We examine the utility of very high redshift Type Ia supernovae for cosmology and systematic uncertainty control. Next generation space surveys such as the Supernova/Acceleration Probe (SNAP) will obtain thousands of supernovae at z>1.7, beyond the design redshift for which the supernovae will be exquisitely characterized. We find that any z gtrsim 2 standard candles' use for cosmological parameter estimation is quite modest and subject to pitfalls; we examine gravitational lensing, redshift calibration, and contamination effects in some detail. The very high redshift supernovae - both thermonuclear and core collapse - will provide copious interesting information on star formation, environment, and evolution. However, the new observational systematics that must be faced, as well as the limited expansion of SN-parameter space afforded, does not point to high value for 1.7<z<3 SNe Ia in controlling evolutionary systematics relative to what SNAP can already achieve at z<1.7. Synergy with observations from JWST and thirty meter class telescopes afford rich opportunities for advances throughout astrophysics.

The 17th International Conference on Arabidopsis Research was held at the University of Madison, Wisconsin from June 27- July 2, 2006. ICAR-2006 included approximately 625 scientists from across the world. The scientific program was of excellent quality featuring 73 talks, including 30 from invited speakers. There were also 6 community-organized workshops (facilitated by conference staff) featuring additional talks on topics including ‘Submitting data to long-term repositories,’ ‘TAIR introductory workshop,’ ‘Web services and demonstration,’ ‘Public engagement: broadening the impact of your research,’ ‘Systems biology approaches to analysis of metabolic and regulatory networks of Arabidopsis,’ and ‘Mechanotransduction in Arabidopsis.’ Approximately 440 posters were presented in general topic areas including, among others, Development, Modeling/Other Systems, Energy, Environment, and Genetic/Epigenetic mechanisms. Graduate students, postdoctoral researchers, junior faculty, and underrepresented minorities made up a significant portion of the oral presentations thereby promoting the training of young scientists and facilitating important career development opportunities for speakers. Several poster sessions provided an opportunity for younger participants to freely meet with more established scientists. The North American Arabidopsis Steering Committee (NAASC) continued its outreach effort and again sponsored two special luncheons to encourage personal and professional development of young scientists and also underrepresented minorities. The ‘Emerging Scientists Luncheon’ …

Following our earlier study on the dynamics of low energy electron attachment to formic acid, we report the results of elastic low-energy electron collisions with formic acid. Momentum transfer and angular differential cross sections were obtained by performing fixed-nuclei calculations employing the complex Kohn variational method. We make a brief description of the technique used to account for the polar nature of this polyatomic target and compare our results with available experimental data.

Exterior complex scaling provides a practical path forfirst-principles studies of atomic and molecular ionizationproblemssince it avoids explicit enforcement of asymptotic boundary conditionsfor 3-body Coulomb breakup. We have used the method of exterior complexscaling, implemented with both the discrete variable representation andB-splines, to obtain the first-order wave function for molecular hydrogencorresponding to a single photon having been absorbed by a correlatedinitial state. These wave functions are used to construct convergedtriple differential cross sections for double photoionization of alignedH2 molecules.

We describe a fast contour descriptor algorithm and its application to a distributed supernova detection system (the Nearby Supernova Factory) that processes 600,000 candidate objects in 80 GB of image data per night. Our shape-detection algorithm reduced the number of false positives generated by the supernova search pipeline by 41% while producing no measurable impact on running time. Fourier descriptors are an established method of numerically describing the shapes of object contours, but transform-based techniques are ordinarily avoided in this type of application due to their computational cost. We devised a fast contour descriptor implementation for supernova candidates that meets the tight processing budget of the application. Using the lowest-order descriptors (F{sub 1} and F{sub -1}) and the total variance in the contour, we obtain one feature representing the eccentricity of the object and another denoting its irregularity. Because the number of Fourier terms to be calculated is fixed and small, the algorithm runs in linear time, rather than the O(n log n) time of an FFT. Constraints on object size allow further optimizations so that the total cost of producing the required contour descriptors is about 4n addition/subtraction operations, where n is the length of the contour.

