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At least 775 records · Page 43

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions

Characterization of the mature protein complement in cells is crucial for a better understanding of cellular processes on a systems-wide scale. Bottom-up proteomic approaches often lead to loss of critical information about an endogenous protein’s actual state due to post translational modifications (PTMs) and other processes. Top-down approaches that involve analysis of the intact protein can address this concern but present significant analytical challenges related to the separation quality needed, measurement sensitivity, and speed that result in low throughput and limited coverage. Here we used single-dimension ultra high pressure liquid chromatography mass spectrometry to investigate the comprehensive ‘intact’ proteome of the Gram negative bacterial pathogen Salmonella Typhimurium. Top-down proteomics analysis revealed 563 unique proteins including 1665 proteoforms generated by PTMs, representing the largest microbial top-down dataset reported to date. Our analysis not only confirmed several previously recognized aspects of Salmonella biology and bacterial PTMs in general, but also revealed several novel biological insights. Of particular interest was differential utilization of the protein S-thiolation forms S-glutathionylation and S-cysteinylation in response to infection-like conditions versus basal conditions, which was corroborated by changes in corresponding biosynthetic pathways. This differential utilization highlights underlying metabolic mechanisms that modulate changes in cellular signaling, and represents to our knowledge the first report of S-cysteinylation in Gram negative bacteria. The demonstrated utility of our simple proteome-wide intact protein level measurement strategy for gaining biological insight should promote broader adoption and applications of top-down proteomics approaches.

Environmental Molecular Sciences Laboratory↗

Deployable Wind-Hybrid Power Systems for Defense and Disaster Response Applications

This report presents an analysis of the performance of deployable energy systems comprised of wind energy systems integrated with diesel generators, photovoltaic systems, and battery storage to meet the load requirements of a representative U.S. Army forward operating base. The analysis is conducted using HOMER, a microgrid analysis software that can search through a wide range of parameters to design and optimize microgrid power systems. The search parameters include the system architecture, the wind and solar resources, and the availability of diesel fuel. The results of the analysis measure the relative performance of the different systems and environments in terms of the overall transportation cost to deploy the system and the ability to provide resilience in terms of meeting mission critical loads.

02 PETROLEUM↗

Assessing the Uncertainty in QUANTEC's Dose–Response Relation of Lung and Spinal Cord With a Bootstrap Analysis

Purpose: To apply a statistical bootstrap analysis to assess the uncertainty in the dose–response relation for the endpoints pneumonitis and myelopathy reported in the QUANTEC review. Methods and Materials: The bootstrap method assesses the uncertainty of the estimated population-based dose-response relation due to sample variability, which reflects the uncertainty due to limited numbers of patients in the studies. A large number of bootstrap replicates of the original incidence data were produced by random sampling with replacement. The analysis requires only the dose, the number of patients, and the number of occurrences of the studied endpoint, for each study. Two dose–response models, a Poisson-based model and the Lyman model, were fitted to each bootstrap replicate using maximum likelihood. Results: The bootstrap analysis generates a family of curves representing the range of plausible dose–response relations, and the 95% bootstrap confidence intervals give an estimated upper and lower toxicity risk. The curve families for the 2 dose–response models overlap for doses included in the studies at hand but diverge beyond that, with the Lyman model suggesting a steeper slope. The resulting distributions of the model parameters indicate correlation and non-Gaussian distribution. For both data sets, the likelihood of the observed data was higher for the Lyman model in >90% of the bootstrap replicates. Conclusions: The bootstrap method provides a statistical analysis of the uncertainty in the estimated dose–response relation for myelopathy and pneumonitis. It suggests likely values of model parameter values, their confidence intervals, and how they interrelate for each model. Finally, it can be used to evaluate to what extent data supports one model over another. For both data sets considered here, the Lyman model was preferred over the Poisson-based model.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

QM Investigation of Rare Earth Ion Interactions with First Hydration Shell Waters and Protein-Based Coordination Models

