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  • 1
    Publication Date: 2015-06-18
    Description: Cell-to-cell variation is a universal feature of life that affects a wide range of biological phenomena, from developmental plasticity to tumour heterogeneity. Although recent advances have improved our ability to document cellular phenotypic variation, the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq) integrated into a programmable microfluidics platform. Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provide insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type-specific accessibility variance across eight cell types. Targeted perturbations of cell cycle or transcription factor signalling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome compartments de novo, linking single-cell accessibility variation to three-dimensional genome organization. Single-cell analysis of DNA accessibility provides new insight into cellular variation of the 'regulome'.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4685948/" 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/PMC4685948/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buenrostro, Jason D -- Wu, Beijing -- Litzenburger, Ulrike M -- Ruff, Dave -- Gonzales, Michael L -- Snyder, Michael P -- Chang, Howard Y -- Greenleaf, William J -- 5U54HG00455805/HG/NHGRI NIH HHS/ -- P50 HG007735/HG/NHGRI NIH HHS/ -- P50HG007735/HG/NHGRI NIH HHS/ -- T32 HG000044/HG/NHGRI NIH HHS/ -- T32HG000044/HG/NHGRI NIH HHS/ -- U19 AI057266/AI/NIAID NIH HHS/ -- U19AI057266/AI/NIAID NIH HHS/ -- U54 HG004558/HG/NHGRI NIH HHS/ -- UH2 AR067676/AR/NIAMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA [2] Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA. ; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA. ; Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA. ; Fluidigm Corporation, South San Francisco, California 94080, USA. ; 1] Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA [2] Department of Applied Physics, Stanford University, Stanford, California 94025, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26083756" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Compartmentation ; Cell Cycle/genetics ; Cell Line ; Cells/classification/*metabolism ; Chromatin/*genetics/*metabolism ; DNA/genetics/metabolism ; Epigenesis, Genetic ; *Epigenomics ; Genome, Human/genetics ; Humans ; Microfluidics ; Signal Transduction ; Single-Cell Analysis/*methods ; Transcription Factors/metabolism ; Transposases/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2008-05-24
    Description: Mineral deposits on the martian surface can elucidate ancient environmental conditions on the planet. Opaline silica deposits (as much as 91 weight percent SiO2) have been found in association with volcanic materials by the Mars rover Spirit. The deposits are present both as light-toned soils and as bedrock. We interpret these materials to have formed under hydrothermal conditions and therefore to be strong indicators of a former aqueous environment. This discovery is important for understanding the past habitability of Mars because hydrothermal environments on Earth support thriving microbial ecosystems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Squyres, S W -- Arvidson, R E -- Ruff, S -- Gellert, R -- Morris, R V -- Ming, D W -- Crumpler, L -- Farmer, J D -- Marais, D J Des -- Yen, A -- McLennan, S M -- Calvin, W -- Bell, J F 3rd -- Clark, B C -- Wang, A -- McCoy, T J -- Schmidt, M E -- de Souza, P A Jr -- New York, N.Y. -- Science. 2008 May 23;320(5879):1063-7. doi: 10.1126/science.1155429.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Astronomy, Space Sciences Building, Cornell University, Ithaca, NY 14853, USA. squyres@astro.cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497295" target="_blank"〉PubMed〈/a〉
    Keywords: Extraterrestrial Environment ; Hot Temperature ; Hydrogen-Ion Concentration ; *Mars ; *Silicon Dioxide ; Spacecraft ; *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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  • 3
    Publication Date: 2010-06-05
