Browsing by Subject "CATALOG"

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  • Vardoulaki, E.; Andrade, E. F. Jimenez; Karim, A.; Novak, M.; Leslie, S. K.; Tisanic, K.; Smolcic, V.; Schinnerer, E.; Sargent, M. T.; Bondi, M.; Zamorani, G.; Magnelli, B.; Bertoldi, F.; Ruiz, N. Herrera; Mooley, K. P.; Delhaize, J.; Myers, S. T.; Marchesi, S.; Koekemoer, A. M.; Gozaliasl, G.; Finoguenov, A.; Middleberg, E.; Ciliegi, P. (2019)
    Context. Given the unprecedented depth achieved in current large radio surveys, we are starting to probe populations of radio sources that have not been studied in the past. However, identifying and categorising these objects, differing in size, shape and physical properties, is becoming a more difficult task. Aims. In this data paper we present and characterise the multi-component radio sources identified in the VLA-COSMOS Large Project at 3 GHz (0.75 arcsec resolution, 2.3 mu Jy beam(-1) rms), i.e. the radio sources which are composed of two or more radio blobs. Methods. The classification of objects into multi-components was done by visual inspection of 351 of the brightest and most extended blobs from a sample of 10,899 blobs identified by the automatic code BLOBCAT. For that purpose we used multi-wavelength information of the field, such as the 1.4 GHz VLA-COSMOS data and the Ultra Deep Survey with the VISTA telescope (UltraVISTA) stacked mosaic available for COSMOS. Results. We have identified 67 multi-component radio sources at 3 GHz: 58 sources with active galactic nucleus (AGN) powered radio emission and nine star-forming galaxies. We report eight new detections that were not observed by the VLA-COSMOS Large Project at 1.4 GHz, due to the slightly larger area coverage at 3 GHz. The increased spatial resolution of 0.75 arcsec has allowed us to resolve (and isolate) multiple emission peaks of 28 extended radio sources not identified in the 1.4 GHz VLA-COSMOS map. We report the multi-frequency flux densities (324 MHz, 325 MHz, 1.4 GHz & 3 GHz), star formation rates, and stellar masses of these objects. We find that multi-component objects at 3 GHz VLA-COSMOS inhabit mainly massive galaxies (>10(10.5)M(circle dot)). The majority of the multi-component AGN lie below the main sequence of star-forming galaxies (SFGs), in the green valley and the quiescent region. Furthermore, we provide detailed descriptions of the objects and find that amongst the AGN there are two head-tail, ten corelobe, nine wide-angle-tail (WAT), eight double-double or Z-/X-shaped, three bent-tail radio sources, and 26 symmetric sources, while amongst the SFGs we find the only star-forming ring seen in radio emission in COSMOS. Additionally, we report a large number (32 out of 58) of disturbed/bent multi-component AGN, 18 of which do not lie within X-ray groups in COSMOS (redshift range 0.08 Conclusion. The high angular resolution and sensitivity of the 3 GHz VLA-COSMOS data set give us the opportunity to identify peculiar radio structures and sub-structures of multi-component objects, and relate them to physical phenomena such as AGN or star-forming galaxies. This study illustrates the complexity of the mu Jy radio-source population; at the sensitivity and resolution of 3 GHz VLA-COSMOS, the radio structures of AGN and SFG both emitting radio continuum emission, become comparable in the absence of clear, symmetrical jets. Thus, disentangling the AGN and SFG contributions using solely radio observations can be misleading in a number of cases. This has implications for future surveys, such as those done by square kilometre array (SKA) and precursors, which will identify hundreds of thousands of multi-component objects.
  • Rooijers, Koos; Kolmeder, Carolin; Juste, Catherine; Dore, Joel; de Been, Mark; Boeren, Sjef; Galan, Pilar; Beauvallet, Christian; de Vos, Willem M.; Schaap, Peter J. (2011)
  • Lehtinen, K.; Bach, U.; Muinonen, K.; Poutanen, M.; Petrov, L. (2016)
    Stellar occultations by asteroids observed at visual wavelengths have been an important tool for studying the size and shape of asteroids and for revising the orbital parameters of asteroids. At radio frequencies, a shadow of an asteroid on the Earth is dominated by diffraction effects. Here, we show, for the first time, that a single observation of an occultation of a compact radio source at a frequency of 5 GHz can be used to derive the effective size of the occulting object and to derive the distance between the observer and the center of the occultation path on the Earth. The derived diameter of the occulting object, asteroid (115) Thyra, is 75 +/- 6 km. The observed occultation profile shows features that cannot be explained by diffraction of a single asteroid.
