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Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors, or NNs) to sequence. We use SAP to assess whether draft data is sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high quality draft with error rates of 10{sup -3}-10{sup -5} ({approx} 8x coverage) of target organisms is suitable for DNA signature prediction. Low quality draft with error rates of {approx} 1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high quality draft of target and low quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation …

We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. …

Although materials that exhibit nearest-neighbor-only antiferromagnetic interactions and geometrical frustration theoretically should not magnetically order in the absence of disorder, few such systems have been observed experimentally. One such system appears to be the pyrochlore Tb{sub 2}Ti{sub 2}O{sub 7}. However, previous structural studies indicated that Tb{sub 2}Ti{sub 2}O{sub 7} is an imperfect pyrochlore. To clarify the situation, we performed neutron powder diffraction (NPD) and x-ray absorption fine structure (XAFS) measurements on samples that were prepared identically to those that show no magnetic order. The NPD measurements show that the long-range structure of Tb{sub 2}Ti{sub 2}O{sub 7} is well ordered with no structural transitions between 4.5 and 600 K. In particular, mean-squared displacements (u{sup 2}'s) for each site follow a Debye model with no offsets. No evidence for Tb/Ti site interchange was observed within an upper limit of 2%. Likewise, no excess or deficiency in the oxygen stoichiometry was observed, within an upper limit of 2% of the nominal pyrochlore value. Tb L{sub III} and Ti K-edge XAFS measurements from 20-300 K similarly indicate a well-ordered local structure. Other aspects of the structure are considered. We conclude that Tb{sub 2}Ti{sub 2}O{sub 7} has, within experimental error, an ideal, disorder-free pyrochlore lattice, …

GaN/InGaN light emitting diodes (LEDs) are commercialized for lighting applications because of the cost efficient way that they produce light of high brightness. Nevertheless, there is significant room for improving their external emission efficiency from typical values below 10 percent to more than 50 percent, which are obtainable by use of other materials systems that, however, do not cover the visible spectrum. In particular, green-light emitting diodes fall short in this respect, which is troublesome since the human eye is most sensitive in this spectral range. In this letter advanced electron microscopy is used to characterize indium segregation in InGaN quantum wells of high-brightness, green LEDs (with external quantum efficiency as high as 15 percent at 75 A/cm2). Our investigations reveal the presence of 1-3 nm wide indium rich clusters in these devices with indium concentrations as large as 0.30-0.40 that narrow the band gap locally to energies as small as 2.65 eV.

The new class of diode-pumped alkali vapor lasers (DPALs) offers high efficiency cw laser radiation at near-infrared wavelengths: cesium 895 nm, rubidium 795 nm, and potassium 770 nm. The working physical principles of DPALs will be presented. Initial 795 nm Rb and 895 nm Cs laser experiments performed using a titanium sapphire laser as a surrogate pump source demonstrated DPAL slope power conversion efficiencies in the 50-70% range, in excellent agreement with device models utilizing only literature spectroscopic and kinetic data. Using these benchmarked models for Rb and Cs, optimized DPALs with optical-optical efficiencies >60%, and electrical efficiencies of 25-30% are projected. DPAL device architectures for near-diffraction-limited power scaling into the high kilowatt power regime from a single aperture will be described. DPAL wavelengths of operation offer ideal matches to silicon and gallium arsenide based photovoltaic power conversion cells for efficient power beaming.

We have developed a 10-plexed PCR assay coupled to a 12-plexed liquid bead array to rapidly screen environmental samples for B. anthracis, Y. pestis, F. tularensis, and B. melitensis. Highly validated species -specific primer sets were used to simultaneously amplify multiple diagnostic regions unique to each individual pathogen. Resolution of the mix of amplified products was achieved by PCR product hybridization to corresponding probe sequences, attached to unique sets of fluorescent beads. The hybridized beads were processed through a flow cytometer, which detected presence and quantity of each PCR product. The assay was optimized to allow for maximum sensitivity in a multiplexed format. A high- throughput demonstration was performed where 384 simulated environmental samples were spiked with different amounts of B. thuringensis spores and pathogen DNA. The samples were robotically processed to extract DNA and arrayed for multiplexed PCR-liquid bead detection. The assay correctly identified the presence or absence of each pathogen and collected over 3,000 individual data points within a single 8-hour shift for approximately $1.20 per sample in a 10-plexed assay.

