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  • Articles  (472,116)
  • American Chemical Society  (340,152)
  • Oxford University Press  (109,458)
  • American Association of Petroleum Geologists (AAPG)
  • Cambridge University Press
  • 2010-2014  (299,943)
  • 1995-1999  (172,173)
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  • 1
    Publication Date: 2020-11-20
    Description: Siwi caldera, in the Vanuatu arc (Tanna island), is a rare volcanic complex where both persistent eruptive activity (Yasur volcano)and rapid block resurgence (Yenkahe horst) can be investigated simultaneously during a post-caldera stage. Here we provide new constraints on the feeding system of this volcanic complex, based on a detailed study of the petrology, geochemistry and volatile content of Yasur^Siwi bulk-rocks and melt inclusions, combined with measurements of the chemical composition and mass fluxes of Yasur volcanic gases. Major and trace element analyses of Yasur^ Siwi volcanic rocks, together with literature data for other volcanic centers, point to a single magmatic series and possibly long-lived feeding of Tanna volcanism by a homogeneous arc basalt. Olivine-hosted melt inclusions show that the parental basaltic magma, which produces basaltic-trachyandesites to trachyandesites by 50^70% crystal fractionation, is moderately enriched in volatiles ( 1wt % H2O, 0·1wt % S and 0·055 wt % Cl). The basaltic-trachyandesite magma, emplaced at between 4^5 km depth and the surface, preserves a high temperature (1107 158C) and constant H2O content ( 1wt %) until very shallow depths, where it degasses extensively and crystallizes. These conditions, maintained over the past 1400 years of Yasur activity, require early water loss during basalt differentiation, prevalent open-system degassing, and a relatively high heat flow ( 109W). Yasur volcano releases on average 13·4 103 tons d 1 of H2O and 680 tons d 1 of SO2, but moderate amounts of CO2 (840 tons d 1), HCl (165 tons d 1), and HF (23 tons d 1). Combined with melt inclusion data, these gas outputs constrain a bulk magma degassing rate of 5 107 m3 a 1, about a half of which is due to degassing of the basaltic-trachyandesite. We compute that 25 km3 of this magma have degassed without erupting and have accumulated beneath Siwi caldera over the past 1000 years, which is one order of magnitude larger than the accumulated volume uplift of the Yenkahe resurgent block. Hence, basalt supply and gradual storage of unerupted degassed basaltictrachyandesite could easily account for (or contribute to) the Yenkahe block resurgence.
    Description: Published
    Description: 1077-1105
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: restricted
    Keywords: Vanuatu arc ; Yasur ; gas fluxes ; volatiles ; melt inclusions ; resurgent block ; volcano thermal budget ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2020-11-26
    Description: So far, the role of appendicularians in the biogeochemical cycling of organic matter has been largely overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepods, and produce numerous fecal pellets and filtering houses contributing to export production by aggregating small marine particles. To study their quantitative impact on biogeochemical flux, we have included this group in the biogeochemical flux model, using a recently developed ecophysiological model. One-dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for the year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore, current biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small-sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than the estimates from mesotrophic sites, showing that appendicularians’ role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made at other sites. Thus, degradation and grazing of appendicularian detritus need better quantification if we are to accurately assess the role of appendicularia in export flux.
    Description: EU-FP6 project SESAME GOCE-036949
    Description: Published
    Description: 855-872
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: BFM ; zooplankton ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2019-07-16
    Description: Petroleum systems located at passive continental margins received increasing attention in the last decade mainly because of deep- and ultra‐deep-water hydrocarbon exploration and production. The high risks associated with these settings originate mainly from the poor understanding of inherent geodynamic processes. The new priority program SAMPLE (South Atlantic Margin Processes and Links with onshore Evolution), established by the German Science Foundation in 2009 for a total duration of 6 years, addresses a number of open questions related to continental breakup and post‐breakup evolution of passive continental margins. 27 sub‐projects take advantage of the exceptional conditions of the South Atlantic as a prime “Geo‐archive.” The regional focus is set on the conjugate margins located east of Brazil and Argentina on one side and west of Angola, Namibia and South Africa on the other (Figure 1) as well as on the Walvis Ridge and the present‐day hotspot of Tristan da Cunha. The economic relevance of the program is demonstrated by support from several petroleum companies, but the main goal is research on fundamental processes behind the evolution of passive continental margins.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Book , peerRev
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  • 4
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    American Chemical Society
    In:  EPIC3Environmental Science and Technology, American Chemical Society, 48, pp. 13451-13458, ISSN: 0013-936X
    Publication Date: 2014-11-21
    Description: Plastic pollution is an emerging global threat for marine wildlife. Many species of birds, reptiles and fishes are directly impaired by plastics as they can get entangled in ropes and drown or they can ingest plastic fragments which, in turn, may clog their stomachs and guts. Microplastics of less than 1 mm can be ingested by small invertebrates but their fate in the digestive organs and their effects on the animals are yet not well understood. We embedded fluorescent microplastics in artificial agarose-based food and offered the food to marine isopods, Idotea emarginata. The isopods did not distinguish between food with and food without microplastics. Upon ingestion, the microplastics were present in the stomach and in the gut but not in the tubules of the midgut gland which is the principal organ of enzyme-secretion and nutrient resorption. The feces contained the same concentration of micro-plastics as the food which indicates that no accumulation of microplastics happens during the gut passage. Long-term bioassays of six weeks showed no distinct effects of continu¬ous micro-plastic consumption on mortality, growth, and intermolt duration. I. emarginata are able to prevent intrusion of particles even smaller than 1 µm into the midgut gland which is facilitated by the complex structure of the stomach including a fine filter system. It separates the midgut gland tubules from the stomach and allows only the passage of fluids and chyme. Our results indicate that micro¬plastics, as administered in the experi¬ments, do not clog the digestive organs of isopods and do not have adverse effects on their life history parameters.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Cambridge University Press
