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  • Oxford University Press  (110,094)
  • American Geophysical Union
  • 2010-2014  (110,527)
  • 1985-1989  (37,601)
  • 1960-1964  (8,348)
  • 1935-1939  (3,910)
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  • 1
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    Mapping Moho depth variations in central Italy from PsMoho-P delay times: Evidence of an E-W transition in the Adriatic Moho at 42°N latitude (2014)
    American Geophysical Union
    Details
    Publication Date: 2020-12-18
    Description: Along the Italian peninsula adjoin two crustal domains, peri-Tyrrhenian and Adriatic, whose boundary is not univocal in central Italy. In this area, we attempt to map the extent of the Moho in the two terrains from variations of the travel time difference between the direct P wave and the P-to-S wave converted at the crust-mantle boundary, called PsMoho. We use teleseismic receiver functions computed at 38 broad-band stations in this and previous studies, and assigned each of the recording sites to the Adriatic or peri-Tyrrhenian terrains based on station location, geologic and geophysical data and interpretation, and consistency of delays with the regional Moho trend. The results of the present study show that the PsMoho arrival time varies from 2.3 to 4.1 s in the peri-Tyrrhenian domain and from 3.7 to 5.5 s in the Adriatic domain. As expected, the lowest time difference is observed along the Tyrrhenian coastline and the largest values are observed in the axial zone of the Apennine chain. A key new result of this study is a sharp E-W boundary in the Adriatic domain that separates a deeper Moho north of about 42 N latitude from a shallower Moho to the south. This feature is constrained for a length of about 40 km by the observations available in this study. The E-W boundary requires a revision of prior mapping of the Moho in central Italy and supports previous hypotheses of lithosphere segmentation.
    Description: Published
    Description: 3929–3938
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: open
    Keywords: teleseismic receiver functions ; Moho discontinuity ; central Italy ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Low-temperature magnetic properties of pelagic carbonates: Oxidation of biogenic magnetite and identification of magnetosome chains (2014)
    American Geophysical Union
    Details
    Publication Date: 2021-02-17
    Description: Pelagic marine carbonates provide important records of past environmental change. We carried out detailed low-temperature magnetic measurements on biogenic magnetite-bearing sediments from the Southern Ocean (Ocean Drilling Program (ODP) Holes 738B, 738C, 689D, and 690C) and on samples containing whole magnetotactic bacteria cells. We document a range of low-temperature magnetic properties, including reversible humped low-temperature cycling (LTC) curves. Different degrees of magnetite oxidation are considered to be responsible for the observed variable shapes of LTC curves. A dipole spring mechanism in magnetosome chains is introduced to explain reversible LTC curves. This dipole spring mechanism is proposed to result from the uniaxial anisotropy that originates from the chain arrangement of biogenic magnetite, similar to published results for uniaxial stable single domain (SD) particles. The dipole spring mechanism reversibly restores the remanence during warming in LTC measurements. This supports a previous idea that remanence of magnetosome chains is completely reversible during LTC experiments. We suggest that this magnetic fingerprint is a diagnostic indicator for intact magnetosome chains, although the presence of isolated uniaxial stable SD particles and magnetically interacting particles can complicate this test. Magnetic measurements through the Eocene section of ODP Hole 738B reveal an interval with distinct magnetic properties that we interpret to originate from less oxidized biogenic magnetite and enrichment of a biogenic “hard” component. Co-occurrence of these two magnetic fingerprints during the late Eocene in the Southern Ocean indicates less oxic conditions, probably due to increased oceanic primary productivity and organic carbon burial.
    Description: Published
    Description: 6049–6065
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: pelagic carbonates ; biogenic magnetite ; rock magnetism ; environmental magnetism ; ODP ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.05. Geomagnetism::04.05.09. Environmental magnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Sudden deep gas eruption nearby Rome's airport of Fiumicino (2014)
    American Geophysical Union
    Details
    Publication Date: 2021-03-24
    Description: On 24 August 2013 a sudden gas eruption from the ground occurred in the Tiber river delta, nearby Rome's international airport of Fiumicino. We assessed that this gas, analogous to other minor vents in the area, is dominantly composed of deep, partially mantle-derived CO2, as in the geothermal gas of the surrounding Roman Comagmatic Province. Increased amounts of thermogenic CH4 are likely sourced from Meso-Cenozoic petroleum systems, overlying the deep magmatic fluids. We hypothesize that the intersection of NE-SW and N-S fault systems, which at regional scale controls the location of the Roman volcanic edifices, favors gas uprising through the impermeable Pliocene and deltaic Holocene covers. Pressurized gas may temporarily be stored below these covers or within shallower sandy, permeable layers. The eruption, regardless the triggering cause—natural or man-made, reveals the potential hazard of gas-charged sediments in the delta, even at distances far from the volcanic edifices.
    Description: Published
    Description: 5632–5636
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: geothermal gas ; deep CO2 ; Tiber river delta ; thermogenic CH4 ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Unraveling the geometry of the New England oroclines (eastern Australia): Constraints from magnetic fabrics (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: The southern New England Orogen (NEO) in eastern Australia is characterized by tight curvatures (oroclines), but the exact geometry of the oroclines and their kinematic evolution are controversial. Here we present new data on the anisotropy ofmagnetic susceptibility (AMS), which provide a petrofabric proxy for the finite strain associated with the oroclines. We focus on a series of preoroclinal Devonian-Carboniferous fore-arc basin rocks, which are aligned parallel to the oroclinal structure, and by examining structural domains, we test whether or not the magnetic fabric is consistent with the strain axes. AMS data show a first-order consistency with the shape of the oroclines, characterized, in most of structural domains, by subparallelism between magnetic lineations, “structural axis” and bedding. With the exception of the Gresford and west Hastings domains, our results are relatively consistent with the existence of the Manning and Nambucca (Hastings) Oroclines. Reconstruction of magnetic lineations to a prerotation (i.e., pre–late Carboniferous) stage, considering available paleomagnetic results, yields a consistent and rather rectilinear NE-SW predeformation fore-arc basin. This supports the validity of AMS as a strain proxy in complex orogens, such as the NEO. In the Hastings Block, magnetic lineations are suborthogonal to bedding, possibly indicating a different deformational history with respect to the rest of the NEO.
    Description: Published
    Description: 2261–2282
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: AMS data, magnetic fabric, oroclines ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism ; 04. Solid Earth::04.07. Tectonophysics::04.07.01. Continents ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Paleomagnetism and magnetic fabric of the Eastern Cordillera of Colombia: Evidence for oblique convergence and non rotational reactivation of a Mesozoic intracontinental rift (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: We report the paleomagnetic and magnetic fabric results of 58 sites from Cretaceous-Miocene marine and continental strata from the Eastern Cordillera (EC) and the Cucuta zone, at the junction between the Santander Massif and the Merida Andes of Colombia. The EC is an intracontinental doubly vergent range inverting a Triassic to Early Cretaceous rift zone. Twenty-three sites reveal nonsystematic tectonic rotations, including unrotated areas of the EC range with respect to stable South America. Our data show that the EC inverted a NNE oriented rift zone and that the orientation of the Mesozoic rift and the mountain chain roughly correspond. Interestingly, magnetic lineations from anisotropy of magnetic susceptibility analysis do not trend parallel to the chain but rather are oblique to the main orogenic trend. By also considering GPS evidence of a ~1 cm/yr ENE displacement of central western Colombia accommodated by the EC, we suggest that the Miocene-Recent deformation event of this belt arises from ENE oblique convergence reactivating a NNE oriented rift zone. Oblique shortening was likely partitioned into pure dip-slip shear characterizing thick-skinned frontal thrust sheets (well known along both chain fronts) and by range-parallel right-lateral strike-slip faults, which have not been identified yet, but likely exist in the axial part of the EC. Finally, the 35° ± 9° clockwise rotation observed in four post-Miocene magnetically overprinted sites from the Cucuta zone reflects late Cenozoic and ongoing right-lateral strike-slip displacement occurring along faults parallel to the Boconó fault system, possibly connected with the right-lateral faults inferred to exist along the axial part of the EC.
    Description: Published
    Description: 2233–2260
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: Paleomagnetism, magnetic fabric, Eastern Cordillera ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.04. Plate boundaries, motion, and tectonics ; 04. Solid Earth::04.07. Tectonophysics::04.07.06. Subduction related processes ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    An analysis of tropical instability waves in a numerical model of the Pacific Ocean - 1. Spatial variability of the waves (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Unstable oscillations confined within the mixed layer close to the equator are generated in wind-forced experiments performed in a multilevel general circulation model configured for the tropical Pacific Ocean. The experiments indicate that the waves develop preferentially in the eastern Pacific along the northern temperature front. However, there is clear evidence of a second unstable region along the southern temperature front in the central Pacific. In both regions the instabilities propagate westward, but in the central Pacific their phase speed is considerably smaller. The differences between the wave characteristics in the eastern and central Pacific are closely correlated to the differences in the time mean conditions of the flow. The eastern instabilities have a structure with two peaks in amplitude: one located on the equator and the other a few degrees north of it. Their dispersion characteristics show many similarities to those of tropical instability waves (TIWs) observed in the Pacific Ocean, while the instabilities which grow in the central Pacific do not have any known observed correspondents. We explore the spatial variability of the simulated waves through a wavelet analysis, which provides detailed results on how the period and wavelength of the instabilities change as a function of longitude, latitude, and depth. The wavelet analysis reveals that in the eastern Pacific and close to the surface the TIWs have a phase speed of-48 cm/s, while in the central Pacific they have a phase speed of-11 cm/s. In particular, the change in the phase speed is due to a change in the dominant period of the TIWs: The period of the central Pacific instabilities is considerably longer than the period of the instabilities present in the eastern Pacific.
    Description: This work was supported by the Department of Commerce/NOAA grant NA56GP0026. One of the authors (SM) was partially supported by a NASA Global Change Fellowship NGT-30288.
    Description: Published
    Description: 29613-29635
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: Ocean modeling ; Equatorial Ocean ; Tropical Instability Waves ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Intensity of the geomagnetic field in Europe for the last 3 ka: Influence of data quality on geomagnetic field modeling (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: One of the main challenges of paleomagnetic research is to obtain high-resolution geomagnetic field intensity reconstructions. For the last millennia, these reconstructions are mostly based on archeomagnetic data. However, the quality of the intensity data available in the databases is very variable, and the high scatter observed in the records clearly suggests that some of them might not be reliable. In this work we investigate how the geomagnetic field intensity reconstructions and, hence, our present knowledge of the geomagnetic field in the past, are affected by the quality of the data selected for modeling the Earth’s magnetic field. For this purpose we rank the European archeointensity data in four quality categories following widely accepted paleomagnetic criteria based on the methodology used during the laboratory treatment of the samples and on the number of specimens retained to calculate the mean intensities. Four geomagnetic field regional models have been implemented by applying the revised spherical cap harmonic analysis to these four groups of input data. Geomagnetic field models strongly depend on the used data set. The model built using all the available data (without any preselection) appears to be the less accurate, indicating some internal inconsistencies of the data set. In addition, some features of this model are clearly dominated by the less reliable archeointensity data, suggesting that such features might not reflect real variations of the past geomagnetic field. On the contrary, the regional model built on selected high-quality intensity data shows a very consistent intensity pattern at the European scale, confirming that the main intensity changes observed in Europe in the recent history of the geomagnetic field occurred at the continental scale.
