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  • Oxford University Press  (103,075)
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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
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    Canadian Science Publishing
    In:  EPIC3Arctic Science, Canadian Science Publishing, 2(2), pp. 33-49, ISSN: 2368-7460
    Publication Date: 2022-08-12
    Description: Manual collection of accurate phenology data is time-consuming and expensive. In this study, we investigate whether repeat colour digital photography can be used (1) to identify phenological patterns, (2) to identify differences in vegetation due to experimental warming and site moisture conditions, and (3) as a proxy for biomass. Pixel values (RGB) were extracted from images taken of permanent plots in long-term warming experiments in three tundra communities at a high Arctic site during one growing season. The Greenness Excess Index (GEI) was calculated from image data at the plot scale (1 × 1 m) as well as for two species, Dryas integrifolia and Salix arctica. GEI values were then compared to corresponding field-based phenology observations. GEI and Normalized Difference Vegetation Index (NDVI) values from a paired set of true colour and infrared images were compared with biomass data. The GEI values followed seasonal phenology at the plot and species scale and correlated well with standardized observations. GEI correlated well with biomass and was able to detect quantitative differences between warmed and control plots and the differences between communities due to site-specific moisture conditions. We conclude that true colour images can be used effectively to monitor phenology and biomass in high Arctic tundra. The simplicity and affordability of the photographic method represents an opportunity to expand observations in tundra ecosystems.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 40
    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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  • 41
    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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  • 42
    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
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  • 43
    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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  • 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 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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  • 45
    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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  • 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 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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  • 47
    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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  • 48
    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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  • 49
    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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  • 50
    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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  • 51
    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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  • 52
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    Unknown
    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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  • 53
    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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  • 54
    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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  • 55
    Publication Date: 2015-07-01
    Description: Because of their rapid maneuverability, extended operational range, and improved personnel safety, unmanned aerial vehicles (UAVs) with vision-based systems have great potential for monitoring, detecting, and fighting forest fires. Over the last decade, UAV-based forest fire fighting technology has shown increasing promise. This paper presents a systematic overview of current progress in this field. First, a brief review of the development and system architecture of UAV systems for forest fire monitoring, detection, and fighting is provided. Next, technologies related to UAV forest fire monitoring, detection, and fighting are briefly reviewed, including those associated with fire detection, diagnosis, and prognosis, image vibration elimination, and cooperative control of UAVs. The final section outlines existing challenges and potential solutions in the application of UAVs to forest firefighting.
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  • 56
    Publication Date: 2018-09-01
    Description: Net CO2 assimilation (AN) is an important physiological indicator that reflects the photosynthetic capacity. The seasonal and spatial variations of AN play an important role in carbon uptake simulations, especially for trees. To gain a clearer understanding of the state of the branch carbon balance, it is necessary to more carefully evaluate the dynamic variation of AN over different gradients in the crown during the growing season. Gas exchange, leaf temperature (Tleaf), vapor pressure deficit (VPD), leaf mass per area (LMA), and relative depth into crown (RDINC) were measured throughout the growing season of planted Larix olgensis A. Henry trees. A semi-empirical model for predicting multilayered crown AN was established by incorporating Tleaf, VPD, LMA, RDINC, and their combinations into a photosynthetic light response (PLR) curve model using re-parameterization. The model was assessed based on goodness of fit (adjusted coefficient of determination ([Formula: see text]), root mean square error (RMSE), and Akaike’s information criterion (AIC)) and on the validation results (mean error (ME), mean absolute error (MAE), precision estimation (P)) and performed well. The multilayered predicted model of crown AN lays the foundation for calculating the multilayered photosynthetic production within the crown and determining the range of the functional crown for individual trees.
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  • 57
    Publication Date: 2015-07-01
    Description: Boreal peatlands in Canada comprise a substantial store of soil organic carbon (peat), and this peat is vulnerable to extensive burning during periods of extended drying. Increased frequency of extreme weather events in boreal regions is expected with future climate change, and the conditions that would support sustained smouldering peat combustion within peatlands may be more common. Organic soils tend to burn by smouldering combustion, a very slow-moving process in fuels such as those found in peatlands. Thus the most extreme conditions for carbon loss to the atmosphere due to the burning of peat likely occur when widespread propagation of flaming combustion leads to widespread initiation of smouldering. To investigate the potential for large-scale, high-intensity fire spread across forested bogs, we examined the fuel conditions in forested bogs necessary to support active crown fire. We measured surface and canopy fine fuels (those available to contribute to the propagating energy flux of the main flaming front) across a postfire chronosequence of forested boreal bog from central Alberta, Canada. We found that fuel load of fine surface material remained relatively constant across the chronosequence and at levels large enough to support crown fire initiation. Black spruce (Picea mariana (Mill.) B.S.P.) regeneration begins to fill in the crown space with increasing time since disturbance and achieves crown bulk densities similar to black spruce upland forests. We estimated that after about 80 years, the black spruce canopy has developed enough available fuel to support active crown fire on between 10% to 40% of days in a typical fire season in central Alberta, Canada. Broad-scale propagation of high-intensity fire across a peatland when coincident with drought-induced lower moisture in deep peatland layers has the potential to lead to a substantial release of stored terrestrial carbon.
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  • 58
    Publication Date: 2018-09-01
    Description: Understanding patterns of aboveground carbon storage across forest types is increasingly important as managers adapt to threats of global change. We combined field measures of aboveground biomass with lidar to model fine-scale biomass in deciduous forests located in two watersheds; one watershed was underlain by sandstone and the other by shale. We measured tree and shrub biomass across three topographic positions for both watersheds and analyzed biomass using mixed models. The watershed underlain by shale had 60% more aboveground biomass than the sandstone watershed. Although spatial patterns of biomass were different across watersheds, both had higher (between about 40% and 55%) biomass values at the toe-slope position than at the ridge-top position. To model fine-scale spatial patterns of biomass, we tested the effectiveness of leaf-on and leaf-off lidar combined with topographic metrics to develop a spatially explicit random forest model of tree and shrub biomass across both watersheds. Leaf-on variables were more important for modeling shrub biomass, while leaf-off variables were more effective at modeling tree biomass. Our model of tree and shrub biomass reflects the distribution of biomass across both watersheds at a fine scale and highlights the potential of abiotic factors such as topography and bedrock to affect carbon storage.
