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  • American Institute of Physics (AIP)  (93,263)
  • Nature Publishing Group  (60,815)
  • 2020-2022  (4)
  • 2010-2014  (61,729)
  • 1985-1989  (50,454)
  • 1980-1984  (17,607)
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  • 1
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    Nature Publishing Group
    In:  EPIC3Nature Geoscience, Nature Publishing Group, 7(5), pp. 376-381, ISSN: 1752-0894
    Publication Date: 2014-07-14
    Description: During the Middle Miocene climate transition about 14 million years ago, the Antarctic ice sheet expanded to near-modern volume. Surprisingly, this ice sheet growth was accompanied by a warming in the surface waters of the Southern Ocean, whereas a slight deep-water temperature increase was delayed by more than 200 thousand years. Here we use a coupled atmosphere–ocean model to assess the relative effects of changes in atmospheric CO2 concentration and ice sheet growth on regional and global temperatures. In the simulations, changes in the wind field associated with the growth of the ice sheet induce changes in ocean circulation, deep-water formation and sea-ice cover that result in sea surface warming and deep-water cooling in large swaths of the Atlantic and Indian ocean sectors of the Southern Ocean. We interpret these changes as the dominant ocean surface response to a 100-thousand-year phase of massive ice growth in Antarctica. A rise in global annual mean temperatures is also seen in response to increased Antarctic ice surface elevation. In contrast, the longer-term surface and deep-water temperature trends are dominated by changes in atmospheric CO2 concentration. We therefore conclude that the climatic and oceanographic impacts of the Miocene expansion of the Antarctic ice sheet are governed by a complex interplay between wind field, ocean circulation and the sea-ice system.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
    Publication Date: 2014-07-17
    Description: Thermokarst lakes formed across vast regions of Siberia and Alaska during the last deglaciation and are thought to be a net source of atmospheric methane and carbon dioxide during the Holocene epoch1, 2, 3, 4. However, the same thermokarst lakes can also sequester carbon5, and it remains uncertain whether carbon uptake by thermokarst lakes can offset their greenhouse gas emissions. Here we use field observations of Siberian permafrost exposures, radiocarbon dating and spatial analyses to quantify Holocene carbon stocks and fluxes in lake sediments overlying thawed Pleistocene-aged permafrost. We find that carbon accumulation in deep thermokarst-lake sediments since the last deglaciation is about 1.6 times larger than the mass of Pleistocene-aged permafrost carbon released as greenhouse gases when the lakes first formed. Although methane and carbon dioxide emissions following thaw lead to immediate radiative warming, carbon uptake in peat-rich sediments occurs over millennial timescales. We assess thermokarst-lake carbon feedbacks to climate with an atmospheric perturbation model and find that thermokarst basins switched from a net radiative warming to a net cooling climate effect about 5,000 years ago. High rates of Holocene carbon accumulation in 20 lake sediments (47 ± 10 grams of carbon per square metre per year; mean ± standard error) were driven by thermokarst erosion and deposition of terrestrial organic matter, by nutrient release from thawing permafrost that stimulated lake productivity and by slow decomposition in cold, anoxic lake bottoms. When lakes eventually drained, permafrost formation rapidly sequestered sediment carbon. Our estimate of about 160 petagrams of Holocene organic carbon in deep lake basins of Siberia and Alaska increases the circumpolar peat carbon pool estimate for permafrost regions by over 50 per cent (ref. 6). The carbon in perennially frozen drained lake sediments may become vulnerable to mineralization as permafrost disappears7, 8, 9, potentially negating the climate stabilization provided by thermokarst lakes during the late Holocene.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 3
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    Nature Publishing Group
    In:  EPIC3Nature, Nature Publishing Group, 512(7514), pp. 290-294, ISSN: 0028-0836
    Publication Date: 2014-09-04
    Description: During glacial periods of the Late Pleistocene, an abundance of proxy data demonstrates the existence of large and repeated millennial-scale warming episodes, known as Dansgaard–Oeschger (DO) events1. This ubiquitous feature of rapid glacial climate change can be extended back as far as 800,000 years before present (BP) in the ice core record2, and has drawn broad attention within the science and policy-making communities alike3. Many studies have been dedicated to investigating the underlying causes of these changes, but no coherent mechanism has yet been identified3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15. Here we show, by using a comprehensive fully coupled model16, that gradual changes in the height of the Northern Hemisphere ice sheets (NHISs) can alter the coupled atmosphere–ocean system and cause rapid glacial climate shifts closely resembling DO events. The simulated global climate responses—including abrupt warming in the North Atlantic, a northward shift of the tropical rainbelts, and Southern Hemisphere cooling related to the bipolar seesaw—are generally consistent with empirical evidence1, 3, 17. As a result of the coexistence of two glacial ocean circulation states at intermediate heights of the ice sheets, minor changes in the height of the NHISs and the amount of atmospheric CO2 can trigger the rapid climate transitions via a local positive atmosphere–ocean–sea-ice feedback in the North Atlantic. Our results, although based on a single model, thus provide a coherent concept for understanding the recorded millennial-scale variability and abrupt climate changes in the coupled atmosphere–ocean system, as well as their linkages to the volume of the intermediate ice sheets during glacials.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2019-03-08
    Description: Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering themvisible fromspace3.Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate thatE. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
    Publication Date: 2020-04-14
    Description: The Asian monsoon (AM) played an important role in the dynastic history of China, yet it remains unknown whether AM-mediated shifts in Chinese societies affect earth surface processes to the point of exceeding natural variability. Here, we present a dust storm intensity record dating back to the first unified dynasty of China (the Qin Dynasty, 221–207 B.C.E.). Marked increases in dust storm activity coincided with unified dynasties with large populations during strong AM periods. By contrast, reduced dust storm activity corresponded to decreased population sizes and periods of civil unrest, which was co-eval with a weakened AM. The strengthened AM may have facilitated the development of Chinese civilizations, destabilizing the topsoil and thereby increasing the dust storm frequency. Beginning at least 2000 years ago, human activities might have started to overtake natural climatic variability as the dominant controls of dust storm activity in eastern China.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
    Publication Date: 2020-11-12
    Description: Antarctic krill, Euphausia superba, supports a valuable commercial fishery in the Southwest Atlantic, which holds the highest krill densities and is warming rapidly. The krill catch is increasing, is concentrated in a small area, and has shifted seasonally from summer to autumn/winter. The fishery is managed by the Commission for the Conservation of Antarctic Marine Living Resources, with the main goal of safeguarding the large populations of krill-dependent predators. Here we show that, because of the restricted distribution of successfully spawning krill and high inter-annual variability in their biomass, the risk of direct fishery impacts on the krill stock itself might be higher than previously thought. We show how management benefits could be achieved by incorporating uncertainty surrounding key aspects of krill ecology into management decisions, and how knowledge can be improved in these key areas. This improved information may be supplied, in part, by the fishery itself.
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
    Publication Date: 2021-02-03
    Description: The dominant feature of large-scale mass transfer in the modern ocean is the Atlantic meridional overturning circulation (AMOC). The geometry and vigour of this circulation influences global climate on various timescales. Palaeoceanographic evidence suggests that during glacial periods of the past 1.5 million years the AMOC had markedly different features from today; in the Atlantic basin, deep waters of Southern Ocean origin increased in volume while above them the core of the North Atlantic Deep Water (NADW) shoaled. An absence of evidence on the origin of this phenomenon means that the sequence of events leading to global glacial conditions remains unclear. Here we present multi-proxy evidence showing that northward shifts in Antarctic iceberg melt in the Indian–Atlantic Southern Ocean (0–50°E) systematically preceded deep-water mass reorganizations by one to two thousand years during Pleistocene-era glaciations. With the aid of iceberg-trajectory model experiments, we demonstrate that such a shift in iceberg trajectories during glacial periods can result in a considerable redistribution of freshwater in the Southern Ocean. We suggest that this, in concert with increased sea-ice cover, enabled positive buoyancy anomalies to ‘escape’ into the upper limb of the AMOC, providing a teleconnection between surface Southern Ocean conditions and the formation of NADW. The magnitude and pacing of this mechanism evolved substantially across the mid-Pleistocene transition, and the coeval increase in magnitude of the ‘southern escape’ and deep circulation perturbations implicate this mechanism as a key feedback in the transition to the ‘100-kyr world’, in which glacial–interglacial cycles occur at roughly 100,000-year periods.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
    Publication Date: 2017-04-04
    Description: The MW 8.8 mega-thrust earthquake and tsunami that occurred on February 27, 2010, offshore Maule region, Chile, was not unexpected. A clearly identified seismic gap existed in an area where tectonic loading has been accumulating since the great 1835 earthquake experienced and described by Darwin during the voyage of the Beagle. Here we jointly invert tsunami and geodetic data (InSAR, GPS, land-level changes), to derive a robust model for the co-seismic slip distribution and induced co-seismic stress changes, and compare them to past earthquakes and the pre-seismic locking distribution. We aim to assess if the Maule earthquake has filled the Darwin gap, decreasing the probability of a future shock . We find that the main slip patch is located to the north of the gap, overlapping the rupture zone of the MW 8.0 1928 earthquake, and that a secondary concentration of slip occurred to the south; the Darwin gap was only partially filled and a zone of high pre-seismic locking remains unbroken. This observation is not consistent with the assumption that distributions of seismic rupture might be correlated with pre-seismic locking, potentially allowing the anticipation of slip distributions in seismic gaps. Moreover, increased stress on this unbroken patch might have increased the probability of another major to great earthquake there in the near future.
    Description: Published
    Description: 173-177
    Description: 3.1. Fisica dei terremoti
    Description: 4.2. TTC - Modelli per la stima della pericolosità sismica a scala nazionale
    Description: JCR Journal
    Description: restricted
    Keywords: Source process ; Chile ; Tsunami ; Joint Inversion ; Seismic Gap ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.06. Subduction related processes ; 05. General::05.01. Computational geophysics::05.01.03. Inverse methods
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2017-04-04
    Description: Studies of past sea-level markers are commonly used to unveil the tectonic history and seismic behavior of subduction zones. We present new evidence on vertical motions of the Hellenic subduction zone as resulting from a suite of Late Pleistocene - Holocene shorelines in western Crete (Greece). Shoreline ages obtained by AMS radiocarbon dating of seashells, together with the reappraisal of shoreline ages from previous works, testify a long-term uplift rate of 2.5-2.7 mm/y. This average value, however, includes periods in which the vertical motions vary significantly: 2.6-3.2 mm/y subsidence rate from 42 ka to 23 ka, followed by ~7.7 mm/y sustained uplift rate from 23 ka to present. The last ~5 ky shows a relatively slower uplift rate of 3.0-3.3 mm/y, yet slightly higher than the long-term average. A preliminary tectonic model attempts at explaining these up and down motions by across-strike partitioning of fault activity in the subduction zone.