    Description: Published
    Description: 2515–2530
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Description: open
    Keywords: Geomagnetism ; Paleomagnetism ; Archeomagnetism ; 04. Solid Earth::04.05. Geomagnetism::04.05.02. Geomagnetic field variations and reversals ; 04. Solid Earth::04.05. Geomagnetism::04.05.05. Main geomagnetic field ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Ultra-thick Triassic dolomites control the rupture behavior of the central Apennine seismicity: Evidence from magnetic modeling of the L’Aquila fault zone (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: High-resolution tomography from the 2009 L’Aquila extensional seismic sequence has shown that the Mw 6.1 main shock and most of the aftershocks occurred within a high velocity body (6.6≤Vp≤6.8 Km/s), located between depths of 3 and 12 km. The nature of the high Vp-body has remained speculative, although exhumed mafic deep crustal and upper mantle rocks (serpentinites) have been favoured. We used 3D magnetic anomaly modelling to investigate the plausibility of these favoured sources for the L’Aquila body. The modelling does not support the presence of high-velocity serpentinites with a 30-50% serpentinization degree and gabbros. Accordingly, we conclude that the high Vp-body may represent non-magnetic upper Triassic and possibly lower Liassic dolomites that have been drilled in neighbouring wells for 2-4 km. This conclusion is also consistent with the lack of a coherent gravity anomaly for the body. We speculate that ultra-thick Triassic dolomites reaching a thickness of 8 km may have been deposited in syntectonic wedges formed at the northern margin of the Ionian Sea, where oceanic spreading occurred in mid-late Triassic times.
    Description: Published
    Description: 6756–6770
    Description: 7A. Geofisica di esplorazione
    Description: JCR Journal
    Description: restricted
    Keywords: L’Aquila earthquake ; seismic tomography ; magnetic anomalies ; magnetic modelling ; dolomites; ; Apennines ; 04. Solid Earth::04.05. Geomagnetism::04.05.04. Magnetic anomalies
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Real-time measurements of the concentration and isotope composition of atmospheric and volcanic CO2 at Mount Etna (Italy) (2014)
    American Geophysical Union
    Details
    Publication Date: 2020-02-24
    Description: We present unprecedented data of real-time measurements of the concentration and isotope composition of CO2 in air and in fumarole-plume gases collected in 2013 during two campaigns at Mount Etna volcano, which were made using a laser-based isotope ratio infrared spectrometer. We performed approximately 360 measurements/h, which allowed calculation of the δ13C values of volcanic CO2. The fumarole gases of Torre del Filosofo (2900mabove sea level) range from 3.24 ± 0.06‰to 3.71 ± 0.09‰, comparable to isotope ratio mass spectrometry (IRMS) measurements of discrete samples collected on the same dates. Plume gases sampled more than 1 km from the craters show a δ13C= 2.2 ± 0.4‰, in agreement with the crater fumarole gases analyzed by IRMS. Measurements performed along ~17km driving track from Catania to Mount Etna show more negative δ13C values when passing through populated centers due to anthropogenic-derived CO2 inputs (e.g., car exhaust). The reported results demonstrate that this technique may represent an important advancement for volcanic and environmental monitoring.
    Description: Published
    Description: 2382–2389
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Real-time data of CO2 content and δ13C in atmospheric/volcanic gases ; This study opens new perspective for the community for volcanic surveillance ; 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::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    The failed eruption of Mt. Etna in December 2005: evidence from volcanic tremor analyses (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Strong changes in seismic radiation, comparable to those preceding and/or accompanying eruptive activity in recent years, were recorded at Mt. Etna volcano, Italy, from November 2005 to January 2006. The amplitude of volcanic tremor peaked in mid-December 2005 after a continuous, slow increase from August 2005 onwards, during which neither effusive nor paroxysmal activity was observed by volcanologists and alpine guides. During this time span, the centroid locations of volcanic tremor moved towards the surface, more and more clustered below the summit craters. The application of pattern classification analysis based on Self-Organizing Maps and fuzzy clustering to volcanic tremor data highlighted variations in the frequency domain as well. These changes were temporally associated with ground deformation variations, as indicative of a mild inflation of the summit of the volcano, and with a conspicuous increase in the SO2 plume-flux emission. Overall, we interpret this evidence as the result of recharging of the volcanic feeder at depth (〉 3 km below sea level) during which magma did not reach the shallow plumbing system.
    Description: Published
    Description: 4989–5005
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: embargoed_20140606
    Keywords: time series analysis ; volcano seismology ; volcano monitoring ; neural network and fuzzy logic ; seismic tomography ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
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    Probabilistic modeling of future volcanic eruptions at Mount Etna (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: The statistical analysis of volcanic activity at Mt Etna was conducted with the twofold aim of (1) constructing a probability map for vent opening of future flank eruptions and (2) forecasting the expected number of eruptive events at the summit craters. The spatiotemporal map of new vent opening at Etna volcano is based on the analysis of spatial locations and frequency of flank eruptions starting from 1610. Thanks to the completeness and accuracy of historical data over the last four centuries, we examined in detail the spatial and temporal distribution of flank eruptions showing that effusive events follow a nonhomogenous Poisson process with space-time varying intensities. After demonstrating the spatial nonhomogeneity and the temporal nonstationarity of flank eruptions at Etna, we calculated the recurrence rates (events expected per unit area per unit time) and produced different spatiotemporal probability maps of new vent opening in the next 1, 10 and 50 years. These probabilistic maps have an immediate use in evaluating the future timing and areas of Etna prone to volcanic hazards. Finally, the results of the analysis of the persistent summit activity during the last 110 years indicate that the hazard rate for eruptive events is not constant with time, differs for each summit crater of Mt Etna, highlighting a general increase in the eruptive frequency starting from the middle of last century and particularly from 1971, when the SE crater was formed.
    Description: This work was developed in the frame of the TecnoLab, the Laboratory for the Technological Advance in Volcano Geophysics organized by INGV-CT, DIEES-UNICT, and DMI-UNICT.
    Description: Published
    Description: 1925-1935
    Description: 1V. Storia e struttura dei sistemi vulcanici
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 4V. Vulcani e ambiente
    Description: 3IT. Calcolo scientifico e sistemi informatici
    Description: JCR Journal
    Description: restricted
    Keywords: Etna ; probabilistic modeling ; eruption ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 05. General::05.01. Computational geophysics::05.01.02. Cellular automata, fuzzy logic, genetic alghoritms, neural networks ; 05. General::05.01. Computational geophysics::05.01.04. Statistical analysis ; 05. General::05.01. Computational geophysics::05.01.05. Algorithms and implementation ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Ocean, sea-ice, atmosphere oscillations in the Southern Ocean as simulated by the SINTEX coupled model (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: 1This study evaluates the Antarctic Circumpolar Wave (ACW) as simulated by the SINTEX coupled model. We found evidence that sea-ice treatment plays a crucial role on simulating the ACW. In particular, SST anomalies at interannual time scales describe a propagating ACW-like pattern when a dynamic thermodynamic sea-ice model is coupled with the ocean, but when sea-ice is relaxed to climatology, anomalies occur as zonally symmetric patterns that do not propagate in longitude. Moreover, from the experiment with an active sea-ice component we saw that ACW-like oscillations are strongly modulated by low frequency variability. Our result adds some extra confidence to previous studies based on relatively short series of observed data.
    Description: This research was supported by the PREDICATE EU project (EVK2 – CT-1999 – 0020,). First author was supported by the PRISM EU project (EVR1 – CT-2001 – 40012).
    Description: Published
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: Antarctic Circumpolar Wave ; General Circulation Models ; air-ice-sea interactions ; 02. Cryosphere::02.04. Sea ice::02.04.01. Atmosphere/sea ice/ocean interaction
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
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    An analysis of tropical instability waves in a numerical model of the Pacific Ocean - 2. Generation and energetics of the waves (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: The instability processes which generate unstable waves with chara- cteristics similar to observed tropical instability waves in the Pacific Ocean are examined through a local energy analysis based on deviations from the time mean flow. Numerical experiments indicate that the waves develop preferentially in the eastern Pacific along the northern temperature front and have a westward phase speed and a structure with two peaks in amplitude: one located on the equator and the other a few degrees north of it. The energy analysis shows that the "two-peak" structure of the eastern waves is explained by two different instability processes which occur at different latitudes. In the time mean sense the region north of the equator is baroclinically unstable, while barotropic instability prevails at the equator. The life cycle of the waves is revealed by the time evolution of the energetics. Baroclinic instability is the dominant triggering mechanism which induces growth of the waves along the northern temperature front. The eddy pressure fluxes radiate energy south of the equator where the rneridional shear between the Equatorial Undercurrent and the South Equatorial Current becomes barotropically unstable. From the numerical simulations, there is evidence of a second unstable region in the central Pacific south of the equator where the instabilities have a lower phase speed. The energy analysis also shows that these waves grow from both barotropic and baroclinic conversions.
    Description: This work was supported by the Department of Com- merce/NOAA under grant NA56GP0026. One of the au- thors (SM) was partially supported by a NASA Global Change Fellowship NGT-30288. Another author (AB) was supported by a UCAR Postdoctoral Fellowship
    Description: Published
    Description: 29637-29661
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: Ocean modeling ; Equatorial Ocean ; Tropical Instability Waves ; Ocean wave generation ; Ocean wave energetics ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
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    Seismo-tectonic behavior of the Pernicana Fault System (Mt Etna): A gauge for volcano flank instability? (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Flank instability at basaltic volcanoes is often related to repeated dike intrusions along rift zones and accompanied by surface fracturing and seismicity. These processes have been mostly studied during specific events, and the lack of longer-term observations hinders their better understanding. Here we analyze ~20 years of deformation of the Pernicana Fault System (PFS), the key structure controlling the instability of the eastern flank of Mt. Etna. We exploit East-West and vertical components of mean deformation velocity, as well as corresponding time series, computed from ERS/ENVISAT (1992–2010) and COSMO-SkyMed (2009–2011) satellite radar sensors via Synthetic Aperture Radar Interferometry techniques. We then integrate and compare this information with field, seismic, and leveling data, collected between 1980 and 2012. We observe transient displacements accompanied by seismicity, overprinted on a long-term background eastward motion (~2 cm/yr). In the last decades, these transient events were preceded by a constant amount of accumulated strain near the PFS. The time of strain accumulation varies between a few years and a few decades, also depending on magma emplacement within the nearby North East Rift, which may increase the strain along the PFS. These results suggest that the amount of deformation near the PFS may be used as a gauge to forecast the occurrence of instability transients on the eastern flank of Etna. In this context, the PFS may provide an ideal, small-scale structure to test the relations between strain accumulation, stress loading, and seismic energy release.
    Description: This work has been partially supported by the Italian Space Agency (ASI) within the SAR4Volcanoes project, agreement I/ 034/11/0.
    Description: Published
    Description: 4398-4409
    Description: 1T. Geodinamica e interno della Terra
    Description: 2T. Tettonica attiva
    Description: 3T. Pericolosità sismica e contributo alla definizione del rischio
    Description: 4T. Fisica dei terremoti e scenari cosismici
    Description: 5T. Sorveglianza sismica e operatività post-terremoto
    Description: 1V. Storia e struttura dei sistemi vulcanici
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 4V. Vulcani e ambiente
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: JCR Journal
    Description: restricted
    Keywords: Volcano flank instability ; Pernicana fault ; Etna ; 04. Solid Earth::04.01. Earth Interior::04.01.99. General or miscellaneous ; 04. Solid Earth::04.03. Geodesy::04.03.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 05. General::05.01. Computational geophysics::05.01.99. General or miscellaneous ; 05. General::05.02. Data dissemination::05.02.99. General or miscellaneous ; 05. General::05.08. Risk::05.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Complete seismic release of tectonic strain and earthquake recurrence in the Apennines (Italy) (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Here I compare estimates of tectonic strain rates from dense Global Positioning System measurements with the seismicity released in the last ~500 years in the Apennines (Italy). The rates of seismic moment accumulation from geodesy and of historical seismic release by earthquakes agree within the uncertainties, ruling out significant aseismic deformation. Within the considered 400 km long section of the Apennines, this balance yields an average recurrence interval of 30–75 years for MW≥6.5 events without requiring a future earthquake larger than those observed historically (MW~7). A minimum estimate of unreleased strain allows MW≥6.5 and MW≥6.9 events to be released in ~35% and ~10% of the central-southern Apennines, respectively. The definition of the seismic potential for smaller events is more uncertain, and their occurrence remains a significant threat throughout the Apennines.
