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  • Oxford University Press  (115,491)
  • 2015-2019  (83,816)
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  • 1
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    Oxford University Press
    Publication Date: 2024-03-23
    Description: "With so much media and political criticism of their shortcomings and failures, it is easy to overlook the fact that many governments work pretty well much of the time. Great Policy Successes turns the spotlight on instances of public policy that are remarkably successful. It develops a framework for identifying and assessing policy successes, paying attention not just to their programmatic outcomes but also to the quality of the processes by which policies are designed and delivered, the level of support and legitimacy they attain, and the extent to which successful performance endures over time. The bulk of the book is then devoted to 15 detailed case studies of striking policy successes from around the world, including Singapore's public health system, Copenhagen and Melbourne's rise from stilted backwaters to the highly liveable and dynamic urban centres they are today, Brazil's Bolsa Familia poverty relief scheme, the US's GI Bill, and Germany's breakthrough labour market reforms of the 2000s. Each case is set in context, its main actors are introduced, key events and decisions are described, the assessment framework is applied to gauge the nature and level of its success, key contributing factors to success are identified, and potential lessons and future challenges are identified. Purposefully avoiding the kind of heavy theorizing that characterizes many accounts of public policy processes, each case is written in an accessible and narrative style ideally suited for classroom use in conjunction with mainstream textbooks on public policy design, implementation, and evaluation.
    Keywords: public policy ; policy evaluation ; government ; governance ; social policy ; health policy ; economic policy ; thema EDItEUR::J Society and Social Sciences::JP Politics and government
    Language: English
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  • 2
    Publication Date: 2021-06-21
    Description: We present the analysis of rotational and translational ground motions from earthquakes recorded during October–November 2016, in association with the Central Italy seismic sequence. We use co-located measurements of the vertical ground rotation rate from a large ring laser gyroscope and the three components of ground velocity from a broad-band seismometer. Both instruments are positioned in a deep underground environment, within the Gran Sasso National Laboratories of the Istituto Nazionale di Fisica Nucleare. We collected dozens of events spanning the 3.5–5.9 magnitude range and epicentral distances between 30 and 70 km. This data set constitutes an unprecedented observation of the vertical rotational motions associated with an intense seismic sequence at local distance. Under the plane-wave approximation we process the data set in order to get an experimental estimation of the events backazimuth. Peak values of rotation rate (PRR) and horizontal acceleration (PGA) are markedly correlated, according to a scaling constant which is consistent with previous measurements from different earthquake sequences. We used a prediction model in use for Italy to calculate the expected PGA at the recording site, obtaining consequently predictions for PRR. Within the modelling uncertainties, predicted rotations are consistent with the observed ones, suggesting the possibility of establishing specific attenuation models for ground rotations, like the scaling of peak velocity and peak acceleration in empirical ground-motion prediction relationships. In a second step, after identifying the direction of the incoming wavefield, we extract phase-velocity data using the spectral ratio of the translational and rotational components. This analysis is performed over time windows associated with the P-coda, S-coda and Lg phase. Results are consistent with independent estimates of shear wave velocities in the shallow crust of the Central Apennines
    Description: Published
    Description: 705-715
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Rotational seismology ; Surface waves and free oscillations ; Wave propagation
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 208(1), pp. 449-467, ISSN: 1365-246X
    Publication Date: 2016-12-03
    Description: The Mozambique Ridge, a prominent basement high in the southwestern Indian Ocean, consists of four major geomorphological segments associated with numerous phases of volcanic activity in the Lower Cretaceous. The nature and origin of the Mozambique Ridge have been intensely debated with one hypothesis suggesting a Large Igneous Province origin. High-resolution seismic reflection data reveal a large number of extrusion centres with a random distribution throughout the southern Mozambique Ridge and the nearby Transkei Rise. Intra-basement reflections emerge from the extrusion centres and are interpreted to represent massive lava flow sequences. Such lava flow sequences are characteristic of eruptions leading to the formation of continental and oceanic flood basalt provinces, hence supporting a Large Igneous Province origin of the Mozambique Ridge. We observe evidence for widespread post-sedimentary magmatic activity that we correlate with a southward propagation of the East African Rift System. Based on our volumetric analysis of the southern Mozambique Ridge we infer a rapid sequential emplacement between ~131 Ma and ~125 Ma, which is similar to the short formation periods of other Large Igneous Provinces like the Agulhas Plateau.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2018-11-09
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
    Publication Date: 2017-05-11
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 6
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    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
    Publication Date: 2017-04-28
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 7
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    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
    Publication Date: 2017-05-11
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 8
    Publication Date: 2017-04-04
    Description: The mineralogy of thermometamorphic granites is relatively simple, making it possible to track the spatial distribution of chemical and mineralogical variations in these rocks and investigate the processes that underpin these metamorphic reactions.We have undertaken a detailed investigation of metagranites from the contact aureole that fringes a quartz diorite intrusion of Late Permian age, emplaced into Carboniferous peraluminous granites of the Gennargentu Igneous Complex (Sardinia, Italy). New data are presented including the petrography of metagranites within a 500 m zone adjacent to the quartz diorite intrusion, the compositions of minerals and bulk-rocks, and the oxygen isotope compositions of separated minerals. We have used these data to assess the mobility of elements, expressed as oxide, in the aureole, and the physical conditions of fluid-assisted thermometamorphism. Modal variations and the oscillatory zoning of plagioclase demonstrate that the shallow (P 200MPa) quartz diorite intrusion was emplaced through a number of magmatic injections.The border zone of the quartz diorite intrusion presents evidence of two main processes: hybridization between andesite and rhyolite magmas and volatile saturation of the mingled magma. Modal differences in the contact zone with respect to the protolith (i.e. peraluminous granite), variations in mineral composition, temperature constraints and K2O, Na2O, SiO2 and Al2O3 indicate that a relatively large volume of the host granite (up to 400 m from the contact) was metasomatized by high-temperature (650^3508C) fluids derived from the mingled zone of the quartz diorite intrusion. In detail, the metasomatic K2O-rich fluid reacted with albite to form K-feldspar, and triggered the recrystallization of quartz and plagioclase to higher calcium concentrations. The progressive increase in the MgO/(MgOþFeO) of chlorite closer to the contact indicates that this phase also recrystallized. The iron released during chlorite recrystallization was buffered by hematite formation in the pores of metasomatic K-feldspar. The Gennargentu metagranites provide evidence that metasomatic fluids can play a major role in driving metamorphic reactions in contact aureoles. For instance, the expected increase of Ca in plagioclase owing to thermal equilibration was not achieved in the high-T zone of the aureole because of fluid-assisted removal of cations.We conclude that caution should be taken when interpreting the processes that underpin contact metamorphism in terms of thermally driven, ionic diffusion alone, because the role of fluids may be significant, if not overwhelming, in the domains closest to the magmatic source.
    Description: Published
    Description: 839-859
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: contact metamorphism ; metasomatism ; red metagranites ; oxygen isotopes ; Gennargentu Igneous Complex ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2017-04-04
    Description: We reply to the comments of De Natale and Pino (2013) on the paper “Are the source models of the M 7.1 1908 Messina Straits earthquake reliable? Insights from a novel inversion and sensitivity analysis of levelling data” by Aloisi et al. (2012). We entirely reject their speculative comments and confirm our viewpoint about the impossibility of discriminating between the two oppositely dipping fault models on the basis of the levelling data alone; we state again that their role as a keystone for modellers is untenable. The comment of De Natale and Pino (2013) are welcomed insofar they give us the possibility to improve our previous analysis, and to criticize the mainstream hypothesis favoring to a low-angle East dipping fault in the Sicilian side of the Messina Straits as responsible of the 1908 destructive earthquake.
    Description: Published
    Description: 1403–1409
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Transient deformation ; Earthquake dynamics ; Earthquake source observations ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2017-04-04
    Description: In order to exploit radon profiles for geophysical purposes and also to estimate its entry indoors, it is necessary to study its transport through porous soils. The great number of involved parameters and processes affecting the emanation of radon from the soil grains and its transport in the source medium has led to many theoretical and/or laboratory studies. The authors report the first results of a laboratory study carried out at the Radioactivity Laboratory of the Department of Physics and Astronomy (University of Catania) by means of a facility for measuring radon concentrations in the sample pores at various depths under well-defined and controlled conditions of physical parameters. In particular, radon concentration vertical profiles extracted in low-moisture samples for different advective fluxes and temperatures were compared with expected concentrations, according to a three-phase transport model developed by Andersen (Risø National Laboratory, Denmark), showing, in general, a good agreement between measurements and model calculations.
    Description: Published
    Description: 575-581
    Description: 4V. Vulcani e ambiente
    Description: JCR Journal
    Description: reserved
    Keywords: Radon ; profile ; geophysic ; porous ; 01. Atmosphere::01.01. Atmosphere::01.01.05. Radiation
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
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    Oxford University Press
    Publication Date: 2017-04-04
    Description: We provide an updated present-day stress map for the Italian territory. Following the World Stress Map (WSM) Project guidelines, we list the different stress indicators, explaining the criteria used to select data. We discuss the data, which will also be included in the 2016 release of the WSM, highlighting the areas for which we have added stress information. Our map displays the minimum horizontal stress orientations inferred from crustal stress indicators down to 40 km depth using data of A–C quality, updated for earthquakes until December 2015. We have completely reviewed all data, and the data set now contains 855 entries, in contrast to the previous 715. The number of data with A–C quality of 630 corresponds to an increase of 26 per cent relative to the previous data set. In particular, the new data set contains the results of the analysis of borehole breakouts, critically reviewed data from earthquake focal mechanisms, data concerning active faults, formal inversions of focal mechanisms of seismic sequences or of restricted areas and one stress determination from overcoring. The new data set defines the stress field in areas not well covered by the previous data: the region north to the Po Plain and the central Adriatic sea, both characterized by a thrust- and strike-faulting regime, the northern Sicilian belt with a prevailing normal-faulting regime, and the Ionian sea with a strike-slip regime.