Here, conventional methods for extracting rare earth metals (REMs) from mined mineral ores are inefficient, expensive, and environmentally damaging. Recent discovery of lanmodulin (LanM), a protein that coordinates REMs with high-affinity and selectivity over competing ions, provides inspiration for new REM refinement methods. Here, we used quantum mechanical (QM) methods to investigate trivalent lanthanide cation (Ln 3+ ) interactions with coordination systems representing bulk solvent water and protein binding sites. Energy decomposition analysis (EDA) showed differences in the energetic components of Ln 3+ interaction with representatives of solvent (water, H 2 O) and protein binding sites (acetate, CH 3 COO – ), highlighting the importance of accurate description of electrostatics and polarization in computational modeling of REM interactions with biological and bioinspired molecules. Relative binding free energies were obtained for Ln 3+ with coordination complexes originating from binding sites in PDB structures of a lanthanum binding peptide (PDB entry 7CCO) and LanM, with explicit consideration of the first hydration shell waters, according to quasi-chemical theory (QCT). Beyond the first shell, the bulk solvent environment was represented with an implicit continuum model. Ln 3+ interactions with (H 2 O) 9 and both binding site models became more favorable, moving down the periodic series. This trend was more pronounced with the protein binding site models than with water, resulting in affinity increasing with periodic number, except for the last REM, Lu 3+ , which bound less favorably than the preceding element, Yb 3+ . Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. Conversely, the previously reported experimental data for LanM show a preference for the earlier lanthanides; this is likely due to longer-range interactions and cooperative effects, which are not represented by the reduced models. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. In contrast to the previously reported experimental data for LanM, the peptide preferentially binds the earlier lanthanides. This difference likely arises due to longer-range interactions and cooperative effects not represented by the peptide. Further investigation of Ln 3+ interactions with whole proteins using polarizable molecular mechanics models with explicit solvent is warranted to understand the influence of longer-ranged interactions, cooperativity, and bulk solvent. Nevertheless, the present work provides new insights into Ln 3+ interactions with biomolecules and presents an effective computational platform for designing specific single-site REM binding peptides more efficiently.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Community-wide Validation of Geospace Model Ground Magnetic Field Perturbation Predictions to Support Model Transition to Operations

In this paper we continue the community-wide rigorous modern space weather model validation efforts carried out within GEM, CEDAR and SHINE programs. In this particular effort, in coordination among the Community Coordinated Modeling Center (CCMC), NOAA Space Weather Prediction Center (SWPC), modelers, and science community, we focus on studying the models' capability to reproduce observed ground magnetic field fluctuations, which are closely related to geomagnetically induced current phenomenon. One of the primary motivations of the work is to support NOAA SWPC in their selection of the next numerical model that will be transitioned into operations. Six geomagnetic events and 12 geomagnetic observatories were selected for validation.While modeled and observed magnetic field time series are available for all 12 stations, the primary metrics analysis is based on six stations that were selected to represent the high-latitude and mid-latitude locations. Events-based analysis and the corresponding contingency tables were built for each event and each station. The elements in the contingency table were then used to calculate Probability of Detection (POD), Probability of False Detection (POFD) and Heidke Skill Score (HSS) for rigorous quantification of the models' performance. In this paper the summary results of the metrics analyses are reported in terms of POD, POFD and HSS. More detailed analyses can be carried out using the event by event contingency tables provided as an online appendix. An online interface built at CCMC and described in the supporting information is also available for more detailed time series analyses.

MAGNETIC↗

Investigation of porous polymer gas chromatographic packings for atmospheric analysis of extraterrestrial bodies

Measurement of the permanent gases in the atmospheres of mission targets is a major objective. A 16 meter long Porapak N column was used on the Venus probe and required a rather high carrier gas flow rate. The researchers have, therefore, surveyed commercial porous polymer types which had some ability to resolve nitrogen, oxygen, argon and carbon monoxide gases. Porapaks N and Q appeared superior to most. Batch to batch variation, however, was quite wide, so the researchers learned how to synthesize porous polymer and investigated some of the factors affecting the separations. A polymer was synthesized which was superior to all commercial products and allowed at least a 50% reduction in length and flow rate of carrier gas. Similar studies were made concerning the separation of hydrocarbons and new porous polymers have been synthesized which represent significant improvements in time of analysis, column, and carrier gas flow rate.