Recent in situ observations in stratiform clouds suggest that mixed phase regimes, here defined as limited cloud volumes containing both liquid and solid water, are constrained to narrow layers (order 100 m) separating all-liquid and fully glaciated volumes (Hallett and Viddaurre, 2005). The Department of Energy Atmospheric Radiation Measurement Program's (DOE-ARM, Ackerman and Stokes, 2003) North Slope of Alaska (NSA) ARM Climate Research Facility (ACRF) recently started collecting routine measurement of radar Doppler velocity power spectra from the Millimeter Cloud Radar (MMCR). Shupe et al. (2004) showed that Doppler spectra has potential to separate the contributions to the total reflectivity of the liquid and solid water in the radar volume, and thus to investigate further Hallett and Viddaurre's findings. The Mixed-Phase Arctic Cloud Experiment (MPACE) was conducted along the NSA to investigate the properties of Arctic mixed phase clouds (Verlinde et al., 2006). We present surface based remote sensing data from MPACE to discuss the fine-scale structure of the mixed-phase clouds observed during this experiment.

It has been proposed that during growth under anaerobic oroxygen-limited conditions Shewanella oneidensis MR-1 uses theserine-isocitrate lyase pathway common to many methylotrophic anaerobes,in which formaldehyde produced from pyruvate is condensed with glycine toform serine. The serine is then transformed through hydroxypyruvate andglycerate to enter central metabolism at phosphoglycerate. To examine itsuse of the serine-isocitrate lyase pathway under anaerobic conditions, wegrew S. oneidensis MR-1 on [1-13C]lactate as the sole carbon source witheither trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor.Analysis of cellular metabolites indicates that a large percentage(>75 percent) of lactate was partially oxidized to either acetate orpyruvate. The 13C isotope distributions in amino acids and other keymetabolites indicate that, under anaerobic conditions, a complete serinepathway is not present, and lactate is oxidized via a highly reversibleserine degradation pathway. The labeling data also suggest significantactivity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase)reactions. Although the tricarboxylic acid (TCA) cycle is often observedto be incomplete in many other anaerobes (absence of 2-oxoglutaratedehydrogenase activity), isotopic labeling supports the existence of acomplete TCA cycle in S. oneidensis MR-1 under TMAO reductioncondition.

A program called ``Innovative Billing?? has been developed to provide individualized energy information for a mass audience?the entireresidential customer base of an electric or gas utility. Customers receive a graph on the bill that compares that customer?s consumption with othersimilar customers for the same month. The program aims to stimulate customers to make ef?ciency improvements. To group as many as severalmillion customers into small ``comparison groups??, an automated method must be developed drawing solely from the data available to the utility.This paper develops and applies methods to compare the quality of resulting comparison groups.A data base of 114,000 customers from a utility billing system was used to evaluate Innovative Billing comparison groups, comparing fouralternative criteria: house characteristics (?oor area, housing type, and heating fuel); street; meter read route; billing cycle. Also, customers wereinterviewed to see what forms of comparison graphs made most sense and led to fewest errors of interpretation. We ?nd that good qualitycomparison groups result from using street name, meter book, or multiple house characteristics. Other criteria we tested, such as entire cycle, entiremeter book, or single house characteristics such as ?oor area, resulted in poor quality comparison groups. This analysis provides a basis forchoosing comparison groups based …

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees …

Global changes in gene expression occur during tumor progression, as indicated by expression profiling of metastatic tumors. How this occurs is poorly understood. SATB1 functions as a genome organizer by folding chromatin via tethering multiple genomic loci and recruiting chromatin remodeling enzymes to regulate chromatin structure and expression of a large number of genes. Here we show that SATB1 is expressed at high levels in aggressive breast cancer cells, and is undetectable in non-malignant breast epithelial cells. Importantly, RNAi-mediated removal of SATB1 from highly-aggressive MDA-MB-231 cells altered the expression levels of over 1200 genes, restored breast-like acinar polarity in three-dimensional cultures, and prevented the metastastic phenotype in vivo. Conversely, overexpression of SATB1 in the less-aggressive breast cancer cell line Hs578T altered the gene expression profile and increased metastasis dramatically in vivo. Thus, SATB1 is a global regulator of gene expression in breast cancer cells, directly regulating crucial metastasis-associated genes, including ERRB2 (HER2/NEU), TGF-{beta}1, matrix metalloproteinase 3, and metastasin. The identification of SATB1 as a protein that re-programs chromatin organization and transcription profiles to promote breast cancer metastasis suggests a new model for metastasis and may provide means of therapeutic intervention.

A general problem when fitting EXAFS data is determining whether particular parameters are statistically significant. The F-test is an excellent way of determining relevancy in EXAFS because it only relies on the ratio of the fit residual of two possible models, and therefore the data errors approximately cancel. Although this test is widely used in crystallography (there, it is often called a 'Hamilton test') and has been properly applied to EXAFS data in the past, it is very rarely applied in EXAFS analysis. We have implemented a variation of the F-test adapted for EXAFS data analysis in the RSXAP analysis package, and demonstrate its applicability with a few examples, including determining whether a particular scattering shell is warranted, and differentiating between two possible species or two possible structures in a given shell.