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  • 59
    Publication Date: 1983-12-01
    Description: The pine-wood nematode, Bursaphelenchusxylophilus (Steiner and Buhrer), was most commonly extracted from Cerambycidae emerging from nematode-infested pines in Minnesota and Wisconsin during 1981 and 1982. The greatest number of nematodes were extracted from Monochamusscutellatus (Say) and Monochamuscarolinensis (Olivier). Low numbers of B. xylophilus were found in some buprestids but no nematodes were found in the curulionid and scolytid beetles examined. Two species of Cerambycidae, Monochamusmannorator (Kiby.) and M. scutellatus were associated with B. xylophilus from balsam fir in Minnesota. Bursaphelenchusxylophilus from insects associated with balsam fir were morphologically different from insects associated with pine. Dauer larvae of B. xylophilus were concentrated in the thoracic segments of M. scutellatus and Monochamusmutator (Lec.) examined. Bursaphelenchusxylophilus was transmitted to twigs during maturation feeding and to logs during oviposition by M. carolinensis, M. mutator, and M. scutellatus.
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  • 60
    Publication Date: 2016-11-01
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  • 61
    Publication Date: 2015-06-01
    Description: Resource development can have significant consequences for the distribution of vegetation cover and for species persistence. Modelling changes to anthropogenic disturbance regimes over time can provide profound insights into the mechanisms that drive land cover change. We analyzed the spatial patterns of anthropogenic disturbance before and after a period of significant oil and gas extraction in two boreal forest subregions in Alberta, Canada. A spatially explicit model was used to map levels of anthropogenic forest crown mortality across 700 000 ha of managed forest over a 60-year period. The anthropogenic disturbance regime varied both spatially and temporally and was outside the historical range of variability characterized by regional fire regimes. Levels of live forest crown within anthropogenic disturbances declined and edge density increased following oil and gas development, whereas patch size varied regionally. In some places, anthropogenic disturbance generated profoundly novel landscapes with spatial patterns that had no historical analogue in the boreal system. The results illustrate that a shift in one sector of the economy can have dramatic outcomes on landscape structure. The results also suggest that any efforts to better align cumulative anthropogenic disturbance patterns with the historic baseline will almost certainly require a concerted and collaborative effort from all of the major stakeholders.
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  • 62
    Publication Date: 1983-12-01
    Description: Alnusrubra Bong, dominates the first 65 – 80 years of a sere that is initiated naturally on the terraces of the Hoh River. Stands of 14, 24, and 65 years were studied to determine to what extent the Alnus stage enriched the nitrogen inventory of the site. Bare sandbars deposited by the river had a mean of 783 kg/ha nitrogen. Alnus communities caused an increase in the nitrogen inventory so that, by 65 years, total community nitrogen was 4659 kg/ha, soils held 3594 kg/ha N in the upper 45 cm, and Alnus trees held 942 kg/ha N. The nitrogen contents of the soil, Alnus wood, bark, and branches, grasses, total aboveground biomass, total belowground biomass, and sticks less than 1 cm diameter all showed significant increases from 14 to 65 years. The A. rubra stage is an important link in the nutrient inventory between unvegetated, recently deposited sandbars and the climax coniferous forests dominated by Tsugaheterophylla (Raf.) Sarg. and Piceasitchensis (Bong.) Carr.
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  • 63
    Publication Date: 2015-08-01
    Description: In many recent studies, the value of forest inventory information in harvest scheduling has been examined. In a previous paper, we demonstrated that making measurement decisions for stands for which the harvest decision is uncertain simultaneously with the harvest decisions may be highly profitable. In that study, the quality of additional measurements was not a decision variable, and the only options were between making no measurements or measuring perfect information. In this study, we introduce data quality into the decision problem, i.e., the decisionmaker can select between making imperfect or perfect measurements. The imperfect information is obtained with a specific scenario tree formulation. Our decision problem includes three types of decisions: harvest decisions, measurement decisions, and decisions about measurement quality. In addition, the timing of the harvests and measurements must be decided. These decisions are evaluated based on two objectives: discounted aggregate income for the planning periods and the end value of the forest at the end of the planning horizon. Solving the bi-objective optimization problem formed using the ε-constraint method showed that imperfect information was mostly sufficient for the harvest timing decisions during the planning horizon but perfect information was required to meet the end-value constraint. The relative importance of the two objectives affects the measurements indirectly by increasing or decreasing the number of certain decisions (i.e., situations in which the optimal decision is identical in all scenarios).
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  • 64
    Publication Date: 2018-04-01
    Description: The contribution of forest biomass to Canada’s energy production is small but growing. As the forest bioenergy industry in Canada expands, there is growing interest in more sustainably managing the wood ash that is generated as a by-product. Despite being rich in nutrients, wood ash is usually landfilled in Canada. Soil applications of ash in Canadian forests could be used to mimic some of the effects of wildfire, to replace nutrients removed during harvesting, to counteract the negative effects of acid deposition, and to improve tree growth. At present, the provincial and territorial processes for obtaining regulatory approval to use wood ash as a forest soil amendment can be challenging to navigate. Furthermore, the costs for obtaining approval and transporting and applying wood ash to the soil can render landfilling a more cost-effective method of ash management. To ensure that wood ash applications in Canadian forests are conducted safely, effectively, and efficiently, experience from European countries could provide a useful starting point for developing best practices. The results of Canadian research trials will assist policy makers and forest managers in refining management guidelines that encourage soil applications of wood ash as a forest management tool while protecting the ecology, water quality, biodiversity, and productivity of Canadian forests.
