clearly understood. Here, we usedSaccharomyces cerevisiaeas a model to study the molecular pathways involved in the function of CdtB fromAggregatibacter actinomycetemcomitans, a cause of aggressive periodontitis. We show thatA.actinomycetemcomitansCdtB (AaCdtB) expression induces S/G2arrest and death in a DNase-catalytic residue and nuclear localization-dependent manner in haploid yeasts. Yeast strains defective in homologous recombination (HR) repair, but not other DNA repair pathways, are hypersensitive to AaCdtB, suggesting that HR is required for survival upon CdtB expression. In addition, yeast does not harbor the substrate for the other activity proposed for CdtB function, which is phosphatidylinositol-3,4,5-triphosphate phosphatase. Thus, these results suggest that direct DNA-damaging activity alone is sufficient for CdtB toxicity. To investigate how CdtB induces cell death, we examined the effect of CdtB in yeast strains with mutations in apoptotic regulators. Our results suggest that yeast death occurs independently of the yeast metacaspase geneYCA1and the apoptosis-inducing factorAIF1but is partially dependent on histone H2B serine 10 phosphorylation. Therefore, we report here the evidence that AaCdtB causes DNA damage that leads to nonapoptotic death in yeast and the first mutation that confers resistance to CdtB.
Morphine Disrupts Interleukin-23 (IL-23)/IL-17-Mediated Pulmonary Mucosal Host Defense against
Streptococcus
pneumoniae
Infection
Authors: Ma Jing , Wang Jinghua , Wan Jing , Charboneau Richard , Chang Yaping , Barke Roderick A. , Roy Sabita 
Published: December 2009

ABSTRACT

S
treptococcus
pneumoniae
is a pathogen that causes serious respiratory disease and meningitis in the immunocompromised drug abuse population. However, the precise mechanisms by which drug abuse compromises the host immune defense to pulmonary
S. pneumoniae
infection is not fully understood. Using a well-established murine model of opiate abuse and
S. pneumoniae
lung infection, we explored the influence of morphine treatment on the interleukin-23 (IL-23)/IL-17 axis and related innate immunity. Impairment of early IL-23/IL-17 production caused by morphine treatment was associated with delayed neutrophil migration and decreased pneumococcal clearance. Furthermore, morphine treatment impaired MyD88-dependent IL-23 production in alveolar macrophages and dendritic cells in response to
in vitro
S. pneumoniae
cell infection. Moreover, morphine treatment significantly inhibited the
S. pneumoniae
-induced phosphorylation of interferon response factor 3 (IRF3), ATF2, and NF-κBp65. T-cell receptor δ (TCRδ)-deficient mice showed a decrease in IL-17 production and a severely weakened capacity to clear lung
S. pneumoniae
infection. Finally, morphine treatment resulted in diminished secretion of antimicrobial proteins S100A9 and S100A8/A9 during early stages of
S. pneumoniae
infection. In conclusion, morphine treatment causes a dysfunction in IL-23-producing dendritic cells and macrophages and IL-17-producing γδT lymphocytes in response to
S. pneumoniae
lung infection. This leads to diminished release of antimicrobial S100A8/A9 proteins, compromised neutrophil recruitment, and more-severe infection.
A SURVEY OF POLYNOMIAL APPROXIMATION ON THE SPHERE
Authors: DAI FENG , WANG KUNYANG 
Published: December 2009

The main purpose of this paper is to survey some of the work on spherical approximation done by the BNU group under the direction of Professor Sun. The equiconvergent operators of Cesàro means, and their interesting applications are described. The Jackson inequality for spherical polynomials and some moduli of smoothness on the sphere are investigated. The equivalence between moduli of smoothness and K-functionals is also discussed. We also describe several weighted polynomial inequalities on the sphere, including the Remez-type and the Nikolskii-type inequalities, the Marcinkiewicz–Zygmund inequality, the Bernstein-type and the Schur-type inequalities. Positive cubature formulas on the sphere, and their relation to the Marcinkiewicz–Zygmund inequality are also discussed. A survey on recent results on asymptotic orders of the n-widths of Sobolev's classes on the sphere is also given.
Motion field texture synthesis
Authors: Ma Chongyang , Wei Li-Yi , Guo Baining , Zhou Kun 
Published: December 2009