    Description: Published
    Description: 5677
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: coastal geomorphology ; tectonic rates ; paleoshorelines ; subduction ; Crete ; 04. Solid Earth::04.04. Geology::04.04.03. Geomorphology ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2017-04-04
    Description: The 2011 Tohoku-oki (Mw 9.1) earthquake is so far the best-observed megathrust rupture, which allowed the collection of unprecedented offshore data. The joint inversion of tsunami waveforms (DART buoys, bottom pressure sensors, coastal wave gauges, and GPS-buoys) and static geodetic data (onshore GPS, seafloor displacements obtained by a GPS/acoustic combination technique), allows us to retrieve the slip distribution on a non-planar fault. We show that the inclusion of near-source data is necessary to image the details of slip pattern (maximum slip ,48 m, up to ,35 m close to the Japan trench), which generated the large and shallow seafloor coseismic deformations and the devastating inundation of the Japanese coast. We investigate the relation between the spatial distribution of previously inferred interseismic coupling and coseismic slip and we highlight the importance of seafloor geodetic measurements to constrain the interseismic coupling, which is one of the key-elements for long-term earthquake and tsunami hazard assessment.
    Description: Published
    Description: 385
    Description: 3.1. Fisica dei terremoti
    Description: N/A or not JCR
    Description: restricted
    Keywords: Tohoku ; Subduction ; Tsunami ; Inverse problem ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.06. Subduction related processes
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
    Publication Date: 2017-04-04
    Description: Improving lava flow hazard assessment is one of the most important and challenging fields of volcanology, and has an immediate and practical impact on society. Here, we present a methodology for the quantitative assessment of lava flow hazards based on a combination of field data, numerical simulations and probability analyses. With the extensive data available on historic eruptions of Mt. Etna, going back over 2000 years, it has been possible to construct two hazard maps, one for flank and the other for summit eruptions, allowing a quantitative analysis of the most likely future courses of lava flows. The effective use of hazard maps of Etna may help in minimizing the damage from volcanic eruptions through correct land use in densely urbanized area with a population of almost one million people. Although this study was conducted on Mt. Etna, the approach used is designed to be applicable to other volcanic areas.
    Description: This work was developed within the framework of TecnoLab, the Laboratory for Technological Advance in Volcano Geophysics organized by INGV-CT, DIEES-UNICT, and DMI-UNICT.
    Description: Published
    Description: 3493
    Description: 1V. Storia e struttura dei sistemi vulcanici
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 4V. Vulcani e ambiente
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: 3IT. Calcolo scientifico e sistemi informatici
    Description: JCR Journal
    Description: restricted
    Keywords: Lava flow hazard ; Etna ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 05. General::05.01. Computational geophysics::05.01.99. General or miscellaneous ; 05. General::05.02. Data dissemination::05.02.99. General or miscellaneous ; 05. General::05.08. Risk::05.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
    Publication Date: 2017-04-04
    Description: In recent decades, geophysical investigations have detected wide magma reservoirs beneath quiescent calderas. However, the discovery of partially melted horizons inside the crust is not sufficient to put constraints on capability of reservoirs to supply cataclysmic eruptions, which strictly depends on the chemical-physical properties of magmas (composition, viscosity, gas content etc.), and thus on their differentiation histories. In this study, by using geochemical, isotopic and textural records of rocks erupted from the high-risk Campi Flegrei caldera, we show that the alkaline magmas have evolved toward a critical state of explosive behaviour over a time span shorter than the repose time of most volcanic systems and that these magmas have risen rapidly toward the surface. Moreover, similar results on the depth and timescale of magma storage were previously obtained for the neighbouring Somma-Vesuvius volcano. This consistency suggests that there might be a unique long-lived magma pool beneath the whole Neapolitan area.
    Description: Published
    Description: article 712
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: N/A or not JCR
    Description: open
    Keywords: magma ; campi flegrei caldera ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
    Publication Date: 2019-07-17
    Description: The mid-Piacenzian climate represents the most geologically recent interval of long-term average warmth relative to the last million years, and shares similarities with the climate projected for the end of the 21st century. As such, it represents a natural experiment from which we can gain insight into potential climate change impacts, enabling more informed policy decisions for mitigation and adaptation. Here, we present the first systematic comparison of Pliocene sea surface temperature (SST) between an ensemble of eight climate model simulations produced as part of PlioMIP (Pliocene Model Intercomparison Project) with the PRISM (Pliocene Research, Interpretation and Synoptic Mapping) Project mean annual SST field. Our results highlight key regional and dynamic situations where there is discord between the palaeoenvironmental reconstruction and the climate model simulations. These differences have led to improved strategies for both experimental design and temporal refinement of the palaeoenvironmental reconstruction.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
    Publication Date: 2019-07-17
    Description: Comparing simulations of key warm periods in Earth history with contemporaneous geological proxy data is a useful approach for evaluating the ability of climate models to simulate warm, high-CO2 climates that are unprecedented in the more recent past. Here we use a global data set of confidence-assessed, proxy-based temperature estimates and biome reconstructions to assess the ability of eight models to simulate warm terrestrial climates of the Pliocene epoch. The Late Pliocene, 3.6–2.6 million years ago, is an accessible geological interval to understand climate processes of a warmer world. We show that model-predicted surface air temperatures reveal a substantial cold bias in the Northern Hemisphere. Particularly strong data–model mismatches in mean annual temperatures (up to 18 °C) exist in northern Russia. Our model sensitivity tests identify insufficient temporal constraints hampering the accurate configuration of model boundary conditions as an important factor impacting on data–model discrepancies. We conclude that to allow a more robust evaluation of the ability of present climate models to predict warm climates, future Pliocene data–model comparison studies should focus on orbitally defined time slices.
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
    Publication Date: 2017-10-18
    Description: Efforts to extract a Greenland ice core with a complete record of the Eemian interglacial (130,000 to 115,000 years ago) have until now been unsuccessful. The response of the Greenland ice sheet to the warmer-than-present climate of the Eemian has thus remained unclear. Here we present the new North Greenland Eemian Ice Drilling (‘NEEM’) ice core and show only a modest ice-sheet response to the strong warming in the early Eemian. We reconstructed the Eemian record from folded ice using globally homogeneous parameters known from dated Greenland and Antarctic ice-core records. On the basis of water stable isotopes, NEEM surface temperatures after the onset of the Eemian (126,000 years ago) peaked at 8 ± 4 degrees Celsius above the mean of the past millennium, followed by a gradual cooling that was probably driven by the decreasing summer insolation. Between 128,000 and 122,000 years ago, the thickness of the northwest Greenland ice sheet decreased by 400 ± 250 metres, reaching surface elevations 122,000 years ago of 130 ± 300 metres lower than the present. Extensive surface melt occurred at the NEEM site during the Eemian, a phenomenon witnessed when melt layers formed again at NEEM during the exceptional heat of July 2012. With additional warming, surface melt might become more common in the future.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Nature Publishing Group
    In:  EPIC3Nature Geoscience, Nature Publishing Group, 7(2), pp. 113-116, ISSN: 1752-0894
    Publication Date: 2018-08-10
    Description: The Antarctic Circumpolar Current is key to the mixing and ventilation of the world’s oceans1, 2, 3, 4, 5. This current flows from west to east between about 45° and 70° S (refs 1, 2, 3) connecting the Atlantic, Pacific and Indian oceans, and is driven by westerly winds and buoyancy forcing. High levels of productivity in the current regulate atmospheric CO2 concentrations6. Reconstructions of the current during the last glacial period suggest that flow speeds were faster7 or similar8 to present, and it is uncertain whether the strength and position of the westerly winds changed9, 10, 11. Here we reconstruct Antarctic Circumpolar Current bottom speeds through the constricting Drake Passage and Scotia Sea during the Last Glacial Maximum and Holocene based on the mean grain size of sortable silt from a suite of sediment cores. We find essentially no change in bottom flow speeds through the region, and, given that the momentum imparted by winds, and modulated by sea-ice cover, is balanced by the interaction of these flows with the seabed, this argues against substantial changes in wind stress. However, glacial flow speeds in the sea-ice zone12 south of 56° S were significantly slower than present, whereas flow in the north was faster, but not significantly so. We suggest that slower flow over the rough topography south of 56° S may have reduced diapycnal mixing in this region during the last glacial period, possibly reducing the diapycnal contribution to the Southern Ocean overturning circulation.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Nature Publishing Group
    In:  EPIC3Scientific Reports, Nature Publishing Group, 4(4119), ISSN: 2045-2322
    Publication Date: 2019-07-17
    Description: Complex network approaches have recently been applied to continuous spatial dynamical systems, like climate, successfully uncovering the system's interaction structure. However the relationship between the underlying atmospheric or oceanic flow's dynamics and the estimated network measures have remained largely unclear. We bridge this crucial gap in a bottom-up approach and define a continuous analytical analogue of Pearson correlation networks for advection-diffusion dynamics on a background flow. Analysing complex networks of prototypical flows and from time series data of the equatorial Pacific, we find that our analytical model reproduces the most salient features of these networks and thus provides a general foundation of climate networks. The relationships we obtain between velocity field and network measures show that line-like structures of high betweenness mark transition zones in the flow rather than, as previously thought, the propagation of dynamical information.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
    Publication Date: 2022-05-25
    Description: © Macmillan Publishers Limited, 2010. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 Unported License. The definitive version was published in Nature Communications 1 (2010): 49, doi:10.1038/ncomms1045.
    Description: Motor innervation to the tetrapod forelimb and fish pectoral fin is assumed to share a conserved spinal cord origin, despite major structural and functional innovations of the appendage during the vertebrate water-to-land transition. In this paper, we present anatomical and embryological evidence showing that pectoral motoneurons also originate in the hindbrain among ray-finned fish. New and previous data for lobe-finned fish, a group that includes tetrapods, and more basal cartilaginous fish showed pectoral innervation that was consistent with a hindbrain-spinal origin of motoneurons. Together, these findings support a hindbrain–spinal phenotype as the ancestral vertebrate condition that originated as a postural adaptation for pectoral control of head orientation. A phylogenetic analysis indicated that Hox gene modules were shared in fish and tetrapod pectoral systems. We propose that evolutionary shifts in Hox gene expression along the body axis provided a transcriptional mechanism allowing eventual decoupling of pectoral motoneurons from the hindbrain much like their target appendage gained independence from the head.
    Description: Th is work was supported by the National Institutes of Health and National Science Foundation.
    Repository Name: Woods Hole Open Access Server
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  • 19
    Publication Date: 2022-05-25
    Description: © Macmillan Publishers Limited, 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 3 (2012): 669, doi:10.1038/ncomms1673.