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  • 65
    Publication Date: 2017-01-01
    Description: Genetic variation and population structure in biomass yield and coppice growth traits were assessed in seven native North American willow species (Salix amygdaloides (AMY), Salix bebbiana (BEB), Salix discolor (DIS), Salix eriocephala (ERI), Salix humilis (HUM), Salix interior (INT), and Salix nigra (NIG)) established together in common-garden field tests on two sites. Differences in biomass yield, coppice stem number, and average single-stem mass were significant at the site, species, population, and genotype (clonal) levels. There were also species × site interactions. Analyses of variance components for these traits showed that only 3%–5% of the total variation in these traits was due to site differences, whereas genetic variation at the species, population, and genotype levels accounted for approximately 10%–39%, 5%–13%, and 12%–23%, respectively. Populations were a significant source of variation in some willow species (e.g., AMY, DIS, ERI, and INT) but not in other species. Tree willows were less prolific in stem sprout production than shrub willows, and ERI coppices produced by far the highest number of stem sprouts per coppice. This multispecies investigation demonstrated strong species and clonal differences, but variation among populations within a species, although significant, was relatively small, indicating that major growth and yield gains can be made through proper species selection and clonal selection within local populations.
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  • 66
    Publication Date: 2018-01-01
    Description: Bud burst is one of the most observable phenological stages in tree species, and its responses to environmental factors are found to be species-specific. Nevertheless, for dioecious plants, whether the bud burst responses are sex specific remains an open question, as do the underlying physiological mechanisms. Here, we investigated the effect of elevated temperature (+2 °C) and drought (30% field capacity) during December–March on bud development, gas exchange, water and nitrogen status, and carbohydrate metabolism in female and male Populus cathayana to understand how nongrowing season warming and drought modifies physiological and phenological traits. Our results showed that at ambient temperature, males experienced earlier bud burst than females. Winter warming significantly delayed bud burst and even synchronized it for both sexes because of the greater responsiveness of males. Although drought exerted little effect on the timing of bud burst, it significantly reduced bud fresh mass and limited bud growth by decreasing gas exchange capacity and nonstructural carbohydrate (NSC) accumulation; moreover, females were more affected by drought stress. The significant sex × watering × temperature interactions for δ13C and NSC indicate that sexual dimorphism in these condition-specific traits would increase along the environmental gradients, implying contrasting life history strategies in different ecological scenarios. The convergence in the time for bud burst caused by elevated temperature might exaggerate the competition among males, thus influencing the sex ratio, structure, and functioning of P. cathayana populations.
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  • 67
    Publication Date: 2016-09-01
    Description: This study considered airborne laser scanning (ALS) based aboveground biomass (AGB) prediction in mountain forests. The study area consisted of a long transect from southern Norway to northern parts of the country with wide ranges of elevation along a long latitudinal gradient (58°N–69°N). This transect was covered by ALS data and field data from 238 plots. AGB was modeled using different types of predictor variables, namely ALS metrics, variables related to growing conditions (elevation, latitude, and climatic variables), and tree species information. Modelling of AGB in the long transect covering diverse mountainous forest conditions was challenging: the RMSE values were rather large (37%–70%). The effects of growing conditions on model predictions were minor. However, species information was essential to improve accuracy. The analysis revealed that when doing inventories of spruce-dominated areas, all plots should be pooled together when the models are developed, whereas if pine or deciduous species dominate the area in question, separate dominant species-wise models should be constructed.
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  • 68
    Publication Date: 2015-08-01
    Description: The impact of root water uptake on duff (both fibric and humic horizons) moisture was investigated at deciduous, mixedwood, and conifer stands in Ontario, Canada. Roots were actively excluded from the duff layer using geotextiles inserted at the duff–mineral soil interface and along the plot edges; liquid and vapour water flow was otherwise not affected by the geotextiles. Root exclusion caused little difference in duff moisture content prior to early June, after which the root exclusion plots remained at 15%–20% volumetric water content, whereas root-intact plots declined to as low as 5% volumetric water content during rain-free periods. Only in the root-intact plots did the duff water content reach sufficiently low levels that duff evaporation was limited by low water content. The net effect of root exclusion was to reduce the cumulative growing season water loss in the duff by 19%–31%, depending on the stand type. Root exclusion also decreased the number of days with a high probability of duff smouldering from as many as 72 days·year−1 to as few as 0 days·year−1. This root exclusion experiment provides a model for short-term duff moisture transitions under thinned forests such as those forests under community wildfire protection.
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  • 69
    Publication Date: 1982-06-01
    Description: Flooding for 30 days induced several changes in Quercusmacrocarpa Michx. seedlings, with stomatal closure among the earliest responses. Stomata remained more closed in flooded than in unflooded plants during the entire experimental period. Leaf water potential was consistently higher in flooded than in unflooded plants. Other responses to flooding included acceleration of ethylene production by stems; formation of hypertrophied lenticels on submerged portions of stems; growth inhibition, with greatest reduction in roots; and formation of a few adventitious roots on submerged portions of the stem above the soil line. Some of the morphological responses to flooding, especially formation of hypertrophied lenticels, appeared to be associated with increased ethylene production. Quercusmacrocarpa seedlings adapted poorly to flooding as shown by failure of stomata to reopen after an early period of flooding and low capacity for production of adventitious roots. The much greater inhibition of root growth than shoot growth by flooding will reduce drought tolerance after floodwaters recede.
