Showing papers by "Swedish Defence Research Agency published in 2007"

Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains

Abstract: Background Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with the genome sequence of Francisella tularensis subspecies novicida U112, which is nonpathogenic to humans.

Simulation of transition and turbulence decay in the Taylor–Green vortex

Abstract: Conventional large-eddy simulation (LES) and monotone integrated LES (MILES) are tested in emulating the dynamics of transition to turbulence in the Taylor–Green vortex (TGV). A variety of subgrid scale (SGS) models and high-resolution numerical methods are implemented in the framework of both incompressible and compressible fluid flow equations. Comparisons of the evolution of characteristic TGV integral measures are made with previously reported and new direct numerical simulation (DNS) data. The computations demonstrate that the convective numerical diffusion effects in the MILES methods can consistently capture the physics of flow transition and turbulence decay without resorting to an explicit SGS model, while providing accurate prediction of established theoretical findings for the kinetic energy dissipation, energy spectra, enstrophy and kinetic energy decay. All approaches tested provided fairly robust computational frameworks.

LES of supersonic combustion in a scramjet engine model

Abstract: In this study, Large Eddy Simulation (LES) has been used to examine supersonic flow and combustion in a model scramjet combustor. The LES model is based on an unstructured finite volume discretization, using total variational diminishing flux reconstruction, of the filtered continuity, momentum, enthalpy, and passive/reactive scalar equations, used to describe the combustion process. The configuration used is similar to the laboratory scrarmjet at the Institute for Chemical Propulsion of the German Aerospace Center (DLR) and consists of a one-sided divergent channel with a wedge-shaped flameholder at the base of which hydrogen is injected. Here, we investigate supersonic flow with hydrogen injection and supersonic flow with hydrogen injection and combustion. For the purpose of validation, the LES results are compared with experimental data for velocity and temperature at different cross-sections. In addition, qualitative comparisons are also made between predicted and measured shadowgraph images. The LES computations are capable of predicting both the non-reacting and reacting flowfields reasonably well-in particular we notice that the LES model identifies and differentiates between peculiarities of the flowfields found in the experiments. (c) 2006 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Hip, thigh and calf muscle atrophy and bone loss after 5-week bedrest inactivity

Abstract: Unloaded inactivity induces atrophy and functional deconditioning of skeletal muscle, especially in the lower extremities. Information is scarce, however, regarding the effect of unloaded inactivity on muscle size and function about the hip. Regional bone loss has been demonstrated in hips and knees of elderly orthopaedic patients, as quantified by computerized tomography (CT). This method remains to be validated in healthy individuals rendered inactive, including real or simulated weightlessness. In this study, ten healthy males were subjected to 5 weeks of experimental bedrest and five matched individuals served as ambulatory controls. Maximum voluntary isometric hip and knee extension force were measured using the strain gauge technique. Cross-sectional area (CSA) of hip, thigh and calf muscles, and radiological density (RD) of the proximal tibial bone were measured using CT. Bedrest decreased (P 0.05), when examined at similar time intervals. The present findings of a substantial loss in hip extensor strength and a smaller, yet significant atrophy of these muscles, demonstrate that hip muscle deconditioning accompanies losses in thigh and calf muscle mass after bedrest. This suggests that comprehensive quantitative studies on impaired locomotor function after inactivity should include all joints of the lower extremity. Our results also demonstrate that a decreased RD, indicating bone mineral loss, can be shown already after 5 weeks of unloaded bedrest, using a standard CT technique.

