bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytomegalovirus Immune Evasion Strategy
Authors: Mueller Kristen L.
Published: April 2010

Cytomegalovirus monkeys can reinfect an already-infected host by evading the CD8
+
T cell–mediated immune response.
Shuttle Vector-Based Transformation System for
Pyrococcus furiosus
Authors: Waege Ingrid , Schmid Georg , Thumann Sybille , Thomm Michael , Hausner Winfried
Published: April 2010

Pyrococcus furiosus
is a model organism for analyses of molecular biology and biochemistry of archaea, but so far no useful genetic tools for this species have been described. We report here a genetic transformation system for
P. furiosus
based on the shuttle vector system pYS2 from
Pyrococcus abyssi
. In the redesigned vector, the
pyrE
gene from
Sulfolobus
was replaced as a selectable marker by the 3-hydroxy-3-methylglutaryl coenzyme A reductase gene (HMG-CoA) conferring resistance of transformants to the antibiotic simvastatin. Use of this modified plasmid resulted in the overexpression of the HMG-CoA reductase in
P. furiosus
, allowing the selection of strains by growth in the presence of simvastatin. The modified shuttle vector replicated in
P. furio
s
us
, but the copy number was only one to two per chromosome. This system was used for overexpression of His
6
-tagged subunit D of the RNA polymerase (RNAP) in
Pyrococcus
cells. Functional RNAP was purified from transformed cells in two steps by Ni-NTA and gel filtration chromatography. Our data provide evidence that expression of transformed genes can be controlled from a regulated gluconeogenetic promoter.
Antibiofilm Activity of the Marine Bacterium
Pseudoalteromonas
sp. Strain 3J6
Authors: Dheilly Alexandra , Soum-Soutéra Emmanuelle , Klein Géraldine L. , Bazire Alexis , Compère Chantal , Haras Dominique , Dufour Alain
Published: April 2010

Biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. In two-species biofilms of marine bacteria grown under dynamic conditions,
Pseudoalteromonas
sp. strain 3J6 formed mixed biofilms with
Bacillus
sp. strain 4J6 but was largely predominant over
Paracoccus
sp. strain 4M6 and
Vibrio
sp. strain D01. The supernatant of
Pseudoalteromonas
sp. 3J6 liquid culture (SN
3J6
) was devoid of antibacterial activity against free-living
Paracoccus
sp. 4M6 and
Vibrio
sp. D01 cells, but it impaired their ability to grow as single-species biofilms and led to higher percentages of nonviable cells in 48-h biofilms. Antibiofilm molecules of SN
3J6
were able to coat the glass surfaces used to grow biofilms and reduced bacterial attachment about 2-fold, which might partly explain the biofilm formation defect but not the loss of cell viability. SN
3J6
had a wide spectrum of activity since it affected all Gram-negative marine strains tested except other
Pseudoalteromonas
strains. Biofilm biovolumes of the sensitive strains were reduced 3- to 530-fold, and the percentages of nonviable cells were increased 3- to 225-fold. Interestingly, SN
3J6
also impaired biofilm formation by three strains belonging to the human-pathogenic species
Pseudomonas aeruginosa
,
Salmonella enterica
, and
Escherichia coli
. Such an antibiofilm activity is original and opens up a variety of applications for
Pseudoalteromonas
sp. 3J6 and/or its active exoproducts in biofilm prevention strategies.
Role of Extracellular DNA in Initial Bacterial Adhesion and Surface Aggregation
Authors: Das Theerthankar , Sharma Prashant K. , Busscher Henk J. , van der Mei Henny C. , Krom Bastiaan P.
Published: April 2010

Extracellular DNA (eDNA) is an important component of the biofilm matrix. We show that removal of eDNA from Gram-positive bacteria reduces initial adhesion to and aggregation of bacteria on surfaces. Thermodynamic analyses indicated that eDNA introduces favorable acid-base interactions, explaining the effect of eDNA on aggregation and adhesion to the surface.
Molecular Pathogenesis of Infections Caused byLegionella pneumophila
Authors: Newton Hayley J. , Ang Desmond K. Y. , van Driel Ian R. , Hartland Elizabeth L.
Published: April 2010

The genusLegionellacontains more than 50 species, of which at least 24 have been associated with human infection. The best-characterized member of the genus,Legionella pneumophila, is the major causative agent of Legionnaires' disease, a severe form of acute pneumonia.L. pneumophilais an intracellular pathogen, and as part of its pathogenesis, the bacteria avoid phagolysosome fusion and replicate within alveolar macrophages and epithelial cells in a vacuole that exhibits many characteristics of the endoplasmic reticulum (ER). The formation of the unusualL. pneumophilavacuole is a feature of its interaction with the host, yet the mechanisms by which the bacteria avoid classical endosome fusion and recruit markers of the ER are incompletely understood. Here we review the factors that contribute to the ability ofL. pneumophilato infect and replicate in human cells and amoebae with an emphasis on proteins that are secreted by the bacteria into theLegionellavacuole and/or the host cell. Many of these factors undermine eukaryotic trafficking and signaling pathways by acting as functional and, in some cases, structural mimics of eukaryotic proteins. We discuss the consequences of this mimicry for the biology of the infected cell and also for immune responses toL. pneumophilainfection.
Cardiac Involvement with Parasitic Infections
Authors: Hidron Alicia , Vogenthaler Nicholas , Santos-Preciado José I. , Rodriguez-Morales Alfonso J. , Franco-Paredes Carlos , Rassi Anis
Published: April 2010

