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  • 1
    Publication Date: 2016-02-06
    Description: : Genomic datasets are often interpreted in the context of large-scale reference databases. One approach is to identify significantly overlapping gene sets, which works well for gene-centric data. However, many types of high-throughput data are based on genomic regions. Locus Overlap Analysis (LOLA) provides easy and automatable enrichment analysis for genomic region sets, thus facilitating the interpretation of functional genomics and epigenomics data. Availability and Implementation: R package available in Bioconductor and on the following website: http://lola.computational-epigenetics.org . Contact : nsheffield@cemm.oeaw.ac.at or cbock@cemm.oeaw.ac.at
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2019
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 3
    Publication Date: 2011-10-12
    Description: Stress has been identified as a major causal factor for many mental disorders. However, our knowledge about the chain of molecular and cellular events translating stress experience into altered behavior is still rather scant. Here, we have characterized a murine ortholog of the putative tumor suppressor gene DRR1 as a unique stress-induced protein in brain. It binds to actin, promotes bundling and stabilization of actin filaments, and impacts on actin-dependent neurite outgrowth. Endogenous DRR1 localizes to some, but not all, synapses, with preference for the presynaptic region. Hippocampal virus-mediated enhancement of DRR1 expression reduced spine density, diminished the probability of synaptic glutamate release, and altered cognitive performance. DRR1 emerges as a protein to link stress with actin dynamics, which in addition is able to act on synaptic function and cognition.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 4
    Publication Date: 2014-09-17
    Description: The Herschel Multi-tiered Extragalactic Survey (HerMES) is the largest Guaranteed Time Key Programme on the Herschel Space Observatory. With a wedding cake survey strategy, it consists of nested fields with varying depth and area totalling ~380 deg 2 . In this paper, we present deep point source catalogues extracted from Herschel -Spectral and Photometric Imaging Receiver (SPIRE) observations of all HerMES fields, except for the later addition of the 270 deg 2 HerMES Large-Mode Survey (HeLMS) field. These catalogues constitute the second Data Release (DR2) made in 2013 October. A sub-set of these catalogues, which consists of bright sources extracted from Herschel -SPIRE observations completed by 2010 May 1 (covering ~74 deg 2 ) were released earlier in the first extensive data release in 2012 March. Two different methods are used to generate the point source catalogues, the sussextractor point source extractor used in two earlier data releases (EDR and EDR2) and a new source detection and photometry method. The latter combines an iterative source detection algorithm, starfinder , and a De-blended SPIRE Photometry algorithm. We use end-to-end Herschel -SPIRE simulations with realistic number counts and clustering properties to characterize basic properties of the point source catalogues, such as the completeness, reliability, photometric and positional accuracy. Over 500 000 catalogue entries in HerMES fields (except HeLMS) are released to the public through the HeDAM ( Herschel Database in Marseille) website ( http://hedam.lam.fr/HerMES ).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2018-12-19
    Description: ACS Energy Letters DOI: 10.1021/acsenergylett.8b02131
    Electronic ISSN: 2380-8195
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 6
    Publication Date: 2008-05-24
    Description: Massive stars end their short lives in spectacular explosions--supernovae--that synthesize new elements and drive galaxy evolution. Historically, supernovae were discovered mainly through their 'delayed' optical light (some days after the burst of neutrinos that marks the actual event), preventing observations in the first moments following the explosion. As a result, the progenitors of some supernovae and the events leading up to their violent demise remain intensely debated. Here we report the serendipitous discovery of a supernova at the time of the explosion, marked by an extremely luminous X-ray outburst. We attribute the outburst to the 'break-out' of the supernova shock wave from the progenitor star, and show that the inferred rate of such events agrees with that of all core-collapse supernovae. We predict that future wide-field X-ray surveys will catch each year hundreds of supernovae in the act of exploding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Soderberg, A M -- Berger, E -- Page, K L -- Schady, P -- Parrent, J -- Pooley, D -- Wang, X-Y -- Ofek, E O -- Cucchiara, A -- Rau, A -- Waxman, E -- Simon, J D -- Bock, D C-J -- Milne, P A -- Page, M J -- Barentine, J C -- Barthelmy, S D -- Beardmore, A P -- Bietenholz, M F -- Brown, P -- Burrows, A -- Burrows, D N -- Bryngelson, G -- Cenko, S B -- Chandra, P -- Cummings, J R -- Fox, D B -- Gal-Yam, A -- Gehrels, N -- Immler, S -- Kasliwal, M -- Kong, A K H -- Krimm, H A -- Kulkarni, S R -- Maccarone, T J -- Meszaros, P -- Nakar, E -- O'Brien, P T -- Overzier, R A -- de Pasquale, M -- Racusin, J -- Rea, N -- York, D G -- England -- Nature. 2008 May 22;453(7194):469-74. doi: 10.1038/nature06997.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Astrophysical Sciences, Princeton University, Ivy Lane, Princeton, New Jersey 08544, USA. alicia@astro.princeton.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497815" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2008-08-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bock, Christoph -- England -- Nature. 2008 Aug 21;454(7207):938. doi: 10.1038/454938a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719562" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells ; *Famous Persons ; Fertilization in Vitro/*ethics/trends ; Humans ; *Parents ; Paternity ; Pluripotent Stem Cells
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2008-09-05