    Description: Na+/K+ pumps move net charge through the cell membrane by mediating unequal exchange of intracellular Na+ and extracellular K+. Most charge moves during transitions that release Na+ to the cell exterior. When pumps are constrained to bind and release only Na+, a membrane voltage-step redistributes pumps among conformations with zero, one, two or three bound Na+, thereby transiently generating current. By applying rapid voltage steps to squid giant axons, we previously identified three components in such transient currents, with distinct relaxation speeds: fast (which nearly parallels the voltage-jump time course), medium speed (τm=0.2–0.5 ms) and slow (τs=1–10 ms). Here we show that these three components are tightly correlated, both in their magnitudes and in the time courses of their changes. The correlations reveal the dynamics of the conformational rearrangements that release three Na+ to the exterior (or sequester them into their binding sites) one at a time, in an obligatorily sequential manner.
    Description: This research was directly supported by the Intramural Research Program of the National Institutes of Health (NIH), NINDS, grants NIH HL36783 to D.C.G., and NIH U54GM087519 and R01GM030376 to F.B.
    Repository Name: Woods Hole Open Access Server
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  • 20
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 2 (2012): 582, doi:10.1038/srep00582.
    Description: Over the last century humans have altered the export of fluvial materials leading to significant changes in morphology, chemistry, and biology of the coastal ocean. Here we present sedimentary, paleoenvironmental and paleogenetic evidence to show that the Black Sea, a nearly enclosed marine basin, was affected by land use long before the changes of the Industrial Era. Although watershed hydroclimate was spatially and temporally variable over the last ~3000 years, surface salinity dropped systematically in the Black Sea. Sediment loads delivered by Danube River, the main tributary of the Black Sea, significantly increased as land use intensified in the last two millennia, which led to a rapid expansion of its delta. Lastly, proliferation of diatoms and dinoflagellates over the last five to six centuries, when intensive deforestation occurred in Eastern Europe, points to an anthropogenic pulse of river-borne nutrients that radically transformed the food web structure in the Black Sea.
    Description: This study was supported by grants OISE 0637108, EAR 0952146, OCE 0602423 and OCE 0825020 from the National Science Foundation and grants from the Woods Hole Oceanographic Institution.
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  • 21
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 3 (2013): 2802, doi:10.1038/srep02802.
    Description: It is usually assumed that metabolic constraints restrict deep-sea corals to cold-water habitats, with ‘deep-sea’ and ‘cold-water’ corals often used as synonymous. Here we report on the first measurements of biological characters of deep-sea corals from the central Red Sea, where they occur at temperatures exceeding 20°C in highly oligotrophic and oxygen-limited waters. Low respiration rates, low calcification rates, and minimized tissue cover indicate that a reduced metabolism is one of the key adaptations to prevailing environmental conditions. We investigated four sites and encountered six species of which at least two appear to be undescribed. One species is previously reported from the Red Sea but occurs in deep cold waters outside the Red Sea raising interesting questions about presumed environmental constraints for other deep-sea corals. Our findings suggest that the present understanding of deep-sea coral persistence and resilience needs to be revisited.
    Keywords: Ecosystem ecology ; Biodiversity ; Genetics ; Metabolism
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  • 22
    Publication Date: 2022-05-25
    Description: © Macmillan Publishers Limited, 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 2 (2011): 293, doi:10.1038/ncomms1297.
    Description: The relative importance of north–south migrations of the intertropical convergence zone (ITCZ) versus El Niño-Southern Oscillation and its associated Pacific Walker Circulation (PWC) variability for past hydrological change in the western tropical Pacific is unclear. Here we show that north–south ITCZ migration was not the only mechanism of tropical Pacific hydrologic variability during the last millennium, and that PWC variability profoundly influenced tropical Pacific hydrology. We present hydrological reconstructions from Cattle Pond, Dongdao Island of the South China Sea, where multi-decadal rainfall and downcore grain size variations are correlated to the Southern Oscillation Index during the instrumental era. Our downcore grain size reconstructions indicate that this site received less precipitation during relatively warm periods, AD 1000–1400 and AD 1850–2000, compared with the cool period (AD 1400–1850). Including our new reconstructions in a synthesis of tropical Pacific records results in a spatial pattern of hydrologic variability that implicates the PWC.
    Description: This work was supported by the Natural Science Foundation of China (NSFC) (40730107) and the Major State Basic Research Development Program of China (973 Program) (No.2010CB428902). DWO acknowledges support from the US NSF.
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  • 23
    Publication Date: 2022-05-25
    Description: © Macmillan Publishers Limited, 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 3 (2012): 620, doi:10.1038/ncomms1636.
    Description: The Mid-Cayman spreading centre is an ultraslow-spreading ridge in the Caribbean Sea. Its extreme depth and geographic isolation from other mid-ocean ridges offer insights into the effects of pressure on hydrothermal venting, and the biogeography of vent fauna. Here we report the discovery of two hydrothermal vent fields on the Mid-Cayman spreading centre. The Von Damm Vent Field is located on the upper slopes of an oceanic core complex at a depth of 2,300 m. High-temperature venting in this off-axis setting suggests that the global incidence of vent fields may be underestimated. At a depth of 4,960 m on the Mid-Cayman spreading centre axis, the Beebe Vent Field emits copper-enriched fluids and a buoyant plume that rises 1,100 m, consistent with 〉 400 °C venting from the world’s deepest known hydrothermal system. At both sites, a new morphospecies of alvinocaridid shrimp dominates faunal assemblages, which exhibit similarities to those of Mid-Atlantic vents.
    Description: This work is supported by a UK NERC award (NE/F017774/1 & NE/F017758/1) to J.T.C., D.P.C., B.J.M., K.S. and P.A.T., Royal Society Travel Grant 2009/R3 to R.C.S., A.M. is supported by SENSEnet, a Marie Curie Initial Training Network (ITN) funded by the European Commission Seventh Framework Programme, Contract Number PITN-GA-2009-237868 and a NASA ASTEP Grant NNX09AB75G to C.R.G. and C.L.V.D., which are gratefully acknowledged.
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  • 24
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Genetics 44 (2012): 121-126, doi:10.1038/ng.1054.
    Description: To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.
    Description: The authors also acknowledge the following funding sources in particular: UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/I000771/1 to S.-A.S. and A.T.; UK BBSRC BB/I025840/1 to S.-A.S.; UK BBSRC BB/I000917/1 to D.F.; EU CarcinoGENOMICS (PL037712) to J.K.; US National Institutes of Health (NIH) 1RC2CA148222-01 to W.H. and the HSCI; US MIRADA LTERS DEB-0717390 and Alfred P. Sloan Foundation (ICoMM) to L.A.-Z.; Swiss Federal Government through the Federal Office of Education and Science (FOES) to L.B. and I.X.; EU Innovative Medicines Initiative (IMI) Open PHACTS 115191 to C.T.E.; US Department of Energy (DOE) DE-AC02- 06CH11357 and Arthur P. Sloan Foundation (2011- 6-05) to J.G.; UK BBSRC SysMO-DB2 BB/I004637/1 and BBG0102181 to C.G.; UK BBSRC BB/I000933/1 to C.S. and J.L.G.; UK MRC UD99999906 to J.L.G.; US NIH R21 MH087336 (National Institute of Mental Health) and R00 GM079953 (National Institute of General Medical Science) to A.L.; NIH U54 HG006097 to J.C. and C.E.S.; Australian government through the National Collaborative Research Infrastructure Strategy (NCRIS); BIRN U24-RR025736 and BioScholar RO1-GM083871 to G.B. and the 2009 Super Science initiative to C.A.S.
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  • 25
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 3 (2012): 803, doi:10.1038/ncomms1811.
    Description: Ventilation and mixing of oceanic gyres is important to ocean-atmosphere heat and gas transfer, and to mid-latitude nutrient supply. The rates of mode water formation are believed to impact climate and carbon exchange between the surface and mid-depth water over decadal periods. Here, a record of 14C/12C (1780–1940), which is a proxy for vertical ocean mixing, from an annually banded coral from Bermuda, shows limited inter-annual variability and a substantial Suess Effect (the decrease in 14C/12C since 1900). The Sargasso Sea mixing rates between the surface and thermocline varied minimally over the past two centuries, despite changes to mean-hemispheric climate, including the Little Ice Age and variability in the North Atlantic Oscillation. This result indicates that regional formation rates of sub-tropical mode water are stable over decades, and that anthropogenic carbon absorbed by the ocean does not return to the surface at a variable rate.
    Description: Funding provided by NSF’s Chemical Oceanography Program OCE - 0526463 and 0961980 and the Stephen Hui Trust Fund.
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  • 26
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 2 (2012): 553, doi:10.1038/srep00553.
    Description: Sea surface temperature imagery, satellite altimetry, and a surface drifter track reveal an unusual tilt in the Gulf Stream path that brought the Gulf Stream to 39.9°N near the Middle Atlantic Bight shelfbreak—200 km north of its mean position—in October 2011, while a large meander brought Gulf Stream water within 12 km of the shelfbreak in December 2011. Near-bottom temperature measurements from lobster traps on the outer continental shelf south of New England show distinct warming events (temperature increases exceeding 6°C) in November and December 2011. Moored profiler measurements over the continental slope show high salinities and temperatures, suggesting that the warm water on the continental shelf originated in the Gulf Stream. The combination of unusual water properties over the shelf and slope in late fall and the subsequent mild winter may affect seasonal stratification and habitat selection for marine life over the continental shelf in 2012.
    Description: Profiler data were made available by the Ocean Observatory Initiative (OOI) during the construction phase of the project. The OOI is funded by the National Science Foundation and managed by the Consortium for Ocean Leadership. Drifter data were provided by Tim Shaw and David Calhoun at Cape Fear Community College.GGGwas supported by NSFGrant OCE-1129125. RET was supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Cooperative Institute for the North Atlantic Region. MA was supported by the Penzance Endowed Fund in Support of Assistant Scientists.
    Keywords: Ecology ; Climate change ; Atmospheric science ; Oceanography
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  • 27
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature 496 (2013): 311-316, doi:10.1038/nature12027.
    Description: The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
    Description: cquisition and storage of Latimeria chalumnae samples was supported by grants from the African Coelacanth Ecosystem Programme of the South African National Department of Science and Technology. Generation of the Latimeria chalumnae and Protopterus annectens sequences by the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University was supported by grants from the National Human Genome Research Institute (NHGRI). K.L.T. is the recipient of a EURYI award from the European Science Foundation.
    Keywords: Genome evolution ; Comparative genomics
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  • 28
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature 499 (2013): 209–213, doi:10.1038/nature12221.
    Description: Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space3. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
    Description: Joint Genome Institute (JGI) contributions were supported by the Office of Science of the US Department of Energy (DOE) under contract no. 7DE-AC02-05CH11231.