    Description: Published
    Description: 1525-1531
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Seismicity and tectonics ; Dynamics: seismotectonics ; Crustal structure ; Europe ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
    Publication Date: 2018-09-20
    Description: The relationships between trachytes and peralkaline rhyolites (i.e. pantellerites and comendites), which occur in many continental rift systems, oceanic islands and continental intraplate settings, is unclear. To fill this gap, we have performed phase equilibrium experiments on two representative metaluminous trachytes from Pantelleria to determine both their pre-eruptive equilibration conditions (pressure, temperature, H2O content and redox state) and liquid lines of descent. Experiments were performed in the temperature range 750–950 C, pressure 0 5–1 5 kbar and fluid saturation conditions with XH2O [¼H2O/(H2OþCO2)] ranging between zero and unity. Redox conditions were fixed below the nickel–nickel oxide buffer (NNO). The results show that at 950 C and melt water contents (H2Omelt) close to saturation, trachytes are at liquidus conditions at all pressures. Clinopyroxene is the liquidus phase, being followed by iron-rich olivine and alkali feldspar. Comparison of experimental and natural phases (abundances and compositions) yields the following pre-eruptive conditions: P¼160 5 kbar, T¼925625 C, H2Omelt¼261wt %, and fO2 between NNO– 0 5 and NNO– 2. A decrease in temperature from 950 C to 750 C, as well as of H2Omelt, promotes a massive crystallization of alkali feldspar to over 80 wt %. Iron-bearing minerals show gradual iron enrichment when T and fO2 decrease, trending towards the compositions of the phenocrysts of natural pantellerites. Despite the metaluminous character of the bulk-rock compositions, residual glasses obtained after 80 wt % crystallization evolve toward comenditic compositions, owing to profuse alkali feldspar crystallization, which decreases the Al2O3 of the melt, leading to a consequent increase in the peralkalinity index [PI¼molar (Na2OþK2O)/Al2O3]. This is the first experimental demonstration that peralkaline felsic derivatives can be produced by low-pressure fractional crystallization of metaluminous mafic magmas. Our results show that the pantelleritic magmas of basalt–trachyte–rhyolite igneous suites require at least 95 wt % of parental basalt crystallization, consistent with trace element evidence. Redox conditions, through their effect on Fe–Ti oxide stabilities, control the final iron content of the evolving melt.
    Description: Published
    Description: 559- 588
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Keywords: peralkaline silicic magmatism ; Pantelleria ; Green Tuff ; petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
    Publication Date: 2019-03-13
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2015. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Mud volcanoes are geological systems often characterized by elevated fluid pressures at depth deviating from hydrostatic conditions. This near-critical state makes mud volcanoes particularly sensitive to external forcing induced by natural or man-made perturbations. We used the Nirano mud volcanic field as a natural laboratory to test pre- and post-seismic effects generated by distant earthquakes.We first characterized the subsurface structure of the Nirano mud volcanic field with a geoelectrical study. Next, we deployed a broad-band seismic station in the area to understand the typical seismic signal generated by the mud volcano. Seismic records show a background noise below 2 s, sometimes interrupted by pulses of drumbeatlike high-frequency signals lasting from several minutes to hours. To date this is the first observation of drumbeat signal observed in mud volcanoes. In 2013 June we recorded a M4.7 earthquake, that occurred approximately 60 km far from our seismic station. According to empirical estimations the Nirano mud volcanic field should not have been affected by the M4.7 earthquake. Yet, before the seismic event we recorded an increasing amplitude of the signal in the 10–20 Hz frequency band. The signal emerged approximately two hours before the earthquake and lasted for about three hours. Our statistical analysis suggests the presence of a possible precursory signal about 10 min before the earthquake.
    Description: Published
    Description: 907–917
    Description: 7A. Geofisica per il monitoraggio ambientale
    Description: JCR Journal
    Keywords: Tomography ; Gas and hydrate systems ; Earthquake interaction, forecasting, and prediction ; Seismicity and tectonics ; Volcano seismology ; Mud volcanism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2017-04-04
    Description: Although there are many methods for investigating tectonic structures, many faults remain hidden, and they can endanger the life and property of people living along them. The slopes of volcanoes are covered with such hidden faults, near which strong earthquakes and gas releases can appear. Revealing hidden faults can therefore contribute significantly to the protection of people living in volcanic areas. In the study, seven different techniques were used for making measurements of in-soil radon concentrations in order to search for hidden faults on the SE flank of the Mt. Etna volcano. These reported methods had previously been proved to be useful tools for investigating fault structures. The main aim of the experiment presented here was to evaluate the usability of these methods in the geological conditions of the Mt. Etna region, and to find the best place for continual radon monitoring using a permanent station in the near future.
    Description: Published
    Description: 70-73
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: Mt. Etna ; soil gas ; hidden faults ; radon ; 04. Solid Earth::04.02. Exploration geophysics::04.02.01. Geochemical exploration
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Oxford University Press
    In:  EPIC3The Natural History of Crustacea, Physiology (Vol. 4), New York, Oxford University Press, 35 p., pp. 285-319, ISBN: 9780199832415
    Publication Date: 2015-03-23
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 37(3), pp. 584-595, ISSN: 0142-7873
    Publication Date: 2015-08-22
    Description: Plankton fractions from a saline lake in Argentina were studied using a combined trophic marker approach. A strong seasonality of biomarkers was characteristic for the different fractions, particularly the variations in the 18:4(n 2 3) and 20:4(n 2 3) fatty acids and the d13C values. The primary production in the lake was mainly driven by diatoms, reflected by the close relation of d13C, chlorophyll a and diatom fatty acid markers. The combined approach of d13C and 20:4(n 2 3) enabled processes in the lipid metabolism of the copepod Boeckella poopoensis to be inferred. The polyunsaturated fatty acid 22:6(n 2 3) and the d15N separated the trophic levels in this food web with copepods at higher trophic level. Nutritional stress and omnivory of B. poopoensis partially explained the d15N variations in mesozooplankton. The d15N signature was probably driven by cyanobacteria in the microplankton and by microbial processes in the nanoplankton fraction. Warmer temperatures may favour the saturation of microalgae fatty acids and the abundance of plankton groups richer in saturated fatty acids. The tendency to unsaturation in mesozooplankton at colder temperatures was probably influenced by diet and metabolic requirements. Future temperature increase and eutrophication-like processes may increase the importance of cyanobacterial and bacterial markers under climate change scenarios.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Oxford University Press
    In:  EPIC3ICES Journal of Marine Science, Oxford University Press, 73, pp. 772-782, ISSN: 1054-3139
    Publication Date: 2016-11-30
    Description: Global warming and ocean acidification are among the most important stressors for aquatic ecosystems in the future. To investigate their direct and indirect effects on a near-natural plankton community, a multiple-stressor approach is needed. Hence, we set up mesocosms in a full-factorial design to study the effects of both warming and high CO2 on a Baltic Sea autumn plankton community, concentrating on the impacts on microzooplankton (MZP). MZP abundance, biomass, and species composition were analysed over the course of the experiment. We observed that warming led to a reduced time-lag between the phytoplankton bloom and an MZP biomass maximum. MZP showed a significantly higher growth rate and an earlier biomass peak in the warm treatments while the biomass maximum was not affected. Increased pCO2 did not result in any significant effects on MZP biomass, growth rate, or species composition irrespective of the temperature, nor did we observe any significant interactions between CO2 and temperature. We attribute this to the high tolerance of this estuarine plankton community to fluctuations in pCO2, often resulting in CO2 concentrations higher than the predicted end-of-century concentration for open oceans. In contrast, warming can be expected to directly affect MZP and strengthen its coupling with phytoplankton by enhancing its grazing pressure.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
    Publication Date: 2022-05-25
    Description: Author Posting. © Crown Copyright, 2015. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 204 (2016): 1-20, doi:10.1093/gji/ggv416.
    Description: The Canada Basin and the southern Alpha-Mendeleev ridge complex underlie a significant proportion of the Arctic Ocean, but the geology of this undrilled and mostly ice-covered frontier is poorly known. New information is encoded in seismic wide-angle reflections and refractions recorded with expendable sonobuoys between 2007 and 2011. Velocity–depth samples within the sedimentary succession are extracted from published analyses for 142 of these records obtained at irregularly spaced stations across an area of 1.9E + 06 km2. The samples are modelled at regional, subregional and station-specific scales using an exponential function of inverse velocity versus depth with regionally representative parameters determined through numerical regression. With this approach, smooth, non-oscillatory velocity–depth profiles can be generated for any desired location in the study area, even where the measurement density is low. Practical application is demonstrated with a map of sedimentary thickness, derived from seismic reflection horizons interpreted in the time domain and depth converted using the velocity–depth profiles for each seismic trace. A thickness of 12–13 km is present beneath both the upper Mackenzie fan and the middle slope off of Alaska, but the sedimentary prism thins more gradually outboard of the latter region. Mapping of the observed-to-predicted velocities reveals coherent geospatial trends associated with five subregions: the Mackenzie fan; the continental slopes beyond the Mackenzie fan; the abyssal plain; the southwestern Canada Basin; and, the Alpha-Mendeleev magnetic domain. Comparison of the subregional velocity–depth models with published borehole data, and interpretation of the station-specific best-fitting model parameters, suggests that sandstone is not a predominant lithology in any of the five subregions. However, the bulk sand-to-shale ratio likely increases towards the Mackenzie fan, and the model for this subregion compares favourably with borehole data for Miocene turbidites in the eastern Gulf of Mexico. The station-specific results also indicate that Quaternary sediments coarsen towards the Beaufort-Mackenzie and Banks Island margins in a manner that is consistent with the variable history of Laurentide Ice Sheet advance documented for these margins. Lithological factors do not fully account for the elevated velocity–depth trends that are associated with the southwestern Canada Basin and the Alpha-Mendeleev magnetic domain. Accelerated porosity reduction due to elevated palaeo-heat flow is inferred for these regions, which may be related to the underlying crustal types or possibly volcanic intrusion of the sedimentary succession. Beyond exploring the variation of an important physical property in the Arctic Ocean basin, this study provides comparative reference for global studies of seismic velocity, burial history, sedimentary compaction, seismic inversion and overpressure prediction, particularly in mudrock-dominated successions.