    Description: Published
    Description: 1155–1162
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Crustal deformation ; Earthquakes ; GPS ; Apennines ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
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    Long-term stress-strain analysis of volcano flank instability: The eastern sector of Etna from 1980 to 2012 (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: We investigated the evolution of seismicity and deformation in the unstable eastern flank of Etna volcano over a 30 year period (from 1980 to 2012). A significant temporal correlation has been revealed between periods of flank acceleration and intensified seismic activity by comparing seismicity along the northern border (Pernicana fault system) of the sliding flank and the deformation of the eastern flank. Two marked phases have been observed in 1984-1986 and in the years following 2002. These two phases are separated by an intermediate phase from 1987 to 2001, in which the flank sliding slowed down and the seismicity dropped drastically. This common temporal evolution in the deformation rate and seismic release supports the hypothesis that the seismicity in the northern border can be viewed as a marker of the response to accommodate the stress exerted by the traction of the eastern flank sliding. This interplay has also been corroborated by finite element method numerical computations that highlight a good correlation between the seismicity pattern and areas of positive stress changes induced by the sliding surface. The two intense phases of flank acceleration are representative of two main different sources: volcano flank instability stretching the eastern sector in the first 1984-1986 phase and magmatic intrusions pushing the eastern flank seaward since the 2002-2003 eruption. Establishing the relationship between flank acceleration and seismic activation therefore contributes to understanding Etna's mechanical behavior and provides insights into the processes regulating the unstable flank response.
    Description: Published
    Description: 5098-5108
    Description: 1V. Storia e struttura dei sistemi vulcanici
    Description: JCR Journal
    Description: restricted
    Keywords: Pernicana ; fault ; volcano-tectonics ; flank instability ; seismicity and deformation ; stress and strain ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 17
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    Magma flow between summit and Pu‘u ‘O‘o at Kılauea Volcano, Hawai‘i (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Volcanic eruptions are often accompanied by spatiotemporal migration of ground deformation, a consequence of pressure changes within magma reservoirs and pathways. We modeled the propagation of pressure variations through the east rift zone (ERZ) of K" ılauea Volcano, Hawai‘i, caused by magma " o-Kupaianaha withdrawal during the early eruptive episodes (1983–1985) of the ongoing Pu‘u ‘ O‘" " eruption. Eruptive activity at the Pu‘u ‘ O‘" o vent was typically accompanied by abrupt deflation that lasted for several hours and was followed by a sudden onset of gradual inflation once the eruptive episode had ended. Similar patterns of deflation and inflation were recorded at K" ılauea’s summit, approximately 15 km to the northwest, albeit with time delays of hours. These delay times can be reproduced by modeling the spatiotemporal changes in magma pressure and flow rate within an elastic-walled dike that traverses K" ılauea’s ERZ. Key parameters that affect the behavior of the magma-dike system are the dike dimensions, the elasticity of the wall rock, the magma viscosity, and to a lesser degree the magnitude and duration of the pressure variations themselves. Combinations of these parameters define a transport efficiency and a pressure diffusivity, which vary somewhat from episode to episode, resulting in variations in delay times. The observed variations in transport efficiency are most easily explained by small, localized changes to the geometry of the magma pathway
    Description: Published
    Description: 2232–2246
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: magma flow ; dikes ; Kilauea ; elastic rock ; magma-rock coupling ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 18
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    The coupling between very long period seismic events, volcanic tremor, and degassing rates at Mount Etna volcano (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: From December 2005 to January 2006, an anomalous degassing episode was observed at Mount Etna, well-correlated with an increase in volcanic tremor, and in the almost complete absence of eruptive activity. In the same period, more than 10,000 very long period (VLP) events were detected. Through moment tensor inversion analyses of the VLP pulses, we obtained quantitative estimates of the volumetric variations associated with these events. This allowed a quantitative investigation of the relationship between VLP seismic activity, volcanic tremor, and gas emission rate at Mount Etna. We found a statistically significant positive correlation between SO2 gas flux and volcanic tremor, suggesting that tremor amplitude can be used as a first-order proxy for the background degassing activity of the volcano. VLP volumetric changes and SO2 gas flux are correlated only for the last part of our observations, following a slight change in the VLP source depth. We calculate that the gas associated with VLP signal genesis contributed less than 5% of the total gas emission. The existence of a linear correlation between VLP and degassing activities indicates a general relationship between these two processes. The effectiveness of such coupling appears to depend upon the particular location of the VLP source, suggesting that conduit geometry might play a significant role in the VLP-generating process. These results are the first report on Mount Etna of a quantitative relationship between the amounts of gas emissions directly estimated through instrumental flux measurements and the quantities of gas mass inferred in the VLP source inversion.
    Description: Published
    Description: 4910-4921
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Very Long Period seismicity ; UV scanners network ; Etna Volcano ; volcano monitoring ; 04. Solid Earth::04.02. Exploration geophysics::04.02.06. Seismic methods ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 19
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    Interaction between magma intrusion and flank dynamics at Mt. Etna in 2008, imaged by integrated dense GPS and DInSAR data (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Global positioning system (GPS) and differential interferometric synthetic aperture radar (DInSAR) data, collected from July 2007 to July 2008 on Mt. Etna, are analyzed to define the dynamics preceding and accompanying the onset of the eruption on 13 May 2008. Short- and long-term comparisons have been made on both GPS and radar data, covering similar time windows. Thanks to the availability of three GPS surveys the year before the eruption onset, an increase in the seaward movement of the NE flank of the volcano has been detected in the few months before the dike intrusion. The GPS ground deformation pattern also shows a slight inflation centered on the western side of the volcano in the preeruptive long-term comparison (from July 2007 to May 2008). The GPS has been integrated with DInSAR data by the SISTEM approach, to take advantage of the different methodologies and provide high spatial sampling of the 3-D ground displacement pattern. We inverted the SISTEM results to model the pressure source causing the observed preeruptive inflation. The subsequent emplacement of the eruptive dike was imaged by two GPS surveys carried out on a dense network over the uppermost part of the volcano on 6 and 13 May, i.e., a few days before and a few hours after the beginning of the eruption. We inverted this comparison to define the position, geometry, and kinematics of the dike. The dike intrusion was also imaged by DInSAR data with temporal baselines of 2-3 months, which confirm strong displacements localized on the summit area, rapidly decreasing toward the middle flanks of the volcano, as detected by very short-term GPS data; furthermore, the comparison between DInSAR and GPS data highlighted the presence of a depressurizing source localized beneath the upper southwestern area, acting just after the dike intrusion. Finally, the long-period (1 year) GPS and DInSAR data were integrated by SISTEM to finely depict the 3-D ground deformation pattern with the highest spatial resolution. The long-period data allowed the complex kinematics of the volcano to be finely imaged and highlighting the interaction between flank dynamics and magma injection.
    Description: Published
    Description: 2818-2835
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: flank dynamics ; eruption ; volcano-tectonics ; GPS ; DInSAR ; data integration ; Etna ; deformation ; volcano ; fault ; 04. Solid Earth::04.03. Geodesy::04.03.07. Satellite geodesy
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  • 20
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    New data from borehole strainmeters to infer lava fountain sources (Etna 2011-2012) (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: In January 2011 eruptive activity resumed at Etna producing a new phase with frequent lava fountain episodes until April 2012. In November 2011, the first two borehole strainmeters were installed, which detected negative strain changes (~ 0.15 - 0.8 strain) during the paroxysmal events. A Finite Element Model was set up to estimate accurately the tilt and volumetric strain, taking into account the real profile of the volcano and the elastic medium heterogeneity. The numerical computations indicated an elongated depressurizing source located at 0 km b.s.l., which underwent a volume change of ~2 x 106 m3 which is the most of the magma volume erupted while a smaller remaining part is accommodated by the magma compressibility. This shallow source cannot accumulate large magma volumes and, thus, favours short term periodic eruptive events with a fairly constant balance between the refilling and the erupted magma.
    Description: Published
    Description: 3579-3584
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: embargoed_20150613
    Keywords: Etna volcano ; lava fountain eruptions ; shallow plumbing system ; borehole strainmeters ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 21
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    Interseismic coupling, seismic potential, and earthquake recurrence on the southern front of the Eastern Alps (NE Italy) (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: Here we use continuous GPS observations to document the geodetic strain accumulation across the South-Eastern Alps (NE Italy). We estimate the interseismic coupling on the intracontinental collision thrust fault and discuss the seismic potential and earthquake recurrence. We invert the GPS velocities using the back slip approach to simultaneously estimate the relative angular velocity and the degree of interseismic coupling on the thrust fault that separates the Eastern Alps and the Venetian-Friulian plain. Comparison between the rigid rotation predicted motion and the shortening observed across the area indicates that the South-Eastern Alpine thrust front absorbs about 70% of the total convergence between the Adria and Eurasia plates. The coupling is computed on a north dipping fault following the continuous external seismogenic thrust front of the South-Eastern Alps. The modeled thrust fault is currently locked from the surface to a depth of ≈10 km. The transition zone between locked and creeping portions of the fault roughly corresponds with the belt of microseismicity parallel and to the north of the mountain front. The estimated moment deficit rate is 1.3 ± 0.4 × 1017 Nm/yr. The comparison between the estimated moment deficit and that released historically by the earthquakes suggests that to account for the moment deficit the following two factors or their combination should be considered: (1) a significant part of the observed interseismic coupling is released aseismically and (2) infrequent “large” events with long return period (〉 1000 years) and with magnitudes larger than the value assigned to the largest historical events (Mw≈ 6.7).
    Description: Published
    Description: 4448-4468
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Eastern Alps; interseismic coupling; seismotectonics; seismic potential; recurrence time; GPS ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk ; 04. Solid Earth::04.07. Tectonophysics::04.07.01. Continents ; 04. Solid Earth::04.07. Tectonophysics::04.07.04. Plate boundaries, motion, and tectonics ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
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  • 22
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    An active oblique-contractional belt at the transition between the Southern Apennines and Calabrian Arc: The Amendolara Ridge, Ionian Sea, Italy (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: High-resolution, single-channel seismic and multibeam bathymetry data collected at the Amendolara Ridge, a key submarine area marking the junction between the Apennine collision belt and the Calabrian subduction forearc, reveal active deformation in a supposedly stable crustal sector. New data, integrated with existing multichannel seismic profiles calibrated with oil-exploratory wells, show that middle to late Pleistocene sediments are deformed in growth folds above blind oblique-reverse faults that bound a regional pop-up. Data analysis indicates that ~10 to 20 km long banks that top the ~80 km long, NW-SE trending ridge are structural culminations above en echelon fault segments. Numeric modeling of bathymetry and stratigraphic markers suggests that three 45° dipping upper crustal (2–10 km) fault segments underlie the ridge, with slip rates up to ~0.5 mm/yr. Segments may be capable with M ~ 6.1–6.3 earthquakes, although an unknown fraction of aseismic slip undoubtedly contributes to deformation. The fault array that bounds the southern flank of the ridge (Amendolara Fault System) parallels a belt of Mw 〈 4.7 strike-slip and thrust earthquakes, which suggest current left-oblique reverse motion on the array. The eastern segment of the array shows apparent morphologic evidence of deformation and might be responsible for Mw ≤ 5.2 historic events. Late Pliocene-Quaternary growth of the oblique contractional belt is related to the combined effects of stalling of Adriatic slab retreat underneath the Apennines and subduction retreat of the Ionian slab underneath Calabria. Deformation localization was controlled by an inherited mechanical interface between the thick Apulian (Adriatic) platform crust and the attenuated Ionian Basin crust.