Parasitic infections previously seen only in developing tropical settings can be currently diagnosed worldwide due to travel and population migration. Some parasites may directly or indirectly affect various anatomical structures of the heart, with infections manifested as myocarditis, pericarditis, pancarditis, or pulmonary hypertension. Thus, it has become quite relevant for clinicians in developed settings to consider parasitic infections in the differential diagnosis of myocardial and pericardial disease anywhere around the globe. Chagas' disease is by far the most important parasitic infection of the heart and one that it is currently considered a global parasitic infection due to the growing migration of populations from areas where these infections are highly endemic to settings where they are not endemic. Current advances in the treatment of African trypanosomiasis offer hope to prevent not only the neurological complications but also the frequently identified cardiac manifestations of this life-threatening parasitic infection. The lack of effective vaccines, optimal chemoprophylaxis, or evidence-based pharmacological therapies to control many of the parasitic diseases of the heart, in particular Chagas' disease, makes this disease one of the most important public health challenges of our time.
Clinical and Laboratory Update on Blastomycosis
Authors: Saccente Michael , Woods Gail L.
Published: April 2010

Blastomycosis is endemic in regions of North America that border the Great Lakes and the St. Lawrence River, as well as in the Mississippi River and Ohio River basins. Men are affected more often than women and children because men are more likely to participate in activities that put them at risk for exposure toBlastomyces dermatitidis. Human infection occurs when soil containing microfoci of mycelia is disturbed and airborne conidia are inhaled. If natural defenses in the alveoli fail to contain the infection, lymphohematogenous dissemination ensues. Normal host responses generate a characteristic pyogranulomatous reaction. The most common sites of clinical disease are the lung and skin; osseous, genitourinary, and central nervous system manifestations follow in decreasing order of frequency. Blastomycosis is one of the great mimickers in medicine; verrucous cutaneous blastomycosis resembles malignancy, and mass-like lung opacities due toB. dermatitidisoften are confused with cancer. Blastomycosis may be clinically indistinguishable from tuberculosis. Diagnosis is based on culture and direct visualization of round, multinucleated yeast forms that produce daughter cells from a single broad-based bud. Although a long course of amphotericin B is usually curative, itraconazole is also highly effective and is the mainstay of therapy for most patients with blastomycosis.
A Global Perspective on Hantavirus Ecology, Epidemiology, and Disease
Authors: Jonsson Colleen B. , Figueiredo Luiz Tadeu Moraes , Vapalahti Olli
Published: April 2010

Hantaviruses are enzootic viruses that maintain persistent infections in their rodent hosts without apparent disease symptoms. The spillover of these viruses to humans can lead to one of two serious illnesses, hantavirus pulmonary syndrome and hemorrhagic fever with renal syndrome. In recent years, there has been an improved understanding of the epidemiology, pathogenesis, and natural history of these viruses following an increase in the number of outbreaks in the Americas. In this review, current concepts regarding the ecology of and disease associated with these serious human pathogens are presented. Priorities for future research suggest an integration of the ecology and evolution of these and other host-virus ecosystems through modeling and hypothesis-driven research with the risk of emergence, host switching/spillover, and disease transmission to humans.
Candida
Infections of the Genitourinary Tract
Authors: Achkar Jacqueline M. , Fries Bettina C.
Published: April 2010

All humans are colonized with
Candida
species, mostly
Candida albicans
, yet some develop diseases due to
Candida
, among which genitourinary manifestations are extremely common. The forms of genitourinary candidiasis are distinct from each other and affect different populations. While vulvovaginal candidiasis affects mostly healthy women, candiduria occurs typically in elderly, hospitalized, or immunocompromised patients and in neonates. Despite its high incidence and clinical relevance, genitourinary candidiasis is understudied, and therefore, important questions about pathogenesis and treatment guidelines remain to be resolved. In this review, we summarize the current knowledge about genitourinary candidiasis.
Sequential XylS-CTD Binding to the Pm Promoter Induces DNA Bending Prior to Activation
Authors: Domínguez-Cuevas Patricia , Ramos Juan-Luís , Marqués Silvia
Published: April 2010

