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 describe modeling and simulation of long-range terrestrial laser communications links between static and mobile platforms. Atmospheric turbulence modeling, along with pointing, tracking and acquisition models are combined to provide an overall capability to estimate communications link performance.

The China Spallation Neutron Source (CSNS) is an accelerator-based high-power project currently in preparation under the direction of the Chinese Academy of Sciences (CAS). The complex is based on an H- linear accelerator, a rapid cycling proton synchrotron accelerating the beam to 1.6 GeV, a solid tungsten target station, and five initial instruments for spallation neutron applications. The facility will operate at 25 Hz repetition rate with a phase-I beam power of about 120 kW. The major challenge is to build a robust and reliable user's facility with upgrade potential at a fractional of ''world standard'' cost.

The AdS/CFT correspondence between conformal field theory and string states in an extended space-time has provided new insights into not only hadron spectra, but also their light-front wavefunctions. We show that there is an exact correspondence between the fifth-dimensional coordinate of anti-de Sitter space z and a specific impact variable {zeta} which measures the separation of the constituents within the hadron in ordinary space-time. This connection allows one to predict the form of the light-front wavefunctions of mesons and baryons, the fundamental entities which encode hadron properties and scattering amplitudes. A new relativistic Schroedinger light-front equation is found which reproduces the results obtained using the fifth-dimensional theory. Since they are complete and orthonormal, the AdS/CFT model wavefunctions can be used as an initial ansatz for a variational treatment or as a basis for the diagonalization of the light-front QCD Hamiltonian. A number of applications of light-front wavefunctions are also discussed.

A sample of PUREX sludge from Tank 4 was characterized, and subsequently combined with a Tank 51 sample (Tank 51-E1) received following Al dissolution, but prior to a supernate decant by the Tank Farm, to perform a settling and washing study to support Sludge Batch 6 preparation. The sludge source for the majority of the Tank 51-E1 sample is Tank 12 HM sludge. The Tank 51-E1 sample was decanted by SRNL prior to use in the settling and washing study. The Tank 4 sample was analyzed for chemical composition including noble metals. The characterization of the Tank 51-E1 sample, used here in combination with the Tank 4 sample, was reported previously. SRNL analyses on Tank 4 were requested by Liquid Waste Engineering (LWE) via Technical Task Request (TTR) HLE-TTR-2009-103. The sample preparation work is governed by Task Technical and Quality Assurance Plan (TTQAP), and analyses were controlled by an Analytical Study Plan and modifications received via customer communications. Additional scope included a request for a settling study of decanted Tank 51-E1 and a blend of decanted Tank 51-E1 and Tank 4, as well as a washing study to look into the fate of undissolved sulfur observed during the Tank 4 …

Electrochemical noise (EN) probes were deployed in two continuous kraft digesters at a variety of locations representative of corrosion throughout the vessels. Current and potential noise, the temperature at each probe location, and the value of up to 60 process parameters (flow rates, liquor chemistry, etc.) were monitored continuously during each experiment. The results indicate that changes in furnish composition and process upsets were invariably associated with concurrent substantial changes in EN activity throughout the vessels. Post-test evaluation of the mild steel electrode materials in both vessels confirmed general corrosion of a magnitude consistent with historical trends in the respective vessels as well as values qualitatively (and semi-quantitatively) related to EN current sums for each electrode pair. Stainless steel electrodes representing 309LSi and 312 overlay repairs exhibited zero wastage corrosion--as did the actual overlays--but the EN data indicated periodic redox activity on the stainless steel that varied with time and position within the vessel. Little or no correlation between EN probe activity and other operational variables was observed in either vessel. Additional details for each digester experiment are summarized.

The objective of this calculation is to estimate the quantity of fissile material that could accumulate in fractures in the rock beneath plutonium-ceramic (Pu-ceramic) and Mixed-Oxide (MOX) waste packages (WPs) as they degrade in the potential monitored geologic repository at Yucca Mountain. This calculation is to feed another calculation (Ref. 31) computing the probability of criticality in the systems described in Section 6 and then ultimately to a more general report on the impact of plutonium on the performance of the proposed repository (Ref. 32), both developed concurrently to this work. This calculation is done in accordance with the development plan TDP-DDC-MD-000001 (Ref. 9), item 5. The original document described in item 5 has been split into two documents: this calculation and Ref. 4. The scope of the calculation is limited to only very low flow rates because they lead to the most conservative cases for Pu accumulation and more generally are consistent with the way the effluent from the WP (called source term in this calculation) was calculated (Ref. 4). Ref. 4 (''In-Drift Accumulation of Fissile Material from WPs Containing Plutonium Disposition Waste Forms'') details the evolution through time (breach time is initial time) of the chemical composition of …