    Description: Published
    Description: 2169–2194
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: partially_open
    Keywords: Active compression ; Growth strata modeling ; High-resolution seismic ; Multibeam bathymetry ; Jonian Sea ; 04. Solid Earth::04.02. Exploration geophysics::04.02.06. Seismic methods ; 04. Solid Earth::04.04. Geology::04.04.01. Earthquake geology and paleoseismology ; 04. Solid Earth::04.04. Geology::04.04.04. Marine geology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy
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  • 23
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    Wave-guide effects in very high rate GPS record of the 6 April 2009, Mw 6.1 L'Aquila, central Italy earthquake (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: A 10 Hz sampling frequency GPS station was installed near L'Aquila a few days before the 6 April 2009 Mw 6.1 earthquake. It recorded displacement waveforms during the main shock and the largest Mw 5.4 aftershock of 7 April. The horizontal components of the main shock contain a high-amplitude (43 cm peak-to-peak) nearly harmonic (1 Hz) wave train not evident in other nearby instrumental records. The persistency of this feature during aftershocks recorded by a temporarily colocated seismological station highlights a local site effect. Traditional models based on near-surface velocity structure and topography variations fail to reproduce the size and frequency band of the observed amplified motion. The amplified wave train can be explained by a low-velocity fault zone layer below the station. This model fits the delay of the large-amplitude nearly harmonic wave train after the S wave phase and is consistent with the variation in the fault excitation efficiency between the two shocks in relation to their different source depth and location. Synthetic calculation of trapped waves in a model consisting of two quarter spaces separated by a 650 m wide low-velocity zone with 50% velocity reduction and Q value of 20 fit well the observed anomalous record. The parameters of the model fault zone layer are consistent with geological evidence of a broad damage zone adjacent to the station and a similar site response found in this crustal zone with ambient noise. Results of shallow seismic surveys and sonic logs from deep wells provide independent constraints on the host rock velocities.
    Description: This work has partially benefited from the activities performed in the NERA project (Network of European Research infrastructures for earthquake risk Assessment and mitigation, 262330), funded by the European Commission FP7 program, and in the FIRB-Abruzzo project, funded by the Italian Ministery of Education, University and Research.
    Description: Published
    Description: 490–501
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: High-rate GPS ; Transient deformation ; L'Aquila earthquake ; fault-guided waves ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
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  • 24
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    Investigation of the complex dynamics and structure of the 2010 Eyjafjallajökull volcanic ash cloud using multispectral images and numerical simulations (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: We investigated the structure and evolution of the 2010 Eyjafjallajökull volcanic cloud and its dispersal over Iceland and Europe integrating satellite multispectral images and numerical simulations. Data acquired by Medium Resolution Imaging Spectrometer (MERIS)and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) have been analyzed to quantify the cloud extent and composition. The VOL-CALPUFF dispersal code was applied to reconstruct the transient and 3-D evolution of the cloud. Source parameters estimated on the base of available a posteriori volcanological data sets have been used. Quantitative comparisons between satellite retrievals and modeling results were performed for two selected instants of time during the first and third eruptive phases on a regional scale. Sensitivity of the model to initial volcanological conditions has been analyzed at continental scale. Several complex non intuitive features of cloud dynamics have been highlighted and strengths and limitations of the adopted methods identified. The main findings are: the level of quantitative agreement between satellite observations and numerical results depends on ash cloud composition (particle sizes and concentration) with better agreement for smaller particles and higher concentrations; the agreement between observations and modeling outcomes also depends on the temporal stability of volcanological conditions and the complexity of the meteorological wind field; the irregular dispersion of ash, as reconstructed from satellite data and numerical modeling, can be well explained by the different response of particle sizes to strong vertical wind-shear, and by resuspension processes acting at ground level; eruptive source conditions are the main source of uncertainty in modeling, especially during an ongoing crisis and at long-range scales.
    Description: Published
    Description: 4729–4747
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Volcanic ash cloud ; Satellite retrieval ; Numerical modelling ; Eyjafjallajokull ; Ash dispersal and deposition ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects
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  • 25
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    Vertical GPS ground motion rates in the Euro-Mediterranean region: New evidence of velocity gradients at different spatial scales along the Nubia-Eurasia plate boundary (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: We use 2.5 to 14 years long position time series from 〉800 continuous Global Positioning System (GPS) stations to study vertical deformation rates in the Euro-Mediterranean region. We estimate and remove common mode errors in position time series using a principal component analysis, obtaining a significant gain in the signal-to-noise ratio of the displacements data. Following the results of a maximum likelihood estimation analysis, which gives a mean spectral index ~ 0.7, we adopt a power law + white noise stochastic model in estimating the final vertical rates and find 95% of the velocities within ±2 mm/yr, with uncertainties from filtered time series ~40% smaller than from the unfiltered ones. We highlight the presence of statistically significant velocity gradients where the stations density is higher. We find undulations of the vertical velocity field at different spatial scales both in tectonically active regions, like eastern Alps, Apennines, and eastern Mediterranean, and in regions characterized by a low or negligible tectonic activity, like central Iberia and western Alps. A correlation between smooth vertical velocities and topographic features is apparent in many sectors of the study area. Glacial isostatic adjustment and weathering processes do not completely explain the measured rates, and a combination of active tectonics and deep-seated geodynamic processes must be invoked. Excluding areas where localized processes are likely, or where subduction processes may be active, mantle dynamics is the most likely process, but regional mantle modeling is required for a better understanding.
    Description: Published
    Description: 6003–6024
    Description: 1T. Geodinamica e interno della Terra
    Description: 2T. Tettonica attiva
    Description: 1R. Reti di monitoraggio e Osservazioni
    Description: JCR Journal
    Description: restricted
    Keywords: GPS ; Geodynamics ; Mediterranean ; Vertical deformation ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 04. Solid Earth::04.03. Geodesy::04.03.06. Measurements and monitoring ; 04. Solid Earth::04.03. Geodesy::04.03.07. Satellite geodesy ; 04. Solid Earth::04.07. Tectonophysics::04.07.01. Continents ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.04. Plate boundaries, motion, and tectonics ; 04. Solid Earth::04.07. Tectonophysics::04.07.06. Subduction related processes
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  • 26
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    Deep structure and tectonics of the northern-central Apennines as seen by regional-scale tomography and 3-D located earthquakes (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: In this study we present new high-resolution, regional-scale, Vp and Vp/Vs models of the northern-central Apennines along with accurate 3-D locations of a large set of local earthquakes. The main velocity anomalies are consistent with the surface geology in the shallow layers and present evidence for fluids stored within the basement at greater depths beneath the extensional belt. The Adria and Tyrrhenian mantle are defined by positive velocity anomalies below 30 km depth, while a low-Vp, high-Vp/Vs region in between indicates the existence of a hydrated wedge. The results yield new constraints on active processes in the Apennines and more generally envisage the evolution of a postcollisional belt. Velocity anomalies and earthquakes are consistent with a complex system of delamination and sinking of the Adria continental lithosphere, with the peeling of the crust identified by intermediate-depth seismicity. Change of seismicity and structural patterns along the belt indicates that this tectonic process is diachronous and that fluids, released by sunken lithosphere, are stored within the crust, conditioning the occurrence of seismicity and the onset of extension.
    Description: Published
    Description: 5391-5403
    Description: 1T. Geodinamica e interno della Terra
    Description: JCR Journal
    Description: restricted
    Keywords: Local earthquake tomography ; tectonic of Apennines ; 04. Solid Earth::04.06. Seismology::04.06.07. Tomography and anisotropy
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  • 27
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    Eruptive processes leading to the most explosive lava fountain at Etna volcano: The 23 November 2013 episode (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: The 23 November 2013 lava fountain at Etna volcano was the most explosive of the last 44 episodes that have occurred at Etna in 2011–2013. We infer the total magma volume erupted by thermal images analysis and show that it was characterized by a very high time-averaged-discharge-rate (TADR) of ~360m3 s 1, having erupted ~1.6 × 106m3 of dense-rock equivalent magma volume in just 45 min, which is more than 3 times the TADR observed during previous episodes. Two borehole dilatometers confirmed the eruption dynamics inferred from the thermal images. When compared to the other lava fountains, this episode can be considered as the explosive end-member. However, the erupted volume was still comparable to the other lava fountain events. We interpret that the 23 November explosive end-member event was caused by more primitive and gas-rich magma entering the system, as demonstrated by the exceptional height reached by the lava fountain.
    Description: Published
    Description: 4912–4919
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Etna eruption ; paroxysmal explosive eruption ; lava fountain ; strainmeters ; lava fountain volume ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 28
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    Progression of spontaneous in-plane shear faults from sub-Rayleigh to compressional wave rupture speeds (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-04-04
    Description: We investigate numerically the passage of spontaneous, dynamic in-plane shear ruptures from initiation to their final rupture speed, using very fine grids. By carrying out more than 120 simulations, we identify two different mechanisms controlling supershear transition. For relatively weaker faults, the rupture speed always passes smoothly and continuously through the range of speeds between the Rayleigh and shear wave speeds (the formerly considered forbidden zone of rupture speeds). This, however, occurs in a very short time, before the ruptures reach the compressional wave speed. The very short time spent in this range of speeds may explain why a jump over these speeds was seen in some earlier numerical and experimental studies and confirms that this speed range is an unstable range, as predicted analytically for steady state, singular cracks. On the other hand, for relatively stronger faults, we find that a daughter rupture is initiated by the main (mother) rupture, ahead of it. The mother rupture continues to propagate at sub-Rayleigh speed and eventually merges with the daughter rupture, whose speed jumps over the Rayleigh to shear wave speed range. We find that this daughter rupture is essentially a “pseudorupture,” in that the two sides of the fault are already separated, but the rupture has negligible slip and slip velocity. After the mother rupture merges with it, the slip, the slip velocity, and the rupture speed become dominated by those of the mother rupture. The results are independent of grid sizes and of methods used to nucleate the initial rupture.
    Description: Published
    Description: 8331–8345
    Description: 4T. Fisica dei terremoti e scenari cosismici
    Description: JCR Journal
    Description: open
    Keywords: Seismic source ; Supershear ruptures ; 04. Solid Earth::04.04. Geology::04.04.06. Rheology, friction, and structure of fault zones
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Paleomagnetic evidence for a post-Eocene 90° CCW rotation of internal Apennine units: A linkage with Corsica-Sardinia rotation? (2014)
    American Geophysical Union
    Details
    Publication Date: 2017-10-06
    Description: We report on an extensive paleomagnetic study (36 sites) of the Tuscan Nappe succession from the Northern Apennines Arc, aimed to reconstruct the tectonic evolution of the internal sector of this chain. We analyzed Eocene pelagic foreland ramp deposits (Scaglia Toscana Formation) and Oligocene–lower Miocene siliciclastic turbidites (Macigno and Falterona Formations). Paleomagnetic results show that the internal sector of the Northern Apennines underwent large counterclockwise (CCW) rotations with respect to the Adria-Africa foreland. A decrease in the rotation magnitude was observed from the southern to the northern sector of the arc (from 91 to 36°). This trend is opposite to that observed in the more external units of Northern Apennines and demonstrates that the oroclinal bending model, which has been proposed for the external units of the chain, is not appropriate to explain the evolution of the internal sector of the arc. On the basis of the observed paleomagnetic pattern, we propose a new tectonic model in which the Tuscan and Falterona-Cervarola units in the southern area were first rotated CCW along with the Corsica-Sardinia block during its lower Miocene rotational drifting and were later involved in the main phases of rotational emplacement and translation toward the outermost sector (Umbria domain), thus yielding the final curved shape of the Northern Apennines chain. Data from this study represent the first paleomagnetic evidence of the influence of the Corsica-Sardinia CCW rotation in the Apennines orogenic wedge deformation, in the general framework of the geodynamic evolution of the Central Mediterranean subduction system.