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  • 70
    Publication Date: 2018-05-01
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  • 71
    Publication Date: 2016-03-01
    Description: As part of the development of the 2011 National Land Cover Database (NLCD) tree canopy cover layer, a pilot project was launched to test the use of high-resolution photography coupled with extensive ancillary data to map the distribution of tree canopy cover over four study regions in the conterminous US. Two stochastic modeling techniques, random forests (RF) and stochastic gradient boosting (SGB), are compared. The objectives of this study were first to explore the sensitivity of RF and SGB to choices in tuning parameters and, second, to compare the performance of the two final models by assessing the importance of, and interaction between, predictor variables, the global accuracy metrics derived from an independent test set, as well as the visual quality of the resultant maps of tree canopy cover. The predictive accuracy of RF and SGB was remarkably similar on all four of our pilot regions. In all four study regions, the independent test set mean squared error (MSE) was identical to three decimal places, with the largest difference in Kansas where RF gave an MSE of 0.0113 and SGB gave an MSE of 0.0117. With correlated predictor variables, SGB had a tendency to concentrate variable importance in fewer variables, whereas RF tended to spread importance among more variables. RF is simpler to implement than SGB, as RF has fewer parameters needing tuning and also was less sensitive to these parameters. As stochastic techniques, both RF and SGB introduce a new component of uncertainty: repeated model runs will potentially result in different final predictions. We demonstrate how RF allows the production of a spatially explicit map of this stochastic uncertainty of the final model.
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  • 72
    Publication Date: 2015-03-01
    Description: Trees form the terrestrial interface with the atmosphere in forested regions. The electrical properties of trees may influence their response to atmospheric conditions and potentially lethal phenomena (e.g., lightning). We review the literature describing electrical properties of trees and provide a tabular summary of the methods and goals of each study. We hypothesized that electrical resistivity varies consistently among species and between growth forms. We surveyed resistivity of eight tree and three vine species in Michigan and Kentucky, and we quantified resistivity over a moisture gradient for wood blocks of four tree species. Resistivity varied predictably with stem diameter and differed among species and growth forms. Specifically, resistivity of trees was approximately 200% higher than resistivity of vines, and resistivity of conifers was 135% higher than that of hardwoods. The regional comparison showed no difference in resistivity of red maple (Acer rubrum L.) and sugar maple (Acer saccharum Marsh.) between Michigan and Kentucky. These results, in combination with interspecific differences observed among wood blocks, suggest that there is a phylogenetic basis for variation in resistivity that reflects differences in anatomy and physiology. Our review and empirical survey provide a framework for studying the ecological effects of lightning in the context of the electrical properties of trees.
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  • 73
    Publication Date: 2018-12-01
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  • 74
    Publication Date: 2015-11-01
    Description: The influence of forest ecology and strategic planning has increased in importance to support the management of mixed-species forests to enhance biodiversity. However, little is known about competitive and facilitative interactions between trees and species in mixed fir–beech–spruce forests, mostly because of a lack of long-term experimental research. In the 1960s, long-term sample plots were established in the Western Carpathians to develop region-specific yield models. Trees in the plots were measured at 5- to 16-year intervals from 1967(69). In 2010, the positions of standing trees in all plots were identified spatially. Stump positions were also identified to record the coordinates of trees that had been removed or had died. The objectives of this study were to evaluate the applicability of widely used competition indices for mature fir–beech–spruce mixed forests and to test whether the tree competition zone changes among species and forest stands of different stocking densities. Results showed that the best competition index was based on the comparison of the basal area of competitors and the subject tree in the radius, which was defined as a function of stand density and species. In addition, beech was found to be a strong self-competitor, which was not the case for silver fir (Abies alba Mill.). Results suggest that simpler competition indices are better suited for such diverse forests, as more complex indices do not describe the competition interactions sufficiently well.
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  • 75
    Publication Date: 2018-09-01
    Description: Wildfires, insect outbreaks, and windstorms are increasingly common forest disturbances. Post-disturbance management often involves salvage logging, i.e., the felling and removal of the affected trees; however, this practice may represent an additional disturbance with effects on ecosystem processes and services. We developed a systematic map to provide an overview of the primary studies on this topic and created a database with information on the characteristics of the retrieved publications, including information on stands, disturbance, intervention, measured outcomes, and study design. Of 4341 retrieved publications, 90 were retained in the systematic map. These publications represented 49 studies, predominantly from North America and Europe. Salvage logging after wildfire was addressed more frequently than after insect outbreaks or windstorms. Most studies addressed logging after a single disturbance event, and replication of salvaged stands rarely exceeded 10. The most frequent response variables were tree regeneration, ground cover, and deadwood characteristics. This document aims to help managers find the most relevant primary studies on the ecological effects of salvage logging. It also aims to identify and discuss clusters and gaps in the body of evidence, relevant for scientists who aim to synthesize previous work or identify questions for future studies.
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  • 76
    Publication Date: 2015-06-01
    Description: The parsimonious taper function proposed by Riemer et al. (1995. Allg. Forst.- Jagdztg. 166(7): 144–147) was fitted for radiata pine (Pinus radiata D. Don) stems in Spain by using a nonlinear mixed modelling approach. Eight candidate models (all possible expansion combinations of the three fixed parameters with random effects) were assessed, and the mixed model with three random effects performed the best according to the goodness-of-fit statistics. An evaluation data set was used to assess the performance of these models in predicting stem diameter along the bole, as well as total stem volume. Four prediction approaches were compared: one subject (tree) specific (SS) and three population specific (ordinary least squares (OLS), mean (M), and population averaged (PA)). The SS responses for a tree were estimated from a prior stem diameter measurement available for that tree, whereas OLS, M, and PA were obtained from the fixed-effects model, from the fixed parameters of mixed-effects models, and by computing mean predictions from the mixed-effects models over the distribution of random effects, respectively. Prediction errors were greater for the M and PA responses than for the OLS response, and therefore, from the prediction point of view, the use of the mixed-effects models is not recommended when an additional stem diameter measurement is not available. The mixed model with three random effects was also selected as the best model for SS estimations. Measurement of an additional stem diameter at a relative tree height of approximately 0.5 provided the best calibrations for stem diameters along the bole and total stem volume predictions. The SS approach increased the flexibility and efficiency of the selected mixed-effects model for localized predictions and thus improved the overall predictive capacity of the base model.