    Keywords: Numerical approximations and analysis ; Spatial analysis ; Controlled source seismology ; Acoustic properties ; Sedimentary basin processes ; Large igneous provinces ; Crustal structure ; Arctic region
    Repository Name: Woods Hole Open Access Server
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  • 19
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    Oxford University Press
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author, 2015. 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 203 (2015): 893-895, doi:10.1093/gji/ggv324.
    Description: The statistics of directional data on a sphere can be modelled either using the Fisher distribution that is conditioned on the magnitude being unity, in which case the sample space is confined to the unit sphere, or using the latitude–longitude marginal distribution derived from a trivariate Gaussian model that places no constraint on the magnitude. These two distributions are derived from first principles and compared. The Fisher distribution more closely approximates the uniform distribution on a sphere for a given small value of the concentration parameter, while the latitude–longitude marginal distribution is always slightly larger than the Fisher distribution at small off-axis angles for large values of the concentration parameter. Asymptotic analysis shows that the two distributions only become equivalent in the limit of large concentration parameter and very small off-axis angle.
    Keywords: Numerical approximations and analysis ; Probability distributions ; Marine magnetics and palaeomagnetics
    Repository Name: Woods Hole Open Access Server
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  • 20
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 7 (2015): 3207-3225, doi:10.1093/gbe/evv210.
    Description: High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes—generically known as restriction site associated DNA sequencing (RAD-seq)—is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for nonmodel species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting “neutral” elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced representation data are available (including transcriptomes and neutral RAD-seq data sets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.
    Description: This research was supported by the Office of Ocean Exploration and Research of the National Oceanic and Atmospheric Administration (NA09OAR4320129 to T.S.); the Division of Ocean Sciences of the National Science Foundation (OCE-1131620 to T.S.); the Astrobiology Science and Technology for Exploring Planets program of the National Aeronautics and Space Administration (NNX09AB76G to T.S.); and the Academic Programs Office (Ocean Ventures Fund to S.H.), the Ocean Exploration Institute (Fellowship support to T.M.S.), and the Ocean Life Institute of the Woods Hole Oceanographic Institution (internal grant to T.M.S. and S.H.).
    Keywords: RAD-seq ; Reduced representation sequencing ; PredRAD ; Experimental design ; Genome size prediction ; Restriction recognition sequence probability
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/vnd.ms-excel
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  • 21
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.
    Description: The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.
    Description: This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14).
    Keywords: RNA editing ; ADAR ; Evolution ; Coral
    Repository Name: Woods Hole Open Access Server
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  • 22
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 6 (2018): coy049, doi:10.1093/conphys/coy049.
    Description: Male baleen whales have long been suspected to have annual cycles in testosterone, but due to difficulty in collecting endocrine samples, little direct evidence exists to confirm this hypothesis. Potential influences of stress or adrenal stress hormones (cortisol, corticosterone) on male reproduction have also been difficult to study. Baleen has recently been shown to accumulate steroid hormones during growth, such that a single baleen plate contains a continuous, multi-year retrospective record of the whale’s endocrine history. As a preliminary investigation into potential testosterone cyclicity in male whales and influences of stress, we determined patterns in immunoreactive testosterone, two glucocorticoids (cortisol and corticosterone), and stable-isotope (SI) ratios, across the full length of baleen plates from a bowhead whale (Balaena mysticetus), a North Atlantic right whale (Eubalaena glacialis) and a blue whale (Balaenoptera musculus), all adult males. Baleen was subsampled at 2 cm (bowhead, right) or 1 cm (blue) intervals and hormones were extracted from baleen powder with methanol, followed by quantification of all three hormones using enzyme immunoassays validated for baleen extract of these species. Baleen of all three males contained regularly spaced peaks in testosterone content, with number and spacing of testosterone peaks corresponding well to SI data and to species-specific estimates of annual baleen growth rate. Cortisol and corticosterone exhibited some peaks that co-occurred with testosterone peaks, while other glucocorticoid peaks occurred independent of testosterone peaks. The right whale had unusually high glucocorticoids during a period with a known entanglement in fishing gear and a possible disease episode; in the subsequent year, testosterone was unusually low. Further study of baleen testosterone patterns in male whales could help clarify conservation- and management-related questions such as age of sexual maturity, location and season of breeding, and the potential effect of anthropogenic and natural stressors on male testosterone cycles.
    Description: This work was supported by (1) the Arizona Board of Regents Technology Research Initiative Fund; (2) the Center for Bioengineering Innovation at Northern Arizona University; (3) the Greenland Institute of Natural Resources; (4) the Woods Hole Oceanographic Institution Ocean Life Institute and (5) Fisheries and Ocean Canada’s (DFO) Priorities and Partnership Strategic Initiatives Fund and Oceans Protection Plan.
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  • 23
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2015. 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 203 (2015): 1-21, doi:10.1093/gji/ggv251.
    Description: We examine along-axis variations in melt content of the axial magma lens (AML) beneath the fast-spreading East Pacific Rise (EPR) using an amplitude variation with angle of incidence (AVA) crossplotting method applied to multichannel seismic data acquired in 2008. The AVA crossplotting method, which has been developed for and, so far, applied for hydrocarbon prospection in sediments, is for the first time applied to a hardrock environment. We focus our analysis on 2-D data collected along the EPR axis from 9°29.8′N to 9°58.4′N, a region which encompasses the sites of two well-documented submarine volcanic eruptions (1991–1992 and 2005–2006). AVA crossplotting is performed for a ∼53 km length of the EPR spanning nine individual AML segments (ranging in length from ∼3.2 to 8.5 km) previously identified from the geometry of the AML and disruptions in continuity. Our detailed analyses conducted at 62.5 m interval show that within most of the analysed segments melt content varies at spatial scales much smaller (a few hundred of metres) than the length of the fine-scale AML segments, suggesting high heterogeneity in melt concentration. At the time of our survey, about 2 yr after the eruption, our results indicate that the three AML segments that directly underlie the 2005–2006 lava flow are on average mostly molten. However, detailed analysis at finer-scale intervals for these three segments reveals AML pockets (from 〉62.5 to 812.5 m long) with a low melt fraction. The longest such mushy section is centred beneath the main eruption site at ∼9°50.4′N, possibly reflecting a region of primary melt drainage during the 2005–2006 event. The complex geometry of fluid flow pathways within the crust above the AML and the different response times of fluid flow and venting to eruption and magma reservoir replenishment may contribute to the poor spatial correlation between incidence of hydrothermal vents and presence of highly molten AML. The presented results are an important step forward in our ability to resolve small-scale characteristics of the AML and recommend the AVA crossplotting as a tool for examining mid-ocean ridge magma-systems elsewhere.
    Description: This research was supported by NSF awards OCE0327872 to J.C.M. and S.M.C., OCE-0327885 to J.P.C., and OCE0624401 to M.R.N.
    Keywords: Mid-ocean ridge processes ; Submarine tectonics and volcanism ; Crustal structure ; Physics of magma and magma bodies
    Repository Name: Woods Hole Open Access Server
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  • 24
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 44 (2016): e157, doi:10.1093/nar/gkw738.
    Description: Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a UAG premature termination codon (PTC) to tryptophan (UGG) was improved from ∼11% to ∼70%. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.
    Description: National Institutes of Health [1R0111223855, 1R01NS64259]; Cystic Fibrosis Foundation Therapeutics [Rosent14XXO]; Infrastructural support was provided by the National Institutes of Health [NIGMS 1P20GM103642, NIMHD 8G12-MD007600]; National Science Foundation [DBI 0115825, DBI 1337284]; Department of Defense [52680-RT-ISP].
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  • 25
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2016. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 208 (2017): 1026-1042, doi:10.1093/gji/ggw435.
    Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the subseafloor conductivity that is assumed to be isotropic. The deep water (ocean layer electrically much thicker than the overburden) seafloor EM response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a half-space, or a stronger and faster response. For an ocean whose electrical thickness is comparable to or much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. These transitions can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire subseafloor resistivity structure with the sea surface. A stronger and faster response occurs when guided energy flow is dominant, while a weaker and slower response occurs when the air interaction is dominant. However, at intermediate offsets for some models, the air interaction can partially or fully reverse the direction of energy flux in the reservoir layer toward rather than away from the source, resulting in a stronger and slower response. The Fréchet derivatives are dominated by preferential sensitivity to the reservoir layer conductivity for all water depths except at high frequencies, but also display a shift with offset from the galvanic to the inductive mode in the underburden and overburden due to the interplay of guided energy flow and the air interaction. This means that the sensitivity to the horizontal conductivity is almost as strong as to the vertical component in the shallow parts of the subsurface, and in fact is stronger than the vertical sensitivity deeper down. However, the sensitivity to horizontal conductivity is still weak compared to the vertical component within thin resistive regions. The horizontal sensitivity is gradually decreased when the water becomes deep. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.