    Description: Published
    Description: 374-392
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: paleomagnetism, Apennines, Tuscany ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism
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    Explosive expansion of a slowly-decompressed magma analog:evidence of delayed bubble nucleation (2014)
    American Geophysical Union
    Details
    Publication Date: 2019-12-05
    Description: While ascending in the plumbing system of volcanoes, magma undergoes decompression at rates spanning several orders of magnitude and set by a number of factors internal and external to the volcano. Slow decompression generally results in an effusive or mildly explosive expansion of the magma, but counterexamples of sudden switches from effusive to explosive eruptive behaviour have been documented at various volcanoes worldwide. The mechanisms involved in this behavior are currently debated, in particular regarding basaltic magmas. Here, we explore the interplay between decompression rate and vesiculation vigour by decompressing a magma analog obtained by dissolving pine resin into acetone in varying proportions. Our mixtures contain solid particles and upon decompression experience the nucleation of acetone bubbles. We find mixtures high in acetone, containing smaller and fewer solid particles, experience strong supersaturation and fragment for very slow decompressions, despite having low viscosity, while mixtures low in acetone, with more and larger solid particles degas efficiently. We interpret our results in terms of delayed bubble nucleation due to a lack of efficient nucleation sites. We discuss how a similar mechanism might induce violent, explosive expansion in volatile-rich and poorly crystalline low-silica magmas, by analogy to previous inferences for rhyolitic magmas.
    Description: Published
    Description: 3067-3084
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: embargoed_20150613
    Keywords: Magma fragmentation ; basaltic magma ; analog laboratory experiments ; slow decompression ; bubble nucleation ; explosive volcanic eruptions ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism
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    Comment on “The winter anomaly in the middlelatitude F region during the solar minimum period observed by the Constellation Observing System for Meteorology, Ionosphere, and Climate” by W. K. Lee, H. Kil, Y.-S. Kwak, Q. Wu, S. Cho, and J. U. Park (2014)
    American Geophysical Union
    Details
    Publication Date: 2020-02-24
    Description: Seasonal or winter anomaly in the F2 layer has been known since the beginning of regular ionospheric observations [e.g., Berkner and Wells, 1938, and references therein], and one may be sure that such a fundamental feature of this phenomenon as its height extent has been analyzed. However, Lee et al. [2011] using radio occultation Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) Ne(h) observations have decided to reconsider this problem starting from the very beginning without any analyses of previous investigations and comparisons to earlier obtained results as if ionospheric F2 layer physics has started with them. Besides, the authors have done some incorrect statements which contradict the present theory of the ionospheric F2 layer. They claim that “The topside plasma density is greater in the summer hemisphere than in the winter hemisphere; … the electron density below the F peak at middle latitudes is also greater during summer than during winter; Therefore, the seasonal anomalous behavior is a phenomenon only near the F-peak height in the Northern Hemisphere; The question is why the seasonal behavior of the ionosphere near the F-peak height is different from the behavior below and above the F peak. ….there was no explanation for the different seasonal behaviors of electron density in the lower F region and at F-peak height”. This is the main contents and results of the paper. Let us consider what was known about winter anomaly before the paper by Lee et al. [2011].
    Description: Published
    Description: 7972–7978
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
    Description: restricted
    Keywords: December anomaly, ionosphere ; 01. Atmosphere::01.02. Ionosphere::01.02.99. General or miscellaneous
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    Multidisciplinary Approach Yields Insight into Mt. Etna 2001 Eruption (2014)
    American Geophysical Union
    Details
    Publication Date: 2020-02-24
    Description: On July 17,2001, lava began pouring down the slopes of Mt. Etna in Sicily signaling the start of the volcano's first flank eruption in nearly 10 years. Etna typically experiences long periods of explosive and effusive activity at the summit, which lies 3350 m a.s.l., interspersed with shorter flank eruptions. During the latter, large volumes of lava can threaten local populations. The Catania Section of the Istituto Nazionale di Geofisica e Vulcanologia (INGV) routinely monitors the volcano with an array of integrated multidisciplinary techniques. During the 2001 flank eruption, researchers obtained the deepest insight yet into the mechanisms that control this fascinating volcano. In particular, by studying ground deformation, seismicity, gravity changes, and geomagnetism, researchers were able to forecast 3 to 4 days in advance the intrusion of a new feeder dike in the upper part of the volcano and follow the propagation of dike emplacement and fissure opening, as well as estimate the volume of the intrusion. During the eruption, volcanology gas geochemistry and petrology were used to distinguish two different magmas erupting at the same time from both this new feeder dike and the summit feeding system, which has been active since January 2001. Effusion rate measurements and thermal mapping of the flow field provided insight into the maximum length the lava flow could reach from the lower vent, and researchers were able to follow the process of tube formation along this flow. The previous flank eruption on Etna occurred between 1991 and 1993, when 235 million of lava poured from within the Valle del Bove (VDB) and formed a lava flow field over 8.5 km long that threatened the town of Zafferana. Since then, eruptive activity at Etna has been restricted to the summit area. A progressive increase in the activity occurred between June 1998 and February 1999, with a succession of 21 paroxysmal episodes from the Southeast Cone (SEC). Then, on February 1999, a fire fountain episode from the SEC indicated the start of the 1999 summit eruption, which produced two lava flow fields. During 2000, there were 66 fire fountain events from the SEC accompanied by small lava flows. Lava flow emission started again from the north base of the SEC in January 2001, and on May 9,2001, small fire fountaining episodes were observed on the summit and northern flank of the SEC.This activity gradually increased in frequency and intensity before the 2001 flank eruption.
    Description: Published
    Description: 653-656
    Description: 3V. Dinamiche e scenari eruttivi
    Description: N/A or not JCR
    Description: restricted
    Keywords: Etna eruption ; volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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    A method for foF2 short-term (1–24 h) forecast using both historical and real-time foF2 observations over European stations: EUROMAP model (2014)
    American Geophysical Union
    Details
    Publication Date: 2020-02-24
    Description: A method for foF2 short-term forecast over Europe has been developed and implemented in the EUROMAP model. The input-driving parameters are 3 h ap indices (converted to ap(τ)), effective ionospheric T index, and real-time foF2 observations. The method includes local (for each station) regression storm models to describe strong negative disturbances under ap(τ)〉30 and training models to describe foF2 variations under ap(τ) ≤ 30. The derived model was tested in two regimes: descriptive when observed 3 h ap indices were used and real forecast when predicted daily Ap were used instead of 3 h ap indices—. In the case of strong negative disturbances the EUROMAP model demonstrates on average the improvement over the lnternational Reference Ionosphere STORM-time correction model (IRI(STORM)) model: 40% in winter, 24% in summer, and 39% in equinox. The average improvement over climatology is 41% in winter, 59% in summer, and 55% in equinox. In the majority of cases this difference is statistically significant. In the case of strong positive disturbances, higher-latitude stations also manifest a significant difference between the twomodels but this difference is insignificant at lower latitude stations. The substitution of 3 h ap input indices for the predicted daily Ap ones decreases the foF2 prediction accuracy in the case of negative disturbances but practically has no effect with positive disturbances. In both cases the proposed method manifests better accuracy than the IRI(STORM) model provides. The obtained results show a real opportunity to provide foF2 forecast with the (1–24 h) lead time on the basis of predicted Ap indices
    Description: Published
    Description: 253-270
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
    Description: restricted
    Keywords: forecast ; 01. Atmosphere::01.02. Ionosphere::01.02.03. Forecasts
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    Modeling the spreading of glacial meltwater from the Amundsen and Bellingshausen Seas (2014)
    American Geophysical Union
    In:  EPIC3Geophysical Research Letters, American Geophysical Union, 41(22), pp. 7942-7949, ISSN: 00948276
    Details
    Publication Date: 2019-07-16
    Description: It has been suggested that an increased melting of continental ice in the Amundsen Sea (AS) and Bellingshausen Sea (BS) is a likely source of the observed freshening of Ross Sea (RS) water. To test this hypothesis, we simulate the spreading of glacial meltwater using the Finite Element Sea Ice/Ice Shelf/Ocean Model. Based on the spatial distribution of simulated passive tracers, most of the basal meltwater from AS ice shelves flows toward the RS with more than half of the melt originating from the Getz Ice Shelf. Further, the model results show that a slight increase of the basal mass loss can substantially intensify the transport of meltwater into the RS due to a strengthening of the melt-driven shelf circulation and the westward flowing coastal current. This supports the idea that the basal melting of AS and BS ice shelves is one of the main sources for the RS freshening.
    Repository Name: EPIC Alfred Wegener Institut
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    A Mid-Holocene Shift and Millennial-Scale Variations in North Pacific Intermediate Water Oxygenation and Upper Ocean Hydrography (2014)
    American Geophysical Union
    In:  EPIC3American Geophysical Union Fall Meeting, San Francisco, CA, USA, 2014-12-15-2014-12-19Washington, D. C., USA, American Geophysical Union
    Details
    Publication Date: 2015-01-05
    Description: The subarctic North Pacific and its marginal seas constitute a key area in which rapid environmental changes over the past decades have been observed in instrumental records, like sea ice decreases, or alterations of nutrient inventories and oxygenation of mid-depth water masses. However, knowledge about the past climatic and oceanographic variability beyond instrumental time series in the subarctic North Pacific and its marginal seas is limited. Few temporally and spatially well-resolved high-resolution and spatially well datasets exist, with spatial and temporal coverage being insufficient to gain a detailed picture of past variations. Our proxydata-based study focuses on a collection of sediment records from the Okhotsk Sea as major source area for well ventilated North Pacific Intermediate Water (NPIW) that cover the last ca. 12,000 years with high temporal and adequate spatial resolution. We decipher rapid changes in NPIW ventilation patterns on centennial to millennial time scales and show that the current ventilation of the mid-depth North Pacific has likely only been prevalent for the last 2 ka. We further provide evidence for a Mid-Holocene shift in mid-depth NPIW ventilation characteristics. Additionally, changes in North Atlantic Deep Water flow speed and patterns are reflected in our records of North Pacific mid-depth water mass dynamics, thus indicating a hemispheric-wide connection between the Atlantic and Pacific regions during the Holocene. Planktic oxygen isotope data suggest a high variability in the stratification of local surface water masses and the formation of sea ice, influencing the formation of new, well ventilated water masses near to our core sites. We compare the main Holocene baseline changes evidenced in our proxy reconstructions to Early Holocene and Pre-Industrial time slice results from the fully-coupled MPI-ESM (COSMOS) Earth System Model, with a focus on the Pacific Ocean to better understand NPIW and upper ocean dynamic changes.