XylS protein, a member of the AraC family of transcriptional regulators, comprises a C-terminal domain (CTD) involved in DNA binding and an N-terminal domain required for effector binding and protein dimerization. In the absence of benzoate effectors, the N-terminal domain behaves as an intramolecular repressor of the DNA binding domain. To date, the poor solubility properties of the full-length protein have restricted XylS analysis to genetic approachesin vivo. To characterize the molecular consequences of XylS binding to its operator, we used a recombinant XylS-CTD variant devoid of the N-terminal domain. The resulting protein was soluble and monomeric in solution and activated transcription from its cognate promoter in an effector-independent manner. XylS binding sites in the Pm promoter present an intrinsic curvature of 35° centered at position −42 within the proximal site. Gel retardation and DNase footprint analysis showed XylS-CTD binding to Pm occurred sequentially: first a XylS-CTD monomer binds to the proximal site overlapping the RNA polymerase binding sequence to form complex I. This first event increased Pm bending to 50° and was followed by the binding of the second monomer, which further increased the observed global curvature to 98°. This generated a concomitant shift in the bending center to a region centered at position −51 when the two sites were occupied (complex II). We propose a model in which DNA structure and binding sequences strongly influence XylS binding events previous to transcription activation.
Mixed Infections and
In Vivo
Evolution in the Human Fungal Pathogen Cryptococcus neoformans
Authors: Desnos-Ollivier Marie , Patel Sweta , Spaulding Adam R. , Charlier Caroline , Garcia-Hermoso Dea , Nielsen Kirsten , Dromer Françoise
Published: April 2010

Koch’s postulates are criteria establishing a causal relationship between a microbe and a disease that lead to the assumption that diseases are caused by a single strain or its evolved forms.
Cryptococcus neoformans
is a life-threatening human fungal pathogen responsible for an estimated 1 million cases of cryptococcosis/year, predominantly meningoencephalitis. To assess the molecular diversity of clinical isolates and gain knowledge of
C. neoformans
biology in the host, we analyzed clinical cultures collected during the prospective CryptoA/D study. Using molecular analysis of unpurified isolates, we demonstrated that mixed infections in humans are more common than previously thought, occurring in almost 20% of patients diagnosed with cryptococcosis. These mixed infections are composed of different mating types, serotypes, and/or genotypes. We also identified genetically related haploid and diploid strains in the same patients. Experimental infections and quantitative PCR show that these ploidy changes can result from endoreplication (duplication of DNA content) and that shuttling between haploid and diploid states can occur, suggesting
in vivo
evolution. Thus, the concept of one strain/one infection does not hold true for
C. neoformans
and may apply to other environmentally acquired fungal pathogens. Furthermore, the possibility of mixed and/or evolving infections should be taken into account when developing therapeutic strategies against these pathogens.

IMPORTANCE
Cryptococcus  neoformans
is a life-threatening human fungal pathogen that is present in the environment and is responsible for an estimated 1 million cases of cryptococcosis/year, predominantly meningoencephalitis in HIV-infected patients. To assess the molecular diversity of clinical isolates and gain knowledge of
C. neoformans
biology in the host, we analyzed clinical cultures collected during a prospective study on cryptococcosis. Using molecular analysis of unpurified isolates, we uncovered an unexpectedly high frequency (almost 20%) of mixed infections. We further demonstrated that these mixed infections could result from infestation by multiple strains acquired from the environment. We also made the serendipitous discovery of
in vivo
evolution leading to endoreplication of the yeasts within the host. Thus, the concept of one strain causing one infection does not hold true for
C. neoformans
and potentially for other environmentally acquired fungal pathogens. The possibility of mixed and/or evolving infections should be taken into account when developing therapeutic strategies against these pathogens.
Rehabilitation for shoulder instability
Authors: Jaggi A , Lambert S
Published: April 2010

Both structural and non-structural components can contribute to shoulder instability. Classification and therefore management must recognise these factors to achieve functional stability. This paper discusses a classification system proposing three types of shoulder instability recognising the structural and non-structural components and that a continuum exists between pathologies. Structural causes can be addressed with surgical intervention, but non-structural causes such as altered neuromuscular control within the rotator cuff should be addressed conservatively. The purpose of this article is to describe the types of instability and guide appropriate management, helping to avoid surgery in inappropriate cases and ensure that effective rehabilitation has been achieved.
First-time anterior shoulder dislocations: has the standard changed?
Authors: Boone Julienne L , Arciero Robert A
Published: April 2010

The traditional treatment of a first-time anterior shoulder dislocation of reduction and a period of immobilisation should be challenged. The purpose of this review is to assimilate and present the current literature on acute anterior shoulder instability. This involves consideration of the pathoanatomy, natural history and the more recent evaluation of treatment outcomes, which appropriately incorporate quality of life measures in addition to recurrences. There is ample evidence to consider primary stabilisation as an option for treatment in the high-risk group, less than 25 years of age.
A new classification system for shoulder instability
Authors: Kuhn John E
Published: April 2010

Glenohumeral joint instability is extremely common yet the definition and classification of instability remains unclear. In order to find the best ways to treat instability, the condition must be clearly defined and classified. This is particularly important so that treatment studies can be compared or combined, which can only be done if the patient population under study is the same. The purpose of this paper was to review the problems with historical methods of defining and classifying instability and to introduce the FEDS system of classifying instability, which was developed to have content validity and found to have high interobserver and intraobserver agreement.
Mechanical and hydraulic characterization of plastic concrete for seepage cut-off walls
Authors: Hinchberger S. , Weck J. , Newson T.
Published: April 2010

