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  • Oxford University Press  (91.771)
  • American Institute of Physics (AIP)  (61.555)
  • International Union of Crystallography
  • Blackwell Publishing Ltd
  • 2020-2023  (55)
  • 2010-2014  (167.686)
  • 1975-1979  (35.679)
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  • 1
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    3-D attenuation image of fluid storage and tectonic interactions across the Pollino fault network (2022)
    Oxford University Press
    Details
    Publikationsdatum: 2022-03-07
    Beschreibung: The Pollino range is a region of slow deformation where earthquakes generally nucleate on low-angle normal faults. Recent studies have mapped fault structures and identified fluid related dynamics responsible for historical and recent seismicity in the area. Here, we apply the coda-normalization method at multiple frequencies and scales to image the 3-D P-wave attenuation (QP) properties of its slowly deforming fault network. The wide-scale average attenuation properties of the Pollino range are typical for a stable continental block, with a dependence of QP on frequency of Q−1 P = (0.0011   0.0008) f (0.36 0.32). Using only waveforms comprised in the area of seismic swarms, the dependence of attenuation on frequency increases [Q−1 P = (0.0373   0.0011) f (−0.59 0.01)], as expected when targeting seismically active faults. A shallow very-low-attenuation anomaly (max depth of 4–5 km) caps the seismicity recorded within the western cluster 1 of the Pollino seismic sequence (2012, maximum magnitude Mw = 5.1). High-attenuation volumes below this anomaly are likely related to fluid storage and comprise the western and northern portions of cluster 1 and the Mercure basin. These anomalies are constrained to the NW by a sharp low-attenuation interface, corresponding to the transition towards the eastern unit of the Apennine Platform under the Lauria mountains. The low-seismicity volume between cluster 1 and cluster 2 (maximum magnitude Mw = 4.3, east of the primary) shows diffuse low-to-average attenuation features. There is no clear indication of fluid-filled pathways between the two clusters resolvable at our resolution. In this volume, the attenuation values are anyway lower than in recognized low-attenuation blocks, like the Lauria Mountain and Pollino Range. As the volume develops in a region marked at surface by small-scale cross-faulting, it suggests no actual barrier between clusters, more likely a system of small locked fault patches that can break in the future. Our model loses resolution at depth, but it can still resolve a 5-to-15-km-deep high-attenuation anomaly that underlies the Castrovillari basin. This anomaly is an ideal deep source for the SE-to-NW migration of historical seismicity. Our novel deep structural maps support the hypothesis that the Pollino sequence has been caused by a mechanism of deep and lateral fluid-induced migration.
    Beschreibung: Natural Environment Research Council (NERC) Centre for Doctoral Training (CDT) in Oil and Gas. University of Aberdeen.
    Beschreibung: Published
    Beschreibung: 536–547
    Beschreibung: 4T. Sismicità dell'Italia
    Beschreibung: JCR Journal
    Schlagwort(e): body waves ; seismic attenuation ; seismic tomography ; 04.06. Seismology
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Sub‐micrometer focusing setup for high‐pressure crystallography at the Extreme Conditions beamline at PETRA III (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publikationsdatum: 2022-06-24
    Beschreibung: Scientific tasks aimed at decoding and characterizing complex systems and processes at high pressures set new challenges for modern X‐ray diffraction instrumentation in terms of X‐ray flux, focal spot size and sample positioning. Presented here are new developments at the Extreme Conditions beamline (P02.2, PETRA III, DESY, Germany) that enable considerable improvements in data collection at very high pressures and small scattering volumes. In particular, the focusing of the X‐ray beam to the sub‐micrometer level is described, and control of the aberrations of the focusing compound refractive lenses is made possible with the implementation of a correcting phase plate. This device provides a significant enhancement of the signal‐to‐noise ratio by conditioning the beam shape profile at the focal spot. A new sample alignment system with a small sphere of confusion enables single‐crystal data collection from grains of micrometer to sub‐micrometer dimensions subjected to pressures as high as 200 GPa. The combination of the technical development of the optical path and the sample alignment system contributes to research and gives benefits on various levels, including rapid and accurate diffraction mapping of samples with sub‐micrometer resolution at multimegabar pressures.
    Beschreibung: Facing the challenges of X‐ray diffraction from tiny samples subjected to multimegabar pressures, instrumentation developments are presented that enable, among other studies, single‐crystal data collection from micrometer‐ to sub‐micrometer‐sized grains. The developments are based on a sub‐micrometer beam capability employing compound refractive lenses operating with a phase correcting plate and a precise motorization solution.
    Schlagwort(e): ddc:548
    Sprache: Englisch
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  • 3
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    Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings (2022)
    Oxford University Press
    Details
    Publikationsdatum: 2022-06-24
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Page, H. N., Bahr, K. D., Cyronak, T., Jewett, E. B., Johnson, M. D., & McCoy, S. J. Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings. Ices Journal of Marine Science, 79(1), (2022): 1–11, https://doi.org/10.1093/icesjms/fsab232.
    Beschreibung: Accurately predicting the effects of ocean and coastal acidification on marine ecosystems requires understanding how responses scale from laboratory experiments to the natural world. Using benthic calcifying macroalgae as a model system, we performed a semi-quantitative synthesis to compare directional responses between laboratory experiments and field studies. Variability in ecological, spatial, and temporal scales across studies, and the disparity in the number of responses documented in laboratory and field settings, make direct comparisons difficult. Despite these differences, some responses, including community-level measurements, were consistent across laboratory and field studies. However, there were also mismatches in the directionality of many responses with more negative acidification impacts reported in laboratory experiments. Recommendations to improve our ability to scale responses include: (i) developing novel approaches to allow measurements of the same responses in laboratory and field settings, and (ii) researching understudied calcifying benthic macroalgal species and responses. Incorporating these guidelines into research programs will yield data more suitable for robust meta-analyses and will facilitate the development of ecosystem models that incorporate proper scaling of organismal responses to in situ acidification. This, in turn, will allow for more accurate predictions of future changes in ecosystem health and function in a rapidly changing natural climate.
    Beschreibung: We would like to thank the Ocean Carbon and Biogeochemistry Program for organizing the fourth U.S. Ocean Acidification Principal Investigators meeting, which is where this synthesis was conceived. HNP was a postdoctoral research fellow at Mote Marine Laboratory. MDJ is a postdoctoral scholar at Woods Hole Oceanographic Institution. SJM is a Norma J. Lang early career fellow of the Phycological Society of America.
    Repository-Name: Woods Hole Open Access Server
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  • 4
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    Spectral elements numerical simulation of the 2009 L’Aquila earthquake on a detailed reconstructed domain (2022)
    Oxford University Press
    Details
    Publikationsdatum: 2022-06-22
    Beschreibung: In this paper we simulate the earthquake that hit the city of L'Aquila on the 6th of April 2009 using SPEED (SPectral Elements in Elastodynamics with Discontinuous Galerkin), an open-source code able to simulate the propagation of seismic waves in complex three-dimensional (3D) domains. Our model includes an accurate 3D recon- struction of the Quaternary deposits, according to the most up-to-date data obtained from the Microzonation studies in Central Italy and a detailed model of the topography incorporated using a newly developed tool (May et al. 2021). The sensitivity of our results with respect to dfferent kinematic seismic sources is inves- tigated. The results obtained are in good agreement with the recordings at the available seismic stations at epicentral distances within a range of 20km. Finally, a blind source prediction scenario application shows a reasonably good agreement between simulations and recordings can be obtained by simulating stochastic rupture realizations with basic input data. These results, although limited to nine simulated scenarios, demonstrate that it is possible to obtain a satisfactory reconstruction of a ground shaking scenario employing a stochastic source constrained on a limited amount of ex-ante information. A similar approach can be used to model future and past earthquakes for which little or no information is typically available, with potential relevant implications for seismic risk assessment.
    Beschreibung: Published
    Beschreibung: 29–49
    Beschreibung: 3T. Fisica dei terremoti e Sorgente Sismica
    Beschreibung: JCR Journal
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Environmental effects and seismogenic source characterization of the December 2020 earthquake sequence near Petrinja, Croatia (2022)
    Oxford University Press
    Details
    Publikationsdatum: 2022-06-22
    Beschreibung: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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.
    Beschreibung: On 29 December 2020, a shallow earthquake of magnitude Mw 6.4 struck northern Croatia, near the town of Petrinja, more than 24 hours after a strong foreshock (Ml 5). We formed a reconnaissance team of European geologists and engineers, from Croatia, Slovenia, France, Italy and Greece, rapidly deployed in the field to map the evidence of coseismic environmental effects. In the epicentral area, we recognized surface deformation, such as tectonic breaks along the earthquake source at the surface, liquefaction features (scattered in the fluvial plains of Kupa, Glina and Sava rivers), and slope failures, both caused by strong motion. Thanks to this concerted, collective and meticulous work, we were able to document and map a clear and unambiguous coseismic surface rupture associated with the main shock. The surface rupture appears discontinuous, consisting of multi-kilometer en échelon right stepping sections, along a NW-SE striking fault that we call the Petrinja-Pokupsko Fault (PPKF). The observed deformation features, in terms of kinematics and trace alignments, are consistent with slip on a right lateral fault, in agreement with the focal solution of the main shock. We found mole tracks, displacement on faults affecting natural features (e. g. drainage channels), scarplets, and more frequently breaks of anthropogenic markers (roads, fences). The surface rupture is observed over a length of ∼13 km from end-to-end, with a maximum displacement of 38 cm, and an average displacement of ∼10 cm. Moreover, the liquefaction extends over an area of nearly 600 km² around the epicenter. Typology of liquefaction features include sand blows, lateral spreading phenomenon along the road and river embankments, as well as sand ejecta of different grain size and matrix. Development of large and long fissures along the fluvial landforms, current or ancient, with massive ejections of sediments is pervasive. These features are sometimes accompanied by small horizontal displacements. Finally, the environmental effects of the earthquake appear to be reasonably consistent with the usual scaling relationships, in particular the surface faulting. This rupture of the ground occurred on or near traces of a fault that shows clear evidence of Quaternary activity. Further and detailed studies will be carried out to characterize this source and related faults in terms of future large earthquakes potential, for their integration into seismic hazard models.
    Beschreibung: Published
    Beschreibung: 1394–1418
    Beschreibung: 2T. Deformazione crostale attiva
    Beschreibung: JCR Journal
    Schlagwort(e): Seismicity and tectonics ; Earthquake hazards ; Coseismic effects ; M6.4 Petrinja earthquake (Croatia)
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Moho depths for Antarctica Region by the inversion of ground-based gravity data (2022)
    Oxford University Press
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    Publikationsdatum: 2022-09-01
    Beschreibung: In the last years the scientific literature has been enriched with new models of the Moho depth in the Antarctica Continent derived by the seismic reflection technique and refraction profiles, receiver functions and seismic surface waves, but also by gravimetric observations over the continent. In particular, the gravity satellite missions of the last two decades have provided data in this remote region of the Earth and have allowed the investigation of the crust properties. Meanwhile, other important contributions in this direction has been given by the fourth International Polar Year (IPY, 2007–2008) which started seismographic and geodetic networks of unprecedented duration and scale, including airborne gravimetry over largely unexplored Antarctic frontiers. In this study, a new model for the Antarctica Moho depths is proposed. This new estimation is based on no satellite gravity measures, thanks to the availability of the gravity database ANTGG2015, that collects gravity data from ground-base, airborne and shipborne campaigns. In this new estimate of the Moho depths the contribution of the gravity measures has been maximized reducing any correction of the gravity measures and avoiding constraints of the solution to seismological observations and to geological evidence. With this approach a pure gravimetric solution has been determined. The model obtained is pretty in agreement with other Moho models and thanks to the use of independent data it can be exploited also for cross-validating different Moho depths solutions.
    Beschreibung: Published
    Beschreibung: 1404–1420
    Beschreibung: 1T. Struttura della Terra
    Beschreibung: JCR Journal
    Schlagwort(e): Antarctica ; Moho ; Gravity inversion ; Collocation ; ANTGG2015
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Distribution of oceanic crust in the Enderby Basin offshore East Antarctica (2022)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 231, pp. 1959-1981
    Details
    Publikationsdatum: 2022-09-16
    Beschreibung: Seismic reflection and refraction data were collected in 2007 and 2012 to reveal the crustal fabric on a single long composite profile offshore Prydz Bay, East Antarctica. A P-wave velocity model provides insights on the crustal fabric, and a gravity-constrained density model is used to describe the crustal and mantle structure. The models show that a 230-km- wide continent–ocean transition separates stretched continental from oceanic crust along our profile. While the oceanic crust close to the continent–ocean boundary is just 3.5–5 km thick, its thickness increases northwards towards the Southern Kerguelen Plateau to 12 km. This change is accompanied by thickening of a lower crustal layer with high P-wave velocities of up to 7.5 km s–1, marking intrusive rocks emplaced beneath the mid-ocean ridge under increasing influence of the Kerguelen plume. Joint interpretations of our crustal model, seismic reflection data and magnetic data sets constrain the age and extent of oceanic crust in the research area. Oceanic crust is shown to continue to around 160 km farther south than has been interpreted in previous data, with profound implications for plate kinematic models of the region. Finally, by combining our findings with a regional magnetic data compilation and regional seismic reflection data we propose a larger extent of oceanic crust in the Enderby Basin than previously known.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 8
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    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity (2022)
    Oxford University Press
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    Publikationsdatum: 2022-10-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.
    Beschreibung: Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
    Beschreibung: This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program.
    Schlagwort(e): Protein evolution ; Domain annotation ; Animal evolution ; Innate immunity
    Repository-Name: Woods Hole Open Access Server
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  • 9
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    Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods (2022)
    Oxford University Press
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    Publikationsdatum: 2022-10-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shoshan, Y., Liscovitch-Brauer, N., Rosenthal, J. J. C., & Eisenberg, E. Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods. Molecular Biology and Evolution, 38(9), (2021): 3775–3788, https://doi.org/10.1093/molbev/msab154.
    Beschreibung: RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
    Beschreibung: This research was supported by a grants from the United States–Israel Binational Science Foundation (BSF), Jerusalem, Israel (BSF2017262 to J.J.C.R. and E.E.), the Israel Science Foundation (3371/20 to E.E.) and the National Science Foundation (IOS 1827509 and 1557748 to J.J.C.R).
    Schlagwort(e): RNA editing ; Adaptation ; Evolution
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 10
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    Interspecific differences in the flow regimes and drag of North Pacific skate egg cases (2022)
    Oxford University Press
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    Publikationsdatum: 2022-10-12
    Beschreibung: Author Posting. © The Author(s), 2022. 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 Integrative & Comparative Biology 62(3), (2022): 805-816, https://doi.org/10.1093/icb/icac108.
    Beschreibung: Skates are a diverse group of dorso-ventrally compressed cartilaginous fish found primarily in high-latitude seas. These slow-growing oviparous fish deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1–4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or “break-away velocity,” each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programing software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.
    Beschreibung: This work was supported by the NSF-REU and FHL Blinks-Beacon for funding JNE. And the Stephen and Ruth Wainwright Endowed Fellowship, BEACON and Hoag Awards, Robert T. Paine Experimental and Field Ecology Award, FHL Award, FHL Marine Science Fund, FHL Student Fund (Kohn), Patricia L. Dudley Endowment for funding KCH.