A variety of animation effects such as herds and fluids contain detailed motion fields characterized by repetitive structures. Such detailed motion fields are often visually important, but tedious to specify manually or expensive to simulate computationally. Due to the repetitive nature, some of these motion fields (e.g. turbulence in fluids) could be synthesized by procedural texturing, but procedural texturing is known for its limited generality.
We apply example-based texture synthesis for motion fields. Our technique is general and can take on a variety of user inputs, including captured data, manual art, and physical/procedural simulation. This data-driven approach enables artistic effects that are difficult to achieve via previous methods, such as heart shaped swirls in fluid animation. Due to the use of texture synthesis, our method is able to populate a large output field from a small input exemplar, imposing minimum user workload. Our algorithm also allows the synthesis of output motion fields not only with the same dimension as the input (e.g. 2D to 2D) but also of higher dimension, such as 3D volumetric outputs from 2D planar inputs. This cross-dimension capability supports a convenient usage scenario, i.e. the user could simply supply 2D images and our method produces a 3D motion field with similar characteristics. The motion fields produced by our method are generic, and could be combined with a variety of large-scale low-resolution motions that are easy to specify either manually or computationally but lack the repetitive structures to be characterized as textures. We apply our technique to a variety of animation phenomena, including smoke, liquid, and group motion.
Automatic bounding of programmable shaders for efficient global illumination
Authors: Velázquez-Armendáriz Edgar , Zhao Shuang , Hašan Miloš , Walter Bruce , Bala Kavita 
Published: December 2009

This paper describes a technique to automatically adapt programmable shaders for use in physically-based rendering algorithms. Programmable shading provides great flexibility and power for creating rich local material detail, but only allows the material to be queried in one limited way: point sampling. Physically-based rendering algorithms simulate the complex global flow of light through an environment but rely on higher level information about the material properties, such as importance sampling and bounding, to intelligently solve high dimensional rendering integrals.
We propose using a compiler to automatically generate interval versions of programmable shaders that can be used to provide the higher level query functions needed by physically-based rendering without the need for user intervention or expertise. We demonstrate the use of programmable shaders in two such algorithms, multidimensional lightcuts and photon mapping, for a wide range of scenes including complex geometry, materials and lighting.
Shadow art
Authors: Mitra Niloy J. , Pauly Mark 
Published: December 2009

"To them, I said, the truth would be literally nothing but the shadows of the images." -Plato, The RepublicShadow art is a unique form of sculptural art where the 2D shadows cast by a 3D sculpture are essential for the artistic effect. We introduce computational tools for the creation of shadow art and propose a design process where the user can directly specify the desired shadows by providing a set of binary images and corresponding projection information. Since multiple shadow images often contradict each other, we present a geometric optimization that computes a 3D shadow volume whose shadows best approximate the provided input images. Our analysis shows that this optimization is essential for obtaining physically realizable 3D sculptures. The resulting shadow volume can then be modified with a set of interactive editing tools that automatically respect the often intricate shadow constraints. We demonstrate the potential of our system with a number of complex 3D shadow art sculptures that go beyond what is seen in contemporary art pieces.
Serializable isolation for snapshot databases
Authors: Cahill Michael J. , Röhm Uwe , Fekete Alan D. 
Published: December 2009

Many popular database management systems implement a multiversion concurrency control algorithm called snapshot isolation rather than providing full serializability based on locking. There are well-known anomalies permitted by snapshot isolation that can lead to violations of data consistency by interleaving transactions that would maintain consistency if run serially. Until now, the only way to prevent these anomalies was to modify the applications by introducing explicit locking or artificial update conflicts, following careful analysis of conflicts between all pairs of transactions.
This article describes a modification to the concurrency control algorithm of a database management system that automatically detects and prevents snapshot isolation anomalies at runtime for arbitrary applications, thus providing serializable isolation. The new algorithm preserves the properties that make snapshot isolation attractive, including that readers do not block writers and vice versa. An implementation of the algorithm in a relational DBMS is described, along with a benchmark and performance study, showing that the throughput approaches that of snapshot isolation in most cases.
Relational query coprocessing on graphics processors
Authors: He Bingsheng , Lu Mian , Yang Ke , Fang Rui , Govindaraju Naga K. , Luo Qiong , Sander Pedro V. 
Published: December 2009

