A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

The combustion of fossil fuels is profoundly altering the chemical composition of the atmosphere. Beginning with the Industrial Revolution, the concentration of carbon dioxide in the atmosphere has increased from approximately 280 to 370 {micro}l l{sup -1} in 2004, and it is expected to exceed 550 {micro}l l{sup -1} by 2050. Tropospheric ozone has risen even more rapidly than CO{sub 2} and average summer concentrations in the Northern Hemisphere are expected to continue to increase by 0.5-2.5% per year over the next 30 years. Although elevated CO{sub 2} stimulates photosynthesis and productivity of terrestrial ecosystems, ozone (O{sub 3}) is deleterious. In addition to directly affecting the physiology and productivity of crops, increased concentrations of tropospheric CO{sub 2} and O{sub 3} are predicted to lower the nutritional quality of leaves, which has the potential to increase herbivory as insects eat more to meet their nutritional demands. We tested the hypothesis that changes in tropospheric chemistry affect the relationship between plants and insect herbivores by changing leaf quality. The susceptibility to herbivory of soybean grown in elevated CO{sub 2} or O{sub 3} was examined using free air gas concentration enrichment (SoyFACE). FACE technology has the advantage that plants are cultivated under realistic …

We have observed 1 event consistent with the signature expected of the rare decay of a positive kaon to a positive pion and a neutrino anti-neutrino pair. In the examined momentum region of 211 to 230 MeV/c in the center of mass of the kaon we estimated the backgrounds to be about 0.08 {+-} 0.03 events. From this observation we estimate the branching ratio to be 4.2{sub {minus}3.5}{sup +9.7} x 10{sup {minus}10}. In this presentation I will explain the experiment, and the analysis techniques. I will also discuss the expected improvements in the near future from the analysis of new data sets.

Single transverse-spin asymmetry in high energy hadronic reaction has been greatly investigated from both experiment and theory sides in the last few years. In this talk, I will summarize some recent theoretical developments, which, in my opinion, help to unvail the mysterious of the single spin asymmetry.

This paper describes a new approach to environmental decision support for salinity management in the San Joaquin Basin of California that focuses on web-based data sharing using YSI Econet technology and continuous data quality management using a novel software tool, Aquarius.

We show that changes in the orientation of the inner accretion disk of Cygnus X-1 affect the shape of the broad Fe K{alpha} emission line emitted from this object, in such a way that eV-level spectral resolution observations (such as those that will be carried out by the ASTRO-E2 satellite) can be used to analyze the dynamics of the disk. We here present a new diagnosis tool, supported by numerical simulations, by which short observations of Cygnus X-1, separated in time, can determine whether its accretion disk actually processes, and if so, determine its period and precession angle. Knowing the precession parameters of Cygnus X-1 would result in a clarification of the origin of such precession, distinguishing between tidal and spin-spin coupling. This approach could also be used for similar studies in other microquasar systems.

The Solid-State, Heat-Capacity Laser (SSHCL) program at Lawrence Livermore National Laboratory is a multigeneration laser development effort scalable to the megawatt power levels. Wavefront quality is a driving metric of its performance. A deformable mirror with over 100 degrees of freedom situated within the cavity is used to correct both the static and dynamic aberrations sensed with a Shack-Hartmann wavefront sensor. The laser geometry is an unstable, confocal resonator with a clear aperture of 10 cm x 10 cm. It operates in a pulsed mode at a high repetition rate (up to 200 Hz) with a correction being applied before each pulse. Wavefront information is gathered in real-time from a low-power pick-off of the high-power beam. It is combined with historical trends of aberration growth to calculate a correction that is both feedback and feed-forward driven. The overall system design, measurement techniques and correction algorithms are discussed. Experimental results are presented.

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We have developed a 3D wavelet-based filter for visualizing structural features in volumetric data. The only variable parameter is a characteristic linear size of the feature of interest. The filtered output contains only those regions that are correlated with the characteristic size, thus denoising the image. We demonstrate the use of the filter by applying it to 3D data from a variety of electron microscopy samples including low contrast vitreous ice cryogenic preparations, as well as 3D optical microscopy specimens.

The advent of CCD cameras and computerized data recording has spurred the development of several new cameras and techniques for recording nanosecond images. We have made a side by side comparison of three nanosecond frame cameras, examining them for both performance and operational characteristics. The cameras include; Micro-Channel Plate/CCD, Image Diode/CCD and Image Diode/Film; combinations of gating/data recording. The advantages and disadvantages of each device will be discussed.

