Showing papers by "DSM published in 2010"

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

Abstract: The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.

Combined Measurement and QCD Analysis of the Inclusive e± p Scattering Cross Sections at HERA

Abstract: A combination is presented of the inclusive deep inelastic cross sections measured by the H1 and ZEUS Collaborations in neutral and charged current unpolarised e(+/-)p scattering at HERA during the period 1994-2000. The data span six orders of magnitude in negative four-momentum-transfer squared, Q(2), and in Bjorken x. The combination method used takes the correlations of systematic uncertainties into account, resulting in an improved accuracy. The combined data are the sole input in a NLO QCD analysis which determines a new set of parton distributions, HERAPDF1.0, with small experimental uncertainties. This set includes an estimate of the model and parametrisation uncertainties of the fit result.

Quasar feedback revealed by giant molecular outflows

Abstract: In the standard scenario for galaxy evolution young star-forming galaxies transform into red bulge-dominated spheroids, where star formation has been quenched. To explain this transformation, a strong negative feedback generated by accretion onto a central super-massive black hole is often invoked. The depletion of gas resulting from quasar-driven outflows should eventually stop star-formation across the host galaxy and lead the black hole to “suicide” by starvation. Direct observational evidence for a major quasar feedback onto the host galaxy is still missing, because outflows previously observed in quasars are generally associated with the ionized component of the gas, which only accounts for a minor fraction of the total gas content, and typically occurrs in the central regions. We used the IRAM PdB Interferometer to observe the CO(1-0) transition in Mrk 231, the closest quasar known. Thanks to the wide band we detected broad wings of the CO line, with velocities of up to 750 km s-1 and spatially resolved on the kpc scale. These broad CO wings trace a giant molecular outflow of about 700 /year, far larger than the ongoing star-formation rate (~200 /year) observed in the host galaxy. This wind will totally expel the cold gas reservoir in Mrk 231 in about 107 yrs, therefore halting the star-formation activity on the same timescale. The inferred kinetic energy in the molecular outflow is ~1.2 × 1044 erg/s, corresponding to a few percent of the AGN bolometric luminosity, which is very close to the fraction expected by models ascribing quasar feedback to highly supersonic shocks generated by radiatively accelerated nuclear winds. Instead, the contribution by the SNe associated with the starburst fall short by several orders of magnitude to account for the kinetic energy observed in the outflow. The direct observational evidence for quasar feedback reported here provides solid support to the scenarios ascribing the observed properties of local massive galaxies to quasar-induced large-scale winds.

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

Abstract: DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org).

The dependence of Type Ia Supernovae luminosities on their host galaxies

Abstract: (Abridged) Precision cosmology with Type Ia supernovae (SNe Ia) makes use of the fact that SN Ia luminosities depend on their light-curve shapes and colours. Using Supernova Legacy Survey (SNLS) and other data, we show that there is an additional dependence on the global characteristics of their host galaxies: events of the same light-curve shape and colour are, on average, 0.08mag (~4.0sigma) brighter in massive host galaxies (presumably metal-rich) and galaxies with low specific star-formation rates (sSFR). SNe Ia in galaxies with a low sSFR also have a smaller slope ("beta") between their luminosities and colours with ~2.7sigma significance, and a smaller scatter on SN Ia Hubble diagrams (at 95% confidence), though the significance of these effects is dependent on the reddest SNe. SN Ia colours are similar between low-mass and high-mass hosts, leading us to interpret their luminosity differences as an intrinsic property of the SNe and not of some external factor such as dust. If the host stellar mass is interpreted as a metallicity indicator, the luminosity trends are in qualitative agreement with theoretical predictions. We show that the average stellar mass, and therefore the average metallicity, of our SN Ia host galaxies decreases with redshift. The SN Ia luminosity differences consequently introduce a systematic error in cosmological analyses, comparable to the current statistical uncertainties on parameters such as w. We show that the use of two SN Ia absolute magnitudes, one for events in high-mass (metal-rich) galaxies, and one for events in low-mass (metal-poor) galaxies, adequately corrects for the differences. Cosmological fits incorporating these terms give a significant reduction in chi^2 (3.8-4.5sigma). We conclude that future SN Ia cosmological analyses should use a correction of this (or similar) form to control demographic shifts in the galaxy population.

Check your cultures! A list of cross-contaminated or misidentified cell lines.