  • Barnes, D.; Davies, J. A.; Harrison, R. A.; Byrne, J. P.; Perry, C. H.; Bothmer, V.; Eastwood, J. P.; Gallagher, P. T.; Kilpua, E. K. J.; Möstl, C.; Rodriguez, L.; Rouillard, A. P.; Odstrcil, D. (2019)
    Recent observations with the Heliospheric Imagers (HIs) onboard the twin NASA Solar Terrestrial Relations Observatory (STEREO) spacecraft have provided unprecedented observations of a large number of coronal mass ejections (CMEs) in the inner heliosphere. In this article we discuss the generation of the HIGeoCAT CME catalogue and perform a statistical analysis of its events. The catalogue was generated as part of the EU FP7 HELCATS (Heliospheric Cataloguing, Analysis and Techniques Service) project (www.helcats-fp7.eu/). It is created by generating time/elongation maps for CMEs using observations from the inner (HI-1) and outer (HI-2) cameras along a position angle close to the CME apex. Next, we apply single-spacecraft geometric-fitting techniques to determine the kinematic properties of these CMEs, including their speeds, propagation directions, and launch times. The catalogue contains a total of 1455 events (801 from STEREO-A and 654 from STEREO-B) from April 2007 to the end of August 2017. We perform a statistical analysis of the properties of CMEs in HIGeoCAT and compare the results with those from the Large Angle Spectrometric Coronagraph (LASCO) CDAW catalogues (Yashiro etal.J.Geophys. Res. Space Phys.109, A07105, 2004) and the COR-2 catalogue of Vourlidas etal. (Astrophys. J.838, 141, 2004) during the same period. We find that the distributions of both speeds and latitudes for the HIGeoCAT CMEs correlate with the sunspot number over the solar cycle. We also find that the HI-derived CME speed distributions are generally consistent with coronagraph catalogues over the solar cycle, albeit with greater absolute speeds due to the differing methods with which each is derived.
  • Weissbrod, Omer; Hormozdiari, Farhad; Benner, Christian; Cui, Ran; Ulirsch, Jacob; Gazal, Steven; Schoech, Armin P.; van de Geijn, Bryce; Reshef, Yakir; Marquez-Luna, Carla; O'Connor, Luke; Pirinen, Matti; Finucane, Hilary K.; Price, Alkes L. (2020)
    Fine-mapping aims to identify causal variants impacting complex traits. We propose PolyFun, a computationally scalable framework to improve fine-mapping accuracy by leveraging functional annotations across the entire genome-not just genome-wide-significant loci-to specify prior probabilities for fine-mapping methods such as SuSiE or FINEMAP. In simulations, PolyFun + SuSiE and PolyFun + FINEMAP were well calibrated and identified >20% more variants with a posterior causal probability >0.95 than identified in their nonfunctionally informed counterparts. In analyses of 49 UK Biobank traits (average n = 318,000), PolyFun + SuSiE identified 3,025 fine-mapped variant-trait pairs with posterior causal probability >0.95, a >32% improvement versus SuSiE. We used posterior mean per-SNP heritabilities from PolyFun + SuSiE to perform polygenic localization, constructing minimal sets of common SNPs causally explaining 50% of common SNP heritability; these sets ranged in size from 28 (hair color) to 3,400 (height) to 2 million (number of children). In conclusion, PolyFun prioritizes variants for functional follow-up and provides insights into complex trait architectures. PolyFun is a computationally scalable framework for functionally informed fine-mapping that makes full use of genome-wide data. It prioritizes more variants than previous methods when applied to 49 complex traits from UK Biobank.
  • van Leeuwen, F.; Muinonen, K.; Fedorets, G.; Granvik, M.; Pentikäinen, H.; Oszkiewicz, D.; Pieniluoma, T.; Gaia Collaboration (2017)
    Context. The first Gaia Data Release contains the Tycho-Gaia Astrometric Solution (TGAS). This is a subset of about 2 million stars for which, besides the position and photometry, the proper motion and parallax are calculated using Hipparcos and Tycho-2 positions in 1991.25 as prior information. Aims. We investigate the scientific potential and limitations of the TGAS component by means of the astrometric data for open clusters. Methods. Mean cluster parallax and proper motion values are derived taking into account the error correlations within the astrometric solutions for individual stars, an estimate of the internal velocity dispersion in the cluster, and, where relevant, the effects of the depth of the cluster along the line of sight. Internal consistency of the TGAS data is assessed. Results. Values given for standard uncertainties are still inaccurate and may lead to unrealistic unit-weight standard deviations of least squares solutions for cluster parameters. Reconstructed mean cluster parallax and proper motion values are generally in very good agreement with earlier Hipparcos-based determination, although the Gaia mean parallax for the Pleiades is a significant exception. We have no current explanation for that discrepancy. Most clusters are observed to extend to nearly 15 pc from the cluster centre, and it will be up to future Gaia releases to establish whether those potential cluster-member stars are still dynamically bound to the clusters. Conclusions. The Gaia DR1 provides the means to examine open clusters far beyond their more easily visible cores, and can provide membership assessments based on proper motions and parallaxes. A combined HR diagram shows the same features as observed before using the Hipparcos data, with clearly increased luminosities for older A and F dwarfs.