Graphics processors (GPUs) have recently emerged as powerful coprocessors for general purpose computation. Compared with commodity CPUs, GPUs have an order of magnitude higher computation power as well as memory bandwidth. Moreover, new-generation GPUs allow writes to random memory locations, provide efficient interprocessor communication through on-chip local memory, and support a general purpose parallel programming model. Nevertheless, many of the GPU features are specialized for graphics processing, including the massively multithreaded architecture, the Single-Instruction-Multiple-Data processing style, and the execution model of a single application at a time. Additionally, GPUs rely on a bus of limited bandwidth to transfer data to and from the CPU, do not allow dynamic memory allocation from GPU kernels, and have little hardware support for write conflicts. Therefore, a careful design and implementation is required to utilize the GPU for coprocessing database queries.
In this article, we present our design, implementation, and evaluation of an in-memory relational query coprocessing system, GDB, on the GPU. Taking advantage of the GPU hardware features, we design a set of highly optimized data-parallel primitives such as split and sort, and use these primitives to implement common relational query processing algorithms. Our algorithms utilize the high parallelism as well as the high memory bandwidth of the GPU, and use parallel computation and memory optimizations to effectively reduce memory stalls. Furthermore, we propose coprocessing techniques that take into account both the computation resources and the GPU-CPU data transfer cost so that each operator in a query can utilize suitable processors—the CPU, the GPU, or both—for an optimized overall performance. We have evaluated our GDB system on a machine with an Intel quad-core CPU and an NVIDIA GeForce 8800 GTX GPU. Our workloads include microbenchmark queries on memory-resident data as well as TPC-H queries that involve complex data types and multiple query operators on data sets larger than the GPU memory. Our results show that our GPU-based algorithms are 2--27x faster than their optimized CPU-based counterparts on in-memory data. Moreover, the performance of our coprocessing scheme is similar to, or better than, both the GPU-only and the CPU-only schemes.
Preventing history forgery with secure provenance
Authors: Hasan Ragib , Sion Radu , Winslett Marianne 
Published: December 2009

As increasing amounts of valuable information are produced and persist digitally, the ability to determine the origin of data becomes important. In science, medicine, commerce, and government, data provenance tracking is essential for rights protection, regulatory compliance, management of intelligence and medical data, and authentication of information as it flows through workplace tasks. While significant research has been conducted in this area, the associated security and privacy issues have not been explored, leaving provenance information vulnerable to illicit alteration as it passes through untrusted environments.
In this article, we show how to provide strong integrity and confidentiality assurances for data provenance information at the kernel, file system, or application layer. We describe Sprov, our provenance-aware system prototype that implements provenance tracking of data writes at the application layer, which makes Sprov extremely easy to deploy. We present empirical results that show that, for real-life workloads, the runtime overhead of Sprov for recording provenance with confidentiality and integrity guarantees ranges from 1% to 13%, when all file modifications are recorded, and from 12% to 16%, when all file read and modifications are tracked.
Causality-based versioning
Authors: Muniswamy-Reddy Kiran-Kumar , Holland David A. 
Published: December 2009

