Data report: electron microprobe investigation of primary minerals in basalts from the west philippine sea basin (ocean drilling program leg 195, site 1201)

The basement cored at Site 1201 (west Philippine Basin) during Ocean Drilling Program Leg 195 consists of a 91-m-thick sequence of basalts, mostly pillow lavas and perhaps one sheet lava flow, with a few intercalations of hyaloclastite and interpillow sedimentary material. Hydrothermal alteration pervasively affected the basalt sequence, giving rise to a variety of secondary minerals such as K-Fe-Mg-clay minerals, oxyhydroxides and clay minerals mixtures, natrolite group zeolites, analcite, alkali feldspar, and carbonate. The primary minerals of pillow and sheet basalts that survived the intense hydrothermal alteration were investigated by electron microprobe with the aim of characterizing their chemical composition and variability. The primary minerals are mostly plagioclase, ranging in composition from bytownite through labradorite to andesine, chromian-magnesian-diopside, and spinels, both Ti magnetite (partially maghemitized) and chromian spinel. Overall, the chemical features of the primary minerals of Site 1201 basalts correspond to the primitive character of the bulk rocks, suggesting that the parent magma of these basalts was a mafic tholeiitic magma that most likely only suffered limited fractional crystallization and crystallized at high temperatures (slightly below 1200°C) and under increasing ƒO2 conditions. The major element composition of clinopyroxene suggests a backarc affinity of the mantle source of Site 1201 basement

Modelling diverse root density dynamics and deep nitrogen uptake — a simple approach

We present a 2-D model for simulation of root density and plant nitrogen (N) uptake for crops grown in agricultural systems, based on a modification of the root density equation originally proposed by Gerwitz and Page in J Appl Ecol 11:773–781, (1974). A root system form parameter was introduced to describe the distribution of root length vertically and horizontally in the soil profile. The form parameter can vary from 0 where root density is evenly distributed through the soil profile, to 8 where practically all roots are found near the surface. The root model has other components describing root features, such as specific root length and plant N uptake kinetics. The same approach is used to distribute root length horizontally, allowing simulation of root growth and plant N uptake in row crops. The rooting depth penetration rate and depth distribution of root density were found to be the most important parameters controlling crop N uptake from deeper soil layers. The validity of the root distribution model was tested with field data for white cabbage, red beet, and leek. The model was able to simulate very different root distributions, but it was not able to simulate increasing root density with depth as seen in the experimental results for white cabbage. The model was able to simulate N depletion in different soil layers in two field studies. One included vegetable crops with very different rooting depths and the other compared effects of spring wheat and winter wheat. In both experiments variation in spring soil N availability and depth distribution was varied by the use of cover crops. This shows the model sensitivity to the form parameter value and the ability of the model to reproduce N depletion in soil layers. This work shows that the relatively simple root model developed, driven by degree days and simulated crop growth, can be used to simulate crop soil N uptake and depletion appropriately in low N input crop production systems, with a requirement of few measured parameters

Scalable Similarity Search for Molecular Descriptors

Similarity search over chemical compound databases is a fundamental task in the discovery and design of novel drug-like molecules. Such databases often encode molecules as non-negative integer vectors, called molecular descriptors, which represent rich information on various molecular properties. While there exist efficient indexing structures for searching databases of binary vectors, solutions for more general integer vectors are in their infancy. In this paper we present a time- and space- efficient index for the problem that we call the succinct intervals-splitting tree algorithm for molecular descriptors (SITAd). Our approach extends efficient methods for binary-vector databases, and uses ideas from succinct data structures. Our experiments, on a large database of over 40 million compounds, show SITAd significantly outperforms alternative approaches in practice.Comment: To be appeared in the Proceedings of SISAP'1

Temperature and volatile organic compound concentrations as controlling factors for chemical composition of alpha-pinene-derived secondary organic aerosol

This work investigates the individual and combined effects of temperature and volatile organic compound precursor concentrations on the chemical composition of particles formed in the dark ozonolysis of alpha-pinene. All experiments were conducted in a 5m(3) Teflon chamber at an initial ozone concentration of 100 ppb and initial alpha-pinene concentrations of 10 and 50 ppb, respectively; at constant temperatures of 20, 0, or -15 degrees C; and at changing temperatures (ramps) from -15 to 20 and from 20 to -15 degrees C. The chemical composition of the particles was probed using a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). A four-factor solution of a positive matrix factorization (PMF) analysis of the combined HR-ToF-AMS data is presented. The PMF analysis and the elemental composition analysis of individual experiments show that secondary organic aerosol particles with the highest oxidation level are formed from the lowest initial alpha-pinene concentration (10 ppb) and at the highest temperature (20 degrees C). A higher initial alpha-pinene concentration (50 ppb) and/or lower temperature (0 or -15 degrees C) results in a lower oxidation level of the molecules contained in the particles. With respect to the carbon oxidation state, particles formed at 0 degrees C are more comparable to particles formed at 15 degrees C than to those formed at 20 degrees C. A remarkable observation is that changes in temperature during particle formation result in only minor changes in the elemental composition of the particles. Thus, the temperature at which aerosol particle formation is induced seems to be a critical parameter for the particle elemental composition. Comparison of the HR-ToF-AMS-derived estimates of the content of organic acids in the particles based on m/z 44 in the mass spectra show good agreement with results from off-line molecular analysis of particle filter samples collected from the same experiments. Higher temperatures are associated with a decrease in the absolute mass concentrations of organic acids (R-COOH) and organic acid functionalities (-COOH), while the organic acid functionalities account for an increasing fraction of the measured particle mass.Peer reviewe