Pollock, G. E.↗

An analysis of the wear behavior of SiC whisker reinforced alumina from 25 to 1200 C

A model is described for predicting the wear behavior of whisker reinforced ceramics. The model was successfully applied to a silicon carbide whisker reinforced alumina ceramic composite subjected to sliding contact. The model compares the friction forces on the whiskers due to sliding, which act to pull or push them out of the matrix, to the clamping or compressive forces on the whiskers due to the matrix, which act to hold the whiskers in the composite. At low temperatures, the whiskers are held strongly in the matrix and are fractured into pieces during the wear process along with the matrix. At elevated temperatures differential thermal expansion between the whiskers and matrix can cause loosening of the whiskers and lead to pullout during the wear process and to higher wear. The model, which represents the combination of elastic stress analysis and a friction heating analysis, predicts a transition temperature at which the strength of the whiskers equals the clamping force holding them in the matrix. Above the transition the whiskers are pulled out of the matrix during sliding, and below the transition the whiskers are simply fractured. The existence of the transition gives rise to a dual wear mode or mechanism behavior for this material which was observed in laboratory experiments. The results from this model correlate well with experimentally observed behavior indicating that the model may be useful in obtaining a better understanding of material behavior and in making material improvements.

Dellacorte, Christopher↗

Geothermal Prospector: Supporting Geothermal Analysis Through Spatial Data Visualization and Querying Tools

Determining opportunities for geothermal energy can involve a significant investment in data collection and analysis. Analysts within a variety of industry and research domains collect and use these data; however, determining the existence and availability of data needed for a specific analysis activity can be challenging and represents one of the initial barriers to geothermal development [2]. This paper describes the motivating factors involved in designing and building the Geothermal Prospector application, how it can be used to reduce risks and costs related to geothermal exploration, and where it fits within the larger collection of tools that is the National Geothermal Data System (NGDS) [5].

15 GEOTHERMAL ENERGY↗

An analysis of the wear behavior of SiC whisker-reinforced alumina from 25 to 1200 C

A model is described for predicting the wear behavior of whisker reinforced ceramics. The model was successfully applied to a silicon carbide whisker reinforced alumina ceramic composite subjected to sliding contact. The model compares the friction forces on the whiskers due to sliding, which act to pull or push them out of the matrix, to the clamping or compressive forces on the whiskers due to the matrix, which act to hold the whiskers in the composite. At low temperatures, the whiskers are held strongly in the matrix and are fractured into pieces during the wear process along with the matrix. At elevated temperatures differential thermal expansion between the whiskers and matrix can cause loosening of the whiskers and lead to pullout during the wear process and to higher wear. The model, which represents the combination of elastic stress analysis and a friction heating analysis, predicts a transition temperature at which the strength of the whiskers equals the clamping force holding them in the matrix. Above the transition the whiskers are pulled out of the matrix during sliding, and below the transition the whiskers are simply fractured. The existence of the transition gives rise to a dual wear mode or mechanism behavior for this material which was observed in laboratory experiments. The results from this model correlate well with experimentally observed behavior indicating that the model may be useful in obtaining a better understanding of material behavior and in making material improvements.

Dellacorte, Christopher↗

SAS4A/SASSYS-1 Lead Verification Test Suite

SAS4A/SASSYS-1 is a simulation tool used to perform deterministic analyses of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal-cooled nuclear reactors. With its origin as SAS1A in the late 1960s, the SAS series of codes has been under continuous use and development for over forty-five years and represents a critical investment in safety analysis capabilities for the U.S. Department of Energy. Although SAS4A/SASSYS-1 was developed to support the analysis of any liquid-metal-cooled nuclear reactor, it has primarily been utilized to design and analyze Sodium Fast Reactors (SFRs). As a result, most of the verification basis for SAS4A/SASSYS-1 utilizes sodium as a coolant and geometry descriptions that are typical of a SFR facility. In this work, new verification problems are defined to extend the applicability of the SAS4A/SASSYS-1 verification basis into Lead Fast Reactor (LFR) design space. A review of the existing SAS4A/SASSYS-1 SFR verification test suite is performed to determine the number of test cases that are SFR specific. SFR specific test cases are replicated using lead as a coolant and system layouts that are representative of LFRs. This report provides definitions and reference solutions for seven new test cases that scope lead-specific features and capabilities of the software. For a verification test to be considered acceptable, comparisons of analytical solutions to SAS4A/SASSYS-1 predictions must produce negligible or justifiable errors. All LFR specific test cases are found to be acceptable.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The development of Gibbs's dyadic and implications for the gradient of a vector field

