Human biospecimens are subjected to collection, processing, and storage that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research that uses human tissues, it is crucial that information on the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications on biospecimen-related research and to help reassure patient contributors and the advocacy community that their contributions are valued and respected.

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

Tracking features and exploring their temporal dynamics can aid scientists in identifying interesting time intervals in a simulation and serve as basis for performing quantitative analyses of temporal phenomena. In this paper, we develop a novel approach for tracking subsets of isosurfaces, such as burning regions in simulated flames, which are defined as areas of high fuel consumption on a temperature isosurface. Tracking such regions as they merge and split over time can provide important insights into the impact of turbulence on the combustion process. However, the convoluted nature of the temperature isosurface and its rapid movement make this analysis particularly challenging. Our approach tracks burning regions by extracting a temperature isovolume from the four-dimensional space-time temperature field. It then obtains isosurfaces for the original simulation time steps and labels individual connected 'burning' regions based on the local fuel consumption value. Based on this information, a boundary surface between burning and non-burning regions is constructed. The Reeb graph of this boundary surface is the tracking graph for burning regions.

Training update with Environmental a health focus. Training conducted as part of the United Negro College Fund Special Programs Corporation/National Library of Medicine - HBCU ACCESS Project at the University of the District of Columbia, Washington, DC on November 2, 2010.

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Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development. Drosophila melanogaster is an important non-mammalian model system that has had a critical role in basic biological discoveries, such as identifying chromosomes as the carriers of genetic information and uncovering the role of genes in development. Because it shares a substantial genic content with humans, Drosophila is increasingly used as a translational model for human development, homeostasis and disease. High-quality maps are needed for all functional genomic elements. Previous studies demonstrated that a …

In this paper, we propose a novel mesh coarsening method called brick coarsening method. The proposed method can be used in conjunction with any graph partitioners and scales to very large meshes. This method reduces problem space by decomposing the original mesh into fixed-size blocks of nodes called bricks, layered in a similar way to conventional brick laying, and then assigning each node of the original mesh to appropriate brick. Our experiments indicate that the proposed method scales to very large meshes while allowing simple RCB partitioner to produce higher-quality partitions with significantly less edge cuts. Our results further indicate that the proposed brick-coarsening method allows more complicated partitioners like PT-Scotch to scale to very large problem size while still maintaining good partitioning performance with relatively good edge-cut metric. Graph partitioning is an important problem that has many scientific and engineering applications in such areas as VLSI design, scientific computing, and resource management. Given a graph G = (V,E), where V is the set of vertices and E is the set of edges, (k-way) graph partitioning problem is to partition the vertices of the graph (V) into k disjoint groups such that each group contains roughly equal number of vertices …

An experts' workshop was convened in Dublin Ireland September 27th – 28th 2010 in support of IEA Ocean Energy Systems Implementing Agreement Annex IV. PNNL was responsible for organizing the content of the workshop, overseeing the contractors (Irish Marine Institute) hosting the event, presenting material on Annex IV and materials applicable to the workshop intent. PNNL is also overseeing a contractor (Wave Energy Center/University of Plymouth – WEC/UP) in the collection and analysis of the Annex IV data. Fifty-eight experts from 8 countries attended the workshop by invitation, spending two days discussing the needs of Annex IV. Presentations by DOE (background on Annex IV), PNNL (process for developing Annex IV; presentation of the draft database for PNNL project, plans for incorporating Annex IV data), WEC/UP on the environmental effect matrix, and four MHK developers (two from the UK, one from Ireland and one from Sweden; each discussing their own projects and lessons learned for measuring and mitigating environmental effects, as well as interactions with consenting [permitting] processes) helped provide background. The workshop participants worked part of the time in the large group and most of the time in four smaller breakout groups. Participants engaged in the process and provided a …

Silo and HDF5 are I/O libraries used by many codes important to the LLNL's Weapons and Complex Integration (WCI) mission. In the past year, modest adjustments and tuning of Silo, HDF5 and the I/O configuration of the BG/P platform, Dawn, were undertaken. A key goal of this work was to improve I/O performance without requiring any changes in the application codes themselves. In particular, the application codes have been allowed to continue to use a simplified yet highly flexible I/O paradigm known as 'Poor Man's Parallel I/O', where scalability is achieved through concurrent, serial I/O to multiple files. The results demonstrate substantial performance gains (better than 50x in many cases) at large scale (greater than 64,000 MPI tasks). They describe key enhancements made to Silo, HDF5 and the I/O configuration of our BG/P platform and present very favorable results from scalability studies over a wide range of operating scenarios.

Familiarize students affiliated with the Student National Medical Association with the National Library of Medicine's online resources that address medical conditions, health disparities, and public health preparedness needs.