    Beschreibung: 2023-07-04
    Repository-Name: Woods Hole Open Access Server
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  • 11
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    Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex (2022)
    Oxford University Press
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    Publikationsdatum: 2022-05-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Wiley, D. N., Silva, T. L., Robuck, A. R., Richardson, D. E., Glancy, S. G., Clancey, E., Giandonato, T., Solow, A. R., Thompson, M. A., Hong, P., Baumann, H., Kaufman, L., & Llopiz, J. K. Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex. Ices Journal of Marine Science, 78(3), (2021): 1023–1037, https://doi.org/10.1093/icesjms/fsaa251.
    Beschreibung: Northern sand lance (Ammodytes dubius) and Atlantic herring (Clupea harengus) represent the dominant lipid-rich forage fish species throughout the Northeast US shelf and are critical prey for numerous top predators. However, unlike Atlantic herring, there is little research on sand lance or information about drivers of their abundance. We use intra-annual measurements of sand lance diet, growth, and condition to explain annual variability in sand lance abundance on the Northeast US Shelf. Our observations indicate that northern sand lance feed, grow, and accumulate lipids in the late winter through summer, predominantly consuming the copepod Calanus finmarchicus. Sand lance then cease feeding, utilize lipids, and begin gonad development in the fall. We show that the abundance of C. finmarchicus influences sand lance parental condition and recruitment. Atlantic herring can mute this effect through intra-guild predation. Hydrography further impacts sand lance abundance as increases in warm slope water decrease overwinter survival of reproductive adults. The predicted changes to these drivers indicate that sand lance will no longer be able to fill the role of lipid-rich forage during times of low Atlantic herring abundance—changing the Northeast US shelf forage fish complex by the end of the century.
    Beschreibung: Research was funded by the Bureau of Ocean Energy Management (IA agreement M17PG0019; DNW, LK, HB, and JKL), including a subaward via the National Marine Sanctuary Foundation (18-11-B-203). Additional support came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project No. R/O-57; JKL, HB, and DNW) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship programme. ARR was funded by an NOAA Nancy Foster Scholarship.
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  • 12
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    Inspecting the Reliability of Geochemical Facies Identified for the Waterworks' Capture Zone in Germany (2022)
    Blackwell Publishing Ltd | Malden, US
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    Publikationsdatum: 2022-09-27
    Beschreibung: Little research attention has been given to validating clusters obtained from the groundwater geochemistry of the waterworks' capture zone with a prevailing lake‐groundwater exchange. To address this knowledge gap, we proposed a new scheme whereby Gaussian finite mixture modeling (GFMM) and Spike‐and‐Slab Bayesian (SSB) algorithms were utilized to cluster the groundwater geochemistry while quantifying the probability of the resulting cluster membership against each other. We applied GFMM and SSB to 13 geochemical parameters collected during different sampling periods at 13 observation points across the Barnim Highlands plateau located in the northeast of Berlin, Germany; this included 10 observation wells, two lakes, and a gallery of drinking production wells. The cluster analysis of GFMM yielded nine clusters, either with a probability ≥0.8, while the SSB produced three hierarchical clusters with a probability of cluster membership varying from 〈0.2 to 〉0.8. The findings demonstrated that the clustering results of GFMM were in good agreement with the classification as per the principal component analysis and Piper diagram. By superimposing the parameter clustering onto the observation clustering, we could identify discrepancies that exist among the parameters of a certain cluster. This enables the identification of different factors that may control the geochemistry of a certain cluster, although parameters of that cluster share a strong similarity. The GFMM results have shown that from 2002, there has been active groundwater inflow from the lakes towards the capture zone. This means that it is necessary to adopt appropriate measures to reverse the inflow towards the lakes.
    Beschreibung: Article impact statement: The probability of cluster membership quantified using an algorithm should be validated against another probabilistic‐based classifier.
    Beschreibung: Federal Ministry of Education and Research http://dx.doi.org/10.13039/501100002347
    Schlagwort(e): ddc:551.9 ; ddc:551.49
    Sprache: Englisch
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  • 13
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    Application of mixed‐effects modelling and rule‐based models to explain copper variation in soil profiles of southern Germany (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publikationsdatum: 2022-10-01
    Beschreibung: Copper (Cu) is an essential element for plants and microorganisms and at larger concentrations a toxic pollutant. A number of factors controlling Cu dynamics have been reported, but information on quantitative relationships is scarce. We aimed to (i) quantitatively describe and predict soil Cu concentrations (CuAR) in aqua regia considering site‐specific effects and effects of pH, soil organic carbon (SOC) and cation exchange capacity (CEC), and (ii) study the suitability of mixed‐effects modelling and rule‐based models for the analysis of long‐term soil monitoring data. Thirteen uncontaminated long‐term monitoring soil profiles in southern Germany were analysed. Since there was no measurable trend of increasing CuAR concentrations with time in the respective depth ranges of the sites, data from different sampling dates were combined and horizon‐specific regression analyses including model simplifications were carried out for 10 horizons. Fixed‐ and mixed‐effects models with the site as a random effect were useful for the different horizons and significant contributions (either of main effects or interactions) of SOC, CEC and pH were present for 9, 8 and 7 horizons, respectively. Horizon‐specific rule‐based cubist models described the CuAR data similarly well. Validations of cubist models and mixed‐effects models for the CuAR concentrations in A horizons were successful for the given population after random splitting into calibration and validation samples, but not after independent validations with random splitting according to sites. Overall, site, CEC, SOC and pH provide important information for a description of CuAR concentrations using the different regression approaches. Highlights: Information on quantitative relationships for factors controlling Cu dynamics is scarce. Site, CEC, SOC and pH provide important information for a description of Cu concentrations. Validations of cubist models and mixed‐effects models for A horizons were successful for a closed population of sites.
    Beschreibung: Bavarian State Ministry of the Environment and Consumer Protection http://dx.doi.org/10.13039/501100010219
    Beschreibung: Ministry of Agriculture and Environment Mecklenburg‐Western Pomerania
    Schlagwort(e): ddc:631.4
    Sprache: Englisch
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  • 14
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    Robust approaches for model‐free small‐angle scattering data analysis (2022)
    Bender, Philipp ; Honecker, Dirk ; Bersweiler, Mathias ; [weitere]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publikationsdatum: 2022-10-04
    Beschreibung: The small‐angle neutron scattering data of nanostructured magnetic samples contain information regarding their chemical and magnetic properties. Often, the first step to access characteristic magnetic and structural length scales is a model‐free investigation. However, due to measurement uncertainties and a restricted q range, a direct Fourier transform usually fails and results in ambiguous distributions. To circumvent these problems, different methods have been introduced to derive regularized, more stable correlation functions, with the indirect Fourier transform being the most prominent approach. Here, the indirect Fourier transform is compared with the singular value decomposition and an iterative algorithm. These approaches are used to determine the correlation function from magnetic small‐angle neutron scattering data of a powder sample of iron oxide nanoparticles; it is shown that with all three methods, in principle, the same correlation function can be derived. Each method has certain advantages and disadvantages, and thus the recommendation is to combine these three approaches to obtain robust results.
    Beschreibung: Three different approaches are compared for determination of the correlation function from the small‐angle neutron scattering data of a powder sample of iron oxide nanoparticles.
    Schlagwort(e): ddc:548
    Sprache: Englisch
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  • 15
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    Millimetre scale aeration of the rhizosphere and drilosphere (2022)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2022-10-04
    Beschreibung: Soil aeration is a critical factor for oxygen‐limited subsoil processes, as transport by diffusion and advection is restricted by the long distance to the free atmosphere. Oxygen transport into the soil matrix is highly dependent on its connectivity to larger pore channels like earthworm and root colonised biopores. Here we hypothesize that the soil matrix around biopores represents different connectivity depending on biopore genesis and actual coloniser. We analysed the soil pore system of undisturbed soil core samples around biopores generated or colonised by roots and earthworms and compared them with the pore system of soil, not in the immediacy of a biopore. Oxygen partial pressure profiles and gas relative diffusion was measured in the rhizosphere and drilosphere from the biopore wall into the bulk soil with microelectrodes. The measurements were linked with structural features such as porosity and connectivity obtained from X‐ray tomography and image analysis. Aeration was enhanced in the soil matrix surrounding biopores in comparison to the bulk soil, shown by higher oxygen concentrations and higher relative diffusion coefficients. Biopores colonised by roots presented more connected lateral pores than earthworm colonised ones, which resulted in enhanced aeration of the rhizosphere compared to the drilosphere. This has influenced biotic processes (microbial turnover/mineralization or root respiration) at biopore interfaces and highlights the importance of microstructural features for soil processes and their dependency on the biopore's coloniser.
    Beschreibung: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Schlagwort(e): ddc:631.4
    Sprache: Englisch
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  • 16
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    An alternative method to evaluate earthquake detection from synthetic Wood–Anderson seismograms: an application in Italy (2022)
    Oxford University Press
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    Publikationsdatum: 2022-08-26
    Beschreibung: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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.
    Beschreibung: Defining the regional variability of minimum magnitude for earthquake detection is crucial for planning seismic networks. Knowing the earthquake detection magnitude values is fundamental for the optimal location of new stations and to select the priority for reactivating the stations of a seismic network in case of a breakdown. In general, the assessment of earthquake detection is performed by analysing seismic noise with spectral or more sophisticated methods. Further, to simulate amplitude values at the recording sites, spectral methods require knowledge of several geophysical parameters including rock density, S-wave velocity, corner frequency, quality factor, site specific decay parameter and so on, as well as a velocity model for the Earth's interior. The simulation results are generally expressed in terms of Mw and therefore a further conversion must be done to obtain the values of local magnitude (ML), which is the parameter commonly used for moderate and small earthquakes in seismic catalogues. Here, the relationship utilized by a seismic network to determine ML is directly applied to obtain the expected amplitude [in mm, as if it were recorded by a Wood–Anderson (WA) seismometer] at the recording site, without any additional assumptions. The station detection estimates are obtained by simply considering the ratio of the expected amplitude with respect to the background noise, also measured in mm. The seismic noise level for the station is estimated starting from four waveforms (each signal lasting 1 min) sampled at various times of the day for a period of one week. The proposed method is tested on Italian seismic events occurring in 2019 by using the locations of 16.879 earthquakes recorded by 374 stations. The first results indicate that by evaluating the station noise level with 5-s windows, a representative sample of the variability in expected noise level is generated for every station, even if only 4 min of signal per day over a week of recordings is used. The method was applied to define the detection level of the Italian National Seismic Network (RSN). The RSN detection level represents a reference for the definition and application of guidelines in the field of monitoring of subsurface industrial activities in Italy. The proposed approach can be successfully applied to define the current performance of a local seismic network (managed by private companies) and to estimate the expected further improvements, requested to fulfil the guidelines with the installation of new seismic stations. This method has been tested in Italy and can be reproduced wherever the local magnitude ML, based on synthetic WA records, is used.
    Beschreibung: Published
    Beschreibung: 1283–1297
    Beschreibung: 4T. Sismicità dell'Italia
    Beschreibung: JCR Journal
    Schlagwort(e): Time-series analysis ; Earthquake ground motions ; Seismic noise ; Induced seismicity ; 04.06. Seismology ; 05.04. Instrumentation and techniques of general interest
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 17
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    Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches (2022)
    Oxford University Press
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    Publikationsdatum: 2022-08-19
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aoki, L. R., Brisbin, M. M., Hounshell, A. G., Kincaid, D. W., Larson, E., Sansom, B. J., Shogren, A. J., Smith, R. S., & Sullivan-Stack, J. Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches. Bioscience, 72(6), (2022): 508-520, https://doi.org/10.1093/biosci/biac020.
    Beschreibung: Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre- and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.
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  • 18
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    Structure determination from unindexed powder data from scratch by a global optimization approach using pattern comparison based on cross‐correlation functions (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2022-06-16
    Beschreibung: A method of ab initio crystal structure determination from powder diffraction data for organic and metal–organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit‐cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL‐GO (`FIt with DEviating Lattice parameters ‐ Global Optimization'). FIDEL‐GO uses a similarity measure based on cross‐correlation functions, which allows the comparison of simulated and experimental powder data even if the unit‐cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit‐cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi‐step procedure with built‐in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user‐controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11‐difluoro‐, 2,9‐dichloro‐ and 2,9‐dichloro‐6,13‐dihydro‐quinacridone, which were solved from powder patterns with 14–20 peaks only, and of the coordination polymer dichloro‐bis(pyridine‐N)copper(II).
    Beschreibung: A new method for the structure determination of molecular crystals from unindexed powder data has been developed and successfully applied. The method performs a global optimization using pattern comparison based on cross‐correlation functions.
    Schlagwort(e): ddc:548
    Sprache: Englisch
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  • 19
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    Response of subsoil organic matter contents and physical properties to long‐term, high‐rate farmyard manure application (2022)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2022-07-26
    Beschreibung: Application of farmyard manure (FYM) is common practice to improve physical and chemical properties of arable soil and crop yields. However, studies on effects of FYM application mainly focussed on topsoils, whereas subsoils have rarely been addressed so far. We, therefore, investigated the effects of 36‐year FYM application with different rates of annual organic carbon (OC) addition (0, 469, 938 and 1875 g C m−2 a−1) on OC contents of a Chernozem in 0–30 cm (topsoil) and 35–45 cm (subsoil) depth. We also investigated its effects on soil structure and hydraulic properties in subsoil. X‐ray computed tomography was used to analyse the response of the subsoil macropore system (≥19 μm) and the distribution of particulate organic matter (POM) to different FYM applications, which were related to contents in total OC (TOC) and water‐extractable OC (WEOC). We show that FYM‐C application of 469 g C m−2 a−1 caused increases in TOC and WEOC contents only in the topsoil, whereas rates of ≥938 g C m−2 a−1 were necessary for TOC enrichment also in the subsoil. At this depth, the subdivision of TOC into different OC sources shows that most of the increase was due to fresh POM, likely by the stimulation of root growth and bioturbation. The increase in subsoil TOC went along with increases in macroporosity and macropore connectivity. We neither observed increases in plant‐available water capacity nor in unsaturated hydraulic conductivity. In conclusion, only very high application of FYM over long periods can increase OC content of subsoil at our study site, but this increase is largely based on fresh, easily degradable POM and likely accompanied by high C losses when considering the discrepancy between OC addition rate by FYM and TOC response in soil. Highlights A new image processing procedure to distinguish fresh and decomposed POM. The increase of subsoil C stock based to a large extend on fresh, labile POM. Potential of arable subsoils for long‐term C storage by large FYM application rates is limited. The increase in TOC has no effect on hydraulic properties of the subsoil.