  • Gaia Collaboration; Eyer, L.; Muinonen, K.; Fedorets, G.; Granvik, M.; Siltala, L. (2019)
    Context. The ESA Gaia mission provides a unique time-domain survey for more than 1.6 billion sources with G less than or similar to 21 mag. Aims. We showcase stellar variability in the Galactic colour-absolute magnitude diagram (CaMD). We focus on pulsating, eruptive, and cataclysmic variables, as well as on stars that exhibit variability that is due to rotation and eclipses. Methods. We describe the locations of variable star classes, variable object fractions, and typical variability amplitudes throughout the CaMD and show how variability-related changes in colour and brightness induce "motions". To do this, we use 22 months of calibrated photometric, spectro-photometric, and astrometric Gaia data of stars with a significant parallax. To ensure that a large variety of variable star classes populate the CaMD, we crossmatched Gaia sources with known variable stars. We also used the statistics and variability detection modules of the Gaia variability pipeline. Corrections for interstellar extinction are not implemented in this article. Results. Gaia enables the first investigation of Galactic variable star populations in the CaMD on a similar, if not larger, scale as was previously done in the Magellanic Clouds. Although the observed colours are not corrected for reddening, distinct regions are visible in which variable stars occur. We determine variable star fractions to within the current detection thresholds of Gaia. Finally, we report the most complete description of variability-induced motion within the CaMD to date. Conclusions. Gaia enables novel insights into variability phenomena for an unprecedented number of stars, which will benefit the understanding of stellar astrophysics. The CaMD of Galactic variable stars provides crucial information on physical origins of variability in a way that has previously only been accessible for Galactic star clusters or external galaxies. Future Gaia data releases will enable significant improvements over this preview by providing longer time series, more accurate astrometry, and additional data types (time series BP and RP spectra, RVS spectra, and radial velocities), all for much larger samples of stars.
  • Gaia Collaboration; Brown, A. G. A.; Muinonen, K.; Fedorets, G.; Granvik, M.; Penttila, A.; Siltala, L. (2021)
    Context. We present the early installment of the third Gaia data release, Gaia EDR3, consisting of astrometry and photometry for 1.8 billion sources brighter than magnitude 21, complemented with the list of radial velocities from Gaia DR2. Aims. A summary of the contents of Gaia EDR3 is presented, accompanied by a discussion on the differences with respect to Gaia DR2 and an overview of the main limitations which are present in the survey. Recommendations are made on the responsible use of Gaia EDR3 results. Methods. The raw data collected with the Gaia instruments during the first 34 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium and turned into this early third data release, which represents a major advance with respect to Gaia DR2 in terms of astrometric and photometric precision, accuracy, and homogeneity. Results. Gaia EDR3 contains celestial positions and the apparent brightness in G for approximately 1.8 billion sources. For 1.5 billion of those sources, parallaxes, proper motions, and the (G(BP) - G(RP)) colour are also available. The passbands for G, G(BP), and G(RP) are provided as part of the release. For ease of use, the 7 million radial velocities from Gaia DR2 are included in this release, after the removal of a small number of spurious values. New radial velocities will appear as part of Gaia DR3. Finally, Gaia EDR3 represents an updated materialisation of the celestial reference frame (CRF) in the optical, the Gaia-CRF3, which is based solely on extragalactic sources. The creation of the source list for Gaia EDR3 includes enhancements that make it more robust with respect to high proper motion stars, and the disturbing effects of spurious and partially resolved sources. The source list is largely the same as that for Gaia DR2, but it does feature new sources and there are some notable changes. The source list will not change for Gaia DR3. Conclusions. Gaia EDR3 represents a significant advance over Gaia DR2, with parallax precisions increased by 30 per cent, proper motion precisions increased by a factor of 2, and the systematic errors in the astrometry suppressed by 30-40% for the parallaxes and by a factor similar to 2.5 for the proper motions. The photometry also features increased precision, but above all much better homogeneity across colour, magnitude, and celestial position. A single passband for G, G(BP), and G(RP) is valid over the entire magnitude and colour range, with no systematics above the 1% level