    Description: Decades of speculation about a warmer, wetter Mars climate in the planet's first billion years postulate a denser CO2-rich atmosphere than at present. Such an atmosphere should have led to the formation of outcrops rich in carbonate minerals, for which evidence has been sparse. Using the Mars Exploration Rover Spirit, we have now identified outcrops rich in magnesium-iron carbonate (16 to 34 weight percent) in the Columbia Hills of Gusev crater. Its composition approximates the average composition of the carbonate globules in martian meteorite ALH 84001. The Gusev carbonate probably precipitated from carbonate-bearing solutions under hydrothermal conditions at near-neutral pH in association with volcanic activity during the Noachian era.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morris, Richard V -- Ruff, Steven W -- Gellert, Ralf -- Ming, Douglas W -- Arvidson, Raymond E -- Clark, Benton C -- Golden, D C -- Siebach, Kirsten -- Klingelhofer, Gostar -- Schroder, Christian -- Fleischer, Iris -- Yen, Albert S -- Squyres, Steven W -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):421-4. doi: 10.1126/science.1189667. Epub 2010 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NASA Johnson Space Center, Houston, TX 77058, USA. richard.v.morris@nasa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20522738" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere ; Carbon Dioxide ; *Carbonates/chemistry ; Climate ; Extraterrestrial Environment ; Ferrous Compounds ; Magnesium ; *Mars ; Meteoroids ; Spacecraft ; Temperature ; *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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  • 4
    Publication Date: 2004-08-07
    Description: Wind-abraded rocks, ripples, drifts, and other deposits of windblown sediments are seen at the Columbia Memorial Station where the Spirit rover landed. Orientations of these features suggest formative winds from the north-northwest, consistent with predictions from atmospheric models of afternoon winds in Gusev Crater. Cuttings from the rover Rock Abrasion Tool are asymmetrically distributed toward the south-southeast, suggesting active winds from the north-northwest at the time (midday) of the abrasion operations. Characteristics of some rocks, such as a two-toned appearance, suggest that they were possibly buried and exhumed on the order of 5 to 60 centimeters by wind deflation, depending on location.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greeley, R -- Squyres, S W -- Arvidson, R E -- Bartlett, P -- Bell, J F 3rd -- Blaney, D -- Cabrol, N A -- Farmer, J -- Farrand, B -- Golombek, M P -- Gorevan, S P -- Grant, J A -- Haldemann, A F C -- Herkenhoff, K E -- Johnson, J -- Landis, G -- Madsen, M B -- McLennan, S M -- Moersch, J -- Rice, J W Jr -- Richter, L -- Ruff, S -- Sullivan, R J -- Thompson, S D -- Wang, A -- Weitz, C M -- Whelley, P -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):810-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geological Sciences, Arizona State University, Box 871404, Tempe, AZ 85287-1404, USA. Greeley@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297660" target="_blank"〉PubMed〈/a〉
    Keywords: Evolution, Planetary ; Extraterrestrial Environment ; *Mars ; Wind
    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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  • 5
    Publication Date: 2004-08-07
    Description: The Miniature Thermal Emission Spectrometer (Mini-TES) on Spirit has studied the mineralogy and thermophysical properties at Gusev crater. Undisturbed soil spectra show evidence for minor carbonates and bound water. Rocks are olivinerich basalts with varying degrees of dust and other coatings. Dark-toned soils observed on disturbed surfaces may be derived from rocks and have derived mineralogy (+/-5 to 10%) of 45% pyroxene (20% Ca-rich pyroxene and 25% pigeonite), 40% sodic to intermediate plagioclase, and 15% olivine (forsterite 45% +/-5 to 10). Two spectrally distinct coatings are observed on rocks, a possible indicator of the interaction of water, rock, and airfall dust. Diurnal temperature data indicate particle sizes from 40 to 80 microm in hollows to approximately 0.5 to 3 mm in soils.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christensen, P R -- Ruff, S W -- Fergason, R L -- Knudson, A T -- Anwar, S -- Arvidson, R E -- Bandfield, J L -- Blaney, D L -- Budney, C -- Calvin, W M -- Glotch, T D -- Golombek, M P -- Gorelick, N -- Graff, T G -- Hamilton, V E -- Hayes, A -- Johnson, J R -- McSween, H Y Jr -- Mehall, G L -- Mehall, L K -- Moersch, J E -- Morris, R V -- Rogers, A D -- Smith, M D -- Squyres, S W -- Wolff, M J -- Wyatt, M B -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):837-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geological Sciences, Arizona State University, Tempe, AZ 85287, USA. phil.christensen@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297667" target="_blank"〉PubMed〈/a〉
    Keywords: Carbonates ; Geologic Sediments ; Interferometry ; Iron Compounds ; Magnesium Compounds ; *Mars ; *Minerals ; Oxides ; Silicates ; Spectrum Analysis ; Temperature ; 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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  • 6
    Publication Date: 2003-06-07
