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  • Oxford University Press  (23)
  • American Association for the Advancement of Science (AAAS)
  • Tübingen: Mohr
  • ZBW - Deutsche Zentralbibliothek für Wirtschaftswissenschaften, Leibniz-Informationszentrum Wirtschaft Kiel, Hamburg
  • 1
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    A framework for installable external tools in Skyline (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-27
    Description: : Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. The Skyline document model contains extensive mass spectrometry data from targeted proteomics experiments performed using selected reaction monitoring, parallel reaction monitoring and data-independent and data-dependent acquisition methods. Researchers have developed software tools that perform statistical analysis of the experimental data contained within Skyline documents. The new external tools framework allows researchers to integrate their tools into Skyline without modifying the Skyline codebase. Installed tools provide point-and-click access to downstream statistical analysis of data processed in Skyline. The framework also specifies a uniform interface to format tools for installation into Skyline. Tool developers can now easily share their tools with proteomics researchers using Skyline. Availability and implementation: Skyline is available as a single-click self-updating web installation at http://skyline.maccosslab.org . This Web site also provides access to installable external tools and documentation. Contact: brendanx@u.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-02
    Description: The class II transactivator (CIITA) is essential for the expression of major histocompatibility complex class II (MHC-II) genes; however, the role of CIITA in gene regulation outside of MHC-II biology is not fully understood. To comprehensively map CIITA-bound loci, ChIP-seq was performed in the human B lymphoblastoma cell line Raji. CIITA bound 480 sites, and was significantly enriched at active promoters and enhancers. The complexity of CIITA transcriptional regulation of target genes was analyzed using a combination of CIITA -null cells, including a novel cell line created using CRISPR/Cas9 tools. MHC-II genes and a few novel genes were regulated by CIITA; however, most other genes demonstrated either diminished or no changes in the absence of CIITA. Nearly all CIITA-bound sites were within regions containing accessible chromatin, and CIITA's presence at these sites was associated with increased histone H3K27 acetylation, suggesting that CIITA's role at these non-regulated loci may be to poise the region for subsequent regulation. Computational genome-wide modeling of the CIITA bound XY box motifs provided constraints for sequences associated with CIITA-mediated gene regulation versus binding. These data therefore define the CIITA regulome in B cells and establish sequence specificities that predict activity for an essential regulator of the adaptive immune response.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    The early evolution of the inner solar system: a meteoritic perspective (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-07
    Description: Formation of the solar system may have been triggered by a stellar wind. From then on, the solar system would have followed a conventional evolutionary path, including the formation of a disk and bipolar jets. The now extinct short-lived radionuclides beryllium-10 and, possibly, manganese-53 that were present in meteorites probably resulted from energetic particle irradiation within the solar system. Calcium-aluminum-rich inclusions (the oldest known solar system solids) and chondrules could have been produced by the bipolar jets, but it is more likely that they formed during localized events in the asteroid belt. The chondritic meteorites formed within the temperature range (100 to 400 kelvin) inferred for the midplane of classical T Tauri disks at 2 to 3 astronomical units from their central stars. However, these meteorites may retain a chemical memory of earlier times when midplane temperatures were much higher. Dissipation of the solar nebula occurred within a few million years of solar system formation, whereas differentiation of asteroidal-sized bodies occurred within 5 to 15 million years. The terrestrial planets took approximately 100 million years to form. Consequently, they would have accreted already differentiated bodies, and their final assembly was not completed until after the solar nebula had dispersed. This implies that water-bearing asteroids and/or icy planetesimals that formed near Jupiter are the likely sources of Earth's water.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'D Alexander, C M -- Boss, A P -- Carlson, R W -- New York, N.Y. -- Science. 2001 Jul 6;293(5527):64-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Terrestrial Magnetism, Carnegie Institution of Washington, 5241 Broad Branch Road, N.W., Washington, DC 20015, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11441173" 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
