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  • Articles  (13)
  • Copernicus  (8)
  • Mineralogical Society of Great Britain and Ireland  (4)
  • American Association for the Advancement of Science (AAAS)  (1)
  • Public Library of Science (PLoS)
  • Mineralogical Society of America
  • 2015-2019  (13)
  • 2018  (13)
  • Geosciences  (13)
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  • Articles  (13)
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  • 2015-2019  (13)
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  • 1
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    Agmantinite, Ag2MnSnS4, a new mineral with a wurtzite derivative structure from the Uchucchacua polymetallic deposit, Lima Department, Peru (2018)
    Mineralogical Society of Great Britain and Ireland
    Details
    Publication Date: 2018
    Description: 〈div data-abstract-type="normal"〉 〈p〉Agmantinite, ideally Ag〈span〉2〈/span〉MnSnS〈span〉4〈/span〉, is a new mineral from the Uchucchacua polymetallic deposit, Oyon district, Catajambo, Lima Department, Peru. It occurs as orange–red crystals up to 100 μm across. Agmantinite is translucent with adamantine lustre and possesses a red streak. It is brittle. Neither fracture nor cleavage were observed. Based on the empirical formula the calculated density is 4.574 g/cm〈span〉3〈/span〉. On the basis of chemically similar compounds the Mohs hardness is estimated at between 2 to 2½. In plane-polarised light agmantinite is white with red internal reflections. It is weakly bireflectant with no observable pleochroism with red internal reflections. Between crossed polars, agmantinite is weakly anisotropic with reddish brown to greenish grey rotation tints. The reflectances (〈span〉R〈/span〉〈span〉min〈/span〉 and 〈span〉R〈/span〉〈span〉max〈/span〉) for the four standard wavelengths are: 19.7 and 22.0 (470 nm); 20.5 and 23.2 (546 nm); 21.7 and 2.49 (589 nm); and 20.6 and 23.6 (650 nm), respectively.〈/p〉 〈p〉Agmantinite is orthorhombic, space group 〈span〉P〈/span〉2〈span〉1〈/span〉〈span〉nm〈/span〉, with unit-cell parameters: 〈span〉a〈/span〉 = 6.632(2), 〈span〉b〈/span〉 = 6.922(2), 〈span〉c〈/span〉 = 8.156(2) Å, 〈span〉V〈/span〉 = 374.41(17) Å〈span〉3〈/span〉, 〈span〉a〈/span〉:〈span〉b〈/span〉:〈span〉c〈/span〉 0.958:1:1.178 and 〈span〉Z〈/span〉 = 2. The crystal structure was refined to 〈span〉R〈/span〉 = 0.0575 for 519 reflections with 〈span〉I 〉〈/span〉 2σ(〈span〉I〈/span〉). Agmantinite is the first known mineral of 〈span〉〈span〉〈img data-mimesubtype="gif" data-type="simple" src="http://static.cambridge.org/resource/id/urn:cambridge.org:id:binary:20190522072108342-0385:S0026461X18001391:S0026461X18001391_inline1.gif"〉 〈span data-mathjax-type="texmath"〉 〈/span〉 〈/span〉〈/span〉〈span〉M〈/span〉〈span〉II〈/span〉〈span〉M〈/span〉〈span〉IV〈/span〉S〈span〉4〈/span〉 type that is derived from wurtzite rather than sphalerite by ordered substitution of Zn, analogous to the substitution pattern for deriving stannite from sphalerite. The six strongest X-ray powder-diffraction lines derived from single-crystal X-ray diffraction data [〈span〉d〈/span〉 in Å (intensity)] are: 3.51 (s), 3.32 (w), 3.11 (vs), 2.42 (w), 2.04 (m) and 1.88 (m). The empirical formula (based on 8 apfu) is (Ag〈span〉1.94〈/span〉Cu〈span〉0.03〈/span〉)〈span〉Σ1.97〈/span〉(Mn〈span〉0.98〈/span〉Zn〈span〉0.05〈/span〉)〈span〉Σ1.03〈/span〉Sn〈span〉0.97〈/span〉S〈span〉4.03〈/span〉.The crystal structure-derived formula is Ag〈span〉2〈/span〉(Mn〈span〉0.69〈/span〉Zn〈span〉0.31〈/span〉)〈span〉Σ1.00〈/span〉SnS〈span〉4〈/span〉 and the simplified formula is Ag〈span〉2〈/span〉MnSnS〈span〉4〈/span〉.〈/p〉 〈p〉The name is for the composition and the new mineral and mineral name have been approved by the International Mineralogical Association Commission on New Minerals, Nomenclature and Classification (IMA2014-083).〈/p〉 〈/div〉
