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.

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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 …

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.

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 …

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 …

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 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.

A relatively new technique for measuring the electron cloud density in storage rings has been developed and successfully demonstrated [S. De Santis, J.M. Byrd, F. Caspers, A. Krasnykh, T. Kroyer, M.T.F. Pivi, and K.G. Sonnad, Phys. Rev. Lett. 100, 094801 (2008).]. We present the experimental results of a systematic application of this technique at the Cornell Electron Storage Ring Test Accelerator. The technique is based on the phase modulation of the TE mode transmitted in a synchrotron beam pipe caused by the periodic variation of the density of electron plasma. Because of the relatively simple hardware requirements, this method has become increasingly popular and has been since successfully implemented in several machines. While the principles of this technique are straightforward, quantitative derivation of the electron cloud density from the measurement requires consideration of several effects, which we address in detail.

Catalysis is a key technology for improving the quality of life while simultaneously reducing the adverse impact of human activities on the environment. The discovery of new catalytic processes and the improvement of existing ones are also critically important for securing the nation's energy supply. The GRC on Catalysis is considered one the most prestigious conference for catalysis research, bringing together leading researchers from both academia, industry and national labs to discuss the latest, most exciting research in catalysis and the future directions for the field. The 2010 GRC on Catalysis will follow time-honored traditions and feature invited talks from the world's leading experts in the fundamentals and applications of catalytic science and technology. We plan to have increased participation from industry. The extended discussions in the company of outstanding thinkers will stimulate and foster new science. The conference will include talks in the following areas: Alternative feedstocks for chemicals and fuels, Imaging and spectroscopy, Design of novel catalysts, Catalyst preparation fundamentals, Molecular insights through theory, Surface Science, Catalyst stability and dynamics. In 2010, the Catalysis conference will move to a larger conference room with a new poster session area that will allow 40 posters per session. The dorm rooms …

A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.

High (≈ 90%) deuterium retention was observed in NSTX gas balance measurements both withand without lithiumization of the carbon plasma facing components. The gas retained in ohmic discharges was measured by comparing the vessel pressure rise after a discharge to that of a gasonly pulse with the pumping valves closed. For neutral beam heated discharges the gas input and gas pumped by the NB cryopanels were tracked. The discharges were followed by outgassing of deuterium that reduced the retention. The relationship between retention and surface chemistry was explored with a new plasma-material interface probe connected to an in-vacuo surface science station that exposed four material samples to the plasma. XPS and TDS analysis showed that the binding of D atoms is fundamentally changed by lithium - in particular atoms are weakly bonded in regions near lithium atoms bound to either oxygen or the carbon matrix.

AC-dipole magnets are typically implemented as a parallel LC resonant circuit. To maximize efficiency, it's beneficial to operate at a high Q. This, however, limits the magnet to a narrow frequency range. Current designs therefore operate at a low Q to provide a wider bandwidth at the cost of efficiency. Dynamically tuning a high Q resonant circuit tries to maintain a high efficiency while providing a wide frequency range. The results of ongoing efforts at BNL to implement dynamically tuned high-Q AC dipoles will be presented.

Here we report the first angle-resolved photoemission measurement on nearly optimally doped multilayer Tl-based superconducting cuprates (Tl-2212 and Tl-1223) and a comparison study to single-layer (Tl-2201) compound. A kink in the band dispersion is found in all three compounds but exhibits different momentum dependence for the single-layer and multilayer compounds, reminiscent to that of Bi-based cuprates. This layer number dependent renormalization effect strongly implies that the spin-resonance mode is unlikely to be responsible for the dramatic renormalization effect near the antinodal region.

A characteristic feature of the copper oxide high-temperature superconductors is the dichotomy between the electronic excitations along the nodal (diagonal) and antinodal (parallel to the Cu-O bonds) directions in momentum space, generally assumed to be linked to the d-wave symmetry of the superconducting state. Angle-resolved photoemission measurements in the superconducting state have revealed a quasiparticle spectrum with a d-wave gap structure that exhibits a maximum along the antinodal direction and vanishes along the nodal direction. Subsequent measurements have shown that, at low doping levels, this gap structure persists even in the high-temperature metallic state, although the nodal points of the superconducting state spread out in finite Fermi arcs. This is the so-called pseudogap phase, and it has been assumed that it is closely linked to the superconducting state, either by assigning it to fluctuating superconductivity or by invoking orders which are natural competitors of d-wave superconductors. Here we report experimental evidence that a very similar pseudogap state with a nodal-antinodal dichotomous character exists in a system that is markedly different from a superconductor: the ferromagnetic metallic groundstate of the colossal magnetoresistive bilayer manganite La{sub 1.2}Sr{sub 1.8}Mn{sub 2}O{sub 7}. Our findings therefore cast doubt on the assumption that the pseudogap state …

We present an Open Automated Demand Response Communications Specifications (OpenADR) data model capable of communicating real-time prices to electricity customers. We also show how the same data model could be used to for other types of dynamic pricing tariffs (including peak pricing tariffs, which are common throughout the United States). Customers participating in automated demand response programs with building control systems can respond to dynamic prices by using the actual prices as inputs to their control systems. Alternatively, prices can be mapped into"building operation modes," which can act as inputs to control systems. We present several different strategies customers could use to map prices to operation modes. Our results show that OpenADR can be used to communicate dynamic pricing within the Smart Grid and that OpenADR allows for interoperability with existing and future systems, technologies, and electricity markets.

colloids ? luminescence ? metal oxides ? nanocrystals ? synthesis design

Active capping is a relatively new approach for treating contaminated sediments. It involves applying chemically reactive amendments to the sediment surface. The main role of active caps is to stabilize contaminants in contaminated sediments, lower the bioavailable pool of contaminants, and reduce the release of contaminants to the water column. Metals are common contaminants in many marine and fresh water environments as a result of industrial and military activities. The mobile, soluble forms of metals are generally considered toxic. Induced chemical precipitation of these metals can shift toxic metals from the aqueous phase to a solid, precipitated phase which is often less bioavailable. This approach can be achieved through application of sequestering agents such as rock phosphates, organoclays, zeolites, clay minerals, and biopolymers (e.g., chitosan) in active capping technology. Active capping holds great potential for a more permanent solution that avoids residual risks resulting from contaminant migration through the cap or breaching of the cap. In addition to identifying superior active capping agents, research is needed to optimize application techniques, application rates, and amendment combinations that maximize sequestration of contaminants. A selected set of active capping treatment technologies has been demonstrated at a few sites, including a field demonstration at …