Abstract: Continuous cell lines consist of cultured cells derived from a specific donor and tissue of origin that have acquired the ability to proliferate indefinitely. These cell lines are well-recognized models for the study of health and disease, particularly for cancer. However, there are cautions to be aware of when using continuous cell lines, including the possibility of contamination, in which a foreign cell line or microorganism is introduced without the handler's knowledge. Cross-contamination, in which the contaminant is another cell line, was first recognized in the 1950s but, disturbingly, remains a serious issue today. Many cell lines become cross-contaminated early, so that subsequent experimental work has been performed only on the contaminant, masquerading under a different name. What can be done in response—how can a researcher know if their own cell lines are cross-contaminated? Two practical responses are suggested here. First, it is important to check the literature, looking for previous work on cross-contamination. Some reports may be difficult to find and to make these more accessible, we have compiled a list of known cross-contaminated cell lines. The list currently contains 360 cell lines, drawn from 68 references. Most contaminants arise within the same species, with HeLa still the most frequently encountered (29%, 106/360) among human cell lines, but interspecies contaminants account for a small but substantial minority of cases (9%, 33/360). Second, even if there are no previous publications on cross-contamination for that cell line, it is essential to check the sample itself by performing authentication testing.

Quasar feedback revealed by giant molecular outflows

Abstract: In the standard scenario for galaxy evolution young star-forming galaxies transform into red bulge-dominated spheroids, where star formation has been quenched. To explain such a transformation, a strong negative feedback generated by accretion onto a super-massive black hole is often invoked. The depletion of gas resulting from quasar-driven outflows should eventually stop star-formation in the host galaxy and lead the black hole to "suicide" for starvation. Direct observational evidence for a major quasar feedback onto the host galaxy is still missing, since outflows previously observed in quasars are generally associated with the ionized component of the gas, which only accounts for a minor fraction of the total gas content, and typically occurring in the central regions. We used the IRAM PdB Interferometer to observe CO(1-0) in Mrk 231, the closest QSO known. Thanks to the wide band we detect broad wings of the CO line, with velocities up to 750 km/s and spatially resolved on the kpc scale. Such broad CO wings trace a giant molecular outflow of about 700 MSun/yr, far larger than the ongoing star-formation rate (~200 MSun/yr) observed in the host galaxy. This wind will totally expel the cold gas reservoir in Mrk 231 in about 1e7 yrs, therefore halting the star-formation activity on the same timescale. The inferred kinetic energy in the molecular outflow is ~1.2e44 erg/s, corresponding to a few percent of the AGN bolometric luminosity, very close to the fraction expected by models ascribing quasar feedback to highly supersonic shocks generated by radiatively accelerated nuclear winds. The direct observational evidence for quasar feedback reported here provides solid support to the scenarios ascribing the observed properties of local massive galaxies to quasar-induced large scale winds.

The Fourth IBIS/ISGRI Soft Gamma-ray Survey Catalog

Abstract: In this paper, we report on the fourth soft gamma-ray source catalog obtained with the IBIS gamma-ray imager on board the INTEGRAL satellite. The scientific data set is based on more than 70 Ms of high-quality observations performed during the first five and a half years of the Core Program and public observations. Compared to previous IBIS surveys, this catalog includes a substantially increased coverage of extragalactic fields, and comprises more than 700 high-energy sources detected in the energy range 17-100 keV, including both transients and faint persistent objects that can only be revealed with longer exposure times. A comparison is provided with the latest Swift/BAT survey results.

The mechanism of the modified Ullmann reaction

Abstract: The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols) made these reactions truly catalytic, with catalyst amounts as low as 1 mol% or even lower. Since these catalysts are homogeneous, it has opened up the possibility to investigate the mechanism of these modified Ullmann reactions. Most authors agree that Cu(I) is the true catalyst even though Cu(0) and Cu(II) catalysts have also shown to be active. It should be noted however that Cu(I) is capable of reversible disproportionation into Cu(0) and Cu(II). In the first step, the nucleophile displaces the halide in the LnCu(I)X complex forming LnCu(I)ZR (Z = O, NR′, S). Quite a number of mechanisms have been proposed for the actual reaction of this complex with the aryl halide: 1. Oxidative addition of ArX forming a Cu(III) intermediate followed by reductive elimination; 2. Sigma bond metathesis; in this mechanism copper remains in the Cu(II) oxidation state; 3. Single electron transfer (SET) in which a radical anion of the aryl halide is formed (Cu(I)/Cu(II)); 4. Iodine atom transfer (IAT) to give the aryl radical (Cu(I)/Cu(II)); 5. π-complexation of the aryl halide with the Cu(I) complex, which is thought to enable the nucleophilic substitution reaction. Initially, the radical type mechanisms 3 and 4 where discounted based on the fact that radical clock-type experiments with ortho-allyl aryl halides failed to give the cyclised products. However, a recent DFT study by Houk, Buchwald and co-workers shows that the modified Ullmann reaction between aryl iodide and amines or primary alcohols proceeds either via an SET or an IAT mechanism. Van Koten has shown that stalled aminations can be rejuvenated by the addition of Cu(0), which serves to reduce the formed Cu(II) to Cu(I); this also corroborates a Cu(I)/Cu(II) mechanism. Thus the use of radical clock type experiments in these metal catalysed reactions is not reliable. DFT calculations from Hartwig seem to confirm a Cu(I)/Cu(III) type mechanism for the amidation (Goldberg) reaction, although not all possible mechanisms were calculated.