There is overwhelming evidence that addiction is a disease of the brain (Leshner, 1997). Yet public perception that addiction is a reflection of moral weakness or a lack of willpower persists. The insidious consequence of this perception is that we lose sight of the fact that there are enormous medical consequences of addiction including the fact that a large fraction of the total deaths from cancer and heart disease are caused by smoking addiction. Ironically the medical school that educates physicians in addiction medicine and the cancer hospital that has a smoking cessation clinic are vanishingly rare and efforts at harm reduction are frequently met with a public indignation. Meanwhile the number of people addicted to substances is enormous and increasing particularly the addictions to cigarettes and alcohol. It is particularly tragic that addiction usually begins in adolescence and becomes a chronic relapsing problem and there are basically no completely effective treatments. Clearly we need to understand how drugs of abuse affect the brain and we need to be creative in using this information to develop effective treatments. Imaging technologies have played a major role in the conceptualization of addiction as a disease of the brain (Fowler et al., 1998a; …

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This report summarizes the objectives, technical barrier, approach, and accomplishments for the development of a novel water-gas-shift (WGS) membrane reactor for hydrogen enhancement and CO reduction. We have synthesized novel CO{sub 2}-selective membranes with high CO{sub 2} permeabilities and high CO{sub 2}/H{sub 2} and CO{sub 2}/CO selectivities by incorporating amino groups in polymer networks. We have also developed a one-dimensional non-isothermal model for the countercurrent WGS membrane reactor. The modeling results have shown that H{sub 2} enhancement (>99.6% H{sub 2} for the steam reforming of methane and >54% H{sub 2} for the autothermal reforming of gasoline with air on a dry basis) via CO{sub 2} removal and CO reduction to 10 ppm or lower are achievable for synthesis gases. With this model, we have elucidated the effects of system parameters, including CO{sub 2}/H{sub 2} selectivity, CO{sub 2} permeability, sweep/feed flow rate ratio, feed temperature, sweep temperature, feed pressure, catalyst activity, and feed CO concentration, on the membrane reactor performance. Based on the modeling study using the membrane data obtained, we showed the feasibility of achieving H{sub 2} enhancement via CO{sub 2} removal, CO reduction to {le} 10 ppm, and high H{sub 2} recovery. Using the membrane synthesized, we have obtained …

Article and CD submitted by writer Kevin Gardner discussing Portsmouth brunswikck and Groton

This paper is the result of an extensive literature review and technology evaluation, performed to determine the status of sensors and measurement technologies.

This paper is the result of an extensive literature review and technology evaluation, performed to determine the status of sensors and measurement technologies.

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set of ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket …

Maintenance of apico-basal polarity in normal breast epithelial acini requires a balance between cell proliferation, cell death, and proper cell-cell and cell-extracellular matrix signaling. Aberrations in any of these processes can disrupt tissue architecture and initiate tumor formation. Here we show that the small GTPase Rap1 is a crucial element in organizing acinar structure and inducing lumen formation. Rap1 activity in malignant HMT-3522 T4-2 cells is appreciably higher than in S1 cells, their non-malignant counterparts. Expression of dominant-negative Rap1 resulted in phenotypic reversion of T4-2 cells, led to formation of acinar structures with correct apico-basal polarity, and dramatically reduced tumor incidence despite the persistence of genomic abnormalities. The resulting acini contained prominent central lumina not observed when other reverting agents were used. Conversely, expression of dominant-active Rap1 in T4-2 cells inhibited phenotypic reversion and led to increased invasiveness and tumorigenicity. Thus, Rap1 acts as a central regulator of breast architecture, with normal levels of activation instructing apical polarity during acinar morphogenesis, and increased activation inducing tumor formation and progression to malignancy.

Analyses of two-particle correlations have provided the chief means for determining spatio-temporal characteristics of relativistic heavy ion collisions. We discuss the theoretical formalism behind these studies and the experimental methods used in carrying them out. Recent results from RHIC are put into context in a systematic review of correlation measurements performed over the past two decades. The current understanding of these results are discussed in terms of model comparisons and overall trends.