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    The neuron-specific protein PGP 9.5 is a ubiquitin carboxyl-terminal hydrolase (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-11-03
    Description: A complementary DNA (cDNA) for ubiquitin carboxyl-terminal hydrolase isozyme L3 was cloned from human B cells. The cDNA encodes a protein of 230 amino acids with a molecular mass of 26.182 daltons. The human protein is very similar to the bovine homolog, with only three amino acids differing in over 100 residues compared. The amino acid sequence deduced from the cDNA was 54% identical to that of the neuron-specific protein PGP 9.5. Purification of bovine PGP 9.5 confirmed that it is also a ubiquitin carboxyl-terminal hydrolase. These results suggest that a family of such related proteins exists and that their expression is tissue-specific.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilkinson, K D -- Lee, K M -- Deshpande, S -- Duerksen-Hughes, P -- Boss, J M -- Pohl, J -- New York, N.Y. -- Science. 1989 Nov 3;246(4930):670-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2530630" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; B-Lymphocytes/enzymology ; Base Sequence ; Cattle ; DNA/genetics ; Humans ; Isoenzymes/genetics ; Molecular Sequence Data ; Neuropeptides/*genetics/isolation & purification ; Sequence Homology, Nucleic Acid ; Thiolester Hydrolases/*genetics/isolation & purification ; Ubiquitin Thiolesterase
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Kepler planet-detection mission: introduction and first results (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-09
    Description: The Kepler mission was designed to determine the frequency of Earth-sized planets in and near the habitable zone of Sun-like stars. The habitable zone is the region where planetary temperatures are suitable for water to exist on a planet's surface. During the first 6 weeks of observations, Kepler monitored 156,000 stars, and five new exoplanets with sizes between 0.37 and 1.6 Jupiter radii and orbital periods from 3.2 to 4.9 days were discovered. The density of the Neptune-sized Kepler-4b is similar to that of Neptune and GJ 436b, even though the irradiation level is 800,000 times higher. Kepler-7b is one of the lowest-density planets (approximately 0.17 gram per cubic centimeter) yet detected. Kepler-5b, -6b, and -8b confirm the existence of planets with densities lower than those predicted for gas giant planets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borucki, William J -- Koch, David -- Basri, Gibor -- Batalha, Natalie -- Brown, Timothy -- Caldwell, Douglas -- Caldwell, John -- Christensen-Dalsgaard, Jorgen -- Cochran, William D -- DeVore, Edna -- Dunham, Edward W -- Dupree, Andrea K -- Gautier, Thomas N 3rd -- Geary, John C -- Gilliland, Ronald -- Gould, Alan -- Howell, Steve B -- Jenkins, Jon M -- Kondo, Yoji -- Latham, David W -- Marcy, Geoffrey W -- Meibom, Soren -- Kjeldsen, Hans -- Lissauer, Jack J -- Monet, David G -- Morrison, David -- Sasselov, Dimitar -- Tarter, Jill -- Boss, Alan -- Brownlee, Don -- Owen, Toby -- Buzasi, Derek -- Charbonneau, David -- Doyle, Laurance -- Fortney, Jonathan -- Ford, Eric B -- Holman, Matthew J -- Seager, Sara -- Steffen, Jason H -- Welsh, William F -- Rowe, Jason -- Anderson, Howard -- Buchhave, Lars -- Ciardi, David -- Walkowicz, Lucianne -- Sherry, William -- Horch, Elliott -- Isaacson, Howard -- Everett, Mark E -- Fischer, Debra -- Torres, Guillermo -- Johnson, John Asher -- Endl, Michael -- MacQueen, Phillip -- Bryson, Stephen T -- Dotson, Jessie -- Haas, Michael -- Kolodziejczak, Jeffrey -- Van Cleve, Jeffrey -- Chandrasekaran, Hema -- Twicken, Joseph D -- Quintana, Elisa V -- Clarke, Bruce D -- Allen, Christopher -- Li, Jie -- Wu, Haley -- Tenenbaum, Peter -- Verner, Ekaterina -- Bruhweiler, Frederick -- Barnes, Jason -- Prsa, Andrej -- New York, N.Y. -- Science. 2010 Feb 19;327(5968):977-80. doi: 10.1126/science.1185402. Epub 2010 Jan 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NASA Ames Research Center, Moffett Field, CA 94035, USA. William.J.Borucki@nasa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20056856" 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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  • 6