This paper describes a series of laboratory tests performed to characterize the mechanical and hydraulic properties of plastic concrete (PL-C). PL-C is used in the construction of seepage cut-off walls in dams and it comprises cement, aggregate, and water mixed with sodium bentonite. The addition of sodium bentonite causes a reduction in strength and improved ductility after failure compared with normal concrete. The mechanical properties of PL-C are studied using a series of unconfined compression tests and confined compression tests performed while simultaneously permeating water through PL-C specimens. Stress relaxation and controlled rate of loading tests are also performed to investigate the rate-sensitivity and time-dependency of plastic concrete. The test results show that the hydraulic conductivity of PL-C increases between two and three orders of magnitude during triaxial compression due to yielding, crack formation, and dilation of the cracks. Such changes in the behaviour of PL-C should be minimized during design by controlling the working strains and using erosion-resistant mixes. In addition to these findings, PL-C exhibits significant time-dependent behaviour similar to that observed for clays, and the variation of compressive strength versus confining stress is comparable to normal strength concrete.
Investigation of a possible submarine landslide at the Var delta front (Nice continental slope, southeast France)
Authors: Sultan N. , Savoye B. , Jouet G. , Leynaud D. , Cochonat P. , Henry P. , Stegmann S. , Kopf A.
Published: April 2010

The Var prodelta progrades across a straight, narrow shelf (less than 2 km wide) with a very steep continental slope reaching locally more than 30°. Historically, the Var delta front is sadly famous for the 1979 catastrophic submarine landslide that resulted in several casualties and infrastructural damage. Geotechnical and geophysical investigations carried out in late 2007 to the east of the 1979 landslide scar provide evidence for the possible occurrence of a new important sedimentary collapse and submarine landslide. Geophysical data acquired in the area show the presence of several seafloor morphological steps rooted to shallow subsurface seismic reflections. Moreover, in situ piezocone measurements demonstrate the presence of several shear zones at the border of the shelf break at different depths below the seafloor. The aim of this technical note is to present and discuss acquired geotechnical and geophysical data in terms of failure mechanisms and submarine landslides. Both geophysical and geotechnical data suggest the start-up of a progressive failure mechanism and reveal the possible occurrence of a submarine landslide and the urgent need for mitigation procedures.
PROBING THE MOMENTUM-DEPENDENT MEDIUM MODIFICATIONS OF THE NUCLEON–NUCLEON ELASTIC CROSS SECTION
Authors: LI QINGFENG , SHEN CAIWAN , DI TORO M.
Published: April 2010

The momentum dependence of the medium modifications on nucleon–nucleon elastic cross sections is investigated with the microscopic transport model UrQMD. The semi-peripheral Au + Au collision at the beam energy Eb = 400A MeV is adopted as an example. It is found that uncertainties of the momentum dependence on medium modifications of cross sections visibly influence the yield and collective flow distributions of free nucleons. In these observables, the elliptic flow is sensitively dependent on detailed forms of the momentum dependence. However, it is weakly influenced by the splitting effect of the neutron–neutron and proton–proton cross sections.
SPHERICALLY SYMMETRIC MASSIVE SCALAR FIELDS IN GENERAL RELATIVITY
Authors: MEHRPOOYA MOHAMMAD , MOMENI D.
Published: April 2010

First, we review some attempts made to find the exact spherically symmetric solutions to Einstein field equations in the presence of scalar fields. Wyman's solution in both the static and the nonstatic scalar field is discussed, and it is shown why in the case of the nonstatic homogenous matter field the static metric cannot be represented in terms of elementary functions. We mention here that if the space–time is static, according to field equations, there are two options for fixing the scalar field: static (time-independent) and nonstatic (time-dependent). All these solutions are limited to the minimally coupled massless scalar fields and also in the absence of the cosmological constant. Then we show that if we are interested to have homogenous isotropic scalar field matter, we can construct a series solution in terms of the scalar field's mass and cosmological constant. This solution is static and possesses a locally flat case as a special choice of the mass of the scalar field and can be interpreted as an effective vacuum. Therefore, the mass of the scalar field eliminates any locally gravitational effect as tidal forces. Finally, we describe why this system is unstable in the language of dynamical systems.
PROJECTION MODELS FOR INTUITIONISTIC FUZZY MULTIPLE ATTRIBUTE DECISION MAKING
Authors: XU ZESHUI , HU HUI
Published: April 2010

The aim of this paper is to investigate the intuitionistic fuzzy multiple attribute decision-making problems where the attribute values are expressed in intuitionistic fuzzy numbers or interval-valued intuitionistic fuzzy numbers. We introduce some notions, such as intuitionistic fuzzy ideal point, interval-valued intuitionistic fuzzy ideal point, the modules of intuitionistic fuzzy numbers, and interval-valued intuitionistic fuzzy numbers. We also introduce the cosine of the included angle between the attribute value vectors of each alternative and the intuitionistic fuzzy ideal point, and the cosine of the included angle between the attribute value vectors of each alternative and the interval-valued intuitionistic fuzzy ideal point. Then we establish two projection models to measure the similarity degrees between each alternative and the intuitionistic fuzzy ideal point, and between each alternative and the interval-valued intuitionistic fuzzy ideal point. Based on the projection models, we can rank the given alternatives and then select the most desirable one. Finally, we illustrate the developed projection models with a numerical example.
THE DIOPHANTINE EQUATION A4 + 2δB2 = Cn
Authors: BENNETT MICHAEL A. , ELLENBERG JORDAN S. , NG NATHAN C.
Published: April 2010