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  • 77
    Publication Date: 2016-05-01
    Description: To better understand climatic origins of annual tree-growth anomalies in boreal forests, we analysed 895 black spruce (Picea mariana (Mill.) B.S.P.) tree-growth series from 46 xeric sites situated along three latitudinal transects in Eastern Canada. We identified interannual (based on comparison with previous year growth) and multidecadal (based on the entire tree-ring width distribution) growth anomalies between 1901 and 2001 at site and transect levels. Growth anomalies occurred mainly at site level and seldom at larger spatial scales. Both positive interannual and multidecadal growth anomalies were strongly associated with below-average temperatures and above-average precipitation during the previous growing season (Junet–1 – Augustt–1). The climatic signature of negative interannual and multidecadal growth anomalies was more complex and mainly associated with current-year climatic anomalies. Between the early and late 20th century, only negative multidecadal anomalies became more frequent. Our results highlight the role of previous growing season climate in controlling tree growth processes and suggest a positive association between climate warming and increases in the frequency of negative multidecadal growth anomalies. Projected climate change may further favour the occurrence of tree-growth anomalies and enhance the role of site conditions as modifiers of tree response to regional climate change.
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  • 78
    Publication Date: 2019-03-01
    Description: A two-year field study was carried out to determine whether inoculating white spruce, Picea glauca (Moench) Voss, with a native endophytic fungus, Phialocephala scopiformis DAOM 229536 Kowalski & Kehr (Helotiales, Ascomycota), decreased the performance of eastern spruce budworm, Choristoneura fumiferana Clemens, developing on these trees. Second instars were reared at three densities in the mid crown and at one density in the lower, mid, and upper crown. Larval survival (i.e., survival of larvae to pupation) was lower on endophyte-inoculated trees than on control trees in the mid crown and especially the upper crown but was similar in the lower crown, resulting in a significant interaction between endophyte and crown level. A similar but marginally insignificant interaction was observed for overall survival up to adult emergence (i.e., total survival). Larval survival and total survival were approximately 22% and 19% lower, respectively, when developing in the upper crown of endophyte-inoculated trees than in control trees. Larval survival remained relatively constant, with increased density on control trees but decreased with density on endophyte-inoculated trees, resulting in a significant interaction between endophyte and larval density. Sex ratios of emerged adults and wing lengths of emerged females were not influenced by the endophyte. Our results suggest that endophytic fungi could be useful additions to integrated pest management programs.
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  • 79
    Publication Date: 2019-05-01
    Description: Quantitative genetic variation of fiber-dimension traits and their relationship with diameter at breast height (DBH) and solid-wood traits (i.e., density and modulus of elasticity (MOE)) was investigated in lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.). A total of 823 increment cores were sampled from 207 half-sib families at two independent progeny trials, aged 34–35 years, located in northern Sweden. High-resolution pith-to-bark profiles were obtained for radial fiber width (RFW), tangential fiber width (TFW), fiber wall thickness (FWT), and fiber coarseness (FC) using SilviScan. Heritabilities ranged from 0.29 to 0.74, and inheritance increased with cambial maturity. Estimated age–age genetic correlations indicate that early selection between ages 5 and 8 years is highly efficient. Our results indicate that selection for a 1% increase in DBH or MOE incurs a negligible effect on fiber-dimension traits and maximum genetic gains are reached when DBH and MOE are considered jointly. Moreover, simultaneous improvement of growth and stiffness is achievable when a selection index with 7 to 10 economical weights for MOE relative to 1 for DBH is incorporated. However, the unfavorable relationship between solid-wood traits and pulp and paper related traits suggests that breeding strategies must be implemented to improve wood quality of lodgepole pine for multiple uses.
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  • 80
    Publication Date: 2019-05-01
    Description: Lack of generalized equations has prevailed in Brazil, because it is assumed that localized or climate-specific equations are needed. This study aimed to develop generalized stem taper and volume equations applicable to 11 eucalyptus clones and evaluate if climate variation impacts the accuracy of the estimates. A total of 693 trees evenly distributed across 11 clones at 21 sites were used for model fittings and predictive validation. The penalized mixed spline (PMS) approach was developed for predicting stem taper and volume along the stem profile. The Schumacher and Hall (1933) equation was used to predict total tree volume, while volume ratio equations were applied to predict merchantable volume. For every fitted equation, an annual climatic variable was included to assess the improvement in model performance. The overall results highlighted that climatic variation does not need to be accounted for in stem taper and volume modeling. All of the equations displayed desirable accuracy, but the generalized PMS equation may be preferred when the forestry enterprise looks to furnish a range of multiple forest products. The generalized total tree volume equation, combined with the ratio equations, is highly recommended when the forestry enterprise produces a single product.
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  • 81
    Publication Date: 2016-03-01
    Description: Wood ash may be an effective soil amendment in North America to restore acidified and low-nutrient forest soils, but little research exists beyond its effects on soil and plants. Eastern Red-backed Salamander (Plethodon cinereus (Green, 1818)) abundance was assessed in a northern hardwood forest 1 year following an ash-addition field trial. Plots were established with fly ash and bottom ash treatments of 0, 1, 4, and 8 Mg·ha−1 (n = 4), and cover boards were positioned both with and without ash beneath. One year following ash additions, salamander abundance had increased under boards with fly ash beneath, and bottom ash had no effect. Soil pH and electrical conductivity increased under cover boards with ash beneath them and for uncovered soil, and the effects were strongest under cover boards with ash beneath. The effects of ash were generally stronger at higher dosages, and fly ash was stronger than bottom ash. The moisture holding capacity of fly ash was 60% higher than the soil and was 63% lower than the soil for bottom ash, but they had little effect on moisture of the forest floor. These results suggest that ash altered salamander abundance via soil pH and moisture and would not inhibit salamander movement over the forest floor.