  • Juvela, Mika; He, Jinhua; Pattle, Katherine; Liu, Tie; Bendo, George; Eden, David J.; Feher, Orsolya; Fich, Michel; Fuller, Gary; Hirano, Naomi; Kim, Kee-Tae; Li, Di; Liu, Sheng-Yuan; Malinen, Johanna; Marshall, Douglas J.; Paradis, Deborah; Parsons, Harriet; Pelkonen, Veli-Matti; Rawlings, Mark G.; Ristorcelli, Isabelle; Samal, Manash R.; Tatematsu, Ken'ichi; Thompson, Mark; Traficante, Alessio; Wang, Ke; Ward-Thompson, Derek; Wu, Yuefang; Yi, Hee-Weon; Yoo, Hyunju (2018)
    Context. Analysis of all-sky Planck submillimetre observations and the IRAS 100 mu m data has led to the detection of a population of Galactic cold clumps. The clumps can be used to study star formation and dust properties in a wide range of Galactic environments. Aims. Our aim is to measure dust spectral energy distribution ( SED) variations as a function of the spatial scale and the wavelength. Methods. We examined the SEDs at large scales using IRAS, Planck, and Herschel data. At smaller scales, we compared JCMT/SCUBA-2 850 mu m maps with Herschel data that were filtered using the SCUBA-2 pipeline. Clumps were extracted using the Fellwalker method, and their spectra were modelled as modified blackbody functions. Results. According to IRAS and Planck data, most fields have dust colour temperatures T-C similar to 14-18K and opacity spectral index values of beta = 1.5-1.9. The clumps and cores identified in SCUBA-2 maps have T similar to 13K and similar beta values. There are some indications of the dust emission spectrum becoming flatter at wavelengths longer than 500 mu m. In fits involving Planck data, the significance is limited by the uncertainty of the corrections for CO line contamination. The fits to the SPIRE data give a median beta value that is slightly above 1.8. In the joint SPIRE and SCUBA-2 850 mu m fits, the value decreases to beta similar to 1.6. Most of the observed T-beta anticorrelation can be explained by noise. Conclusions. The typical submillimetre opacity spectral index fi of cold clumps is found to be similar to 1.7. This is above the values of diffuse clouds, but lower than in some previous studies of dense clumps. There is only tentative evidence of a T-beta anticorrelation and beta decreasing at millimetre wavelengths.
  • Malinen, J.; Montier, L.; Montillaud, J.; Juvela, M.; Ristorcelli, I.; Clark, S. E.; Berne, O.; Bernard, J.-Ph.; Pelkonen, V.-M.; Collins, D. C. (2016)
    The nearby cloud L1642 is one of only two known very high latitude (b| > 30 deg) clouds actively forming stars. It is a rare example of star formation in isolated conditions, and can reveal important details of star formation in general, e.g. of the effect of magnetic fields. We compareHerschel dust emission structures and magnetic field orientation revealed byPlanck polarization maps in L1642. The high-resolution (similar to 20 arcsec)Herschel data reveal a complex structure including a dense, compressed central clump, and low-density striations. ThePlanck polarization data (at 10 arcmin resolution) reveal an ordered magnetic field pervading the cloud and aligned with the surrounding striations. There is a complex interplay between the cloud structure and large-scale magnetic field. This suggests that the magnetic field is closely linked to the formation and evolution of the cloud. CO rotational emission confirms that the striations are connected with the main clumps and likely to contain material either falling into or flowing out of the clumps. There is a clear transition from aligned to perpendicular structures approximately at a column density ofN(H) = 1.6 x 10(21) cm(-2). Comparing theHerschel maps with thePlanck polarization maps shows the close connection between the magnetic field and cloud structure even in the finest details of the cloud.
  • de Moraes, Pedro L. R.; Sennikov, Alexander N. (2021)
    Cyperus megapotamicus (A. Spreng.) Kunth is a nomenclatural synonym of Rhynchospora megapotamica (A. Spreng.) H. Pfeiff. but was originally misapplied to a species of Cyperus. Contrary to the rules, both species names are in current use in different genera. We here clarify the perpetuated taxonomic and nomenclatural confusion regarding the identity of C. megapotamicus sensu Kunth and related names and conclude that Cyperus jaeggii Boeckeler is the correct name to be adopted. We provide an amended circumscription of this species, with Cyperus mauryi Kuntze and Pycreus nematodes Schrad. ex C. B. Clarke as its newly proposed heterotypic synonyms. Additionally, lectotypes are designated for the names Scirpus megapotamicus A. Spreng., Rhynchospora maculata Maury, Rhynchospora luzuliformis var. elongata Kuntze, Rhynchospora luzuliformis var. subcapitata Kuntze, Cyperus jaeggii, Cyperus mauryi and Pycreus nematodes.