In a previous paper, the second author proved that the equation [Formula: see text] had no integral solutions for prime p > 211 and (A,B,C) = 1. In the present paper, we explain how to extend this result to smaller exponents, and to the related equation [Formula: see text]
MOTIVIC DOUBLE SHUFFLE
Authors: SOUDÈRES ISMAEL
Published: April 2010

The goal of this paper is to give an elementary proof of the double shuffle relations directly for the Goncharov and Manin motivic multiple zeta values. The shuffle relation is straightforward, but for the stuffle, we use a modification of a method first introduced by Cartier for the purpose of proving stuffle for the real multiple zeta values. We will use both the representation of multiple zeta values on the moduli spaces of curve introduced by Goncharov and Manin and we will apply suitable blow-up sequences to the representation of multiple zeta values as integral over a cube.
Geometric containers for efficient shortest-path computation
Authors: Wagner Dorothea , Willhalm Thomas , Zaroliagis Christos
Published: April 2010

A fundamental approach in finding efficiently best routes or optimal itineraries in traffic information systems is to reduce the search space (part of graph visited) of the most commonly used shortest path routine (Dijkstra's algorithm) on a suitably defined graph. We investigate reduction of the search space while simultaneously retaining data structures, created during a preprocessing phase, of size linear (i.e., optimal) to the size of the graph. We show that the search space of Dijkstra's algorithm can be significantly reduced by extracting geometric information from a given layout of the graph and by encapsulating precomputed shortest-path information in resulted geometric objects (containers). We present an extensive experimental study comparing the impact of different types of geometric containers using test data from real-world traffic networks. We also present new algorithms as well as an empirical study for the dynamic case of this problem, where edge weights are subject to change and the geometric containers have to be updated and show that our new methods are two to three times faster than recomputing everything from scratch. Finally, in an appendix, we discuss the software framework that we developed to realize the implementations of all of our variants of Dijkstra's algorithm. Such a framework is not trivial to achieve as our goal was to maintain a common code base that is, at the same time, small, efficient, and flexible, as we wanted to enhance and combine several variants in any possible way.
Using random sampling to build approximate tries for efficient string sorting
Authors: Sinha Ranjan , Zobel Justin
Published: April 2010

Algorithms for sorting large datasets can be made more efficient with careful use of memory hierarchies and reduction in the number of costly memory accesses. In earlier work, we introduced burstsort, a new string-sorting algorithm that on large sets of strings is almost twice as fast as previous algorithms, primarily because it is more cache efficient. Burstsort dynamically builds a small trie that is used to rapidly allocate each string to a bucket. In this paper, we introduce new variants of our algorithm: SR-burstsort, DR-burstsort, and DRL-burstsort. These algorithms use a random sample of the strings to construct an approximation to the trie prior to sorting. Our experimental results with sets of over 30 million strings show that the new variants reduce, by up to 37%, cache misses further than did the original burstsort, while simultaneously reducing instruction counts by up to 24%. In pathological cases, even further savings can be obtained.
Algorithms for pure Nash equilibria in weighted congestion games
Authors: Panagopoulou Panagiota N. , Spirakis Paul G.
Published: April 2010

In large-scale or evolving networks, such as the Internet, there is no authority possible to enforce a centralized traffic management. In such situations, game theory, and especially the concepts of Nash equilibria and congestion games [Rosenthal 1973] are a suitable framework for analyzing the equilibrium effects of selfish routes selection to network delays. We focus here onsingle-commoditynetworks where selfish users select paths to route their loads (represented by arbitrary integerweights). We assume that individual link delays are equal to the total load of the link. We then focus on the algorithm suggested in Fotakis et al. [2005], i.e., a potential-based method for findingpureNash equilibria in such networks. A superficial analysis of this algorithm gives an upper bound on its time, which is polynomial inn(the number of users) and the sum of their weightsW. This bound can be exponential innwhen some weights are exponential. We provide strong experimental evidence that this algorithm actually converges to a pure Nash equilibrium inpolynomial time. More specifically, our experimental findings suggest that the running time is a polynomial function ofnand logW. In addition, we propose an initial allocation of users to paths that dramatically accelerates this algorithm, compared to an arbitrary initial allocation. A by-product of our research is the discovery of a weighted potential function when link delays areexponentialto their loads. This asserts the existence of pure Nash equilibria for these delay functions and extends the result of Fotakis et al. [2005].
Multiword atomic read/write registers on multiprocessor systems
Authors: Larsson Andreas , Gidenstam Anders , Ha Phuong H. , Papatriantafilou Marina , Tsigas Philippas
Published: April 2010