    Beschreibung: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Schlagwort(e): ddc:631.4
    Sprache: Englisch
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  • 20
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    Site dependence of the magnetocaloric effect in Mn5−xFexSi3 (2022)
    Ait Haddouch, Mohammed ; Abboushi, Nour ; Sharma, Neetika ; [weitere]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2022-12-06
    Beschreibung: The nuclear and magnetic structures of Mn3Fe2Si3 are investigated in the temperature range from 20 to 300 K. The magnetic properties of Mn3Fe2Si3 were measured on a single crystal. The compound undergoes a paramagnetic to antiferromagnetic transition at TN2 ≃ 120 K and an antiferromagnetic to antiferromagnetic transition at TN1 ≃ 69 K. A similar sequence of magnetic phase transitions is found for the parent compound Mn5Si3 upon temperature variation, but the field‐driven transition observed in Mn5Si3 is not found in Mn3Fe2Si3, resulting in a strongly reduced magnetocaloric effect. Structurally, the hexagonal symmetry found for both compounds under ambient conditions is preserved in Mn3Fe2Si3 through both magnetic transitions, indicating that the crystal structure is only weakly affected by the magnetic phase transition, in contrast to Mn5Si3 where both transitions distort the nuclear structure. Both compounds feature a collinear high‐temperature magnetic phase AF2 and transfer into a non‐collinear phase AF1 at low temperature. While one of the distinct crystallographic sites remains disordered in the AF2 phase in the parent compound, the magnetic structure in the AF2 phase involves all magnetic atoms in Mn3Fe2Si3. These observations imply that the distinct sites occupied by the magnetic atoms play an important role in the magnetocaloric behaviour of the family.
    Beschreibung: The nuclear and magnetic structures of Mn3Fe2Si3 are determined and the magnetic properties are compared with those of the parent compound Mn5Si3. The results imply that the distinct magnetic sites play an important role in the magnetocaloric behaviour of the family. image
    Schlagwort(e): ddc:548 ; magnetocaloric effect ; magnetic structure ; neutron diffraction ; synchrotron diffraction ; site dependence
    Sprache: Englisch
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  • 21
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    Environmental drivers and trends in forage fish occupancy of the Northeast US shelf (2022)
    Oxford University Press
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    Publikationsdatum: 2022-05-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Deroba, J. J., Richardson, D. E., Ji, R., & Llopiz, J. K. Environmental drivers and trends in forage fish occupancy of the Northeast US shelf. Ices Journal of Marine Science, 78(10), (2021): 3687–3708, https://doi.org/10.1093/icesjms/fsab214.
    Beschreibung: The Northeast US shelf ecosystem is undergoing unprecedented changes due to long-term warming trends and shifts in regional hydrography leading to changes in community composition. However, it remains uncertain how shelf occupancy by the region's dominant, offshore small pelagic fishes, also known as forage fishes, has changed throughout the late 20th and early 21st centuries. Here, we use species distribution models to estimate the change in shelf occupancy, mean weighted latitude, and mean weighted depth of six forage fishes on the Northeast US shelf, and whether those trends were linked to coincident hydrographic conditions. Our results suggest that observed shelf occupancy is increasing or unchanging for most species in both spring and fall, linked both to gear shifts and increasing bottom temperature and salinity. Exceptions include decreases to observed shelf occupancy by sand lance and decreases to Atlantic herring's inferred habitat suitability in the fall. Our work shows that changes in shelf occupancy and inferred habitat suitability have varying coherence, indicating complex mechanisms behind observed shelf occupancy for many species. Future work and management can use these results to better isolate the aspects of forage fish life histories that are important for determining their occupancy of the Northeast US shelf.
    Beschreibung: Funding came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project number R/O-57; RJ and JKL) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE1655686; RJ and JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship program.
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  • 22
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    Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland) (2022)
    Oxford University Press
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    Publikationsdatum: 2022-10-28
    Beschreibung: Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a relocation strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide on horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area.
    Beschreibung: Published
    Beschreibung: 1244–1257
    Beschreibung: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Beschreibung: JCR Journal
    Schlagwort(e): Physics - Geophysics; Physics - Geophysics
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 23
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    Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations (2022)
    Oxford University Press
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    Publikationsdatum: 2022-11-10
    Beschreibung: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sassenhagen, I., Erdner, D., Lougheed, B., Richlen, M., & SjÖqvist, C. Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations. Journal of Plankton Research, 44(4), (2022): 559-572, https://doi.org/10.1093/plankt/fbac034.
    Beschreibung: The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (〈5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.
    Beschreibung: This work was supported by the Olle Engkvist foundation [200-0564 to I.S.]; the Swedish Research Council (Vetenskapsrådet) [2018-04992 to B.C.L.]; the Academy of Finland [321609 to C.S.]; the National Science Foundation [NSF OCE-1841811 to D.L.E. and M.L.R.]; and the National Institute of Environmental Health [NIEHS P01ES028949 to M.L.R.].
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  • 24
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    HTD2: a single‐crystal X‐ray diffractometer for combined high‐pressure/low‐temperature experiments at laboratory scale (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2022-12-15
    Beschreibung: High‐pressure (HP) X‐ray diffraction experiments at low temperature (LT) require dedicated instruments as well as non‐standard sample environments and measuring strategies. This is especially true when helium cryogenic temperatures below 80 K are targeted. Furthermore, only experiments on single‐crystalline samples provide the prerequisites to study subtle structural changes in the p–T phase diagram under extreme LT and HP conditions in greater detail. Due to special hardware requirements, such measurements are usually in the realm of synchrotron beamlines. This contribution describes the design of an LT/HP diffractometer (HTD2) to perform single‐crystal X‐ray diffraction experiments using a laboratory source in the temperature range 400 〉 T 〉 2 K while applying pressures of up to 20 GPa.
    Beschreibung: The design and operation of a newly commissioned single‐crystal X‐ray diffractometer (HTD2) are presented. The device enables experiments under simultaneous low‐temperature and high‐pressure conditions using a laboratory X‐ray source.
    Schlagwort(e): ddc:548 ; HTD2 ; low temperature ; high pressure ; single crystals ; instrumentation
    Sprache: Englisch
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  • 25
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    On incoherent diffractive imaging (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2022-04-07
    Beschreibung: Incoherent diffractive imaging (IDI) promises structural analysis with atomic resolution based on intensity interferometry of pulsed X‐ray fluorescence emission. However, its experimental realization is still pending and a comprehensive theory of contrast formation has not been established to date. Explicit expressions are derived for the equal‐pulse two‐point intensity correlations, as the principal measured quantity of IDI, with full control of the prefactors, based on a simple model of stochastic fluorescence emission. The model considers the photon detection statistics, the finite temporal coherence of the individual emissions, as well as the geometry of the scattering volume. The implications are interpreted in view of the most relevant quantities, including the fluorescence lifetime, the excitation pulse, as well as the extent of the scattering volume and pixel size. Importantly, the spatiotemporal overlap between any two emissions in the sample can be identified as a crucial factor limiting the contrast and its dependency on the sample size can be derived. The paper gives rigorous estimates for the optimum sample size, the maximum photon yield and the expected signal‐to‐noise ratio under optimal conditions. Based on these estimates, the feasibility of IDI experiments for plausible experimental parameters is discussed. It is shown in particular that the mean number of photons per detector pixel which can be achieved with X‐ray fluorescence is severely limited and as a consequence imposes restrictive constraints on possible applications.
    Beschreibung: Starting from a simple model of stochastic fluorescence emission, a theory is derived of contrast formation and signal‐to‐noise ratio for incoherent diffractive imaging; its feasibility for plausible experimental parameters is discussed. image
    Schlagwort(e): ddc:548
    Sprache: Englisch
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  • 26
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    How to Find Aquifer Statistics Utilizing Pumping Tests? Two Field Studies Using welltestpy (2021)
    Blackwell Publishing Ltd | Malden, US
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    Publikationsdatum: 2022-04-01
    Beschreibung: We present a workflow to estimate geostatistical aquifer parameters from pumping test data using the Python package welltestpy. The procedure of pumping test analysis is exemplified for two data sets from the Horkheimer Insel site and from the Lauswiesen site, Germany. The analysis is based on a semi‐analytical drawdown solution from the upscaling approach Radial Coarse Graining, which enables to infer log‐transmissivity variance and horizontal correlation length, beside mean transmissivity, and storativity, from pumping test data. We estimate these parameters of aquifer heterogeneity from type‐curve analysis and determine their sensitivity. This procedure, implemented in welltestpy, is a template for analyzing any pumping test. It goes beyond the possibilities of standard methods, for example, based on Theis' equation, which are limited to mean transmissivity and storativity. A sensitivity study showed the impact of observation well positions on the parameter estimation quality. The insights of this study help to optimize future test setups for geostatistical aquifer analysis and provides guidance for investigating pumping tests with regard to aquifer statistics using the open‐source software package welltestpy.
    Beschreibung: Article impact statement: We present a workflow to infer parameters of subsurface heterogeneity from pumping test data exemplified at two sites using welltestpy.
    Beschreibung: German Federal Environmental Foundation (DBU) http://dx.doi.org/10.13039/100007636
    Schlagwort(e): ddc:551.49
    Sprache: Englisch
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  • 27
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    Importance of sources of variability, scales and experimental design: A case study about the effects of biochar and slurry application on soil properties in agricultural silty loam soils (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publikationsdatum: 2022-04-01
    Beschreibung: In designed experiments, different sources of variability and an adequate scale of measurement need to be considered, but not all approaches in common usage are equally valid. In order to elucidate the importance of sources of variability and choice of scale, we conducted an experiment where the effects of biochar and slurry applications on soil properties related to soil fertility were studied for different designs: (a) for a field‐scale sampling design with either a model soil (without natural variability) as an internal control or with composited soils, (b) for a design with a focus on amendment variabilities, and (c) for three individual field‐scale designs with true field replication and a combined analysis representative of the population of loess‐derived soils. Three silty loam sites in Germany were sampled and the soil macroaggregates were crushed. For each design, six treatments (0, 0.15 and 0.30 g slurry‐N kg−1 with and without 30 g biochar kg−1) were applied before incubating the units under constant soil moisture conditions for 78 days. CO2 fluxes were monitored and soils were analysed for macroaggregate yields and associated organic carbon (C). Mixed‐effects models were used to describe the effects. For all soil properties, results for the loess sites differed with respect to significant contributions of fixed effects for at least one site, suggesting the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils to be made and showed that site:slurry:biochar and site:slurry interactions were not negligible for macroaggregate yields. The use of a model soil as an internal control enabled observation of variabilities other than those related to soils or amendments. Experiments incorporating natural variability in soils or amendments resulted in partially different outcomes, indicating the need to include all important sources of variability. Highlights Effects of biochar and slurry applications were studied for different designs and mixed‐effects models were used to describe the effects. Including an internal control allowed observation of, e.g., methodological and analytical variabilities. The results suggested the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils. The results indicated the need to include all important sources of variability.
    Schlagwort(e): ddc:631.4
    Sprache: Englisch
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  • 28
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    Do tree species affect decadal changes in soil organic carbon and total nitrogen stocks in Danish common garden experiments? (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publikationsdatum: 2022-04-01
    Beschreibung: Temperate forest soils are often considered as an important sink for atmospheric carbon (C), thereby buffering anthropogenic CO2 emissions. However, the effect of tree species composition on the magnitude of this sink is unclear. We resampled a tree species common garden experiment (six sites) a decade after initial sampling to evaluate whether forest floor (FF) and topsoil organic carbon (Corg) and total nitrogen (Nt) stocks changed in dependence of tree species (Norway spruce—Picea abies L., European beech—Fagus sylvatica L., pedunculate oak—Quercus robur L., sycamore maple—Acer pseudoplatanus L., European ash—Fraxinus excelsior L. and small‐leaved lime—Tilia cordata L.). Two groups of species were identified in terms of Corg and Nt distribution: (1) Spruce with high Corg and Nt stocks in the FF developed as a mor humus layer which tended to have smaller Corg and Nt stocks and a wider Corg:Nt ratio in the mineral topsoil, and (2) the broadleaved species, of which ash and maple distinguished most clearly from spruce by very low Corg and Nt stocks in the FF developed as mull humus layer, had greater Corg and Nt stocks, and narrow Corg:Nt ratios in the mineral topsoil. Over 11 years, FF Corg and Nt stocks increased most under spruce, while small decreases in bulk mineral soil (esp. in 0–15 cm and 0–30 cm depth) Corg and Nt stocks dominated irrespective of species. Observed decadal changes were associated with site‐related and tree species‐mediated soil properties in a way that hinted towards short‐term accumulation and mineralisation dynamics of easily available organic substances. We found no indication for Corg stabilisation. However, results indicated increasing Nt stabilisation with increasing biomass of burrowing earthworms, which were highest under ash, lime and maple and lowest under spruce. Highlights We studied if tree species differences in topsoil Corg and Nt stocks substantiate after a decade. The study is unique in its repeated soil sampling in a multisite common garden experiment. Forest floors increased under spruce, but topsoil stocks decreased irrespective of species. Changes were of short‐term nature. Nitrogen was most stable under arbuscular mycorrhizal species.
    Beschreibung: Deutsche Forschungsgemeinschaff (DFG)
    Schlagwort(e): ddc:551.9 ; ddc:631.41
    Sprache: Englisch
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  • 29
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    Natural Radioactivity of the Crystalline Basement Rocks of the Peloritani Mountains (North-Eastern Sicily, Italy): Measurements and Radiological Hazard (2021)
    Oxford University Press
    Details
    Publikationsdatum: 2022-03-02
    Beschreibung: Crystalline rocks can produce dangerous radiation levels on the basis of their content in radioisotopes. Here, we report radiological data from 10 metamorphic and igneous rock samples collected from the crystalline basement of the Peloritani Mountains (southern Italy). In order to evaluate the radiological properties of these rocks, the gamma radiation and the radon emanation have been measured. Moreover, since some of these rocks are employed as building materials, we assess the potential hazard for population connected to their use. Gamma spectroscopy was used to measure the 226Ra, 232Th and 40K activity concentration, whereas the radon emanation was investigated by using a RAD 7 detector. The results show 226Ra, 232Th and 40K activity concentration values ranging from (17 ± 4) to (56 ± 8) Bq kg-1, (14 ± 3) to (77 ± 14) Bq kg-1 and (167 ± 84) to (1760 ± 242) Bq kg-1, respectively. Values of the annual effective dose equivalent outdoor range from 0.035 to 0.152 mSv y-1, whereas the gamma index is in the range of 0.22-0.98. The 222Rn emanation coefficient and the 222Rn surface exhalation rate vary from (0.63 ± 0.3) to (8.27 ± 1.6)% and from (0.12 ± 0.03) to (2.75 ± 0.17) Bq m-2 h-1, respectively. The indoor radon derived from the building use of these rocks induces an approximate contribution to the annual effective dose ranging from 8 to 176 μSv y-1. All the obtained results suggest that the crystalline rocks from the Peloritani Mountains are not harmful for the residential population, even though they induce annual effective doses due to terrestrial gamma radiation above the worldwide average values. Moreover, their use as building materials does not produce significant health hazards connected to the indoor radon exposure.
    Beschreibung: Published
    Beschreibung: 452–464
    Beschreibung: 6A. Geochimica per l'ambiente e geologia medica
    Beschreibung: JCR Journal
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 30
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    Transfer learning: Improving neural network based prediction of earthquake ground shaking for an area with insufficient training data (2021)
    Oxford University Press
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    Publikationsdatum: 2022-03-16
    Beschreibung: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. 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.
