Showing papers by "Swedish Defence Research Agency published in 2005"

The complete genome sequence of Francisella tularensis, the causative agent of tularemia.

Abstract: Francisella tularensis is one of the most infectious human pathogens known. In the past, both the former Soviet Union and the US had programs to develop weapons containing the bacterium. We report the complete genome sequence of a highly virulent isolate of F. tularensis (1,892,819 bp). The sequence uncovers previously uncharacterized genes encoding type IV pili, a surface polysaccharide and iron-acquisition systems. Several virulence-associated genes were located in a putative pathogenicity island, which was duplicated in the genome. More than 10% of the putative coding sequences contained insertion-deletion or substitution mutations and seemed to be deteriorating. The genome is rich in IS elements, including IS630 Tc-1 mariner family transposons, which are not expected in a prokaryote. We used a computational method for predicting metabolic pathways and found an unexpectedly high proportion of disrupted pathways, explaining the fastidious nutritional requirements of the bacterium. The loss of biosynthetic pathways indicates that F. tularensis is an obligate host-dependent bacterium in its natural life cycle. Our results have implications for our understanding of how highly virulent human pathogens evolve and will expedite strategies to combat them.

Recycling revisited - life cycle comparisons of global warming impact and total energy use of waste management strategies

Abstract: Recycling of waste materials has been analysed from a life cycle perspective in a number of studies over the past 10-15 years Publications comparing the global warming impact and total energy use

A Mutant of Francisella tularensis Strain SCHU S4 Lacking the Ability To Express a 58-Kilodalton Protein Is Attenuated for Virulence and Is an Effective Live Vaccine

Abstract: Francisella tularensis subsp. tularensis (type A) strain SCHU S4 is a prototypic strain of the pathogen that is highly virulent for humans and other mammals. Its intradermal (i.d.) 50% lethal dose ...

Spatial and temporal b value anomalies preceding the devastating off coast of NW sumatra earthquake of December 26, 2004

Abstract: [1] Spatial and temporal variations of b values are studied by means of 624 earthquakes in the Andaman-Nicobar Islands region during a five-year period preceding the giant shock on December 26, 2004. Sliding time and space windows containing 50 events are used. Temporal variations reveal two significant drops in b value which coincide with the occurrence of two large shocks (Ms ≥ 7.0) towards the end of 2002 and with the Mw = 9.0 event in 2004. The spatial distribution shows accumulation of stresses (low b) around the epicentres of the 2002 and 2004 events and an event in North Andaman. The area of high stress around the 2004 epicenter extends in NNW-SSE direction over an area about 450 km long.

Protozoan Acanthamoeba polyphaga as a Potential Reservoir for Campylobacter jejuni

Abstract: We showed by a laboratory experiment that four different Campylobacter jejuni strains are able to infect the protozoan Acanthamoeba polyphaga. C. jejuni cells survived for longer periods when cocultured with amoebae than when grown in culture alone. The infecting C. jejuni cells aggregated in amoebic vacuoles, in which they were seen to be actively moving. Furthermore, a resuscitation of bacterial cultures that were previously negative in culturability tests was observed after reinoculation into fresh amoeba cultures. After spontaneous rupture of the amoebae, C. jejuni could be detected by microscopy and culturability tests. Our results indicate that amoebae may serve as a nonvertebrate reservoir for C. jejuni in the environment.

Evolution of subspecies of Francisella tularensis.

Abstract: Analysis of unidirectional genomic deletion events and single nucleotide variations suggested that the four subspecies of Francisella tularensis have evolved by vertical descent. The analysis indicated an evolutionary scenario where the highly virulent F. tularensis subsp. tularensis (type A) appeared before the less virulent F. tularensis subsp. holarctica (type B). Compared to their virulent progenitors, attenuated strains of F. tularensis exhibited specific unidirectional gene losses.

Well-Posed Boundary Conditions for the Navier--Stokes Equations

Abstract: In this article we propose a general procedure that allows us to determine both the number and type of boundary conditions for time dependent partial differential equations. With those, well-posedness can be proven for a general initial-boundary value problem. The procedure is exemplified on the linearized Navier--Stokes equations in two and three space dimensions on a general domain.