The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea

Abstract: Dinoroseobacter shibae DFL12T, a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12T is able to synthesize the vitamins B1 and B12 for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B12 are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B12 was confirmed to be functional, and D. shibae DFL12T was shown to provide the growth-limiting vitamins B1 and B12 to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12T is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12T has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12T shows the most complex viral defense system of all Rhodobacterales sequenced to date.

Fragmentation and mass segregation in the massive dense cores of Cygnus X

Abstract: Massive dense cores (MDCs) are the high-mass equivalent of the so-called dense cores in nearby star-forming regions With typical sizes of 01 pc, they could form either a few high-mass stars, or a cluster of low-mass stars We present high-angular resolution continuum observations obtained with the IRAM Plateau de Bure interferometer at 13 and 35 mm towards the six most massive and youngest (IR-quiet) dense cores in the Cygnus X complex Located at only 17 kpc, the Cygnus X region offers the opportunity of reaching small enough scales (of the order of 1700 AU at 13 mm) to separate individual collapsing objects, and thus to observe and constrain the result of the fragmentation process The cores are sub-fragmented with a total of 23 fragments inside 5 cores Only the most compact MDC, CygX-N63, may host a single proto-stellar object with an envelope as massive as ˜60 M_ȯ The fragments in the other cores have sizes and separations similar to low-mass pre-stellar condensations and Class 0 young stellar objects in nearby protoclusters, and are most probably self-gravitating objects (M > Mvir) In addition to CygX-N63, a total of 8 objects are found to be probable precursors of OB stars with their envelope masses ranging from 84 to 30 M_ȯ inside a FWHM of 4000 AU The level of fragmentation is globally higher than in the turbulence regulated, monolithic collapse scenario, but it is also not as high as expected in a pure gravo-turbulent scenario where the distribution of mass is dominated by low-mass protostars/stars Here, the fractions of the total MDC masses in the high-mass proto-stellar fragments are found to be as high as 37, 58, and 100% in CygX-N12, CygX-N53, and CygX-N63, respectively These high fractions of mass in the proto-stellar fragments are also indicative of a high efficiency of core formation in the MDCs The increase in the core formation efficiency as a function of average density in the MDCs is proposed to be caused by the increasing importance of self-gravity leading to gravitational collapse on the scale of the MDCs At the same time, the observed MDCs tend to fragment into a few proto-stellar objects within their central regions We are therefore probably witnessing the primordial mass segregation of clusters The physical origin of the fragmentation into a few high-mass objects is not yet clear, and will be investigated in the future by studying the kinematics of the MDCs

Nutrition and immunity: an update

Abstract: Immunity encompasses all mechanisms and responses used by the organism to defend itself against bacteria, viruses or parasites. Adequate supply and balance of nutrients are required for proper efficiency of the host defences. Research has identified dietary factors that affect human and animal immune responses like amino acids, fatty acids, minerals and vitamins. Some of these nutrients have been proven to have specific actions on immunity when provided at pharmacological doses. This paper will review these nutrients and their current use in aquaculture. The immune system is an efficient but complex system. Its complexity has made the assessment of the effects of diets difficult. Nevertheless, the standardization of methodology as well as the use of new techniques at the cell or the gene level should help to better understand the mechanisms of immune modulation. This paper will review the major functions of fish and shrimp immune system and the methodologies used. Cellular and humoral functions including cytokines will be discussed in relation to potential means to modulate them and the underlying mechanism. A better understanding of the mechanisms of modulation of the immune functions should help in the discovery of new dietary factors to improve the immune status of the animal, leading to better disease resistance.