The Lawrence Livermore National Laboratory (LLNL) Chemical & Biological National Security Program (CBNP) provides science, technology, and integrated systems for chemical and biological security. Our approach is to develop and field systems that dramatically improve the nation's capabilities to prevent, prepare for, detect, and respond to terrorist use of chemical or biological weapons.

Current grid development projects are being designed such that they require end users to be authenticated under the auspices of a ''recognized'' organization, called a Virtual Organization (VO). A VO must establish resource-usage agreements with grid resource providers. The VO is responsible for authorizing its members for grid computing privileges. The individual sites and resources typically enforce additional layers of authorization. The VOX project developed at Fermilab is an extension of VOMS, developed jointly for DataTAG by INFN and for DataGrid by CERN. The VOX project provides set of services that facilitate grid users registration with a VO, administration of VO members, as well as control access of grid users to a particular site. The current state of deployment and future steps to improve the prototype and implement some new features will be discussed.

Laboratory experiments on wave propagation through saturated and partially saturated porous media have often been conducted on porous cylinders that were initially fully saturated and then allowed to dry while continuing to acquire data on the wave behavior. Since it is known that drying typically progresses from outside to inside, a sensible physical model of this process is concentric cylinders having different saturation levels--the simplest example being a fully dry outer cylindrical shell together with a fully wet inner cylinder. We use this model to formulate the equations for wave dispersion in porous cylinders for patchy saturation (i.e. drainage) conditions. In addition to multiple modes of propagation obtained numerically from these dispersion relations, we find two distinct analytical expressions for torsional wave modes. We solve the dispersion relation for torsional waves for two examples: Massillon sandstone and Sierra White granite. The drainage analysis appears to give improved agreement with the data for both these materials.

Article on the transcriptional regulator AlgR controlling cyanide production in Pseudomonas aeruginosa.

The redshift distribution of well-defined samples of distant early-type galaxies offers a means to test the predictions of monolithic and hierarchical galaxy formation scenarios. NICMOS maps of the entire Hubble Deep Field North in the F110W and F160W filters, when combined with the available WFPC2 data, allow us to calculate photometric redshifts and determine the morphological appearance of galaxies at rest-frame optical wavelengths out to z {approx} 2.5. Here we report results for two subsamples of early-type galaxies, defined primarily by their morphologies in the F160W band, which were selected from the NICMOS data down to H{sub 160AB} < 24.0. A primary subsample is defined as the 34 galaxies with early-type galaxy morphologies and early-type galaxy spectral energy distributions. The secondary subsample is defined as those 42 objects which have early-type galaxy morphologies with non-early type galaxy spectral energy distributions. The observed redshift distributions of our two early-type samples do not match that predicted by a monolithic collapse model, which shows an overabundance at z > 1.5. A (V/V{sub max}) test confirms this result. When the effects of passive luminosity evolution are included in the calculation, the mean value of Vmax for the primary sample is 0.22 {+-} 0.05, and …

Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest …

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I'd like to welcome you to the Agent 2004 conference. As most of you are aware, this conference is the fifth in a series of meetings that began in 1999. A conference followed the next year in 2000. The 2001 conference was skipped because of some conflicts with other conferences, and the conferences have proceeded annually since then. We have the proceedings of the previous conferences available here on CDs. One CD has the proceedings from 1999, 2000, and 2002; the other contains last year's proceedings. The purpose of these conferences is to advance the state of the computational social sciences and to integrate the social sciences with the decision sciences and something that is traditionally known as the management sciences. Those of you in the operations/research area are familiar with the traditional school of modeling simulation that emerged from that scientific area. This conference will bring together a different group of people to talk about the topic of agent-based theories and simulations. This fifth agent conference is one of a group of conferences held annually around the country. Most of you are probably aware of the CASOS Conference held at Carnegie Mellon University, usually in July. UCLA holds the …