The 2010 Gordon Research Conference on Polymer Physics will provide outstanding lectures and discussions in this critical field that impacts every industrial sector from electronics to transportation to medicine to textiles to energy generation and storage. Fundamental topics range from mechanical properties of soft gels to new understanding in polymer crystallization to energy conversion and transmission to simulating polymer dynamics at the nanoscale. This international conference will feature 22 invited lectures, wherein the opening 10 minutes are specifically designed for a general polymer physics audience. In addition, poster sessions and informal activities provide ample opportunity to discuss the latest advances in polymer physics. The technical content of the meeting will include new twists on traditional polymer physics topics, recent advances in previously underrepresented topics, and emerging technologies enabled by polymer physics. Here is a partially listing of targeted topics: (1) electrically-active and light-responsive polymers and polymer-based materials used in energy conversion and storage; (2) polymers with hierarchical structures including supramolecular assemblies, ion-containing polymers, and self-assembled block polymers; (3) mechanical and rheological properties of soft materials, such as hydrogels, and of heterogeneous materials, particularly microphase separated polymers and polymer nanocomposites; and (4) crystallization of polymers in dilute solutions, polymer melts, and …

The National Ignition Facility (NIF) is the largest and most energetic laser in the world contained in a complex the size of a football stadium. From the initial laser pulse, provided by telecommunication style infrared nanoJoule pulsed lasers, to the final 192 laser beams (1.8 Mega Joules total energy in the ultraviolet) converging on a target the size of a pencil eraser, laser safety is of paramount concern. In addition to this, there are numerous high-powered (Class 3B and 4) diagnostic lasers in use that can potentially send their laser radiation travelling throughout the facility. With individual beam paths of up to 1500 meters and a workforce of more than one thousand, the potential for exposure is significant. Simple laser safety practices utilized in typical laser labs just don't apply. To mitigate these hazards, NIF incorporates a multi layered approach to laser safety or 'Defense in Depth.' Most typical high-powered laser operations are contained and controlled within a single room using relatively simplistic controls to protect both the worker and the public. Laser workers are trained, use a standard operating procedure, and are required to wear Personal Protective Equipment (PPE) such as Laser Protective Eyewear (LPE) if the system is …

Airborne electromagnetic (AEM) surveys were flown during fiscal year (FY) 2008 within the 600 Area in an attempt to characterize the underlying subsurface and to aid in the closure and remediation design study goals for the 200-PO-1 Groundwater Operable Unit (OU). The rationale for using the AEM surveys was that airborne surveys can cover large areas rapidly at relatively low costs with minimal cultural impact, and observed geo-electrical anomalies could be correlated with important subsurface geologic and hydrogeologic features. Initial interpretation of the AEM surveys indicated a tenuous correlation with the underlying geology, from which several anomalous zones likely associated with channels/erosional features incised into the Ringold units were identified near the River Corridor. Preliminary modeling resulted in a slightly improved correlation but revealed that more information was required to constrain the modeling (SGW-39674, Airborne Electromagnetic Survey Report, 200-PO-1 Groundwater Operable Unit, 600 Area, Hanford Site). Both time-and frequency domain AEM surveys were collected with the densest coverage occurring adjacent to the Columbia River Corridor. Time domain surveys targeted deeper subsurface features (e.g., top-of-basalt) and were acquired using the HeliGEOTEM{reg_sign} system along north-south flight lines with a nominal 400 m (1,312 ft) spacing. The frequency domain RESOLVE system acquired electromagnetic …

Savannah River Remediation (SRR) is preparing Tank 6F for closure. The first step in preparing the tank for closure is mechanical sludge removal. In mechanical sludge removal, personnel add liquid (e.g., inhibited water or supernate salt solution) to the tank to form a slurry. They mix the liquid and sludge with pumps, and transfer the slurry to another tank for further processing. Mechanical sludge removal effectively removes the bulk of the sludge from a tank, but is not able to remove all of the sludge. In Tank 6F, SRR estimated a sludge heel of 5,984 gallons remained after mechanical sludge removal. To remove this sludge heel, SRR performed chemical cleaning. The chemical cleaning included two oxalic acid strikes, a spray wash, and a water wash. SRR conducted the first oxalic acid strike as follows. Personnel added 110,830 gallons of 8 wt % oxalic acid to Tank 6F and mixed the contents of Tank 6F with two submersible mixer pumps (SMPs) for approximately four days. Following the mixing, they transferred 115,903 gallons of Tank 6F material to Tank 7F. The SMPs were operating when the transfer started and were shut down approximately five hours after the transfer started. SRR collected a …