Tracking the impact of environment on the galaxy stellar mass function up to z ~ 1 in the 10 k zCOSMOS sample

Abstract: We study the impact of the environment on the evolution of galaxies in the zCOSMOS 10 k sample in the redshift range 0.1 ≤ z ≤ 1.0 over an area of ~1.5 deg^2. The considered sample of secure spectroscopic redshifts contains about 8500 galaxies, with their stellar masses estimated by SED fitting of the multiwavelength optical to near-infrared (NIR) photometry. The evolution of the galaxy stellar mass function (GSMF) in high and low density regions provides a tool to study the mass assembly evolution in different environments; moreover, the contributions to the GSMF from different galaxy types, as defined by their SEDs and their morphologies, can be quantified. At redshift z ~ 1, the GSMF is only slightly dependent on environment, but at lower redshifts the shapes of the GSMFs in high- and low-density environments become extremely different, with high density regions exhibiting a marked bimodality, not reproducible by a single Schechter function. As a result of this analysis, we infer that galaxy evolution depends on both the stellar mass and the environment, the latter setting the probability of a galaxy to have a given mass: all the galaxy properties related to the stellar mass show a dependence on environment, reflecting the difference observed in the mass functions. The shapes of the GSMFs of early- and late-type galaxies are almost identical for the extremes of the density contrast we consider, ranging from isolated galaxies to rich group members. The evolution toward z = 0 of the transition mass M_(cross), i.e., the mass at which the early- and late-type GSMFs match each other, is more rapid in high density environments, because of a difference in the evolution of the normalisation of GSMFs compared to the total one in the considered environment. The same result is found by studying the relative contributions of different galaxy types, implying that there is a more rapid evolution in overdense regions, in particular for intermediate stellar masses. The rate of evolution is different for sets of galaxy types divided on the basis of their SEDs or their morphologies, tentatively suggesting that the migration from the blue cloud to the red sequence occurs on a shorter timescale than the transformation from disc-like morphologies to ellipticals. Our analysis suggests that environmental mechanisms of galaxy transformation start to be more effective at z < 1. The comparison of the observed GSMFs to the same quantities derived from a set of mock catalogues based on semi-analytical models shows disagreement, in both low and high density environments: in particular, blue galaxies in sparse environments are overproduced in the semi-analytical models at intermediate and high masses, because of a deficit of star formation suppression, while at z < 0.5 an excess of red galaxies is present in dense environments at intermediate and low masses, because of the overquenching of satellites.

ISX is a retinoic acid-sensitive gatekeeper that controls intestinal β,β-carotene absorption and vitamin A production

Abstract: The uptake of dietary lipids from the small intestine is a complex process that depends on the activities of specific membrane receptors with yet unknown regulatory mechanisms. Using both mouse models and human cell lines, we show here that intestinal lipid absorption by the scavenger receptor class B type 1 (SR-BI) is subject to control by retinoid signaling. Retinoic acid via retinoic acid receptors induced expression of the intestinal transcription factor ISX. ISX then repressed the expression of SR-B1 and the carotenoid-15,15′-oxygenase Bcmo1. BCMO1 acts downstream of SR-BI and converts absorbed β,β-carotene to the retinoic acid precursor, retinaldehyde. Using BCMO1-knockout mice, we demonstrated increased intestinal SR-BI expression and systemic β,β-carotene accumulation. SR-BI-dependent accumulation of β,β-carotene was prevented by dietary retinoids that induced ISX expression. Thus, our study revealed a diet-responsive regulatory network that controls β,β-carotene absorption and vitamin A production by negative feedback regulation. The role of SR-BI in the intestinal absorption of other dietary lipids, including cholesterol, fatty acids, and tocopherols, implicates retinoid signaling in the regulation of lipid absorption more generally and has clinical implications for diseases associated with dyslipidemia.—Lobo, G. P., Hessel, S., Eichinger, A., Noy, N., Moise, A. R., Wyss, A., Palczewski, K., von Lintig, J. ISX is a retinoic acid-sensitive gatekeeper that controls intestinal β,β-carotene absorption and vitamin A production.