    Description: The Thermal Emission Imaging System (THEMIS) on Mars Odyssey has produced infrared to visible wavelength images of the martian surface that show lithologically distinct layers with variable thickness, implying temporal changes in the processes or environments during or after their formation. Kilometer-scale exposures of bedrock are observed; elsewhere airfall dust completely mantles the surface over thousands of square kilometers. Mars has compositional variations at 100-meter scales, for example, an exposure of olivine-rich basalt in the walls of Ganges Chasma. Thermally distinct ejecta facies occur around some craters with variations associated with crater age. Polar observations have identified temporal patches of water frost in the north polar cap. No thermal signatures associated with endogenic heat sources have been identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christensen, Philip R -- Bandfield, Joshua L -- Bell, James F 3rd -- Gorelick, Noel -- Hamilton, Victoria E -- Ivanov, Anton -- Jakosky, Bruce M -- Kieffer, Hugh H -- Lane, Melissa D -- Malin, Michael C -- McConnochie, Timothy -- McEwen, Alfred S -- McSween, Harry Y Jr -- Mehall, Greg L -- Moersch, Jeffery E -- Nealson, Kenneth H -- Rice, James W Jr -- Richardson, Mark I -- Ruff, Steven W -- Smith, Michael D -- Titus, Timothy N -- Wyatt, Michael B -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2056-61. Epub 2003 Jun 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geological Sciences, Arizona State University, Tempe, AZ 85287-6305, USA. phil.christensen@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12791998" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide ; Extraterrestrial Environment ; Geologic Sediments ; Geological Phenomena ; Geology ; *Mars ; Seasons ; Temperature ; 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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  • 7
    Publication Date: 2004-08-07
    Description: The Spirit landing site in Gusev Crater on Mars contains dark, fine-grained, vesicular rocks interpreted as lavas. Pancam and Mini-Thermal Emission Spectrometer (Mini-TES) spectra suggest that all of these rocks are similar but have variable coatings and dust mantles. Magnified images of brushed and abraded rock surfaces show alteration rinds and veins. Rock interiors contain 〈/=25% megacrysts. Chemical analyses of rocks by the Alpha Particle X-ray Spectrometer are consistent with picritic basalts, containing normative olivine, pyroxenes, plagioclase, and accessory FeTi oxides. Mossbauer, Pancam, and Mini-TES spectra confirm the presence of olivine, magnetite, and probably pyroxene. These basalts extend the known range of rock compositions composing the martian crust.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McSween, H Y -- Arvidson, R E -- Bell, J F 3rd -- Blaney, D -- Cabrol, N A -- Christensen, P R -- Clark, B C -- Crisp, J A -- Crumpler, L S -- Des Marais, D J -- Farmer, J D -- Gellert, R -- Ghosh, A -- Gorevan, S -- Graff, T -- Grant, J -- Haskin, L A -- Herkenhoff, K E -- Johnson, J R -- Jolliff, B L -- Klingelhoefer, G -- Knudson, A T -- McLennan, S -- Milam, K A -- Moersch, J E -- Morris, R V -- Rieder, R -- Ruff, S W -- De Souza, P A Jr -- Squyres, S W -- Wanke, H -- Wang, A -- Wyatt, M B -- Yen, A -- Zipfel, J -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):842-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996-1410, USA. mcsween@utk.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297668" target="_blank"〉PubMed〈/a〉
    Keywords: Extraterrestrial Environment ; Geologic Sediments ; Iron Compounds ; Magnesium Compounds ; *Mars ; *Minerals ; Oxides ; *Silicates ; Spectroscopy, Mossbauer ; Spectrum Analysis ; 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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  • 8
    Publication Date: 2004-08-07
    Description: The Mars Exploration Rover Spirit has traversed a fairly flat, rock-strewn terrain whose surface is shaped primarily by impact events, although some of the landscape has been altered by eolian processes. Impacts ejected basaltic rocks that probably were part of locally formed lava flows from at least 10 meters depth. Some rocks have been textured and/or partially buried by windblown sediments less than 2 millimeters in diameter that concentrate within shallow, partially filled, circular impact depressions referred to as hollows. The terrain traversed during the 90-sol (martian solar day) nominal mission shows no evidence for an ancient lake in Gusev crater.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grant, J A -- Arvidson, R -- Bell, J F 3rd -- Cabrol, N A -- Carr, M H -- Christensen, P -- Crumpler, L -- Des Marais, D J -- Ehlmann, B L -- Farmer, J -- Golombek, M -- Grant, F D -- Greeley, R -- Herkenhoff, K -- Li, R -- McSween, H Y -- Ming, D W -- Moersch, J -- Rice, J W Jr -- Ruff, S -- Richter, L -- Squyres, S -- Sullivan, R -- Weitz, C -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):807-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Earth and Planetary Studies, National Air and Space Museum, Smithsonian Institution, Washington, DC 20560, USA. grantj@nasm.si.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297659" target="_blank"〉PubMed〈/a〉
