Experimental evidence of thermal fluctuations on the X-ray absorption near-edge structure at the aluminum K-edge

After a review of temperature-dependent experimental x-ray absorption near-edge structure (XANES) and related theoretical developments, we present the Al K-edge XANES spectra of corundum and beryl for temperature ranging from 300K to 930K. These experimental results provide a first evidence of the role of thermal fluctuation in XANES at the Al K-edge especially in the pre-edge region. The study is carried out by polarized XANES measurements of single crystals. For any orientation of the sample with respect to the x-ray beam, the pre-edge peak grows and shifts to lower energy with temperature. In addition temperature induces modifications in the position and intensities of the main XANES features. First-principles DFT calculations are performed for both compounds. They show that the pre-edge peak originates from forbidden 1s to 3s transitions induced by vibrations. Three existing theoretical models are used to take vibrations into account in the absorption cross section calculations: i) an average of the XANES spectra over the thermal displacements of the absorbing atom around its equilibrium position, ii) a method based on the crude Born-Oppenheimer approximation where only the initial state is averaged over thermal displacements, iii) a convolution of the spectra obtained for the atoms at the equilibrium positions with an approximate phonon spectral function. The theoretical spectra so obtained permit to qualitatively understand the origin of the spectral modifications induced by temperature. However the correct treatment of thermal fluctuation in XANES spectroscopy requires more sophisticated theoretical tools

Early MicroRNA expression profile as a prognostic biomarker for the development of pelvic inflammatory disease in a mouse model of chlamydial genital infection

It is not currently possible to predict the probability of whether a woman with a chlamydial genital infection will develop pelvic inflammatory disease (PID). To determine if specific biomarkers may be associated with distinct chlamydial pathotypes, we utilized two Chlamydia muridarum variants (C. muridarum Var001 [CmVar001] and CmVar004) that differ in their abilities to elicit upper genital tract pathology in a mouse model. CmVar004 has a lower growth rate in vitro and induces pathology in only 20% of C57BL/6 mouse oviducts versus 83.3% of oviducts in CmVar001-infected mice. To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. CmVar004 infection induced significantly lower levels of CXCL1, CXCL2, tumor necrosis factor alpha (TNF-α), and CCL2 in comparison to CmVar001 infection with similar rRNA (rs16) levels for Chlamydiae. A combination of microRNA (miRNA) sequencing and quantitative real-time PCR (qRT-PCR) analysis of 134 inflammation-related miRNAs was performed 24 h postinfection to determine if the chemokine/cytokine responses would also be reflected in miRNA expression profiles. Interestingly, 12 miRNAs (miR-135a-5p, miR298-5p, miR142-3p, miR223-3p, miR299a-3p, miR147-3p, miR105, miR325-3p, miR132-3p, miR142-5p, miR155-5p, and miR-410-3p) were overexpressed during CmVar004 infection compared to CmVar001 infection, inversely correlating with the respective chemokine/cytokine responses. To our knowledge, this is the first report demonstrating that early biomarkers elicited in the host can differentiate between two pathological variants of chlamydiae and be predictive of upper tract disease. © 2014 Yeruva et al

A group-galaxy cross-correlation function analysis in zCOSMOS

We present a group-galaxy cross-correlation analysis using a group catalog produced from the 16,500 spectra from the optical zCOSMOS galaxy survey. Our aim is to perform a consistency test in the redshift range 0.2 < z < 0.8 between the clustering strength of the groups and mass estimates that are based on the richness of the groups. We measure the linear bias of the groups by means of a group-galaxy cross-correlation analysis and convert it into mass using the bias-mass relation for a given cosmology, checking the systematic errors using realistic group and galaxy mock catalogs. The measured bias for the zCOSMOS groups increases with group richness as expected by the theory of cosmic structure formation and yields masses that are reasonably consistent with the masses estimated from the richness directly, considering the scatter that is obtained from the 24 mock catalogs. An exception are the richest groups at high redshift (estimated to be more massive than 10^13.5 M_sun), for which the measured bias is significantly larger than for any of the 24 mock catalogs (corresponding to a 3-sigma effect), which is attributed to the extremely large structure that is present in the COSMOS field at z ~ 0.7. Our results are in general agreement with previous studies that reported unusually strong clustering in the COSMOS field.Comment: 13 pages, 9 figures, published in Ap