  • Ade, P. A. R.; Juvela, M.; Keihanen, E.; Kurki-Suonio, H.; Poutanen, T.; Suur-Uski, A. -S.; Planck Collaboration (2013)
  • Ade, P. A. R.; Aghanim, N.; Arnaud, M.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Barrena, R.; Bartolo, N.; Battaner, E.; Benabed, K.; Benoit-Levy, A.; Bernard, J. -P.; Bersanelli, M.; Bielewicz, P.; Bikmaev, I.; Boehringer, H.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Burenin, R.; Burigana, C.; Butler, R. C.; Calabrese, E.; Carvalho, P.; Catalano, A.; Chamballu, A.; Chiang, H. C.; Chon, G.; Christensen, P. R.; Churazov, E.; Clements, D. L.; Colombo, L. P. L.; Comis, B.; Couchot, F.; Curto, A.; Cuttaia, F.; Dahle, H.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Diego, J. M.; Dole, H.; Dore, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Ensslin, T. A.; Eriksen, H. K.; Finelli, F.; Flores-Cacho, I.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Frejsel, A.; Fromenteau, S.; Galeotta, S.; Ganga, K.; Genova-Santos, R. T.; Giard, M.; Gilfanov, M.; Giraud-Heraud, Y.; Gjerlow, E.; Gonzalez-Nuevo, J.; Gorski, K. M.; Gruppuso, A.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Hempel, A.; Henrot-Versille, S.; Hernandez-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Hurier, G.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Khamitov, I.; Kisner, T. S.; Kneissl, R.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lamarre, J. -M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Leonardi, R.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vornle, M.; Lopez-Caniego, M.; Lubin, P. M.; Macias-Perez, J. F.; Maino, D.; Mandolesi, N.; Maris, M.; Martin, P. G.; Martinez-Gonzalez, E.; Masi, S.; Matarrese, S.; Mazzotta, P.; Melin, J. -B.; Mendes, L.; Mennella, A.; Migliaccio, M.; Miville-Deschenes, M. -A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Norgaard-Nielsen, H. U.; Novikov, D.; Novikov, I.; Oxborrow, C. A.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Perdereau, O.; Perotto, L.; Perrotta, F.; Pettorino, V.; Piacentini, F.; Piat, M.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Popa, L.; Pratt, G. W.; Prunet, S.; Puget, J. -L.; Rachen, J. P.; Reinecke, M.; Remazeilles, M.; Renault, C.; Ricciardi, S.; Ristorcelli, I.; Rocha, G.; Roman, M.; Rosset, C.; Rossetti, M.; Roudier, G.; Rubino-Martin, J. A.; Rusholme, B.; Sandri, M.; Scott, D.; Spencer, L. D.; Stolyarov, V.; Sudiwala, R.; Sunyaev, R.; Sutton, D.; Suur-Uski, A. -S.; Sygnet, J. -F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vibert, L.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; Yvon, D.; Zacchei, A.; Zonca, A. (2015)
    We present the results of approximately three years of observations of Planck Sunyaev-Zeldovich (SZ) sources with the Russian-Turkish 1.5m telescope (RTT150), as a part of the optical follow-up programme undertaken by the Planck collaboration. During this time period approximately 20% of all dark and grey clear time available at the telescope was devoted to observations of Planck objects. Some observations of distant clusters were also done at the 6 m Bolshoi Telescope Alt-azimutalnyi (BTA) of the Special Astrophysical Observatory of the Russian Academy of Sciences. In total, deep, direct images of more than one hundred fields were obtained in multiple filters. We identified 47 previously unknown galaxy clusters, 41 of which are included in the Planck catalogue of SZ sources. The redshifts of 65 Planck clusters were measured spectroscopically and 14 more were measured photometrically. We discuss the details of cluster optical identifications and redshift measurements. We also present new spectroscopic redshifts for 39 Planck clusters that were not included in the Planck SZ source catalogue and are published here for the first time.
  • Raju, Sajan C.; Lagström, Sonja; Ellonen, Pekka; de Vos, Willem M.; Eriksson, Johan G.; Weiderpass, Elisabete; Rounge, Trine B. (2018)
    Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 +/- 0.097 and 13.56 +/- 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.