    Beschreibung: In a recent study (Jozinovi\'c et al, 2020) we showed that convolutional neural networks (CNNs) applied to network seismic traces can be used for rapid prediction of earthquake peak ground motion intensity measures (IMs) at distant stations using only recordings from stations near the epicenter. The predictions are made without any previous knowledge concerning the earthquake location and magnitude. This approach differs from the standard procedure adopted by earthquake early warning systems (EEWSs) that rely on location and magnitude information. In the previous study, we used 10 s, raw, multistation waveforms for the 2016 earthquake sequence in central Italy for 915 events (CI dataset). The CI dataset has a large number of spatially concentrated earthquakes and a dense station network. In this work, we applied the CNN model to an area around the VIRGO gravitational waves observatory sited near Pisa, Italy. In our initial application of the technique, we used a dataset consisting of 266 earthquakes recorded by 39 stations. We found that the CNN model trained using this smaller dataset performed worse compared to the results presented in the original study by Jozinovi\'c et al. (2020). To counter the lack of data, we adopted transfer learning (TL) using two approaches: first, by using a pre-trained model built on the CI dataset and, next, by using a pre-trained model built on a different (seismological) problem that has a larger dataset available for training. We show that the use of TL improves the results in terms of outliers, bias, and variability of the residuals between predicted and true IMs values. We also demonstrate that adding knowledge of station positions as an additional layer in the neural network improves the results. The possible use for EEW is demonstrated by the times for the warnings that would be received at the station PII.
    Beschreibung: RISE (Union's Horizon 2020 research and innovation programme, grant agreement No.821115)
    Beschreibung: Published
    Beschreibung: 704–718
    Beschreibung: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Beschreibung: JCR Journal
    Schlagwort(e): Physics - Geophysics; Physics - Geophysics ; machine learning ; ground motion prediction ; seismology
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 31
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    Azimuthal anisotropy from Eikonal Tomography: example from ambient-noise measurements in the AlpArray network (2021)
    Oxford University Press
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    Publikationsdatum: 2021-12-24
    Beschreibung: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. 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.
    Beschreibung: Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150,000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the Eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wavefronts that affect the phase travel-time measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the travel-time field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at midcrustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E-W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
    Beschreibung: German Science Foundation (SPP-2017, Project Ha 2403/21-1); Swiss National Science Foundation SINERGIA Project CRSII2-154434/1 (Swiss-AlpArray); Progetto Pianeta Dinamico, finanziamento MUR-INGV, Task S2 – 2021
    Beschreibung: Published
    Beschreibung: 151–170
    Beschreibung: 1T. Struttura della Terra
    Beschreibung: JCR Journal
    Schlagwort(e): Seismic anisotropy ; Seismic interferometry ; Seismic tomography ; Wave propagation ; Continental tectonics: compressional ; 04.01. Earth Interior ; 04.06. Seismology
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    The focal mechanism of the 7 September 1920, Mw 6.5 earthquake: insights into the seismotectonics of the Lunigiana–Garfagnana area, Tuscany, Italy (2021)
    Oxford University Press
    Details
    Publikationsdatum: 2021-12-15
    Beschreibung: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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.
    Beschreibung: To understand the seismotectonics and the seismic hazard of the study sector of the Northern Apennines (Italy), one of the most important earthquakes of magnitude Mw = 6.5 which struck the Lunigiana and Garfagnana areas (Tuscany) on 7 September 1920 should be studied. Given the early instrumental epoch of the event, neither geometric and kinematic information on the fault-source nor its fault-plane solution were available. Both areas were candidates for hosting the source fault and there was uncertainty between a normal fault with Apenninic direction or an anti-Apenninic strike-slip. We retrieved 11 focal parameters (including the fault-plane solution) of the 1920 earthquake. Only macroseismic intensity information (from 499 inhabited centres) through the KF-NGA inversion technique was used. This technique uses a Kinematic model of the earthquake source and speeds up the calculation by a Genetic Algorithm with Niching. The result is a pure dip-slip focal solution. The intrinsic ambiguities of the KF-NGA method (±180° on the rake angle; choice of the fault plane between the two nodal planes) were solved with field and seismotectonic evidence. The earthquake was generated by a normal fault (rake angle = 265° ± 8°) with an Apennine direction (114° ± 5°) and dipping 38° ± 6° towards SW. The likely candidate for hosting the source-fault in 1920 is the Compione-Comano fault that borders the NE edge of the Lunigiana graben. The KF-NGA algorithm proved to be invaluable for studying the kinematics of early instrumental earthquakes and allowed us to uniquely individuate, for the first time ever, the seismogenic source of the 1920 earthquake. Our findings have implications in hazard computation and seismotectonic contexts.
    Beschreibung: Published
    Beschreibung: 1465–1477
    Beschreibung: 4T. Sismicità dell'Italia
    Beschreibung: JCR Journal
    Schlagwort(e): Inverse theory ; Body waves ; Earthquake source observations ; Seismicity and tectonics ; Dynamics: seismotectonics ; Fractures, faults, and high strain deformation zones ; 04.06. Seismology
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 33
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    Intraplate Basalt Alkalinity Modulated by a Lithospheric Mantle Filter at the Dunedin Volcano (New Zealand) (2021)
    Oxford University Press
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    Publikationsdatum: 2021-12-22
    Beschreibung: Systematic variations in the crystal cargo and whole-rock isotopic compositions of mantle-derived basalts in the intraplate Dunedin Volcano (New Zealand) indicate the influence of a complex mantle-to-crust polybaric plumbing system. Basaltic rocks define a compositional spectrum from low-alkali basalts through mid-alkali basalts to high-alkali basalts. High-alkali basalts display clinopyroxene crystals with sector (hourglass) and oscillatory zoning (Mg#61–82) as well as Fe-rich green cores (Mg#43–69), whereas low-alkali basalts are characterized by clinopyroxenes with unzoned overgrowths (Mg#69–83) on resorbed mafic cores (Mg#78–88), coexisting with reversely zoned plagioclase crystals (An43–68 to An60–84 from core to rim). Complex magma dynamics are indicated by distinctive compositional variations in clinopyroxene phenocrysts, with Cr-rich zones (Mg#74–87) indicating continuous recharge by more mafic magmas. Crystallization of olivine, clinopyroxene and titanomagnetite occurred within a polybaric plumbing system extending from upper mantle to mid-crustal depths (485–1059 MPa and 1147–1286°C), whereas crystallization of plagioclase with subordinate clinopyroxene and titanomagnetite proceeded towards shallower crustal levels. The compositions of high-alkali basalts and mid-alkali basalts resemble those of ocean island basalts and are characterized by FOZO-HIMU isotopic signatures (87Sr/86Sri = 0.70277–0.70315, 143Nd/144Ndi = 0.51286–0.51294 and 206Pb/204Pb = 19.348–20.265), whereas low-alkali basalts have lower incompatible element abundances and isotopic compositions trending towards EMII (87Sr/86Sri = 0.70327–70397, 143Nd/144Ndi = 0.51282–0.51286 and 206Pb/204Pb = 19.278–19.793). High- and mid-alkali basalt magmas mostly crystallized in the lower crust, whereas low-alkali basalt magma recorded deeper upper mantle clinopyroxene crystallization before eruption. The variable alkaline character and isotope composition may result from interaction of low-alkaline melts derived from the asthenosphere with melts derived from lithospheric mantle, possibly initiated by asthenospheric melt percolation. The transition to more alkaline compositions was induced by variable degrees of melting of metasomatic lithologies in the lithospheric mantle, leading to eruption of predominantly small-volume, high-alkali magmas at the periphery of the volcano. Moreover, the lithosphere imposed a filtering effect on the alkalinity of these intraplate magmas. As a consequence, the eruption of low-alkali basalts with greater asthenospheric input was concentrated at the centre of the volcano, where the plumbing system was more developed.
    Beschreibung: Published
    Beschreibung: egab062
    Beschreibung: 2V. Struttura e sistema di alimentazione dei vulcani
    Beschreibung: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Beschreibung: 4V. Processi pre-eruttivi
    Beschreibung: JCR Journal
    Schlagwort(e): alkali basalts ; Dunedin Volcano ; thermobarometry ; primary magma ; lithospheric mantle filter ; Igneous Petrology ; Thermobarometry ; Mantle melting and metasomatism ; Magmatic plumbing systems
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172 (2021)
    Oxford University Press
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    Publikationsdatum: 2022-05-27
    Beschreibung: Author Posting. © Oxford University Press, 2021. This article is posted here by permission of [publisher] for personal use, not for redistribution. The definitive version was published in Lund, S., Acton, G., Clement, B., Okada, M., & Keigwin, L. On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172. Geophysical Journal International, 225(2), (2021): 1129-1141, https://doi.org/10.1093/gji/ggaa564.
    Beschreibung: Palaeomagnetic secular variation (PSV) and excursion data obtained across MIS 8 (243–300 ka) from the western North Atlantic Ocean ODP (Ocean Drilling Program) sites 1060–1063 show composite high-resolution PSV records (both directions and relative palaeointensity) developed for each site and intercompared. Two methods of chronostratigraphy allow us to date these records. First, we used published results that compared the calcium carbonate records of ODP Leg 172 sediments and tuned them with Milankovich cyclicity. We also compared our palaeointensity records with the PISO-1500 global palaeointensity record that was dated with oxygen isotope stratigraphy. We prefer the PISO-1500 record to date our cores. Two excursions are preserved in our PSV records—Excursions 8α and 9α. Our revised age estimates for both excursions are 8α (236.7–239.8 ka) and 9α (283.7–286.9 ka). We have compared shipboard measurements of the two excursions with u-channel measurements of selected excursion intervals. Excursion 8α is interpreted as a ‘Class II’ excursion (local reversal) with in-phase inclination and declination changes; Excursion 9α is a ‘Class I’ excursion with 90° out-of-phase inclination and declination changes. Averaged directions (after removal of true excursional directions) and relative palaeointensity in 3 and 9 ka overlapping intervals show significant PSV directional variability over 104 yr timescales that is regionally correlatable among the four sites. A notable pattern of angular dispersion variability involves most time spent with low (∼10°) dispersion, with three shorter intervals of high (∼25°) dispersion. The relative palaeointensity variability also shows significant variability over 104 yr timescales with three notable intervals of low palaeointensity in all four records and a direct correspondence between the three low-palaeointensity intervals and the three intervals of high angular dispersion. The two magnetic field excursions occur in two of the three low-palaeointensity/high-dispersion intervals. This suggests that the geomagnetic field operates in two states between reversals, one with regular to high palaeointensity and low directional variability and one with low palaeointensity and significantly higher directional variability and excursions.
    Schlagwort(e): Geomagnetic excursions ; Palaeointensity ; Palaeomagnetic secular variation
    Repository-Name: Woods Hole Open Access Server
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  • 35
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    Urban pluvial flood adaptation: Results of a household survey across four German municipalities (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2022-09-30
    Beschreibung: In recent years, German cities were heavily impacted by pluvial flooding and related damage is projected to increase due to climate change and urbanisation. It is important to ask how to improve urban pluvial flood risk management. To understand the current state of property level adaptation, a survey was conducted in four municipalities that had recently been impacted by pluvial flooding. A hybrid framework based on the Protection Motivation Theory (PMT) and the Protection Action Decision Model (PADM) was used to investigate drivers of adaptive behaviour through both descriptive and regression analyses. Descriptive statistics revealed that participants tended to instal more low‐ and medium‐cost measures than high‐cost measures. Regression analyses showed that coping appraisal increased protection motivation, but that the adaptive behaviour also depends on framing factors, particularly homeownership. We further found that, while threat appraisal solely affects protection motivation and responsibility appraisal affects solely maladaptive thinking, coping appraisal affects both. Our results indicate that PMT is a solid starting point to study adaptive behaviours in the context of pluvial flooding, but we need to go beyond that by, for instance, considering factors of the PADM, such as responsibility, ownership, or respondent age, to fully understand this complex decision‐making process.
    Beschreibung: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Schlagwort(e): ddc:551.489 ; ddc:363.34
    Sprache: Englisch
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  • 36
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    Developmental exposure to domoic acid disrupts startle response behavior and circuitry in zebrafish (2021)
    Oxford University Press
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    Publikationsdatum: 2022-06-07
    Beschreibung: Author Posting. © The Author(s), 2021. 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 Toxicological Sciences 182(20), (2021): 310-326, https://doi.org/10.1093/toxsci/kfab066.
    Beschreibung: Harmful algal blooms produce potent neurotoxins that accumulate in seafood and are hazardous to human health. Developmental exposure to the harmful algal bloom toxin, domoic acid (DomA), has behavioral consequences well into adulthood, but the cellular and molecular mechanisms of DomA developmental neurotoxicity are largely unknown. To assess these, we exposed zebrafish embryos to DomA during the previously identified window of susceptibility and used the well-known startle response circuit as a tool to identify specific neuronal components that are targeted by exposure to DomA. Exposure to DomA reduced startle responsiveness to both auditory/vibrational and electrical stimuli, and even at the highest stimulus intensities tested, led to a dramatic reduction of one type of startle (short-latency c-starts). Furthermore, DomA-exposed larvae had altered kinematics for both types of startle responses tested, exhibiting shallower bend angles and slower maximal angular velocities. Using vital dye staining, immunolabeling, and live imaging of transgenic lines, we determined that although the sensory inputs were intact, the reticulospinal neurons required for short-latency c-starts were absent in most DomA-exposed larvae. Furthermore, axon tracing revealed that DomA-treated larvae also showed significantly reduced primary motor neuron axon collaterals. Overall, these results show that developmental exposure to DomA targets large reticulospinal neurons and motor neuron axon collaterals, resulting in measurable deficits in startle behavior. They further provide a framework for using the startle response circuit to identify specific neural populations disrupted by toxins or toxicants and to link these disruptions to functional consequences for neural circuit function and behavior.
    Beschreibung: This research was supported by a WHOI Von Damm and Ocean Ridge Initiative Fellowships to J.M.P. and the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381).
    Beschreibung: 2022-06-07
    Schlagwort(e): domoic acid ; harmful algal blooms ; harmful algal bloom toxins ; developmental toxicity ; startle response ; escape response ; startle circuit
    Repository-Name: Woods Hole Open Access Server
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    Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands (2021)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands. Bioscience, 70(12), (2020): 1108-1119, doi:10.1093/biosci/biaa140.
    Beschreibung: Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.
    Beschreibung: This work was supported by the following funding sources: National Science Foundation (NSF) grant no. DEB 1902712 to LAD, JLB, DSJ, and TJM; NSF grant no. DEB 1902695 to AEG; NSF grant no. DEB 1902704 to JAN; NSF grant no. DEB 1354214 to TJM; NSF grant no. DEB 1350491 to JLB; NSF grant no. OCE 1637630 to AEG and LAD; and additional funding from the Dorr Foundation, the Department of the Interior Northeast Climate Science Center (grant no. DOI G12AC00001), and a Bullard Fellowship (Harvard University) to LAD and from the National Academies of Science, Medicine, and Engineering Gulf Research Program to JAN. Resources purchased with funds from the NSF Biological Field Stations and Marine Laboratories program (grant no. DBI 1722553, to Northeastern University) were used to generate the data for the manuscript. Initial conversations on the effects of nutrient enrichment in marshes with Scott Warren and Bruce Peterson were critical in informing the work described in the manuscript. Sam Kelsey and Jane Tucker contributed to much of the N cycling biogeochemistry; Caitlin Bauer, Frankie Leach, Paige Weber, Emily Geoghegan and Sophie Drew assisted with field work; and Joe Vineis assisted with metagenomic analysis. This is contribution 3941 from the Virginia Institute of Marine Science. The data were compiled from multiple published sources. Links to published data can be found here: https://pie-lter.ecosystems.mbl.edu/data. The sequence data used to derive figure 6 are publicly available on the MG-RAST website under project number mgp84173.