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  • 82
    Publication Date: 2016-05-01
    Description: Forest health deteriorated in eastern North America as a result of depletion of available soil base cations by elevated inputs of acid deposition. We experimentally restored available calcium (Ca) to soils of a forested watershed at Hubbard Brook, New Hampshire, and measured the response of fine root biomass 14 years after treatment. In this northern hardwood forest, fine root (
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  • 83
    Publication Date: 1983-10-01
    Description: Root elongation of greenhouse-grown Alaskan taiga tree seedlings increased with increasing root temperature in all six species examined and was most temperature sensitive in warm-adapted aspen (Populustremuloides Michx.). Root elongation was slower in fine than large roots and in black spruce (Piceamariana (Mill.) B.S.P.) was less temperature sensitive in fine than in large roots. Root elongation in the laboratory was slowest in black spruce, which has an inherently slow growth rate, and most rapid in poplar (Populusbalsamifera L.) and aspen, which grow more rapidly. In contrast, field root elongation rates tended to be highest in black spruce from cold wet sites, suggesting that site factors other than soil temperature (e.g., moisture) predominated over genetic differences among species in determining field root elongation rates. The seasonal pattern of root elongation was closely correlated with soil temperature and reached maximum rates in July for all tree species (except aspen medium-sized roots). Most roots of each species were in the top 20 cm of soil. However, root growth penetrated to greater depth in warm compared with cold sites. Root biomass in a 130-year black spruce forest (1230 g/m2) comprised only 15% of total tree biomass. Root biomass of 25-year aspen and 60-year poplar sites (517 and 5385 g/m2, respectively) comprised a greater proportion (57% in poplar) of total tree biomass than in spruce.
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  • 84
    Publication Date: 2019-03-01
    Description: Vegetation–soil systems differentially influence the ecosystem processes related to the carbon cycle, particularly when one tree species is dominant over wide geographic regions that are undergoing climate change. The objective of this study was to quantify the stocks of ecosystem carbon in three vegetation–soil systems along a highland elevational gradient in central Mexico. The vegetation–soil systems, from lower to higher elevation, were dominated by Alnus jorullensis Kunth, Abies religiosa (Kunth) Schltdl. & Cham., and Pinus hartwegii Lindl., respectively. Above- and below-ground tree biomass was determined in each system, along with the litter, coarse woody material, roots, and litterfall. The A. religiosa system had the greatest stock of aboveground biomass carbon (216 ± 31 Mg C·ha−1). The A. jorullensis system had the greatest production of litterfall (3.1 ± 0.08 Mg·ha−1·year−1); however, the carbon content of this litter layer (1.2 ± 0.32 Mg C·ha−1) was lower than that of P. hartwegii (10.1 ± 0.28 Mg C·ha−1). Thus, the litter layer in the A. jorullensis system had markedly the shortest residence time (8 years), suggesting high rates of litter decomposition. The soil carbon stock (at soil depth of 1 m) was greater in A. jorullensis (189 Mg C·ha−1) and P. hartwegii (137 Mg C·ha−1) than in A. religiosa (68 Mg C·ha−1). The A. religiosa and A. jorullensis systems had the highest and lowest total ecosystem C content (301 and 228 Mg C·ha−1, respectively). Upward migration of the A. religiosa system in response to global climate change, however, could cause losses by 2030 of 187 Mg C·ha−1 associated with aboveground biomass.
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  • 85
    Publication Date: 2018-05-01
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  • 86
    Publication Date: 2017-08-01
    Description: Conifer winter damage results primarily from loss of cold hardiness during unseasonably warm days in late winter and early spring, and such damage may increase in frequency and severity under a warming climate. In this study, the dehardening dynamics of lodgepole pine (Pinus contorta Dougl. ex. Loud), jack pine (Pinus banksiana Lamb.), white spruce (Picea glauca (Moench) Voss), and black spruce (Picea mariana (Mill.) B.S.P.) were examined in relation to thermal accumulation during artificial dehardening in winter (December) and spring (March) using relative electrolyte leakage and visual assessment of pine needles and spruce shoots. Results indicated that all four species dehardened at a similar rate and to a similar extent, despite considerably different thermal accumulation requirements. Spring dehardening was comparatively faster, with black spruce slightly hardier than the other conifers at the late stage of spring dehardening. The difference, however, was relatively small and did not afford black spruce significant protection during seedling freezing tests prior to budbreak in late March and early May. The dehardening curves and models developed in this study may serve as a tool to predict cold hardiness by temperature and to understand the potential risks of conifer cold injury during warming–freezing events prior to budbreak.
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  • 87
    Publication Date: 2018-06-01
    Description: Model-based inference is an alternative to probability-based inference for small areas or remote areas for which probability sampling is difficult. Model-based mean square error estimators incorporate three components: prediction covariance, residual variance, and residual covariance. The latter two components are often considered negligible, particularly for large areas, but no thresholds that justify ignoring them have been reported. The objectives of the study were threefold: (i) to compare analytical and bootstrap estimators of model parameter covariances as the primary factors affecting prediction covariance; (ii) to estimate the contribution of residual variance to overall variance; and (iii) to estimate thresholds for residual spatial correlation that justify ignoring this component. Five datasets were used, three from Europe, one from Africa, and one from North America. The dependent variable was either forest volume or biomass and the independent variables were either Landsat satellite image bands or airborne laser scanning metrics. Three conclusions were noteworthy: (i) analytical estimators of the model parameter covariances tended to be biased; (ii) the effects of residual variance were mostly negligible; and (iii) the effects of spatial correlation on residual covariance vary by multiple factors but decrease with increasing study area size. For study areas greater than 75 km2 in size, residual covariance could generally be ignored.