  • Kolmeder, Carolin A.; de Vos, Willem M. (2021)
    It is known for more than 100 years that the intestinal microbes are important for the host's health and the last decade this is being intensely studied with a focus on the mechanistic aspects. Among the fundamental functions of the intestinal microbiome are the priming of the immune system, the production of essential vitamins and the energy harvest from foods. By now, several dozens of diseases, both intestinal and non-intestinal related, have been associated with the intestinal microbiome. Initially, this was based on the description of the composition between groups of different health status or treatment arms based on phylogenetic approaches based on the 16S rRNA gene sequences. This way of analysis has mostly moved to the analysis of all the genes or transcripts of the microbiome i.e. metagenomics and meta-transcriptomics. Differences are regularly found but these have to be taken with caution as we still do not know what the majority of genes of the intestinal microbiome are capable of doing. To circumvent this caveat researchers are studying the proteins and the metabolites of the microbiome and the host via metaproteomics and metabolomics approaches. However, also here the complexity is high and only a fraction of signals obtained with high throughput instruments can be identified and assigned to a known protein or molecule. Therefore, modern microbiome research needs advancement of existing and development of new analytical techniques. The usage of model systems like intestinal organoids where samples can be taken and processed rapidly as well as microfluidics systems may help. This review aims to elucidate what we know about the functionality of the human intestinal microbiome, what technologies are advancing this knowledge, and what innovations are still required to further evolve this actively developing field. (C) 2020 The Authors. Published by Elsevier B.V.
  • Kilpua, E. K. J.; Fontaine, D.; Moissard, C.; Ala-Lahti, M.; Palmerio, E.; Yordanova, E.; Good, S. W.; Lumme, E.; Osmane, A.; Palmroth, M.; Turc, L.; Kalliokoski, Milla (2019)
    We present a statistical study of interplanetary conditions and geospace response to 89 coronal mass ejection-driven sheaths observed during Solar Cycles 23 and 24. We investigate in particular the dependencies on the driver properties and variations across the sheath. We find that the ejecta speed principally controls the sheath geoeffectiveness and shows the highest correlations with sheath parameters, in particular in the region closest to the shock. Sheaths of fast ejecta have on average high solar wind speeds, magnetic (B) field magnitudes, and fluctuations, and they generate efficiently strong out-of-ecliptic fields. Slow-ejecta sheaths are considerably slower and have weaker fields and field fluctuations, and therefore they cause primarily moderate geospace activity. Sheaths of weak and strong B field ejecta have distinct properties, but differences in their geoeffectiveness are less drastic. Sheaths of fast and strong ejecta push the subsolar magnetopause significantly earthward, often even beyond geostationary orbit. Slow-ejecta sheaths also compress the magnetopause significantly due to their large densities that are likely a result of their relatively long propagation times and source near the streamer belt. We find the regions near the shock and ejecta leading edge to be the most geoeffective parts of the sheath. These regions are also associated with the largest B field magnitudes, out-of-ecliptic fields, and field fluctuations as well as largest speeds and densities. The variations, however, depend on driver properties. Forecasting sheath properties is challenging due to their variable nature, but the dependence on ejecta properties determined in this work could help to estimate sheath geoeffectiveness through remote-sensing coronal mass ejection observations.
  • Gaia Collaboration; Brown, A. G. A.; Muinonen, K.; Fedorets, G.; Granvik, M.; Siltala, L. (2018)
    Context. We present the second Gaia data release, Gaia DR2, consisting of astrometry, photometry, radial velocities, and information on astrophysical parameters and variability, for sources brighter than magnitude 21. In addition epoch astrometry and photometry are provided for a modest sample of minor planets in the solar system. Aims. A summary of the contents of Gaia DR2 is presented, accompanied by a discussion on the differences with respect to Gaia DR1 and an overview of the main limitations which are still present in the survey. Recommendations are made on the responsible use of Gaia DR2 results. Methods. The raw data collected with the Gaia instruments during the first 22 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium (DPAC) and turned into this second data release, which represents a major advance with respect to Gaia DR1 in terms of completeness, performance, and richness of the data products. Results. Gaia DR2 contains celestial positions and the apparent brightness in G for approximately 1.7 billion sources. For 1.3 billion of those sources, parallaxes and proper motions are in addition available. The sample of sources for which variability information is provided is expanded to 0 : 5 million stars. This data release contains four new elements: broad-band colour information in the form of the apparent brightness in the G(BP) (330-680 nm) and G(RP) (630-1050 nm) bands is available for 1.4 billion sources; median radial velocities for some 7 million sources are presented; for between 77 and 161 million sources estimates are provided of the stellar effective temperature, extinction, reddening, and radius and luminosity; and for a pre-selected list of 14 000 minor planets in the solar system epoch astrometry and photometry are presented. Finally, Gaia DR2 also represents a new materialisation of the celestial reference frame in the optical, the Gaia-CRF2, which is the first optical reference frame based solely on extragalactic sources. There are notable changes in the photometric system and the catalogue source list with respect to Gaia DR1, and we stress the need to consider the two data releases as independent. Conclusions. Gaia DR2 represents a major achievement for the Gaia mission, delivering on the long standing promise to provide parallaxes and proper motions for over 1 billion stars, and representing a first step in the availability of complementary radial velocity and source astrophysical information for a sample of stars in the Gaia survey which covers a very substantial fraction of the volume of our galaxy.