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    Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw (2021)
    Oxford University Press
    Details
    Publikationsdatum: 2022-05-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirschberger, C., Sleight, V. A., Criswell, K. E., Clark, S. J., & Gillis, J. A. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Molecular Biology and Evolution, (2021): msab123, https://doi.org/10.1093/molbev/msab123
    Beschreibung: The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralising BMP and endothelin signalling pathways and their effectors, the joint markers nkx3.2 and gdf5 and pro-chondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, while differences in notch signalling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the dorsoventral axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
    Beschreibung: This work was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship to CH, by a Wolfson College Junior Research Fellowship and MBL Whitman Early Career Fellowship to VAS, and by a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377) and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) to JAG.
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  • 39
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    The challenges of detecting and attributing ocean acidification impacts on marine ecosystems (2021)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Doo, S. S., Kealoha, A., Andersson, A., Cohen, A. L., Hicks, T. L., Johnson, Z., I., Long, M. H., McElhany, P., Mollica, N., Shamberger, K. E. F., Silbiger, N. J., Takeshita, Y., & Busch, D. S. The challenges of detecting and attributing ocean acidification impacts on marine ecosystems. ICES Journal of Marine Science, 77(7-8), (2020): 2411-2422, https://doi.org/10.1093/icesjms/fsaa094.
    Beschreibung: A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
    Beschreibung: SSD was funded by NSF OCE (grant # 1415268). DSB and PM were supported by the NOAA Ocean Acidification Program and Northwest Fisheries Science Center, MHL was supported by NSF OCE (grant # 1633951), ZIJ was supported by NSF OCE (grant # 1416665) and DOE EERE (grant #DE-EE008518), NJS was supported by NSF OCE (grant # 1924281), ALC was supported by NSF OCE (grant # 1737311), and AA was supported by NSF OCE (grant # 1416518). KEFS, AK, and TLH were supported by Texas A&M University. This is CSUN Marine Biology contribution (# 306).
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    Characterizing the culturable surface microbiomes of diverse marine animals (2021)
    Oxford University Press
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    Publikationsdatum: 2022-10-26
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keller, A. G., Apprill, A., Lebaron, P., Robbins, J., Romano, T. A., Overton, E., Rong, Y., Yuan, R., Pollara, S., & Whalen, K. E. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology, 97(4), (2021): fiab040, https://doi.org/10.1093/femsec/fiab040.
    Beschreibung: Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
    Beschreibung: Funding was provided by the National Science Foundation (Biological Oceanography) award #1657808 and National Institutes of Health grants 1R21-AI119311–01 to K. E. Whalen, as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. This constitutes scientific manuscript #298 from the Sea Research Foundation.
    Schlagwort(e): Bacteria ; SSU rRNA ; Coral ; Whale ; Microbiome ; Skin
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  • 41
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    Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carroll, E. L., Ott, P. H., McMillan, L. F., Galletti Vernazzani, B., Neveceralova, P., Vermeulen, E., Gaggiotti, O. E., Andriolo, A., Baker, C. S., Bamford, C., Best, P., Cabrera, E., Calderan, S., Chirife, A., Fewster, R. M., Flores, P. A. C., Frasier, T., Freitas, T. R. O., Groch, K., Hulva, P., Kennedy, A., Leaper, R., Leslie, M. S., Moore, M., Oliveira, L., Seger, J., Stepien, E. N., Valenzuela, L. O., Zerbini, A., & Jackson, J. A. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. Journal of Heredity, 111(3), (2020): 263-276, doi:10.1093/jhered/esaa010.
    Beschreibung: As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.
    Beschreibung: This work was supported by the EU BEST 2.0 medium grant 1594 and UK DARWIN PLUS grant 057 and additional funding from the World Wildlife Fund GB107301. The collection of the Chile–Peru sample was supported by the Global Greengrants Fund and the Pacific Whale Foundation. The collection of the Brazilian samples was supported through grants by the Brazilian National Research Council to Paulo H. Ott (CNPq proc. n° 144064/98-7) and Paulo A.C. Flores (CNPq proc. n° 146609/1999-9) and with support from the World Wildlife Fund (WWF-Brazil). The collection of the South African samples was supported by the Global Greengrants Fund, the Pacific Whale Foundation and Charles University Grant Agency (1140217). E.L.C. was partially supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand. This study forms part of the Ecosystems component of the British Antarctic Survey Polar Sciences for Planet Earth Programme, funded by the Natural Environment Research Council.
    Schlagwort(e): population structure ; connectivity ; migration ; gene flow
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    A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lasek-Nesselquist, E., & Johnson, M. D. A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses. Genome Biology and Evolution, 11(11), (2019): 3218–3232, doi:10.1093/gbe/evz233.
    Beschreibung: Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium—M. rubrum, M. major, and M. chamaeleon—being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination—particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate—requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
    Beschreibung: We thank David Beaudoin and Holly V. Moeller for their assistance in collecting cells and extracting RNA. We thank the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory for the generous use of their servers. This work was supported in part by a National Science Foundation grant to both authors (IOS 1354773).
    Schlagwort(e): Mesodinium ; Litostomatea ; ciliate phylogenomics ; mixed-species transcriptomes ; sequence contamination
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    Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N., Zhu, W., Wang, Z., Wang, Z., Ju, B., Ci, W., Lu, X., Yu, D., Wang, Q., Aluru, N., Oliveri, P., Zhang, Y. E., Martindale, M. Q., & Liu, J. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 6(5), (2019):993-1003, doi:10.1093/nsr/nwz064.
    Beschreibung: Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.
    Beschreibung: This work was supported by the National Key Research and Development Program of China (2018YFC1003303), the Strategic Priority Research Program of the CAS (XDB13040200), the National Natural Science Foundation of China (91519306, 31425015), the Youth Innovation Promotion Association of the CAS and the Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SMC016).
    Schlagwort(e): DNA methylation ; evolution ; development ; reprogramming
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    Spatially regulated editing of genetic information within a neuron (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Diaz Quiroz, J. F., Montiel-Gonzalez, Maria F., Nemes, Sonya E., Rangan, K. J., Levinson, S. R., Eisenberg, E., & Rosenthal, J. J. C. Spatially regulated editing of genetic information within a neuron. Nucleic Acids Research, (2020): gkaa172, doi: 10.1093/nar/gkaa172.
    Beschreibung: In eukaryotic cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic information is sequestered within the nucleus. This arrangement imposes constraints on how the information can be tailored for different cellular regions, particularly in cells with complex morphologies like neurons. Although messenger RNAs (mRNAs), and the proteins that they encode, can be differentially sorted between cellular regions, the information itself does not change. RNA editing by adenosine deamination can alter the genome’s blueprint by recoding mRNAs; however, this process too is thought to be restricted to the nucleus. In this work, we show that ADAR2 (adenosine deaminase that acts on RNA), an RNA editing enzyme, is expressed outside of the nucleus in squid neurons. Furthermore, purified axoplasm exhibits adenosine-to-inosine activity and can specifically edit adenosines in a known substrate. Finally, a transcriptome-wide analysis of RNA editing reveals that tens of thousands of editing sites (〉70% of all sites) are edited more extensively in the squid giant axon than in its cell bodies. These results indicate that within a neuron RNA editing can recode genetic information in a region-specific manner.
    Beschreibung: National Science Foundation (NSF) [IOS1557748 to J.R.]; United States–Israel Binational Science Foundation [BSF2013094 to J.R. and E.E.]; The Grass Foundation grant in support of the Doryteuthis pealeii Genome Project, and a gift by Mr. Edward Owens. Funding for open access charge: United States–Israel Binational Science Foundation [BSF2013094].
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
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    Publikationsdatum: 2022-10-27
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Beschreibung: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Beschreibung: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Schlagwort(e): Cephalopod ; Invertebrate ; Genome assembly
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    Advancing an interdisciplinary framework to study seed dispersal ecology (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beckman, N. G., Asian, C. E., Rogers, H. S., Kogan, O., Bronstein, J. L., Bullock, J. M., Hartig, F., HilleRisLambers, J., Zhou, Y., Zurell, D., Brodie, J. F., Bruna, E. M., Cantrell, R. S., Decker, R. R., Efiom, E., Fricke, E. C., Gurski, K., Hastings, A., Johnson, J. S., Loiselle, B. A., Miriti, M. N., Neubert, M. G., Pejchar, L., Poulsen, J. R., Pufal, G., Razafindratsima, O. H., Sandor, M. E., Shea, K., Schreiber, S., Schupp, E. W., Snell, R. S., Strickland, C., & Zambrano, J. Advancing an interdisciplinary framework to study seed dispersal ecology. Aob Plants, 12(2), (2020): plz048, doi:10.1093/aobpla/plz048.
    Beschreibung: Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity and interdependent processes occurring over multiple spatial and temporal scales. Current population models often use simple phenomenological descriptions of dispersal processes, limiting their ability to examine the role of population persistence and spread, especially under global change. To move seed dispersal ecology forward, we need to evaluate the impact of any single seed dispersal event within the full spatial and temporal context of a plant’s life history and environmental variability that ultimately influences a population’s ability to persist and spread. In this perspective, we provide guidance on integrating empirical and theoretical approaches that account for the context dependency of seed dispersal to improve our ability to generalize and predict the consequences of dispersal, and its anthropogenic alteration, across systems. We synthesize suitable theoretical frameworks for this work and discuss concepts, approaches and available data from diverse subdisciplines to help operationalize concepts, highlight recent breakthroughs across research areas and discuss ongoing challenges and open questions. We address knowledge gaps in the movement ecology of seeds and the integration of dispersal and demography that could benefit from such a synthesis. With an interdisciplinary perspective, we will be able to better understand how global change will impact seed dispersal processes, and potential cascading effects on plant population persistence, spread and biodiversity.
    Beschreibung: 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).
    Schlagwort(e): Analytical models ; demography ; global change ; individual-based models ; long-distance seed dispersal ; population models ; seed dispersal
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    PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: Author Posting. © The Author(s), 2020. 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 Toxicological Sciences (2020): kfaa158, doi:10.1093/toxsci/kfaa158.
    Beschreibung: Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
    Beschreibung: National Institute of Health National Institute of Environmental Health Sciences Outstanding New Environmental Scientist (NIH R01ES024915 to N.A.); Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) (Grant P01ES028938); National Science Foundation (Grant OCE-1840381) to M. E. Hahn, J. J. Stegeman, N.A., and S.K.].
    Beschreibung: 2021-10-16
    Schlagwort(e): dioxin-like PCBs ; development ; zebrafish ; epitranscriptomics ; m6A ; MeRIP
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  • 48
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    Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lamb, D. C., Hargrove, T. Y., Zhao, B., Wawrzak, Z., Goldstone, J. V., Nes, W. D., Kelly, S. L., Waterman, M. R., Stegeman, J. J., & Lepesheva, G. I. Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases. Molecular Biology and Evolution, (2020): msaa260, doi:10.1093/molbev/msaa260.
    Beschreibung: Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an “orphan” P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in 〉1,000 bacteria from nine different phyla, 〉50 of them being natural CYP51fx fusion proteins.
    Beschreibung: The study was supported by National Institutes of Health (Grant No. R01 GM067871 to G.I.L.) and by a UK-USA Fulbright Scholarship and the Royal Society (to D.C.L.).
    Schlagwort(e): sterol biosynthesis ; evolution ; cytochrome P450 ; CYP51 redox partner ; crystallography
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  • 49
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    Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies (2020)
    Oxford University Press
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zemeckis, D. R., Dean, M. J., DeAngelis, A. I., Van Parijs, S. M., Hoffman, W. S., Baumgartner, M. F., Hatch, L. T., Cadrin, S. X., & McGuire, C. H. Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies. ICES Journal of Marine Science, 76(6), (2019): 1610-1625, doi: 10.1093/icesjms/fsz064.
    Beschreibung: Effective fishery management measures to protect fish spawning aggregations require reliable information on the spatio-temporal distribution of spawning. Spawning closures have been part of a suite of fishery management actions to rebuild the Gulf of Maine stock of Atlantic cod (Gadus morhua), but difficulties remain with managing rebuilding. The objective of this study was to identify the spatial and temporal distribution of cod spawning during winter in Massachusetts Bay to improve our understanding of cod spawning dynamics and inform fisheries management. Spawning was investigated in collaboration with commercial fishermen during three winter spawning seasons (October 2013–March 2016) using acoustic telemetry and passive acoustic monitoring equipment deployed in fixed-station arrays and mounted on mobile autonomous gliders. Tagged cod exhibited spawning site fidelity and spawning primarily occurred from early November through January with a mid-December peak and some inter-annual variability. The spatial distribution of spawning was generally consistent among years with multiple hotspots in areas 〉50 m depth. Current closures encompass most of spawning, but important areas are recommended for potential modifications. Utilizing multiple complementary technologies and deployment strategies in collaboration with commercial fishermen enabled a comprehensive description of spawning and provides a valuable model for future studies.
    Beschreibung: Year 1 was jointly funded by The Nature Conservancy and Massachusetts Division of Marine Fisheries. The remainder of this research was funded through the 2013–2014 NOAA Saltonstall Kennedy grant program (Award No. NA14NMF4270027) with additional support from the Nature Conservancy and Cabot Family Charitable Foundation.
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  • 50
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    Physical modeling and validation of porpoises' directional emission via hybrid metamaterials (2020)
    Oxford University Press
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dong, E., Zhang, Y., Song, Z., Zhang, T., Cai, C., & Fang, N. X. Physical modeling and validation of porpoises' directional emission via hybrid metamaterials. National Science Review, 6(5), (2019): 921-928, doi:10.1093/nsr/nwz085.
    Beschreibung: In wave physics and engineering, directional emission sets a fundamental limitation on conventional simple sources as their sizes should be sufficiently larger than their wavelength. Artificial metamaterial and animal biosonar both show potential in overcoming this limitation. Existing metamaterials arranged in periodic microstructures face great challenges in realizing complex and multiphase biosonar structures. Here, we proposed a physical directional emission model to bridge the gap between porpoises’ biosonar and artificial metamaterial. Inspired by the anatomical and physical properties of the porpoise's biosonar transmission system, we fabricated a hybrid metamaterial system composed of multiple composite structures. We validated that the hybrid metamaterial significantly increased directivity and main lobe energy over a broad bandwidth both numerically and experimentally. The device displayed efficiency in detecting underwater target and suppressing false target jamming. The metamaterial-based physical model may be helpful to achieve the physical mechanisms of porpoise biosonar detection and has diverse applications in underwater acoustic sensing, ultrasound scanning, and medical ultrasonography.
    Beschreibung: E.D., Y.Z., Z.S., T.Z. and C.C. acknowledge the financial support in part by the National Key Research and Development Program of China (2018YFC1407504), the National Natural Science Foundation of China (41676023, 41276040 and 41422604). N.X.F. acknowledges the support from the MIT Energy Initiative grant. Z.S. thanks the China Scholarship Council for the financial support of his oversea study in Woods Hole Oceanographic Institution.