    In:  EPIC3Antarctic Science, Cambridge University Press, 26(6), pp. 625-635, ISSN: 0954-1020
    Publication Date: 2014-11-27
    Description: A common precursor to ice shelf disintegration, most notably that of Larsen B Ice Shelf, is unusually intense or prolonged surface melt and the presence of surface standing water. However, there has been little research into detailed patterns of melt on ice shelves or the nature of summer melt ponds. We investigated surface melt on Larsen C Ice Shelf at high resolution using Envisat advanced synthetic aperture radar (ASAR) data and explored melt ponds in a range of satellite images. The improved spatial resolution of SAR over alternative approaches revealed anomalously long melt duration in western inlets. Meteorological modelling explained this pattern by föhn winds which were common in this region.Melt ponds are difficult to detect using optical imagery because cloud-free conditions are rare in this region and ponds quickly freeze over, but can be monitored using SAR in all weather conditions. Melt ponds up to tens of kilometres in length were common in Cabinet Inlet, where melt duration was most prolonged. The pattern of melt explains the previously observed distribution of ice shelf densification, which in parts had reached levels that preceded the collapse of Larsen B Ice Shelf,suggesting a potential role for föhn winds in promoting unstable conditions on ice shelves.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    Oxford University Press
    In:  EPIC3Journal of Experimental Botany, Oxford University Press, ISSN: 0022-0957
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
    Publication Date: 2012-02-03
    Description: This handbook defines the discipline of historical seismology by comprehensively detailing the latest research methodologies for studying historical earthquakes and tsunamis. It describes the many historical sources that contain references to seismic phenomena, discusses the critical problems of interpreting such sources, and presents a summary of the various theories proposed (from ancient Greek to modern times) to explain the causes of earthquakes – indispensable factors for understanding historical earthquake descriptions. The text presents numerous examples of interpretations and misinterpretations of historical earthquakes and tsunamis in order to illustrate the key techniques, with a chapter devoted to an explanation of the date and time systems used throughout history in Mediterranean Europe and the Near East. The authors also tie historical seismology research to archaeological investigations and demonstrate how new scientific databases and catalogues can be compiled from information derived from the methodologies described. This is an important new reference for scientists, engineers, historians and archaeologists on the methodologies for analysing earthquakes and tsunamis of the past. Illustrated with examples from a broad geographic region (including Europe, North Africa, the Middle East, central Asia and the Americas), the book provides a valuable foundation for understanding the Earth’s seismic past and potential future seismic hazard.
    Description: Published
    Description: 3.10. Storia ed archeologia applicate alle Scienze della Terra
    Description: open
    Keywords: Historical earthquakes ; historical tsunamis ; historical seismology ; archaeoseismology ; earthquake catalogues ; databases ; 04. Solid Earth::04.06. Seismology::04.06.05. Historical seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book
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  • 8
    Publication Date: 2017-04-04
    Description: Crystal-rich lithic clasts occurring in volcanic deposits are key tools to understand processes of storage, cooling, and fractionation of magmas in pre-eruptive volcanic systems. These clasts, indeed, represent snapshots of the magma-chamber/host-rock interface before eruptions and provide information on crystallization, differentiation, and degrees of interaction between magma and wall-rocks. In this study, with the aim to shed light on magma-carbonate interaction and CO2 emission in volcanic areas, we focused on the petrology of cumulate and skarn rocks by using as case study a suite of mafic and calcite-bearing lithic clasts from the Colli Albani Volcanic District. By means of phase relations, bulk rock chemistry, phase compositions, and stable isotope data we have recognized different types of cumulates and skarns. Cumulates containing either clinopyroxene±olivine associated with Cr-bearing spinel or glass+phlogopite have been divided in primitive and differentiated, respectively. Primitive cumulates originate at the interface between a relatively primitive magma and carbonate-bearing rocks and show evidences of olivine instability (i.e. heteradcumulate texture) due to carbonate assimilation. Differentiated cumulates, characterized by Ca-rich olivines, phlogopite, and glass containing calcite, form from a differentiated magma in a system open to CaO-contamination. Skarns has been divided in exoskarns, characterized by xenomorphic texture and abundant calcite, and endoskarns, characterized by hypidiomorphic texture, Ca-Tschermak-rich mineral phases, and interstitial glass. Exoskarns formed by means of solid state reactions in a dolostone protolith whereas endoskarns crystallized at subliquidus temperature from a silicate melt that experienced exoskarns assimilation. Our study evidences that magma-carbonate interaction can not be considered a one step process exhausting just after the formation of skarn shells. Magma and carbonate rocks, when in contact, continuously interact leading to the formation of exoskarns, endoskarns, cumulates (primitive and differentiated ones), and differentiated melts. Finally, by means of oxygen and carbon isotope compositions of calcite in equilibrium with skarns, we demonstrate that carbonate assimilation represents a source of massive CO2 degassing mechanism due to the consumption of calcite and removing of CO2 during the decarbonation process.
    Description: Sapienza Universita' di Roma INGV-DPC [Project V 3.1, Colli Albani].
