PNNL Information Technology Benchmarking

Benchmarking is a methodology for searching out industry best practices that lead to superior performance. It is exchanging information, not just with any organization, but with organizations known to be the best within PNNL, in industry, or in dissimilar industries with equivalent functions. It is used as a continuous improvement tool for business and technical processes, products, and services. Information technology--comprising all computer and electronic communication products and services--underpins the development and/or delivery of many PNNL products and services. This document describes the Pacific Northwest National Laboratory's (PNNL's) approach to information technology (IT) benchmarking. The purpose is to engage other organizations in the collaborative process of benchmarking in order to improve the value of IT services provided to customers. TM document's intended audience consists of other US Department of Energy (DOE) national laboratories and their IT staff. Although the individual participants must define the scope of collaborative benchmarking, an outline of IT service areas for possible benchmarking is described

Airborne multiwavelength High Spectral Resolution Lidar (HSRL-2) observations during TCAP 2012 : Vertical profiles of optical and microphysical properties of a smoke/urban haze plume over the northeastern coast of the US

© Author(s) 2014. This work is distributed under the Creative Commons Attribution 3.0 License.We present measurements acquired by the world's first airborne 3 backscatter (β) + 2 extinction (α) High Spectral Resolution Lidar (HSRL-2). HSRL-2 measures particle backscatter coefficients at 355, 532, and 1064 nm, and particle extinction coefficients at 355 and 532 nm. The instrument has been developed by the NASA Langley Research Center. The instrument was operated during Phase 1 of the Department of Energy (DOE) Two-Column Aerosol Project (TCAP) in July 2012. We observed pollution outflow from the northeastern coast of the US out over the western Atlantic Ocean. Lidar ratios were 50-60 sr at 355 nm and 60-70 sr at 532 nm. Extinction-related Ångström exponents were on average 1.2-1.7, indicating comparably small particles. Our novel automated, unsupervised data inversion algorithm retrieved particle effective radii of approximately 0.2 μm, which is in agreement with the large Ångström exponents. We find good agreement with particle size parameters obtained from coincident in situ measurements carried out with the DOE Gulfstream-1 aircraft.Peer reviewedFinal Published versio

A New N-terminal Recognition Domain in Caveolin-1 Interacts with Sterol Carrier Protein-2 (SCP-2)

Although plasma membrane domains, such as caveolae, provide an organizing principle for signaling pathways and cholesterol homeostasis in the cell, relatively little is known regarding specific mechanisms, whereby intracellular lipid-binding proteins are targeted to caveolae. Therefore, the interaction between caveolin-1 and sterol carrier protein-2 (SCP-2), a protein that binds and transfers both cholesterol and signaling lipids (e.g., phosphatidylinositides and sphingolipids), was examined by yeast two-hybrid, in vitro binding and fluorescence resonance energy transfer (FRET) analyses. Results of the in vivo and in vitro assays identified for the first time the N-terminal amino acids (aa) 1−32 amphipathic α helix of SCP-2 functionally interacted with caveolin-1. This interaction was independent of the classic caveolin-1 scaffolding domain, in which many signaling proteins interact. Instead, SCP-2 bound caveolin-1 through a new domain identified in the N-terminal domain of caveolin-1 between aa 34−40. Modeling studies suggested that electrostatic interactions between the SCP-2 N-terminal aa 1−32 amphipathic α-helical domain (cationic, positively charged face) and the caveolin-1 N-terminal aa 33−59 α helix (anionic, negatively charged face) may significantly contribute to this interaction. These findings provide new insights on how SCP-2 enhances cholesterol retention within the cell as well as regulates the distribution of signaling lipids, such as phosphoinositides and sphingolipids, at plasma membrane caveolae

Genetic Introgression and the Survival of Florida Panther Kittens

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0–1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data

HSRL-2 aerosol optical measurements and microphysical retrievals vs. airborne in situ measurements during DISCOVER-AQ 2013: : an intercomparison study