    Keywords: Electrical properties ; Marine electromagnetics
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  • 26
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioscience 67 (2017): 760–768, doi:10.1093/biosci/bix059.
    Description: As the sampling frequency and resolution of Earth observation imagery increase, there are growing opportunities for novel applications in population monitoring. New methods are required to apply established analytical approaches to data collected from new observation platforms (e.g., satellites and unmanned aerial vehicles). Here, we present a method that estimates regional seasonal abundances for an understudied and growing population of gray seals (Halichoerus grypus) in southeastern Massachusetts, using opportunistic observations in Google Earth imagery. Abundance estimates are derived from digital aerial survey counts by adapting established correction-based analyses with telemetry behavioral observation to quantify survey biases. The result is a first regional understanding of gray seal abundance in the northeast US through opportunistic Earth observation imagery and repurposed animal telemetry data. As species observation data from Earth observation imagery become more ubiquitous, such methods provide a robust, adaptable, and cost-effective solution to monitoring animal colonies and understanding species abundances.
    Description: We would like to thank generous support from International Fund for Animal Welfare, the Bureau of Ocean Energy, and the Oak Foundation for funding support for the telemetry devices.
    Keywords: Abundance estimation ; Gray seals (Halichoerus grypus) ; Cape Cod ; Remote sensing ; Earth observation
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  • 27
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Epigenetics 4 (2018): dvy005, doi:10.1093/eep/dvy005.
    Description: There is growing evidence that environmental toxicants can affect various physiological processes by altering DNA methylation patterns. However, very little is known about the impact of toxicant-induced DNA methylation changes on gene expression patterns. The objective of this study was to determine the genome-wide changes in DNA methylation concomitant with altered gene expression patterns in response to 3, 3’, 4, 4’, 5-pentachlorobiphenyl (PCB126) exposure. We used PCB126 as a model environmental chemical because the mechanism of action is well-characterized, involving activation of aryl hydrocarbon receptor, a ligand-activated transcription factor. Adult zebrafish were exposed to 10 nM PCB126 for 24 h (water-borne exposure) and brain and liver tissues were sampled at 7 days post-exposure in order to capture both primary and secondary changes in DNA methylation and gene expression. We used enhanced Reduced Representation Bisulfite Sequencing and RNAseq to quantify DNA methylation and gene expression, respectively. Enhanced reduced representation bisulfite sequencing analysis revealed 573 and 481 differentially methylated regions in the liver and brain, respectively. Most of the differentially methylated regions are located more than 10 kilobases upstream of transcriptional start sites of the nearest neighboring genes. Gene Ontology analysis of these genes showed that they belong to diverse physiological pathways including development, metabolic processes and regeneration. RNAseq results revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and energy metabolism in response to polychlorinated biphenyl exposure. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting that the relationship between methylation and gene expression is dynamic and complex, involving multiple layers of regulation.
    Description: This work was supported by the National Institute of Health Outstanding New Environmental Scientist Award to NA (NIH R01ES024915) and Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) grant P01ES021923 and National Science Foundation Grant OCE-1314642 to M. Hahn, J. Stegeman, NA and SK].
    Repository Name: Woods Hole Open Access Server
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  • 28
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 1072–1087, doi:10.1093/gji/ggy203.
    Description: An earthquake rupture process can be kinematically described by rupture velocity, duration and spatial extent. These key kinematic source parameters provide important constraints on earthquake physics and rupture dynamics. In particular, core questions in earthquake science can be addressed once these properties of small earthquakes are well resolved. However, these parameters of small earthquakes are poorly understood, often limited by available data sets and methodologies. The Incorporated Research Institutions for Seismology Community Wavefield Experiment in Oklahoma deployed ∼350 three-component nodal stations within 40 km2 for a month, offering an unprecedented opportunity to test new methodologies for resolving small earthquake finite source properties in high resolution. In this study, we demonstrate the power of the nodal data set to resolve the variations in the seismic wavefield over the focal sphere due to the finite source attributes of an M2 earthquake within the array. The dense coverage allows us to tightly constrain rupture area using the second moment method even for such a small earthquake. The M2 earthquake was a strike-slip event and unilaterally propagated towards the surface at 90 per cent local S-wave speed (2.93 km s−1). The earthquake lasted ∼0.019 s and ruptured Lc ∼70 m and Wc ∼45 m. With the resolved rupture area, the stress-drop of the earthquake is estimated as 7.3 MPa for Mw 2.3. We demonstrate that the maximum and minimum bounds on rupture area are within a factor of two, much lower than typical stress-drop uncertainty, despite a suboptimal station distribution. The rupture properties suggest that there is little difference between the M2 Oklahoma earthquake and typical large earthquakes. The new three-component nodal systems have great potential for improving the resolution of studies of earthquake source properties.
    Description: WF is currently supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship. JM was partially supported by SCEC grant #17177 at Woods Hole Oceanographic Institution. This research was supported by the Southern California Earthquake Center (Contribution No. 8014). SCEC is funded by NSF Cooperative Agreement EAR-1033462 and USGS Cooperative Agreement G12AC20038.
    Keywords: Inverse theory ; Waveform inversion ; Body waves ; Earthquake dynamics ; Earthquake source observations ; Seismic instruments
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  • 29
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 942–958, doi:10.1093/gji/ggy316.
    Description: Surface waves recorded by global arrays have proven useful for locating tectonic earthquakes and in detecting slip events depleted in high frequency, such as glacial quakes. We develop a novel method using an aggregation of small- to continental-scale arrays to detect and locate seismic sources with Rayleigh waves at 20–50 s period. The proposed method is a hybrid approach including first dividing a large aperture aggregate array into Delaunay triangular subarrays for beamforming, and then using the resolved surface wave propagation directions and arrival times from the subarrays as data to formulate an inverse problem to locate the seismic sources and their origin times. The approach harnesses surface wave coherence and maximizes resolution of detections by combining measurements from stations spanning the whole U.S. continent. We tested the method with earthquakes, glacial quakes and landslides. The results show that the method can effectively resolve earthquakes as small as ∼M3 and exotic slip events in Greenland. We find that the resolution of the locations is non-uniform with respect to azimuth, and decays with increasing distance between the source and the array when no calibration events are available. The approach has a few advantages: the method is insensitive to seismic event type, it does not require a velocity model to locate seismic sources, and it is computationally efficient. The method can be adapted to real-time applications and can help in identifying new classes of seismic sources.
    Description: WF is currently supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship. This work was supported by National Science Foundation grant EAR-1358520 at Scripps Institution of Oceanography, UC San Diego.
    Repository Name: Woods Hole Open Access Server
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  • 30
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2017. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 211 (2017): 1046–1061, doi:10.1093/gji/ggx360.
    Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically-polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the sub-seafloor conductivity that is assumed to be transversely anisotropic, with a vertical-to-horizontal resistivity ratio of 3:1. For an ocean whose electrical thickness is comparable to that of the overburden, the seafloor electromagnetic response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a halfspace, or a stronger and faster response, and displays little to no evidence for the air interaction. For an ocean whose electrical thickness is much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets, and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. By comparison to the isotropic case with the same horizontal conductivity, transverse anisotropy stretches the Poynting vector and the electric field response from a thin resistive layer to much longer offsets. These phenomena can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire sub-seafloor resistivity structure with the sea surface. The Fréchet derivatives are dominated by preferential sensitivity to the vertical conductivity in the reservoir layer and overburden at short offsets. The horizontal conductivity Fréchet derivatives are weaker than to comparable to the vertical derivatives at long offsets in the substrate. This means that the sensitivity to the horizontal conductivity is present in the shallow parts of the subsurface. In the presence of transverse anisotropy, it is necessary to go to higher frequencies to sense the horizontal conductivity in the overburden as compared to an isotropic model with the same horizontal conductivity. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.
    Description: This work was supported at WHOI by an Independent Research and Development award, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.
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  • 31
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 214 (2018): 2224–2235, doi:10.1093/gji/ggy201.
    Description: The key kinematic earthquake source parameters: rupture velocity, duration and area, shed light on earthquake dynamics, provide direct constraints on stress drop, and have implications for seismic hazard. However, for moderate and small earthquakes, these parameters are usually poorly constrained due to limitations of the standard analysis methods. Numerical experiments by Kaneko and Shearer demonstrated that standard spectral fitting techniques can lead to roughly one order of magnitude variation in stress-drop estimates that do not reflect the actual rupture properties even for simple crack models. We utilize these models to explore an alternative approach where we estimate the rupture area directly. For the suite of models, the area averaged static stress drop is nearly constant for models with the same underlying friction law, yet corner-frequency-based stress-drop estimates vary by a factor of 5–10 even for noise-free data. Alternatively, we simulated inversions for the rupture area as parametrized by the second moments of the slip distribution. A natural estimate for the rupture area derived from the second moments is A = πLcWc, where Lc and Wc are the characteristic rupture length and width. This definition yields estimates of stress drop that vary by only 10 per cent between the models but are slightly larger than the true area averaged values. We simulate inversions for the second moments for the various models and find that the area can be estimated well when there are at least 15 available measurements of apparent duration at a variety of take-off angles. The improvement compared to azimuthally averaged corner-frequency-based approaches results from the second moments accounting for directivity and removing the assumption of a circular rupture area, both of which bias the standard approach. We also develop a new method that determines the minimum and maximum values of rupture area that are consistent with a particular data set at the 95 per cent confidence level. For the Kaneko and Shearer models with 20+ randomly distributed observations and ∼10 per cent noise levels, we find that the maximum and minimum bounds on rupture area typically vary by a factor of two and that the minimum stress drop is often more tightly constrained than the maximum.