    Print ISSN: 0026-461X
    Electronic ISSN: 1471-8022
    Topics: Geosciences
    Published by Mineralogical Society of Great Britain and Ireland
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  • 2
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    Structural and chemical study of weishanite, (Au,Ag,Hg), from the Keystone mine, Colorado, USA. (2018)
    Mineralogical Society of Great Britain and Ireland
    Details
    Publication Date: 2018
    Description: 〈div data-abstract-type="normal"〉〈p〉Structural data for weishanite, an alloy of Au, Ag and Hg, were collected for the first time from a crystal from the Keystone Mine, Colorado, USA. The structure was solved in the space group 〈span〉P〈/span〉6〈span〉3〈/span〉/〈span〉mmc〈/span〉 with the unit cell 〈span〉a〈/span〉 = 2.9348(8) and 〈span〉c〈/span〉 = 4.8215(18) Å] and refined to 〈span〉R〈/span〉 = 0.0299 for 40 observed reflections [4σ(〈span〉F〈/span〉) level] and four parameters and to 〈span〉R〈/span〉 = 0.0356 for all 47 independent reflections. The weishanite structure can be considered a derivative of the zinc structure, with Au, Ag and Hg disordered in the same structural position. On this basis, we suggest that the formula is normalized to 1 atom with 〈span〉Z〈/span〉 = 2, leading, for the sample investigated, to Au〈span〉0.41〈/span〉Ag〈span〉0.31〈/span〉Hg〈span〉0.28〈/span〉 (electron microprobe data). Accordingly, weishanite can be considered the Au-rich isotype of schachnerite. A comparison with other Au/Ag-Hg alloys is presented together with a critical discussion about the nomenclature rules to be applied to alloys and simple metals.〈/p〉〈/div〉
    Print ISSN: 0026-461X
    Electronic ISSN: 1471-8022
    Topics: Geosciences
    Published by Mineralogical Society of Great Britain and Ireland
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  • 3
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    Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-04-20
    Description: Gliomas with histone H3 lysine27-to-methionine mutations (H3K27M-glioma) arise primarily in the midline of the central nervous system of young children, suggesting a cooperation between genetics and cellular context in tumorigenesis. Although the genetics of H3K27M-glioma are well characterized, their cellular architecture remains uncharted. We performed single-cell RNA sequencing in 3321 cells from six primary H3K27M-glioma and matched models. We found that H3K27M-glioma primarily contain cells that resemble oligodendrocyte precursor cells (OPC-like), whereas more differentiated malignant cells are a minority. OPC-like cells exhibit greater proliferation and tumor-propagating potential than their more differentiated counterparts and are at least in part sustained by PDGFRA signaling. Our study characterizes oncogenic and developmental programs in H3K27M-glioma at single-cell resolution and across genetic subclones, suggesting potential therapeutic targets in this disease.