    Description: Published
    Description: 2307-2332
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: magma/carbonate interaction ; CO2 degassing ; c umulate and skarn ; Colli Albani ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2017-04-04
    Description: An integrated bio-, magneto- and cyclostratigraphic study of the Ypresian/Lutetian (Early/Middle Eocene) transition along the Otsakar section resulted in the identification of the C22n/C21r chron boundary and of the calcareous nannofossil CP12a/b zonal boundary; the latter is the main correlation criterion of the Lutetian Global Stratotype Section and Point (GSSP) recently defined at Gorrondatxe (Basque Country). By counting precession-related mudstone–marl couplets of 21 ka, the time lapse between both events was calculated to be 819 ka. This suggests that the age of the CP12a/b boundary, and hence that of the Early/Middle Eocene boundary, is 47.76 Ma, 250 ka younger than previously thought. This age agrees with, and is supported by, estimates from Gorrondatxe based on the time lapse between the Lutetian GSSP and the C21r/C21n boundary. The duration of Chron C21r is estimated at 1.326 Ma. Given that the base of the Eocene is dated at 55.8 Ma, the duration of the Early Eocene is 8 Ma, 0.8 Ma longer than in current time scales. The Otsakar results further show that the bases of planktonic foraminiferal zones E8 and P10 are younger than the CP12a/b boundary. The first occurrence of Turborotalia frontosa, being approximately 550 ka older that the CP12a/b boundary, is the planktonic foraminiferal event that lies closest to the Early/Middle Eocene boundary. The larger foraminiferal SBZ12/13 boundary is located close to the CP12a/b boundary and correlates with Chron C21r, not with the C22n/C21r boundary.
    Description: In press
    Description: 1-19
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: Eocene ; Ypresian–Lutetian boundary ; biostratigraphy ; magnetostratigraphy ; cyclostratigraphy ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2017-04-03
    Description: An integrated bio-, magneto- and cyclostratigraphic study of the Ypresian/Lutetian (Early/Middle Eocene) transition along the Otsakar section resulted in the identification of the C22n/C21r chron boundary and of the calcareous nannofossil CP12a/b zonal boundary; the latter is the main correlation criterion of the Lutetian Global Stratotype Section and Point (GSSP) recently defined at Gorrondatxe (Basque Country). By counting precession-related mudstone–marl couplets of 21 ka, the time lapse between both events was calculated to be 819 ka. This suggests that the age of the CP12a/b boundary, and hence that of the Early/Middle Eocene boundary, is 47.76 Ma, 250 ka younger than previously thought. This age agrees with, and is supported by, estimates from Gorrondatxe based on the time lapse between the Lutetian GSSP and the C21r/C21n boundary. The duration of Chron C21r is estimated at 1.326 Ma. Given that the base of the Eocene is dated at 55.8 Ma, the duration of the Early Eocene is 8 Ma, 0.8 Ma longer than in current time scales. The Otsakar results further show that the bases of planktonic foraminiferal zones E8 and P10 are younger than the CP12a/b boundary. The first occurrence of Turborotalia frontosa, being approximately 550 ka older that the CP12a/b boundary, is the planktonic foraminiferal event that lies closest to the Early/Middle Eocene boundary. The larger foraminiferal SBZ12/13 boundary is located close to the CP12a/b boundary and correlates with Chron C21r, not with the C22n/C21r boundary.
    Description: Published
    Description: 442-460
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: Eocene ; Ypresian–Lutetian boundary ; biostratigraphy ; magnetostratigraphy ; cyclostratigraphy. ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
    Publication Date: 2017-04-04
    Description: Stratigraphic, structural, palaeocurrent and palaeomagnetic analyses of Upper Albian deep-water deposits in and around the Deba block (Northern Iberia) are presented. Results indicate an anticlockwise vertical-axis rotation of this block by 35◦ during a maximum time span of c. 1 Ma (Late Albian intra-C. auritus ammonite Subzone). This Albian syndepositional block rotation is interpreted to be the consequence of the coeval activity of conjugatemajor sinistral strike-slip faults and minor (antithetic) dextral strike-slip faults, which border the Deba block. On the base of conservative estimations, a minimum block-rotation rate of 35◦ Ma−1 and a sinistral strike-slip rate of 1.2 kmMa−1 are calculated. As a consequence of the interaction of the rotated Deba block with adjacent nonrotated blocks, its corners experienced coeval transpressive (NW and SE corners) and transtensional deformations (SW and, possibly, NE corners). At the transtensional SW corner, two domal highreflective seismic structures have been recorded and interpreted as high-level magmatic laccoliths. These magmatic intrusions triggered the development of a mineralizing hydrothermal system, which vented to the Late Albian seafloor warm to hot hydrocarbon-rich fluids. Vented hydrocarbon was generated from Albian organic-rich sediments by contact alteration with hydrothermal fluids.