    Repository Name: EPIC Alfred Wegener Institut
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    Liquid water in snow (2014)
    American Geophysical Union
    In:  EPIC3Workshop at the Institute for Snow and Avalanche Research, EOS, Davos, Switzerland, American Geophysical Union
    Details
    Publication Date: 2019-07-17
    Description: From 2-4 April 2014 about 50 researchers attended the workshop „Liquid water in snow – measurements techniques and modeling approaches“ that took place at the Institute for Snow and Avalanche Research (SLF) in Davos, Switzerland – the first one since 1982 in Innsbruck, Austria. This is the report thereof.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Miscellaneous , notRev
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    The Opening of the Arctic-Atlantic Gateway: Tectonic, Oceanographic and Climatic Dynamics - an IODP Initiative (2014)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting, San Francisco, 2014-12-15-2014-12-19American Geophysical Union
    Details
    Publication Date: 2014-08-03
    Description: The modern polar cryosphere reflects an extreme climate state with profound temperature gradients towards high-latitudes. It developed in association with stepwise Cenozoic cooling, beginning with ephemeral glaciations and the appearance of sea ice in the late middle Eocene. The polar ocean gateways played a pivotal role in changing the polar and global climate, along with declining greenhouse gas levels. The opening of the Drake Passage finalized the oceanographic isolation of Antarctica, some 40 Ma ago. The Arctic Ocean was an isolated basin until the early Miocene when rifting and subsequent sea-floor spreading started between Greenland and Svalbard, initiating the opening of the Fram Strait / Arctic-Atlantic Gateway (AAG). Although this gateway is known to be important in Earth’s past and modern climate, little is known about its Cenozoic development. However, the opening history and AAG’s consecutive widening and deepening must have had a strong impact on circulation and water mass exchange between the Arctic Ocean and the North Atlantic. To study the AAG’s complete history, ocean drilling at two primary sites and one alternate site located between 73°N and 78°N are proposed. These sites will provide unprecedented sedimentary records that will unveil (1) the history of shallow-water exchange between the Arctic Ocean and the North Atlantic, and (2) the development of the AAG to a deep-water connection and its influence on the global climate system. The specific overarching goals of our proposal are to study: • the influence of distinct tectonic events in the development of the AAG and the formation of deep water passage on the North Atlantic and Arctic paleoceanography, and • the role of the AAG in the climate transition from the Paleogene greenhouse to the Neogene icehouse for the long-term (~50 Ma) climate history of the northern North Atlantic.
    Repository Name: EPIC Alfred Wegener Institut
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    Post-seismic viscoelastic deformation and stress transfer after the 1960 M9.5 Valdivia, Chile earthquake : effects on the 2010 M8.8 Maule, Chile earthquake (2014)
    Oxford University Press
    Details
    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
    Repository Name: Woods Hole Open Access Server
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    Palaeoenvironmental conditions in the Gulf of Alaska (NE Pacific) during the Mid Pleistocene Transition (2014)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting, San Francisco, CA, USA, 2014-12-14-2014-12-19American Geophysical Union
    Details
    Publication Date: 2022-09-29
    Description: The Mid Pleistocene Transition (MPT) constitutes a fundamental shift in Earth's climate system from a 41 ka to a 100 ka periodicity in glacial oscillations. The exact timing and mechanism(s) that caused this change from a low- to high-amplitude glacial variability are still under debate and only recently Pena & Goldstein (2014) suggested that a disruption of the thermohaline circulation at about 900 ka BP and a subsequent change in ocean circulation might have acted as a trigger for the onset of 100 ka glacial-interglacial cycles. Most studies targeting the MPT are based on Atlantic sediment records whereas only few data sets are available from the North Pacific (see e.g. Clark et al., 2006 and McClymont et al., 2013 for reviews). IODP Expedition 341 distal deep-water site U1417 in the Gulf of Alaska (subpolar NE Pacific) now provided a continuous sediment record for reconstructing Miocene to Late Pleistocene changes in the sea surface conditions and how these relate to orbital and millennial scale climate variability. Here we present organic geochemical biomarker data covering the 1.5 Ma to 0.1 Ma time interval with special focus on the MPT. Alkenone, sterol, n-alkane and C25 highly branched isoprenoid data are used to reconstruct sea surface temperatures, primary productivity and terrigenous organic matter input (via sea ice, icebergs, meltwater discharge or aeolian transport). In addition, the diatom concentration and the species composition of the diatom assemblage deliver information on changes in palaeoproductivity and nutrient (silicate) availability. A major change in the environmental setting between 1.2 and 0.8 Ma is recorded by the biomarkers. This shift seems to be associated with a significant cooling of the surface waters in the Gulf of Alaska. Matching this shift, a significant change in the main components of the diatom community occurred between 1.2 and 0.8 Ma. References Clark, P.U., Archer, D., Pollard, D., Blum, J.D., Rial, J.A., Brovkin, V., Mix, A.C., Pisias, N.G., Roy, M., 2006. Quaternary Science Reviews, 25, (23–24), 3150-3184. McClymont, E.L., Sosdian, S.M., Rosell-Melé, A., Rosenthal, Y., 2013. Earth-Science Reviews, 123, 173-193. Pena, L.D. and Goldstein, S.L., 2014. Science, 345, 318-322.
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  • 40
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    Climate-Ice Sheet Interactions through the Pliocene-Pleistocene: Preliminary Results from IODP Expedition 341 (Gulf of Alaska) (2014)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting, San Francisco, CA, USA, 2014-12-14-2014-12-19American Geophysical Union
    Details
    Publication Date: 2022-09-29
    Description: Since the Pliocene, global climate history is distinguished by the transition into a colder world, dominated by the onset and intensification of major Northern Hemisphere glaciations which have also changed in their duration and intensity. Potential drivers for these events include falling atmospheric CO2, progressive sub-glacial erosion, tectonic uplift, and associated feedbacks. At present, isolating climate as the driver of evolving continental ice volume since the Pliocene is hindered by the limited long term data sets which directly link climate changes to evidence for ice-sheet advance/retreat, erosion, and tectonic evolution over million year timescales. IODP Expedition 341 drilled a cross-margin transect in the Gulf of Alaska from ice-proximal sites on the continental shelf to distal sites in the deep Pacific. This study focuses on the distal site (Site U1417, c.4190 m water depth) which contains variable biogenic and terrigenous contributions, and evidence for deposition through pelagic, mass movement and glacial processes. Our aim is to investigate links between north-east Pacific paleoceanography and the history of the north-west Cordilleran ice sheet, neither of which are fully understood given limited data pre-dating the Last Glacial Maximum. We reconstruct SSTs during the mid-Pliocene, Plio-Pleistocene Transition (PPT) and mid-Pleistocene transition (MPT) using the UK37’ index. We consider the interaction between SSTs and primary production by examining the absolute and relative abundances of plankton biomarkers (e.g. for haptophytes, diatoms and dinoflagellates), carbon/nitrogen ratios, stable isotopes (δ13C, δ15N) and diatom assemblages. Links between these climatic events and the north-west Cordilleran ice-sheet advance/retreat history are initially made using shipboard stratigraphy; emerging data sets on ice-rafting from members of the Expedition 341 Scientific Party will refine these relationships.
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  • 41
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    Arctic sea ice variability during the last deglaciation: a biomarker approach (2014)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting, San Francisco, CA, USA, 2014-12-14-2014-12-19American Geophysical Union
    Details
    Publication Date: 2022-09-29
    Description: The last transition from full glacial to current interglacial conditions was accompanied by distinct short-term climate fluctuations caused by changes in the global ocean circulation system. Most palaeoceanographic studies focus on the documentation of the behaviour of the Atlantic Meridional Overturning Circulation (AMOC) during the last deglaciation in response to freshwater forcing events. In this respect, the role of Arctic sea ice remained relatively unconsidered - primarily because of the difficulty of its reconstruction. Here we present new proxy data on late glacial (including the Last Glacial Maximum; LGM) and deglacial sea ice variability in the Arctic Ocean and its main gateway - the Fram Strait - and how these changes in sea ice coverage contributed to AMOC perturbations observed during Heinrich Event 1 and the Younger Dryas. Recurrent short-term advances and retreats of sea ice in Fram Strait, prior and during the LGM, are in line with a variable (or intermittent) North Atlantic heat flow along the eastern corridor of the Nordic Seas. Possibly in direct response to the initial freshwater discharge from melting continental ice-sheets, a permanent sea ice cover established only at about 19 ka BP (i.e. post-LGM) and lasted until 17.6 ka BP, when an abrupt break-up of this thick ice cover and a sudden discharge of huge amounts of sea ice and icebergs through Fram Strait coincided with the weakening of the AMOC during Heinrich Event 1. Similarly, another sea ice maximum at about 12.8 ka BP is associated with the slowdown of the AMOC during the Younger Dryas. The new data sets clearly highlight the important role of Arctic sea ice for the re-organisation of the oceanographic setting in the North Atlantic during the last deglaciation. Further studies and sensitivity experiments to identify crucial driving (and feedback) mechanisms within the High Latitude ice-ocean-atmosphere system will contribute the understanding of rapid climate changes.
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  • 42
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    Late Pleistocene biogenic sedimentation in the Gulf of Alaska: A biogeochemical perspective from IODP Expedition 341 (2014)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting, San Francisco, CA, USA, 2014-12-14-2014-12-19American Geophysical Union
    Details
    Publication Date: 2022-09-29
    Description: Reconstructing the timing and nature of past changes in aquatic productivity in the Gulf of Alaska (GoA) can shed light on the primary processes driving biogeochemical cycling over geologic timescales. Here, we present sedimentologic, physical property, stable isotope, and biogenic opal concentration data from IODP Expedition 341 Sites U1417 and U1419 and identify intervals where diatom ooze lithofacies and geochemical evidence for increased algal productivity are prevalent during the Pleistocene. Sites U1417 and U1419 are located in the center and the margin of the Fe-limited GoA, respectively, and they offer the potential to characterize past changes in biogeochemical cycling during different Pleistocene time intervals. Site U1419 cores were collected from a small slope basin at the edge of the continental shelf. Sediment cores reveal two prominent ~6-m-thick intervals of diatomaceous ooze. Between these intervals are numerous 20-cm-thick sections of biogenic-rich sediment, interbedded with gray mud that commonly contains lonestones. Based on preliminary age models, the two diatom ooze intervals likely correspond to the Holocene and MIS 3, while the intervening interbedded glacigenic and biogenic sediment can broadly be ascribed to MIS 2. Diatomaceous ooze and diatom-rich sediments are generally characterized by lower magnetic susceptibility, natural gamma ray, bulk density, and higher b* color reflectance. Initial C & N concentration and stable isotopic data show elevated concentrations and more positive stable isotope values during the Holocene and MIS 3, which approximate the isotopic signature of modern phytoplankton measured in the GoA. Within the glacial period, the biogenic-rich intervals are also characterized by more positive C and N isotopic values. When combined with the shipboard physical property data, the stable isotopic results are indicative of millennial-scale variations in productivity and/or changes in glacial ice extent in the GoA during the last glacial period. We will discuss these results in the context of an improved isotope stratigraphy and ongoing work examining multiple interglacial productivity variations at Site U1417.