InN nanorods were grown on a, c-, and r-plane of sapphire and also on Si (111) and GaN (0001) by non-catalytic, template-free hydride metal-organic vapor phase epitaxy and studied by transmission electron microscopy, electron energy loss (EELS) and photoluminescence (PL) at room temperature. These nanocrystals have different shapes and different faceting depending on the substrate used and their crystallographic orientation. EELS measurements have confirmed the high purity of these crystals. The observed PL peak was in the range of 0.9-0.95 eV. The strongest PL intensity was observed for the nanocrystals with the larger diameters.

The CALPHAD approach is applied to kinetic studies of phase transformations and aging of prototypes of Ni-Cr-Mo-based alloys selected for waste disposal canisters in the Yucca Mountain Project (YMP). Based on a previous study on alloy stability for several candidate alloys, the thermodynamic driving forces together with a newly developed mobility database have been used to analyze diffusion-controlled transformations in these Ni-based alloys. Results on precipitation of the Ni{sub 2}Cr-ordered phase in Ni-Cr and Ni-Cr-Mo alloys, and of the complex P- and {delta}-phases in a surrogate of Alloy 22 are presented, and the output from the modeling are compared with experimental data on aging.

The need to consider aqueous and sorption kinetics andmicrobiological processes arises in many subsurface problems. Ageneral-rate expression has been implemented into the TOUGHREACTsimulator, which considers multiple mechanisms (pathways) and includesmultiple product, Monod, and inhibition terms. This paper presents aformulation for incorporating kinetic rates among primary species intomass-balance equations. The space discretization used is based on aflexible integral finite difference approach that uses irregular griddingto model bio-geologic structures. A general multi-region model forhydrological transport interacted with microbiological and geochemicalprocesses is proposed. A 1-D reactive transport problem with kineticbiodegradation and sorption was used to test the enhanced simulator,which involves the processes that occur when a pulse of water containingNTA (nitrylotriacetate) and cobalt is injected into a column. The currentsimulation results agree very well with those obtained with othersimulators. The applicability of this general multi-region model wasvalidated by results from a published column experiment ofdenitrification and sulfate reduction. The matches with measured nitrateand sulfate concentrations were adjusted with the interficial areabetween mobile hydrological and immobile biological regions. Resultssuggest that TOUGHREACT can not only be a useful interpretative tool forbiogeochemical experiments, but also can produce insight into processesand parameters of microscopic diffusion and their interplay withbiogeochemical reactions. The geometric- and process-based multi-regionmodel may provide …

Precise gamma-ray thermal neutron capture cross sectionshave been measured at the Budapest Reactor for all elements withZ=1-83,92 except for He and Pm. These measurements and additional datafrom the literature been compiled to generate the Evaluated Gamma-rayActivation File (EGAF), which is disseminated by LBNL and the IAEA. Thesedata are nearly complete for most isotopes with Z<20 so the totalradiative thermal neutron capture cross sections can be determineddirectly from the decay scheme. For light isotopes agreement with therecommended values is generally satisfactory although large discrepanciesexist for 11B, 12,13C, 15N, 28,30Si, 34S, 37Cl, and 40,41K. Neutroncapture decay data for heavier isotopes are typically incomplete due tothe contribution of unresolved continuum transitions so only partialradiative thermal neutron capture cross sections can be determined. Thecontribution of the continuum to theneutron capture decay scheme arisesfrom a large number of unresolved levels and transitions and can becalculated by assuming that the fluctuations in level densities andtransition probabilities are statistical. We have calculated thecontinuum contribution to neutron capture decay for the palladiumisotopes with the Monte Carlo code DICEBOX. These calculations werenormalized to the experimental cross sections deexciting low excitationlevels to determine the total radiative thermal neutron capture crosssection. The resulting palladium cross sections values were determinedwith a precision …

A model study on fractured systems was performed using aconcept that treats isotropic cracked systems as ensembles of crackedgrains by analogy to isotropic polycrystalline elastic media. Theapproach has two advantages: (a) Averaging performed is ensembleaveraging, thus avoiding the criticism legitimately leveled at mosteffective medium theories of quasistatic elastic behavior for crackedmedia based on volume concentrations of inclusions. Since crack effectsare largely independent of the volume they occupy in the composite, sucha non-volume-based method offers an appealingly simple modelingalternative. (b) The second advantage is that both polycrystals andfractured media are stiffer than might otherwise be expected, due tonatural bridging effects of the strong components. These same effectshave also often been interpreted as crack-crack screening inhigh-crack-density fractured media, but there is no inherent conflictbetween these two interpretations of this phenomenon. Results of thestudy are somewhat mixed. The spread in elastic constants observed in aset of numerical experiments is found to be very comparable to the spreadin values contained between the Reuss and Voigt bounds for thepolycrystal model. However, computed Hashin-Shtrikman bounds are much tootight to be in agreement with the numerical data, showing thatpolycrystals of cracked grains tend to violate some implicit assumptionsof the Hashin-Shtrikman bounding approach. However, the self-consistentestimates obtained for …