    Keywords: Genetics, Medicine, Diseases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , 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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    Structural and chemical study of weishanite, (Au,Ag,Hg), from the Keystone mine, Colorado, USA. (2018)
    Mineralogical Society of Great Britain and Ireland
    Details
    Publication Date: 2018-05-29
    Print ISSN: 0026-461X
    Electronic ISSN: 1471-8022
    Topics: Geosciences
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  • 5
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    Investigation of the oxidation of methyl vinyl ketone (MVK) by OH radicals in the atmospheric simulation chamber SAPHIR (2018)
    Copernicus
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    Publication Date: 2018-06-07
    Description: The photooxidation of methyl vinyl ketone (MVK) was investigated in the atmospheric simulation chamber SAPHIR for conditions at which organic peroxy radicals (RO2) mainly reacted with NO (“high NO” case) and for conditions at which other reaction channels could compete (“low NO” case). Measurements of trace gas concentrations were compared to calculated concentration time series applying the Master Chemical Mechanism (MCM version 3.3.1). Product yields of methylglyoxal and glycolaldehyde were determined from measurements. For the high NO case, the methylglyoxal yield was (19 ± 3) % and the glycolaldehyde yield was (65 ± 14) %, consistent with recent literature studies. For the low NO case, the methylglyoxal yield reduced to (5 ± 2) % because other RO2 reaction channels that do not form methylglyoxal became important. Consistent with literature data, the glycolaldehyde yield of (37 ± 9) % determined in the experiment was not reduced as much as implemented in the MCM, suggesting additional reaction channels producing glycolaldehyde. At the same time, direct quantification of OH radicals in the experiments shows the need for an enhanced OH radical production at low NO conditions similar to previous studies investigating the oxidation of the parent VOC isoprene and methacrolein, the second major oxidation product of isoprene. For MVK the model–measurement discrepancy was up to a factor of 2. Product yields and OH observations were consistent with assumptions of additional RO2 plus HO2 reaction channels as proposed in literature for the major RO2 species formed from the reaction of MVK with OH. However, this study shows that also HO2 radical concentrations are underestimated by the model, suggesting that additional OH is not directly produced from RO2 radical reactions, but indirectly via increased HO2. Quantum chemical calculations show that HO2 could be produced from a fast 1,4-H shift of the second most important MVK derived RO2 species (reaction rate constant 0.003 s−1). However, additional HO2 from this reaction was not sufficiently large to bring modelled HO2 radical concentrations into agreement with measurements due to the small yield of this RO2 species. An additional reaction channel of the major RO2 species with a reaction rate constant of (0.006 ± 0.004) s−1 would be required that produces concurrently HO2 radicals and glycolaldehyde to achieve model–measurement agreement. A unimolecular reaction similar to the 1,5-H shift reaction that was proposed in literature for RO2 radicals from MVK would not explain product yields for conditions of experiments in this study. A set of H-migration reactions for the main RO2 radicals were investigated by quantum chemical and theoretical kinetic methodologies, but did not reveal a contributing route to HO2 radicals or glycolaldehyde.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 6
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    A comprehensive organic nitrate chemistry: insights into the lifetime of atmospheric organic nitrates (2018)
    Copernicus
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    Publication Date: 2018-10-26