  • Clerc, N.; Ramos-Ceja, M. E.; Ridl, J.; Lamer, G.; Brunner, H.; Hofmann, F.; Comparat, J.; Pacaud, F.; Käfer, F.; Reiprich, T. H.; Merloni, A.; Schmid, C.; Brand, T.; Wilms, J.; Friedrich, P.; Finoguenov, A.; Dauser, T.; Kreykenbohm, I. (2018)
    Context. Studies of galaxy clusters provide stringent constraints on models of structure formation. Provided that selection effects are under control, large X-ray surveys are well suited to derive cosmological parameters, in particular those governing the dark energy equation of state. Aims. We forecast the capabilities of the all-sky eROSITA (extended ROentgen Survey with an Imaging Telescope Array) survey to be achieved by the early 2020s. We bring special attention to modelling the entire chain from photon emission to source detection and cataloguing. Methods. The selection function of galaxy clusters for the upcoming eROSITA mission is investigated by means of extensive and dedicated Monte-Carlo simulations. Employing a combination of accurate instrument characterisation and a state-of-the-art source detection technique, we determine a cluster detection efficiency based on the cluster fluxes and sizes. Results. Using this eROSITA cluster selection function, we find that eROSITA will detect a total of approximately 10(5) clusters in the extra-galactic sky. This number of clusters will allow eROSITA to put stringent constraints on cosmological models. We show that incomplete assumptions on selection effects, such as neglecting the distribution of cluster sizes, induce a bias in the derived value of cosmological parameters. Conclusions. Synthetic simulations of the eROSITA sky capture the essential characteristics impacting the next-generation galaxy cluster surveys and they highlight parameters requiring tight monitoring in order to avoid biases in cosmological analyses.
  • Ahumada, Romina; Prieto, Carlos Allende; Almeida, Andres; Andrews, Brett H.; Anguiano, Borja; Armengaud, Eric; Aubert, Marie; Avila, Santiago; Avila-Reese, Vladimir; Badenes, Carles; Balland, Christophe; Barger, Kat; Barrera-Ballesteros, Jorge K.; Basu, Sarbani; Bautista, Julian; Beaton, Rachael L.; Beers, Timothy C.; Benavides, B. Izamar T.; Bender, Chad F.; Bernardi, Mariangela; Bovy, Jo; Brandt, W. N.; Brinkmann, Jonathan; Brownstein, Joel R.; Bundy, Kevin; Burgasser, Adam; Burtin, Etienne; Cano-Diaz, Mariana; Capasso, Raffaella; Cappellari, Michele; Carrera, Ricardo; Chabanier, Solene; Chaplin, William; Chapman, Michael; Cherinka, Brian; Chiappini, Cristina; Choi, Peter Doohyun; Chojnowski, S. Drew; Chung, Haeun; Clerc, Nicolas; Coffey, Damien; Comerford, Julia M.; Comparat, Johan; da Costa, Luiz; Cousinou, Marie-Claude; Covey, Kevin; Crane, Jeffrey D.; Cunha, Katia; Ilha, Gabriele da Silva; Dai, Yu Sophia; Damsted, Sanna B.; Darling, Jeremy; Dawson, Kyle; De, Nikhil; de la Macorra, Axel; Lee, Nathan De; de Andrade Queiroz, Anna Barbara; Machado, Alice Deconto; de la Torre, Sylvain; Dell'Agli, Flavia; des Bourboux, Helion du Mas; Diamond-Stanic, Aleksandar M.; Dillon, Sean; Donor, John; Drory, Niv; Duckworth, Chris; Dwelly, Tom; Ebelke, Garrett; Eftekharzadeh, Sarah; Eigenbrot, Arthur Davis; Elsworth, Yvonne P.; Eracleous, Mike; Erfanianfar, Ghazaleh; Escoffier, Stephanie; Fan, Xiaohui; Farr, Emily; Fernandez-Trincado, Jose G.; Feuillet, Diane; Finoguenov, Alexis; Fofie, Patricia; Fraser-McKelvie, Amelia; Frinchaboy, Peter M.; Fromenteau, Sebastien; Fu, Hai; Galbany, Lluis; Garcia, Rafael A.; Garcia-Hernandez, D. A.; Oehmichen, Luis Alberto Garma; Ge, Junqiang; Maia, Marcio Antonio Geimba; Geisler, Doug; Gelfand, Joseph; Goddy, Julian; Gonzalez-Perez, Violeta; Green, Paul; Grier, Catherine J.; Hekker, S.; Hogg, David W.; Holtzman, Jon A.; Horta, Danny; Hou, Jiamin; Hsieh, Bau-Ching; Huber, Daniel; Hunt, Jason A. S.; Chitham, J. Ider; Iv, Charles C. Kirkpatrick; McDermid, Richard