    Keywords: Genetic variation
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  • 29
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature 499 (2013): 431–437, doi:10.1038/nature12352.
    Description: Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
    Description: The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. We also thank the CeBiTec Bioinformatics Resource Facility, which is supported byBMBF grant 031A190. B.P.H. and J.A.D. were supported by the NASA Exobiology grant EXO-NNX11AR78GandNSFOISE 096842and B.P.H. by a generous contribution from G. Fullmer through the UNLV Foundation. S.M.S was supported by NSF grants OCE-0452333 and OCE-1136727, and the WHOI’s Andrew W. Mellon Fund for Innovative Research; and S.J.H. by the Canadian Foundation for Innovation, the British Columbia Knowledge Development Fund, the National Sciences and Engineering Research Council (NSERC) of Canada and the TULA foundation funded Centre for Microbial Diversity and Evolution (CMDE), and the Canadian Institute for Advanced Research (CIFAR). R.S. was supported by NSF grants DEB-841933, EF-826924, OCE-1232982, OCE-821374 and OCE-1136488, and the Deep Life I grant by the Alfred P. Sloan Foundation. P.H.was supported by a Discovery Outstanding Researcher Award (DORA) from the Australian Research Council, grant DP120103498.
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  • 30
    Publication Date: 2022-05-25
    Description: © The Author(s), 2014]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 6648, doi:10.1038/srep06648.
    Description: Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.
    Description: This research was supported by grants from the National Natural Science Foundation of China (Grant Nos. 41030211 and 41302022), the National Basic Research Program of China (Grant No. 2011CB808800), and State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Nos GBL11410 and GBL11201).
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  • 31
    Publication Date: 2022-05-25
    Description: © International Society for Microbial Ecology, 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 5 (2011): 1748–1758, doi:10.1038/ismej.2011.48.
    Description: A novel hydrothermal field has been discovered at the base of Lōihi Seamount, Hawaii, at 5000 mbsl. Geochemical analyses demonstrate that ‘FeMO Deep’, while only 0.2 °C above ambient seawater temperature, derives from a distal, ultra-diffuse hydrothermal source. FeMO Deep is expressed as regional seafloor seepage of gelatinous iron- and silica-rich deposits, pooling between and over basalt pillows, in places over a meter thick. The system is capped by mm to cm thick hydrothermally derived iron-oxyhydroxide- and manganese-oxide-layered crusts. We use molecular analyses (16S rDNA-based) of extant communities combined with fluorescent in situ hybridizations to demonstrate that FeMO Deep deposits contain living iron-oxidizing Zetaproteobacteria related to the recently isolated strain Mariprofundus ferroxydans. Bioenergetic calculations, based on in-situ electrochemical measurements and cell counts, indicate that reactions between iron and oxygen are important in supporting chemosynthesis in the mats, which we infer forms a trophic base of the mat ecosystem. We suggest that the biogenic FeMO Deep hydrothermal deposit represents a modern analog for one class of geological iron deposits known as ‘umbers’ (for example, Troodos ophilolites, Cyprus) because of striking similarities in size, setting and internal structures.
    Description: Funding has been provided by the NSF Microbial Observatories Program (KJE, DE, BT, HS and CM), by the Gordon and Betty Moore Foundation (KJE), the College of Letters, Arts, and Sciences at the University of Southern California (KJE) and by the NASA Astrobiology Institute (KJE, DE).
    Keywords: Geomicrobiology ; Deep biosphere ; Hydrothermal ; Iron bacteria ; Iron oxidation
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  • 32
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.
    Description: Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.
    Description: This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University.
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  • 33
    Publication Date: 2022-05-25
    Description: © International Society for Microbial Ecology, 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 5 (2011): 1565–1567, doi:10.1038/ismej.2011.39.
    Description: Interest in sampling of diverse environments, combined with advances in high-throughput sequencing, vastly accelerates the pace at which new genomes and metagenomes are generated. For example, as of January 2011, 12 500 user-generated metagenomes have been submitted to the public MG-RAST Annotation server (http://metagenomics. nmpdr.org; Meyer et al., 2008), 490% of which were produced using high-throughput sequencing methodologies. We have entered into an era of ‘mega-sequencing projects’ that include the Genomic Encyclopaedia of Bacteria and Archaea project (http://www.jgi.doe.gov/programs/GEBA), the Microbial Earth Project (http://genome.jgi-psf. org/programs/bacteria-archaea/MEP/index.jsf), the Human Microbiome Project (http://nihroadmap.nih. gov/hmp), the Metagenomics of the Human Intestinal Tract consortium (http://www.metahit.eu), the Terragenome Initiative (http://www.terragenome. org), the Tara Oceans Expedition (http://oceans. taraexpeditions.org), the National Ecological Observatory Network (NEON-http://www.neoninc.org), the International Census of Marine Microbes (ICoMM-http://icomm.mbl.edu), Microbial Inventory Research Across Diverse Aquatic Long-Term Ecological Research Sites (http://amarallab.mbl. edu/mirada/mirada.html), the Earth Microbiome Project (http://www.earthmicrobiome.org) and other funded and unfunded projects, with many more visionary projects on the horizon.
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  • 34
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    Nature Publishing Group
    In:  EPIC3Nature Communications, Nature Publishing Group, 5, pp. 5520, ISSN: 2041-1723
    Publication Date: 2016-06-13
    Description: One of the most abrupt and yet unexplained past rises in atmospheric CO2 (〉10 p.p.m.v. in two centuries) occurred in quasi-synchrony with abrupt northern hemispheric warming into the Bølling/Allerød, ~14,600 years ago. Here we use a U/Th-dated record of atmospheric Δ14C from Tahiti corals to provide an independent and precise age control for this CO2 rise. We also use model simulations to show that the release of old (nearly 14C-free) carbon can explain these changes in CO2 and Δ14C. The Δ14C record provides an independent constraint on the amount of carbon released (~125 Pg C). We suggest, in line with observations of atmospheric CH4 and terrigenous biomarkers, that thawing permafrost in high northern latitudes could have been the source of carbon, possibly with contribution from flooding of the Siberian continental shelf during meltwater pulse 1A. Our findings highlight the potential of the permafrost carbon reservoir to modulate abrupt climate changes via greenhouse-gas feedbacks.
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  • 35
    Publication Date: 2014-12-17
    Description: Interior Antarctica is among the most remote places on Earth and was thought to be beyond the reach of human impacts when Amundsen and Scott raced to the South Pole in 1911. Here we show detailed measurements from an extensive array of 16 ice cores quantifying substantial toxic heavy metal lead pollution at South Pole and throughout Antarctica by 1889 – beating polar explorers by more than 22 years. Unlike the Arctic where lead pollution peaked in the 1970s, lead pollution in Antarctica was as high in the early 20th century as at any time since industrialization. The similar timing and magnitude of changes in lead deposition across Antarctica, as well as the characteristic isotopic signature of Broken Hill lead found throughout the continent, suggest that this single emission source in southern Australia was responsible for the introduction of lead pollution into Antarctica at the end of the 19th century and remains a significant source today. An estimated 660 t of industrial lead have been deposited over Antarctica during the past 130 years as a result of mid-latitude industrial emissions, with regional-to-global scale circulation likely modulating aerosol concentrations. Despite abatement efforts, significant lead pollution in Antarctica persists into the 21st century.
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  • 36
    Publication Date: 2021-10-20
    Description: Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of 〉10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p 〈 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
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  • 37
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature 500 (2013): 453–457, doi:10.1038/nature12326.
    Description: Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years1. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing2. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873)3, and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
    Description: This work was supported by Genoscope-CES (where most of the sequencing was performed), by US National Science Foundation grants MCB-0821956 and MCB-1121334 to I.A., by German Research Foundation grant HA 5163/2-1 to O.H., by grant 11.G34.31.0008 fromthe Ministry of Education and Science of the Russian Federation to A.S.K., by grant NSF CAREER number 0644282 to M.K., by US National Science Foundation grant MCB-0923676 to D.B.M.W., by FRFC grant 2.4.655.09.F from the Belgian Fonds National de la Recherche Scientifique (FNRS) and a start-up grant from the University of Namur to K.V.D.; J.F.F. and K.V.D. thank also J.-P. Descy (University of Namur) for funding support.
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  • 38
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 4342, doi:10.1038/ncomms5342.
    Description: Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.
    Description: This work was mainly supported by Howard Hughes Medical Institute. H.P. is currently supported by the Allen Institute for Brain Science. R.W.T. and A.M. were supported by a grant MH071739 (MERIT).
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  • 39
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 5385, doi:10.1038/ncomms6385.
    Description: Submarine mud volcanoes are important sources of methane to the water column. However, the temporal variability of their mud and methane emissions is unknown. Methane emissions were previously proposed to result from a dynamic equilibrium between upward migration and consumption at the seabed by methane-consuming microbes. Here we show non-steady-state situations of vigorous mud movement that are revealed through variations in fluid flow, seabed temperature and seafloor bathymetry. Time series data for pressure, temperature, pH and seafloor photography were collected over 431 days using a benthic observatory at the active Håkon Mosby Mud Volcano. We documented 25 pulses of hot subsurface fluids, accompanied by eruptions that changed the landscape of the mud volcano. Four major events triggered rapid sediment uplift of more than a metre in height, substantial lateral flow of muds at average velocities of 0.4 m per day, and significant emissions of methane and CO2 from the seafloor.
    Description: Participation of the Sentry AUV and TETHYS team from WHOI was funded by the Arctic Research Initiative of WHOI’s Ocean and Climate Change Institute and the NASA ASTEP grant NNX09AB76G. Additional funds were made available by the AWI, the Max Planck Society and the DFG METEOR/MERIAN programme, as well as the Leibniz programme to A.B.
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  • 40
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 4102, doi:10.1038/ncomms5102.
    Description: Tropical south-western Pacific temperatures are of vital importance to the Great Barrier Reef (GBR), but the role of sea surface temperatures (SSTs) in the growth of the GBR since the Last Glacial Maximum remains largely unknown. Here we present records of Sr/Ca and δ18O for Last Glacial Maximum and deglacial corals that show a considerably steeper meridional SST gradient than the present day in the central GBR. We find a 1–2 °C larger temperature decrease between 17° and 20°S about 20,000 to 13,000 years ago. The result is best explained by the northward expansion of cooler subtropical waters due to a weakening of the South Pacific gyre and East Australian Current. Our findings indicate that the GBR experienced substantial meridional temperature change during the last deglaciation, and serve to explain anomalous deglacial drying of northeastern Australia. Overall, the GBR developed through significant SST change and may be more resilient than previously thought.