    Description: The cores of most galaxies are thought to harbour supermassive black holes, which power galactic nuclei by converting the gravitational energy of accreting matter into radiation. Sagittarius A* (Sgr A*), the compact source of radio, infrared and X-ray emission at the centre of the Milky Way, is the closest example of this phenomenon, with an estimated black hole mass that is 4,000,000 times that of the Sun. A long-standing astronomical goal is to resolve structures in the innermost accretion flow surrounding Sgr A*, where strong gravitational fields will distort the appearance of radiation emitted near the black hole. Radio observations at wavelengths of 3.5 mm and 7 mm have detected intrinsic structure in Sgr A*, but the spatial resolution of observations at these wavelengths is limited by interstellar scattering. Here we report observations at a wavelength of 1.3 mm that set a size of 37(+16)(-10) microarcseconds on the intrinsic diameter of Sgr A*. This is less than the expected apparent size of the event horizon of the presumed black hole, suggesting that the bulk of Sgr A* emission may not be centred on the black hole, but arises in the surrounding accretion flow.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doeleman, Sheperd S -- Weintroub, Jonathan -- Rogers, Alan E E -- Plambeck, Richard -- Freund, Robert -- Tilanus, Remo P J -- Friberg, Per -- Ziurys, Lucy M -- Moran, James M -- Corey, Brian -- Young, Ken H -- Smythe, Daniel L -- Titus, Michael -- Marrone, Daniel P -- Cappallo, Roger J -- Bock, Douglas C-J -- Bower, Geoffrey C -- Chamberlin, Richard -- Davis, Gary R -- Krichbaum, Thomas P -- Lamb, James -- Maness, Holly -- Niell, Arthur E -- Roy, Alan -- Strittmatter, Peter -- Werthimer, Daniel -- Whitney, Alan R -- Woody, David -- England -- Nature. 2008 Sep 4;455(7209):78-80. doi: 10.1038/nature07245.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology (MIT) Haystack Observatory, Off Route 40, Westford, Massachusetts 01886, USA. sdoeleman@haystack.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18769434" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2011-11-15
    Description: In the mammalian genome, 5'-CpG-3' dinucleotides are frequently methylated, correlating with transcriptional silencing. Genome-wide demethylation is thought to occur only twice during development, in primordial germ cells and in the pre-implantation embryo. These demethylation events are followed by de novo methylation, setting up a pattern inherited throughout development and modified only at tissue-specific loci. We studied DNA methylation in differentiating mouse erythroblasts in vivo by using genomic-scale reduced representation bisulfite sequencing (RRBS). Demethylation at the erythroid-specific beta-globin locus was coincident with global DNA demethylation at most genomic elements. Global demethylation was continuous throughout differentiation and required rapid DNA replication. Hence, DNA demethylation can occur globally during somatic cell differentiation, providing an experimental model for its study in development and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230325/" 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/PMC3230325/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shearstone, Jeffrey R -- Pop, Ramona -- Bock, Christoph -- Boyle, Patrick -- Meissner, Alexander -- Socolovsky, Merav -- DK32520/DK/NIDDK NIH HHS/ -- R01 HL084168/HL/NHLBI NIH HHS/ -- R01 HL084168-02/HL/NHLBI NIH HHS/ -- R01 HL084168-03/HL/NHLBI NIH HHS/ -- R01 HL084168-04/HL/NHLBI NIH HHS/ -- R01 HL084168-04S1/HL/NHLBI NIH HHS/ -- R01 HL084168-05/HL/NHLBI NIH HHS/ -- T32-130807/PHS HHS/ -- New York, N.Y. -- Science. 2011 Nov 11;334(6057):799-802. doi: 10.1126/science.1207306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22076376" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CpG Islands ; *DNA Methylation ; DNA Replication ; Dinucleoside Phosphates/metabolism ; Embryo, Mammalian ; Erythroblasts/*metabolism ; *Erythropoiesis ; Gene Expression Regulation, Developmental ; Genome ; Liver/embryology ; Locus Control Region ; Long Interspersed Nucleotide Elements ; Mice ; S Phase ; Sequence Analysis, DNA ; Transcription, Genetic ; beta-Globins/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2015-01-13
    Description: The functional capacity of a battery is observed to decrease, often quite dramatically, as discharge rate demands increase. These capacity losses have been attributed to limited ion access and low electrical conductivity, resulting in incomplete electrode use. A strategy to improve electronic conductivity is the design of bimetallic materials that generate a silver matrix in situ during cathode reduction. Ex situ x-ray absorption spectroscopy coupled with in situ energy-dispersive x-ray diffraction measurements on intact lithium/silver vanadium diphosphate (Li/Ag2VP2O8) electrochemical cells demonstrate that the metal center preferentially reduced and its location in the bimetallic cathode are rate-dependent, affecting cell impedance. This work illustrates that spatial imaging as a function of discharge rate can provide needed insights toward improving realizable capacity of bimetallic cathode systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kirshenbaum, Kevin -- Bock, David C -- Lee, Chia-Ying -- Zhong, Zhong -- Takeuchi, Kenneth J -- Marschilok, Amy C -- Takeuchi, Esther S -- New York, N.Y. -- Science. 2015 Jan 9;347(6218):149-54. doi: 10.1126/science.1257289.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Brookhaven National Laboratory, 2 Center Street, Upton, NY 11973-5000, USA. ; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA. ; Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260-4200, USA. ; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA. Department of Materials Science and Engineering, Stony Brook University, Stony Brook, NY 11794-2275, USA. kenneth.takeuchi.1@stonybrook.edu amy.marschilok@stonybrook.edu esther.takeuchi@stonybrook.edu. ; Brookhaven National Laboratory, 2 Center Street, Upton, NY 11973-5000, USA. Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA. Department of Materials Science and Engineering, Stony Brook University, Stony Brook, NY 11794-2275, USA. kenneth.takeuchi.1@stonybrook.edu amy.marschilok@stonybrook.edu esther.takeuchi@stonybrook.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25574017" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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