This report talks about Integrated Safety Management Summit i Knoxville, TN

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's …

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We have studied the oxidation of carbon monoxide over a lanthanum substituted perovskite (La0.5Sr0.5CoO3-d) catalyst prepared by spray pyrolysis. Under the assumption of a first-order kinetics mechanism for CO, it has been found that the activation energy barrier of the reaction changes from 80 to 40 kJ mol-1 at a threshold temperature of ca. 320 oC. In situ XPS near-ambient pressure ( 0.2 torr) shows that the gas phase oxygen concentration over the sample decreases sharply at ca. 300 oC. These two observations suggest that the oxidation of CO undergoes a change of mechanism at temperatures higher than 300 oC.

Article on 7-chloro-2-methylamino-5-phenyl-3H-1, 4-benzodiazepine-4-oxide, 7-chloro-1, 3-dihydro-1-methyl-5-phenyl-2H-1, 4-benzodiazepin-2-one, and 7-chloro-5-(2-chlorophenyl)-3-hydroxy-1, 3-dihydro-1, 4-benzodiazepin-2-one in (propane-1, 2-diol + water) at a temperature of 303.2 K.

This report talks about Approach to a Fully Integrated Performance Assurance System.

This report addresses the development of the Hanford site chronic beryllium disease prevention program.

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Tritium reservoirs are constructed from welded stainless steel forgings. While these steels are highly resistant to the embrittling effects of hydrogen isotopes and helium from tritium decay; they are not immune. Tritium embrittlement is an enhanced form of hydrogen embrittlement because of the presence of helium-3 from tritium decay which nucleates as nanometer-sized bubbles on dislocations, grain boundaries, and other microstructural defects. Steels with decay helium bubble microstructures are hardened and less able to deform plastically and become more susceptible to embrittlement by hydrogen and its isotopes. Ductility, elongation-to-failure, and fracture toughness are reduced by exposures to tritium and the reductions increase with time as helium-3 builds into the material from tritium permeation and radioactive decay. Material and forging specifications have been developed for optimal material compatibility with tritium. These specifications cover composition, mechanical properties, and select microstructural characteristics like grain size, flow-line orientation, inclusion content, and ferrite distribution. For many years, the forming process of choice for reservoir manufacturing was high-energy-rate forging (HERF), principally because the DOE forging facility owned only HERF hammers. Today, some reservoir forgings are being made that use a conventional, more common process known as press forging (PF or CF). One of the chief differences …

The chiral supramolecular catalyst Ga{sub 4}L{sub 6} [L = 1,5-bis(2,3-dihydroxybenzoylamino)naphthalene] is a molecular tetrahedron that catalyzes the 3-aza-Cope rearrangement of allyl enammonium cations. This catalysis is accomplished by preorganizing the substrate in a reactive conformation within the host. This work demonstrates that through the use of enantiopure assembly, its chiral cavity is capable of catalyzing the 3-aza-Cope rearrangement enantioselectively, with yields of 21-74% and enantiomeric excesses from 6 to 64% at 50 C. At lower temperatures, the enantioselectivity improved, reaching 78% ee at 5 C. This is the highest enantioselectivity to date induced by the chiral cavity of a supramolecular assembly.

The authors demonstrate distribution of a 2850 MHz rf signal over stabilized optical fiber links. For a 2.2 km link they measure an rms drift of 19.4 fs over 60 h, and for a 200 m link an rms drift of 8.4 fs over 20 h. The rf signals are transmitted as amplitude modulation on a continuous optical carrier. Variations in the delay length are sensed using heterodyne interferometry and used to correct the rf phase. The system uses standard fiber telecommunications components.

Article on the effects of different concentrations of poly(vinyl pyrrolidone) on the solubility of lamotrigine and diazepam in ethanol and water mixtures at 298.2 K.

Francisella tularensis, the causative agent of the zoonotic disease tularemia, has recently gained increased attention due to the emergence of tularemia in geographical areas where the disease has been previously unknown, and the organism's potential as a bioterrorism agent. Although F. tularensis has an extremely broad host range, the bacterial reservoir in nature has not been conclusively identified. In this study, the ability of virulent F. tularensis strains to survive and replicate in the amoeba Acanthamoeba castellanii was explored. We observe that A. castellanii trophozoites rapidly encyst in response to F. tularensis infection and that this rapid encystment phenotype (REP) is caused by factor(s) secreted by amoebae and/or F. tularensis into the co-culture media. Further, our results indicate that in contrast to LVS, virulent strains of F. tularensis can survive in A. castellanii cysts for at least 3 weeks post infection and that induction of rapid amoeba encystment is essential for survival. In addition, our data indicate that pathogenic F. tularensis strains block lysosomal fusion in A. castellanii. Taken together, these data suggest that the interactions between F. tularensis strains and amoeba may play a role in the environmental persistence of F. tularensis.

Sub-micron sized airborne particulate matter is not collected well on regular quartz or glass fiber filter papers. We used a micro-orifice uniform deposit impactor (MOUDI) to size fractionate particulate matter (PM) into six size fractions and deposit it on specially designed high purity thin aluminum disks. The MOUDI separated PM into fractions 56-100 nm, 100-180 nm, 180-320 nm, 320-560 nm, 560-1000 nm, and 1000-1800 nm. Since MOUDI have low flow rates, it takes several days to collect sufficient carbon on 47 mm foil disks. The small carbon mass (20-200 microgram C) and large aluminum substrate ({approx}25 mg Al) presents several challenges to production of graphite targets for accelerator mass spectrometry (AMS) analysis. The Al foil consumes large amounts of oxygen as it is heated and tends to melt into quartz combustion tubes, causing gas leaks. We describe sample processing techniques to reliably produce graphitic targets for {sup 14}C-AMS analysis of PM deposited on Al impact foils.