    Description: Funding was provided by Deutsche Forschungsgemeinschaft (FE 615/4-1), Australian Research Council (Discovery grant DP1094001), Australia and New Zealand IODP Consortium, Australian Institute of Nuclear Science and Engineering, Natural Environmental Research Council (NE/H014136/1, NE/H014268/1), the Cooperative Research Program of the Center for Advanced Marine Core Research (10B039, 11A013, 11B041), Ministry of Earth Sciences, Govt. of India (with partial support from DST & ISRO-GBP) and Japan Society for the Promotion of Science (JSPS NEXT-GR031).
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  • 41
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 6 (2012): 1901-1915, doi:10.1038/ismej.2012.31.
    Description: Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global ‘dark ocean’ mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content.
    Description: CSR was supported by an NSF Postdoctoral Fellowship in Biological Informatics (DBI-0532893). The research was supported by National Science Foundation awards: ANT 0632389 (to AEM and JJG), and ANT 0632278 and 0217282 (to HWD), all from the Antarctic Organisms and Ecosystems Program.
    Keywords: Antarctic bacterioplankton ; Metagenomics ; Chemolithoautotrophy
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  • 42
    Publication Date: 2022-05-26
    Description: © Macmillan Publishers, 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Oncogene 32 (2013): 1135–1143, doi:10.1038/onc.2012.135.
    Description: Neurofibromatosis type 2 patients develop schwannomas, meningiomas and ependymomas resulting from mutations in the tumor suppressor gene, NF2, encoding a membrane-cytoskeleton adapter protein called merlin. Merlin regulates contact inhibition of growth and controls the availability of growth factor receptors at the cell surface. We tested if microtubule-based vesicular trafficking might be a mechanism by which merlin acts. We found that schwannoma cells, containing merlin mutations and constitutive activation of the Rho/Rac family of GTPases, had decreased intracellular vesicular trafficking relative to normal human Schwann cells. In Nf2−/− mouse Schwann (SC4) cells, re-expression of merlin as well as inhibition of Rac or its effector kinases, MLK and p38SAPK, each increased the velocity of Rab6 positive exocytic vesicles. Conversely, an activated Rac mutant decreased Rab6 vesicle velocity. Vesicle motility assays in isolated squid axoplasm further demonstrated that both mutant merlin and active Rac specifically reduce anterograde microtubule-based transport of vesicles dependent upon the activity of p38SAPK kinase. Taken together, our data suggest loss of merlin results in the Rac-dependent decrease of anterograde trafficking of exocytic vesicles, representing a possible mechanism controlling the concentration of growth factor receptors at the cell surface.
    Description: This work was supported by NIH R01 CA118032 (to NR), and MBL research fellowships (to NR and GM), NIH R01 NS23868 (to STB).
    Keywords: Merlin ; NF2 ; Rac ; Trafficking ; Exocytosis
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  • 43
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 4170, doi:10.1038/srep04170.
    Description: Estimating abundance of Antarctic minke whales is central to the International Whaling Commission's conservation and management work and understanding impacts of climate change on polar marine ecosystems. Detecting abundance trends is problematic, in part because minke whales are frequently sighted within Antarctic sea ice where navigational safety concerns prevent ships from surveying. Using icebreaker-supported helicopters, we conducted aerial surveys across a gradient of ice conditions to estimate minke whale density in the Weddell Sea. The surveys revealed substantial numbers of whales inside the sea ice. The Antarctic summer sea ice is undergoing rapid regional change in annual extent, distribution, and length of ice-covered season. These trends, along with substantial interannual variability in ice conditions, affect the proportion of whales available to be counted by traditional shipboard surveys. The strong association between whales and the dynamic, changing sea ice requires reexamination of the power to detect trends in whale abundance or predict ecosystem responses to climate change.
    Description: This work received funding from the following institutions: Alfred Wegener Institute for Polar and Marine Research (AWI); Dutch Ministry of Agriculture, Nature and Food Quality (EL & I); German Federal Ministry of Food, Agriculture and Consumer Protection (BMELV); German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU); the Institute for Marine Resources and Ecosystem Studies (Wageningen IMARES); Johann Heinrich von Thu¨nen Institute (Federal Research Institute for Rural Areas, Forestry and Fisheries); the Netherlands Polar Programme (NPP) of the Netherlands Organisation for Scientific Research (NOW); Research and Technology Centre Westcoast (FTZ) of the University Kiel. RW was funded by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme (proposal Nu 253407 (call reference: FP7- PEOPLE-2009-IIF).
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  • 44
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 8 (2014): 1-3, doi:10.1038/ismej.2013.176.
    Description: The need for metadata standards for microbe sampling in the built environment.
    Description: We would like to thank the Alfred P Sloan Foundation grant FP047325-01-PR for support for this project.
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  • 45
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 5024, doi:10.1038/srep05024.
    Description: Climate change is a major threat to global biodiversity. Antarctic ecosystems are no exception. Investigating past species responses to climatic events can distinguish natural from anthropogenic impacts. Climate change produces ‘winners’, species that benefit from these events and ‘losers’, species that decline or become extinct. Using molecular techniques, we assess the demographic history and population structure of Pygoscelis penguins in the Scotia Arc related to climate warming after the Last Glacial Maximum (LGM). All three pygoscelid penguins responded positively to post-LGM warming by expanding from glacial refugia, with those breeding at higher latitudes expanding most. Northern (Pygoscelis papua papua) and Southern (Pygoscelis papua ellsworthii) gentoo sub-species likely diverged during the LGM. Comparing historical responses with the literature on current trends, we see Southern gentoo penguins are responding to current warming as they did during post-LGM warming, expanding their range southwards. Conversely, Adélie and chinstrap penguins are experiencing a ‘reversal of fortunes’ as they are now declining in the Antarctic Peninsula, the opposite of their response to post-LGM warming. This suggests current climate warming has decoupled historic population responses in the Antarctic Peninsula, favoring generalist gentoo penguins as climate change ‘winners’, while Adélie and chinstrap penguins have become climate change ‘losers’.
    Description: We thank the Zoological Society of London, Quark Expeditions, Exodus Travels ltd., Oceanites, the Holly Hill Charitable Trust, the Charities Advisory Trust and an U.S. National Science Foundation (NSF) Office of Polar Programs grant (ANT-0739575) for funding.
    Keywords: Climate-change ecology ; Molecular ecology ; Molecular evolution ; Population genetics
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  • 46
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 5316, doi:10.1038/srep05316.
    Description: During the propagation of coherent mesoscale eddies, they directly or indirectly induce many effects and interactions at different scales, implying eddies are actually serving as a kind of energy carrier or energy source for these eddy-related dynamic processes. To quantify this dynamically significant energy flow, the multi-year averaged horizontal eddy energy fluxes (EEFs) were estimated by using satellite altimetry data and a two-layer model based on hydrographic climatology. There is a strong net westward transport of eddy energy estimated at the mean value of ~13.3 GW north of 5°N and ~14.6 GW at the band 5°S ~ 44°S in the Southern Hemisphere. However, poleward of 44°S east-propagating eddies carry their energy eastward with an averaged net flux of ~3.2 GW. If confirmed, it would signify that geostrophic eddies not only contain the most of oceanic kinetic energy (KE), but also carry and spread a significant amount of energy with them.
    Description: This study is supported by Grants XDA11010202, 2011CB403505, 2013CB430303; Projects 41306016, U1033002, 40976021 of NNSFC and LTOZZ1304.
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  • 47
    facet.materialart.
    Unknown
    Nature Publishing Group
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Climate Change 4 (2014): 862-863, doi:10.1038/nclimate2386.
    Description: Low oxygen levels in tropical oceans shape marine ecosystems and biogeochemistry with climate change expected to expand these regions. Now, a study indicates that regional dynamics control tropical oxygen trends, bucking projected global reductions in ocean oxygen.
    Description: 2015-03-25
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  • 48
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 4274, doi:10.1038/ncomms5274.
    Description: Ecological connections between surface waters and the deep ocean remain poorly studied despite the high biomass of fishes and squids residing at depths beyond the euphotic zone. These animals likely support pelagic food webs containing a suite of predators that include commercially important fishes and marine mammals. Here we deploy pop-up satellite archival transmitting tags on 15 Chilean devil rays (Mobula tarapacana) in the central North Atlantic Ocean, which provide movement patterns of individuals for up to 9 months. Devil rays were considered surface dwellers but our data reveal individuals descending at speeds up to 6.0 m s−1 to depths of almost 2,000 m and water temperatures 〈4 °C. The shape of the dive profiles suggests that the rays are foraging at these depths in deep scattering layers. Our results provide evidence of an important link between predators in the surface ocean and forage species occupying pelagic habitats below the euphotic zone in ocean ecosystems.
    Description: This research was partially supported by the Portuguese Foundation for Science and Technology/Ministry of Education and Science (FCT/MCTES-MEC) through individual support to P.A. (Cieˆncia 2008/POPH/QREN) and J.F. (SFRH/BPD/66532/2009) and the LARSyS Strategic Project (PEst/OE/EEI/LA00009/2011). This study was support by the US National Science Foundation (OCE 0825148 to S.R.T. and G.B.S.), The Harrison Foundation, Rodney and Elizabeth Berens, the King Abdullah University of Science and Technology (baseline research funds to M.L.B.) and the Woods Hole Oceanographic Institution.
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  • 49
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 5848, doi:10.1038/srep05848.
    Description: Interior Antarctica is among the most remote places on Earth and was thought to be beyond the reach of human impacts when Amundsen and Scott raced to the South Pole in 1911. Here we show detailed measurements from an extensive array of 16 ice cores quantifying substantial toxic heavy metal lead pollution at South Pole and throughout Antarctica by 1889 – beating polar explorers by more than 22 years. Unlike the Arctic where lead pollution peaked in the 1970s, lead pollution in Antarctica was as high in the early 20th century as at any time since industrialization. The similar timing and magnitude of changes in lead deposition across Antarctica, as well as the characteristic isotopic signature of Broken Hill lead found throughout the continent, suggest that this single emission source in southern Australia was responsible for the introduction of lead pollution into Antarctica at the end of the 19th century and remains a significant source today. An estimated 660 t of industrial lead have been deposited over Antarctica during the past 130 years as a result of mid-latitude industrial emissions, with regional-to-global scale circulation likely modulating aerosol concentrations. Despite abatement efforts, significant lead pollution in Antarctica persists into the 21st century.
    Description: This work primarily was supported by the U.S. National Science Foundation Division of Polar Programs (research grants 9903744, 0538427, 0538416, 0968391, 1142166, 0632031; instrument grants 0216552, 0421412).
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  • 50
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 7366, doi:10.1038/srep07366.
    Description: The magnitude of flooding in New York City by Hurricane Sandy is commonly believed to be extremely rare, with estimated return periods near or greater than 1000 years. However, the brevity of tide gauge records result in significant uncertainties when estimating the uniqueness of such an event. Here we compare resultant deposition by Hurricane Sandy to earlier storm-induced flood layers in order to extend records of flooding to the city beyond the instrumental dataset. Inversely modeled storm conditions from grain size trends show that a more compact yet more intense hurricane in 1821 CE probably resulted in a similar storm tide and a significantly larger storm surge. Our results indicate the occurrence of additional flood events like Hurricane Sandy in recent centuries, and highlight the inadequacies of the instrumental record in estimating current flood risk by such extreme events.