    Schlagwort(e): porpoise's physical model ; metamaterials ; biosonar ; directional emission
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  • 51
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    Mantle upwelling beneath the South China Sea and links to surrounding subduction systems (2020)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, J., Xu, Y., Sun, Z., & Zhou, Z. Mantle upwelling beneath the South China Sea and links to surrounding subduction systems. National Science Review, 6(5), (2019): 877-881, doi:10.1093/nsr/nwz123.
    Beschreibung: The evolution of the South China Sea (SCS) is directly linked to the complex subduction systems of the surrounding Pacific, Philippine Sea and Indo-Australian Plates (Fig. 1a). Major advances in the last several years are providing new insights into the SCS-mantle dynamics, through regional seismic imaging of the upper mantle [1,2], unprecedented IODP drilling expeditions (349/367/368/368X) [3–5] that obtained the oceanic basement basalt samples for the first time, geochemical analyses of the SCS-mantle source compositions [6–8] and geodynamic modeling [9,10]. Furthermore, new geological mapping, seismic imaging [11,12] and IODP drilling [13,14] have revealed evidence for significantly greater magma production at the northern SCS rifted margin, in comparison to the magma-poor end-member of the Atlantic rifted margins. This paper provides a new perspective of the SCS-mantle dynamics inspired by new observations and geodynamic modeling. We first highlight new geophysical evidence for a broad region of low-seismic-velocity anomalies in the upper mantle beneath the northern SCS, abundant magmatism during continental breakup and post-seafloor spreading, and geochemical evidence for recycled oceanic components beneath the SCS. We then present new models of layered flows in the mantle beneath the SCS, revealing two modes of plate- and subduction-driven mantle upwelling, including (i) narrow centers of mantle upwelling at shallow depths induced by divergent plate motion at seafloor-spreading centers and (ii) broad zones of mantle upwelling as a result of subduction-induced mantle-return flows at greater depths. These new observations and geodynamic studies suggest strong links between mantle upwelling beneath the SCS and surrounding subducting plates.
    Beschreibung: This work was supported by the National Natural Science Foundation of China (41890813, 91628301, U1606401, 41976066, 91858207 and 41706056), the Chinese Academy of Sciences (Y4SL021001, QYZDY-SSW-DQC005 and 133244KYSB20180029), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou, GML2019ZD0205), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100), the State Oceanic Administration (GASI-GEOGE-02) and China Ocean Mineral Resources R&D Association (DY135-S2–1-04).
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  • 52
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    The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling (2020)
    Oxford University Press
    Details
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sun, Z., Lin, J., Qiu, N., Jian, Z., Wang, P., Pang, X., Zheng, J., & Zhu, B. The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling. National Science Review, 6(5), (2019): 871-876, doi:10.1093/nsr/nwz116.
    Beschreibung: Magmatism plays a key role in the process of continental margin breakup and ocean formation. Even in the extremely magma-poor Iberia and Newfoundland margin, studies of field outcrops have shown that syn-rift magmatism had participated in rifting from a very early stage and contributed directly to the rifting process. The final transition from exhumed continental mantle to the ocean formation is also triggered by the accumulation and eruption of magma [1]. Therefore, Atlantic-type passive continental margins are classified into two end-members: magma-poor (non-volcanic) and magma-rich (volcanic). The differences between them lie in whether a large amount of intrusive and extrusive magmatism from the mantle plume/hotspot is involved in the syn-rift and breakup stages. A magma-rich margin [2] should include the following characteristics: (i) a high-velocity lower crust (HVLC) caused by syn-rift mafic magma underplating; (ii) continental crust intruded by abundant sills and dikes; (iii) a large volume of seaward-dipping reflectors (SDRs) caused by flood basalt eruption or tuffs. All other margins are classified as magma-poor margins.
    Beschreibung: We thank the research team project of Guangdong Natural Science Foundation (2017A030312002), IODP-China and South China Sea Deep Project (91628301) and K.C. Wong Education Foundation (GJTD-2018-13) for providing support for the research. This research was also supported by the China National Science and Technology Major Project (2016ZX05026–003), the joint foundation of the National Natural Science Foundation of China and Guangdong province (U1301233), as well as the National Natural Science Foundation of China (41576070 and 41890813).
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  • 53
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    Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? (2020)
    Oxford University Press
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    Publikationsdatum: 2022-10-26
    Beschreibung: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, W. M., Alexander, H., Bier, R. L., Miller, D. R., Muscarella, M. E., Pitz, K. J., & Smith, H. Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? FEMS Microbiology Ecology, (2020): fiaa115, doi: 10.1093/femsec/fiaa115.
    Beschreibung: Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
    Beschreibung: This work was supported by the National Science Foundation [OCE-1356192].
    Schlagwort(e): Auxotrophy ; Microbial community stability ; Microbial interactions ; Aquatic
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  • 54
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    The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting (2020)
    Oxford University Press
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    Publikationsdatum: 2022-10-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, P., Huang, C., Lin, J., Jian, Z., Sun, Z., & Zhao, M. The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting. National Science Review, 6(5), (2019): 902-913, doi:10.1093/nsr/nwz135.
    Beschreibung: The South China Sea, as ‘a non-volcanic passive margin basin’ in the Pacific, has often been considered as a small-scale analogue of the Atlantic. The recent ocean drilling in the northern South China Sea margin found, however, that the Iberian model of non-volcanic rifted margin from the Atlantic does not apply to the South China Sea. In this paper, we review a variety of rifted basins and propose to discriminate two types of rifting basins: plate-edge type such as the South China Sea and intra-plate type like the Atlantic. They not only differ from each other in structure, formation process, lifespan and geographic size, but also occur at different stages of the Wilson cycle. The intra-plate rifting occurred in the Mesozoic and gave rise to large oceans, whereas the plate-edge rifting took place mainly in the mid-Cenozoic, with three-quarters of the basins concentrated in the Western Pacific. As a member of the Western Pacific system of marginal seas, the South China Sea should be studied not in isolation on its origin and evolution, but in a systematic context to include also its neighboring counterparts.
    Beschreibung: This work was supported by the National Natural Science Foundation of China as a part of the ‘South China Sea Deep’ Project (91128000).
    Schlagwort(e): Rifting ; Marginal basin ; Passive margin ; South China Sea ; Western Pacific ; Subduction
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  • 55
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    Large Diversity in Nitrogen- and Sulfur-Containing Compatible Solute Profiles in Polar and Temperate Diatoms (2020)
    Oxford University Press
    In:  Integrative and Comparative Biology, 60 (6). pp. 1401-1413.
    Details
    Publikationsdatum: 2022-01-07
    Beschreibung: Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allows them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter, and include precursors to climate active compounds (e.g., dimethyl sulfide [DMS]), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggests different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles.
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  • 56
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    Post-seismic viscoelastic deformation and stress transfer after the 1960 M9.5 Valdivia, Chile earthquake : effects on the 2010 M8.8 Maule, Chile earthquake (2014)
    Oxford University Press
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    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Beschreibung: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Beschreibung: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Schlagwort(e): Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
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  • 57
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    Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates (2014)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Beschreibung: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Beschreibung: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Schlagwort(e): Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
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  • 58
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    Magnetotelluric data, stable distributions and impropriety: an existential combination (2014)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Beschreibung: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Beschreibung: This work was supported by NSF grant EAR0809074.
    Schlagwort(e): Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
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  • 59
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    Virus infection of Haptolina ericina and Phaeocystis pouchetii implicates evolutionary conservation of programmed cell death induction in marine haptophyte–virus interactions (2014)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Beschreibung: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Beschreibung: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Schlagwort(e): Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
    Repository-Name: Woods Hole Open Access Server
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    The evolution of the four subunits of voltage-gated calcium channels : ancient roots, increasing complexity, and multiple losses (2014)
    Oxford University Press
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    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Beschreibung: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Schlagwort(e): Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
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    Multi-events earthquake early warning algorithm using a Bayesian approach (2014)
    Oxford University Press
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    Publikationsdatum: 2014-12-13
    Beschreibung: Current earthquake early warning (EEW) systems lack the ability to appropriately handle multiple concurrent earthquakes, which led to many false alarms during the 2011 Tohoku earthquake sequence in Japan. This paper uses a Bayesian probabilistic approach to handle multiple concurrent events for EEW. We implement the theory using a two-step algorithm. First, an efficient approximate Bayesian model class selection scheme is used to estimate the number of concurrent events. Then, the Rao-Blackwellized Importance Sampling method with a sequential proposal probability density function is used to estimate the earthquake parameters, that is hypocentre location, origin time, magnitude and local seismic intensity. A real data example based on 2 months data (2011 March 9–April 30) around the time of the 2011 M 9 Tohoku earthquake is studied to verify the proposed algorithm. Our algorithm results in over 90 per cent reduction in the number of incorrect warnings compared to the existing EEW system operating in Japan.
    Schlagwort(e): Seismology
    Print ISSN: 0956-540X
    Digitale ISSN: 1365-246X
    Thema: Geologie und Paläontologie
    Publiziert von Oxford University Press im Namen von The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation (2014)
    Oxford University Press
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    Publikationsdatum: 2014-12-13
    Beschreibung: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
    Digitale ISSN: 1759-6653
    Thema: Biologie
    Publiziert von Oxford University Press
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    A catalogue of 2D photometric decompositions in the SDSS-DR7 spectroscopic main galaxy sample: preferred models and systematics (2014)
    Oxford University Press
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    Publikationsdatum: 2014-12-12
    Beschreibung: We present a catalogue of 2D, point spread function-corrected de Vacouleurs, Sérsic, de Vacouleurs+Exponential, and Sérsic+Exponential fits of ~7 x 10 5 spectroscopically selected galaxies drawn from the Sloan Digital Sky Survey (SDSS) Data Release 7. Fits are performed for the SDSS r band utilizing the fitting routine galfit and analysis pipeline pymorph . We compare these fits to prior catalogues. Fits are analysed using a physically motivated flagging system. The flags suggest that more than 90 per cent of two-component fits can be used for analysis. We show that the fits follow the expected behaviour for early and late galaxy types. The catalogues provide a robust set of structural and photometric parameters for future galaxy studies. We show that some biases remain in the measurements, e.g. the presence of bars significantly affect the bulge measurements although the bulge ellipticity may be used to separate barred and non-barred galaxies, and about 15 per cent of bulges of two-component fits are also affected by resolution. The catalogues are available in electronic format. We also provide an interface for generating postage stamp images of the 2D model and residual as well as the 1D profile. These images can be generated for a user-uploaded list of galaxies on demand.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
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    The influence of charge injection from intermediate connectors on the performance of tandem organic light-emitting devices (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: Charge generation in a typical intermediate connector, composed of “n-type doped layer/transition metal oxide (TMO)/hole transporting layer (HTL),” of a tandem organic light-emitting device (OLED) has recently been found to arise from charge transfer at the TMO/HTL interfaces. In this paper, we investigate the effect of hole injection barriers from intermediate connectors on the performance of tandem OLEDs. The hole injection barriers are caused by the offset of the highest occupied molecular orbital (HOMO) energy levels between HTLs contained in the intermediate connector and the top electroluminescence (EL) unit. We also find that although charge generation can occur at the interfaces between the TMO and a wide variety of HTLs of different HOMO values, an increase in the hole injection barrier however limits the electroluminescence efficiency of the top EL units. In the case of large hole injection barriers, significant charge accumulation in the HTLs makes the intermediate connector lose its functionality gradually over operating time, and limits device stability.
    Print ISSN: 0021-8979
    Digitale ISSN: 1089-7550
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Effect of electron trap states on spin-dependent transport characteristics in CoFe/MgO/n+-Si junctions investigated by Hanle effect measurements and inelastic electron tunneling spectroscopy (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-09
    Beschreibung: Spin-dependent transport properties in CoFe/MgO/n + -Si junctions were investigated by Hanle effect measurements and inelastic electron tunneling (IET) spectroscopy. The CoFe/MgO/n + -Si junctions examined in this study exhibited two different Hanle curves. In the low bias region, broad Hanle signals were mainly observed; in the high bias region, narrow Hanle signals were mainly observed. The d 2 I / dV 2 - V curves (which correspond to IET spectra) contain several peaks originating from phonon modes and other peaks originating from electron trap states. At the bias voltage where electron trap states are observed, Δ d 2 I / dV 2 depends on the magnetic field and the full width at half-maximum of the Δ d 2 I / dV 2 – H curves corresponds to that of the broad Hanle signals. These results indicate that electron trap states are located in the low energy region and cause a decrease in spin lifetime.
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Carrier thermalization under stimulated emission in In0.17Ga0.83N epilayer at room temperature (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-09
    Beschreibung: We elucidate a strong room temperature stimulated emission (SE) of In 0.17 Ga 0.83 N epilayer grown by molecular beam epitaxy under the subpicosecond pulse excitation. The SE peak at 428 nm emerges on the higher energy side of the spontaneous emission in photoluminescence spectra when the excitation density exceeds the threshold of ∼3.68 mJ/cm 2 . Nondegenerate transient differential reflectivity measurements show that a multi-stage carrier thermalization from excited states to localized edge states and stimulated emission dominate the decay processes of photogenerated carriers under various excitation densities. Our results indicate that the existence of phonon bottleneck effect could result in a slow thermalization process in the InGaN material even under the condition of stimulated emission.
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Frustrated incomplete donor ionization in ultra-low resistivity germanium films (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-09
    Beschreibung: The relationship between carrier concentration and donor atomic concentration has been determined in n -type Ge films doped with P. The samples were carefully engineered to minimize non-active dopant incorporation by using specially designed P(SiH 3 ) 3 and P(GeH 3 ) 3 hydride precursors. The in situ nature of the doping and the growth at low temperatures, facilitated by the Ge 3 H 8 and Ge 4 H 10 Ge sources, promote the creation of ultra-low resistivity films with flat doping profiles that help reduce the errors in the concentration measurements. The results show that Ge deviates strongly from the incomplete ionization expected when the donor atomic concentration exceeds N d  = 10 17  cm −3 , at which the energy separation between the donor and Fermi levels ceases to be much larger than the thermal energy. Instead, essentially full ionization is seen even at the highest doping levels beyond the solubility limit of P in Ge. The results can be explained using a model developed for silicon by Altermatt and coworkers, provided the relevant model parameter is properly scaled. The findings confirm that donor solubility and/or defect formation, not incomplete ionization, are the major factors limiting the achievement of very high carrier concentrations in n -type Ge. The commercially viable chemistry approach applied here enables fabrication of supersaturated and fully ionized prototypes with potential for broad applications in group-IV semiconductor technologies.
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Reduction of skin effect losses in double-level-T-gate structure (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-09
    Beschreibung: We developed a T-gate technology based on selective wet etching yielding 200 nm wide T-gate structures used for fabrication of High Electron Mobility Transistors (HEMT). Major advantages of our process are the use of only standard photolithographic process and the ability to generate T-gate stacks. A HEMT fabricated on AlGaN/GaN/sapphire with gate length L g  = 200 nm and double-stacked T-gates exhibits 60 GHz cutoff frequency showing ten-fold improvement compared to 6 GHz for the same device with 2  μ m gate length. HEMTs with a double-level-T-gate (DLTG) structure exhibit up to 35% improvement of f max value compared to a single T-gate device. This indicates a significant reduction of skin effect losses in DLTG structure compared to its standard T-gate counterpart. These results agree with the theoretical predictions.