Modern multiprocessor systems offer advanced synchronization primitives, built in hardware, to support the development of efficient parallel algorithms. In this article, we develop a simple and efficient algorithm, the READERSFIELD algorithm, for atomic registers (variables) of arbitrary length. The simplicity and better complexity of the algorithm is achieved via the utilization of two such common synchronization primitives. In this article, we also experimentally evaluate the performance of our algorithm, together with lock-based approaches and a practical, previously previously known algorithm that is based that is based only on read and write primitives. The experimental evaluation is performed on three well-known parallel architectures. This evaluation clearly shows that both algorithms are practical and that as the size of the register increases the READERSFIELD algorithm performs better, following its analytical evaluation.
Automated reaction mapping
Authors: Crabtree John D. , Mehta Dinesh P.
Published: April 2010

Automated reaction mapping is a fundamental first step in the analysis of chemical reactions and opens the door to the development of sophisticated chemical kinetic tools. This article formulates the reaction mapping problem as an optimization problem. The problem is shown to be NP-Complete for general graphs. Five algorithms based on canonical graph naming and enumerative combinatoric techniques are developed to solve the problem. Unlike previous formulations based on limited configurations or classifications, our algorithms are uniquely capable of mapping any reaction that can be represented as a set of chemical graphs optimally. This is due to the direct use of Graph Isomorphism as the basis for these algorithms as opposed to the more commonly used Maximum Common Subgraph. Experimental results on chemical and biological reaction databases demonstrate the efficiency of our algorithms.
Geometric algorithms for optimal airspace design and air traffic controller workload balancing
Authors: Basu Amitabh , Mitchell Joseph S. B. , Sabhnani Girish Kumar
Published: April 2010

The National Airspace System (NAS) is designed to accommodate a large number of flights over North America. For purposes of workload limitations for air traffic controllers, the airspace is partitioned into approximately 600 sectors; each sector is observed by one or more controllers. In order to satisfy workload limitations for controllers, it is important that sectors be designed carefully according to the traffic patterns of flights, so that no sector becomes overloaded. We formulate and study the airspace sectorization problem from an algorithmic point-of-view, modeling the problem of optimal sectorization as a geometric partition problem with constraints. The novelty of the problem is that it partitions data consisting of trajectories of moving points, rather than static point set partitioning that is commonly studied. First, we formulate and solve the 1D version of the problem, showing how to partition a line into “sectors” (intervals) according to historical trajectory data. Then, we apply the 1D solution framework to design a 2D sectorization heuristic based on binary space partitions. We also devise partitions based on balanced “pie partitions” of a convex polygon.

We evaluate our 2D algorithms experimentally, applying our algorithms to actual historical flight track data for the NAS. We compare the workload balance of our methods to that of the existing set of sectors for the NAS and find that our resectorization yields competitive and improved workload balancing. In particular, our methods yield an improvement by a factor between 2 and 3 over the current sectorization in terms of the time-average and the worst-case workloads of the maximum workload sector. An even better improvement is seen in the standard deviations (over all sectors) of both time-average and worst-case workloads.
GPU-Quicksort
Authors: Cederman Daniel , Tsigas Philippas
Published: April 2010

In this article, we describe GPU-Quicksort, an efficient Quicksort algorithm suitable for highly parallel multicore graphics processors. Quicksort has previously been considered an inefficient sorting solution for graphics processors, but we show that in CUDA, NVIDIA's programing platform for general-purpose computations on graphical processors, GPU-Quicksort performs better than the fastest-known sorting implementations for graphics processors, such as radix and bitonic sort. Quicksort can thus be seen as a viable alternative for sorting large quantities of data on graphics processors.
A software component quality framework
Authors: Alvaro Alexandre , Santana de Almeida Eduardo , Romero de Lemos Meira Silvio
Published: April 2010

One of the major problems with Component-Based Software Engineering (CBSE) is the quality of the components used in a system. The reliability of a component-based software system depends on the reliability of the components that is made of. In CBSE, the proper search, selection and evaluation process of components is considered the cornerstone for the development of any effective component-based system. So far the software industry was concentrated on the functional aspects of components, leaving aside the difficult task of assessing their quality. In this way, we propose a software component quality framework to evaluate the quality of software components in an efficient way. Moreover, an experimental study was accomplished in order to evaluate the viability of the proposed framework.
System/network design-space exploration based on TLM for networked embedded systems
Authors: Bombieri Nicola , Fummi Franco , Quaglia Davide
Published: April 2010

This article presents a methodology for the design of Networked Embedded Systems (NESs), which extends Transaction Level Modeling (TLM) to perform system/network design-space exploration. As a result, a new design dimension is added to the traditional TLM refinement process to represent network configuration alternatives. Each network configuration can be used to drive both architecture exploration and system validation after each refinement step. A system/network simulation taxonomy is investigated aiming at precisely identifying the role of cosimulation in system/network design-space exploration. Furthermore, a general criterion to map functionalities to system and network models is presented. As a case study, the proposed methodology is applied to the design of a Voice-over-IP client.
Link layer driver architecture for unified radio power management in wireless sensor networks
Authors: Klues Kevin , Xing Guoliang , Lu Chenyang
Published: April 2010