    Description: Published
    Description: 986-1001
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: block rotation ; palaeocurrent ; palaeomagnetism ; Albian ; Basque–Cantabrian Basin ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel of Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 149-151, ISBN: 9781107641655
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 13
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 109-111, ISBN: 9781107641655
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel of Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 97-100, ISBN: 9781107641655
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel of Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 129-131, ISBN: 9781107641655
    Publication Date: 2015-03-08
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  • 16
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel of Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 133-136, ISBN: 9781107641655
    Publication Date: 2015-03-08
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  • 17
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 411-484, ISBN: 9781107641655
    Publication Date: 2017-01-13
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  • 18
    Publication Date: 2017-04-04
    Description: Stromboli is known for its persistent degassing and rhythmic strombolian activity occasionally punctuated by paroxysmal eruptions. The basaltic pumice and scoria emitted during paroxysms and strombolian activity, respectively, differ in their textures, crystal contents and glass matrix compositions, which testify to distinct conditions of crystallization, degassing and magma ascent. We present here an extensive dataset on major elements and volatiles (CO2, H2O, S and Cl) in olivine-hosted melt inclusions and embayments from pyroclasts emplaced during explosive eruptions of variable magnitude. Magma saturation pressures were assessed from the dissolved amounts of H2O and CO2 taking into account the melt composition evolution. Both pressures and melt inclusion compositions indicate that (1) Ca-basaltic melts entrapped in high-Mg olivines (Fo89–90) generate Stromboli basalts through crystal fractionation, and (2) the Stromboli plumbing system can be imaged as a succession of magma ponding zones connected by dikes. The 7–10 km interval, where magmas are stored and differentiate, is periodically recharged by new magma batches, possibly ranging from Ca-basalts to basalts, with a CO2-rich gas phase. These deep recharges promote the formation of bubbly basalt blobs, which are able to intrude the shallow plumbing system (2–4 km), where CO2 gas fluxing enhances H2O loss, crystallization and generation of crystal-rich, dense, degassed magma. Chlorine partitioning into the H2O–CO2-bearing gas phase accounts for its efficient degassing (≥69%) under the open-system conditions of strombolian activity. Paroxysms, however, are generated through predominantly closed-system ascent of basaltic magma batches from the deep storage zone. In this situation crystallization is negligible and sulfur exsolution starts at ≤170 MPa. Chlorine remains dissolved in the melt until lower pressures, only 16% being lost upon eruption. Finally, we propose a continuum in explosive eruption energy, from strombolian activity to large paroxysmal events, ultimately controlled by variable pressurization of the deep feeding system associated with magma and gas recharges.
    Description: Published
    Description: 603-626
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; melt inclusions ; magmatic volatiles ; CO2 fluxing ; magma degassing ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 19
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    Oxford University Press
    In:  EPIC3Ocean Acidification, Oxford, Oxford University Press, pp. 291-311, ISBN: 978-0-19-959109-1
    Publication Date: 2014-04-15
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Cambridge University Press
    In:  EPIC3Antarctic Science, Cambridge University Press, 26(1), pp. 80-92, ISSN: 0954-1020
    Publication Date: 2019-07-17
    Description: Understanding the regional and seasonal distribution of seismic research surveys in the Southern Ocean is essential for assessing their acoustic impact on the marine environment. An analysis of the navigation data and cruise table in the Seismic Data Library System for Cooperative Research (SDLS) shows that a fairly extensive network of seismic lines is now available for the Southern Ocean. However, line spacing ranges from tens to hundreds of kilometres, and some almost unsurveyed areas still exist. The seasonal distribution of the seismic profile lengths shows periods with increased survey activity between 1976/77 and 2001/02, but only moderate levels of activity between 2002/03 and 2010/11. The corresponding line spacing is large, and lines are widely distributed over the Southern Ocean. None of the eight Antarctic regions considered here have experienced seismic survey activity during all summer seasons in the last 35 years. Instead, periods with survey activity are interspersed by periods with no survey activity. The average survey length ranges from ~2600 km/season off the Antarctic Peninsula to ~260 km/season off Enderby Land. Compared to the industrial seismic exploration off Norway the acoustic impact of the seismic research activity in the Southern Ocean is at least ~150 times lower.
    Repository Name: EPIC Alfred Wegener Institut
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  • 21
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    American Chemical Society
    In:  EPIC3Environ. Sci. Technol., American Chemical Society, 46, pp. 11327-11335
    Publication Date: 2019-07-17
    Description: In this study, we investigated if industrial high-density polyethylene (HDPE) particles, a model microplastic free of additives, ranging 〉 0− 80 μm are ingested and taken up into the cells and tissue of the blue mussel Mytilus edulis L. The effects of exposure (up to 96 h) and plastic ingestion were observed at the cellular and subcellular level. Microplastic uptake into the gills and digestive gland was analyzed by a new method using polarized light microscopy. Mussel health status was investigated incorporating histological assessment and cytochemical biomarkers of toxic effects and early warning. In addition to being drawn into the gills, HDPE particles were taken up into the stomach and transported into the digestive gland where they accumulated in the lysosomal system after 3 h of exposure. Our results show notable histological changes upon uptake and a strong inflammatory response demonstrated by the formation of granulocytomas after 6 h and lysosomal membrane destabilization, which significantly increased with longer exposure times. We provide proof of principle that microplastics are taken up into cells and cause significant effects on the tissue and cellular level, which can be assessed with standard cytochemical biomarkers and polarized light microscopy for microplastic tracking in tissue.
    Repository Name: EPIC Alfred Wegener Institut
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  • 22
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    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 34(5), pp. 399-415, ISSN: 0142-7873
    Publication Date: 2019-07-17
    Description: This study investigates the relationships between the spring phytoplankton community and environmental factors in the Brazil-Malvinas confluence region. Phytoplankton community composition was determined by the high performance liquid chromatography/CHEMTAX approach, complemented with microscopic examination. Abiotic factors included temperature, salinity, dissolved inorganic macronutrients (ammonium, nitrite, nitrate, phosphate and silicate), water column stability and upper mixed layer depth (UMLD). These environmental variables were reasonably informative to explain the variability of the phytoplankton communities (44% of variation explained). Cluster and canonical correspondence analyses allowed discrimination of four zones (coastal, Sub-Antarctic, tropical and intermediate zones), also identifiable in the T–S diagrams and in the nutrient spatial distribution patterns. The presence of nutrient-rich Sub-Antarctic waters was a major oceanographic feature, associated with diatoms and dinoflagellates. However, in the Sub-Antarctic zone, biomass was particularly low, probably as a result of grazing pressure, as suggested by chemical and biological indicators. In contrast, in oligotrophic tropical waters, phytoplankton was mainly composed by small nanoflagellates and cyanobacteria. A large intermediate zone was also dominated by nanoflagellates, mainly Phaeocystis antarctica, probably favored by strong water column stability. The coastal zone exhibited fairly similar conditions to those in the intermediate zone, but with deeper UMLD, a favorable condition for diatom growth. These results emphasize the importance of the properties of water masses and also biological processes such as grazing in structuring phytoplankton communities in the region.