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  • 88
    Publication Date: 1983-10-01
    Description: The patterns of translocation of carbon in different-age tissues of four common moss species in a black spruce (Piceamariana (Mill.) B.S.P.) dominated forest near Fairbanks, Alaska, were studied by 14C labelling and carbohydrate analysis. A simple, in-vial combustion technique was developed for combustion of small (
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  • 89
    Publication Date: 1982-12-01
    Description: Water stress of subalpine conifer species may be measured with the pressure chamber after several hours of tissue storage. Tissue samples stored in cool, humid vials exhibited very little change in xylem pressure potential over a 4-h period. However, xylem pressure potential declined steadily when a source of water vapor was not available. Xylem pressure potentials of current-year and 1-year-old needles of lodgepole pine (Pinuscontorta var. latifolia Engelm.) were slightly lower than those of older needles.
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  • 90
    Publication Date: 2017-05-01
    Description: The ability to rapidly estimate wind speed beneath a forest canopy or near the ground surface in any vegetation is critical to practical wildland fire behavior models. The common metric of this wind speed is the “mid-flame” wind speed, UMF. However, the existing approach for estimating UMF has some significant shortcomings. These include the assumptions that both the within-canopy wind speed and the canopy structure are uniform with depth (z) throughout the canopy and that the canopy roughness length (z0) and displacement height (d) are the same regardless of canopy structure and foliage density. The purpose of this study is to develop and assess a model of canopy wind and Reynolds stress that eliminates these shortcomings and thereby provide a more physically realistic method for calculating UMF. The present model can be used for canopies of arbitrary plant surface distribution and leaf area, and the single function that describes the within-canopy wind speed is shown to reproduce observed canopy wind speed profiles across a wide variety of canopies. An equally simple analytical expression for the within-canopy Reynolds stress, [Formula: see text], also provides a reasonable description of the observed vertical profiles of Reynolds stress. In turn, [Formula: see text] is used to calculate z0 and d. Tests of operational performance are also discussed.
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  • 91
    Publication Date: 2019-01-01
    Description: Wildland fire dynamics are a complex three-dimensional turbulent process. Cellular automata (CA) is an efficient tool to predict fire dynamics, but the main parameters of the method are challenging to estimate. To overcome this challenge, we compute statistical distributions of the key parameters of a CA model using infrared images from controlled burns. Moreover, we apply this analysis to different spatial scales and compare the experimental results with a simple statistical model. By performing this analysis and making this comparison, several capabilities and limitations of CA are revealed.
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  • 92
    Publication Date: 2019-02-01
    Description: It has recently become clear that the regeneration density of serotinous species within a burned area declines with local fire intensity. It is assumed that this occurs because variation in local fire intensity leads to variation in incident heat fluxes and, ultimately, seed necrosis. We argue here that this same relationship between incident heat flux and seed necrosis is important at the scale of individual plant crowns. Using Picea mariana (Mill.) B.S.P. (black spruce), we show that postfire seed viability increases with crown height, depth into the crown, and angle from wind direction (with the windward side enjoying greater viability). All three effects are what one would expect given the physics of buoyant plumes, interactions of moving fire lines with wake flow around cylinders, and heat transfer in porous bodies such as a tree crown. We conclude by discussing the broader consequences of cone cluster size and global change on regeneration in serotinous species.
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  • 93
    Publication Date: 2019-02-01
    Description: Forest attributes such as volume or basal area are concentrated at tree locations and are absent elsewhere. It is, therefore, more meaningful to consider the amount of forest attributes at a prefixed spatial grain, within regular plots of prefixed size centered at the points of the study area. In this way, the diversity of attributes within plots also can be considered and quantified by suitable indexes, giving rise to a diversity surface defined on the continuum of points constituting the area. We analyze the estimation of diversity surfaces when a sample of plots is selected by a probabilistic sampling scheme and diversity within nonsampled plots is estimated using an inverse distance weighting interpolator. We discuss the design-based asymptotic properties of the resulting maps when the survey area remains fixed and the number of sampled points increases. Because diversity surfaces share suitable mathematical properties, if the schemes adopted to select sample points ensure an even coverage of the study areas avoiding large portions of non-sampled zones, it can be proven that the estimated maps approach the true maps.
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  • 94
    Publication Date: 2015-10-01
    Description: Lightning strikes millions of trees worldwide each year, yet structured lightning damage surveys are relatively rare. Estimates drawn from the literature suggest that lightning directly or indirectly kills up to 4% of large canopy trees in a stand annually. Lightning is a major cause of death for pines in southeastern US forests and for large cacti in some deserts, but its landscape-level effects exclusive of fire at higher latitudes are poorly known. We quantified damage to trees from lightning and other sources in hemlock–hardwood forests of the Huron Mountain Region of Michigan, USA. This region receives ca. 100 cloud-to-ground lightning flashes per year, with most occurring in May to August. We recorded abiotic and biotic damage on 309 trees distributed among nine transects, each 〉2 km long. None of the transect trees had lightning scars, and we observed only 14 clear cases of lightning damage among thousands of trees examined during associated meander surveys (each ca. 0.5 ha). This damage was more commonly associated with emergent stature (50% of struck trees) and higher rates of biotic damage (50%) than we observed in the 309 transect trees (22% emergent status and 16% incidence of biotic damage). Nearly all (93%) of the lightning damaged trees were conifers, suggesting that either susceptibility to, or response to, lightning strikes has a phylogenetic basis. These preliminary results provide a foundation for comparative studies in other forests. Accurate quantification of lightning-induced tree mortality will improve forest turnover models and facilitate predictions of future forest structure under conditions of increased lightning frequency.