Towards demonstration of photonic payload for telecom satellites

To address the challenges of the Digital Agenda for Europe (DAE) and also to remain in line with the evolution of terrestrial communications in a globally connected world, a major increase in telecoms satellites capacity is required in the near future. With telecom satellites payloads based on traditional RF equipment, increase in capacity and flexibility has always translated into a more or less linear increase in equipment count, mass, power consumption and power dissipation. The main challenge of next generation of High Throughput Satellites (HTS) is therefore to provide a ten-fold-increased capacity with enhanced flexibility while maintaining the overall satellite within a "launchable" volume and mass envelope [1], [2], [3]. Photonic is a very promising technology to overcome the above challenges. The ability of Photonic to handle high data rates and high frequencies, as well as enabling reduced size, mass, immunity to EMI and ease of harness routing (by using fibre-optic cables) is critical in this scenario

Slater-Pauling Behavior of the Half-Ferromagnetic Full-Heusler Alloys

Using the full-potential screened Korringa-Kohn-Rostoker method we study the full-Heusler alloys based on Co, Fe, Rh and Ru. We show that many of these compounds show a half-metallic behavior, however in contrast to the half-Heusler alloys the energy gap in the minority band is extremely small. These full-Heusler compounds show a Slater-Pauling behavior and the total spin-magnetic moment per unit cell (M_t) scales with the total number of valence electrons (Z_t) following the rule: M_t=Z_t-24. We explain why the spin-down band contains exactly 12 electrons using arguments based on the group theory and show that this rule holds also for compounds with less than 24 valence electrons. Finally we discuss the deviations from this rule and the differences compared to the half-Heusler alloys.Comment: 10 pages, 8 figures, revised figure 3, new text adde

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads. Combinatorial sequence tagging can be used to examine hundreds of samples with far fewer primers than is required when sequence tags are incorporated at only a single end. The number of reads generated permitted saturating or near-saturating analysis of samples of the vaginal microbiome. The large number of reads al- lowed an in-depth analysis of errors, and we found that PCR-induced errors composed the vast majority of non-organism derived species variants, an ob- servation that has significant implications for sequence clustering of similar high-throughput data. We show that the short reads are sufficient to assign organisms to the genus or species level in most cases. We suggest that this method will be useful for the deep sequencing of any short nucleotide region that is taxonomically informative; these include the V3, V5 regions of the bac- terial 16S rRNA genes and the eukaryotic V9 region that is gaining popularity for sampling protist diversity.Comment: 28 pages, 13 figure

The XMM-Newton Wide-Field Survey in the COSMOS field (XMM-COSMOS): demography and multiwavelength properties of obscured and unobscured luminous AGN

We report the final optical identifications of the medium-depth (~60 ksec), contiguous (2 deg^2) XMM-Newton survey of the COSMOS field. XMM-Newton has detected ~800 X-ray sources down to limiting fluxes of ~5x10^{-16}, ~3x10^{-15}, and ~7x10^{-15} erg/cm2/s in the 0.5-2 keV, 2-10 keV and 5-10 keV bands, respectively. The work is complemented by an extensive collection of multi-wavelength data from 24 micron to UV, available from the COSMOS survey, for each of the X-ray sources, including spectroscopic redshifts for ~50% of the sample, and high-quality photometric redshifts for the rest. The XMM and multiwavelength flux limits are well matched: 1760 (98%) of the X-ray sources have optical counterparts, 1711 (~95%) have IRAC counterparts, and 1394 (~78%) have MIPS 24micron detections. Thanks to the redshift completeness (almost 100%) we were able to constrain the high-luminosity tail of the X-ray luminosity function confirming that the peak of the number density of logL_X>44.5 AGN is at z~2. Spectroscopically-identified obscured and unobscured AGN, as well as normal and starforming galaxies, present well-defined optical and infrared properties. We devised a robust method to identify a sample of ~150 high redshift (z>1), obscured AGN candidates for which optical spectroscopy is not available. We were able to determine that the fraction of the obscured AGN population at the highest (L_X>10^{44} erg s^{-1}) X-ray luminosity is ~15-30% when selection effects are taken into account, providing an important observational constraint for X-ray background synthesis. We studied in detail the optical spectrum and the overall spectral energy distribution of a prototypical Type 2 QSO, caught in a stage transitioning from being starburst dominated to AGN dominated, which was possible to isolate only thanks to the combination of X-ray and infrared observations.Comment: ApJ, in press. 59 pages, 14 figures, 2 Tables. A few typos corrected and a reference added. Table 2 is also available at http://www.mpe.mpg.de/XMMCosmos/xmm53_release ; a version of the paper in ApJ format (27 pages) is available at http://www.mpe.mpg.de/XMMCosmos/xmm53_release/brusa_xmmcosmos_optid.pd