The spectrum of ideal magnetohydrodynamic (MHD) pressure-driven (ballooning) modes in strongly nonaxisymmetric toroidal systems is difficult to analyze numerically owing to the singular nature of ideal MHD caused by lack of an inherent scale length. In this paper, ideal MHD is regularized by using a k-space cutoff, making the ray tracing for the WKB ballooning formalism a chaotic Hamiltonian billiard problem. The minimum width of the toroidal Fourier spectrum needed for resolving toroidally localized ballooning modes with a global eigenvalue code is estimated from the Weyl formula. This phase-space-volume estimation method is applied to ballooning-unstable plasma equilibria in the H-1NF helical axis stellarator and the Large Helical Device (LHD).

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During the course of deactivation and decommissioning (D&D) of the K-Basins, the basins will be partially filled with grout so as to immobilize residual equipment and debris. Some of this residual debris, principally empty fuel canisters, identification tags, and long-handled tools, contain aluminum metal. The aluminum metal will corrode when contacted with the high pH grout, resulting in the generation of hydrogen. Pacific Northwest National Laboratory (PNNL) evaluated existing experimental and analytical studies of this issue to (1) determine whether sufficient hydrogen will be generated and collected during the K-Basins grouting activity to potentially create the conditions for hydrogen deflagration/explosion and (2) identify process constraints that will provide assurance that the conditions for hydrogen deflagration/explosion will not exist. Based on the review of available experimental and analytical studies, it was concluded that the likelihood of generating a flammable mixture of hydrogen from interaction of residual aluminum metal with grout is low but not zero. However, a flammable mixture of hydrogen will not be generated anywhere in the basin facility during grouting of the KE Basin as long as the following conditions are met: (1) The residual aluminum metal inventory in the basin, especially the fuel canisters, are not stacked on …

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Russian pulsating mixer pump (PMP) technology was identified in FY 1996 during technical exchanges between the U.S. Department of Energy (DOE) Tanks Focus Area Retrieval and Closure program, the DOE Environmental Management International Programs, and delegates from Russia as a technology that could be implemented in tank waste retrieval operations in the United States. The PMP is basically a jet mixer powered by a pressure/vacuum supply system. A prototype PMP was provided by the Russian Mining and Chemical Combine and evaluated as a potential retrieval tool in FY 1997 at Pacific Northwest National Laboratory (PNNL). Based on this evaluation, Oak Ridge National Laboratory (ORNL) and DOE staff determined that a modified PMP would meet project needs for bulk mobilization of sludge from one or more of the Gunite and Associated Tanks (GAAT) at ORNL. In FY 1998, PMP technology was selected for deployment in one of the GAAT to mobilize settled solids. Deployment of the PMP was expected to reduce operation and maintenance costs required to utilize more expensive retrieval systems. The following series of cold tests and inspections were conducted on one of the three PMP units provided to verify the acceptability and readiness of the mixing system for …

This project is intended to enhance the ability to use seismic data for the determination of rock and fluid properties through an improved understanding of the physics underlying the relationships between seismic attributes and formation.

Judge's decision on action challenging the legality of a recommendation made by Donald H. Rumsfeld, the Secretary of Defense, in the Department of Defense Report to the Defense Base Closure and Realignment Commission.

This report describes the selection of water compositions for the total system performance assessment (TSPA) model of results from the thermal-hydrological-chemical (THC) seepage model documented in ''Drift-Scale THC Seepage Model'' (BSC 2004 [DIRS 169856]). The selection has been conducted in accordance with ''Technical Work Plan for: Near-Field Environment and Transport: Coupled Processes (Mountain-Scale TH/THC/THM, Drift-Scale THC Seepage, and Post-Processing Analysis for THC Seepage) Report Integration'' (BSC 2004 [DIRS 171334]). This technical work plan (TWP) was prepared in accordance with AP-2.27Q, ''Planning for Science Activities''. Section 1.2.3 of the TWP describes planning information pertaining to the technical scope, content, and management of this report. The post-processing analysis for THC seepage (THC-PPA) documented in this report provides a methodology for evaluating the near-field compositions of water and gas around a typical waste emplacement drift as these relate to the chemistry of seepage, if any, into the drift. The THC-PPA inherits the conceptual basis of the THC seepage model, but is an independently developed process. The relationship between the post-processing analysis and other closely related models, together with their main functions in providing seepage chemistry information for the Total System Performance Assessment for the License Application (TSPA-LA), are illustrated in Figure 1-1. The …