DISCOVERY OF A SUPERLUMINAL Fe K ECHO AT THE GALACTIC CENTER: THE GLORIOUS PAST OF Sgr A* PRESERVED BY MOLECULAR CLOUDS

Abstract: We present the result of a study of the X-ray emission from the galactic center (GC) molecular clouds (MCs) within 15 arcmin from Sgr A*. We use XMM-Newton data (about 1.2 Ms of observation time) spanning about eight years. The MC spectra show all the features characteristic of reflection: (1) intense Fe Kα, with equivalent width of about 0.7-1 keV, and the associated Kβ line; (2) flat power-law continuum, and (3) a significant Fe K edge (τ ~ 0.1-0.3). The diffuse low ionization Fe K emission follows the MC distribution, nevertheless not all MC are Fe K emitters. The long baseline monitoring allows the characterization of the temporal evolution of the MC emission. A complex pattern of variations is shown by the different MCs, with some having constant Fe K emission, some increasing, and some decreasing. In particular, we observe an apparent superluminal motion of a light front illuminating a molecular nebula. This might be due to a source outside the MC (such as Sgr A* or a bright and long outburst of a X-ray binary), though it cannot be due to low energy cosmic rays or a source located inside the cloud. We also observe a decrease of the X-ray emission from G0.11-0.11, behavior similar to that of Sgr B2. The line intensities, clouds dimensions, columns densities, and positions with respect to Sgr A* are consistent with being produced by the same Sgr A* flare. The required high luminosity (about 1.5 × 1039 erg s–1) can hardly be produced by a binary system, while it is in agreement with a flare of Sgr A* fading about 100 years ago. The low intensity of the Fe K emission coming from the 50 and the 20 km s–1 MC places an upper limit of 1036 erg s–1 to the mean luminosity of Sgr A* in the last 60-90 years. The Fe K emission and variations from these MC might have been produced by a single flare of Sgr A*.

CMS Tracking Performance Results from early LHC Operation.

Abstract: The first LHC pp collisions at centre-of-mass energies of 0.9 and 2.36 TeV were recorded by the CMS detector in December 2009. The trajectories of charged particles produced in the collisions were reconstructed using the all-silicon Tracker and their momenta were measured in the 3.8 T axial magnetic field. Results from the Tracker commissioning are presented including studies of timing, efficiency, signal-to-noise, resolution, and ionization energy. Reconstructed tracks are used to benchmark the performance in terms of track and vertex resolutions, reconstruction of decays, estimation of ionization energy loss, as well as identification of photon conversions, nuclear interactions, and heavy-flavour decays.

The sequence of a 1.8-Mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways

Abstract: Plasmids are mobile genetic elements that play a key role in the evolution of bacteria by mediating genome plasticity and lateral transfer of useful genetic information. Although originally considered to be exclusively circular, linear plasmids have also been identified in certain bacterial phyla, notably the actinomycetes. In some cases, linear plasmids engage with chromosomes in an intricate evolutionary interplay, facilitating the emergence of new genome configurations by transfer and recombination or plasmid integration. Genome sequencing of Streptomyces clavuligerus ATCC 27064, a Gram-positive soil bacterium known for its production of a diverse array of biotechnologically important secondary metabolites, revealed a giant linear plasmid of 1.8 Mb in length. This megaplasmid (pSCL4) is one of the largest plasmids ever identified and the largest linear plasmid to be sequenced. It contains more than 20% of the putative protein-coding genes of the species, but none of these is predicted to be essential for primary metabolism. Instead, the plasmid is densely packed with an exceptionally large number of gene clusters for the potential production of secondary metabolites, including a large number of putative antibiotics, such as staurosporine, moenomycin, beta-lactams, and enediynes. Interestingly, cross-regulation occurs between chromosomal and plasmid-encoded genes. Several factors suggest that the megaplasmid came into existence through recombination of a smaller plasmid with the arms of the main chromosome. Phylogenetic analysis indicates that heavy traffic of genetic information between Streptomyces plasmids and chromosomes may facilitate the rapid evolution of secondary metabolite repertoires in these bacteria.

High-order harmonic and attosecond pulse generation on plasma mirrors: basic mechanisms

Abstract: When an intense femtosecond laser pulse hits an optically polished surface, it generates a dense plasma that itself acts as a mirror, known as the plasma mirror. As this mirror reflects the high-intensity laser field, its nonlinear temporal response can lead to a periodic temporal distortion of the reflected wave, associated with a train of attosecond light pulses, and, in the frequency domain, to the generation of high-order harmonics of the laser. This tutorial presents detailed theoretical and numerical analysis of the two dominant harmonic generation mechanisms identified so far, coherent wake emission and the relativistic oscillating mirror. Parametric studies of the emission efficiency are presented for these two regimes, and the phase properties of the corresponding harmonics are discussed. This theoretical study is complemented by a synthesis of recent experimental results, which establishes that these two mechanisms indeed dominate harmonic generation on plasma mirrors.