    Keywords: Extraterrestrial Environment ; Geologic Sediments ; *Mars ; Minerals ; Silicates ; Volcanic Eruptions ; 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
    Publication Date: 2004-12-04
    Description: The Miniature Thermal Emission Spectrometer (Mini-TES) on Opportunity investigated the mineral abundances and compositions of outcrops, rocks, and soils at Meridiani Planum. Coarse crystalline hematite and olivine-rich basaltic sands were observed as predicted from orbital TES spectroscopy. Outcrops of aqueous origin are composed of 15 to 35% by volume magnesium and calcium sulfates [a high-silica component modeled as a combination of glass, feldspar, and sheet silicates (approximately 20 to 30%)], and hematite; only minor jarosite is identified in Mini-TES spectra. Mini-TES spectra show only a hematite signature in the millimeter-sized spherules. Basaltic materials have more plagioclase than pyroxene, contain olivine, and are similar in inferred mineral composition to basalt mapped from orbit. Bounce rock is dominated by clinopyroxene and is close in inferred mineral composition to the basaltic martian meteorites. Bright wind streak material matches global dust. Waterlain rocks covered by unaltered basaltic sands suggest a change from an aqueous environment to one dominated by physical weathering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christensen, P R -- Wyatt, M B -- Glotch, T D -- Rogers, A D -- Anwar, S -- Arvidson, R E -- Bandfield, J L -- Blaney, D L -- Budney, C -- Calvin, W M -- Fallacaro, A -- Fergason, R L -- Gorelick, N -- Graff, T G -- Hamilton, V E -- Hayes, A G -- Johnson, J R -- Knudson, A T -- McSween, H Y Jr -- Mehall, G L -- Mehall, L K -- Moersch, J E -- Morris, R V -- Smith, M D -- Squyres, S W -- Ruff, S W -- Wolff, M J -- New York, N.Y. -- Science. 2004 Dec 3;306(5702):1733-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geological Sciences, Arizona State University, Tempe, AZ 85287, USA. phil.christensen@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15576609" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium Sulfate ; Extraterrestrial Environment ; Ferric Compounds ; Geologic Sediments ; Iron Compounds ; Magnesium Compounds ; Magnesium Sulfate ; *Mars ; *Minerals ; Silicates ; Spacecraft ; Sulfates ; 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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  • 10
    Publication Date: 2012-05-05
    Description: The rover Opportunity has investigated the rim of Endeavour Crater, a large ancient impact crater on Mars. Basaltic breccias produced by the impact form the rim deposits, with stratigraphy similar to that observed at similar-sized craters on Earth. Highly localized zinc enrichments in some breccia materials suggest hydrothermal alteration of rim deposits. Gypsum-rich veins cut sedimentary rocks adjacent to the crater rim. The gypsum was precipitated from low-temperature aqueous fluids flowing upward from the ancient materials of the rim, leading temporarily to potentially habitable conditions and providing some of the waters involved in formation of the ubiquitous sulfate-rich sandstones of the Meridiani region.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Squyres, S W -- Arvidson, R E -- Bell, J F 3rd -- Calef, F 3rd -- Clark, B C -- Cohen, B A -- Crumpler, L A -- de Souza, P A Jr -- Farrand, W H -- Gellert, R -- Grant, J -- Herkenhoff, K E -- Hurowitz, J A -- Johnson, J R -- Jolliff, B L -- Knoll, A H -- Li, R -- McLennan, S M -- Ming, D W -- Mittlefehldt, D W -- Parker, T J -- Paulsen, G -- Rice, M S -- Ruff, S W -- Schroder, C -- Yen, A S -- Zacny, K -- New York, N.Y. -- Science. 2012 May 4;336(6081):570-6. doi: 10.1126/science.1220476.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Astronomy, Cornell University, Ithaca, NY 14853, USA. squyres@astro.cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556248" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium Sulfate ; Extraterrestrial Environment ; Geological Phenomena ; *Mars ; Meteoroids ; Silicates ; Spacecraft ; *Water ; Zinc
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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