Resolving the shocked gas in HH54 with Herschel: CO line mapping at high spatial and spectral resolution

The HH54 shock is a Herbig-Haro object, located in the nearby Chamaeleon II cloud. Observed CO line profiles are due to a complex distribution in density, temperature, velocity, and geometry. Resolving the HH54 shock wave in the far-infrared cooling lines of CO constrain the kinematics, morphology, and physical conditions of the shocked region. We used the PACS and SPIRE instruments on board the Herschel space observatory to map the full FIR spectrum in a region covering the HH54 shock wave. Complementary Herschel-HIFI, APEX, and Spitzer data are used in the analysis as well. The observed features in the line profiles are reproduced using a 3D radiative transfer model of a bow-shock, constructed with the Line Modeling Engine code (LIME). The FIR emission is confined to the HH54 region and a coherent displacement of the location of the emission maximum of CO with increasing J is observed. The peak positions of the high-J CO lines are shifted upstream from the lower J CO lines and coincide with the position of the spectral feature identified previously in CO(10-9) profiles with HIFI. This indicates a hotter molecular component in the upstream gas with distinct dynamics. The coherent displacement with increasing J for CO is consistent with a scenario where IRAS12500-7658 is the exciting source of the flow, and the 180 K bow-shock is accompanied by a hot (800 K) molecular component located upstream from the apex of the shock and blueshifted by -7 km s$^{-1}$. The spatial proximity of this knot to the peaks of the atomic fine-structure emission lines observed with Spitzer and PACS ([OI]63, 145 $\mu$m) suggests that it may be associated with the dissociative shock as the jet impacts slower moving gas in the HH54 bow-shock.Comment: 6 pages, 5 figure

Engineering yeast for high-level production of stilbenoid antioxidants

Stilbenoids, including resveratrol and its methylated derivatives, are natural potent antioxidants, produced by some plants in trace amounts as defense compounds. Extraction of stilbenoids from natural sources is costly due to their low abundance and often limited availability of the plant. Here we engineered the yeast Saccharomyces cerevisiae for production of stilbenoids on a simple mineral medium typically used for industrial production. We applied a pull-push-block strain engineering strategy that included overexpression of the resveratrol biosynthesis pathway, optimization of the electron transfer to the cytochrome P450 monooxygenase, increase of the precursors supply, and decrease of the pathway intermediates degradation. Fed-batch fermentation of the final strain resulted in a final titer of 800 mg l(-1) resveratrol, which is by far the highest titer reported to date for production of resveratrol from glucose. We further integrated heterologous methyltransferases into the resveratrol platform strain and hereby demonstrated for the first time de novo biosynthesis of pinostilbene and pterostilbene, which have better stability and uptake in the human body, from glucose

Bias and temperature dependence of the 0.7 conductance anomaly in Quantum Point Contacts

The 0.7 (2e^2/h) conductance anomaly is studied in strongly confined, etched GaAs/GaAlAs quantum point contacts, by measuring the differential conductance as a function of source-drain and gate bias as well as a function of temperature. We investigate in detail how, for a given gate voltage, the differential conductance depends on the finite bias voltage and find a so-called self-gating effect, which we correct for. The 0.7 anomaly at zero bias is found to evolve smoothly into a conductance plateau at 0.85 (2e^2/h) at finite bias. Varying the gate voltage the transition between the 1.0 and the 0.85 (2e^2/h) plateaus occurs for definite bias voltages, which defines a gate voltage dependent energy difference $\Delta$. This energy difference is compared with the activation temperature T_a extracted from the experimentally observed activated behavior of the 0.7 anomaly at low bias. We find \Delta = k_B T_a which lends support to the idea that the conductance anomaly is due to transmission through two conduction channels, of which the one with its subband edge \Delta below the chemical potential becomes thermally depopulated as the temperature is increased.Comment: 9 pages (RevTex) with 9 figures (some in low resolution

High-pressure, low-abundance water in bipolar outflows. Results from a Herschel-WISH survey

(Abridged) We present a survey of the water emission in a sample of more than 20 outflows from low mass young stellar objects with the goal of characterizing the physical and chemical conditions of the emitting gas. We have used the HIFI and PACS instruments on board the Herschel Space Observatory to observe the two fundamental lines of ortho-water at 557 and 1670 GHz. These observations were part of the "Water In Star-forming regions with Herschel" (WISH) key program, and have been complemented with CO and H2 data. We find that the emission from water has a different spatial and velocity distribution from that of the J=1-0 and 2-1 transitions of CO, but it has a similar spatial distribution to H2, and its intensity follows the H2 intensity derived from IRAC images. This suggests that water traces the outflow gas at hundreds of kelvins responsible for the H2 emission, and not the component at tens of kelvins typical of low-J CO emission. A warm origin of the water emission is confirmed by a remarkable correlation between the intensities of the 557 and 1670 GHz lines, which also indicates the emitting gas has a narrow range of excitations. A non-LTE radiative transfer analysis shows that while there is some ambiguity on the exact combination of density and temperature values, the gas thermal pressure nT is constrained within less than a factor of 2. The typical nT over the sample is 4 10^{9} cm^{-3}K, which represents an increase of 10^4 with respect to the ambient value. The data also constrain within a factor of 2 the water column density. When this quantity is combined with H2 column densities, the typical water abundance is only 3 10^{-7}, with an uncertainty of a factor of 3. Our data challenge current C-shock models of water production due to a combination of wing-line profiles, high gas compressions, and low abundances.Comment: 21 pages, 13 figures. Accepted for publication in A&