Image Decomposition and Separation Using Sparse Representations: An Overview

Abstract: This paper gives essential insights into the use of sparsity and morphological diversity in image decomposition and source separation by reviewing our recent work in this field. The idea to morphologically decompose a signal into its building blocks is an important problem in signal processing and has far-reaching applications in science and technology. Starck , proposed a novel decomposition method-morphological component analysis (MCA)-based on sparse representation of signals. MCA assumes that each (monochannel) signal is the linear mixture of several layers, the so-called morphological components, that are morphologically distinct, e.g., sines and bumps. The success of this method relies on two tenets: sparsity and morphological diversity. That is, each morphological component is sparsely represented in a specific transform domain, and the latter is highly inefficient in representing the other content in the mixture. Once such transforms are identified, MCA is an iterative thresholding algorithm that is capable of decoupling the signal content. Sparsity and morphological diversity have also been used as a novel and effective source of diversity for blind source separation (BSS), hence extending the MCA to multichannel data. Building on these ingredients, we will provide an overview the generalized MCA introduced by the authors in and as a fast and efficient BSS method. We will illustrate the application of these algorithms on several real examples. We conclude our tour by briefly describing our software toolboxes made available for download on the Internet for sparse signal and image decomposition and separation.

Jet-regulated cooling catastrophe

Abstract: We present the first implementation of active galactic nuclei (AGN) feedback in the form of momentum-driven jets in an adaptive mesh refinement (AMR) cosmological resimulation of a galaxy cluster. The jets are powered by gas accretion on to supermassive black holes (SMBHs) which also grow by mergers. Throughout its formation, the cluster experiences different dynamical states: both a morphologically perturbed epoch at early times and a relaxed state at late times allowing us to study the different modes of black hole (BH) growth and associated AGN jet feedback. BHs accrete gas efficiently at high redshift (z > 2), significantly pre-heating proto-cluster haloes. Gas-rich mergers at high redshift also fuel strong, episodic jet activity, which transports gas from the proto-cluster core to its outer regions. At later times, while the cluster relaxes, the supply of cold gas on to the BHs is reduced leading to lower jet activity. Although the cluster is still heated by this activity as sound waves propagate from the core to the virial radius, the jets inefficiently redistribute gas outwards and a small cooling flow develops, along with low-pressure cavities similar to those detected in X-ray observations. Overall, our jet implementation of AGN feedback quenches star formation quite efficiently, reducing the stellar content of the central cluster galaxy by a factor of 3 compared to the no-AGN case. It also dramatically alters the shape of the gas density profile, bringing it in close agreement with the β model favoured by observations, producing quite an isothermal galaxy cluster for gigayears in the process. However, it still falls short in matching the lower than universal baryon fractions which seem to be commonplace in observed galaxy clusters.

Apparatus and methods for conduits and materials

Abstract: The present invention provides apparatus and methods for a conduit, such as an implantable conduit for a vessel. The conduit may comprise a main member and a side-branch member. The conduit may be implanted with the side-branch member initially disposed within the main member. When positioned, the side-branch member may then be extended from within the main member and into a vessel side-branch. The materials for the conduit may include circumferentially distensible and/or low recoil materials. The materials for the conduit may be constructed by various techniques and may include materials with enhanced flexibility and kink resistance.

Hydroxytyrosol promotes mitochondrial biogenesis and mitochondrial function in 3T3-L1 adipocytes.

Abstract: Hydroxytyrosol (HT) in extra-virgin olive oil is considered one of the most important polyphenolic compounds responsible for the health benefits of the Mediterranean diet for lowering incidence of cardiovascular disease, the most common and most serious complication of diabetes. We propose that HT may prevent these diseases by a stimulation of mitochondrial biogenesis that leads to enhancement of mitochondrial function and cellular defense systems. In the present study, we investigated effects of HT that stimulate mitochondrial biogenesis and promote mitochondrial function in 3T3-L1 adipocytes. HT over the concentration range of 0.1–10 μmol/L stimulated the promoter transcriptional activation and protein expression of peroxisome proliferator-activated receptor (PPAR) coactivator 1 alpha (PPARGC1α, the central factor for mitochondrial biogenesis) and its downstream targets; these included nuclear respiration factors 1 and 2 and mitochondrial transcription factor A, which leads to an increase in mitochondrial DNA (mtDNA) and in the number of mitochondria. Knockdown of Ppargc1α by siRNA blocked HT's stimulating effect on Complex I expression and mtDNA copy number. The HT treatment resulted in an enhancement of mitochondrial function, including an increase in activity and protein expression of Mitochondrial Complexes I, II, III and V; increased oxygen consumption; and a decrease in free fatty acid contents in the adipocytes. The mechanistic study of the PPARGC1α activation signaling pathway demonstrated that HT is an activator of 5′AMP-activated protein kinase and also up-regulates gene expression of PPARα, CPT-1 and PPARγ. These data suggest that HT is able to promote mitochondrial function by stimulating mitochondrial biogenesis.