M.; Minniti, Dante; Minsley, Rebecca; Mosser, Benoit; Myers, Adam D.; Nandra, Kirpal; do Nascimento, Janaina Correa; Nevin, Rebecca Jean; Newman, Jeffrey A.; Nidever, David L.; Nitschelm, Christian; Noterdaeme, Pasquier; O'Connell, Julia E.; Olmstead, Matthew D.; Oravetz, Daniel; Oravetz, Audrey; Osorio, Yeisson; Pace, Zachary J.; Padilla, Nelson; Palanque-Delabrouille, Nathalie; Pan, Hsi-An; Pan, Kaike; Parker, James; Peirani, Sebastien; Perez-Fournon, Ismael; Perez-Rafols, Ignasi; Petitjean, Patrick; Pieri, Matthew M.; Pinsonneault, Marc; Poovelil, Vijith Jacob; Povick, Joshua Tyler; Price-Whelan, Adrian M.; Raddick, M. Jordan; Raichoor, Anand; Ray, Amy; Rembold, Sandro Barboza; Rezaie, Mehdi; Riffel, Rogemar A.; Riffel, Rogerio; Rix, Hans-Walter; Robin, Annie C.; Roman-Lopes, A.; Rowlands, Kate; Rubin, Kate H. R.; Salvato, Mara; Sanchez, Ariel G.; Sanchez-Menguiano, Laura; Sanchez-Gallego, Jose R. (2020)
    This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17).
  • Verbeke, C.; Pomoell, J.; Poedts, S. (2019)
    Aims. We introduce a new model for coronal mass ejections (CMEs) that has been implemented in the magnetohydrodynamics (MHD) inner heliosphere model EUHFORIA. Utilising a linear force-free spheromak (LFFS) solution, the model provides an intrinsic magnetic field structure for the CME. As a result, the new model has the potential to predict the magnetic components of CMEs at Earth. In this paper, we present the implementation of the new model and show the capability of the new model. Methods. We present initial validation runs for the new magnetised CME model by considering the same set of events as used in the initial validation run of EUHFORIA that employed the Cone model. In particular, we have focused on modelling the CME that was responsible for creating the largest geomagnetic disturbance (Dst index). Two scenarios are discussed: one where a single magnetised CME is launched and another in which we launch all five Earth-directed CMEs that were observed during the considered time period. Four out of the five CMEs were modelled using the Cone model. Results. In the first run, where the propagation of a single magnetized CME is considered, we find that the magnetic field components at Earth are well reproduced as compared to in-situ spacecraft data. Considering a virtual spacecraft that is separated approximately seven heliographic degrees from the position of Earth, we note that the centre of the magnetic cloud is missing Earth and a considerably larger magnetic field strength can be found when shifting to that location. For the second run, launching four Cone CMEs and one LFFS CME, we notice that the simulated magnetised CME is arriving at the same time as in the corresponding full Cone model run. We find that to achieve this, the speed of the CME needs to be reduced in order to compensate for the expansion of the CME due to the addition of the magnetic field inside the CME. The reduced initial speed of the CME and the added magnetic field structure give rise to a very similar propagation of the CME with approximately the same arrival time at 1 au. In contrast to the Cone model, however, the magnetised CME is able to predict the magnetic field components at Earth. However, due to the interaction between the Cone model CMEs and the magnetised CME, the magnetic field amplitude is significantly lower than for the run using a single magnetised CME. Conclusions. We have presented the LFFS model that is able to simulate and predict the magnetic field components and the propagation of magnetised CMEs in the inner heliosphere and at Earth. We note that shifting towards a virtual spacecraft in the neighbourhood of Earth can give rise to much stronger magnetic field components. This gives the option of adding a grid of virtual spacecrafts to give a range of values for the magnetic field components.