This is an Open Access article distributed under the Creative Commons Attribution 3.0 License, https://creativecommons.org/licenses/by/3.0/. © Author(s) 2017. Published by Copernicus Publications on behalf of the European Geosciences Union.We present a detailed evaluation of remotely-sensed aerosol microphysical properties obtained from an advanced, multi-wavelength High Spectral Resolution Lidar (HSRL-2) during the 2013 NASA DISCOVER-AQ field campaign. Vertically resolved retrievals of fine mode aerosol number, surface area, and volume concentration as well as aerosol effective radius are compared to 108 co-located, airborne in situ measurement profiles in the wintertime San Joaquin Valley, California, and in summertime Houston, Texas. An algorithm for relating the dry in situ aerosol properties to those obtained by the HSRL at ambient relative humidity is discussed. We show that the HSRL-2 retrievals of ambient fine mode aerosol surface area and volume concentrations agree with the in situ measurements to within 25% and 10%, respectively, once hygroscopic growth adjustments have been applied to the dry in situ data. Despite this excellent agreement for the microphysical properties, extinction and backscatter coefficients at ambient relative humidity derived from the in situ aerosol measurements using Mie theory are consistently smaller than those measured by the HSRL, with average differences of 31% 5% and 53% 11% for California and Texas, respectively. This low bias in the in situ estimates is attributed to the presence of coarse mode aerosol that are detected by HSRL-2 but that are too large to be well sampled by the in situ instrumentation. Since the retrieval of aerosol volume is most relevant to current regulatory efforts targeting fine particle mass (PM2:5), these findings highlight the advantages of an advanced 3+2 HSRL for constraining the vertical distribution of the aerosol volume or mass loading relevant for air quality.Peer reviewedFinal Published versio

An Integrated Approach for Characterizing Aerosol Climate Impacts and Environmental Interactions

Aerosols exert myriad influences on the earth's environment and climate, and on human health. The complexity of aerosol-related processes requires that information gathered to improve our understanding of climate change must originate from multiple sources, and that effective strategies for data integration need to be established. While a vast array of observed and modeled data are becoming available, the aerosol research community currently lacks the necessary tools and infrastructure to reap maximum scientific benefit from these data. Spatial and temporal sampling differences among a diverse set of sensors, nonuniform data qualities, aerosol mesoscale variabilities, and difficulties in separating cloud effects are some of the challenges that need to be addressed. Maximizing the long-term benefit from these data also requires maintaining consistently well-understood accuracies as measurement approaches evolve and improve. Achieving a comprehensive understanding of how aerosol physical, chemical, and radiative processes impact the earth system can be achieved only through a multidisciplinary, inter-agency, and international initiative capable of dealing with these issues. A systematic approach, capitalizing on modern measurement and modeling techniques, geospatial statistics methodologies, and high-performance information technologies, can provide the necessary machinery to support this objective. We outline a framework for integrating and interpreting observations and models, and establishing an accurate, consistent, and cohesive long-term record, following a strategy whereby information and tools of progressively greater sophistication are incorporated as problems of increasing complexity are tackled. This concept is named the Progressive Aerosol Retrieval and Assimilation Global Observing Network (PARAGON). To encompass the breadth of the effort required, we present a set of recommendations dealing with data interoperability; measurement and model integration; multisensor synergy; data summarization and mining; model evaluation; calibration and validation; augmentation of surface and in situ measurements; advances in passive and active remote sensing; and design of satellite missions. Without an initiative of this nature, the scientific and policy communities will continue to struggle with understanding the quantitative impact of complex aerosol processes on regional and global climate change and air quality

Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus

Background. Bracoviruses (BVs), a group of double-stranded DNA viruses with segmented genomes, are mutualistic endosymbionts of parasitoid wasps. Virus particles are replication deficient and are produced only by female wasps from proviral sequences integrated into the wasp genome. Virus particles are injected along with eggs into caterpillar hosts, where viral gene expression facilitates parasitoid survival and therefore perpetuation of proviral DNA. Here we describe a 223 kbp region of Glyptapanteles indiensis genomic DNA which contains a part of the G. indiensis bracovirus (GiBV) proviral genome. Results. Eighteen of ∼24 GiBV viral segment sequences are encoded by 7 non-overlapping sets of BAC clones, revealing that some proviral segment sequences are separated by long stretches of intervening DNA. Two overlapping BACs, which contain a locus of 8 tandemly arrayed proviral segments flanked on either side by ∼35 kbp of non-packaged DNA, were sequenced and annotated. Structural and compositional analyses of this cluster revealed it exhibits a G+C and nucleotide composition distinct from the flanking DNA. By analyzing sequence polymorphisms in the 8 GiBV viral segment sequences, we found evidence for widespread selection acting on both protein-coding and non-coding DNA. Comparative analysis of viral and proviral segment sequences revealed a sequence motif involved in the excision of proviral genome segments which is highly conserved in two other bracoviruses. Conclusion. Contrary to current concepts of bracovirus proviral genome organization our results demonstrate that some but not all GiBV proviral segment sequences exist in a tandem array. Unexpectedly, non-coding DNA in the 8 proviral genome segments which typically occupies ∼70% of BV viral genomes is under selection pressure suggesting it serves some function(s). We hypothesize that selection acting on GiBV proviral sequences maintains the genetic island-like nature of the cluster of proviral genome segments described herein. In contrast to large differences in the predicted gene composition of BV genomes, sequences that appear to mediate processes of viral segment formation, such as proviral segment excision and circularization, appear to be highly conserved, supporting the hypothesis of a single origin for BVs. © 2007 Desjardins et al; licensee BioMed Central Ltd

Thermal and Hydraulic Design of the Consolidated Edison Thorium Reactor

ABS>The thermal and hydraulic analyses, both steady state and transient for the CETR are presented. Methods of calculations are discussed and results of analyses are presented. Steady-state analyses are included for pressure drops, flow distribution, orificing, burnout, fuel and burnout cannot occur at any attainable reactor power in the CETR as designed. Bulk boiling of the coolant does not occur at any point in the core during normal steadystate operation. Bulk boiling is permitted during transients because very few fuel channels are involved and the resulting effects on over-all reactor performance are small. Local boiling of the coolant may occur in the reactor during normal steady-state operation and has no appreciable effect on reactor operation except a slight increase in friction pressure drop. The heat-transfer characteristics of the core are actually improved. The hydraulic transient analyses show that no risk of core damage exists for the total loss of forced coolant flow from either maximum or minimum initial flow conditions. (auth

THERMAL AND HYDRAULIC DESIGN OF THE CONSOLIDATED EDISON THORIUM REACTOR

ABS>The thermal and hydraulic analyses, both steady state and transient for the CETR are presented. Methods of calculations are discussed and results of analyses are presented. Steady-state analyses are included for pressure drops, flow distribution, orificing, burnout, fuel and burnout cannot occur at any attainable reactor power in the CETR as designed. Bulk boiling of the coolant does not occur at any point in the core during normal steadystate operation. Bulk boiling is permitted during transients because very few fuel channels are involved and the resulting effects on over-all reactor performance are small. Local boiling of the coolant may occur in the reactor during normal steady-state operation and has no appreciable effect on reactor operation except a slight increase in friction pressure drop. The heat-transfer characteristics of the core are actually improved. The hydraulic transient analyses show that no risk of core damage exists for the total loss of forced coolant flow from either maximum or minimum initial flow conditions. (auth

Aerosol optical and microphysical retrievals from a hybrid multiwavelength lidar data set - DISCOVER-AQ 2011

© Author(s) 2014. This open access work is distributed under the Creative Commons Attribution 3.0 License (https://creativecommons.org/licenses/by/3.0/).Retrievals of aerosol microphysical properties (effective radius, volume and surface-area concentrations) and aerosol optical properties (complex index of refraction and single-scattering albedo) were obtained from a hybrid multiwavelength lidar data set for the first time. In July 2011, in the Baltimore-Washington DC region, synergistic profiling of optical and microphysical properties of aerosols with both airborne (in situ and remote sensing) and ground-based remote sensing systems was performed during the first deployment of DISCOVER-AQ. The hybrid multiwavelength lidar data set combines ground-based elastic backscatter lidar measurements at 355 nm with airborne High-Spectral-Resolution Lidar (HSRL) measurements at 532 nm and elastic backscatter lidar measurements at 1064 nm that were obtained less than 5 km apart from each other. This was the first study in which optical and microphysical retrievals from lidar were obtained during the day and directly compared to AERONET and in situ measurements for 11 cases. Good agreement was observed between lidar and AERONET retrievals. Larger discrepancies were observed between lidar retrievals and in situ measurements obtained by the aircraft and aerosol hygroscopic effects are believed to be the main factor in such discrepancies.Peer reviewe