Versioning file systems provide the ability to recover from a variety of failures, including file corruption, virus and worm infestations, and user mistakes. However, using versions to recover from data-corrupting events requires a human to determine precisely which files and versions to restore. We can create more meaningful versions and enhance the value of those versions by capturing the causal connections among files, facilitating selection and recovery of precisely the right versions after data corrupting events.
We determine when to create new versions of files automatically using the causal relationships among files. The literature on versioning file systems usually examines two extremes of possible version-creation algorithms: open-to-close versioning and versioning on every write. We evaluate causal versions of these two algorithms and introduce two additional causality-based algorithms: Cycle-Avoidance and Graph-Finesse.
We show that capturing and maintaining causal relationships imposes less than 7% overhead on a versioning system, providing benefit at low cost. We then show that Cycle-Avoidance provides more meaningful versions of files created during concurrent program execution, with overhead comparable to open/close versioning. Graph-Finesse provides even greater control, frequently at comparable overhead, but sometimes at unacceptable overhead. Versioning on every write is an interesting extreme case, but is far too costly to be useful in practice.
Surface Melting over Ice Shelves and Ice Sheets as Assessed from Modeled Surface Air Temperatures
Authors: Fyke Jeremy G. , Carter Lionel , Mackintosh Andrew , Weaver Andrew J. , Meissner Katrin J. 
Published: December 2009

Abstract
Summer surface melting plays an important role in the evolution of ice shelves and their progenitor ice sheets. To explore the magnitude of surface melt occurring over modern ice shelves and ice sheets in a climate scenario forced by anthropogenic emissions of carbon dioxide (CO2), a coupled climate model was used to simulate the distribution of summer melt at high latitudes and project the future evolution of high-melt regions in both hemispheres. Forcing of the climate model with CO2 emissions resulting from combustion of the present-day fossil-fuel resource base resulted in expansion of high-melt regions, as defined by the contour marking 200 positive degree-days per year, in the Northern Hemisphere and the Antarctic Peninsula and the introduction of high summer melt over the Ross, Ronne-Filchner, and Amery ice shelves as well as a large portion of the West Antarctic Ice Sheet (WAIS) and most of the Greenland Ice Sheet (GIS) by the year 2500. Capping CO2 concentrations at present-day levels avoided significant summer melt over the large Antarctic shelves, the WAIS, and much of the GIS.
Role for ADAP in shear flow–induced platelet mechanotransduction
Authors: Kasirer-Friede Ana , Ruggeri Zaverio M. , Shattil Sanford J. 
Published: December 2009

AbstractBinding of platelets to fibrinogen via integrin αIIbβ3 stimulates cytoskeletal reorganization and spreading. These responses depend on tyrosine phosphorylation of multiple proteins by Src family members and Syk. Among Src substrates in platelets is adhesion- and degranulation-promoting adapter protein (ADAP), an adapter with potential binding partners: SLP-76, VASP, and SKAP-HOM. During studies of platelet function under shear flow, we discovered that ADAP−/− mouse platelets, unlike ADAP+/+ platelets, formed unstable thrombi in response to carotid artery injury. Moreover, fibrinogen-adherent ADAP−/− platelets in shear flow ex vivo showed reduced spreading and smaller zones of contact with the matrix. These abnormalities were not observed under static conditions, and they could not be rescued by stimulating platelets with a PAR4 receptor agonist or by direct αIIbβ3 activation with MnCl2, consistent with a defect in outside-in αIIbβ3 signaling. ADAP+/+ platelets subjected to shear flow assembled F-actin–rich structures that colocalized with SLP-76 and the Rac1 exchange factor, phospho-Vav1. In contrast, platelets deficient in ADAP, but not those deficient in VASP or SKAP-HOM, failed to form these structures. These results establish that ADAP is an essential component of αIIbβ3-mediated platelet mechanotransduction that promotes F-actin assembly and enables platelet spreading and thrombus stabilization under fluid shear stress.
Identification of iGb3 and iGb4 in melanoma B16F10-Nex2 cells and the iNKT cell-mediated antitumor effect of dendritic cells primed with iGb3
Authors: Dias Bianca R , Rodrigues Elaine G , Nimrichter Leonardo , Nakayasu Ernesto S , Almeida Igor C , Travassos Luiz R 
Published: December 2009