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  • 23
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 123-127, ISBN: 9781107641655
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
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  • 24
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 1-32, ISBN: 9781107641655
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
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  • 25
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 35-94, ISBN: 9781107641655
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
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  • 26
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Description: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Description: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Keywords: Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
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  • 27
    Publication Date: 2022-05-25
    Description: © 2010 The Authors. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 365-378, doi:10.1093/icesjms/fsp262.
    Description: A commercial acoustic system, originally designed for seafloor applications, has been adapted for studying fish with swimbladders. The towed system contains broadband acoustic channels collectively spanning the frequency range 1.7–100 kHz, with some gaps. Using a pulse-compression technique, the range resolution of the echoes is ~20 and 3 cm in the lower and upper ranges of the frequencies, respectively, allowing high-resolution imaging of patches and resolving fish near the seafloor. Measuring the swimbladder resonance at the lower frequencies eliminates major ambiguities normally associated with the interpretation of fish echo data: (i) the resonance frequency can be used to estimate the volume of the swimbladder (inferring the size of fish), and (ii) signals at the lower frequencies do not depend strongly on the orientation of the fish. At-sea studies of Atlantic herring demonstrate the potential for routine measurements of fish size and density, with significant improvements in accuracy over traditional high-frequency narrowband echosounders. The system also detected patches of scatterers, presumably zooplankton, at the higher frequencies. New techniques for quantitative use of broadband systems are presented, including broadband calibration and relating target strength and volume-scattering strength to quantities associated with broadband signal processing.
    Description: The research was supported by the US Office of Naval Research, grants number N00014-04-1-0440 and N00014-04-1-0475, NOAA/CICOR cooperative agreement NA17RJ1223, NOAA/ National Marine Fisheries Service, and the J. Seward Johnson Chair of the WHOI Academic Programs Office.
    Keywords: Acoustic scattering ; Broadband ; Echosounder ; Fish ; Resonance
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  • 28
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Description: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Description: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
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  • 29
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Description: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Description: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Keywords: Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
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  • 30
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in Journal of Plankton Research 32 (2010): 1355-1368, doi:10.1093/plankt/fbq062.
    Description: Increasing availability and extent of biological ocean time series (from both in situ and satellite data) have helped reveal significant phenological variability of marine plankton. The extent to which the range of this variability is modified as a result of climate change is of obvious importance. Here we summarize recent research results on phenology of both phytoplankton and zooplankton. We suggest directions to better quantify and monitor future plankton phenology shifts, including (i) examining the main mode of expected future changes (ecological shifts in timing and spatial distribution to accommodate fixed environmental niches vs. evolutionary adaptation of timing controls to maintain fixed biogeography and seasonality), (ii) broader understanding of phenology at the species and community level (e.g. for zooplankton beyond Calanus and for phytoplankton beyond chlorophyll), (iii) improving and diversifying statistical metrics for indexing timing and trophic synchrony and (iv) improved consideration of spatio-temporal scales and the Lagrangian nature of plankton assemblages to separate time from space changes.
    Description: This study was supported by NSF grants to R.J.: OCE-0727033, 0815838 and 0732152. NSF grants to A.C.T.: OCE-0535386, 0815051 and 0814413. NSF grant to J.A.R.: OCE 0815336.
    Keywords: Plankton ; Phenology ; Life history ; Climate change
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  • 31
    Publication Date: 2022-05-25
    Description: Author Posting. © Cambridge University Press, 2013. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 731 (2013): 545-578, doi:10.1017/jfm.2013.361 .
    Description: A significant amount of research effort has been made to understand the boundary layer instability and the generation and evolution of turbulence subject to periodic/oscillatory flows. However, little is known about bottom boundary layers driven by highly transient and intermittent free-stream flow forcing, such as solitary wave motion. To better understand the nature of the instability mechanisms and turbulent flow characteristics subject to solitary wave motion, a large number of direct numerical simulations are conducted. Different amplitudes of random initial fluctuating velocity field are imposed. Two different instability mechanisms are observed within the range of Reynolds number studied. The first is a short-lived, nonlinear, long-wave instability which is observed during the acceleration phase, and the second is a broadband instability that occurs during the deceleration phase. Transition from a laminar to turbulent state is observed to follow two different breakdown pathways: the first follows the sequence of $K$-type secondary instability of a near-wall boundary layer at comparatively lower Reynolds number and the second one follows a breakdown path similar to that of free shear layers. Overall characteristics of the flow are categorized into four regimes as: (i) laminar; (ii) disturbed laminar; (iii) transitional; and (iv) turbulent. Our categorization into four regimes is consistent with earlier works. However, this study is able to provide more specific definitions through the instability characteristics and the turbulence breakdown process.
    Description: This study is supported by National Science Foundation (CMMI-1135026; OCE- 1130217; OCE-1131016).
    Description: 2014-08-28
    Keywords: Coastal engineering ; Solitary waves ; Turbulent flows
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  • 32
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial 2.5 License. The definitive version was published in Genome Biology and Evolution 2 (2010): 304, doi:10.1093/gbe/evq022.