Aluminum and other metal abundances were determined in 21 red giants in the globular clusters NGC 6752 and M80 as part of a larger study to determine whether the aluminum distribution on the red giant branch is related to the second parameter effect that causes clusters of similar metallicity to display different horizontal branch morphologies. The observations were obtained of the Al I lines near 6700 Angstroms with the CTIO Blanco 4-m telescope and Hydra multi-object spectrograph. The spectra have a resolving power of 18000 or 9400, with typical S/N ratios of 100-200. Mean [Fe/H] values obtained from the spectra are -1.58 for NGC 6751 and -1.73 for M80; this represents the spectroscopic iron abundance determination for M80. Both NGC 6752 and M80 display a spread in aluminum abundance with mean [Al/Fe] ratios of +0.51 and +0.37 respectively. No trend in the variation of the mean AI abundance with position on the giant branch is discernible in either cluster with our small sample.

The construction of the National Ignition Facility (NIF) building and laser beampaths at the Lawrence Livermore National Laboratory has been completed. This 8-year design/construction effort has successfully erected a 450,000 sq ft building and filled its interior with a complex of large-scale optical benches. These benches support all of the large-aperture optic elements of the NIF and the environmentally controlled enclosures that protect each of the 192 laser beamlines as they propagate from the injection laser system, through large aperture amplification stages, and into the target chamber. Even though this facility is very large, nearly 200 m long, 100 m wide, and 30 m tall, stringent mechanical performance requirements have been achieved throughout including temperature control <0.3 C, laser-beam pointing stability on target < 50 {micro}rms, and level 100 surface cleanliness on internal components. This presentation will provide an historical perspective explaining the basis of the design, technical details describing the techniques of construction and a chronological progression of the construction activities from ground breaking to beampath completion.

We describe a method of improving the appearance of a low vertex count mesh in a manner that is guided by rendered images of the original, detailed mesh. This approach is motivated by the fact that greedy simplification methods often yield meshes that are poorer than what can be represented with a given number of vertices. Our approach relies on edge swaps and vertex teleports to alter the mesh connectivity, and uses the downhill simplex method to simultaneously improve vertex positions and surface attributes. Note that this is not a simplification method--the vertex count remains the same throughout the optimization. At all stages of the optimization the changes are guided by a metric that measures the differences between rendered versions of the original model and the low vertex count mesh. This method creates meshes that are geometrically faithful to the original model. Moreover, the method takes into account more subtle aspects of a model such as surface shading or whether cracks are visible between two interpenetrating parts of the model.

The instruments tested included a 9-inch sphere Portable Neutron Rem Counter Model PNR-4 manufactured by Eberline Instrument Corporation, Santa Fe, N.M.; an Andersson-Braum type Remmeter; and Hankins-type albedo neutron dosimeters composed of cadmium-enclosed TLDs. The standard neutron source at the NBS reactor was used. The observed and calculated response curves are presented and discussed. (WHK)

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With the first four of its eventual 192 beams now executing shots, the National Ignition Facility (NIF) at the Lawrence Livermore National Laboratory is already the world's largest and most energetic laser. The optical system performance requirements that are in place for NIF are derived from the goals of the missions it is designed to serve. These missions include inertial confinement fusion (ICF) research and the study of matter at extreme energy densities and pressures. These mission requirements have led to a design strategy for achieving high quality focusable energy and power from the laser and to specifications on optics that are important for an ICF laser. The design of NIF utilizes a multipass architecture with a single large amplifier type that provides high gain, high extraction efficiency and high packing density. We have taken a systems engineering approach to the practical implementation of this design that specifies the wavefront parameters of individual optics in order to achieve the desired cumulative performance of the laser beamline. This presentation provides a detailed look at the causes and effects of performance degradation in large laser systems and how NIF has been designed to overcome these effects. We will also present results of …

It has been suggested that x-ray free electron lasers will enable single-particle diffraction imaging of biological molecules. In this paper we present a model to estimate the required pulse parameters based on a trade-off between minimizing image degradation due to damage and maximizing the image signal-to-noise ratio. We discuss several means to alleviate the photon requirements, and compare the requirements with existing or planned x-ray sources such as short-pulse x-ray free-electron lasers.

Magnetorheological finishing (MRF) techniques have been developed to manufacture continuous phase plates (CPP's) and custom phase corrective structures on polished fused silica surfaces. These phase structures are important for laser applications requiring precise manipulation and control of beam-shape, energy distribution, and wavefront profile. The MRF's unique deterministic-sub-aperture polishing characteristics make it possible to imprint complex topographical information onto optical surfaces at spatial scale-lengths approaching 1 mm. In this study, we present the results of experiments and model calculations that explore imprinting two-dimensional sinusoidal structures. Results show how the MRF removal function impacts and limits imprint fidelity and what must be done to arrive at a high quality surface. We also present several examples of this imprinting technology for fabrication of phase correction plates and CPPs for use at high fluences.