Evaluating Strategies for Defending Electric Power Networks Against Antagonistic Attacks

Abstract: We show how concepts from game theory can be used to find and evaluate strategies for defending an electric power system against antagonistic attacks. Consequently, the interaction between the antagonist and the defender of the system is envisaged as a game. In a numerical example, we study the performance of different defense strategies against a number of attack scenarios. Particularly, we study whether there is a dominant defense strategy and an optimal allocation of resources between protection of components and recovery

On the justification and extension of mixed models in LES

Abstract: A reformulation of the large eddy simulation (LES) equations is presented, based on an alternative decomposition of the subgrid stress tensor leading to modified Leonard, cross, and Reynolds terms, which are all individually frame indifferent. The new Leonard tensor, identical to the scale similarity model proposed by Bardina et al(J. Bardina, J. H. Ferziger and W. C. Reynolds, 1980, AIAA Paper 80-1357), is computable and thus becomes an integral part of the LES equations, so this formulation clearly emphasizes the difference between Reynolds averaged Navier–Stokes (RANS) and LES. The remaining modified cross and Reynolds terms can be regrouped further into a reconstructable part and a true subgrid component, where we here use an approximate deconvolution model and a subgrid viscosity model for the respective parts. This structure justifies the use of a dissipative model term in mixed models based on, e.g., the scale similarity model. The reformulated LES model is tested on two basic flows, the Taylor Gre...

An experimental and computational study of a multi-swirl gas turbine combustor

Abstract: The turbulent flow and flame dynamics within a lean direct fuel injection (LDI) multi-swirl gas turbine combustor is examined using a combination of state-of-the-art diagnostic methods, including laser doppler velocimetry (LDV), particle imaging velocimetry (PIV) and fine bead thermocouples, and modern computational methods, such as flamelet-based large eddy simulations (LES). The computations provide unsteady field data of any quantity of interest, but are to some extent model dependent, whereas the laboratory studies often can capture only end-results of the real processes with limited details. The combined perspectives can thus provide mutual validation of diagnostics and models, and a more complete understanding of the physical and chemical processes involved, including also interdependencies between processes that are very difficult to characterize in the laboratory. In turn, this provides an improved framework for modification of present gas turbine combustors and for the design of future generations. Good agreement between LES and experimental data is found both for the non-reacting and reacting regimes studied. Both cases were found to be sensitive to the inflow into the swirler, and to the confinement. The non-reacting case is dominated by an annular swirling jet, a central recirculation zone (CRZ) and a weak precessing vortex core, oscillating at ∼250 Hz. For the reacting case the CRZ remains, and dominates the flow in the upstream section of the combustor including the flame and the resulting wall jets. Longitudinal pressure fluctuations at ∼380 Hz (420 Hz in the experiments) are also observed in the reacting case.

A Framework for Vulnerability Assessment of Electric Power Systems

Abstract: The infrastructure of a society consists of facilities such as communications, power supplies, transportation, water supplies, and the stock of buildings. In a broad definition of infrastructure, it is also possible to include basic societal functions like education, national defense, and financial and judicial systems. Here, the notion critical infrastructure will refer to the collection of large technical systems, for example electric power grids, which form the basis for most activities in a modern society, and are of great importance for the economic prosperity. Today, critical infrastructure protection is also considered to be a matter of national security.1

Mid-infrared ZGP OPO pumped by near-degenerate narrowband type-I PPKTP parametric oscillator.

Abstract: The total pulse energy of the signal and idler in a near-degenerate type-I periodically poled KTiOPO4 (PPKTP) optical parametrical oscillator (OPO) was spectrally confined within a 2 nm spectral bandwidth at 2.13 μm. This was achieved by using a volume Bragg grating as the output coupler. Both the signal and the idler from the PPKTP OPO were then simultaneously used to pump a mid-infrared ZnGeP2 (ZGP) OPO. The 2 nm bandwidth was narrower than the ZGP crystal acceptance bandwidth and, thus, made efficient conversion in the second OPO possible. A total slope efficiency of 10% from 1.06 μm to the 3.5–5 μm region was demonstrated, generating 250 μJ in the mid-IR with only 3.6 mJ of 1.06 μm pump energy. This corresponds to a Nd:YAG pump to mid-IR conversion efficiency of 7%.