Quantified HI Morphology I: Multi-Wavelengths Analysis of the THINGS Galaxies

Galaxy evolution is driven to a large extent by interactions and mergers with other galaxies and the gas in galaxies is extremely sensitive to the interactions. One method to measure such interactions uses the quantified morphology of galaxy images. Well-established parameters are Concentration, Asymmetry, Smoothness, Gini, and M20 of a galaxy image. Thus far, the application of this technique has mostly been restricted to restframe ultra-violet and optical images. However, with the new radio observatories being commissioned (MeerKAT, ASKAP, EVLA, WSRT/APERTIF, and ultimately SKA), a new window on the neutral atomic hydrogen gas (HI) morphology of a large numbers of galaxies will open up. The quantified morphology of gas disks of spirals can be an alternative indicator of the level and frequency of interaction. The HI in galaxies is typically spatially more extended and more sensitive to low-mass or weak interactions. In this paper, we explore six morphological parameters calculated over the extent of the stellar (optical) disk and the extent of the gas disk for a range of wavelengths spanning UV, Optical, Near- and Far-Infrared and 21 cm (HI) of 28 galaxies from The HI Nearby Galaxy Survey (THINGS). Though the THINGS sample is small and contains only a single ongoing interaction, it spans both non-interacting and post-interacting galaxies with a wealth of multi-wavelength data. We find that the choice of area for the computation of the morphological parameters is less of an issue than the wavelength at which they are measured. The signal of interaction is as good in the HI as in any of the other wavelengths in which morphology has been used to trace the interaction rate to date, mostly star-formation dominated ones (near- and far-ultraviolet). The Asymmetry and M20 parameters are the ones which show the most promise as tracers of interaction in 21 cm line observations.Comment: 16 pages, 11 figure, table 1, accepted by MNRAS, appendix not include

The zCOSMOS 20k Group Catalog

We present an optical group catalog between 0.1 < z < 1 based on 16,500 high-quality spectroscopic redshifts in the completed zCOSMOS-bright survey. The catalog published herein contains 1498 groups in total and 192 groups with more than five observed members. The catalog includes both group properties and the identification of the member galaxies. Based on mock catalogs, the completeness and purity of groups with three and more members should be both about 83% with respect to all groups that should have been detectable within the survey, and more than 75% of the groups should exhibit a one-to-one correspondence to the "real" groups. Particularly at high redshift, there are apparently more galaxies in groups in the COSMOS field than expected from mock catalogs. We detect clear evidence for the growth of cosmic structure over the last seven billion years in the sense that the fraction of galaxies that are found in groups (in volume-limited samples) increases significantly with cosmic time. In the second part of the paper, we develop a method for associating galaxies that only have photo-z to our spectroscopically identified groups. We show that this leads to improved definition of group centers, improved identification of the most massive galaxies in the groups, and improved identification of central and satellite galaxies, where we define the former to be galaxies at the minimum of the gravitational potential wells. Subsamples of centrals and satellites in the groups can be defined with purities up to 80%, while a straight binary classification of all group and non-group galaxies into centrals and satellites achieves purities of 85% and 75%, respectively, for the spectroscopic sample.Comment: 26 pages, 21 figures, published in ApJ (along with machine-readable tables