    Description: Reduction of various biological processes is a hallmark of the parasitic lifestyle. Generally, the more intimate the association between parasites and hosts the stronger the parasite relies on its host's physiology for survival and reproduction. However, some systems have been held to be indispensable, for example, the core pathways of carbon metabolism that produce energy from sugars. Even the most hardened anaerobes that lack oxidative phosphorylation and the tricarboxylic acid cycle have retained glycolysis and some downstream means to generate ATP. Here we describe the deep-coverage genome resequencing of the pathogenic microsporidiian, Enterocytozoon bieneusi, which shows that this parasite has crossed this line and abandoned complete pathways for the most basic carbon metabolism. Comparing two genome sequence surveys of E. bieneusi to genomic data from four other microsporidia reveals a normal complement of 353 genes representing 30 functional pathways in E. bieneusi, except that only 2 out of 21 genes collectively involved in glycolysis, pentose phosphate, and trehalose metabolism are present. Similarly, no genes encoding proteins involved in the processing of spliceosomal introns were found. Altogether, E. bieneusi appears to have no fully functional pathway to generate ATP from glucose. Therefore, this intracellular parasite relies on transporters to import ATP from its host.
    Description: This work was supported by grants from the Canadian Institutes for Health Research (MOP-84265), the National Institutes of Health (NIH AI31788, R21 AI52792, and R21 AI064118), and the National Science Foundation (MCB- 0135272). N.C. is a Scholar of the Canadian Institute for Advanced Research and is supported by a fellowship from the Swiss National Science Foundation (NSF) (PA00P3- 124166). D.E. is supported by the Swiss NSF. P.J.K. is a Fellow of the Canadian Institute for Advanced Research and a Senior Scholar of the Michael Smith Foundation for Health Research.
    Keywords: Microsporidia ; Parasite ; Glycolysis ; Carbon metabolism ; Reduction ; Evolution
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  • 33
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    Cambridge University Press
    Publication Date: 2022-05-25
    Description: Author Posting. © Cambridge University Press, 2012. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 692 (2012): 1-4, doi:10.1017/jfm.2011.468.
    Description: Salt fingers are a form of double-diffusive convection that can occur in a wide variety of fluid systems, ranging from stellar interiors and oceans to magma chambers. Their amplitude has long been difficult to quantify, and a variety of mechanisms have been proposed. Radko & Smith (J. Fluid Mech., this issue, vol. 692, 2012, pp. 5–27) have developed a new theory that balances the basic growth rate with that of secondary instabilities that act on the finite amplitude fingers. Their approach promises a way forward for computationally challenging systems with vastly different scales of decay for momentum, heat and dissolved substances.
    Description: 2013-01-24
    Keywords: Double diffusive convection ; Instability ; Ocean processes
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  • 34
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    Cambridge University Press
    Publication Date: 2022-05-25
    Description: Author Posting. © Cambridge University Press, 2013. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 726 (2013): 371-403, doi:10.1017/jfm.2013.231.
    Description: Nonlinear stratified spindown of an along-isobath current over an insulated slope is shown to develop asymmetries in the vertical circulation and vertical relative vorticity field. During spindown, cyclonic vorticity is weakened to a greater extent than anticyclonic vorticity near the boundary because of buoyancy advection. As a consequence, Ekman pumping is weakened over Ekman suction. Momentum advection can weaken Ekman pumping and strengthen Ekman suction. Time-dependent feedback between the geostrophic flow and the frictional secondary circulation induces asymmetry in cyclonic and anticyclonic vorticity away from the boundary. Buoyancy advection over a slope can modify the secondary circulation such that anticyclonic vorticity decays faster than cyclonic vorticity outside the boundary layer. In contrast, momentum advection can cause cyclonic vorticity to spin down faster than anticyclonic vorticity. A scaling and analytical solutions are derived for when buoyancy advection over a slope can have a more significant impact than momentum advection on these asymmetries. In order to test this scaling and analytical solutions, numerical experiments are run in which both buoyancy and momentum advection are active. These solutions are contrasted with homogeneous or stratified spindown over a flat bottom, in which momentum advection controls the asymmetries. These results are applied to ocean currents over continental shelves and slopes.
    Description: 2014-06-05
    Keywords: Geophysical flows ; Ocean circulation ; Topographic effects
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  • 35
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Description: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Description: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Keywords: Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
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  • 36
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 193(3), pp. 1399-1414, ISSN: 0956-540X
    Publication Date: 2019-07-16
    Description: The Boreas Basin is located in the Norwegian-Greenland Sea between Northeast Greenland and Svalbard. Towards the east, it is bounded by the ultraslow mid-ocean Knipovich Ridge. Here, we present a 340-km-long seismic refraction line acquired during the expedition ARK-XXIV/3 of research vessel Polarstern in 2009, using 18 ocean bottom seismometers. It crosses the central Boreas Basin from the Knipovich Ridge to the Northeast Greenland margin. Thus, the line provides the first reliable crustal structure information of this basin. In addition, the gravity data acquired parallel to the seismic refraction line are used to calculate a 2.5-D gravity model. The P-wave velocity model shows an unusual ∼3-km-thin oceanic crust with seismic velocities less than 6.3 km s−1, indicating the absence of a significant oceanic layer 3. Mantle velocities vary between 7.5 kms−1 in the uppermost mantle and 8.0 km s−1 at approximately 15 km depth. The low velocities within the upper mantle may be explained by 13 per cent serpentinisation, which is negligible at about 15 km depth. Furthermore, the S-wave velocity model shows low Vp/Vs ratios in the mantle, indicating a highly serpentinised mantle at shallow depths. The gravity model has crustal densities between 2.3 and 2.9 g cm−3, which also point towards the absence of a significant thick oceanic layer 3. The results of our seismic refraction line and other geophysical data indicate that the entire Boreas Basin opened at ultraslow spreading rates since at least ∼28 Ma. No evidence for an extinct spreading ridge in the centre of the Boreas Basin was found.
    Repository Name: EPIC Alfred Wegener Institut
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  • 37
    Publication Date: 2022-05-26
    Description: Author Posting. © Cambridge University Press, 2011. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 686 (2011): 534-567, doi:10.1017/jfm.2011.345.