Wireless Sensor Networks (WSNs) represent a new generation of networked embedded systems that must achieve long lifetimes on scarce amounts of energy. Since radio communication accounts for the primary source of power drain in these networks, a large number of different radio power management protocols have been proposed. However, the lack of operating system support for flexibly integrating them with a diverse set of applications and network platforms has made them difficult to use. This article focuses on providing link layer support toward realizing a unified power management architecture (UPMA) for WSNs. In contrast to existing monolithic approaches, we provide (i) a set of standard interfaces that separate link layer power management protocols from common MAC level functionality, (ii) an architectural framework that allows applications to easily swap out different power-management protocols depending on its needs, and (iii) a mechanism for coordinating multiple applications with different power management requirements. We have implemented our approach on both the Mica2 and Telosb radio drivers in TinyOS-2.0, the second generation of the de facto standard operating system for WSNs. Microbenchmark results show that our approach can coordinate the power-management requirements of multiple applications in a platform independent fashion while incurring negligible overhead.
Brief encounters
Authors: Kostakos Vassilis , O'Neill Eamonn , Penn Alan , Roussos George , Papadongonas Dikaios
Published: April 2010

Moving human-computer interaction off the desktop and into our cities requires new approaches to understanding people and technologies in the built environment. We approach the city as a system, with human, physical and digital components and behaviours. In creating effective and usable urban pervasive computing systems, we need to take into account the patterns of movement and encounter amongst people, locations, and mobile and fixed devices in the city. Advances in mobile and wireless communications have enabled us to detect and record the presence and movement of devices through cities. This article makes a number of methodological and empirical contributions. We present a toolkit of algorithms and visualization techniques that we have developed to model and make sense of spatial and temporal patterns of mobility, presence, and encounter. Applying this toolkit, we provide an analysis of urban Bluetooth data based on a longitudinal dataset containing millions of records associated with more than 70000 unique devices in the city of Bath, UK. Through a novel application of established complex network analysis techniques, we demonstrate a significant finding on the relationship between temporal factors and network structure. Finally, we suggest how our understanding and exploitation of these data may begin to inform the design and use of urban pervasive systems.
Reasoning about online algorithms with weighted automata
Authors: Aminof Benjamin , Kupferman Orna , Lampert Robby
Published: April 2010

We describe an automata-theoretic approach for the competitive analysis of
online algorithms
. Our approach is based on
weighted automata
, which assign to each input word a cost in R
≥0
. By relating the “unbounded look ahead” of optimal offline algorithms with nondeterminism, and relating the “no look ahead” of online algorithms with determinism, we are able to solve problems about the competitive ratio of online algorithms, and the memory they require, by reducing them to questions about
determinization
and
approximated determinization
of weighted automata.
Dynamic pricing for impatient bidders
Authors: Bansal Nikhil , Chen Ning , Cherniavsky Neva , Rurda Atri , Schieber Baruch , Sviridenko Maxim
Published: April 2010

We study the following problem related to pricing over time. Assume there is a collection of bidders, each of whom is interested in buying a copy of an item of which there is an unlimited supply. Every bidder is associated with a time interval over which the bidder will consider buying a copy of the item, and a maximum value the bidder is willing to pay for the item. On every time unit, the seller sets a price for the item. The seller's goal is to set the prices so as to maximize revenue from the sale of copies of items over the time period.

In the first model considered, we assume that all bidders are
impatient
, that is, bidders buy the item at the first time unit within their bid interval that they can afford the price. To the best of our knowledge, this is the first work that considers this model. In the offline setting, we assume that the seller knows the bids of all the bidders in advance. In the online setting we assume that at each time unit the seller only knows the values of the bids that have arrived before or at that time unit. We give a polynomial time offline algorithm and prove upper and lower bounds on the competitiveness of deterministic and randomized online algorithms, compared with the optimal offline solution. The gap between the upper and lower bounds is quadratic.

We also consider the
envy-free
model in which bidders are sold the item at the minimum price during their bid interval, as long as it is not over their limit value. We prove tight bounds on the competitiveness of deterministic online algorithms for this model, and upper and lower bounds on the competitiveness of randomized algorithms with quadratic gap. The lower bounds for the randomized case in both models use a novel general technique.
Mechanism design for fractional scheduling on unrelated machines
Authors: Christodoulou George , Koutsoupias Elias , Kovács Annamária
Published: April 2010

Scheduling on unrelated machines is one of the most general and classical variants of the task scheduling problem. Fractional scheduling is the LP-relaxation of the problem, which is polynomially solvable in the nonstrategic setting, and is a useful tool to design deterministic and randomized approximation algorithms.

The mechanism design version of the scheduling problem was introduced by Nisan and Ronen. In this article, we consider the mechanism design version of the fractional variant of this problem. We give lower bounds for any fractional truthful mechanism. Our lower bounds also hold for any (randomized) mechanism for the integral case. In the positive direction, we propose a truthful mechanism that achieves approximation 3/2 for 2 machines, matching the lower bound. This is the first new tight bound on the approximation ratio of this problem, after the tight bound of 2, for 2 machines, obtained by Nisan and Ronen. For
n
machines, our mechanism achieves an approximation ratio of
n
+1/2.