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Wake effects on drift in two-dimensional inviscid incompressible flows (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-12
    Beschreibung: This investigation analyzes the effect of vortex wakes on the Lagrangian displacement of particles induced by the passage of an obstacle in a two-dimensional incompressible and inviscid fluid. In addition to the trajectories of individual particles, we also study their drift and the corresponding total drift areas in the Föppl and Kirchhoff potential flow models. Our findings, which are obtained numerically and in some regimes are also supported by asymptotic analysis, are compared to the wakeless potential flow which serves as a reference. We show that in the presence of the Föppl vortex wake, some of the particles follow more complicated trajectories featuring a second loop. The appearance of an additional stagnation point in the Föppl flow is identified as a source of this effect. It is also demonstrated that, while the total drift area increases with the size of the wake for large vortex strengths, it is actually decreased for small circulation values. On the other hand, the Kirchhoff flow model is shown to have an unbounded total drift area. By providing a systematic account of the wake effects on the drift, the results of this study will allow for more accurate modeling of hydrodynamic stirring.
    Print ISSN: 1070-6631
    Digitale ISSN: 1089-7666
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Anomalous magnetic configuration of Mn2NiAl ribbon and the role of hybridization in the martensitic transformation of Mn50Ni50−xAlx ribbons (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-09
    Beschreibung: The magnetic configuration of Mn 2 NiAl ribbon has been investigated. In contrast to Ni 2 MnAl, the compound Mn 2 NiAl with considerable disorder does exhibit ferromagnetism and, due to exchange interaction competition, both ferromagnetic and antiferromagnetic moment orientations can coexist between nearest neighbor Mn atoms. This is unexpected in Heusler alloys. Regarding the mechanism of the martensitic transformation in Mn 50 Ni 50− x Al x , it is found that increasing the Al content results in an unusual change in the lattice constant, a decrease of the transformation entropy change, and enhancement of the calculated electron localization. These results indicate that the p-d covalent hybridization between Mn (or Ni) and Al atoms gradually increases at the expense of the d-d hybridization between Ni and Mn atoms. This leads to an increased stability of the austenite phase and a decrease of the martensitic transformation temperature. For 11 ≤  x  ≤ 14, Mn 50 Ni 50− x Al x ferromagnetic shape memory alloys are obtained.
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Continuous electrowetting at the low concentration electrolyte-insulator-semiconductor junction (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-09
    Beschreibung: Electrowetting (EW) has applications including displays, microactuation, miniaturized chemistry, adaptive optics, and energy harvesting—understanding the physics of EW junctions is of key importance. Here, the roles of semiconductor space-charge and electric double layer in continuous EW at an electrolyte-insulator-semiconductor junction are considered. A model is formulated in terms of experimental parameters—applied voltage, zero-bias wetting contact angle, semiconductor type and doping, insulator thickness and dielectric constant, and electrolyte concentration and dielectric constant. The model predicts, and experiments indicate, that the EW behavior is diminished for low concentration solutions (∼1–10 nM) and lowly doped silicon (10 14 –10 15  cm −3 ).
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Effect of the helicity injection rate and the Lundquist number on spheromak sustainment (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-12
    Beschreibung: The dynamics of the magnetic relaxation process during the sustainment of spheromak configurations at different helicity injection rates is studied. The three-dimensional activity is recovered using time-dependent resistive magnetohydrodynamic simulations. A cylindrical flux conserver with concentric electrodes is used to model configurations driven by a magnetized coaxial gun. Magnetic helicity is injected by tangential boundary flows. Different regimes of sustainment are identified and characterized in terms of the safety factor profile. The spatial and temporal behavior of fluctuations is described. The dynamo action is shown to be in close agreement with existing experimental data. These results are relevant to the design and operation of helicity injected devices, as well as to basic understanding of the plasma relaxation mechanism in quasi-steady state.
    Print ISSN: 1070-664X
    Digitale ISSN: 1089-7674
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Filamentary structure of plasma produced by compression of puffing deuterium by deuterium or neon plasma sheath on plasma-focus discharge (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-12
    Beschreibung: The present experiments were performed on the PF-1000 plasma focus device at a current of 2 MA with the deuterium injected from the gas-puff placed in the axis of the anode face. The XUV frames showed, in contrast with the interferograms, the fine structure: filaments and spots up to 1 mm diameter. In the deuterium filling, the short filaments are registered mainly in the region of the internal plasmoidal structures and their number correlates with the intensity of neutron production. The longer filamentary structure was recorded close to the anode after the constriction decay. The long curve-like filaments with spots were registered in the big bubble formed after the pinch phase in the head of the umbrella shape of the plasma sheath. Filaments can indicate the filamentary structure of the current in the pinch. Together with the filaments, small compact balls a few mm in diameter were registered by both interferometry and XUV frame pictures. They emerge out of the dense column and their life-time can be greater than hundreds of ns.
    Print ISSN: 1070-664X
    Digitale ISSN: 1089-7674
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Generation of energetic protons in the interaction of Gaussian laser pulses with surface modulated targets (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-12
    Beschreibung: The radiation pressure acceleration of protons in the interaction of Gaussian laser pulses and surface modulated targets is examined by multi-dimensional particle-in-cell simulations. It is shown that strong longitudinal quasi-static magnetic field is generated on the modulated surface of the target, which significantly enhances the transverse diffusion of electrons. This is beneficial for suppressing the transverse Rayleigh-Taylor instability. Finally, the surface of the accelerated proton beams becomes smoother than that in the case of the planar target, and a final mono-energetic proton beam is obtained by using the surface modulated target.
    Print ISSN: 1070-664X
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    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Rejuvenated bouncing of non-Newtonian droplet via nanoparticle enwrapping (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-09
    Beschreibung: We have studied the impact dynamics of non-Newtonian droplets containing poly-(ethylene oxide) (PEO) by using a high speed camera. To get a deeper insight into the droplet-substrate interaction on droplet impact behavior, both the bare droplet and the liquid marbles have been investigated. The usually observed anti-rebound phenomenon caused by the PEO additives can be rejuvenated by enwrapment of droplets with nanoparticles. The presence of PEO in bare droplets greatly enhances the contact line friction and leads to irreversible impalement of the surface structure. Whereas for liquid marbles, the nanoparticle shell on the droplet surface inhibits the impalement. Our results clearly demonstrate that it is the droplet-substrate friction rather than the bulk rheological properties of the liquid that plays the essential role in the anti-rebound effect.
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    The H I-dominated low-surface-brightness galaxy KKR 17 (2014)
    Oxford University Press
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    Publikationsdatum: 2014-12-13
    Beschreibung: We present new narrow-band (Hα and [O  iii ]) images and optical spectrophotometry of H  ii regions for a gas-rich low-surface-brightness irregular galaxy, KKR 17. The central surface brightness of the galaxy is μ 0 ( B ) = 24.15 ± 0.03 mag s –2 . The galaxy was detected by the Arecibo Legacy Fast ALFA survey (ALFALFA). Its mass is dominated by neutral hydrogen (H  i ) gas. In contrast, both the stellar masses of the bright H  ii and diffuse stellar regions are small. In addition, the fit to the spectral energy distribution to each region shows the stellar populations of H  ii and diffuse regions are different. The bright H  ii region contains a large fraction of O-type stars, revealing recent strong star formation, whereas the diffuse region is dominated by median age stars with a typical age of ~600 Myr. Using McGaugh's abundance model, we found that the average metallicity of KKR 17 is 12 + (O/H) = 8.0 ± 0.1. The star-formation rate of KKR 17 is 0.21 ± 0.04 M  yr –1 , which is ~1/5 of our Milky Way's. Based on the analysis results for young stellar clusters in the H  ii region, the bright H  ii region has two sub-components with different velocities and metallicities. This may be caused by the outflow of massive stars or merging events. However, the mechanism triggering star formation in the H  ii region is still uncertain.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
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    A multiwavelength study of the M dwarf binary YY Geminorum (2014)
    Oxford University Press
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    Publikationsdatum: 2014-12-13
    Beschreibung: We review the results of the 1988 multiwavelength campaign on the late-type eclipsing binary YY Geminorum. Observations include: broad-band optical and near-infrared photometry, simultaneous optical and ultraviolet ( IUE ) spectroscopy, X-ray ( Ginga ) and radio (VLA) data. From models fitted to the optical light curves, fundamental physical parameters have been determined together with evidence for transient maculations (spots) located near quadrature longitudes and intermediate latitudes. Eclipses were observed at optical, ultraviolet and radio wavelengths. Significant drops in 6 cm radio emission near the phases of both primary and secondary eclipse indicate relatively compact radio emitting volumes that may lie between the binary components. IUE observations during secondary eclipse are indicative of a uniform chromosphere saturated with Mg  ii emission and an extended volume of Lyα emission. Profile fitting of high-dispersion Hα spectra confirms the chromospheric saturation and indicates significant Hα opacity to heights of a few per cent of the photospheric radius. There is evidence for an enhanced Hα emission region visible near phase 0.25–0.35 which may be associated with a large spot on the primary and with two small optical flares which were also observed at other wavelengths: one in microwave radiation and the other in X-rays. For both flares, L X / L opt is consistent with energy release in closed magnetic structures.
    Print ISSN: 0035-8711
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    Thema: Physik
    Publiziert von Oxford University Press
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    Effects of heating power on divertor in-out asymmetry and scrape-off layer flow in reversed field on Experimental Advanced Superconducting Tokamak (2014)
    American Institute of Physics (AIP)
    Details
    Publikationsdatum: 2014-12-13
    Beschreibung: The dependence of divertor asymmetry and scrape-off layer (SOL) flow on heating power has been investigated in the Experimental Advanced Superconducting Tokamak (EAST). Divertor plasma exhibits an outboard-enhanced in-out asymmetry in heat flux in lower single null configuration for in reversed (ion ∇ B drift direction toward the upper X-point) field directions. Upper single null exhibits an inboard-favored asymmetry in low heating power condition, while exhibits an outboard-favored asymmetry when increasing the heating power. Double null has the strongest in-out asymmetry in heat flux, favoring the outer divertor. The in-out asymmetry ratios of q t , out / q t , in and P out / P total increase with the power across the separatrix P loss , which is probably induced by the enhanced radial particle transport due to a large pressure gradient. The characteristics of the measured SOL parallel flow under various discharge conditions are consistent with the Pfirsch-Schlüter (PS) flow with the parallel Mach number M ∥ decreasing with the line averaged density but increasing with P loss , in the same direction as the PS flow. The contributions of both poloidal E × B drift and parallel flow on poloidal particle transport in SOL on EAST are also assessed.
    Print ISSN: 1070-664X
    Digitale ISSN: 1089-7674
    Thema: Physik
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    Effects of magnetic islands on drift wave instability (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: Magnetic islands have been implemented in the gyrokinetic toroidal code to study the effects of the islands on microturbulence. The pressure profile flattening is verified in the simulation with the islands. Simulations of ion temperature gradient instability find that different toroidal modes are linearly coupled together and that toroidal spectra become broader when the island width increases. The real frequencies and growth rates of different toroidal modes approach each other with the averaged value independent of the island width. The linear mode structures are enhanced at the island separatrices and weakened at the island centers, consistent with the flattening of the pressure profile inside the islands.
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    Slow motion of a circular cylinder in a plane Poiseuille flow in a microchannel (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: The slow motion of a circular cylinder in a plane Poiseuille flow in a microchannel is analyzed for a wide range of cylinder radii and positions across the channel. The cylinder translates parallel to the channel walls and rotates about its axis. The Stokes approximation is used and the problem is solved analytically using the Papkovich-Fadle eigenfunction expansion and the least-squares method. The stream function and the pressure distribution of the flow field are obtained as results. The force and moment exerted on the cylinder, and the pressure change far from the cylinder, are calculated and shown as functions of the size and location of the cylinder. The results confirm some reciprocal relations exactly. In particular, the translational and rotational velocities of the drifting cylinder in the existing Poiseuille flow are determined. The induced pressure change, when the cylinder drifts in the Poiseuille flow, is also calculated. Some typical streamline patterns, depending on the size and location of the cylinder, are shown and discussed. When the cylinder translates and/or rotates in the channel blocked at infinity, a series of Moffatt eddies appears far from the cylinder in the channel, as expected.
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    Elastocapillary flows in flexible tubes (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: Interactions between capillary and elastic effects are relevant to a variety of applications from micro- and nano-scale manufacturing to biological systems. In this work, we investigate capillary flows in flexible, millimeter-scale cylindrical elastic tubes. We demonstrate that surface tension can cause sufficiently flexible tubes to collapse and coalesce spontaneously through non-axisymmetric buckling, and develop criteria for the initial deformation and complete collapse of a circular tube. Experimental results for capillary rise and evaporation of a liquid in a flexible tube are presented, and several regimes are seen for the equilibrium state of a flexible tube deforming under capillary pressure. Deformations of the tube walls are measured in different regimes and compared with a shell theory model. Analysis and experimental results show that despite the complex and non-axisymmetric deformed shapes of cylindrical structures, the elastocapillary length used in previous literature for flat plates and sheets can be used to predict the behavior of flexible tubes.
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    Oblique ion-acoustic cnoidal waves in two temperature superthermal electrons magnetized plasma (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: A study is presented for the oblique propagation of ion acoustic cnoidal waves in a magnetized plasma consisting of cold ions and two temperature superthermal electrons modelled by kappa-type distributions. Using the reductive perturbation method, the nonlinear Korteweg de-Vries equation is derived, which further gives the solutions with a special type of cnoidal elliptical functions. Both compressive and rarefactive structures are found for these cnoidal waves. Nonlinear periodic cnoidal waves are explained in terms of plasma parameters depicting the Sagdeev potential and the phase curves. It is found that the density ratio of hot electrons to ions μ significantly modifies compressive/refractive wave structures. Furthermore, the combined effects of superthermality of cold and hot electrons κ c , κ h , cold to hot electron temperature ratio σ , angle of propagation and ion cyclotron frequency ω ci have been studied in detail to analyze the height and width of compressive/refractive cnoidal waves. The findings in the present study could have important implications in understanding the physics of electrostatic wave structures in the Saturn's magnetosphere where two temperature superthermal electrons are present.
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    Smart monitoring system based on adaptive current control for superconducting cable test (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: A smart monitoring system for superconducting cable test is proposed with an adaptive current control of a superconducting transformer secondary. The design, based on Fuzzy Gain Scheduling, allows the controller parameters to adapt continuously, and finely, to the working variations arising from transformer nonlinear dynamics. The control system is integrated in a fully digital control loop, with all the related benefits, i.e., high noise rejection, ease of implementation/modification, and so on. In particular, an accurate model of the system, controlled by a Fuzzy Gain Scheduler of the superconducting transformer, was achieved by an experimental campaign through the working domain at several current ramp rates. The model performance was characterized by simulation, under all the main operating conditions, in order to guide the controller design. Finally, the proposed monitoring system was experimentally validated at European Organization for Nuclear Research (CERN) in comparison to the state-of-the-art control system [P. Arpaia, L. Bottura, G. Montenero, and S. Le Naour, “Performance improvement of a measurement station for superconducting cable test,” Rev. Sci. Instrum.83, 095111 (2012)] of the Facility for the Research on Superconducting Cables, achieving a significant performance improvement: a reduction in the system overshoot by 50%, with a related attenuation of the corresponding dynamic residual error (both absolute and RMS) up to 52%.