    Description: Most of the nearly zonal, multiple, alternating jets observed in the oceans are latent, that is, their amplitudes are weak relative to the ambient mesoscale eddies. Yet, relatively strong jets are often observed in dynamical simulations. To explore mechanisms controlling the degree of latency, we analyse solutions of an idealized, eddy-resolving and flat-bottom quasigeostrophic model, in which dynamically generated mesoscale eddies maintain and interact with a set of multiple zonal jets. We find that the degree of the latency is controlled primarily by the bottom friction: the larger the friction parameter, the more latent are the jets; and the degree of the latency is substantial for a realistic range of the oceanic bottom friction coefficient. This result not only provides a plausible explanation for the latency of the oceanic jets, but it may also be relevant to the prominent atmospheric multiple jets observed on giant gas planets, such as Jupiter. We hypothesize that these jets can be so strong because of the relative absence of the bottom friction. The mechanism controlling the latency in our solutions is understood in terms of the changes induced in the linear eigenmodes of the time–mean flow by varying the bottom friction coefficient; these changes, in turn, affect and modify the jets. Effects of large Reynolds numbers on the eddies, jets, and the latency are also discussed.
    Description: Funding was provided: for P.B. by NSF grants OCE 0725796 and OCE 0845150, for J.T.F. by NSF grant OCE 0845150, for I.K. by NSF grant OCE 0842834, and for S.K. by the University Research Fellowship from the Royal Society. S.K. also acknowledges support from the Mary Sears Grant from the Woods Hole Oceanographic Institution.
    Description: 2012-09-27
    Keywords: Geostrophic turbulence ; Quasi-geostrophic flows ; Waves in rotating fluids
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  • 38
    Publication Date: 2022-05-26
    Description: Author Posting. © Cambridge University Press, 2013. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 738 (2014): 143-183, doi:10.1017/jfm.2013.583.
    Description: We investigate and quantify stirring due to chaotic advection within a steady, three-dimensional, Ekman-driven, rotating cylinder flow. The flow field has vertical overturning and horizontal swirling motion, and is an idealization of motion observed in some ocean eddies. The flow is characterized by strong background rotation, and we explore variations in Ekman and Rossby numbers, E and Ro, over ranges appropriate for the ocean mesoscale and submesoscale. A high-resolution spectral element model is used in conjunction with linear analytical theory, weakly nonlinear resonance analysis and a kinematic model in order to map out the barriers, manifolds, resonance layers and other objects that provide a template for chaotic stirring. As expected, chaos arises when a radially symmetric background state is perturbed by a symmetry-breaking disturbance. In the background state, each trajectory lives on a torus and some of the latter survive the perturbation and act as barriers to chaotic transport, a result consistent with an extension of the KAM theorem for three-dimensional, volume-preserving flow. For shallow eddies, where E is O(1), the flow is dominated by thin resonant layers sandwiched between KAM-type barriers, and the stirring rate is weak. On the other hand, eddies with moderately small E experience thicker resonant layers, wider-spread chaos and much more rapid stirring. This trend reverses for sufficiently small E, corresponding to deep eddies, where the vertical rigidity imposed by strong rotation limits the stirring. The bulk stirring rate, estimated from a passive tracer release, confirms the non-monotonic variation in stirring rate with E. This result is shown to be consistent with linear Ekman layer theory in conjunction with a resonant width calculation and the Taylor–Proudman theorem. The theory is able to roughly predict the value of E at which stirring is maximum. For large disturbances, the stirring rate becomes monotonic over the range of Ekman numbers explored. We also explore variation in the eddy aspect ratio.
    Description: L.J.P., I.I.R., T.M.O. and P.W. have been supported on DOD (MURI) grant N000141110087, administered by the Office of Naval Research. I.I.R. and L.J.P. received additional support from Grant NSF-OCE-0725796 from the National Science Foundation.
    Description: 2014-12-05
    Keywords: Chaotic advection ; Geophysical and geological flows ; Ocean processes
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  • 39
    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2014. This article is posted here by permission of American Chemical Society for personal use, not for redistribution. The definitive version was published in Environmental Science and Technology 38 (2014): 4732–4738, doi:10.1021/es4053076.
    Description: We present an extensive survey of floating plastic debris in the eastern North and South Pacific Oceans from more than 2500 plankton net tows conducted between 2001 and 2012. From these data we defined an accumulation zone (25 to 41°N, 130 to 180°W) in the North Pacific subtropical gyre that closely corresponds to centers of accumulation resulting from the convergence of ocean surface currents predicted by several oceanographic numerical models. Maximum plastic concentrations from individual surface net tows exceeded 106 pieces km–2, with concentrations decreasing with increasing distance from the predicted center of accumulation. Outside the North Pacific subtropical gyre the median plastic concentration was 0 pieces km–2. We were unable to detect a robust temporal trend in the data set, perhaps because of confounded spatial and temporal variability. Large spatiotemporal variability in plastic concentration causes order of magnitude differences in summary statistics calculated over short time periods or in limited geographic areas. Utilizing all available plankton net data collected in the eastern Pacific Ocean (17.4°S to 61.0°N; 85.0 to 180.0°W) since 1999, we estimated a minimum of 21 290 t of floating microplastic.
    Description: This work was supported by Sea Education Association, NFWF-NOAA Marine Debris Program (Nos. 2009-0062-002, NA10OAR4320148, Amend. 71), and NSF (Nos. OCE-0087528, OCE-1155379, OCE-1260403, OCE-1352422).
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  • 40
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Description: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Description: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Keywords: Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
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  • 41
    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2011. This article is posted here by permission of American Chemical Society for personal use, not for redistribution. The definitive version was published in Environmental Science and Technology 45 (2011): 9931–9935, doi:10.1021/es202816c.