    Description: This work was supported by USGS NEHRP Award G17AP00029. The research was supported by the Southern California Earthquake Center (SCEC; Contribution No. 8013). SCEC is funded by NSF Cooperative Agreement EAR-1033462 and USGS Cooperative Agreement G12AC20038. YK was supported by both public funding from the Government of New Zealand and the Royal Society of New Zealand’s Rutherford Discovery Fellowship.
    Keywords: Earthquake dynamics ; Earthquake source observations ; Body waves
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  • 32
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    Oxford University Press
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 713–735, doi:10.1093/gji/ggy313.
    Description: Gas flux in volcanic conduits is often associated with long-period oscillations known as seismic tremor (Lesage et al.; Nadeau et al.). In this study, we revisit and extend the ‘magma wagging’and ‘whirling’models for seismic tremor, in order to explore the effects of gas flux on the motion of a magma column surrounded by a permeable vesicular annulus (Jellinek & Bercovici; Bercovici et al.; Liao et al.). We find that gas flux flowing through the annulus leads to a Bernoulli effect, which causes waves on the magma column to become unstable and grow. Specifically, the Bernoulli effects are associated with torques and forces acting on the magma column, increasing its angular momentum and energy. As the displacement of the magma column becomes large due to the Bernoulli effect, frictional drag on the conduit wall decelerates the motions of the column, restoring them to small amplitude. Together, the Bernoulli effect and the damping effect contribute to a self-sustained wagging-and-whirling mechanism that help explain the longevity of long-period seismic tremor.
    Description: This work was supported by National Science Foundation grants EAR-1344538 and EAR-1645057
    Keywords: Physics of magma and magma bodies ; Volcano seismology ; Volcanic gases
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  • 33
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 460–473, doi:10.1093/gji/ggy152.
    Description: In this work, we present a new methodology to predict grain-size distributions from geophysical data. Specifically, electric conductivity and magnetic susceptibility of seafloor sediments recovered from electromagnetic profiling data are used to predict grain-size distributions along shelf-wide survey lines. Field data from the NW Iberian shelf are investigated and reveal a strong relation between the electromagnetic properties and grain-size distribution. The here presented workflow combines unsupervised and supervised machine-learning techniques. Non-negative matrix factorization is used to determine grain-size end-members from sediment surface samples. Four end-members were found, which well represent the variety of sediments in the study area. A radial basis function network modified for prediction of compositional data is then used to estimate the abundances of these end-members from the electromagnetic properties. The end-members together with their predicted abundances are finally back transformed to grain-size distributions. A minimum spatial variation constraint is implemented in the training of the network to avoid overfitting and to respect the spatial distribution of sediment patterns. The predicted models are tested via leave-one-out cross-validation revealing high prediction accuracy with coefficients of determination (R2) between 0.76 and 0.89. The predicted grain-size distributions represent the well-known sediment facies and patterns on the NW Iberian shelf and provide new insights into their distribution, transition and dynamics. This study suggests that electromagnetic benthic profiling in combination with machine learning techniques is a powerful tool to estimate grain-size distribution of marine sediments.
    Description: This work was funded through DFG Research Center/Cluster of Excellence ‘The Ocean in the Earth System’ and was part of MARUM Research Area SD
    Keywords: Neural networks ; Fuzzy logic ; Statistical methods ; Electrical properties ; Magnetic properties ; Marine electromagnetics ; Controlled source electromagnetics (CSEM)
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  • 34
    Publication Date: 2021-11-09
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2019. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: The Amatrice–Norcia–Visso sequence is characterized by complex behaviour that is somewhat atypical of main-shock–aftershock sequences, as there were multiple large main shocks that continued for months. In this study we focus on the Amatrice sequence (main shock 2016 August 24, Mw = 5.97) to evaluate the apparent stress values and magnitude-dependent scaling in order to improve our knowledge of processes that control small and large earthquakes within this active region of Italy. Apparent stress is proportional to the ratio of radiated seismic energy and seismic moment, and as such, these stress parameters play an important role in hazard prediction as they have a strong effect on the observed and predicted ground shaking. We analyse 83 events of the sequence from 2016 August 24 to October 16, within a radius of 20 km from the main shock and with an Mw ranging between 5.97 and 2.72. Taking advantage of the averaging nature of coda waves, we analyse coda-envelope-based spectral ratios between neighbouring event pairs.We use equations proposed byWalter et al. to consider stable, low-frequency and high-frequency spectral ratio levelswhich provide measures of the corner frequency and apparent stress ratios of the events within the sequence. The results demonstrate non-self-similar behaviour within the sequence, suggesting a change in dynamics between the largest events and the smaller aftershocks. The apparent stress and corner frequency estimates are compared to those obtained by Malagnini and Munaf`o who utilized hundreds of direct S-wave spectral ratio measurements to obtain their results. Although our analysis is based only on 83 events, our results are in very good agreement, demonstrating once more that the use of coda waves is very stable and provides lower variance measures than those using direct waves. A comparison with recent Central Apennines source scaling models derived from various seismic sequences (1997–1998 Colfiorito, 2002 San Giuliano di Puglia, 2009 L’Aquila) shows that the Amatrice sequence source scaling in this study is well represented by the models proposed by Pacor et al. and Malagnini and Mayeda.
    Description: Published
    Description: 446-455
    Description: 3T. Sorgente sismica
    Description: JCR Journal
    Keywords: Coda waves; Earthquake dynamics; Earthquake source observations; Amatrice ; earthquake stress parameters
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 35
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioinformatics 31 (2015): 1872-1874, doi:10.1093/bioinformatics/btv045.
    Description: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users.
    Description: The Encyclopedia Of Life Rubenstein Fellows Program [CRDF EOL-33066-13/E33066], the LifeWatchGreece Research Infrastructure [384676-94/GSRT/ NSRF(C&E)] and the Novo Nordisk Foundation Center for Protein Research [NNF14CC0001].
    Repository Name: Woods Hole Open Access Server
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  • 36
    Publication Date: 2022-06-20
    Description: A major uncertainty in determining the mass balance of the Antarctic ice sheet from measurements of satellite gravimetry, and to a lesser extent satellite altimetry, is the poorly known correction for the ongoing deformation of the solid Earth caused by glacial isostatic adjustment (GIA). Although much progress has been made in consistently modeling the ice-sheet evolution throughout the last glacial cycle, as well as the induced bedrock deformation caused by these load changes, forward models of GIA remain ambiguous due to the lack of observational constraints on the ice sheet's past extent and thickness and mantle rheology beneath the continent. As an alternative to forward-modeling GIA, we estimate GIA from multiple space-geodetic observations: Gravity Recovery and Climate Experiment (GRACE), Envisat/ICESat and Global Positioning System (GPS). Making use of the different sensitivities of the respective satellite observations to current and past surface-mass (ice mass) change and solid Earth processes, we estimate GIA based on viscoelastic response functions to disc load forcing. We calculate and distribute the viscoelastic response functions according to estimates of the variability of lithosphere thickness and mantle viscosity in Antarctica. We compare our GIA estimate with published GIA corrections and evaluate its impact in determining the ice-mass balance in Antarctica from GRACE and satellite altimetry. Particular focus is applied to the Amundsen Sea Sector in West Antarctica, where uplift rates of several centimetres per year have been measured by GPS. We show that most of this uplift is caused by the rapid viscoelastic response to recent ice-load changes, enabled by the presence of a low-viscosity upper mantle in West Antarctica. This paper presents the second and final contributions summarizing the work carried out within a European Space Agency funded study, REGINA (www.regina-science.eu).
    Repository Name: EPIC Alfred Wegener Institut
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  • 37
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 1822-1837, doi: 10.1093/gji/ggz253.
    Description: Joint inversion of multiple electromagnetic data sets, such as controlled source electromagnetic and magnetotelluric data, has the potential to significantly reduce uncertainty in the inverted electrical resistivity when the two data sets contain complementary information about the subsurface. However, evaluating quantitatively the model uncertainty reduction is made difficult by the fact that conventional inversion methods—using gradients and model regularization—typically produce just one model, with no associated estimate of model parameter uncertainty. Bayesian inverse methods can provide quantitative estimates of inverted model parameter uncertainty by generating an ensemble of models, sampled proportional to data fit. The resulting posterior distribution represents a combination of a priori assumptions about the model parameters and information contained in field data. Bayesian inversion is therefore able to quantify the impact of jointly inverting multiple data sets by using the statistical information contained in the posterior distribution. We illustrate, for synthetic data generated from a simple 1-D model, the shape of parameter space compatible with controlled source electromagnetic and magnetotelluric data, separately and jointly. We also demonstrate that when data sets contain complementary information about the model, the region of parameter space compatible with the joint data set is less than or equal to the intersection of the regions compatible with the individual data sets. We adapt a trans-dimensional Markov chain Monte Carlo algorithm for jointly inverting multiple electromagnetic data sets for 1-D earth models and apply it to surface-towed controlled source electromagnetic and magnetotelluric data collected offshore New Jersey, USA, to evaluate the extent of a low salinity aquifer within the continental shelf. Our inversion results identify a region of high resistivity of varying depth and thickness in the upper 500 m of the continental shelf, corroborating results from a previous study that used regularized, gradient-based inversion methods. We evaluate the joint model parameter uncertainty in comparison to the uncertainty obtained from the individual data sets and demonstrate quantitatively that joint inversion offers reduced uncertainty. In addition, we show how the Bayesian model ensemble can subsequently be used to derive uncertainty estimates of pore water salinity within the low salinity aquifer.