Numerical models of geologic storage of carbon dioxide (CO2)in brine-bearing formations use characteristic curves to represent theinteractions of non-wetting-phase CO2 and wetting-phase brine. When aproblem includes both injection of CO2 (a drainage process) and itssubsequent post-injection evolution (a combination of drainage andwetting), hysteretic characteristic curves are required to correctlycapture the behavior of the CO2 plume. In the hysteretic formulation,capillary pressure and relative permeability depend not only on thecurrent grid-block saturation, but also on the history of the saturationin the grid block. For a problem that involves only drainage or onlywetting, a non-hysteretic formulation, in which capillary pressure andrelative permeability depend only on the current value of the grid-blocksaturation, is adequate. For the hysteretic formulation to be robustcomputationally, care must be taken to ensure the differentiability ofthe characteristic curves both within and beyond the turning-pointsaturations where transitions between branches of the curves occur. Twoexample problems involving geologic CO2 storage are simulated withTOUGH2, a multiphase, multicomponent code for flow and transport codethrough geological media. Both non-hysteretic and hysteretic formulationsare used, to illustrate the applicability and limitations ofnon-hysteretic methods.The first application considers leakage of CO2from the storage formation to the ground surface, while the secondexamines the role of heterogeneity within the storageformation.

The recent discoveries of nonmolecular phases of simple molecular solids [1,2] demonstrate the proof-of-the-principles for producing exotic phases by application of high pressure. Modern advances in theoretical and computational methodologies now make possible to explain or even predict novel structures and properties in a relatively wide range of length scales on the basis of thermodynamic stability [3]. Equally important in materials research is the recent developments in advanced x-ray and laser diagnostics that enable in-situ observations at the formidable pressure-temperature conditions [4]. Having benefited by all these developments, we discuss the first principle of the pressure-induced chemistry, 'Mbar Chemistry', with a few examples that may have important implications in materials research.

We examine ionizing radiation (IR) sensitivity and epistasisrelationships of several Saccharomyces mutants affectingpost-translational modifications of histones H2B and H3. Mutantsbre1delta, lge1delta, and rtf1delta, defective in histone H2B lysine 123ubiquitination, show IR sensitivity equivalent to that of the dot1deltamutant that we reported on earlier, consistent with published findingsthat Dot1p requires H2B K123 ubiquitination to fully methylate histone H3K79. This implicates progressive K79 methylation rather thanmono-methylation in IR resistance. The set2delta mutant, defective in H3K36 methylation, shows mild IR sensitivity whereas mutants that abolishH3 K4 methylation resemble wild type. The dot1delta, bre1delta, andlge1delta mutants show epistasis for IR sensitivity. The paf1deltamutant, also reportedly defective in H2B K123 ubiquitination, confers nosensitivity. The rad6delta, rad51null, rad50delta, and rad9deltamutations are epistatic to bre1? and dot1delta, but rad18delta andrad5delta show additivity with bre1delta, dot1delta, and each other. Thebre1delta rad18delta double mutant resembles rad6delta in sensitivity;thus the role of Rad6p in ubiquitinating H2B accounts for its extrasensitivity compared to rad18delta. We conclude that IR resistanceconferred by BRE1 and DOT1 is mediated through homologous recombinationalrepair, not postreplication repair, and confirm findings of a G1checkpoint role for the RAD6/BRE1/DOT1 pathway.