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    Kepler-16: a transiting circumbinary planet (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-17
    Description: We report the detection of a planet whose orbit surrounds a pair of low-mass stars. Data from the Kepler spacecraft reveal transits of the planet across both stars, in addition to the mutual eclipses of the stars, giving precise constraints on the absolute dimensions of all three bodies. The planet is comparable to Saturn in mass and size and is on a nearly circular 229-day orbit around its two parent stars. The eclipsing stars are 20 and 69% as massive as the Sun and have an eccentric 41-day orbit. The motions of all three bodies are confined to within 0.5 degrees of a single plane, suggesting that the planet formed within a circumbinary disk.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doyle, Laurance R -- Carter, Joshua A -- Fabrycky, Daniel C -- Slawson, Robert W -- Howell, Steve B -- Winn, Joshua N -- Orosz, Jerome A -- Prsa, Andrej -- Welsh, William F -- Quinn, Samuel N -- Latham, David -- Torres, Guillermo -- Buchhave, Lars A -- Marcy, Geoffrey W -- Fortney, Jonathan J -- Shporer, Avi -- Ford, Eric B -- Lissauer, Jack J -- Ragozzine, Darin -- Rucker, Michael -- Batalha, Natalie -- Jenkins, Jon M -- Borucki, William J -- Koch, David -- Middour, Christopher K -- Hall, Jennifer R -- McCauliff, Sean -- Fanelli, Michael N -- Quintana, Elisa V -- Holman, Matthew J -- Caldwell, Douglas A -- Still, Martin -- Stefanik, Robert P -- Brown, Warren R -- Esquerdo, Gilbert A -- Tang, Sumin -- Furesz, Gabor -- Geary, John C -- Berlind, Perry -- Calkins, Michael L -- Short, Donald R -- Steffen, Jason H -- Sasselov, Dimitar -- Dunham, Edward W -- Cochran, William D -- Boss, Alan -- Haas, Michael R -- Buzasi, Derek -- Fischer, Debra -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1602-6. doi: 10.1126/science.1210923.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Carl Sagan Center for the Study of Life in the Universe, SETI Institute, 189 Bernardo Avenue, Mountain View, CA 94043, USA. ldoyle@seti.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921192" 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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  • 7
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    Kepler-47: a transiting circumbinary multiplanet system (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-08-31
    Description: We report the detection of Kepler-47, a system consisting of two planets orbiting around an eclipsing pair of stars. The inner and outer planets have radii 3.0 and 4.6 times that of Earth, respectively. The binary star consists of a Sun-like star and a companion roughly one-third its size, orbiting each other every 7.45 days. With an orbital period of 49.5 days, 18 transits of the inner planet have been observed, allowing a detailed characterization of its orbit and those of the stars. The outer planet's orbital period is 303.2 days, and although the planet is not Earth-like, it resides within the classical "habitable zone," where liquid water could exist on an Earth-like planet. With its two known planets, Kepler-47 establishes that close binary stars can host complete planetary systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Orosz, Jerome A -- Welsh, William F -- Carter, Joshua A -- Fabrycky, Daniel C -- Cochran, William D -- Endl, Michael -- Ford, Eric B -- Haghighipour, Nader -- MacQueen, Phillip J -- Mazeh, Tsevi -- Sanchis-Ojeda, Roberto -- Short, Donald R -- Torres, Guillermo -- Agol, Eric -- Buchhave, Lars A -- Doyle, Laurance R -- Isaacson, Howard -- Lissauer, Jack J -- Marcy, Geoffrey W -- Shporer, Avi -- Windmiller, Gur -- Barclay, Thomas -- Boss, Alan P -- Clarke, Bruce D -- Fortney, Jonathan -- Geary, John C -- Holman, Matthew J -- Huber, Daniel -- Jenkins, Jon M -- Kinemuchi, Karen -- Kruse, Ethan -- Ragozzine, Darin -- Sasselov, Dimitar -- Still, Martin -- Tenenbaum, Peter -- Uddin, Kamal -- Winn, Joshua N -- Koch, David G -- Borucki, William J -- New York, N.Y. -- Science. 2012 Sep 21;337(6101):1511-4. Epub 2012 Aug 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Astronomy Department, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA. orosz@sciences.sdsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22933522" 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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  • 8