    Description: We gratefully acknowledge funding support from National Science Foundation grants 1458392 and 1459035. We thank the captain and crew of the R.V. Marcus G. Langseth for a successful cruise and the Marine EM Lab at Scripps Institution of Oceanography for providing the instrumentation. We also thank Chris Armerding, Marah Dahn, John Desanto, Jimmy Elsenbeck, Matt Folsom, Keiichi Ishizu, Jeff Pepin, Charlotte Wiman and Georgie Zelenak for participating in the cruise. We gratefully acknowledge Alberto Malinverno for the idea to use a Monte Carlo scheme to estimate the distribution of pore fluid salinity, and William Menke for many constructive conversations and suggestions.
    Keywords: Controlled source electromagnetics (CSEM) ; Joint inversion ; Magnetotellurics ; Statistical methods ; Marine electromagnetics ; Probability distributions
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  • 38
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 2122-2135, doi: 10.1093/gji/ggz272.
    Description: We have conducted the first passive Ocean Bottom Seismograph (OBS) experiment near the Challenger Deep at the southernmost Mariana subduction zone by deploying and recovering an array of 6 broad-band OBSs during December 2016–June 2017. The obtained passive-source seismic records provide the first-ever near-field seismic observations in the southernmost Mariana subduction zone. We first correct clock errors of the OBS recordings based on both teleseismic waveforms and ambient noise cross-correlation. We then perform matched filter earthquake detection using 53 template events in the catalogue of the US Geological Survey and find 〉7000 local earthquakes during the 6-month OBS deployment period. Results of the two independent approaches show that the maximum clock drifting was ∼2 s on one instrument (OBS PA01), while the rest of OBS waveforms had negligible time drifting. After timing correction, we locate the detected earthquakes using a newly refined local velocity model that was derived from a companion active source experiment in the same region. In total, 2004 earthquakes are located with relatively high resolution. Furthermore, we calibrate the magnitudes of the detected earthquakes by measuring the relative amplitudes to their nearest relocated templates on all OBSs and acquire a high-resolution local earthquake catalogue. The magnitudes of earthquakes in our new catalogue range from 1.1 to 5.6. The earthquakes span over the Southwest Mariana rift, the megathrust interface, forearc and outer-rise regions. While most earthquakes are shallow, depths of the slab earthquakes increase from ∼100 to ∼240 km from west to east towards Guam. We also delineate the subducting interface from seismicity distribution and find an increasing trend in dip angles from west to east. The observed along-strike variation in slab dip angles and its downdip extents provide new constraints on geodynamic processes of the southernmost Mariana subduction zone.
    Description: We express our appreciation to the science parties and crew members of the R/V Shiyan 3 for deployment and collection of the OBS instruments during the Mariana expeditions. This study is supported by the Hong Kong Research Grant Council Grants (No. 14313816), Faculty of Science at CUHK, Chinese Academy of Sciences (No. Y4SL021001, QYZDY-SSW-DQC005, 133244KYSB20180029), the National Natural Science Foundation of China (No. 41890813, 91628301, 41676042, U1701641, 41576041, 91858207 and U1606401), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100). Generic Mapping Tools (Wessel & Smith 1991) and PSSAC (developed by Prof Lupei Zhu) are used for data analysis and figure preparation in this study. Constructive comments from Dr Lidong Bie and two anonymous reviewers are helpful in improving the manuscript.
    Keywords: Seismicity and tectonics ; Dynamics: seismotectonics ; Subduction zone processes
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  • 39
    Publication Date: 2022-05-26
    Description: Author Posting. © Oxford University Press, 2016. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 205 (2016): 728-743, doi:10.1093/gji/ggw044.
    Description: While elasticity is a defining characteristic of the Earth's lithosphere, it is often ignored in numerical models of long-term tectonic processes in favour of a simpler viscoplastic description. Here we assess the consequences of this assumption on a well-studied geodynamic problem: the growth of normal faults at an extensional plate boundary. We conduct 2-D numerical simulations of extension in elastoplastic and viscoplastic layers using a finite difference, particle-in-cell numerical approach. Our models simulate a range of faulted layer thicknesses and extension rates, allowing us to quantify the role of elasticity on three key observables: fault-induced topography, fault rotation, and fault life span. In agreement with earlier studies, simulations carried out in elastoplastic layers produce rate-independent lithospheric flexure accompanied by rapid fault rotation and an inverse relationship between fault life span and faulted layer thickness. By contrast, models carried out with a viscoplastic lithosphere produce results that may qualitatively resemble the elastoplastic case, but depend strongly on the product of extension rate and layer viscosity U × ηL. When this product is high, fault growth initially generates little deformation of the footwall and hanging wall blocks, resulting in unrealistic, rigid block-offset in topography across the fault. This configuration progressively transitions into a regime where topographic decay associated with flexure is fully accommodated within the numerical domain. In addition, high U × ηL favours the sequential growth of multiple short-offset faults as opposed to a large-offset detachment. We interpret these results by comparing them to an analytical model for the fault-induced flexure of a thin viscous plate. The key to understanding the viscoplastic model results lies in the rate-dependence of the flexural wavelength of a viscous plate, and the strain rate dependence of the force increase associated with footwall and hanging wall bending. This behaviour produces unrealistic deformation patterns that can hinder the geological relevance of long-term rifting models that assume a viscoplastic rheology.
    Description: This work was supported by NSF grants OCE-11-54238 (JAO, MDB), EAR-10-10432 (MDB) and OCE-11-55098 (GI), as well as a WHOI Deep Exploration Institute grant and start-up support from the University of Idaho (EM).
    Keywords: Mid-ocean ridge processes ; Continental tectonics: extensional ; Lithospheric flexure ; Mechanics, theory, and modelling
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  • 40
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 4 (2016): cow014, doi:10.1093/conphys/cow014.
    Description: Reproduction of mysticete whales is difficult to monitor, and basic parameters, such as pregnancy rate and inter-calving interval, remain unknown for many populations. We hypothesized that baleen plates (keratinous strips that grow downward from the palate of mysticete whales) might record previous pregnancies, in the form of high-progesterone regions in the sections of baleen that grew while the whale was pregnant. To test this hypothesis, longitudinal baleen progesterone profiles from two adult female North Atlantic right whales (Eubalaena glacialis) that died as a result of ship strike were compared with dates of known pregnancies inferred from calf sightings and post-mortem data. We sampled a full-length baleen plate from each female at 4 cm intervals from base (newest baleen) to tip (oldest baleen), each interval representing ∼60 days of baleen growth, with high-progesterone areas then sampled at 2 or 1 cm intervals. Pulverized baleen powder was assayed for progesterone using enzyme immunoassay. The date of growth of each sampling location on the baleen plate was estimated based on the distance from the base of the plate and baleen growth rates derived from annual cycles of stable isotope ratios. Baleen progesterone profiles from both whales showed dramatic elevations (two orders of magnitude higher than baseline) in areas corresponding to known pregnancies. Baleen hormone analysis shows great potential for estimation of recent reproductive history, inter-calving interval and general reproductive biology in this species and, possibly, in other mysticete whales.
    Description: This work was supported by the Eppley Foundation for Research, the National Oceanographic and Atmospheric Administration Marine Mammal Health and Stranding Program and the Woods Hole Oceanographic Institution Ocean Life Institute.
    Keywords: Baleen ; Cetacea ; Marine mammals ; Pregnancy ; Progesterone ; Reproduction
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  • 41
    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 7 (2015): 457-464, doi:10.1093/gbe/evu289.
    Description: The uptake and transport of vitamin B12 (cobalamin; Cbl) in mammals involves a refined system with three evolutionarily related transporters: transcobalamin 1 (Tcn1), transcobalamin 2 (Tcn2), and the gastric intrinsic factor (Gif). Teleosts have a single documented binder with intermediate features to the human counterparts. Consequently, it has been proposed that the expansion of Cbl binders occurred after the separation of Actinopterygians. Here, we demonstrate that the diversification of this gene family took place earlier in gnathostome ancestry. Our data indicates the presence of single copy orthologs of the Sarcopterygii/Tetrapoda duplicates Tcn1 and Gif, and Tcn2, in Chondrichthyes. In addition, a highly divergent Cbl binder was found in the Elasmobranchii. We unveil a complex scenario forged by genome, tandem duplications and lineage-specific gene loss. Our findings suggest that from an ancestral transporter, exhibiting large spectrum and high affinity binding, highly specific Cbl transporters emerged through gene duplication and mutations at the binding pocket.
    Description: This work was funded by the Fundação para a Ciência e a Tecnologia (FCT) project PEst-C/MAR/LA0015/2013. PhD grant SFRH/BD/84238/2012 awarded to M.L-.M. Postdoctoral grant SFRH/BPD/72519/2010 awarded to R.R.
    Keywords: Cobalamin transport ; Genome duplications ; Gnathostomes
    Repository Name: Woods Hole Open Access Server
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  • 42
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2016. 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 205 (2016): 785-795, doi:10.1093/gji/ggw036.