In this paper, we review the history of the dyadic as developed by Gibbs. This mathematical construct appeared in the second part of Gibbs's pamphlet on vector analysis (published in 1884), and it represented the first known development of a Cartesian theory of tensors. Gibbs made extensive use of the dyadic to express his theory of linear vector functions, that is, functions that acted on vectors and mapped them to new vectors. The dyadic proved to be a capable vehicle in Gibbs's hands, and his theory for dyadics (which we would now call second-order Cartesian tensors) was relatively advanced. The theory detailed notions such as the decomposition of vectors and conditions under which a tensor would have an inverse. While Gibbs's theory for linear operators expressed by dyadics was robust, it did not seem to garner the attention that the more conventional vector analysis (published in the first half of his pamphlet in 1881) did. Perhaps in part because of the general unfamiliarity with the dyadic, two distinct and conflicting definitions of the gradient of a vector field have arisen in the literature. The details of these differences in notation, possible reasons for the difference, and a potential resolution are proposed.

97 MATHEMATICS AND COMPUTING↗

Rapid Process to Generate Beam Envelopes for Optical System Analysis

The task of evaluating obstructions in the optical throughput of an optical system requires the use of two disciplines, and hence, two models: optical models for the details of optical propagation, and mechanical models for determining the actual structure that exists in the optical system. Previous analysis methods for creating beam envelopes (or cones of light) for use in this obstruction analysis were found to be cumbersome to calculate and take significant time and resources to complete. A new process was developed that takes less time to complete beam envelope analysis, is more accurate and less dependent upon manual node tracking to create the beam envelopes, and eases the burden on the mechanical CAD (computer-aided design) designers to form the beam solids. This algorithm allows rapid generation of beam envelopes for optical system obstruction analysis. Ray trace information is taken from optical design software and used to generate CAD objects that represent the boundary of the beam envelopes for detailed analysis in mechanical CAD software. Matlab is used to call ray trace data from the optical model for all fields and entrance pupil points of interest. These are chosen to be the edge of each space, so that these rays produce the bounding volume for the beam. The x and y global coordinate data is collected on the surface planes of interest, typically an image of the field and entrance pupil internal of the optical system. This x and y coordinate data is then evaluated using a convex hull algorithm, which removes any internal points, which are unnecessary to produce the bounding volume of interest. At this point, tolerances can be applied to expand the size of either the field or aperture, depending on the allocations. Once this minimum set of coordinates on the pupil and field is obtained, a new set of rays is generated between the field plane and aperture plane (or vice-versa). These rays are then evaluated at planes between the aperture and field, at a desired number of steps perceived necessary to build up the bounding volume or cone shape. At each plane, the ray coordinates are again evaluated using the convex hull algorithm to reduce the data to a minimal set. When all of the coordinates of interest are obtained for every plane of the propagation, the data is formatted into an xyz file suitable for FRED optical analysis software to import and create a STEP file of the data. This results in a spiral-like structure that is easily imported by mechanical CAD users who can then use an automated algorithm to wrap a skin around it and create a solid that represents the beam.

Howard, Joseph↗

Structural Analysis of Components of the Students for the Exploration and Development of Space Satellite (SEDSAT) for the Small Expendable Deployer System (SEDS) Project Office

During the time frame allocated by the delivery order, members of the UAH Applied Research Program, with the cooperation of representatives from NASA investigated and conducted stress analysis of the SEDSAT1 satellite. The main area of concern was with the design of the deployable 10 m antennas. The placement of the holes for the antenna door hinge pin was too close to the edge of the antenna canister. Because of the load placed on the hinge pin, the stress analysis of this area suggested that more space would be needed between the holes and the edge of the material. Due to other conflicts, SEDSATI was removed from flying on the space shuttle and moved to the Delta Launch Vehicle. This changed many of the design requirements for the mounting and deployment of the satellite that forced a new design for the satellite. Once this happened, the stress analysis became obsolete, and the task was concluded.