The Final Optics Damage Inspection (FODI) system automatically acquires and utilizes the Optics Inspection (OI) system to analyze images of the final optics at the National Ignition Facility (NIF). During each inspection cycle up to 1000 images acquired by FODI are examined by OI to identify and track damage sites on the optics. The process of tracking growing damage sites on the surface of an optic can be made more effective by identifying and removing signals associated with debris or reflections. The manual process to filter these false sites is daunting and time consuming. In this paper we discuss the use of machine learning tools and data mining techniques to help with this task. We describe the process to prepare a data set that can be used for training and identifying hardware reflections in the image data. In order to collect training data, the images are first automatically acquired and analyzed with existing software and then relevant features such as spatial, physical and luminosity measures are extracted for each site. A subset of these sites is 'truthed' or manually assigned a class to create training data. A supervised classification algorithm is used to test if the features can predict the …

Hydrogen and oxygen generation due to the radiolysis of water is a recognized hazard in pipe systems used in the nuclear industry, where the accumulation of hydrogen and oxygen at high points in the pipe system is expected, and explosive conditions exist. Pipe ruptures at nuclear facilities were attributed to hydrogen explosions inside pipelines, in nuclear facilities, i.e., Hamaoka, Nuclear Power Station in Japan, and Brunsbuettel in Germany. Prior to these accidents an ignition source for hydrogen was questionable, but these accidents, demonstrated that a mechanism was, in fact, available to initiate combustion and explosion. Hydrogen explosions may occur simultaneously with water hammer accidents in nuclear facilities, and a theoretical mechanism to relate water hammer to hydrogen deflagrations and explosions is presented herein.

Pyrophoric reagents represent an important class of reactants because they can participate in many different types of reactions. They are very useful in organic synthesis and in industrial applications. The Occupational Safety and Health Administration (OSHA) and the National Fire Protection Association (NFPA) define Pyrophorics as substances that will self-ignite in air at temperatures of 130 F (54.4 C) or less. However, the U.S. Department of Transportation (DOT) uses criteria different from the auto-ignition temperature criterion. The DOT defines a pyrophoric material as a liquid or solid that, even in small quantities and without an external ignition source, can ignite within five minutes after coming in contact with air when tested according to the United Nations Manual of Tests and Criteria. The Environmental Protection Agency has adopted the DOT definition. Regardless of which definition is used, oxidation of the pyrophoric reagents by oxygen or exothermic reactions with moisture in the air (resulting in the generation of a flammable gas such as hydrogen) is so rapid that ignition occurs spontaneously. Due to the inherent nature of pyrophoric substances to ignite spontaneously upon exposure to air, special precautions must be taken to ensure their safe handling and use. Pyrophoric gases (such as …

The goal of this year's effort is to measure the {sup 238}Pu(n,f) and {sup 238}Pu(n,2n) cross section from 100 keV to 20 MeV. We designed a surrogate experiment that used the reaction {sup 239}Pu(a,a{prime}x) as a surrogate for {sup 238}Pu(n,x). The experiment was conducted using the STARS/LIBERACE experimental facility located at the 88 Inch Cyclotron at Lawrence Berkeley National Laboratory in January 2010. A description of the experiment and status of the data analysis is given. In order to obtain a reliable {sup 238}Pu(n,x) cross section we designed the experiment using the surrogate ratio technique. This technique allows one to measure a desired, unknown, cross section relative to a known cross section. In the present example, the {sup 238}Pu(n,x) cross section of interest is determined relative to the known {sup 235}U(n,x) cross section. To increase confidence in the results, and to reduce overall uncertainties, we are also determining the {sup 238}Pu(n,x) cross section relative to the known {sup 234}U(n,x) cross section. The compound nuclei of interest for this experiment were produced using inelastic alpha scattering. For example, {sup 236}U(a,a{prime}x) served as a surrogate for {sup 235}U(n,x); analogous reactions were considered for the other cross sections. Surrogate experiments determine the probabilities …

The purpose of the ASME/DOE Gen IV Task 7 Part I is to review the current experience on various high temperature reactor intermediate heat exchanger (IHX) concepts. There are several different IHX concepts that could be envisioned for HTR/VHTR applications in a range of temperature from 850C to 950C. The concepts that will be primarily discussed herein are: (1) Tubular Helical Coil Heat Exchanger (THCHE); (2) Plate-Stamped Heat Exchanger (PSHE); (3) Plate-Fin Heat Exchanger (PFHE); and (4) Plate-Machined Heat Exchanger (PMHE). The primary coolant of the NGNP is potentially subject to radioactive contamination by the core as well as contamination from the secondary loop fluid. To isolate the radioactivity to minimize radiation doses to personnel, and protect the primary circuit from contamination, intermediate heat exchangers (IHXs) have been proposed as a means for separating the primary circuit of the NGNP (Next Generation Nuclear Plant) or other process heat application from the remainder of the plant. This task will first review the different concepts of IHX that could be envisioned for HTR/VHTR applications in a range of temperature from 850 to 950 C. This will cover shell-and-tube and compact designs (including the platefin concept). The review will then discuss the maturity …