Vortex-Generator Model and Its Application to Flow Control

Abstract: A new vortex-generator model is introduced, the jBAY model, which provides an efficient method for computational-fluid-dynamics (CFD) simulation of flow systems with vortex-generator arrays. The ...

Selective mass scaling for explicit finite element analyses

Abstract: Due to their inherent lack of convergence problems explicit finite element techniques are widely used for analysing non-linear mechanical processes. In many such processes the energy content in the ...

Flocking with Obstacle Avoidance: A New Distributed Coordination Algorithm Based on Voronoi Partitions

Abstract: A new distributed coordination algorithm for multi-vehicle systems is presented in this paper. The algorithm combines a particular choice of navigation function with Voronoi partitions. This results not only in obstacle avoidance and motion to the goal, but also in a desirable geographical distribution of the vehicles. Our algorithm is decentralized in that each vehicle needs only to know the position of neigh boring vehicles, but no other inter-vehicle communication or centralized control are required. The algorithm gives a natural priority to safety, goal convergence, and formation keeping, in that (1) collision avoidance is guaranteed under all circumstances, (2) the vehicles will move toward the goal as long as a given optimization problem is feasible, and (3) if prior criteria admit, the vehicles tend to a desirable lattice formation. These theoretical properties are discussed in the paper and the performance of the algorithm is illustrated in simulations with realistic models of twenty all-terrain vehicles. Planned experimental evaluation using customized miniature cars is also briefly described.

Forensic Identification of Neat Ricin and of Ricin from Crude Castor Bean Extracts by Mass Spectrometry

Abstract: The protein toxin ricin, which originates from the seeds of Ricinus communis plants, has been the subject of increased interest, due to its potential terrorist use. Exceptionally, this toxin is also subject to the Chemical Weapons Convention. In this paper, it is shown that mass spectrometry can be used to unambiguously verify the presence of ricin in crude toxin preparations. It is demonstrated that MALDI MS can be used for screening, either by direct analysis or by trypsin digestion and peptide mapping. Purified ricin from several varieties of R. communis was characterized by LC-ES MS(/MS). A crude ricin preparation from a single bean was similarly characterized. An LC method was set up with product ion MS/MS detection of selected marker peptides specific for ricin: T5, T7, T11, T12, and T13 from the A-chain and T3, T5, T14, T19, and T20 from the B-chain. This method was then used to unambiguously identify ricin in a crude preparation of ricin. The MALDI MS molecular weight analysis and the marker peptides LC-ES MS/MS analysis give a forensic level of identification of ricin when combined with activity testing.

Change detection for low-frequency SAR ground surveillance

Abstract: Change detection using ultra-wideband synthetic aperture radar (SAR) images in the low end of the VHF band is shown to provide excellent performance for detection of vehicle-sized objects in forest concealment. Two different change detection algorithms are discussed and their performance evaluated. The two algorithms are based on similar statistical hypothesis testing, but differ in that one operates on complex (coherent change detection) whereas the other uses magnitude (incoherent change detection) image data. Algorithm evaluation is performed using radar data acquired with the airborne CARABAS-II SAR in northern Sweden. The data were collected during a change detection experiment with concealed vehicles in boreal forests (stand volume ca. 100 m/sup 3//ha). Results show that coherent change detection gives slightly better performance using full spatial resolution of the images, whereas the incoherent change detection gives better performance when spatial averaging (2/spl times/2 resolution cells) is included. A comparison with detecting vehicles using only single-pass images shows an increase of false alarms of one to two orders of magnitude at the same probability of detection.

Proteomic analysis of anti-Francisella tularensis LVS antibody response in murine model of tularemia.