    Description: Funding for this work was provided by the Hudson River Foundation Expedited Grant #004/12E, the Hudson River Foundation Graduate Fellowship 02–13, the National Science Foundation (RAPID grant #1313859 and instrument and facility support via grant IF-0949313), and the Dalio Explore Fund.
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  • 51
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3993-4000 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: This paper describes the application of an adaptive learning system comprising an associative memory to the characterization of ultrasonic phenomena. The mapping of source and waveform data and vice versa can be performed by utilizing the off-diagonal cross-correlation portions of the associative memory. It is suggested that a more general description of the ultrasonic phenomena can be obtained if the diagonal, autocorrelation portions of the memory are also utilized. In this case, the memory is applicable for the autoassociative optimal filtering of experimental data. Experiments are described which utilize such an adaptive system, running on a laboratory minicomputer, to process the signals from a transient ultrasonic source in a plate specimen. It is shown how the system learns from the experimental pattern vectors, formed from the ultrasonic waveforms and encoded information about the source. The source characteristics are recovered by the recall procedure from the detected ultrasonic signals and vice versa. Also, the changes in the wave phenomenon corresponding to changes in the boundary conditions of the specimen can be detected from the discrepancy between the presented and the learned signals.
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  • 52
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A new type of solid-state sensor for the detection of minute concentrations of hydrogen gas has been developed. The sensor was made of thin, commercially available polyvinylidene fluoride (PVDF) pyroelectric film, sputter coated with Pd. An infrared laser beam served to produce alternating temperature gradients on the Pd-PVDF and on reference Al-Ni-PVDF films, which, in turn, generated ac voltages due to the photopyroelectric (P2E) effect. Exposure to hydrogen gas was shown to produce an increased differential signal between the Pd and reference electrodes; this was tentatively attributed to the adsorption and dissociation of hydrogen molecules on the Pd surface, which caused a shift on the Pd-PVDF pyroelectric coefficient, due to interactions at the Pd-PVDF interface. The differential signal was found to be proportional to the square root of the hydrogen partial pressure at very low concentrations (〈1000 ppm). A semiquantitative interpretation of the differential signal has been achieved using simple gas-solid interaction theory and the combination of the Langmuir isotherm with the photopyroelectric theory in the range of 4–200 Pa. For high pressures (〉200 Pa) the paper is limited only to a phenomenological description. The thickness of the palladium layer has been found to play an important role with respect to the signal response. Presently, hydrogen concentrations as small as 40 ppm, in a flowing H2+N2 mixture, have been detected. The influence of gas flow rate has also been studied. Other characteristics such as the response times, the reversibility, and the durability of the Pd-PVDF-P2E hydrogen detector will also be presented.
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  • 53
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4010-4012 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The quenching cross sections of Ne metastable levels by N2 and CO were measured to be (in A(ring)2 units): 8.3±0.4, 8.7±0.4 for 3s(3/2)2 level and 8.0±0.4, 9.1±0.4 for 3s(1/2)0 level, respectively, at 443 K. The metastables are produced by a pulsed electron beam and their population was monitored by fluorescence induced by a cw dye laser.
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  • 54
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4013-4018 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The generation of quasi-static uniform electric fields by a slotted conducting spherical shell is fully analyzed for an arbitrary number of slots pairs, and optimum surface potential and slots position are determined. Numerical results for spherical shells with up to 14 slots are discussed.
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  • 55
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4001-4009 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: This paper discusses a theoretical as well as experimental study of the performance of electro-optic sampling using a noncontact electro-optic probe, i.e., external electro-optic sampling. Sensitivity, temporal resolution, and the capacitive loading effect of this system are calculated by analysis of a static electric field coupled to an electro-optic crystal placed in close proximity to transmission lines such as microstrip lines and coplanar strips. Full-wave analysis is also applied to investigate effect of the electro-optic crystal on the transient property of high-speed electrical signals. Based on these analytical considerations, we have developed an external electro-optic sampling system using precise probe-positioning technology, which improves the measurement reproducibility. A temporal resolution of 0.5 ps and a spatial resolution of 1 μm are confirmed with this system.
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  • 56
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4089-4094 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Experimental and theoretical studies of a fundamental mode large-orbit gyrotron designed to produce high-power rf radiation in the TE11 mode at about 1 GHz are reported. Theoretical calculations performed as part of the experimental design process are presented. Results of initial experiments are reported in which 500–1000 MW of rf radiation was observed at frequencies 700 and 1200 MHz, consistent with theoretical expectations. The estimated eletronic efficiency of the device is about 10%. Gas cell breakdown patterns produced by the rf pulse are consistent with operation in the desired TE11 mode.
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  • 57
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4104-4111 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: As a second in a series of theoretical models for the electrical discharge machining (EDM) process, an erosion model for the anode material is presented. As with our point heat-source model in the previous article, the present model also accepts power rather than temperature as the boundary condition at the plasma/anode interface. A constant fraction of the total power supplied to the gap is transferred to the anode. The power supplied is assumed to produce a Gaussian-distributed heat flux on the surface of the anode material. Furthermore, the area upon which the flux is incident is assumed to grow with time. The model is capable of showing, via the determined migrating melt fronts, the rapid melting of the anodic material as well as the subsequent resolidification of the material foation from plasma dynamics modeling could improve substantially our results.
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  • 58
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4112-4122 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Designs are proposed, based on a series of one-dimensional calculations, for layered, hollow cylindrical targets to be placed on the axis of an imploding, hollow Z-pinch plasma that can create the approximate plasma conditions, as well as radiation spectrum, for a photoionization pumped, Ne-like recombination laser. The lasant must reach the Ne-like state and be at the appropriate density at the same time that the photoionizing pump radiation is present, placing severe constraints on designs for such targets. Target designs are further constrained by the fact that the 3s-2p resonance line, which depopulates the lower lasing state, must not be highly trapped and by the fact that the upper lasing state must not be collisionally depopulated. We find that hollow, cylindrical targets consisting of a few-micron-thick CH strongback, coated on the inside with a thin layer of Ni lasant and on the outside with an Al converter layer, can be optimized to achieve appropriate conditions for lasing and modest levels of gain.
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  • 59
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4163-4175 
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    Topics: Physics
    Notes: The trigatron has been in widespread use as a demand-triggered, high-voltage switch for more than 40 years. In spite of the popularity and maturity of the technology, there persists an uncertainty over the basic physical mechanism(s) responsible for triggering breakdown in the devices. We present the results of an empirical study of trigatrons that directly demonstrates that breakdown is initiated by a streamer launched from the trigger pin, independent of the trigger spark. We compare our results with those of previous workers, and discuss the generality of our conclusions.
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  • 60
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4181-4183 
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    Topics: Physics
    Notes: Reaction kinetics for the direct synthesis process of compound GaSb from Ga and Sb metals was studied by observing viscosity changes of the melt during the reaction process. The mole fraction of Ga (cGa) was obtained during synthesis using the equation; log η=cGa(log ηGa +log ηSb)+(1−2cGa)log ηGaSb, where η is the viscosity of the total system, and ηGa,ηSb, and ηGaSb are the viscosities of molten Ga metal, molten Sb metal, and molten GaSb, respectively. The reaction rate was obtained from the variation of the mole fraction of reactant cGa. Assuming a second-order reaction, the activation energy was estimated to be 15.5 kcal/mol.
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  • 61
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4184-4187 
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    Topics: Physics
    Notes: A PbTe flux has been used for n-type (Te) doping of GaAs, GaSb, and AlGaSb. The effects of surface accumulation and Te desorption were noticeable in secondary-ion mass spectroscopy profiles of GaAs layers grown at temperatures in excess of 540 °C. Te accumulation was not apparent in GaSb layers grown at temperatures up to 630 °C, but Te desorption occurred from GaSb at temperatures above 540 °C. The donor ionization energy of Te in AlxGa1−xSb is 44 meV for 0.4〈X〈0.5, i.e., significantly lower than the ionization energies of S or Se in similar material.
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  • 62
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4284-4287 
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    Topics: Physics
    Notes: The low-frequency excess electrical noise has been measured on carbon fibers with a wide range of crystalline perfection and corresponding electrical and mechanical properties. Fibers include those prepared from ex-PAN and ex-pitch polymers, and a catalytic-chemical vapor deposited filament. The extensional (Young's) moduli of these fibers varied from about 220 to 890 GPa (35–130 Msi), while the electrical resistivities varied from about 19 to 1 μΩ m. The low-frequency electrical noise of each fiber was found to be proportional to I2 and to vary as 1/f α, where f is the frequency and α is about 1.15. The most striking feature of the results was the strong dependence of the normalized noise power on the degree of crystalline perfection.
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  • 63
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4279-4283 
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    Topics: Physics
    Notes: The densities of states of the conduction and valence bands of silicon and GaAs have been calculated at 300 K for the case of an electron-hole plasma, which can occur at high-injection levels in bipolar devices or in bulk material under intense optical excitation. The results show considerable narrowing of the band gap, which needs to be included in the analysis of device measurements or the interpretation of photoluminescence data. Furthermore, the band-gap narrowing that results from dopant ions is reduced by excess carriers because of the reduced free-carrier screening radius.
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  • 64
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4288-4294 
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    Topics: Physics
    Notes: We investigate the transient response of photogenerated carriers to an external electric field in bulk GaAs. The results of our Monte Carlo simulations indicate that the initial velocity rise times are a strong function of the carrier density. This is caused by a combination of the hot-phonon effect and the enhanced electron-hole scattering within the plasma. Contrary to some previous suggestions, the hot-phonon effect alone is insufficient to explain the initial velocity behavior seen experimentally. The steady-state velocity is limited by the electron-hole scattering.
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  • 65
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4312-4316 
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    Topics: Physics
    Notes: Data obtained on a set of GaAs/AlGaAs double-barrier quantum-well resonant tunneling structures are compared with model calculations of the ideal case where scattering is negligible and tunneling is coherent throughout the entire structure. The comparison points to interface roughness in the well as the most likely cause for the observed large valley currents. The currents at low biases, before resonance sets in, are also studied. Their magnitude is found to be consistent also with the sequential tunneling picture.