    Description: The impacts on the ocean of releases of radionuclides from the Fukushima Dai-ichi nuclear power plants remain unclear. However, information has been made public regarding the concentrations of radioactive isotopes of iodine and cesium in ocean water near the discharge point. These data allow us to draw some basic conclusions about the relative levels of radionuclides released which can be compared to prior ocean studies and be used to address dose consequences as discussed by Garnier-Laplace et al. in this journal.(1) The data show peak ocean discharges in early April, one month after the earthquake and a factor of 1000 decrease in the month following. Interestingly, the concentrations through the end of July remain higher than expected implying continued releases from the reactors or other contaminated sources, such as groundwater or coastal sediments. By July, levels of 137Cs are still more than 10 000 times higher than levels measured in 2010 in the coastal waters off Japan. Although some radionuclides are significantly elevated, dose calculations suggest minimal impact on marine biota or humans due to direct exposure in surrounding ocean waters, though considerations for biological uptake and consumption of seafood are discussed and further study is warranted.
    Description: Funding for this work to KOB is from the Gordon and Betty Moore Foundation as well as the Chemical Oceanography Program of the US National Science Foundation.
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  • 42
    Publication Date: 2022-05-26
    Description: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Description: This work was supported by NSF grant EAR0809074.
    Keywords: Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
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  • 43
    Publication Date: 2022-05-26
    Description: Author Posting. © Foundation for Environmental Conservation, 2009. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Environmental Conservation 36 (2009): 268-276, doi:10.1017/S0376892910000032.
    Description: No-take marine reserves are widely recognized as an effective conservation tool for protecting marine resources. Despite considerable empirical evidence that abundance and biomass of fished species increase within marine reserve boundaries, the potential for reserves to provide fisheries and conservation benefits to adjacent waters remains heavily debated. This paper uses statistical and population models to evaluate published empirical data on adult spillover from marine reserves and shows that spillover is a common phenomenon for species that respond positively to reserve protection, but at relatively small scales, detectable on average up to 800 m from reserve boundaries. At these small scales, local fisheries around reserves were likely unsustainable in 12 of 14 cases without the reserve, and spillover partially or fully offsets losses in catch due to reserve closure in the other two cases. For reserves to play a role in sustaining and replenishing larger-scale fished stocks, networks of reserves may be necessary, but as few exist this is difficult to evaluate. The results suggest reserves can simultaneously meet conservation objectives and benefit local fisheries adjacent to their boundaries.
    Description: Support was provided by a grant from the David and Lucille Packard Foundation to NCEAS for ecosystem-based management ofmarine systems, the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) funded by the David and Lucile Packard Foundation and the Gordon and Betty Moore Foundation (contribution number 348), the Sustainable Fisheries Group supported by the Paul G. Allen Family Foundation and the Bahamas Biocomplexity Project (US NSF Biocomplexity grantOCE-0119976) andUS EPA Science to Achieve Results (R832223).
    Keywords: Adult fish movement ; Fisheries ; Global ; Marine protected areas ; No-take reserves ; Spillover effect ; Synthesis
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  • 44
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Description: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Description: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Keywords: Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
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  • 45
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Description: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Keywords: Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
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  • 46
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): 7132-7149, doi:10.1093/nar/gks467.
    Description: The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
    Description: Office of Science (BER), U.S. Department of Energy [DE-FG02-07ER64388 to D.S. and DE-FG02- 08ER64511 to M.H.S.]; National Aeronautics and Space Administration, NASA Astrobiology Institute [NNA08CN84A to D.S.].
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  • 47
    Publication Date: 2022-05-26
    Description: Author Posting. © Cambridge University Press, 2014. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 752 (2014): R2, doi:10.1017/jfm.2014.389.
    Description: A model of the total volume flux and entrainment occurring in two coalescing axisymmetric turbulent plumes is developed and compared with laboratory experiments. The dynamical evolution of the two plumes is divided into three regions. In region 1, where the plumes are separate, the entrainment in each plume is unaffected by the other plume, although the two plumes are drawn together due to the entrainment of ambient fluid between them. In region 2 the two plumes touch each other but are not yet merged. In this region the total entrainment is a function of both the dynamics of the touching plumes and the reduced surface area through which entrainment occurs. In region 3 the two plumes are merged and the entrainment is equivalent to that in a single plume. We find that the total volume flux after the two plumes touch and before they merge increases linearly with distance from the sources, and can be expressed as a function of the known total volume fluxes at the touching and merging heights. Finally, we define an ‘effective’ entrainment constant, αeff, as the value of α needed to obtain the same total volume flux in two independent plumes as that occurring in two coalescing plumes. The definition of αeff allows us to find a single expression for the development of the total volume flux in the three different dynamical regions. This single expression will simplify the representation of coalescing plumes in more complex models, such as in large-scale geophysical convection, in which plume dynamics are not resolved. Experiments show that the model provides an accurate measure of the total volume flux in the two coalescing plumes as they evolve through the three regions.
    Description: The authors gratefully acknowledge the National Science Foundation (grant OCE-0824636) and the Office of Naval Research (grant N00014-09-1-0844) for their support of the 2013 WHOI Geophysical Fluid Dynamics Summer School where this project was initiated. Support to C.C. was given by the National Science Foundation project OCE-1130008.
    Description: 2015-07-11
    Keywords: Mixing ; Plumes/thermals ; Turbulent mixing
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  • 48
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    Environmental science & technology 29 (1995), S. 108-116 
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    Biochemistry 34 (1995), S. 801-807 
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    Biochemistry 34 (1995), S. 847-856 
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