    Print ISSN: 0034-6748
    Digitale ISSN: 1089-7623
    Thema: Elektrotechnik, Elektronik, Nachrichtentechnik , Physik
    Publiziert von American Institute of Physics (AIP)
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    Characterization of solid state nuclear track detectors of the polyallyl-diglycol-carbonate (CR-39/PM-355) type for light charged particle spectroscopy (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: This paper presents a method which uses the characteristics of the etch pits induced in a polyallyl-diglycol-carbonate (PADC) detector of the CR-39/PM-355 type to estimate particle energy. This method is based on the data provided by a semiautomatic system that selects tracks according to two parameters, crater diameters, and mean gray level values. In this paper we used the results of the calibration measurements that were obtained in our laboratory in the period 2000–2014. Combining the information on the two parameters it is possible to determine unambiguously the incident projectile energy values. The paper presents the results of an attempt to estimate the energy resolution of the method when analyzing the tracks produced in the CR-39/PM-355 detector by energetic ions such as alpha particles, protons, and deuterons. We discuss the energy resolution of the measurement of light charged particle energy which is based on the parameters (crater diameter and mean gray level value) of tracks induced in solid state nuclear track detectors of the PADC type.
    Print ISSN: 0034-6748
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    Thema: Elektrotechnik, Elektronik, Nachrichtentechnik , Physik
    Publiziert von American Institute of Physics (AIP)
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    Automated electrostatic probe device of high resolution and accuracy (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-13
    Beschreibung: In this work, an automated apparatus for driving single electrostatic probes and acquiring the plasma-related data has been designed and fabricated. The voltage range of the present system is ±110 V with an adjustable voltage step as low as 3 mV. Voltage and current measurements are carried out with high resolution and high accuracy circuits, both based on 16 bit analog-to-digital converters. The code embedded in a micro-controller, schedules the operation of the device and transfers the experimental data to a personal computer. The modular design of the system makes possible its modification and thus increases its adaptability to different plasma setups. Finally, the reliable operation of the entire device is confirmed by tests in Electron Cyclotron Resonance plasma.
    Print ISSN: 0034-6748
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    Thema: Elektrotechnik, Elektronik, Nachrichtentechnik , Physik
    Publiziert von American Institute of Physics (AIP)
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    Goos-Hänchen effect and bending of spin wave beams in thin magnetic films (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: For magnon spintronic applications, the detailed knowledge of spin wave (SW) beam dispersion, transmission (reflection) of SWs passing through (reflected from) interfaces, or borders or the scattering of SWs by inhomogeneities is crucial. These wave properties are decisive factors on the usefulness of a particular device. Here, we demonstrate, using micromagnetic simulations supported by an analytical model, that the Goos-Hänchen (GH) shift exists for SW reflecting from thin film edge and that with the effect becomes observable. We show that this effect will exist for a broad range of frequencies in the dipole-exchange range, with the magnetization degree of pinning at the film edge as the crucial parameter, whatever its nature. Moreover, we have also found that the GH effect can be accompanied or even dominating by a bending of the SW beam due to the inhomogeneity of the internal magnetic field. This inhomogeneity, created by demagnetizing field taking place at the film edge, causes gradual change of SWs refractive index. The refraction of the SW beams by the non-uniformity of the magnetic field enables the exploration of graded index magnonics and metamaterial properties for the transmission and processing of information at nanoscale.
    Print ISSN: 0003-6951
    Digitale ISSN: 1077-3118
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
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    Heat-driven spin transport in a ferromagnetic metal (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: As a non-magnetic heavy metal is attached to a ferromagnet, a vertically flowing heat-driven spin current is converted to a transverse electric voltage, which is known as the longitudinal spin Seebeck effect (SSE). If the ferromagnet is a metal, this voltage is also accompanied by voltages from two other sources, i.e., the anomalous Nernst effect in both the ferromagnet and the proximity-induced ferromagnetic boundary layer. By properly identifying and carefully separating those different effects, we find that in this pure spin current circuit the additional spin current drawn by the heavy metal generates another significant voltage by the ferromagnetic metal itself which should be present in all relevant experiments.
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    Confocal shift interferometry of coherent emission from trapped dipolar excitons (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: We introduce a confocal shift-interferometer based on optical fibers. The presented spectroscopy allows measuring coherence maps of luminescent samples with a high spatial resolution even at cryogenic temperatures. We apply the spectroscopy onto electrostatically trapped, dipolar excitons in a semiconductor double quantum well. We find that the measured spatial coherence length of the excitonic emission coincides with the point spread function of the confocal setup. The results are consistent with a temporal coherence of the excitonic emission down to temperatures of 250 mK.
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    Enhanced hydrogen evolution rates at high pH with a colloidal cadmium sulphide–platinum hybrid system (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: We demonstrate enhanced hydrogen generation rates at high pH using colloidal cadmium sulphide nanorods decorated with Pt nanoparticles. We introduce a simplified procedure for the decoration and subsequent hydrogen generation, reducing both the number of working steps and the materials costs. Different Pt precursor concentrations were tested to reveal the optimal conditions for the efficient hydrogen evolution. A sharp increase in hydrogen evolution rates was measured at pH 13 and above, a condition at which the surface charge transfer was efficiently mediated by the formation of hydroxyl radicals and further consumption by the sacrificial triethanolamine hole scavenger.
    Digitale ISSN: 2166-532X
    Thema: Maschinenbau
    Publiziert von American Institute of Physics (AIP)
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    Enhancement of the electrical characteristics of metal-free phthalocyanine films using cold isostatic pressing (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: Spatial gaps between grains and other grains, substrates, or electrodes in organic electronic devices are one of the causes of the reduction in the electrical characteristics. In this study, we demonstrate that cold isostatic pressing (CIP) is an effective method to crush the gaps and enhance the electrical characteristics. CIP of metal-free phthalocyanine (H 2 PC) films induced a decrease in the film thickness by 34%–40% because of the gap crush. The connection of smaller grains into a larger grain and planarization of the film surface were also observed in the CIP film. The crystal axes of the H 2 PC crystallites were rearranged from the a-axis to the c-axis of the α-phase crystal structure in a direction perpendicular to the substrate by CIP, indicating favorable hole injection and transport in this direction because of a better overlap of π orbitals. Thermally stimulated current measurements showed that deep hole traps disappeared and the total hole-trap density decreased after CIP. These CIP-induced changes of the film thicknesses, crystal axes and the hole traps lead to a marked increase in the hole mobility of the H 2 PC films from 2.0 × 10 −7 to 4.0 × 10 −4 cm 2 /V s by 2000 times in the perpendicular direction. We believe that these findings are important for unveiling the underlying carrier injection and transport mechanisms of organic films and for enhancing the performance of future organic electronic devices.
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    Quantized spin waves in single Co/Pt dots detected by anomalous Hall effect based ferromagnetic resonance (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: Anomalous Hall effect (AHE) based ferromagnetic resonance (FMR) measurements were carried out on perpendicularly magnetized Co/Pt multilayer single dots of 0.4–3  μ m in diameter. The resonance behavior was measured by detecting the decrease of perpendicular magnetization component due to magnetization precession. Resonance behavior was observed as a clear decrease of Hall voltages, and the obtained resonance fields were consistent with the results of vector-network-analyzer FMR. Spin-waves with cylindrical symmetry became significant by decreasing the dot diameter, and quantized multiple resonances were observed in the dot of 0.4 μm in diameter. The AHE based FMR proposed here is a powerful method to approach magnetization dynamics including spin waves and non-linear behavior excited in a finite nanostructure.
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    An efficient radiative cooling approximation for use in hydrodynamic simulations (2014)
    Oxford University Press
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    Publikationsdatum: 2014-12-14
    Beschreibung: To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive. Stamatellos and collaborators introduced a scheme for smoothed particle hydrodynamics (SPH) simulations based on the notion of polytropic pseudo-clouds that uses only local quantities to estimate cooling rates. The computational approach is extremely efficient and works well in cases close to spherical symmetry, such as in star formation problems. Unfortunately, the method, which takes the local gravitational potential as an input, can be inaccurate when applied to non-spherical configurations, limiting its usefulness when studying discs or stellar collisions, among other situations of interest. Here, we introduce the ‘pressure scale height method,’ which incorporates the fluid pressure scaleheight into the determination of column densities and cooling rates, and show that it produces more accurate results across a wide range of physical scenarios while retaining the computational efficiency of the original method. The tested models include spherical polytropes as well as discs with specified density and temperature profiles. We focus on applying our techniques within an SPH code, although our method can be implemented within any particle-based Lagrangian or grid-based Eulerian hydrodynamic scheme. Our new method may be applied in a broad range of situations, including within the realm of stellar interactions, collisions, and mergers.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
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    Time dependent potentials associated with exceptional orthogonal polynomials (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: We introduce a method for generating rational extensions of time-dependent potentials, such that the associated Schrödinger equation admits solutions in terms of exceptional orthogonal polynomials. Our method is applicable to position-dependent Schrödinger equations, as well as to their conventional counterparts for constant mass.
    Print ISSN: 0022-2488
    Digitale ISSN: 1089-7658
    Thema: Mathematik , Physik
    Publiziert von American Institute of Physics (AIP)
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    Existence of the Stark-Wannier quantum resonances (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: In this paper, we prove the existence of the Stark-Wannier quantum resonances for one-dimensional Schrödinger operators with smooth periodic potential and small external homogeneous electric field. Such a result extends the existence result previously obtained in the case of periodic potentials with a finite number of open gaps.
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    Thema: Mathematik , Physik
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    Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.
    Digitale ISSN: 1931-9223
    Thema: Chemie und Pharmazie , Physik
    Publiziert von American Institute of Physics (AIP)
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    How to efficiently select an arbitrary Clifford group element (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: We give an algorithm which produces a unique element of the Clifford group on n qubits ( C n ) from an integer 0 ≤ i 〈 C n (the number of elements in the group). The algorithm involves O ( n 3 ) operations and provides, in addition to a canonical mapping from the integers to group elements g , a factorization of g into a sequence of at most 4 n symplectic transvections. The algorithm can be used to efficiently select random elements of C n which are often useful in quantum information theory and quantum computation. We also give an algorithm for the inverse map, indexing a group element in time O ( n 3 ).
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    Thema: Mathematik , Physik
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    Erratum: “Symmetry principles in quantum systems theory” [J. Math. Phys. 52, 113510 (2011)] (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Print ISSN: 0022-2488
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    Thema: Mathematik , Physik
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    Experimental study of global-scale turbulence in a librating ellipsoid (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: We present laboratory experimental results demonstrating that librational forcing of an ellipsoidal container of water can produce intense motions through the mechanism of a libration driven elliptical instability (LDEI). These libration studies are conducted using an ellipsoidal acrylic container filled with water. A particle image velocimetry method is used to measure the 2D velocity field in the equatorial plane over hundreds libration cycles for a fixed Ekman number, E = 2 × 10 −5 . In doing so, we recover the libration induced base flow and a time averaged zonal flow. Further, we show that LDEI in non-axisymmetric container geometries is capable of driving both intermittent and saturated turbulent motions in the bulk fluid. Additionally, we measure the growth rate and amplitude of the LDEI induced excited flow in a fully ellipsoidal container at more extreme parameters than previously studied [Noir et al. , “Experimental study of libration-driven flows in nonaxisymmetric containers,” Phys. Earth Planet. Inter. 204-205 , 1 (2012); Cébron et al. , Phys. Fluids 24 , 061703, “Libration driven elliptical instability,” (2012)]. Excitation of bulk filling turbulence by librational forcing provides a mechanism for transferring rotational energy into turbulent fluid motion and thus can play an important role in the thermal evolution, interior dynamics, and magneto-hydrodynamics of librating bodies, as appear to be common in solar system settings [e.g., Comstock and Bills, “A solar system survey of forced librations in longitude,” J. Geophys. Res. Planets 108 , 1 (2003)].
    Print ISSN: 1070-6631
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    Thema: Physik
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    Miscible heavy-light displacement flows in an inclined two-dimensional channel: A numerical approach (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: We numerically study the displacement flow of two iso-viscous Newtonian fluids in an inclined two-dimensional channel, formed by two parallel plates. The results are complementary to our previous studies on displacement flows in pipes and channels. The heavier displacing fluid moves the lighter displaced fluid in the downward direction. Three dimensionless groups largely describe these flows: the densimetric Froude number ( Fr ), the Reynolds number ( Re ), and the duct inclination (β). As a first order approximation, we are able to classify different flow regimes phenomenologically in a two-dimensional ( Fr ; Re cosβ/ Fr )-plane and provide leading order expressions for the transitions between different regimes. The stabilizing and/or de-stabilizing effects of the imposed mean flow on buoyant exchange flows (zero imposed velocity) are described for a broad range of dimensionless parameters.
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    Symmetric model of compressible granular mixtures with permeable interfaces (2014)
    American Institute of Physics (AIP)
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    Publikationsdatum: 2014-12-16
    Beschreibung: Compressible granular materials are involved in many applications, some of them being related to energetic porous media. Gas permeation effects are important during their compaction stage, as well as their eventual chemical decomposition. Also, many situations involve porous media separated from pure fluids through two-phase interfaces. It is thus important to develop theoretical and numerical formulations to deal with granular materials in the presence of both two-phase interfaces and gas permeation effects. Similar topic was addressed for fluid mixtures and interfaces with the Discrete Equations Method (DEM) [R. Abgrall and R. Saurel, “Discrete equations for physical and numerical compressible multiphase mixtures,” J. Comput. Phys. 186 (2), 361-396 (2003)] but it seemed impossible to extend this approach to granular media as intergranular stress [K. K. Kuo, V. Yang, and B. B. Moore, “Intragranular stress, particle-wall friction and speed of sound in granular propellant beds,” J. Ballist. 4 (1), 697-730 (1980)] and associated configuration energy [J. B. Bdzil, R. Menikoff, S. F. Son, A. K. Kapila, and D. S. Stewart, “Two-phase modeling of deflagration-to-detonation transition in granular materials: A critical examination of modeling issues,” Phys. Fluids 11 , 378 (1999)] were present with significant effects. An approach to deal with fluid-porous media interfaces was derived in Saurel et al. [“Modelling dynamic and irreversible powder compaction,” J. Fluid Mech. 664 , 348-396 (2010)] but its validity was restricted to weak velocity disequilibrium only. Thanks to a deeper analysis, the DEM is successfully extended to granular media modelling in the present paper. It results in an enhanced version of the Baer and Nunziato [“A two-phase mixture theory for the deflagration-to-detonation transition (DDT) in reactive granular materials,” Int. J. Multiphase Flow 12 (6), 861-889 (1986)] model as symmetry of the formulation is now preserved. Several computational examples are shown to validate and illustrate method’s capabilities.
    Print ISSN: 1070-6631
    Digitale ISSN: 1089-7666
    Thema: Physik
    Publiziert von American Institute of Physics (AIP)
    Standort Signatur Erwartet Verfügbarkeit
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