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  • 66
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4317-4324 
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    Topics: Physics
    Notes: The microstructures of three ZnO varistor materials with different Bi2O3 contents have been evaluated by analytical electron microscopy in combination with x-ray diffractometry. The results have been correlated to microelectrode measurements, where breakdown voltages of individual ZnO junctions were measured, and also to current/voltage characteristics of bulk specimens. The volume fraction of the continuous intergranular network of Bi-rich phases, which lies along the triple junctions of the ZnO grains, increases with increasing Bi2O3 content, The conductivity of this network is strongly influenced by its internal microstructure. It was found that increased volume fractions of δ-Bi2O3 and less interpenetration between α-Bi2O and δ-Bi2O3 increases the conductivity of the network. Individual ZnO/ZnO grain boundaries exhibited breakdowns at 3.2 and 3.6 V, depending upon whether they contained segregated Bi atoms or thin Bi-rich amorphous films. The current/voltage characteristics of heterojunctions between ZnO and intergranular Bi2O3 were asymmetrical with respect to the polarity of the applied voltage. It was found that α-Bi2O3 and δ-Bi2O3 give rise to different breakdowns for electrons traveling from the Bi2O3 into an adjacent ZnO grain.
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 4325-4328 
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    Topics: Physics
    Notes: Isothermal anneal experiments have been conducted over a wide temperature range from 300 to 900 °C for polycrystalline YBa2 Cu3 O7−x samples in air. The phase transformation and oxygen contents of the annealed samples were studied and determined by x-ray diffraction and iodine titration. Oxygen diffusion coefficients at different temperatures were determined by a novel technique based on direct observation of the oxygen diffusion fronts by polarized light microscopy. The activation energy for the diffusion of oxygen in YBa2 Cu3 O7−x was obtained by an Arrhenius plot of the diffusion coefficients at different temperatures. The tetragonal-to-orthorhombic phase transformation controlled by oxygen diffusion is discussed.
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    Journal of Applied Physics 66 (1989), S. 4329-4337 
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    Topics: Physics
    Notes: In the limit of negligible exchange and anisotropy (except uniaxial), certain shapes of magnetic samples in certain subsaturating field configurations can be analyzed analytically to obtain magnetization and domain wall patterns. Here we consider two cases: (1) generalized cylindrical objects of arbitrary cross section (with several specific examples given) and (2) a general ellipsoid. We also discuss a "tipping instability'' which might occur in an ellipsoid with uniaxial anisotropy, resulting in a sudden transition from a "curling'' state to a "transverse vortex'' state.
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    Journal of Applied Physics 66 (1989), S. 4338-4344 
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    Topics: Physics
    Notes: Fe multilayered films with various intermediate layers are formed. Their magnetic properties and film structures are examined to understand the mechanism originating soft magnetic properties. The soft magnetic properties change with the lattice mismatches between Fe and intermediate layers, showing low coercive force and high relative permeability at lattice mismatches from 0.4 to 1.2%. It is thought that the lattice mismatches above 0.4% decrease Fe crystallite size and improve soft magnetic properties. Although Fe crystallite size is small at the lattice mismatches above 1.2%, the soft magnetic properties are poor. This is because the large lattice mismatch increases internal stress and magnetic anisotropy energy. This report indicates that the good soft magnetic properties are obtained when both Fe crystallite size and internal stress are small.
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    Journal of Applied Physics 66 (1989), S. 4345-4349 
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    Topics: Physics
    Notes: The advantage of a film with high saturation magnetic flux density for perpendicular magnetic recording is investigated through computer simulations and read/write measurements. A single-pole head using Fe-C/Ni-Fe multilayered film with a saturation magnetic flux density of 2.0 T is fabricated. Read/write tests are performed with the Co-Cr double-layer media. It is shown that the recording ability of this head is very high and does not change with increasing Co-Cr layer coercivity. Computer simulations show that the recording ability also increases when using film with high saturation magnetic flux density for the back layer of a double-layer medium. The upper limit of saturation magnetization of the recording layer can be extended by increasing coercivity. Thus, the higher saturation magnetization medium, which offers higher output voltage and resolution, can be used by applying film with high saturation magnetic flux density for the main pole and the back layer.
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    Journal of Applied Physics 66 (1989), S. 4350-4359 
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    Topics: Physics
    Notes: In this paper we study the dielectric response of materials which display a dc conductivity at low frequencies. A framework based on the generalized Master equation and time dependent transition rates is argued to be applicable to disordered materials and exhibits an interesting fractal dynamics. The relationship of this framework to the "Distribution of transition rates'' theory and the models put forward by Ngai [Comments Solid State Phys. 9, 141 (1980] and by Dissado and Hill [J. Chem. Soc. Faraday Trans. 2, 80, 291 (1984)] is discussed. Model calculations of the dielectric response by means of the above-mentioned three theories are carried out and are compared to experimental results on Al2O3 and SiOxNy thin films. The theories can be distinguished only when the exponent of the power law at high frequencies is close to unity. The Dissado–Hill model is in better agreement with experiments than the other theories, but important discrepancies can easily be seen.
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    Journal of Applied Physics 66 (1989), S. 4381-4386 
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    Topics: Physics
    Notes: Band-gap narrowing of GaAs as a function of doping concentration has been measured using photoluminescence spectroscopy on samples grown by molecular beam epitaxy. Both n- (Si) and p- (Be) doped samples with concentrations varying from 3×1017 to 3×1018 cm−3 have been measured. The experimental results obtained from a line-shape analysis of the spectra taking tailing effects into account are in good agreement with recent theoretical calculations. A simple expression for the band-gap narrowing as a function of concentration for both n-and p-doped GaAs is given.
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    Journal of Applied Physics 66 (1989), S. 4387-4392 
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    Notes: We propose that short-period doping superlattices are suitable for the enhancement of a third-order susceptibility arising from free carriers in nonparabolic energy subbands. The inherent advantage lies in the ability to simply engineer the superlattice potential profile, yielding control of miniband energy dispersion. We consider short-period GaAs doping superlattices composed of uniformly doped donor and acceptor layers, and planar-doped n- and p-type monolayers separated by intrinsic regions. Calculations of the electronic structure of compensated and n-type noncompensated n-i-p-i superlattices incorporating miniband dispersion at nonzero temperature are reported. We show that small modulations of the superlattice potential lead to large subband nonparabolicities and we calculate a twentyfold improvement in the third-order susceptibility over bulk GaAs at room temperature, comparable to that predicted for GaAs/AlGaAs compositional superlattices.
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    Journal of Applied Physics 66 (1989), S. 4418-4424 
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    Topics: Physics
    Notes: The physical mechanism of photostimulated luminescence (PSL) of RbBr:Tl, resulting from x-ray irradiation, has been investigated. Spectroscopic methods have been utilized to identify the bromine F center as the occupied electron trap. By means of absorption studies the charge state of the dopant Tl was found to be monovalent. The spectral emission showed the characteristic Jahn–Teller splitting of the 3P1 state of the Tl+ and its known temperature dependence. PSL lifetime and efficiency experiments have been conducted in the temperature regime from liquid helium to 500 K to understand the charge transport from the F center to the activator and have been compared with corresponding data obtained from direct optical excitation into the A band of the Tl+. The observed temperature dependencies of both lifetimes could be explained by the properties of the s2 ion Tl+. As a resulting model for the PSL process a tunneling from the relaxed excited state of the F center to an excited state of the Tl2+ ion following photostimulation is suggested. The temporal, thermal, and spectral behavior of the subsequent radiative fraction of the deexcitation process is solely determined by the properties of the Tl+ ion in the RbBr matrix.
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    Journal of Applied Physics 66 (1989), S. 4425-4430 
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    Topics: Physics
    Notes: Experiments were conducted in which a high-power CO2 TEA laser interacted with metallic cathode in a high-vacuum (10−8 Torr) diode. For power densities lower than 5×107 W/cm2, no current was detected. For power densities in the range of 5×107–5×108 W/cm2, the Cu cathode emitted a maximum current of 40 mA. At a higher power density level, a circuit-limited current of 8 A was detected. The jump of a few orders of magnitude in the current is attributed to breakdown of the diode gap. The experimental results are similar to those of a triggered vacuum gap, and a thorough comparison is presented in this paper. The influence of the pressure in the vacuum chamber on the current magnitude shows the active role that adsorbed gas molecules have in the initial breakdown. When the cathode material was changed from metal to metal oxide, much lower laser power densities were required to reach the breakdown current region.
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  • 76
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    Journal of Applied Physics 66 (1989), S. 4393-4407 
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    Topics: Physics
    Notes: The intrinsic magneto-optical readout performance in reflection is calculated for bismuth and cobalt-substituted iron-garnet films on a multilayer interference mirror at 800-, 633-, 488-, and 420-nm wavelengths and is compared with that of a trilayer medium composed of an antireflection layer, a rare-earth transition-metal film, and a metallic mirror. It is found, when disregarding inhomogeneities, like irregular domain shape, ripple of the magnetic anisotropy, and surface roughness, that iron garnets are superior to rare-earth transition-metal films at blue to near-ultraviolet wavelengths if operated at thicknesses where optical interference occurs in the magnetic layer. Optical transmittance at these thicknesses is sufficiently high so that multilevel recording media can be conceived. In contrast, the optical absorption of rare-earth transition-metal alloys is much higher so that only thicknesses much above interference conditions are feasible, thus precluding them from multilevel recording.This comparative study is supplemented by calculating the magneto-optical performance in reflection of a recently reported multilayer medium composed of an antireflection coating and a periodically repeated sandwich of 4-A(ring) Co and 9-A(ring) Pt layers. In contrast to conventional rare-earth transition-metal films, the magneto-optical Kerr effects of this material do not degrade when decreasing the wavelength from 800 to 400 nm, but still do not reach the performance of bismuth-iron garnets in the green to ultraviolet spectrum. For the garnet system Y3−xBixFe5O12 the spectra of the real and imaginary parts of the diagonal and off-diagonal component of the dielectric tensor εij are reported in the range of photon energies between 1 and 5 eV, i.e., 1240- and 248-nm wavelengths and a bismuth concentration up x=1.4 Bi3+ atoms per garnet formula. In addition, the off-diagonal components ε'12 and ε(large-closed-square)12 are parametrized in terms of paramagnetic optical transitions, taking the spectra for x=1.25 as a typical example. Furthermore, optical and magneto-optical spectra are presented for Co2+- and Co3+- substituted iron garnets and barium hexaferrite BaFe12O19.Finally, the spectral dependence of the magneto-optical figure of merit 2aitch-thetaF/α of (Y,Bi)3Fe5O12 and amorphous TbFe is compared. Furthermore, high-resolution transmission electron micrographs and x-ray double-crystal diffractograms are presented that elucidate the perfect epitaxial alignment of single-crystalline iron-garnet films and the columnar morphology of polycrystalline iron-garnet films prepared by rf magnetron sputtering. The initial nucleation period of polycrystalline garnet films can be influenced by low-energy ion bombardment for improving the film texture. Under favorable sputtering conditions single- and polycrystalline bismuth-iron garnet films develop a perpendicular magnetic anisotopy. It is not yet clear whether sputtered iron-garnet films can meet the critical requirements on magnetic wall coercivity and magnetic remanence.