Experimental Investigation and Mathematical Modeling of Design Parameters for Efficient Stirrers in Mode-Stirred Reverberation Chambers

Abstract: In this paper, we have investigated the design parameters for efficient stirring in reverberation chambers. We have measured the efficiency of the stirrer in terms of the lowest possible frequency for which it gives a certain number of uncorrelated samples. Rotating stirrers, when rotated about their axes, generate cylindrical volumes. The impact of a change of the stirrer diameter is approximately cubic compared with the change of the stirrer height. The efficiency of stirrers that are translated is proportional to the stepping increment and to the square root of the area of projection of the stirrer on a plane orthogonal to the direction of translation

Genome Sequencing Shows that European Isolates of Francisella tularensis Subspecies tularensis Are Almost Identical to US Laboratory Strain Schu S4

Abstract: Background Francisella tularensis causes tularaemia, a life-threatening zoonosis, and has potential as a biowarfare agent. F. tularensis subsp. tularensis, which causes the most severe form of tularaemia, is usually confined to North America. However, a handful of isolates from this subspecies was obtained in the 1980s from ticks and mites from Slovakia and Austria. Our aim was to uncover the origins of these enigmatic European isolates. Methodology/Principal Findings We determined the complete genome sequence of FSC198, a European isolate of F. tularensis subsp. tularensis, by whole-genome shotgun sequencing and compared it to that of the North American laboratory strain Schu S4. Apparent differences between the two genomes were resolved by re-sequencing discrepant loci in both strains. We found that the genome of FSC198 is almost identical to that of Schu S4, with only eight SNPs and three VNTR differences between the two sequences. Sequencing of these loci in two other European isolates of F. tularensis subsp. tularensis confirmed that all three European isolates are also closely related to, but distinct from Schu S4. Conclusions/Significance The data presented here suggest that the Schu S4 laboratory strain is the most likely source of the European isolates of F. tularensis subsp. tularensis and indicate that anthropogenic activities, such as movement of strains or animal vectors, account for the presence of these isolates in Europe. Given the highly pathogenic nature of this subspecies, the possibility that it has become established wild in the heartland of Europe carries significant public health implications.

Solvent-Assisted Trypsin Digestion of Ricin for Forensic Identification by LC-ESI MS/MS

Abstract: The castor bean plant (Ricinus communis) is used in large quantities for oil production and is also a common ornamental garden plant. However, the beans contain 1-3% of the highly toxic protein ricin, a type II ribosome-inactivating protein that is covered by the Chemical Weapons Convention, and there have been a number of reports concerning the use, or alleged use, of the toxin in terrorist and criminal activities. In the study reported here, we investigated the potential utility of organic solvent-assisted trypsin digestion of crude extracts containing the closely related toxins ricin or abrin to prepare samples for peptide analysis by liquid chromatography combined with electrospray ionization quadrupole time-of-flight tandem mass spectrometry. Diagnostic tryptic fragments of the toxins were detected and unambiguously identified by this procedure. The sample preparation protocol substantially reduces the sample preparation time, from overnight to an hour, and thus greatly reduces the total time required for analyses, to less than 2 h. Furthermore, the reported procedure leaves the disulfide bonds in the protein intact. This is highly relevant in the context of the Chemical Weapons Convention, since the disulfide bond connecting the two chains of ricin indicates the presence of an intact toxin and provides additional forensic evidence for the analytical results.

Linear feedback control and estimation applied to instabilities in spatially developing boundary layers

Abstract: This paper presents the application of feedback control to spatially developing boundary layers. It is the natural follow-up of Hogberg & Henningson (J. Fluid Mech. vol. 470, 2002, p. 151), whe ...

Canonical Insertion-Deletion Markers for Rapid DNA Typing of Francisella tularensis

Abstract: To develop effective and accurate typing of strains of Francisella tularensis, a potent human pathogen and a putative bioterrorist agent, we combined analysis of insertion-deletion (indel) markers with multiple-locus variable-number tandem repeat analysis (MLVA). From 5 representative F. tularensis genome sequences, 38 indel markers with canonical properties, i.e., capable of sorting strains into major genetic groups, were selected. To avoid markers with a propensity for homoplasy, we used only those indels with 2 allelic variants and devoid of substantial sequence repeats. MLVA included sequences with much diversity in copy number of tandem repeats. The combined procedure allowed subspecies division, delineation of clades A.I and A.II of subspecies tularensis, differentiation of Japanese strains from other strains of subspecies holarctica, and high-resolution strain typing. The procedure uses limited amounts of killed bacterial preparations and, because only 1 single analytic method is needed, is time- and cost-effective.