    Description: Organic nitrate chemistry is the primary control over the lifetime of nitrogen oxides (NOx) in rural and remote continental locations. As NOx emissions decrease, organic nitrate chemistry becomes increasingly important to urban air quality. However, the lifetime of individual organic nitrates and the reactions that lead to their production and removal remain relatively poorly constrained, causing organic nitrates to be poorly represented by models. Guided by recent laboratory and field studies, we developed a detailed gas-phase chemical mechanism representing most of the important individual organic nitrates. We use this mechanism within the Weather Research and Forecasting (WRF) model coupled with Chemistry (WRF-Chem) to describe the role of organic nitrates in nitrogen oxide chemistry and in comparisons to observations. We find the daytime lifetime of total organic nitrates with respect to all loss mechanisms to be 2.6 h in the model. This is consistent with analyses of observations at a rural site in central Alabama during the Southern Oxidant and Aerosol Study (SOAS) in summer 2013. The lifetime of the first-generation organic nitrates is ∼2 h versus the 3.2 h lifetime of secondary nitrates produced by oxidation of the first-generation nitrates. The different generations are subject to different losses, with dry deposition to the surface being the dominant loss process for the second-generation organic nitrates and chemical loss being dominant for the first-generation organic nitrates. Removal by hydrolysis is found to be responsible for the loss of ∼30  % of the total organic nitrate pool.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 7
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    Electrodynamic balance–mass spectrometry of single particles as a new platform for atmospheric chemistry research (2018)
    Copernicus
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    Publication Date: 2018-01-08
    Description: New analytical techniques are needed to improve our understanding of the intertwined physical and chemical processes that affect the composition of aerosol particles in the Earth's atmosphere, such as gas–particle partitioning and homogenous or heterogeneous chemistry, and their ultimate relation to air quality and climate. We describe a new laboratory setup that couples an electrodynamic balance (EDB) to a mass spectrometer (MS). The EDB stores a single laboratory-generated particle in an electric field under atmospheric conditions for an arbitrarily long length of time. The particle is then transferred via gas flow to an ionization region that vaporizes and ionizes the analyte molecules before MS measurement. We demonstrate the feasibility of the technique by tracking evaporation of polyethylene glycol molecules and finding agreement with a kinetic model. Fitting data to the kinetic model also allows determination of vapor pressures to within a factor of 2. This EDB–MS system can be used to study fundamental chemical and physical processes involving particles that are difficult to isolate and study with other techniques. The results of such measurements can be used to improve our understanding of atmospheric particles.
    Print ISSN: 1867-1381
    Electronic ISSN: 1867-8548
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 8
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    Identification of organic hydroperoxides and peroxy acids using atmospheric pressure chemical ionization–tandem mass spectrometry (APCI-MS/MS): application to secondary organic aerosol (2018)
    Copernicus
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    Publication Date: 2018-05-30
    Description: Molecules with hydroperoxide functional groups are of extreme importance to both the atmospheric and biological chemistry fields. In this work, an analytical method is presented for the identification of organic hydroperoxides and peroxy acids (ROOH) by direct infusion of liquid samples into a positive-ion atmospheric pressure chemical ionization–tandem mass spectrometer ((+)-APCI-MS/MS). Under collisional dissociation conditions, a characteristic neutral loss of 51 Da (arising from loss of H2O2+NH3) from ammonium adducts of the molecular ions ([M + NH4]+) is observed for ROOH standards (i.e. cumene hydroperoxide, isoprene-4-hydroxy-3-hydroperoxide (ISOPOOH), tert-butyl hydroperoxide, 2-butanone peroxide and peracetic acid), as well as the ROOH formed from the reactions of H2O2 with aldehydes (i.e. acetaldehyde, hexanal, glyoxal and methylglyoxal). This new ROOH detection method was applied to methanol extracts of secondary organic aerosol (SOA) material generated from ozonolysis of α-pinene, indicating a number of ROOH molecules in the SOA material. While the full-scan mass spectrum of SOA demonstrates the presence of monomers (m∕z = 80–250), dimers (m∕z = 250–450) and trimers (m∕z = 450–600), the neutral loss scan shows that the ROOH products all have masses less than 300 Da, indicating that ROOH molecules may not contribute significantly to the SOA oligomeric content. We anticipate this method could also be applied to biological systems with considerable value.
