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  • 1
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    The Amphimedon queenslandica genome and the evolution of animal complexity (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-08-06
    Description: Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130542/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130542/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Srivastava, Mansi -- Simakov, Oleg -- Chapman, Jarrod -- Fahey, Bryony -- Gauthier, Marie E A -- Mitros, Therese -- Richards, Gemma S -- Conaco, Cecilia -- Dacre, Michael -- Hellsten, Uffe -- Larroux, Claire -- Putnam, Nicholas H -- Stanke, Mario -- Adamska, Maja -- Darling, Aaron -- Degnan, Sandie M -- Oakley, Todd H -- Plachetzki, David C -- Zhai, Yufeng -- Adamski, Marcin -- Calcino, Andrew -- Cummins, Scott F -- Goodstein, David M -- Harris, Christina -- Jackson, Daniel J -- Leys, Sally P -- Shu, Shengqiang -- Woodcroft, Ben J -- Vervoort, Michel -- Kosik, Kenneth S -- Manning, Gerard -- Degnan, Bernard M -- Rokhsar, Daniel S -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-03/HG/NHGRI NIH HHS/ -- R01 HG004164-04/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA. mansi@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686567" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/genetics ; Cell Adhesion/genetics ; Cell Cycle/genetics ; Cell Polarity/genetics ; Cell Proliferation ; *Evolution, Molecular ; Genes/genetics ; Genome/*genetics ; Genomics ; Humans ; Immunity, Innate/genetics ; Models, Biological ; Neurons/metabolism ; Phosphotransferases/chemistry/genetics ; Phylogeny ; Porifera/anatomy & histology/cytology/*genetics/immunology ; Sequence Analysis, DNA ; Signal Transduction/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Do the Kepler AGN light curves need reprocessing? (2015)
    Oxford University Press
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    Publication Date: 2015-08-30
    Description: We gauge the impact of spacecraft-induced effects on the inferred variability properties of the light curve of the Seyfert 1 AGN Zw 229-15 observed by Kepler . We compare the light curve of Zw 229-15 obtained from the Kepler MAST data base with a reprocessed light curve constructed from raw pixel data. We use the first-order structure function, SF( t ), to fit both light curves to the damped power-law PSD (power spectral density) of Kasliwal et al. On short time-scales, we find a steeper log PSD slope ( = 2.90 to within 10 per cent) for the reprocessed light curve as compared to the light curve found on MAST ( = 2.65 to within 10 per cent) – both inconsistent with a damped random walk (DRW) which requires  = 2. The log PSD slope inferred for the reprocessed light curve is consistent with previous results that study the same reprocessed light curve. The turnover time-scale is almost identical for both light curves (27.1 and 27.5 d for the reprocessed and MAST data base light curves). Based on the obvious visual difference between the two versions of the light curve and on the PSD model fits, we conclude that there remain significant levels of spacecraft-induced effects in the standard pipeline reduction of the Kepler data. Reprocessing the light curves will change the model inferenced from the data but is unlikely to change the overall scientific conclusions reached by Kasliwal et al. – not all AGN light curves are consistent with the DRW.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Are the variability properties of the Kepler AGN light curves consistent with a damped random walk? (2015)
    Oxford University Press
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    Publication Date: 2015-07-03
    Description: We test the consistency of active galactic nuclei (AGN) optical flux variability with the damped random walk (DRW) model. Our sample consists of 20 multiquarter Kepler AGN light curves including both Type 1 and 2 Seyferts, radio-loud and -quiet AGN, quasars, and blazars. Kepler observations of AGN light curves offer a unique insight into the variability properties of AGN light curves because of the very rapid (11.6–28.6 min) and highly uniform rest-frame sampling combined with a photometric precision of 1 part in 10 5 over a period of 3.5 yr. We categorize the light curves of all 20 objects based on visual similarities and find that the light curves fall into five broad categories. We measure the first-order structure function of these light curves and model the observed light curve with a general broken power-law power spectral density (PSD) characterized by a short-time-scale power-law index and turnover time-scale . We find that less than half the objects are consistent with a DRW and observe variability on short time-scales (~2 h). The turnover time-scale ranges from ~10–135 d. Interesting structure function features include pronounced dips on rest-frame time-scales ranging from 10–100 d and varying slopes on different time-scales. The range of observed short-time-scale PSD slopes and the presence of dip and varying slope features suggests that the DRW model may not be appropriate for all AGN. We conclude that AGN variability is a complex phenomenon that requires a more sophisticated statistical treatment.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Finding rare AGN: X-ray number counts of Chandra sources in Stripe 82 (2013)
    Oxford University Press
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    Publication Date: 2013-05-26
    Description: We present the first results of a wide-area X-ray survey within the Sloan Digital Sky Survey Stripe 82, a 300 deg 2 region of the sky with a substantial investment in multiwavelength coverage. We analysed archival Chandra observations that cover 6.2 deg 2 within Stripe 82 (‘Stripe 82 ACX’), reaching 4.5 flux limits of 1.2  x 10 –15 , 5.4  x 10 –15 and 2.9  x 10 –15  erg s –1  cm –2 in the soft (0.5–2 keV), hard (2–7 keV) and full (0.5–7 keV) bands, to find 480, 137 and 705 X-ray sources, respectively. 214 sources are detected only in the full band and 4 sources are detected solely in the soft band. Utilizing data products from the Chandra Source Catalog, we construct independent $\mathrm{{\rm l}og}\, N{\rm -}\mathrm{{\rm l}og}\,S$ relationships, detailing the number density of X-ray sources as a function of flux. The soft and full bands show general agreement with previous Chandra surveys; the hard band number counts agree among Stripe 82 ACX, XBoötes and XDEEP2, but all three are somewhat systematically lower than the counts derived from Chandra Multiwavelength Project. We compare the luminosity distribution of Stripe 82 ACX with the smaller, deeper Chandra Deep Field -South, Extended Chandra Deep Field -South and Chandra -COSMOS surveys to illustrate the benefit of wide-area surveys in locating high-luminosity and/or high-redshift active galactic nuclei (AGN). Finally, we compare the identified AGN with predictions from population synthesis models, noting that prior to any spectroscopic follow-up campaign, we have already located roughly half the high-luminosity quasars at high redshift expected to lie within the survey area. However, our data also suggest that refinements to population synthesis models will be required.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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