Abstract: Francisella tularensis live vaccine strain infection of mice has been established as an experimental model of tularemia that is suitable for studies of immune mechanisms against the intracellular pathogen. In this study, the model was used to explore immunogenic repertoire of F. tularensis with the aim of identifying new molecules able to activate the host immune system, potential bacterial markers with vaccine, and diagnostic applications. Immunoproteomic approach based on the combination of two-dimensional gel electrophoresis, immunoblotting, and mass spectrometry was applied. Globally, 36 different proteins were identified, which strongly reacted with sera from experimentally infected mice, including several putative virulence markers of intracellular pathogens as nucleoside diphosphate kinase, isocitrate dehydrogenase, RNA-binding protein Hfq, and molecular chaperone ClpB. Of them, 27 proteins are described for the first time as immunorelevant Francisella proteins. When comparing murine immunoproteome of F. tularensis with our previous data from human patients, 25 of the total of 50 identified murine sera immunoreactive spots were recognized by human sera collected from patients suffering from tularemia, as well. Immune sera from two Lps gene congenic strains of mice, C3H/HeN (Lpsn) and C3H/HeJ (Lpsd), represented murine immunoproteome in this study. The spectrum of immunoreactive spots detected by two-dimensional immunoblotting varied throughout the course of infection depending on murine strain. Nevertheless, the antibody patterns of the two strains showed significant homogeneity in being directed against almost identical subset of antigens.

LES studies of the flow in a swirl gas combustor

Abstract: Environmental and other practical concerns have led to the development of compact gas turbine combustors burning lean mixtures leading to potentially low CO and NO x emissions. The compact design requires efficient atomization and mixing together with a compact premixed flame. Associated with these requirements are higher temperatures, increased heat transfer, and thermal load, thus increasing the danger of combustion instabilities (causing performance deterioration and excessive mechanical loads), and possible off-design operation. Numerical simulations of reacting flows are well suited to address these issues. To this end, large eddy simulation (LES) is particularly promising. The philosophy behind LES is to explicitly simulate the large scales of the flow and the thermochemistry, affected by boundary conditions whilst modeling only the small scales, including the interaction between the flow and the combustion processes. Here, we examine the flow and the flame in a model gas turbine combustor (General Electric’s lean premixed dry low NO x LM6000) to evaluate the potential of LES for design studies of engineering applications and to study the effects of the combustor confinement geometry on the flow and on the flame dynamics. Two LES models, a Monotone Integrated LES model with 1 and 2 step Ahrrenius chemistry, and a fractal flame-wrinkling LES model coupled to a conventional one-equation eddy-viscosity subgrid model, are used. Reasonable agreement is found when comparing predictions with experimental data and with other LES computations of the same case. Furthermore, the combustor confinement geometry is found to strongly affect the vortical flow, and hence also the flame and its dynamics.

Compensating strategies in collaborative remembering in very old couples.

Abstract: This study investigates collaborative memory performance in very old married couples working in two types of participant constellations, and with two types of memory tasks, i.e. working as couples, or as individuals in episodic or semantic memory tasks. Sixty-two old married couples were a priori classified as high or low on two dimensions suggested to be important for successful collaboration, i.e. responsibility (how division of responsibility was organized) and agreement (how they mutually agreed on each other's view). The episodic memory task was immediate recall of short stories. The semantic memory tasks were to answer questions about names, places, and concepts. The results suggested that: (1) groups outperformed a single individual, but (2) groups in general suffered from collaboration relative to the predicted potential in episodic tasks only, thus replicating earlier results. Nevertheless, (3) the couples scoring high on division of responsibility achieved the same productivity as nominal pairs (i.e. the predicted potential); (4) the couples scoring high on the agreement dimension showed that they were not as affected by collaboration, but then performed less well in "absolute" performance. Finally, the results were discussed in terms of optimal compensation strategies, especially for elderly couples.

Secondary Bending in Multi Fastener, Composite-to-Aluminium Single Shear Lap Joints

Abstract: A novel technique to study secondary bending due to the eccentric load path in single shear, composite-to-aluminium lap joints has been developed and used in a parametric study. The method is bas ...