FADING HARD X-RAY EMISSION FROM THE GALACTIC CENTER MOLECULAR CLOUD Sgr B2

Abstract: The center of our Galaxy harbors a four million solar mass black hole that is unusually quiet: its present X-ray luminosity is more than 10 orders of magnitude less than its Eddington luminosity. The observation of iron fluorescence and hard X-ray emission from some of the massive molecular clouds surrounding the Galactic center has been interpreted as an echo of a past 10(39) erg s(-1) flare. Alternatively, low-energy cosmic rays propagating inside the clouds might account for the observed emission, through inverse bremsstrahlung of low-energy ions or bremsstrahlung emission of low-energy electrons. Here, we report the observation of a clear decay of the hard X-ray emission from the molecular cloud Sgr B2 during the past seven years, thanks to more than 20 Ms of INTEGRAL exposure. This confirms the decay previously observed comparing the 6.4 keV line fluxes measured by various X-ray instruments, but without intercalibration effects. The measured decay time is 8.2 +/- 1.7 yr, compatible with the light crossing time of the molecular cloud core. Such a short timescale rules out inverse bremsstrahlung by cosmic-ray ions as the origin of the X ray emission. We also obtained 2-100 keV broadband X-ray spectra by combining INTEGRAL and XMM-Newton data and compared them with detailed models of X-ray emission due to irradiation of molecular gas by (1) low-energy cosmic-ray electrons and (2) hard X-rays. Both models can reproduce the data equally well, but the time variability constraints and the huge cosmic-ray electron luminosity required to explain the observed hard X-ray emission strongly favor the scenario in which the diffuse emission of Sgr B2 is scattered and reprocessed radiation emitted in the past by Sgr A*. The spectral index of the illuminating power-law source is found to be Gamma similar to 2 and its luminosity 1.5-5 x 10(39) erg s(-1), depending on the relative positions of Sgr B2 and Sgr A*. Using recent parallax measurements that place Sgr B2 in front of Sgr A*, we find that the period of intense activity of Sgr A* ended between 75 and 155 years ago.

The X-shooter pipeline

Abstract: The X-shooter data reduction pipeline, as part of the ESO-VLT Data Flow System, provides recipes for Paranal Science Operations, and for Data Product and Quality Control Operations at Garching headquarters. At Paranal, it is used for the quick-look data evaluation. The pipeline recipes can be executed either with EsoRex at the command line level or through the Gasgano graphical user interface. The recipes are implemented with the ESO Common Pipeline Library (CPL). X-shooter is the first of the second generation of VLT instruments. It makes possible to collect in one shot the full spectrum of the target from 300 to 2500 nm, subdivided in three arms optimised for UVB, VIS and NIR ranges, with an efficiency between 15% and 35% including the telescope and the atmosphere, and a spectral resolution varying between 3000 and 17,000. It allows observations in stare, offset modes, using the slit or an IFU, and observing sequences nodding the target along the slit. Data reduction can be performed either with a classical approach, by determining the spectral format via 2D-polynomial transformations, or with the help of a dedicated instrument physical model to gain insight on the instrument and allowing a constrained solution that depends on a few parameters with a physical meaning. In the present paper we describe the steps of data reduction necessary to fully reduce science observations in the different modes with examples on typical data calibrations and observations sequences.