    Description: An L-configured, three-component short period seismic array was deployed on the Ross Ice Shelf, Antarctica during November 2014. Polarization analysis of ambient noise data from these stations shows linearly polarized waves for frequency bands between 0.2 and 2 Hz. A spectral peak at about 1.6 Hz is interpreted as the resonance frequency of the water column and is used to estimate the water layer thickness below the ice shelf. The frequency band from 4 to 18 Hz is dominated by Rayleigh and Love waves propagating from the north that, based on daily temporal variations, we conclude were generated by field camp activity. Frequency–slowness plots were calculated using beamforming. Resulting Love and Rayleigh wave dispersion curves were inverted for the shear wave velocity profile within the firn and ice to ∼150 m depth. The derived density profile allows estimation of the pore close-off depth and the firn–air content thickness. Separate inversions of Rayleigh and Love wave dispersion curves give different shear wave velocity profiles within the firn. We attribute this difference to an effective anisotropy due to fine layering. The layered structure of firn, ice, water and the seafloor results in a characteristic dispersion curve below 7 Hz. Forward modelling the observed Rayleigh wave dispersion curves using representative firn, ice, water and sediment structures indicates that Rayleigh waves are observed when wavelengths are long enough to span the distance from the ice shelf surface to the seafloor. The forward modelling shows that analysis of seismic data from an ice shelf provides the possibility of resolving ice shelf thickness, water column thickness and the physical properties of the ice shelf and underlying seafloor using passive-source seismic data.
    Description: PDB, AD and PG were supported by NSF Grant PLR 1246151. RAS was supported by NSF Grant PLR-1246416. DAW, RA and AN were supported under NSF Grants PLR-1142518, 1141916 and 1142126, respectively. PDB also received support from the California Department of Parks and Recreation, Division of Boating and Waterways under contract 11-106-107.
    Keywords: Glaciology ; Surface waves and free oscillations ; Seismic anisotropy ; Antarctica
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  • 43
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in ICES Journal of Marine Science 76(4), (2010): 781-786, doi:10.1093/icesjms/fsy194.
    Description: Whales are federally protected by the Marine Mammal Protection Act; endangered species, such as the North Atlantic right whale, receive additional protection under the Endangered Species Act. However, their regulations have failed to satisfy conservation and animal welfare concerns. From 1990 to 2011 the North Atlantic right whale (Eubalaena glacialis, NARW) population grew at a mean of 2.8% annually. However, population trends reversed since 2011; the species is in decline, with only ∼100 reproductively active females remaining. This failure is driven by vessel collisions and increasingly fatal and serious entanglement in fixed fishing gear, whose rope strength has increased substantially. Chronic entanglement, drag, and associated morbidity have been linked to poor fecundity. Genuine solutions involve designating areas to be avoided and speed restrictions for ships and removing fishing trap ropes from the water column. A trap fishing closure for NARW habitat in the Cape Cod Bay (U.S.) area has been in place seasonally since 2015. 2017 mortalities in Eastern Canada elicited substantive management changes whereby the 2018 presence of NARW in active trap fishing areas resulted in an effective closure. To avoid these costly closures, the traditional trap fishery model of rope end lines attached to surface marker buoys has to be modified so that traps are marked virtually, and retrieved with gear that does not remain in the water column except during trap retrieval. Consumer demand for genuinely whale-safe products will augment and encourage the necessary regulatory changes so that trap fisheries conserve target and nontarget species.
    Description: I thank Mark Baumgartner, Scott Kraus, Tim Werner, Amy Knowlton, Heather Pettis, Scott Landry, Stormy Mayo, Fred Penney, and Beth Casoni for discussions on this topic and Natalie Renier for drawing Figures 5 and 6. Funding was provided by the Woods Hole Oceanographic Institution Independent Research and Development Program.
    Description: 2020-01-10
    Keywords: end line ; entanglement ; large whale ; rope removal ; trap
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  • 44
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International, 219(1), (2019): 464-478, doi:10.1093/gji/ggz315.
    Description: The electromagnetic (EM) field generated by ocean tidal flow is readily detectable in both satellite magnetic field data, and in ocean-bottom measurements of electric and magnetic fields. The availability of accurate charts of tidal currents, constrained by assimilation of modern satellite altimetry data, opens the possibility of using tidal EM fields as a source to image mantle electrical resistivity beneath the ocean basins, as highlighted by the recent success in defining the globally averaged lithosphere–asthenosphere boundary (LAB) with satellite data. In fact, seafloor EM data would be expected to provide better constraints on the structure of resistive oceanic lithosphere, since the toroidal magnetic mode, which can constrain resistive features, is a significant component of the tidal EM field within the ocean, but is absent above the surface (in particular in satellite data). Here we consider this issue in more detail, using a combination of simplified theoretical analysis and 1-D and 3-D numerical modelling to provide a thorough discussion of the sensitivity of satellite and seafloor data to subsurface electrical structure. As part of this effort, and as a step toward 3-D inversion of seafloor tidal data, we have developed a new flexible 3-D spherical-coordinate finite difference scheme for both global and regional scale modelling, with higher resolution models nested in larger scale solutions. We use the new 3-D model, together with Monte Carlo simulations of errors in tidal current estimates, to provide a quantitative assessment of errors in the computed tidal EM signal caused by uncertainty in the tidal source. Over the open ocean this component of error is below 0.01 nT in Bz at satellite height and 0.05 nT in Bx on the seafloor, well below typical signal levels. However, as coastlines are approached error levels can increase substantially. Both analytical and 3-D modelling demonstrate that the seafloor magnetic field is most sensitive to the lithospheric resistance (the product of resistivity and thickness), and is more weakly influenced (primarily in the phase) by resistivity of the underlying asthenosphere. Satellite data, which contain only the poloidal magnetic mode, are more sensitive to the conductive asthenosphere, but have little sensitivity to lithospheric resistance. For both seafloor and satellite data’s changes due to plausible variations in Earth parameters are well above error levels associated with source uncertainty, at least in the ocean interior. Although the 3-D modelling results are qualitatively consistent with theoretical analysis, the presence of coastlines and bathymetric variations generates a complex response, confirming that quantitative interpretation of ocean tidal EM fields will require a 3-D treatment. As an illustration of the nested 3-D scheme, seafloor data at five magnetic and seven electric stations in the northeastern Pacific (41○N, 165○W) are fit with trial-and-error forward modelling of a local domain. The simulation results indicate that the lithospheric resistance is roughly 7 × 108 Ωm2. The phase of the seafloor data in this region are inconsistent with a sharp transition between the resistive lithosphere and conductive asthenosphere.
    Description: This work has been supported by National Natural Science Foundation of China grants 41804072 and 41574104, and NSF grant EAR-1447109. Special thanks to Dr Benjamin Murphy who provided the conductivity-depth profile for 1-D earth model, Dr Min Ding who provided valuable discussion about the oceanic lithosphere and Dr Jeffery Love who provided comments on the stylistics of the manuscript.
    Keywords: Composition and structure of the mantle ; Pacific Ocean ; Electromagnetic theory ; Geomagnetic induction ; Satellite magnetics
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  • 45
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 9 (2017): 659-676, doi:10.1093/gbe/evx023.
    Description: Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.
    Description: This work was primarily supported by a grant from the National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398 to J.K.C., D.L.C., M.E.H., S.I.K., M.F.O., J.R.S., W.W., and A.W.). Further support was provided by the National Institute of Environmental Health Sciences (1R01ES021934-01 to A.W., P42ES7373 to T.H.H., P42ES007381 to M.E.H., and R01ES019324 to J.R.S.), the National Institute of General Medical Sciences (P20GM103423 and P20GM104318 to B.L.K.), and the National Science Foundation (DBI-0640462 and XSEDE-MCB100147 to D.G.).
    Keywords: Population genomics ; Genome sequence ; Comparative genomics ; Adaptation ; Genetic diversity
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  • 46
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 5 (2017): cox061, doi:10.1093/conphys/cox061.
    Description: Recent studies have demonstrated that some hormones are present in baleen powder from bowhead (Balaena mysticetus) and North Atlantic right (Eubalaena glacialis) whales. To test the potential generalizability of this technique for studies of stress and reproduction in large whales, we sought to determine whether all major classes of steroid and thyroid hormones are detectable in baleen, and whether these hormones are detectable in other mysticetes. Powdered baleen samples were recovered from single specimens of North Atlantic right, bowhead, blue (Balaenoptera [B.]musculus), sei (B. borealis), minke (B. acutorostrata), fin (B. physalus), humpback (Megaptera novaeangliae) and gray (Eschrichtius robustus) whales. Hormones were extracted with a methanol vortex method, after which we tested all species with commercial enzyme immunoassays (EIAs, Arbor Assays) for progesterone, testosterone, 17β-estradiol, cortisol, corticosterone, aldosterone, thyroxine and tri-iodothyronine, representing a wide array of steroid and thyroid hormones of interest for whale physiology research. In total, 64 parallelism tests (8 species × 8 hormones) were evaluated to verify good binding affinity of the assay antibodies to hormones in baleen. We also tested assay accuracy, although available sample volume limited this test to progesterone, testosterone and cortisol. All tested hormones were detectable in baleen powder of all species, and all assays passed parallelism and accuracy tests. Although only single individuals were tested, the consistent detectability of all hormones in all species indicates that baleen hormone analysis is likely applicable to a broad range of mysticetes, and that the EIA kits tested here perform well with baleen extract. Quantification of hormones in baleen may be a suitable technique with which to explore questions that have historically been difficult to address in large whales, including pregnancy and inter-calving interval, age of sexual maturation, timing and duration of seasonal reproductive cycles, adrenal physiology and metabolic rate.