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    Kepler-62: a five-planet system with planets of 1.4 and 1.6 Earth radii in the habitable zone (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-04-20
    Description: We present the detection of five planets--Kepler-62b, c, d, e, and f--of size 1.31, 0.54, 1.95, 1.61 and 1.41 Earth radii (R plus sign in circle), orbiting a K2V star at periods of 5.7, 12.4, 18.2, 122.4, and 267.3 days, respectively. The outermost planets, Kepler-62e and -62f, are super-Earth-size (1.25 R plus sign in circle 〈 planet radius 〈/= 2.0 R plus sign in circle) planets in the habitable zone of their host star, respectively receiving 1.2 +/- 0.2 times and 0.41 +/- 0.05 times the solar flux at Earth's orbit. Theoretical models of Kepler-62e and -62f for a stellar age of ~7 billion years suggest that both planets could be solid, either with a rocky composition or composed of mostly solid water in their bulk.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borucki, William J -- Agol, Eric -- Fressin, Francois -- Kaltenegger, Lisa -- Rowe, Jason -- Isaacson, Howard -- Fischer, Debra -- Batalha, Natalie -- Lissauer, Jack J -- Marcy, Geoffrey W -- Fabrycky, Daniel -- Desert, Jean-Michel -- Bryson, Stephen T -- Barclay, Thomas -- Bastien, Fabienne -- Boss, Alan -- Brugamyer, Erik -- Buchhave, Lars A -- Burke, Chris -- Caldwell, Douglas A -- Carter, Josh -- Charbonneau, David -- Crepp, Justin R -- Christensen-Dalsgaard, Jorgen -- Christiansen, Jessie L -- Ciardi, David -- Cochran, William D -- DeVore, Edna -- Doyle, Laurance -- Dupree, Andrea K -- Endl, Michael -- Everett, Mark E -- Ford, Eric B -- Fortney, Jonathan -- Gautier, Thomas N 3rd -- Geary, John C -- Gould, Alan -- Haas, Michael -- Henze, Christopher -- Howard, Andrew W -- Howell, Steve B -- Huber, Daniel -- Jenkins, Jon M -- Kjeldsen, Hans -- Kolbl, Rea -- Kolodziejczak, Jeffery -- Latham, David W -- Lee, Brian L -- Lopez, Eric -- Mullally, Fergal -- Orosz, Jerome A -- Prsa, Andrej -- Quintana, Elisa V -- Sanchis-Ojeda, Roberto -- Sasselov, Dimitar -- Seader, Shawn -- Shporer, Avi -- Steffen, Jason H -- Still, Martin -- Tenenbaum, Peter -- Thompson, Susan E -- Torres, Guillermo -- Twicken, Joseph D -- Welsh, William F -- Winn, Joshua N -- New York, N.Y. -- Science. 2013 May 3;340(6132):587-90. doi: 10.1126/science.1234702. Epub 2013 Apr 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NASA Ames Research Center, Moffett Field, CA 94035, USA. william.j.borucki@nasa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23599262" target="_blank"〉PubMed〈/a〉
    Keywords: Exobiology ; Extraterrestrial Environment ; Models, Theoretical ; *Planets ; Stars, Celestial ; *Water
    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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  • 9
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    Single-proton spin detection by diamond magnetometry (2015)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2015
    Description: 〈p〉Extending magnetic resonance imaging to the atomic scale has been a long-standing aspiration, driven by the prospect of directly mapping atomic positions in molecules with three-dimensional spatial resolution. We report detection of individual, isolated proton spins by a nitrogen-vacancy (NV) center in a diamond chip covered by an inorganic salt. The single-proton identity was confirmed by the Zeeman effect and by a quantum coherent rotation of the weakly coupled nuclear spin. Using the hyperfine field of the NV center as an imaging gradient, we determined proton-NV distances of less than 1 nm.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Natural Sciences in General
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  • 10
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    Stellar cosmogony: formation and evolution of low mass stars (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-06-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boss, A P -- New York, N.Y. -- Science. 1989 Jun 30;244(4912):1598.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17817283" 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
    Published by American Association for the Advancement of Science (AAAS)
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