AbstractBackgroundCD1d-restricted iNKT cells are protective against murine melanoma B16F10-Nex2 growing subcutaneously in syngeneic C57Bl/6 mice as inferred from the fast tumor development in CD1d-KO in comparison with wild type animals. CD1d glycoproteins are related to the class I MHC molecules, and are involved in the presentation, particularly by dentritic cells (DC), of lipid antigens to iNKT cells. In the present work we attempted to identify the endogenous lipid mediator expressed in melanoma cells inducing such immunesurveillance response and study the possibility of protecting animals challenged with tumor cells with lipid-primed DC.ResultsCrude cytosolic and membrane fractions fromin vivogrowing melanoma contained iNKT-stimulating substances. Lipids were then extracted from these cells and one of the fractions (i.e. F3A) was shown to prime bone marrow-derived dendritic cells (BMDC) to stimulate iNKT murine hybridoma (DN32D3) cells to produce IL-2. The active fraction was analyzed by electrospray ionization-mass spectrometry (ESI-LIT-MS) and both iGb3 and iGb4 were identified along with GM3. When iGb3 was incubated with BMDC and tested with DN32D3 cells, IL-2 was equally produced indicating iNKT cell activation. GM3 consistently inhibited this response. To assess the antitumor response-induced by iGb3, a cytotoxicity assayin vitrowas used with [3H]-thymidine labeled B16F10-Nex2 cells. At target/effector (iGb3-activated iNKT) cell ratio of 100-1-100-4tumor cell lysis was shown. The antitumor activityin vivowas tested in mice challenged i.v. with B16F10-Nex2 cells and treated with iGb3- or α-galactosylceramide-primed DCs. A 4-fold lower tumor load in the lungs was observed with either treatment.ConclusionOur results show the expression of globo and isoglobohexosylceramides in murine melanoma B16F10-Nex2. The expression of iGb3 and its precursor, iGb4, on tumor cells may prime an effective iNKT cell-dependent antitumor response, modulated negatively by GM3 which is also produced in these cells. iGb3-primed BMDC exerted a significant iNKT cell-mediated anti-tumor activity in mice challenged with melanoma cells.
A rapid and efficient method for studies of virus interaction at the host cell surface using enteroviruses and real-time PCR
Authors: Jonsson Nina , Gullberg Maria , Israelsson Stina , Lindberg A Michael 
Published: December 2009

Abstract

Background
Measuring virus attachment to host cells is of great importance when trying to identify novel receptors. The presence of a usable receptor is a major determinant of viral host range and cell tropism. Furthermore, identification of appropriate receptors is central for the understanding of viral pathogenesis and gives possibilities to develop antiviral drugs. Attachment is presently measured using radiolabeled and subsequently gradient purified viruses. Traditional methods are expensive and time-consuming and not all viruses are stable during a purification procedure; hence there is room for improvement. Real-time PCR (RT-PCR) has become the standard method to detect and quantify virus infections, including enteroviruses, in clinical samples. For instance, primers directed to the highly conserved 5' untranslated region (5'UTR) of the enterovirus genome enable detection of a wide spectrum of enteroviruses. Here, we evaluate the capacity of the RT-PCR technology to study enterovirus host cell interactions at the cell surface and compare this novel implementation with an established assay using radiolabeled viruses.

Results
Both purified and crude viral extracts of CVB5 generated comparable results in attachment studies when analyzed with RT-PCR. In addition, receptor binding studies regarding viruses with coxsackie- and adenovirus receptor (CAR) and/or decay accelerating factor (DAF) affinity, further demonstrated the possibility to use RT-PCR to measure virus attachment to host cells. Furthermore, the RT-PCR technology and crude viral extracts was used to study attachment with low multiplicity of infection (0.05 × 10-4TCID50/cell) and low cell numbers (250), which implies the range of potential implementations of the presented technique.

Conclusion
We have implemented the well-established RT-PCR technique to measure viral attachment to host cells with high accuracy and reproducibility, at low cost and with less effort than traditional methods. Furthermore, replacing traditional methods with RT-PCR offers the opportunity to use crude virus containing extracts to investigate attachment, which could be considered as a step towards viral attachment studies in a more natural state.