    Print ISSN: 1867-1381
    Electronic ISSN: 1867-8548
    Topics: Geosciences
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  • 9
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    Agmantinite, Ag2MnSnS4, a new mineral with a wurtzite derivative structure from the Uchucchacua polymetallic deposit, Lima Department, Peru (2018)
    Mineralogical Society of Great Britain and Ireland
    Details
    Publication Date: 2018-07-02
    Description: Agmantinite, ideally Ag2MnSnS4, is a new mineral from the Uchucchacua polymetallic deposit, Oyon district, Catajambo, Lima Department, Peru. It occurs as orange–red crystals up to 100 μm across. Agmantinite is translucent with adamantine lustre and possesses a red streak. It is brittle. Neither fracture nor cleavage were observed. Based on the empirical formula the calculated density is 4.574 g/cm3. On the basis of chemically similar compounds the Mohs hardness is estimated at between 2 to 2½. In plane-polarised light agmantinite is white with red internal reflections. It is weakly bireflectant with no observable pleochroism with red internal reflections. Between crossed polars, agmantinite is weakly anisotropic with reddish brown to greenish grey rotation tints. The reflectances (Rmin and Rmax) for the four standard wavelengths are: 19.7 and 22.0 (470 nm); 20.5 and 23.2 (546 nm); 21.7 and 2.49 (589 nm); and 20.6 and 23.6 (650 nm), respectively.Agmantinite is orthorhombic, space group P21nm, with unit-cell parameters: a = 6.632(2), b = 6.922(2), c = 8.156(2) Å, V = 374.41(17) Å3, a:b:c 0.958:1:1.178 and Z = 2. The crystal structure was refined to R = 0.0575 for 519 reflections with I > 2σ(I). Agmantinite is the first known mineral of ${M}_{ m 2}^{ m I} $MIIMIVS4 type that is derived from wurtzite rather than sphalerite by ordered substitution of Zn, analogous to the substitution pattern for deriving stannite from sphalerite. The six strongest X-ray powder-diffraction lines derived from single-crystal X-ray diffraction data [d in Å (intensity)] are: 3.51 (s), 3.32 (w), 3.11 (vs), 2.42 (w), 2.04 (m) and 1.88 (m). The empirical formula (based on 8 apfu) is (Ag1.94Cu0.03)Σ1.97(Mn0.98Zn0.05)Σ1.03Sn0.97S4.03.The crystal structure-derived formula is Ag2(Mn0.69Zn0.31)Σ1.00SnS4 and the simplified formula is Ag2MnSnS4.The name is for the composition and the new mineral and mineral name have been approved by the International Mineralogical Association Commission on New Minerals, Nomenclature and Classification (IMA2014-083).
    Print ISSN: 0026-461X
    Electronic ISSN: 1471-8022
    Topics: Geosciences
    Published by Mineralogical Society of Great Britain and Ireland
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  • 10
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    Using collision-induced dissociation to constrain sensitivity of ammonia chemical ionization mass spectrometry (NH4+-CIMS) to oxygenated volatile organic compounds (2018)
    Copernicus
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    Publication Date: 2018-12-12
    Description: Chemical ionization mass spectrometers (CIMS) routinely detect hundreds of oxidized organic compounds in the atmosphere. A major limitation of these instruments is the uncertainty in their sensitivity to many of the detected ions. We describe the development of a new high-resolution time-of-flight chemical ionization mass spectrometer that operates in one of two ionization modes: using either ammonium ion ligand switching reactions as NH4+-CIMS or proton transfer reactions as PTR-MS. Switching between the modes can be done within two minutes. The NH4+-CIMS mode of the new instrument has sensitivities of up to 67 000 dcps ppbv−1 (duty cycle corrected ion counts per second/parts per billion by volume) and detection limits between 1 and 60 pptv at 2σ for a 1s integration time for numerous oxygenated volatile organic compounds. We present a mass spectrometric voltage scanning procedure based on collision-induced dissociation that allows us to determine the stability of ammonium-organic ions detected by the NH4+-CIMS. Using this procedure, we can effectively constrain the sensitivity of the ammonia chemical ionization mass-spectrometer to a wide range of detected oxidized volatile organic compounds for which no calibration standards exist. We demonstrate the application of this procedure by quantifying the composition of secondary organic aerosols in a series of laboratory experiments.
    Electronic ISSN: 1867-8610
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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