    Description: This work was supported by (1) the Center for Bioengineering Innovation at Northern Arizona University and (2) the New England Aquarium.
    Keywords: Baleen ; Cetaceans ; Hormones ; Marine mammals ; Reproduction ; Stress
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  • 47
    Publication Date: 2022-05-26
    Description: Author Posting. © Author(s), 2017. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 212 (2018): 1429–1449, doi:10.1093/gji/ggx488.
    Description: We conducted detailed analyses of a global array of trenches, revealing systematic intra- and intertrench variations in plate bending characteristics. The intratrench variations of the Manila and Mariana Trenches were analysed in detail as end-member cases of the relatively young (16–36 Ma) and old (140–160 Ma) subducting plates, respectively. Meanwhile, the intertrench variability was investigated for a global array of additional trenches including the Philippine, Kuril, Japan, Izu-Bonin, Aleutian, Tonga-Kermadec, Middle America, Peru, Chile, Sumatra and Java Trenches. Results of the analysis show that the trench relief (W0) and width (X0) of all systems are controlled primarily by the faulting-reduced elastic thickness near the trench axis (Tme) and affected only slightly by the initial unfaulted thickness (TMe) of the incoming plate. The reduction in Te has caused significant deepening and narrowing of trench valleys. For the cases of relatively young or old plates, the plate age could be a dominant factor in controlling the trench bending shape, regardless the variations in axial loadings. Our calculations also show that the axial loading and stresses of old subducting plates can vary significantly along the trench axis. In contrast, the young subducting plates show much smaller values and variations in axial loading and stresses.
    Description: This work was supported by Chinese Academy of Sciences Grants (Y4SL021001, QYZDY-SSW-DQC005, YZ201325 and YZ201534), National Natural Science Foundation of China Grants (91628301, U1606401, 41376063 and 41706056) and HKSAR Research Grant Council Grants (24601515, 14313816).
    Keywords: Lithospheric flexure ; Subduction zone processes
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  • 48
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aslan, C., Beckman, N. G., Rogers, H. S., Bronstein, J., Zurell, D., Hartig, F., Shea, K., Pejchar, L., Neubert, M., Poulsen, J., HilleRisLambers, J., Miriti, M., Loiselle, B., Effiom, E., Zambrano, J., Schupp, G., Pufal, G., Johnson, J., Bullock, J. M., Brodie, J., Bruna, E., Cantrell, R. S., Decker, R., Fricke, E., Gurski, K., Hastings, A., Kogan, O., Razafindratsima, O., Sandor, M., Schreiber, S., Snell, R., Strickland, C., & Zhou, Y. Employing plant functional groups to advance seed dispersal ecology and conservation. AoB Plants, 11(2), (2019):plz006, doi:10.1093/aobpla/plz006.
    Description: Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether single species and entire ecosystems will be resilient to global change. Building on current frameworks, we here posit that seed dispersal ecology should adopt plant functional groups as analytical units to reduce this complexity to manageable levels. Functional groups can be used to distinguish, for their constituent species, whether it matters (i) if seeds are dispersed, (ii) into what context they are dispersed and (iii) what vectors disperse them. To avoid overgeneralization, we propose that the utility of these functional groups may be assessed by generating predictions based on the groups and then testing those predictions against species-specific data. We suggest that data collection and analysis can then be guided by robust functional group definitions. Generalizing across similar species in this way could help us to better understand the population and community dynamics of plants and tackle the complexity of seed dispersal as well as its disruption.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio‐Environmental Synthesis Center under the US National Science Foundation Grant DBI‐1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1- 1). Contributions by the authors C.A. led the development of the concepts, writing, and revising of the manuscript with input from N.G.B. and H.S.R. All authors contributed to the development of concepts and are listed in order of contribution and alphabetical order within each level of contribution.
    Keywords: dependency ; directed dispersal ; dispersal vectors ; generalization ; mutualism ; seed dispersal effectiveness
    Repository Name: Woods Hole Open Access Server
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Alexander, H., Johnson, L. K., & Brown, C. T.. Keeping it light: (re)analyzing community-wide datasets without major infrastructure. Gigascience, 8(2),(2019): giy159, doi:10.1093/gigascience/giy159.
    Description: DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.
    Description: Funding was provided by the Gordon and Betty Moore Foundation (award GBMF4551 to C.T.B.).
    Keywords: reproducibility ; data reuse ; open data
    Repository Name: Woods Hole Open Access Server
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    Publication Date: 2022-05-26
    Description: © International Council for the Exploration of the Sea, 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ICES Journal of Marine Science 73 (2016): 1839-1850, doi: 10.1093/icesjms/fsw086.
    Description: For terrestrial and marine benthic ecologists, landscape ecology provides a framework to address issues of complexity, patchiness, and scale—providing theory and context for ecosystem based management in a changing climate. Marine pelagic ecosystems are likewise changing in response to warming, changing chemistry, and resource exploitation. However, unlike spatial landscapes that migrate slowly with time, pelagic seascapes are embedded in a turbulent, advective ocean. Adaptations from landscape ecology to marine pelagic ecosystem management must consider the nature and scale of biophysical interactions associated with organisms ranging from microbes to whales, a hierarchical organization shaped by physical processes, and our limited capacity to observe and monitor these phenomena across global oceans. High frequency, multiscale, and synoptic characterization of the 4-D variability of seascapes are now available through improved classification methods, a maturing array of satellite remote sensing products, advances in autonomous sampling of multiple levels of biological complexity, and emergence of observational networks. Merging of oceanographic and ecological paradigms will be necessary to observe, manage, and conserve species embedded in a dynamic seascape mosaic, where the boundaries, extent, and location of features change with time.
    Description: This work was supported by NASA grant NNX14AP62A “National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)” funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), the NOAA Integrated Ocean Observing System (IOOS) Program Office, and the LenFest Ocean Program.
    Keywords: Biodiversity ; Conservation ; Landscape ; Ocean observations ; Pelagic ; Phytoplankton ; Seascape
    Repository Name: Woods Hole Open Access Server
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    Oxford University Press
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 2165-2178, doi: 10.1093/gji/ggz280.
    Description: A multitaper estimator is proposed that accommodates time-series containing gaps without using any form of interpolation. In contrast with prior missing-data multitaper estimators that force standard Slepian sequences to be zero at gaps, the proposed missing-data Slepian sequences are defined only where data are present. The missing-data Slepian sequences are frequency independent, as are the eigenvalues that define the energy concentration within the resolution bandwidth, when the process bandwidth is [−1/2,1/2) for unit sampling and the sampling scheme comprises integer multiples of unity. As a consequence, one need only compute the ensuing missing-data Slepian sequences for a given sampling scheme once, and then the spectrum at an arbitrary set of frequencies can be computed using them. It is also shown that the resulting missing-data multitaper estimator can incorporate all of the optimality features (i.e. adaptive-weighting, F-test and reshaping) of the standard multitaper estimator, and can be applied to bivariate or multivariate situations in similar ways. Performance of the missing-data multitaper estimator is illustrated using length of day, seafloor pressure and Nile River low stand time-series.
    Description: The length of day utilized in Section 3 are available from http://hpiers.obspm.fr. The pressure data used in Section 4 are available from https://doi.org/10.1029/2018JC014586. A Matlab function MDmwps.m to compute missing-data power spectra is available from the Mathworks file exchange website. The author thanks Jeff Park and editor F.J. Simons for thorough reviews. This work was supported by an Internal Research and Development award at WHOI, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.
    Keywords: Fourier analysis ; Numerical approximations and analysis ; Statistical methods ; Time-series analysis
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, L. K., Alexander, H., & Brown, C. T. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience, 8(4), (2019): giy158, doi: 10.1093/gigascience/giy158.
    Description: Background: De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines,” on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. Results: New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. Conclusions: Given current bioinformatics approaches, there is no single “best” reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
    Description: Funding was provided by the Gordon and Betty Moore Foundation under award number GBMF4551 to C.T.B. Jetstream cloud platform was used with XSEDE allocation TG-BIO160028 [66, 67].
    Keywords: marine microbial eukaryote ; transcriptome assembly ; automated pipeline ; re-analysis
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  • 53
    Publication Date: 2024-04-05
    Description: Secondary microseismic noise is generated by non-linear interactions between ocean waves at the ocean surface. We present here the theory for computing the site effect of the ocean layer upon body waves generated by noise sources distributed along the ocean surface. By defining the wavefield as the superposition of plane waves, we show that the ocean site effect can be described as the constructive interference of multiply reflected P waves in the ocean that are then converted to either P or SV waves at the ocean–crust interface. We observe that the site effect varies strongly with period and ocean depth, although in a different way for body waves than for Rayleigh waves. We also show that the ocean site effect is stronger for P waves than for S waves. We validate our computation by comparing the theoretical noise body wave sources with the sources inferred from beamforming analysis of the three seismogram components recorded by the Southern California Seismic Network. We use rotated traces for the beamforming analysis, and we show that we clearly detect P waves generated by ocean gravity wave interactions along the track of typhoon Ioke (2006 September). We do not detect the corresponding SV waves, and we demonstrate that this is because their amplitude is too weak.
    Description: Published
    Description: 1096-1106
    Description: 1T. Geodinamica e interno della Terra
    Description: JCR Journal
    Description: restricted
    Keywords: Body waves ; Site effects ; Theoretical Seismology ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Oxford University Press
    In:  Oxford, Oxford University Press, vol. 16B, no. 2, pp. 125-169, (ISBN: 3-7643-7143-9)
    Publication Date: 1990
    Keywords: Textbook of geophysics ; Textbook of geology
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