    Repository Name: EPIC Alfred Wegener Institut
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    Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates (2014)
    Oxford University Press
    Details
    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
    Repository Name: Woods Hole Open Access Server
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    Magnetotelluric data, stable distributions and impropriety: an existential combination (2014)
    Oxford University Press
    Details
    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
    Repository Name: Woods Hole Open Access Server
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    Virus infection of Haptolina ericina and Phaeocystis pouchetii implicates evolutionary conservation of programmed cell death induction in marine haptophyte–virus interactions (2014)
    Oxford University Press
    Details
    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
    Repository Name: Woods Hole Open Access Server
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    The evolution of the four subunits of voltage-gated calcium channels : ancient roots, increasing complexity, and multiple losses (2014)
    Oxford University Press
    Details
    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
    Repository Name: Woods Hole Open Access Server
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    Three‐dimensional compressional wave attenuation tomography for the crust and uppermost mantle of Northern and central California (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
    Print ISSN: 2169-9313
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    Topics: Geosciences , Physics
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    Constraints on fluid flow processes in the Hellenic Accretionary Complex (eastern Mediterranean Sea) from numerical modeling (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
    Print ISSN: 2169-9313
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    Savani : A variable resolution whole‐mantle model of anisotropic shear velocity variations based on multiple data sets (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 50
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    Numerical modeling of convective erosion and peridotite‐melt interaction in big mantle wedge: Implications for the destruction of the North China Craton (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 51
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    Pn anisotropy in Mesozoic western Pacific lithosphere (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Flow of supersonic jets across flat plates: Implications for ground‐level flow from volcanic blasts (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 53
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    Sensitivity of Coulomb stress change to the parameters of the Coulomb failure model: A case study using the 2008 M w 7.9 Wenchuan earthquake (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
    Print ISSN: 2169-9313
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    Earthquake model experiments in a viscoelastic fluid: A scaling of decreasing magnitudes of earthquakes with depth (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 55
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    Resolving the fine‐scale density structure of shallow oceanic mantle by Bayesian inversion of localized geoid anomalies (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 56
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    Upper mantle Q structure beneath old seafloor in the western Pacific (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 57
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    Nongeocentric axial dipole field behavior during the Mono Lake excursion (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
    Print ISSN: 2169-9313
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  • 58
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    Bayesian inversion for the filtered flow at the Earth's core‐mantle boundary (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 59
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    Pockmark formation and evolution in deep water Nigeria: Rapid hydrate growth versus slow hydrate dissolution (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 60
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    Late Pleistocene‐Holocene right slip rate and paleoseismology of the Nayband fault, western margin of the Lut block, Iran (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 61
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    Earthquake ruptures modulated by waves in damaged fault zones (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Zagros “phantom earthquakes” reassessed—The interplay of seismicity and deep salt flow in the Simply Folded Belt? (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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  • 63
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    A cascading failure during the 24 May 2013 great Okhotsk deep earthquake (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Microstructural controls on the physical and mechanical properties of edifice‐forming andesites at Volcán de Colima, Mexico (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Influence of atmospheric structure and topography on infrasonic wave propagation (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Band‐limited topographic mass distribution generates full‐spectrum gravity field: Gravity forward modeling in the spectral and spatial domains revisited (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Source parameter scaling and radiation efficiency of microearthquakes along the Irpinia fault zone in southern Apennines, Italy (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Interpreting subsurface volcanic structures using geologically constrained 3‐D gravity inversions: Examples of maar‐diatremes, Newer Volcanics Province, southeastern Australia (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    A unified theory of microseisms and hum (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Active tectonics and earthquake potential of the Myanmar region (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Stratified seismic anisotropy and the lithosphere‐asthenosphere boundary beneath eastern North America (2014)
    American Geophysical Union
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    Publication Date: 2014-04-01
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    Multi-events earthquake early warning algorithm using a Bayesian approach (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: Current earthquake early warning (EEW) systems lack the ability to appropriately handle multiple concurrent earthquakes, which led to many false alarms during the 2011 Tohoku earthquake sequence in Japan. This paper uses a Bayesian probabilistic approach to handle multiple concurrent events for EEW. We implement the theory using a two-step algorithm. First, an efficient approximate Bayesian model class selection scheme is used to estimate the number of concurrent events. Then, the Rao-Blackwellized Importance Sampling method with a sequential proposal probability density function is used to estimate the earthquake parameters, that is hypocentre location, origin time, magnitude and local seismic intensity. A real data example based on 2 months data (2011 March 9–April 30) around the time of the 2011 M 9 Tohoku earthquake is studied to verify the proposed algorithm. Our algorithm results in over 90 per cent reduction in the number of incorrect warnings compared to the existing EEW system operating in Japan.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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    A catalogue of 2D photometric decompositions in the SDSS-DR7 spectroscopic main galaxy sample: preferred models and systematics (2014)
    Oxford University Press
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    Publication Date: 2014-12-12
    Description: We present a catalogue of 2D, point spread function-corrected de Vacouleurs, Sérsic, de Vacouleurs+Exponential, and Sérsic+Exponential fits of ~7 x 10 5 spectroscopically selected galaxies drawn from the Sloan Digital Sky Survey (SDSS) Data Release 7. Fits are performed for the SDSS r band utilizing the fitting routine galfit and analysis pipeline pymorph . We compare these fits to prior catalogues. Fits are analysed using a physically motivated flagging system. The flags suggest that more than 90 per cent of two-component fits can be used for analysis. We show that the fits follow the expected behaviour for early and late galaxy types. The catalogues provide a robust set of structural and photometric parameters for future galaxy studies. We show that some biases remain in the measurements, e.g. the presence of bars significantly affect the bulge measurements although the bulge ellipticity may be used to separate barred and non-barred galaxies, and about 15 per cent of bulges of two-component fits are also affected by resolution. The catalogues are available in electronic format. We also provide an interface for generating postage stamp images of the 2D model and residual as well as the 1D profile. These images can be generated for a user-uploaded list of galaxies on demand.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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    The H I-dominated low-surface-brightness galaxy KKR 17 (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-13
    Description: We present new narrow-band (Hα and [O  iii ]) images and optical spectrophotometry of H  ii regions for a gas-rich low-surface-brightness irregular galaxy, KKR 17. The central surface brightness of the galaxy is μ 0 ( B ) = 24.15 ± 0.03 mag s –2 . The galaxy was detected by the Arecibo Legacy Fast ALFA survey (ALFALFA). Its mass is dominated by neutral hydrogen (H  i ) gas. In contrast, both the stellar masses of the bright H  ii and diffuse stellar regions are small. In addition, the fit to the spectral energy distribution to each region shows the stellar populations of H  ii and diffuse regions are different. The bright H  ii region contains a large fraction of O-type stars, revealing recent strong star formation, whereas the diffuse region is dominated by median age stars with a typical age of ~600 Myr. Using McGaugh's abundance model, we found that the average metallicity of KKR 17 is 12 + (O/H) = 8.0 ± 0.1. The star-formation rate of KKR 17 is 0.21 ± 0.04 M  yr –1 , which is ~1/5 of our Milky Way's. Based on the analysis results for young stellar clusters in the H  ii region, the bright H  ii region has two sub-components with different velocities and metallicities. This may be caused by the outflow of massive stars or merging events. However, the mechanism triggering star formation in the H  ii region is still uncertain.
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    A multiwavelength study of the M dwarf binary YY Geminorum (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: We review the results of the 1988 multiwavelength campaign on the late-type eclipsing binary YY Geminorum. Observations include: broad-band optical and near-infrared photometry, simultaneous optical and ultraviolet ( IUE ) spectroscopy, X-ray ( Ginga ) and radio (VLA) data. From models fitted to the optical light curves, fundamental physical parameters have been determined together with evidence for transient maculations (spots) located near quadrature longitudes and intermediate latitudes. Eclipses were observed at optical, ultraviolet and radio wavelengths. Significant drops in 6 cm radio emission near the phases of both primary and secondary eclipse indicate relatively compact radio emitting volumes that may lie between the binary components. IUE observations during secondary eclipse are indicative of a uniform chromosphere saturated with Mg  ii emission and an extended volume of Lyα emission. Profile fitting of high-dispersion Hα spectra confirms the chromospheric saturation and indicates significant Hα opacity to heights of a few per cent of the photospheric radius. There is evidence for an enhanced Hα emission region visible near phase 0.25–0.35 which may be associated with a large spot on the primary and with two small optical flares which were also observed at other wavelengths: one in microwave radiation and the other in X-rays. For both flares, L X / L opt is consistent with energy release in closed magnetic structures.
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    An efficient radiative cooling approximation for use in hydrodynamic simulations (2014)
    Oxford University Press
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    Publication Date: 2014-12-14
    Description: To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive. Stamatellos and collaborators introduced a scheme for smoothed particle hydrodynamics (SPH) simulations based on the notion of polytropic pseudo-clouds that uses only local quantities to estimate cooling rates. The computational approach is extremely efficient and works well in cases close to spherical symmetry, such as in star formation problems. Unfortunately, the method, which takes the local gravitational potential as an input, can be inaccurate when applied to non-spherical configurations, limiting its usefulness when studying discs or stellar collisions, among other situations of interest. Here, we introduce the ‘pressure scale height method,’ which incorporates the fluid pressure scaleheight into the determination of column densities and cooling rates, and show that it produces more accurate results across a wide range of physical scenarios while retaining the computational efficiency of the original method. The tested models include spherical polytropes as well as discs with specified density and temperature profiles. We focus on applying our techniques within an SPH code, although our method can be implemented within any particle-based Lagrangian or grid-based Eulerian hydrodynamic scheme. Our new method may be applied in a broad range of situations, including within the realm of stellar interactions, collisions, and mergers.
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    Magnetic resonance tomography using elongated transmitter and in-loop receiver arrays for time-efficient 2-D imaging of subsurface aquifer structures (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Surface nuclear magnetic resonance (surface-NMR) is a promising technique for exploring shallow subsurface aquifer structures. Surface-NMR can be applied in environments that are characterized as a 1-D layered Earth. The technique utilizes a single loop and is referred to as magnetic resonance sounding. The technique referred to as magnetic resonance tomography (MRT) allows complex 2-D aquifer structures to be explored. Currently, MRT requires multiple loops and a roll along measurement scheme, which causes long survey time. We propose a loop layout using an elongated transmitter and an in-loop receiver arrays (ETRA) to conduct a 2-D survey with just one measurement. We present a comprehensive comparison between the new layout and the common approaches based on sensitivity and resolution analyses and show synthetic and field data. The results show that ETRA generates subsurface images at sufficient resolution with significantly lower survey times than other loop layouts.
    Keywords: Geomagnetism, Rock Magnetism and Palaeomagnetism
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Integrated velocity field from ground and satellite geodetic techniques: application to Arenal volcano (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Measurements of ground deformation can be used to identify and interpret geophysical processes occurring at volcanoes. Most studies rely on a single geodetic technique, or fit a geophysical model to the results of multiple geodetic techniques. Here we present a methodology that combines GPS, Total Station measurements and InSAR into a single reference frame to produce an integrated 3-D geodetic velocity surface without any prior geophysical assumptions. The methodology consists of five steps: design of the network, acquisition and processing of the data, spatial integration of the measurements, time series computation and finally the integration of spatial and temporal measurements. The most significant improvements of this method are (1) the reduction of the required field time, (2) the unambiguous detection of outliers, (3) an increased measurement accuracy and (4) the construction of a 3-D geodetic velocity field. We apply this methodology to ongoing motion on Arenal's western flank. Integration of multiple measurement techniques at Arenal volcano revealed a deformation field that is more complex than that described by individual geodetic techniques, yet remains consistent with previous studies. This approach can be applied to volcano monitoring worldwide and has the potential to be extended to incorporate other geodetic techniques and to study transient deformation.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Galactic outflow and diffuse gas properties at z 〉= 1 using different baryonic feedback models (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: We measure and quantify properties of galactic outflows and diffuse gas at z ≥ 1 in cosmological hydrodynamical simulations. Our novel subresolution model, Multi-Phase Particle Integrator (MUPPI), implements supernova feedback using fully local gas properties, where the wind velocity and mass loading are not given as input. We find the following trends at z  = 2 by analysing central galaxies having a stellar mass higher than 10 9 M . The outflow velocity and mass outflow rate ( $\dot{M}_{\rm out}$ ) exhibit positive correlations with galaxy mass and with the star formation rate (SFR). However, most of the relations present a large scatter. The outflow mass loading factor () is between 0.2 and 10. The comparison effective model generates a constant outflow velocity, and a negative correlation of with halo mass. The number fraction of galaxies where outflow is detected decreases at lower redshifts, but remains more than 80 per cent over z  = 1–5. The outflow velocity correlation with SFR becomes flatter at z  = 1, and displays a negative correlation with halo mass in massive galaxies. Our study demonstrates that both the MUPPI and effective models produce significant outflows at ~1/10 of the virial radius; at the same time shows that the properties of outflows generated can be different from the input speed and mass loading in the effective model. Our MUPPI model, using local properties of gas in the subresolution recipe, is able to develop galactic outflows whose properties correlate with global galaxy properties , and consistent with observations.