The Supernova/Acceleration Probe (SNAP) is a proposed space-based experiment designed to study the dark energy and alternative explanations of the acceleration of the Universes expansion by performing a series of complementary systematics-controlled astrophysical measurements. We here describe a self-consistent reference mission design that can accomplish this goal with the two leading measurement approaches being the Type Ia supernova Hubble diagram and a wide-area weak gravitational lensing survey. This design has been optimized to first order and is now under study for further modification and optimization. A 2-m three-mirror anastigmat wide-field telescope feeds a focal plane consisting of a 0.7 square-degree imager tiled with equal areas of optical CCDs and near infrared sensors, and a high efficiency low-resolution integral field spectrograph. The instrumentation suite provides simultaneous discovery and light-curve measurements of supernovae and then can target individual objects for detailed spectral characterization. The SNAP mission will discover thousands of Type Ia supernovae out to z = 3 and will obtain high-signal-to-noise calibrated light-curves and spectra for a subset of > 2000 supernovae at redshifts between z = 0.1 and 1.7 in a northern field and in a southern field. A wide-field survey covering one thousand square degrees in both northern and …

We report results from the first experiments to explore the evolution of the Rayleigh-Taylor (RT) instability from intentionally three-dimensional (3D) initial conditions at an embedded, decelerating interface in a high-Reynolds-number flow. The experiments used {approx}5 kJ of laser energy to produce a blast wave in polyimide and/or brominated plastic having an initial pressure of {approx}50 Mbars. This blast wave shocked and then decelerated the perturbed interface between first material and a lower-density, C foam. This caused the formation of a decelerating interface with an Atwood number {approx}2/3, producing a long-term positive growth rate for the RT instability. The initial perturbations were a 3D perturbation in an ''egg-crate'' pattern with feature spacings of 71 {micro}m in two orthogonal directions and peak-to-valley amplitudes of 5 {micro}m. The resulting RT spikes were observed to overtake the shock waves at the undisturbed, ''free-fall'' rate, and to subsequently deliver material from behind the interface to the forward shock. This result is unanticipated by prior simulations and models.

The authors present the results of narrow-band and broad-band imaging with the Very Large Telescope of the field surrounding the radio galaxy TN J0924-2201 at z = 5.2. 14 candidate Ly{alpha} emitters with an observed equivalent width of at least 124 {angstrom} were detected. Spectroscopy of 8 of these objects revealed 6 having redshifts similar to that of the radio galaxy. The density of emitters near the radio galaxy is a factor 3-4 higher than in the field, and comparable to the density of Ly{alpha} emitters in the protocluster 1338-1942 at z = 4.1. The Ly{alpha} emitters near TN J0924-2201 could therefore be part of a structure that will evolve into a 10{sup 15} M{sub {circle_dot}} cluster. These observations confirm that substantial clustering of Ly{alpha} emitters occur at z > 5 and strengthen the idea that radio galaxies in the early Universe pinpoint regions of high density.

The NASA Space Radiation Laboratory (NSRL) was constructed in collaboration with NASA for the purpose of performing radiation effect studies for the NASA space program. The results of commissioning of this new facility were reported in [l]. In this report we will describe the results of the first run. The NSRL is capable of making use of heavy ions in the range of 0.05 to 3 GeV/n slow extracted from BNL's AGS Booster. Many modes of operation were explored during the first run, demonstrating all the capabilities designed into the system. Heavy ion intensities from 100 particles per pulse up to 12 x 10{sup 9} particles per pulse were delivered to a large variety of experiments, providing a dose range up to 70 Gy/min over a 5 x 5 cm{sup 2} area. Results presented will include those related to the production of beams that are highly uniform in both the transverse and longitudinal planes of motion [2].