Development of effective and durable breast cancer treatment strategies requires a mechanistic understanding of the influence of the microenvironment on response. Previous work has shown that cellular signaling pathways and cell morphology are dramatically influenced by three-dimensional (3D) cultures as opposed to traditional two-dimensional (2D) monolayers. Here, we compared 2D and 3D culture models to determine the impact of 3D architecture and extracellular matrix (ECM) on HER2 signaling and on the response of HER2-amplified breast cancer cell lines to the HER2-targeting agents Trastuzumab, Pertuzumab and Lapatinib. We show that the response of the HER2-amplified AU565, SKBR3 and HCC1569 cells to these anti-HER2 agents was highly dependent on whether the cells were cultured in 2D monolayer or 3D laminin-rich ECM gels. Inhibition of {beta}1 integrin, a major cell-ECM receptor subunit, significantly increased the sensitivity of the HER2-amplified breast cancer cell lines to the humanized monoclonal antibodies Trastuzumab and Pertuzumab when grown in a 3D environment. Finally, in the absence of inhibitors, 3D cultures had substantial impact on HER2 downstream signaling and induced a switch between PI3K-AKT- and RAS-MAPKpathway activation in all cell lines studied, including cells lacking HER2 amplification and overexpression. Our data provide direct evidence that breast cancer cells are …

Prostate epithelial cells grown embedded in laminin-rich extracellular matrix (lrECM) undergo morphological changes that closely resemble their architecture in vivo. In this study, growth characteristics of three human prostate epithelial sublines derived from the same cellular lineage, but displaying different tumorigenic and metastatic properties in vivo, were assessed in three-dimensional (3D) lrECM gels. M12, a highly tumorigenic and metastatic subline, was derived from the parental prostate epithelial P69 cell line by selection in nude mice and found to contain a deletion of 19p-q13.1. The stable reintroduction of an intact human chromosome 19 into M12 resulted in a poorly tumorigenic subline, designated F6. When embedded in lrECM gels, the nontumorigenic P69 line produced acini with clearly defined lumena. Immunostaining with antibodies to {beta}-catenin, E-cadherin or {alpha}6-, {beta}4- and {beta}1-integrins showed polarization typical of glandular epithelium. In contrast, the metastatic M12 subline produced highly disorganized cells with no evidence of polarization. The F6 subline reverted to acini-like structures exhibiting basal polarity marked with integrins. Reducing either vimentin levels via siRNA interference or {beta}1-integrin expression by the addition of the blocking antibody, AIIB2, reorganized the M12 subline into forming polarized acini. The loss of vimentin significantly reduced M12-Vim tumor growth when assessed by …

Cosmic-rays with energies up to 3x1020 eV have been observed. The nuclear composition of these cosmic rays is unknown but if the incident nuclei are protons then the corresponding center of mass energy is sqrt snn = 700 TeV. High energy muons can be used to probe the composition of these incident nuclei. The energy spectra of high-energy (> 1 TeV) cosmic ray induced muons have been measured with deep underground or under-ice detectors. These muons come from pion and kaon decays and from charm production in the atmosphere. Terrestrial experiments are most sensitive to far-forward muons so the production rates aresensitive to high-x partons in the incident nucleus and low-x partons in the nitrogen/oxygen targets. Muon measurements can complement the central-particle data collected at colliders.This paper will review muon production data and discuss some non-perturbative (soft) models that have been used to interpret the data. I will show measurements of TeV muon transverse momentum (pT) spectra in cosmic-ray air showers fromMACRO, and describe how the IceCube neutrino observatory and the proposed Km3Net detector will extend these measurements to a higher pT region where perturbative QCD should apply. With a 1 km2 surface area, the full IceCube detector should observe …

Article on switchgrass (Panicum virgatum) possessing a divergent family of cinnamoyl CoA reductases with distinct biochemical properties.

Various forms of matter may be produced in ultra-relativistic heavy ion collisions. These are the Quark GluonPlasma, the Color Glass Condensate , the Glasma and Quarkyoninc Matter. A novel effect that may beassociated with topological charge fluctuations is the Chiral Magnetic Effect. I explain these concepts andexplain how they may be seen in ultra-relatvistic heavy ion collisions

To provide polarized electron-proton collisions of {radical}s = 100 GeV; addition of a 10 GeV electron accelerator to the existing RHIC facility is currently under study. Two design lines are under consideration: a self-polarizing electron ring, and an energy recovery linac. While the latter provides significantly higher luminosities, it is technologically very challenging. We present both design approaches and discuss their advantages and limitations.

Article discussing research on the correlation and prediction of solute transfer to chloroalkanes from both water and the gas phase.

The reweighting method is applied to improve the chiral property of domain-wall fermions. One way to achieve this is to enlarge L{sub s}, the size of fifth dimension, which controls the size of the induced chiral symmetry breaking. While this is a type of reweighting method for shifting the action parameter, it seems non-trivial since this reweighting means change of the five dimensional lattice volume. In this report, we address issues in this direction of reweighting and evaluate its effectiveness.

The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.