The National Ignition Facility (NIF) at the Lawrence Livermore National Laboratory is a stadium-sized facility containing a 192-beam, 1.8-Megajoule, 500-Terawatt, ultraviolet laser system together with a 10-meter diameter target chamber with room for nearly 100 experimental diagnostics. NIF will be the world's largest and most energetic laser experimental system, providing a scientific center to study inertial confinement fusion and matter at extreme energy densities and pressures. NIF's energetic laser beams will compress fusion targets to conditions required for thermonuclear bum, liberating more energy than required to initiate the fusion reactions. Other NIF experiments will study physical processes at temperatures approaching 10{sup 8} K and 10{sup 11} bar, conditions that exist naturally only in the interior of stars, planets and in nuclear weapons. NIF has completed the first phases of its laser commissioning program. The first four beams of NIF have generated 106 kilojoules of infrared light and over 16 kJ at the third harmonic (351 nm). NIF's target experimental systems are being commissioned and experiments have begun. This paper provides a detailed look the NIF laser systems, laser and optical performance and results from recent laser commissioning shots, and plans for commissioning diagnostics for experiments on NIF.

Arithmetic coding achieves a superior coding rate when encoding a binary source, but its lack of speed makes it an inferior choice when true high-performance encoding is needed. We present our work on a practical implementation of fast entropy coders for binary messages utilizing only bit shifts and table lookups. To limit code table size we limit our code lengths with a type of variable-to-variable (VV) length code created from source string merging. We refer to these codes as ''merged codes''. With merged codes it is possible to achieve a desired level of speed by adjusting the number of bits read from the source at each step. The most efficient merged codes yield a coder with a worst-case inefficiency of 0.4%, relative to the Shannon entropy. Using a hybrid Golomb-VV Bin Coder we are able to achieve a compression ratio that is competitive with other state-of-the-art coders, at a superior throughput.

The High Performance Storage System (HPSS) provides scalable hierarchical storage management (HSM), archive, and file system services. Its design, implementation and current dominant use are focused on HSM and archive services. It is also a general-purpose, global, shared, parallel file system, potentially useful in other application domains. When HPSS design and implementation began over a decade ago, scientific computing power and storage capabilities at a site, such as a DOE national laboratory, was measured in a few 10s of gigaops, data archived in HSMs in a few 10s of terabytes at most, data throughput rates to an HSM in a few megabytes/s, and daily throughput with the HSM in a few gigabytes/day. At that time, the DOE national laboratories and IBM HPSS design team recognized that we were headed for a data storage explosion driven by computing power rising to teraops/petaops requiring data stored in HSMs to rise to petabytes and beyond, data transfer rates with the HSM to rise to gigabytes/s and higher, and daily throughput with a HSM in 10s of terabytes/day. This paper discusses HPSS architectural, implementation and deployment experiences that contributed to its success in meeting the above orders of magnitude scaling targets. We also discuss …

Rockfishes (Sebastes spp.) support one of the most economically important fisheries of the Pacific Northwest and it is essential for sustainable management that age estimation procedures be validated for these species. Atmospheric testing of thermonuclear devices during the 1950s and 1960s created a global radiocarbon ({sup 14}C) signal in the ocean environment that scientists have identified as a useful tracer and chronological marker in natural systems. In this study, we first demonstrated that fewer samples are necessary for age validation using the bomb-generated {sup 14}C signal by emphasizing the utility of the time-specific marker created by the initial rise of bomb-{sup 14}C. Second, the bomb-generated {sup 14}C signal retained in fish otoliths was used to validate the age and age estimation methodology of the quillback rockfish (Sebastes maliger) in the waters of southeast Alaska. Radiocarbon values from the first year's growth of quillback rockfish otoliths were plotted against estimated birth year producing a {sup 14}C time series spanning 1950 to 1985. The initial rise of bomb-{sup 14}C from pre-bomb levels ({approx} -90 {per_thousand}) occurred in 1959 {+-} 1 year and {sup 14}C levels rose relatively rapidly to peak {Delta}{sup 14}C values in 1967 (+105.4 {per_thousand}), with a subsequent declining trend …

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We report on new measurements of the Cabibbo-Kobayashi-Maskawa matrix elements |V{sub cb}| and |V{sub ub}| with inclusive and exclusive semileptonic B decays, highlighting the recent precision measurements with the BABAR detector at the PEP-II asymmetric-energy B Factory at SLAC.