The ATLAS Collaboration at CERN is preparing for the data taking and analysis at the LHC that will start in 2007. Therefore, a series of Data Challenges was started in 2002 whose goals are the validation of the Computing Model, of the complete software suite, of the data model, and to ensure the correctness of the technical choices to be made. A major feature of the first Data Challenge was the preparation and the deployment of the software required for the production of large event samples as a worldwide-distributed activity. It should be noted that it was not an option to ''run everything at CERN'' even if we had wanted to; the resources were not available at CERN to carry out the production on a reasonable time-scale. The great challenge of organizing and then carrying out this large-scale production at a significant number of sites around the world had the refore to be faced. However, the benefits of this are manifold: apart from realizing the required computing resources, this exercise created worldwide momentum for ATLAS computing as a whole. This report describes in detail the main steps carried out in DC1 and what has been learned from them as a …

Using data from the FOCUS (E831) experiment at Fermilab, the authors present a new measurement for the Cabibbo-suppressed decay mode D{sup 0} {yields} K{sup +}K{sup -}{pi}{sup +}{pi}{sup -}. They measure: {Lambda}(D{sup 0} {yields} K{sup +}K{sup -}{pi}{sup +}{pi}{sup -})/{Lambda}(D{sup 0} {yields} K{sup -}{pi}{sup -}{pi}{sup +}{pi}{sup +}) = 0.0295 {+-} 0.0011 {+-} 0.0008. An amplitude analysis has been performed in order to determine the resonant substructure of this decay mode. The dominant components are the decays D{sup 0} {yields} K{sub 1}(1270){sup +} K{sup -}, D{sup 0} {yields} K{sub 1}(1400){sup +}K{sup -} and D{sup 0} {yields} {rho}(770){sup 0}{phi}(1020).

The authors present an analysis of the decay D{sup 0} {yields} K{sup +}{pi}{sup -} based on FOCUS data. From a sample of 234 signal events, they find a branching ratio of {Lambda}(D{sup 0} {yields} K{sup +}{pi}{sup -})/{Lambda}(D{sup 0} {yields} K{sup -}{pi}{sup +}) = (0.429{sub -0.061}{sup +0-.063} {+-} 0.027)% under the assumptions of no mixing and no CP violation. Allowing for CP violation, the find a branching ratio of (0.435{sub -0.061}{sup +0.063} {+-} 0.028)% and a CP asymmetry of 0.178{sub -0.141}{sup +0.144} {+-} 0.041. The branching ratio for the case of mixing with no CP violation is (0.381{sub -0.163}{sup +0.167} {+-} 0.092)%. They also present limits on charm mixing.

Plasmodium falciparum is unable to synthesize purine bases and relies upon purine salvage and purine recycling to meet its purine needs. We report that purines formed as products of the polyamine pathway are recycled in a novel pathway in which 5'-methylthioinosine is generated by adenosine deaminase. The action of P. falciparum purine nucleoside phosphorylase is a convergent step of purine salvage, converting both 5'-methylthioinosine and inosine to hypoxanthine. We used accelerator mass spectrometry to verify that 5'-methylthioinosine is an active nucleic acid precursor in P. falciparum. Prior studies have shown that inhibitors of purine salvage enzymes kill malaria, but potent malaria-specific inhibitors of these enzymes have not previously been described. 5'-methylthio-Immucillin-H, a transition state analogue inhibitor that is selective for malarial over human purine nucleoside phosphorylase, kills P. falciparum in culture. Immucillins are currently in clinical trials for other indications and may have application as antimalarials.

The authors present a measurement of the cross section for Z production times the branching fraction to {tau} leptons, {sigma} {center_dot} Br(Z {yields} {tau}{sup +}{tau}{sup -}), in p{bar p} collisions at {radical}s = 1.96 TeV in the channel in which one {tau} decays into {mu}{nu}{sub {mu}}{nu}{sub {tau}}, and the other into hadrons + {nu}{sub {tau}} or e{nu}{sub e}{nu}{sub {tau}}. The data sample corresponds to an integrated luminosity of 226 pb{sup -1} collected with the D0 detector at the Fermilab Tevatron collider. The final sample contains 2008 candidate events with an estimated background of 55%. From this they obtain {sigma} {center_dot} Br(Z {yields} {tau}{sup +}{tau}{sup -}) = 237 {+-} 15(stat) {+-} 18(sys) {+-} 15(lum) pb, in agreement with the standard model prediction.