Proteomics analysis of the Francisella tularensis LVS response to iron restriction: induction of the F. tularensis pathogenicity island proteins IglABC.

Abstract: Francisella tularensis is a highly virulent, facultative intracellular pathogen that causes tularemia in humans and animals. Although it is one of the most infectious bacterial pathogens, little is known about its virulence mechanisms. In this study, the response of F. tularensis live vaccine strain to iron depletion, which simulates the environment within the host, was investigated. In order to detect alterations in protein synthesis, metabolic labeling, followed by 2D-PAGE analysis was used. Globally, 141 protein spots were detected whose levels were significantly altered in the iron-restricted medium. About 65% of the spots were successfully identified using mass spectrometric approaches. Importantly, among the proteins produced at an increased level during iron-limited growth, three proteins were found encoded by the igl operon, located in the F. tularensis pathogenicity island I (FPI). Of these, the IglC and IglA proteins were previously reported to be necessary for full virulence of F. tularensis. These results, obtained at the proteome level, support and confirm recently published data showing that the igl operon genes are transcribed in response to iron limitation.

Involvement of NADPH oxidase and iNOS in rodent pulmonary cytokine responses to urban air and mineral particles.

Abstract: Involvement of NADPH oxidase and iNOS in rodent pulmonary cytokine responses to urban air and mineral particles.

Creating a European SCADA Security Testbed

Abstract: Supervisory control and data acquisition (SCADA) systems are commonly used to monitor and control critical infrastructure assets. However, over the past two decades, they have evolved from closed, proprietary systems to open networks comprising commodity platforms running common operating systems and TCP/IP stacks. The open architecture and increased connectivity provide more functionality and reduce costs, but they significantly increase the vulnerabilities and the exposure to threats. Since SCADA systems and the critical infrastructureassets they control must have 24-7 availability, it is imperative to understand and manage the risk. This paper makes the case for a European SCADA security testbed that can be used to analyze vulnerabilities threats and the impact of attacks, ultimately helping design new architectures and robust security solutions. The paper also discusses testbed requirements, deployment strategies and potential hurdles.

On Flux-Limiting-Based Implicit Large Eddy Simulation

Abstract: Recent progress in understanding the theoretical basis and effectiveness of implicit large eddy simulation (ILES) is reviewed in both incompressible and compressible flow regimes. We use a modified equation analysis to show that the leading-order truncation error terms introduced by certain hybrid high resolution methods provide implicit subgrid scale (SGS) models similar in form to those of conventional mixed SGS models. Major properties of the implicit SGS model are related to the choice of high-order and low-order scheme components, the choice of a flux limiter, which determines how these schemes are blended locally depending on the flow, and the designed balance of the dissipation and dispersion contributions to the numerical solution. Comparative tests of ILES and classical LES in the Taylor-Green vortex case show robustness in capturing established theoretical findings for transition and turbulence decay.

Bile salt-stimulated lipase and pancreatic lipase-related protein 2 are the dominating lipases in neonatal fat digestion in mice and rats.