Gasification of black liquor (BLG) has distinct advantages over direct combustion in Tomlinson recovery boilers. In this project we seek to resolve causticizing issues in order to make pressurized BLG even more efficient and cost-effective. One advantage of BLG is that the inherent partial separation of sulfur and sodium during gasification lends itself to the use of proven high yield variants to conventional kraft pulping which require just such a separation. Processes such as polysulfide, split sulfidity, ASAQ, and MSSAQ can increase pulp yield from 1% to 10% over conventional kraft but require varying degrees of sulfur/sodium separation, which requires additional [and costly] processing in a conventional Tomlinson recovery process. However during gasification, the sulfur is partitioned between the gas and smelt phases, while the sodium all leaves in the smelt; thus creating the opportunity to produce sulfur-rich and sulfur-lean white liquors for specialty pulping processes. A second major incentive of BLG is the production of a combustible product gas, rich in H2 and CO. This product gas (a.k.a. “syngas”) can be used in gas turbines for combined cycle power generation (which is twice as efficient as the steam cycle alone), or it can be used as a precursor to …

In our laboratory at LLNL, an effort is underway to investigate the underlying complexity of 5f electronic structure with spin-resolved photoelectron spectroscopy using chiral photonic excitation, i.e. Fano Spectroscopy. Our previous Fano measurements with Ce indicate the efficacy of this approach and theoretical calculations and spectral simulations suggest that Fano Spectroscopy may resolve the controversy concerning Pu electronic structure and electron correlation. To this end, we have constructed and commissioned a new Fano Spectrometer, testing it with the relativistic 5d system Pt. Here, our preliminary photoelectron spectra of the UO{sub 2} system are presented. X-ray photoelectron spectroscopy has been used to characterize a sample of UO{sub 2} grown on an underlying substrate of Uranium. Both AlK{alpha} (1487 eV) and MgK{alpha} (1254 eV) emission were utilized as the excitation. Using XPS and comparing to reference spectra, it has been shown that our sample is clearly UO{sub 2}.

The purpose of this task was to perform an Independent Validation Review to evaluate the successful implementation and effectiveness of Safety Basis controls, including new and revised controls, to support the implementation of a new DSA/TSR for B239. This task addresses Milestone 2 of FY10 PEP 7.6.6. As the first IVR ever conducted on a LLNL nuclear facility, it was designated a pilot project. The review follows the outline developed for Milestone 1 of the PEP, which is based on the DOE Draft Guide for Performance of Independent Verification Review of Safety Basis Controls. A formal Safety Basis procedure will be developed later, based on the lessons learned with this pilot project. Note, this review is termed a ''Validation'' in order to be consistent with the PEP definition and address issues historically raised about verification mechanisms at LLNL. Validation is intended to confirm that implementing mechanisms realistically establish the ability of TSR LCO, administrative control or safety management program to accomplish its intended safety function and that the controls are being implemented. This effort should not, however, be confused with a compliance assessment against all relevant DOE requirements and national standards. Nor is it used as a vehicle to question …

The complexities of resonance in multi-degree of freedom systems (multi-DOF) may be clarified using graphic presentations. Multi-DOF systems represent actual systems, such as beams or springs, where multiple, higher order, natural frequencies occur. Resonance occurs when a cyclic load is applied to a structure, and the frequency of the applied load equals one of the natural frequencies. Both equations and graphic presentations are available in the literature for single degree of freedom (SDOF) systems, which describe the response of spring-mass-damper systems to harmonically applied, or cyclic, loads. Loads may be forces, moments, or forced displacements applied to one end of a structure. Multi-DOF systems are typically described only by equations in the literature, and while equations certainly permit a case by case analysis for specific conditions, graphs provide an overall comprehension not gleaned from single equations. In fact, this collection of graphed equations provides novel results, which describe the interactions between multiple natural frequencies, as well as a comprehensive description of increased vibrations near resonance.

Detonation velocities for high explosives can be in the 7 to 8 km/s range. Previous work has shown that these velocities may be measured by inserting an optical fiber probe into the explosive assembly and recording the velocity time history using a Fabry-Perot velocimeter. The measured velocity using this method, however, is the actual velocity multiplied times the refractive index of the fiber core, which is on the order of 1.5. This means that the velocimeter diagnostic must be capable of measuring velocities as high as 12 km/s. Until recently, a velocity of 12 km/s was beyond the maximum velocity limit of a homodyne-based velocimeter. The limiting component in a homodyne system is usually the digitizer. Recently, however, digitizers have come on the market with 20 GHz bandwidth and 50 GS/s sample rate. Such a digitizer coupled with high bandwidth detectors now have the total bandwidth required to make velocity measurements in the 12 km/s range. This paper describes measurements made of detonation velocities using a high bandwidth homodyne system.