Maddux, Gary A.↗

The Solsticial Pause on Mars: A Planetary Wave Reanalysis - Part 1

Large-scale planetary waves are diagnosed from an analysis of profiles retrieved from the Thermal Emission Spectrometer aboard the Mars Global Surveyor spacecraft during its scientific mapping phase. The analysis is conducted by assimilating thermal profiles and total dust opacity retrievals into a Mars global circulation model. Transient waves are largest throughout the northern hemisphere autumn, winter and spring period and almost absent during the summer. The southern hemisphere exhibits generally weaker transient wave behavior. A striking feature of the low-altitude transient waves in the analysis is that they show a broad subsidiary minimum in amplitude centred on the winter solstice, a period when the thermal contrast between the summer hemisphere and the winter pole is strongest and baroclinic wave activity might be expected to be strong. This behavior, here called the 'solsticial pause,' is present in every year of the analysis. This strong pause is under-represented in many independent model experiments, which tend to produce relatively uniform baroclinic wave activity throughout the winter. This paper documents and diagnoses the transient wave solsticial pause found in the analysis; a companion paper investigates the origin of the phenomenon in a series of model experiments.

Lewis, Stephen R.↗

Advanced feature extraction in remote sensing using artificial intelligence and geographic information systems

Traditional computer-assisted image-analysis techniques in remote sensing lag well behind human abilities in terms of both speed and accuracy. A fundamental limitation of computer-assisted techniques is their inability to assimilate a variety of different data types leading to an interpretation in a manner similar to human image interpretation. Expert systems and computer-vision techniques are proposed as a potential solution to these limitations. Some aspects of human expertise in image analysis may be codified into expert systems. Image understanding and symbolic reasoning provide a means of assimilating spatial information and spatial reasoning into the analysis procedure. Knowledge-based image-analysis systems incorporate many of these concepts and have been implemented for some well defined problem domains. Geographic information systems represent an excellent environment for this type of analysis, providing both analytic tools and contextual information to the analysis procedure.

Estes, John E.↗

Identifying Human Factors Issues in Aircraft Maintenance Operations

Maintenance operations incidents submitted to the Aviation Safety Reporting System (ASRS) between 1986-1992 were systematically analyzed in order to identify issues relevant to human factors and crew coordination. This exploratory analysis involved 95 ASRS reports which represented a wide range of maintenance incidents. The reports were coded and analyzed according to the type of error (e.g, wrong part, procedural error, non-procedural error), contributing factors (e.g., individual, within-team, cross-team, procedure, tools), result of the error (e.g., aircraft damage or not) as well as the operational impact (e.g., aircraft flown to destination, air return, delay at gate). The main findings indicate that procedural errors were most common (48.4%) and that individual and team actions contributed to the errors in more than 50% of the cases. As for operational results, most errors were either corrected after landing at the destination (51.6%) or required the flight crew to stop enroute (29.5%). Interactions among these variables are also discussed. This analysis is a first step toward developing a taxonomy of crew coordination problems in maintenance. By understanding what variables are important and how they are interrelated, we may develop intervention strategies that are better tailored to the human factor issues involved.

Veinott, Elizabeth S.↗

Coupled-cluster Green's function: Analysis of properties originating in the exponential parametrization of the ground-state wave function

In this paper we derive basic properties of the Green’s function matrix elements stemming from the exponential coupled cluster (CC) parametrization of the ground-state wave function. We demon- strate that all intermediates used to express retarded (or equivalently, ionized) part of the Green’s function in the ω-representation can be expressed through connected diagrams only. Similar proper- ties are also shared by the first order ω-derivatives of the retarded part of the CC Green’s function. This property can be extended to any order ω-derivatives of the Green’s function. Through the Dyson equation of CC Green’s function, the derivatives of corresponding CC self-energy can be evaluated analytically. In analogy to the CC Green’s function, the corresponding CC self-energy is expressed in terms of connected diagrams only. Moreover, the ionized part of the CC Green’s func- tion satisfies the non-homogeneous linear system of ordinary differential equations, whose solution may be represented in the exponential form. Our analysis can be easily generalized to the advanced part of the CC Green’s function.

74 ATOMIC AND MOLECULAR PHYSICS↗

Slycat Enables Synchronized 3D Comparison of Surface Mesh Ensembles [Brief]

In support of analyst requests for Mobile Guardian Transport studies, researchers at Sandia National Laboratories have expanded data types for the Slycat ensemble-analysis and visualization tool to include 3D surface meshes. This new capability represents a significant advance in our ability to perform detailed comparative analysis of simulation results. Analyzing mesh data rather than images provides greater flexibility for post-processing exploratory analysis.

36 MATERIALS SCIENCE↗