Motivated by the fact that all the known deterministic and randomized mechanisms for the problem assign each task independently from the others, we focus on an interesting subclass of allocation algorithms, the
task-independent
algorithms. We give a lower bound of
n
+1/2, that holds for every (not only monotone) allocation algorithm that takes independent decisions. Under this consideration, our truthful independent mechanism is the best that we can hope from this family of algorithms.
Labeling schemes for vertex connectivity
Authors: Korman Amos
Published: April 2010

This article studies labeling schemes for the vertex connectivity function on general graphs. We consider the problem of assigning short labels to the nodes of any
n
-node graph is such a way that given the labels of any two nodes
u
and
v
, one can decide whether
u
and
v
are
k
-vertex connected in
G
, that is, whether there exist
k
vertex disjoint paths connecting
u
and
v
. This article establishes an upper bound of
k
2
log
n
on the number of bits used in a label. The best previous upper bound for the label size of such a labeling scheme is 2

k

log
n
.
Formal definitions and complexity results for trust relations and trust domains fit for TTPs, the web of trust, PKIs, and ID-based cryptography
Authors: Kramer Simon , Goré Rajeev , Okamoto Eiji
Published: April 2010

We propose computational, declarative definitions of the concepts of weak and strong trust relations between interacting agents, and trust domains of trust-related agents in distributed systems. Our definitions yield computational complexity results for deciding potential and actual trust relationships and membership in trust domains. We instantiate our trust concepts in four major applications of trust, namely: Trusted Third Parties (TTPs), the Web of Trust, Public-Key Infrastructures (PKIs), and Identity-Based Cryptography. Finally, we point out computational means for building trust, and by that, building up trust relations and trust domains. Our defining principle for weak and strong trust is (common) belief in and knowledge of agent correctness, respectively
Central administration of interleukin-4 exacerbates hypothalamic inflammation and weight gain during high-fat feeding
Authors: Oh-I Shinsuke , Thaler Joshua P. , Ogimoto Kayoko , Wisse Brent E. , Morton Gregory J. , Schwartz Michael W.
Published: April 2010

In peripheral tissues, the link between obesity and insulin resistance involves low-grade inflammation induced by macrophage activation and proinflammatory cytokine signaling. Since proinflammatory cytokines are also induced in the hypothalamus of animals placed on a high-fat (HF) diet and can inhibit neuronal signal transduction pathways required for normal energy homeostasis, hypothalamic inflammation is hypothesized to contribute to the pathogenesis of diet-induced obesity (DIO). We addressed this hypothesis by perturbing the inflammatory milieu of the hypothalamus in adult male Wistar rats using intracerebroventricular (icv) administration of interleukin-4 (IL-4), a Th2 cytokine that promotes alternative activation (M2) of macrophages and microglia. During HF feeding, icv IL-4 administration increased hypothalamic proinflammatory cytokine gene expression and caused excess weight gain. Intracerebroventricular pretreatment with PS1145, an inhibitor of IKKβ (a key intracellular mediator of inflammatory signaling), blocked both IL-4 effects, suggesting a causal relationship between IL-4-induced weight gain and hypothalamic inflammation. These observations add to growing evidence linking hypothalamic inflammation to obesity pathogenesis.
Hyperinsulinemic euglycemic step clamping with tracer glucose infusion and labeled glucose infusate for assessment of acute insulin resistance in pigs
Authors: Gjessing Petter Fosse , Fuskevåg Ole-Martin , Hagve Martin , Revhaug Arthur , Irtun Øivind
Published: April 2010

The present study aimed to establish hyperinsulinemic euglycemic step clamping with tracer glucose infusion and labeled glucose infusate (step hot-GINF HEC) for assessment of acute insulin resistance in anesthetized pigs and to arrange for combination with invasive investigative methods. Tracer enrichment was measured during d-[6,6-2H2]glucose infusion before and after surgical instrumentation ( n = 8). Insulin dose-response characteristics were determined by two step hot-GINF HEC procedures, with accordingly labeled glucose infusates performed at a total of six insulin infusion rates ranging from 0.2 to 2.0 mU·kg−1·min−1 ( n = 8). Finally, three-step hot-GINF HEC (0.4, 1.2, and 2.0 mU·kg−1·min−1) was performed subsequent to major surgical trauma ( n = 8). Tracer enrichment, basal glucose kinetics, and circulating levels of C-peptide, cortisol, glucagon, and catecholamines were not influenced by surgical instrumentation. Mean intraindividual coefficient of variance levels for glucose infusion rates and repeatedly measured insulin, glucose, and tracer enrichment indicated stable clamping conditions. Basal and maximal insulin-stimulated glucose utilization was twice as high as in humans at ∼5.5 and 21 mg·kg−1·min−1. Surgical trauma elicited pronounced peripheral and moderate hepatic insulin unresponsiveness (45% lower whole body glucose disposal and 19% less suppressed endogenous glucose release) and apparently diminished metabolic insulin clearance. Step hot-GINF HEC seems suitable for assessment of acute insulin resistance in anesthetized pigs, and combination with invasive investigative methods requiring surgical instrumentation can be accomplished without the premises for utilization of the technique being altered, but attention must be paid to alterations in metabolic insulin clearance.