Variable sampling of the empirical mode decomposition of two-dimensional signals

Abstract: Previous work on empirical mode decomposition in two dimensions typically generates a residue with many extrema points. In this paper we propose an improved method to decompose an image into a number of intrinsic mode functions and a residue image with a minimum number of extrema points. We further propose a method for the variable sampling of the two-dimensional empirical mode decomposition. Since traditional frequency concept is not applicable in this work, we introduce the concept of empiquency, shortform for empirical mode frequency, to describe the signal oscillations. The very special properties of the intrinsic mode functions are used for variable sampling in order to reduce the number of parameters to represent the image. This is done blockwise using the occurrence of extrema points of the intrinsic mode function to steer the sampling rate of the block. A method of using overlapping 7 × 7 blocks is introduced to overcome blocking artifacts and to further reduce the number of parameters required to represent the image. The results presented here shows that an image can be successfully decomposed into a number of intrinsic mode functions and a residue image with a minimum number of extrema points. The results also show that subsampling offers a way to keep the total number of samples generated by empirical mode decomposition approximately equal to the number of pixels of the original image.

Multiscale convergence and reiterated homogenization of parabolic problems

Abstract: Reiterated homogenization is studied for divergence structure parabolic problems of the form ∂ uɛ/∂t−div (a(x,x/ɛ,x/ɛ2,t,t/ɛ k)∇uɛ)=f. It is shown that under standard assumptions on the function a(x, y1,y2,t,τ) the sequence {uɛ} of solutions converges weakly in L2 (0,T; H01(Ω)) to the solution u of the homogenized problem ∂u/∂t− div(b(x,t)∇u)=f.

Steady-State Computations Using Summation-by-Parts Operators

Abstract: This paper concerns energy stability on curvilinear grids and its impact on steady-state calulations. We have done computations for the Euler equations using fifth order summation-by-parts block and diagonal norm schemes. By imposing the boundary conditions weakly we obtain a fifth order energy-stable scheme. The calculations indicate the significance of energy stability in order to obtain convergence to steady state. Furthermore, the difference operators are improved such that faster convergence to steady state are obtained.

Emissions of Polychlorinated Dibenzodioxins and Dibenzofurans and Polychlorinated Biphenyls from Uncontrolled Burning of Garden and Domestic Waste (Backyard Burning)

Abstract: To assess emissions of dioxins (chlorinated dibenzodioxins and dibenzofurans) and PCB from uncontrolled domestic combustion of waste ("backyard burning"),test combustions in barrels and open fires ...

Array interpolation and DOA MSE reduction

Abstract: Interpolation or mapping of data from a given real array to data from a virtual array of more suitable geometry is well known in array signal processing. This operation allows arrays of any geometry to be used with fast direction-of-arrival (DOA) estimators designed for linear arrays. In an earlier companion paper , a first-order condition for zero DOA bias under such mapping was derived and was also used to construct a design algorithm for the mapping matrix that minimized the DOA estimate bias. This bias-minimizing theory is now extended to minimize not only bias, but also to consider finite sample effects due to noise and reduce the DOA mean-square error (MSE). An analytical first-order expression for mapped DOA MSE is derived, and a design algorithm for the transformation matrix that minimizes this MSE is proposed. Generally, DOA MSE is not reduced by minimizing the size of the mapping errors but instead by rotating these errors and the associated noise subspace into optimal directions relative to a certain gradient of the DOA estimator criterion function. The analytical MSE expression and the design algorithm are supported by simulations that show not only conspicuous MSE improvements in relevant scenarios, but also a more robust preprocessing for low signal-to-noise ratios (SNRs) as compared with the pure bias-minimizing design developed in the previous paper.

Nonuniformity correction of infrared focal plane arrays

Abstract: The non-linearity of the responsivity of infrared (IR) focal plane arrays (FPA) is a major concern when IR images are evaluated. This will affect both the detection and classification ability of the IR sensor. The nonuniformity correction (NUC) method proposed here is based on polynomial fitting to pixel responsivities. It is applied to infrared data obtained from two cooled multi-band sensors in the MWIR region. The method is shown to give both suitable data restoration and a simple and efficient computer implementation. Bad pixels were identified by evaluating the coefficents obtained from the multi degree polynomial. Bad pixels were also replaced by using a nearest neighbour-hood algorithm. The NUC method, including the bad pixel identification and replacement, was implemented in a user friendly GUI (graphic user interface) for calibration of registered IR data.