Hydroxytyrosol protects against oxidative damage by simultaneous activation of mitochondrial biogenesis and phase II detoxifying enzyme systems in retinal pigment epithelial cells

Abstract: Studies in this laboratory have previously shown that hydroxytyrosol, the major antioxidant polyphenol in olives, protects ARPE-19 human retinal pigment epithelial cells from oxidative damage induced by acrolein, an environmental toxin and endogenous end product of lipid oxidation, that occurs at increased levels in age-related macular degeneration lesions. A proposed mechanism for this is that protection by hydroxytyrosol against oxidative stress is conferred by the simultaneous activation of two critically important pathways, viz., induction of phase II detoxifying enzymes and stimulation of mitochondrial biogenesis. Cultured ARPE-19 cells were pretreated with hydroxytyrosol and challenged with acrolein. The protective effects of hydroxytyrosol on key factors of mitochondrial biogenesis and phase II detoxifying enzyme systems were examined. Hydroxytyrosol treatment simultaneously protected against acrolein-induced inhibition of nuclear factor-E2-related factor 2 (Nrf2) and peroxisome proliferator-activated receptor coactivator 1 alpha (PPARGC1α) in ARPE-19 cells. The activation of Nrf2 led to activation of phase II detoxifying enzymes, including γ-glutamyl-cysteinyl-ligase, NADPH (nicotinamide adenine dinucleotide phosphate)-quinone-oxidoreductase 1, heme-oxygenase-1, superoxide dismutase, peroxiredoxin and thioredoxin as well as other antioxidant enzymes, while the activation of PPARGC1α led to increased protein expression of mitochondrial transcription factor A, uncoupling protein 2 and mitochondrial complexes. These results suggest that hydroxytyrosol is a potent inducer of phase II detoxifying enzymes and an enhancer of mitochondrial biogenesis. Dietary supplementation of hydroxytyrosol may contribute to eye health by preventing the degeneration of retinal pigment epithelial cells induced by oxidative stress.

High-redshift elliptical galaxies: are they (all) really compact?

Abstract: We investigate the properties of 12 ultramassive passively evolving early-type galaxies (ETGs) at z_(phot) > 1.4 in the COSMOS 2 deg^2 field. These 12 ETGs were selected as pBzKs, have accurate 1.4 ≲ z_(phot) ≲ 1.7, high Sersic index profiles typical of ellipticals, no detection at 24 μm, resulting in a complete ETG sample at M* > 2.5 × 10^(11) M_⊙ (Chabrier initial mass function). Contrary to the previous claims, the half-light radii estimated in very high signal-to-noise ratio imaging data from Hubble Space Telescope+Advanced Camera for Surveys (ACS) are found to be large for most of the sample, consistent with local ellipticals. If the high-redshift ETGs with M* < 2.5 × 10^(11) M_⊙ are really small in size and compact as reported in the previous studies, our result may suggest a 'downsizing' scenario, whereby the most massive ETGs reach their final structure earlier and faster than the lower mass ones. However, simulating galaxies with morphological properties fixed to those of local ETGs with the same stellar mass show that the few compact galaxies that we still recover in our sample can be understood in terms of fluctuations due to noise preventing the recovery of the extended low surface brightness haloes in the light profile. Such haloes, typical of Sersic profiles, extending even up to 40 kpc, are indeed seen in our sample.

Galaxy counterparts of metal-rich damped Lyα absorbers – I. The case of the z= 2.35 DLA towards Q 2222−0946

Abstract: We have initiated a survey using the newly commissioned X-shooter spectrograph to target candidate relatively metal-rich damped Lyα absorbers (DLAs). Our rationale is that highmetallicity DLAs due to the luminosity–metallicity relation likely will have the most luminous galaxy counterparts. In addition, the spectral coverage of X-shooter allows us to search for not only Lyα emission, but also rest-frame optical emission lines. We have chosen DLAs where the strongest rest-frame optical lines ([O II], [O III], Hβ and Hα) fall in the nearinfrared atmospheric transmission bands. In this first paper resulting from the survey, we report on the discovery of the galaxy counterpart of the zabs = 2.354 DLA towards the z = 2.926 quasar Q 2222−0946. This DLA is amongst the most metal-rich z > 2 DLAs studied so far at comparable redshifts and there is evidence for substantial depletion of refractory elements on to dust grains. We measure metallicities from Zn II ,S iII ,N iII ,M nII and Fe II of −0.46 ± 0.07, −0.51 ± 0.06, −0.85 ± 0.06, −1.23 ± 0.06 and −0.99 ± 0.06, respectively. The galaxy is detected in the Lyα ,[ OIII] λλ4959, 5007 and Hα emission lines at an impact parameter of about 0.8 arcsec (6 kpc at zabs = 2.354). Based on the Hα line, we infer a

Measurement of the Charm and Beauty Structure Functions using the H1 Vertex Detector at HERA

Abstract: Inclusive charm and beauty cross sections are measured in e-p and e+p neutral current collisions at HERA in the kinematic region of photon virtuality 5