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    Multiplex sequencing of pooled mitochondrial genomes--a crucial step toward biodiversity analysis using mito-metagenomics (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
    Keywords: Genomics
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    Topics: Biology
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    Easy quantitative assessment of genome editing by sequence trace decomposition (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The efficacy and the mutation spectrum of genome editing methods can vary substantially depending on the targeted sequence. A simple, quick assay to accurately characterize and quantify the induced mutations is therefore needed. Here we present TIDE, a method for this purpose that requires only a pair of PCR reactions and two standard capillary sequencing runs. The sequence traces are then analyzed by a specially developed decomposition algorithm that identifies the major induced mutations in the projected editing site and accurately determines their frequency in a cell population. This method is cost-effective and quick, and it provides much more detailed information than current enzyme-based assays. An interactive web tool for automated decomposition of the sequence traces is available. TIDE greatly facilitates the testing and rational design of genome editing strategies.
    Keywords: Targeted gene modification
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    Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients ( r 2 ) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.
    Keywords: Nucleic acid structure, Protein-nucleic acid interaction
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    Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity ( T m ), nuclease stability, activity in vitro and in vivo , RNase H activation and cleavage patterns (both human and E. coli ) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro , while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo , the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.
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    qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: In an isogenic cell population, phenotypic heterogeneity among individual cells is common and critical for survival of the population under different environment conditions. DNA modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The single molecule real-time (SMRT) sequencing technology provides a unique platform for detecting a wide range of DNA modifications, including N6-methyladenine (6-mA), N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic haploid cells, in which the same loci of the genome are differentially modified. We tested the reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556. qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal population of ST556. Subsequent biochemical analyses revealed that the recognition sequences of two type I restriction–modification (R-M) systems are responsible for the intercellular heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA modification.
    Keywords: Nucleic acid modification, Computational Methods
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    Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
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    In silico prediction of splice-altering single nucleotide variants in the human genome (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies.
    Keywords: RNA characterisation and manipulation, Computational Methods
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    AGO2 and SETDB1 cooperate in promoter-targeted transcriptional silencing of the androgen receptor gene (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: In mammals, RNA interference is primarily a post-transcriptional mechanism. Evidence has accumulated for additional role in transcriptional gene silencing (TGS) but the question for a good paradigm for small interfering antigene RNA (agRNA)-induced chromatin modification remains unanswered. Here, we show that SETDB1, a histone H3-lysine 9 (H3K9)-specific methyltransferase, cooperates with Argonaute-2 (AGO2) and plays an essential role in agRNA-induced TGS. The androgen receptor ( AR ) gene was transcriptionally silenced by agRNA targeted to its promoter, and we show that this repression was mitigated by knockdown of SETDB1 or AGO2 . Chromatin immunoprecipitation demonstrated that agRNA-driven AGO2 was first targeted to the AR promoter, followed by SETDB1. SIN3A and HDAC1/2, the components of the SIN3-HDAC complex, immunoprecipitated with SETDB1, and localized at the agRNA-targeted promoter. Agreeing with the presence of SETDB1, trimethyl-H3K9 was enriched in the AR promoter. Both EZH2 and trimethyl-H3K27 were also present in the targeted locus; accordingly, EZH2 immunoprecipitated with SETDB1. DNA methylation level was not significantly changed, suggesting the absence of de novo methylating activity in agRNA-induced AR promoter. Our results demonstrate that SETDB1, together with AGO2, plays an essential role in TGS through recruiting chromatin remodeler and/or other modifiers, consequently creating a repressive chromatin milieu at the targeted promoter.
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    The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: LEF/TCFs direct the final step in Wnt/β-catenin signalling by recruiting β-catenin to genes for activation of transcription. Ancient, non-vertebrate TCFs contain two DNA binding domains, a High Mobility Group box for recognition of the Wnt Response Element (WRE; 5'-CTTTGWWS-3') and the C-clamp domain for recognition of the GC-rich Helper motif (5'-RCCGCC-3'). Two vertebrate TCFs (TCF-1/TCF7 and TCF-4/TCF7L2) use the C-clamp as an alternatively spliced domain to regulate cell-cycle progression, but how the C-clamp influences TCF binding and activity genome-wide is not known. Here, we used a doxycycline inducible system with ChIP-seq to assess how the C-clamp influences human TCF1 binding genome-wide. Metabolic pulse-labeling of nascent RNA with 4'Thiouridine was used with RNA-seq to connect binding to the Wnt transcriptome. We find that the C-clamp enables targeting to a greater number of gene loci for stronger occupancy and transcription regulation. The C-clamp uses Helper sites concurrently with WREs for gene targeting, but it also targets TCF1 to sites that do not have readily identifiable canonical WREs. The coupled ChIP-seq/4'Thiouridine-seq analysis identified new Wnt target genes, including additional regulators of cell proliferation. Thus, C-clamp containing isoforms of TCFs are potent transcriptional regulators with an expanded transcriptome directed by C-clamp-Helper site interactions.
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    Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.
    Keywords: Genomics
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    Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html .
    Keywords: Nucleic acid structure, Computational Methods
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    EDITORIAL: NAR AWARDS 2014 (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
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    DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R 2 N 2 stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and extensive ATP hydrolysis (~170 ATP/s/monomer) are required for site-specific DNA cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed positions (6–7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'. Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII enzymes may employ a unique catalytic mechanism for DNA cleavage.
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    Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Emerging evidence points to roles for tRNA modifications and tRNA abundance in cellular stress responses. While isolated instances of stress-induced tRNA degradation have been reported, we sought to assess the effects of stress on tRNA levels at a systems level. To this end, we developed a next-generation sequencing method that exploits the paucity of ribonucleoside modifications at the 3'-end of tRNAs to quantify changes in all cellular tRNA molecules. Application of this tRNA-seq method to Saccharomyces cerevisiae identified all 76 expressed unique tRNA species out of 295 coded in the yeast genome, including all isoacceptor variants, with highly precise relative (fold-change) quantification of tRNAs. In studies of stress-induced changes in tRNA levels, we found that oxidation (H 2 O 2 ) and alkylation (methylmethane sulfonate, MMS) stresses induced nearly identical patterns of up- and down-regulation for 58 tRNAs. However, 18 tRNAs showed opposing changes for the stresses, which parallels our observation of signature reprogramming of tRNA modifications caused by H 2 O 2 and MMS. Further, stress-induced degradation was limited to only a small proportion of a few tRNA species. With tRNA-seq applicable to any organism, these results suggest that translational control of stress response involves a contribution from tRNA abundance.
    Keywords: Nucleic acid modification, Transcriptome Mapping - Monitoring Gene Expression
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    Rad51/Dmc1 paralogs and mediators oppose DNA helicases to limit hybrid DNA formation and promote crossovers during meiotic recombination (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: During meiosis programmed DNA double-strand breaks (DSBs) are repaired by homologous recombination using the sister chromatid or the homologous chromosome (homolog) as a template. This repair results in crossover (CO) and non-crossover (NCO) recombinants. Only CO formation between homologs provides the physical linkages guiding correct chromosome segregation, which are essential to produce healthy gametes. The factors that determine the CO/NCO decision are still poorly understood. Using Schizosaccharomyces pombe as a model we show that the Rad51/Dmc1-paralog complexes Rad55-Rad57 and Rdl1-Rlp1-Sws1 together with Swi5-Sfr1 play a major role in antagonizing both the FANCM-family DNA helicase/translocase Fml1 and the RecQ-type DNA helicase Rqh1 to limit hybrid DNA formation and promote Mus81-Eme1-dependent COs. A common attribute of these protein complexes is an ability to stabilize the Rad51/Dmc1 nucleoprotein filament, and we propose that it is this property that imposes constraints on which enzymes gain access to the recombination intermediate, thereby controlling the manner in which it is processed and resolved.
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    Electronic ISSN: 1362-4962
    Topics: Biology
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    Landscape of target:guide homology effects on Cas9-mediated cleavage (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: To study target sequence specificity, selectivity, and reaction kinetics of Streptococcus pyogenes Cas9 activity, we challenged libraries of random variant targets with purified Cas9::guide RNA complexes in vitro . Cleavage kinetics were nonlinear, with a burst of initial activity followed by slower sustained cleavage. Consistent with other recent analyses of Cas9 sequence specificity, we observe considerable (albeit incomplete) impairment of cleavage for targets mutated in the PAM sequence or in ‘seed’ sequences matching the proximal 8 bp of the guide. A second target region requiring close homology was located at the other end of the guide::target duplex (positions 13–18 relative to the PAM). Sequences flanking the guide+PAM region had measurable (albeit modest) effects on cleavage. In addition, the first-base Guanine constraint commonly imposed by gRNA expression systems has little effect on overall cleavage efficiency. Taken together, these studies provide an in vitro understanding of the complexities of Cas9–gRNA interaction and cleavage beyond the general paradigm of site determination based on the ‘seed’ sequence and PAM.
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    Identification of tri-phosphatase activity in the biogenesis of retroviral microRNAs and RNAP III-generated shRNAs (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Transcripts possessing a 5'-triphosphate are a hallmark of viral transcription and can trigger the host antiviral response. 5'-triphosphates are also found on common host transcripts transcribed by RNA polymerase III (RNAP III), yet how these transcripts remain non-immunostimulatory is incompletely understood. Most microRNAs (miRNAs) are 5'-monophosphorylated as a result of sequential endonucleolytic processing by Drosha and Dicer from longer RNA polymerase II (RNAP II)-transcribed primary transcripts. In contrast, bovine leukemia virus (BLV) expresses subgenomic RNAP III transcripts that give rise to miRNAs independent of Drosha processing. Here, we demonstrate that each BLV pre-miRNA is directly transcribed by RNAP III from individual, compact RNAP III type II genes. Thus, similar to manmade RNAP III-generated short hairpin RNAs (shRNAs), the BLV pre-miRNAs are initially 5'-triphosphorylated. Nonetheless, the derivative 5p miRNAs and shRNA-generated 5p small RNAs (sRNAs) possess a 5'-monophosphate. Our enzymatic characterization and small RNA sequencing data demonstrate that BLV 5p miRNAs are co-terminal with 5'-triphosphorylated miRNA precursors (pre-miRNAs). Thus, these results identify a 5'-tri-phosphatase activity that is involved in the biogenesis of BLV miRNAs and shRNA-generated sRNAs. This work advances our understanding of retroviral miRNA and shRNA biogenesis and may have implications regarding the immunostimulatory capacity of RNAP III transcripts.
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    A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses—the so-called transfer function—and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.
    Keywords: Synthetic Biology and Assembly Cloning, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al. , 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.
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    Synergetic regulation of translational reading-frame switch by ligand-responsive RNAs in mammalian cells (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Distinct translational initiation mechanisms between prokaryotes and eukaryotes limit the exploitation of prokaryotic riboswitch repertoire for regulatory RNA circuit construction in mammalian application. Here, we explored programmed ribosomal frameshifting (PRF) as the regulatory gene expression platform for engineered ligand-responsive RNA devices in higher eukaryotes. Regulation was enabled by designed ligand-dependent conformational rearrangements of the two cis-acting RNA motifs of opposite activity in -1 PRF. Particularly, RNA elements responsive to trans-acting ligands can be tailored to modify co-translational RNA refolding dynamics of a hairpin upstream of frameshifting site to achieve reversible and adjustable -1 PRF attenuating activity. Combined with a ligand-responsive stimulator, synthetic RNA devices for synergetic translational-elongation control of gene expression can be constructed. Due to the similarity between co-transcriptional RNA hairpin folding and co-translational RNA hairpin refolding, the RNA-responsive ligand repertoire provided in prokaryotic systems thus becomes accessible to gene-regulatory circuit construction for synthetic biology application in mammalian cells.
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    Topics: Biology
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