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  • 95
    Publication Date: 2017-08-01
    Description: Canada’s National Forest Carbon Monitoring Accounting and Reporting System (NFCMARS) quantifies the carbon (C) dynamics and greenhouse gas (GHG) emissions and removals of Canada’s managed forest to fulfill reporting obligations under international climate conventions. Countries are also requested to assess the uncertainty associated with these estimates, which we report here. We used Monte Carlo simulation to quantify uncertainty of carbon stock and flux estimates from the Carbon Budget Model of the Canadian Forest Sector (CBM-CFS3), the core ecosystem model of the NFCMARS. We evaluated the impacts of model algorithms, parameters, and the input data used to describe forest characteristics and disturbance rates. Under our assumptions, 95% confidence interval widths averaged 16.2 Pg C (+8.3 and –7.9 Pg C, or ±15%) for total ecosystem C stock and 32.2 Tg C·year−1 (+16.6 and –15.6 Tg C·year−1) for net biome production relative to an overall simulation median of –0.8 Tg C·year−1 from 1990 to 2014. The largest sources of uncertainty were related to factors determining biomass increment and the parameters used to model soil and dead organic matter C dynamics. Opportunities to reduce uncertainty and associated research challenges were identified.
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  • 96
    Publication Date: 2015-05-01
    Description: Constraints of the physical environment affect forest growth and forest operations. At a local scale, these constraints are generally considered during forest operations. At regional or continental scales, they are often integrated to larger assessments of the potential for a given land unit to be managed. In this study, we propose an approach to analyze the integration of physical-environment constraints in forest management activities at the regional scale (482 000 km2). The land features that pose constraints to forest management (i.e., hydromorphic organic deposits, dead-ice moraines, washed till, glacial block fields, talus, and active aeolian deposits, slopes 〉 40%) were evaluated within 1114 land districts. To distinguish land districts that can be suitably managed from those where constraints are too important for sustainable timber production, we carried out a sensitivity analysis of physical constraints for the 1114 land districts. After analysis of two portions of the study area under management, a land district was considered suitable for management when more than 20% of its land area consists of features imposing few constraints or, for mountain-type relief districts, when more than 40% of the land area consists of features imposing few constraints. These cutoff values were defined by expert opinion, based on sensitivity analyses performed on the entire study area, on analyses of two different sectors with different types of constraints and on a strong understanding of the study area. Our results show that land districts where the physical environment posed significant constraints covered 7.5% of the study area (36 000 km2). This study shows that doing an a priori classification of land units based on permanent environmental features could facilitate the identification of areas that are not suitable for forest management activities.
    Print ISSN: 0045-5067
    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 97
    Publication Date: 2016-11-01
    Print ISSN: 0045-5067
    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 98
    Publication Date: 1983-02-01
    Description: The aboveground biomass of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) and annual production over 7 years was studied in relation to thinning and nitrogen fertilization. Biomass yield of both treatments increased during the first 3–4 years then decreased for fertilization but not with thinning. Treatments doubled biomass production of individual trees over the study period when applied separately and quadrupled it when combined. Annual biomass production per unit of foliage (E) increased during the first 3–4 years, but was at or below control level after 7 years. The increased E accounted for 20, 37, and 27% of the stemwood dry matter response to thinning, fertilization and the combined treatments, respectively; the remainder was attributed to an increase in foliage biomass. Thinning, but not fertilization, influenced distribution of radial growth along the stem, increasing growth only below the top one-third of the stem. This pattern was related to crown development.
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    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 99
    Publication Date: 2015-10-01
    Description: Over the period 1883–2013, recruitment of subalpine limber pine (Pinus flexilis E. James) and Great Basin bristlecone pine (Pinus longaeva D.K. Bailey) above the upper tree line, below the lower tree line, and across middle-elevation forest borders occurred at localized sites across four mountain ranges in the western Great Basin. A synchronous pulse at all ecotones occurred between 1963 and 2000 (limber pine) and between 1955 and 1978 (bristlecone pine) when pines expanded 225 m beyond forest borders. Little recruitment occurred before this interval or in the 21st century. No obvious environmental factors distinguished recruitment locations from nonrecruitment locations. Where their ranges overlap, limber pine has leapfrogged above bristlecone pine by 300 m. Limber pine tree-ring chronologies, developed to compare radial-growth responses with recruitment, showed dominant pulses of increased growth during the same interval as recruitment. Significant climate correlations of growth and recruitment indicated lead and lag effects as much as 6 years and complex relationships with climate variables, corroborating the importance of cumulative climate effects relative to any single year. Water relations were the most important drivers of growth and recruitment and interacted with growing-season minimum and maximum temperatures. These results underscore the importance of studying ecotones at all margins when evaluating conifer response to climate change.
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    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 100
    Publication Date: 1981-09-01
    Description: In order to test the hypothesis that the deterioration of trembling aspen (Populustremuloides Michx.) is related to variations in climate, soil properties, and genotype, 59 trembling aspen clones were sampled in Michigan, Wisconsin, Minnesota, and Ontario. A longevity index (LI) was calculated by taking the difference between predicted basal area from normal yield tables and measured basal area for each clone. Correlations of environmental variables with LI indicate that aspen longevity decreases with increasing mean annual temperature. Under similar temperature regimes, aspen growing on xeric sites and on sites low in exchangeable Ca are most susceptible to early breakup. Since there were negligible differences in soil properties between nine pairs of adjacent deteriorating and relatively well stocked clones, we hypothesize that, under similar environmental conditions, variation in the timing of deterioration may be due to genotypic differences between clones.
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    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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