Abstract: During infancy, the basic conditions for digestion of dietary fat differ from later in life. The bile salt–stimulated lipase (BSSL) is an enzyme expressed in the exocrine pancreas and in some species (including human) also in the lactating mammary gland and secreted with the milk. The aim of this study was to compare the ontogeny of four pancreatic lipases [BSSL, pancreatic triglyceride lipase (PL), pancreatic lipase-related protein 2 (PLRP2), and phospholipase A2 (PLA2)] in one species that supplies BSSL with milk (the mouse) and one that does not (the rat). We followed expression of the four pancreatic lipases from postnatal d 1 until after weaning in both species. We found that BSSL and PLRP2, two lipases with broad substrate specificity, dominated. It was not until weaning that significant expression of PL and PLA2 were induced. Thus, BSSL and PLRP2 seem to be responsible for fat digestion as long as milk is the main food. Moreover, the early temporal pattern of BSSL expression differed between species. We speculate that the milk-borne BSSL is able to compensate for a slower ontogeny of pancreatic BSSL expression in the mouse.

Wide-Angle Shift-Map PE for a Piecewise Linear Terrain—A Finite-Difference Approach

Abstract: A wide-angle parabolic wave equation solution is presented using shift-map and finite-difference techniques. The corresponding split-step Fourier solution is well known. The solution using finite-difference technique, where the standard parabolic wave equation is modified into the so-called Claerbout equation allowing propagation angles up to 45deg from the paraxial direction, is also well known. Here, we present an extension to that solution in which the shift-map technique is incorporated into the finite-difference scheme allowing a varying terrain to be considered. The result is a solution that corresponds to the well known split-step solution, which is believed to perform well for terrain slopes up to 10deg-15deg and discontinuous slope changes on the order of 15deg-20deg. This solution is a first-order one with respect to the terrain slope. However, when using the finite-difference technique, it is also possible to find a second-order solution with respect to the terrain slope. This new solution performs well for slopes up to about 15deg and discontinuous slope changes up to about 30deg, which is an improvement.

Type II secretion and type IV pili of Francisella.

Abstract: Francisella tularensis genomes encode homologues of type IV pili. Though several F. tularensis genes required for Tfp expression are homologous to genes required for type II secretion (T2S), these gene clusters mainly bear structural signatures that are typical of Tfp. There is preliminary evidence that different F. tularensis subspecies express Tfp-like surface structures, but there are also some interesting differences between the subspecies. One difference between the nonpathogenic subspecies novicida (F. novicida) and the highly pathogenic type A strains is in sequence of one of the predicted pilin genes, pilA. In contrast, type B strains show several differences compared to type A strains, two predicted pilin genes and the pilT gene are pseudogenes, while pilA is identical to pilA that is encoded by the type A strains. This is likely significant as PilA contributes to virulence of type B strains while PilT is essential for Tfp retraction in other bacterial pathogens. Tfp-mediated protein secretion is only evident in in vitro grown F. novicida. Surprisingly, secretion of several F. novicida proteins was dependent on pilA and other genes with postulated roles in Tfp expression. F. novicida secretion mutants were more virulent in the mouse infection model. Thus, in F. novicida, Tfp gene clusters serve both T2S and Tfp assembly and it is tempting to speculate that evolution of the pathogenic subspecies involved loss of functional T2S via structural changes of PilA and additional genes, including those that encode some of the Tfp-secreted proteins.

Cross-eye jamming of monopulse radar

Abstract: Radar seeking missiles present a serious threat towards ships and aircraft. In cross-eye jamming a missile seeker is deflected by signals from two onboard antennas transmitting out of phase with signals of nearly equal strength. The limits on cross-eye performance imposed by scattering have been studied when scattering takes place far from the propagation path. It will be shown that a digital cross-eye system with several antenna units can be seriously affected by scattering from sea waves and terrain.

Genomic deletion marking an emerging subclone of Francisella tularensis subsp. holarctica in France and the Iberian Peninsula.

Abstract: Francisella tularensis subsp. holarctica is widely disseminated in North America and the boreal and temperate regions of the Eurasian continent. Comparative genomic analyses identified a 1.59-kb genomic deletion specific to F. tularensis subsp. holarctica isolates from Spain and France. Phylogenetic analysis of strains carrying this deletion by multiple-locus variable-number tandem repeat analysis showed that the strains comprise a highly related set of genotypes, implying that these strains were recently introduced or recently emerged by clonal expansion in France and the Iberian Peninsula.