Ambipolar diffusion redistributes magnetic flux in weakly ionized plasmas and plays a critical role in star formation. Simulations of ambipolar diffusion using explicit MHD codes are prohibitively expensive for the level of ionization observed in molecular clouds ({approx}&lt; 10{sup -6}) since an enormous number of time steps is required to represent the dynamics of the dominant neutral component with a time step determined by the trace ion component. Here we show that ambipolar diffusion calculations can be significantly accelerated by the 'heavy-ion approximation', in which the mass density of the ions is increased and the collisional coupling constant with the neutrals decreased such that the product remains constant. In this approximation, the ambipolar diffusion time and the ambipolar magnetic Reynolds number remain unchanged. We present three tests of the heavy-ion approximation: C-type shocks, the Wardle instability, and the 1D collapse of a magnetized slab. We show that this approximation is quite accurate provided that (1) the square of the Alfven Mach number is small compared to the ambipolar diffusion Reynolds number for dynamical problems, and that (2) the ion mass density is negligible for quasi-static problems; a specific criterion is given for the magnetized slab problem. The first condition can …

The importance of microenvironment and context in regulation of tissue-specific genes is finally well established. DNA exposure to, or sequestration from, nucleases can be used to detect differences in higher order chromatin structure in intact cells without disturbing cellular or tissue architecture. To investigate the relationship between chromatin organization and tumor phenotype, we utilized an established 3-D assay where normal and malignant human breast cells can be easily distinguished by the morphology of the structures they make (acinus-like vs tumor-like, respectively). We show that these phenotypes can be distinguished also by sensitivity to AluI digestion where the malignant cells are resistant to digestion relative to non-malignant cells. Reversion of the T4-2 breast cancer cells by either cAMP analogs, or a phospatidylinositol 3-kinase (P13K) inhibitor not only reverted the phenotype, but also the chromatin sensitivity to AluI. By using different cAMP-analogs, we show that the cAMP-induced phenotypic reversion, polarization, and shift in DNA organization act through a cAMP-dependent-protein-kinase A-coupled signaling pathway. Importantly, inhibitory antibody to fibronectin also reverted the malignant phenotype, polarized the acini, and changed chromatin sequestration. These experiments show not only that modifying the tumor microenvironment can alter the organization of tumor cells but also that architecture of the …

For long-lived intermediate-level radioactive waste, the useof concrete as engineering barrier and Callovian-Oxfordian clay asgeological barrier at a depth of 500 m is considered in the Frenchdisposal concept (ANDRA, 2005). Upon emplacement, initially unsaturatedconcrete is expected to experience coupled processes involving heating,re-saturation with groundwater from the clay formation, gas exchanges andgeochemical reactions. After an early period of re-saturation, solutetransport is supposed to be diffusion-controlled because of the extremelylow permeability of the two media. These coupled processes may lead tochanges in the porosity of the concrete or clay barriers. In the presentpaper, a fully coupled Thermo-Hydro-Chemical (THC) response of atwo-phase (gas and solution) mass-transfer model was evaluated and testedby a sensitivity analysis. This study is an extension of a previous modelapplied to an isothermal and fully saturated concrete/clay interface(Burnol et al., 2005); it investigated the coupled effect of temperatureand unsaturated conditions assuming no production of H2(g). The systemwas simulated for a 2000-year period, which covers the most predominantthermal perturbation.

We present strange particle spectra and yields measured atmid-rapidity in sqrt text s=200 GeV proton-proton (p+p) collisions atRHIC. We find that the previously observed universal transverse mass(mathrm mT \equiv\sqrt mathrm p_T 2+\mathrm m2) scaling of hadronproduction in p+p collisions seems to break down at higher \mt and thatthere is a difference in the shape of the \mt spectrum between baryonsand mesons. We observe mid-rapidity anti-baryon to baryon ratios nearunity for Lambda and Xi baryons and no dependence of the ratio ontransverse momentum, indicating that our data do not yet reach thequark-jet dominated region. We show the dependence of the mean transversemomentum (\mpt) on measured charged particle multiplicity and on particlemass and infer that these trends are consistent with gluon-jet dominatedparticle production. The data are compared to previous measurements fromCERN-SPS, ISR and FNAL experiments and to Leading Order (LO) and Next toLeading order (NLO) string fragmentation model predictions. We infer fromthese comparisons that the spectral shapes and particle yields from $p+p$collisions at RHIC energies have large contributions from gluon jetsrather than quark jets.

A summary is given of presentations and discussions in theLaser-Plasma Acceleration Working Group at the 2006 Advanced AcceleratorConcepts Workshop. Presentation highlights include: widespreadobservation of quasi-monoenergetic electrons; good agreement betweenmeasured and simulated beam properties; the first demonstration oflaser-plasma acceleration up to 1 GeV; single-shot visualization of laserwakefield structure; new methods for measuring<100 fs electronbunches; and new methods for "machining" laser-plasma acceleratorstructures. Discussion of future direction includes: developing a roadmapfor laser-plasma acceleration beyond 1 GeV; a debate over injection andguiding; benchmarking simulations with improved wake diagnostics;petawatt laser technology for future laser-plasmaaccelerators.