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    Journal of Applied Physics 66 (1989), S. 4441-4443 
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    Topics: Physics
    Notes: Chemical analysis of the surface of an oxidized silicon-germanium mixture by Rutherford backscattering reported recently showed that the silicon is oxidized, but not the germanium. This result provides evidence that the effective oxygen concentration at the silica-silicon interface is low, which is contrary to a slow interface reaction. Strain in the oxide film can result in linear-parabolic oxidation kinetics without a slow interface reaction.
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    Journal of Applied Physics 66 (1989), S. 4539-4541 
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    Notes: Low energy inelastic electron tunneling spectra are presented for thermally formed oxides on copper films. Thinner oxide tunnel barriers are observed to contain interfacial gradients as evidenced by spectral intensity asymmetries between forward and reverse bias, whereas thicker oxides appear to be more uniform in composition. Spectral results are in good qualitative agreement with reported studies of bulk cuprous oxides, and the semiconducting nature of the oxide layers is reflected in a negative temperature coefficient of resistivity of the tunnel junctions.
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    Journal of Applied Physics 66 (1989), S. 4547-4548 
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    Topics: Physics
    Notes: Optical waveguide profiles of He+ ion implanted polymethylmethacrylate have been analyzed. The surface index increases by up to 3% and the depth profile of the index is consistent with a diffusion limited decomposition of the target. This was confirmed by 77- or 300-K implants with a capping layer to inhibit decomposition.
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    Journal of Applied Physics 66 (1989), S. 4544-4546 
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    Topics: Physics
    Notes: Infrared absorption spectroscopy was used to study the oxidation of hydrogenated amorphous silicon carbide (a-Si:C:H) films prepared by the glow-discharge decomposition of gaseous mixtures of silane and methane. It has been found that carbon-rich samples incorporate oxygen when exposed to air, as detected by an increased absorption of the Si-O-Si stretching vibration band. The analysis of the infrared spectra of samples annealed in air at room temperature and at 200 °C indicates that, except for their oxidation rate, no appreciable difference exists in the mechanisms of oxygen incorporation in the films at the two temperatures. The oxidation kinetics suggests an open porous structure for these carbon-rich films. On the contrary, samples having a low carbon content appear to oxidize on the surface only, in a way similar to amorphous silicon.
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    Journal of Applied Physics 66 (1989), S. 4554-4556 
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    Topics: Physics
    Notes: Thin-film transistors have been made using nickel phthalocyanine (PcNi) as active component. The characteristics of these transistors are studied with positive and negative gate-source and drain-source polarizations. The channel conductivity was p type. Very different thicknesses of PcNi layer are used, showing that in the two polarizations the effects are interfacial.
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    Journal of Applied Physics 66 (1989), S. 4560-4561 
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    Notes: A technique for measuring the field-effect mobility of a gateless In0.53Ga047As/In0.52Al0.48As heterojunction has been developed by using the nonpersistent photoconductive effect. Subband depopulation in a parallel magnetic field is consistent with the "universal'' depopulation observed in InAs, InSb, and HgCdTe metal-oxide-semiconductor field-effect transistors.
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    Journal of Applied Physics 66 (1989), S. 3445-3452 
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    Notes: Transmission versus voltage operating characteristics of a GaAs/AlGaAs multiple-quantum-well light modulator have been measured at temperatures between 4.3 and 290 K. At 4.3 K, the linewidth of the heavy-hole exciton absorption is 1.3 meV, and the modulation ratio is greater than 1000 at a 9-V bias. At room temperature, the exciton resonance is broadened to 5.3 meV by phonon scattering and the maximum modulation ratio is 4.93 at 12 V. The measured temperature and voltage dependence of the exciton absorption energies, linewidths, and intensities have been used with a simple model for the modulator's optical transmission to calculate the operating characteristics as a function of material quality. The upper limit on the room-temperature transmission modulation ratio is estimated to be 5.4 for a device fabricated from 100 quantum wells of width 100 A(ring).
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    Journal of Applied Physics 66 (1989), S. 3574-3578 
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    Topics: Physics
    Notes: Adhesion-induced deformations of a polyurethane substrate in contact with cross-linked polystyrene spheres, having diameters ranging from less than 2 μm to approximately 12.5 μm were observed using scanning electron microscopy. The diameters of the contact areas were measured from the micrographs. It was found that the contact radius varied as the particle radius raised to the 0.75±0.05 power. Experimental results are compared to the predictions of various adhesion models. The results are also discussed in terms of the Dupré work of adhesion.
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    Journal of Applied Physics 66 (1989), S. 3579-3584 
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    Topics: Physics
    Notes: We have observed very rapid migration of silicon atoms along the grain boundaries of electron-beam-annealed polycrystalline silicon film in a silicon-on-insulator (SOI) island structure with a capped layer consisting of Si3N4 and SiO2 films. A considerable amount of mass transport was observed in the SOI structure at a temperature high enough to melt grain boundaries but not high enough to melt the entire polycrystalline silicon film. Our results support the notion that electromigration of Si+4 ions in molten silicon at the grain boundaries is responsible for the rapid migration of silicon atoms.
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    Journal of Applied Physics 66 (1989), S. 3542-3547 
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    Topics: Physics
    Notes: Traditionally, the chemical composition of surfaces prepared by various chemical, thermal, and plasma oxidation are analyzed by x-ray photoelectron spectroscopy. In this work, both x-ray wide-angle and glancing angle diffraction techniques were used, not only to investigate chemical composition, but also to characterize the structural features of the chemical oxide grown on an InP (100) surface in both HCl and HNO3 etches. These oxides all showed different degrees of preferred orientation with respect to the substrate. In 1M–8M HCl etches, the gradient composition, identified as crystalline hydrous InPO4, was the predominant phase and the rest was mainly composed of hydrous InPO4-based oxides. Coherent hydrated layers, also identified as hydrous InPO4, were obtained in HNO3 etches. In addition, the observation that InI -InIII mixed valence and InI chloro compounds are produced helped clarify the understanding of the dissolution mechanism of InP.
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    Journal of Applied Physics 66 (1989), S. 3698-3702 
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    Topics: Physics
    Notes: To understand the behavior of a YBa2Cu3O7−x weak link (constriction), a simple model of two Josephson junctions in series with each other is proposed. Electronic simulation of this two-junction array under various conditions generates dc and ac IV curves. Some of these curves duplicate very well what has been observed on a real YBa2Cu3O7−x weak link, while others predict phenomena that have not yet been observed. These results suggest the possible applicability of this model to explain the complicated experimental features of a YBa2Cu3O7−x weak link.
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3717-3722 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The superconductive properties in the Bi(Pb)-Sr-Ca-Cu-O system with nominal composition of Bi2−x Pbx Sr2 Ca2 Cu3 Oy (x=0, 0.2, 0.4, and 0.6) and annealed at 860 °C for 240 h were studied using dc resistivity and ac susceptibility measurements. For x=0.2 and 0.4, the bulk zero resistivity temperatures were found to be ∼103 K. For x=0 and 0.6, these temperatures were found to be ∼73–75 K. The ac susceptibility data show enrichment of the volume fraction of the high-Tc phase in compositions with x=0.2 and 0.4. Tc of this phase is constant at 107 K for all values of x. The enhancement of the bulk zero resistivity temperature for x=0.2 and 0.4 is due to the improved intergranular coupling of the high-Tc phase, although the resulting weak-link behavior reflects a low current carrying capacity in these materials. The presence of the low-Tc phase (∼65 K) is still visible in the susceptibility data. For x=0.6, the intergranular coupling of the high-Tc phase is almost destroyed; however, the coupling of the low-Tc phase is better than when x=0. Powder x-ray diffraction and scanning electron microscopy data show the formation of large grains of the calcium plumbate, Ca2PbO4 phase with increasing Pb up to x=0.6. The large grains of the Ca2 PbO4 phase may incorporate other impurity phases within it when x=0.6, cleaning up the remaining grain boundaries, thereby improving the intergranular coupling within this material. Energy dispersive x-ray analysis indicates that some Pb is incorporated into the structure of both superconducting phases.
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  • 89
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3723-3726 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A possible pairing mechanism involving the collective oscillations ("dipolons'') of the crystal-field-generated dipoles of the oxygen ions in the CuO2 planes in the superconductor YBa2Cu3O7−δ has been used to estimate, in the framework of the BCS theory, the variation of Tc as a function of δ, which compares very well with the experimental observations.
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  • 90
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3727-3730 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The demagnetizing energy of thin magnetic films can be written in terms of the Fourier components of the magnetization distribution. This formalism is used to investigate the structure of jagged domain walls in both perpendicular and in-plane media. Also introduced is a set of correlation functions and their relationship to demagnetizing energy density in media with random magnetization distribution.
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  • 91
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 2828-2832 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The resonance spectrum of composite plates made of alternating piezoelectric ceramic and epoxy elements is studied both theoretically and experimentally in the frequency range below the thickness resonance. The transmissivity of the finite structure to plate modes is calculated, taking into account the effective plate velocities of the two constituent materials and the finite number of elements in the structure. The results are in excellent agreement with the electrically excited acoustical resonances of samples with different geometry and number of elements. In particular, the effects of the finite size on the number and frequency of modes, as well as their selection rules in the given experimental setup, are successfully interpreted. New "surface'' resonances, attributed to the end elements, are observed in the stopbands when the surface elements have lower impedance.
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  • 92
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 2819-2827 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Thirty-seven of 97 AlxGa1−xAs laser diodes from three tests conducted in vacuum (10−6 Torr) at a −20 °C heat sink temperature (Tj∼0 °C) failed catastrophically. Causes of failure varied from testing error to defects in the metallization. In all cases, p-side anomalies allowed indium solder (and probably gold in addition to indium in one case) to migrate into the GaAs bulk, causing the observed failures. The results of this research show that the integrity of the p-side metallization is crucial for reliable operation. Stringent controls have been implemented in the design and processing of the p-side metallization and catastrophic failures due to p-side anomalies have not been observed in subsequent life tests. A correlation was made between shifts in the forward voltage at 1 mA (Vf at 1 mA) and the specific failure mechanisms found in this research. In all cases Vf at 1 mA was found to decrease. The amount of decrease depended on the failure mechanism. A quantitative model is presented that explains the shift in Vf as a function of the type of defect in the active region.
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  • 93
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 2833-2837 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: To accurately evaluate the integrity of the interfaces of a multilayered structure using ultrasonic pulse echo methods, we must understand the wave propagation in the structure and identify the appropriate interface signal. However, the signal is often complicated by the material and defect characteristics of the preceding interfaces. We have derived generalized mathematical formulas for the reflected mode time and the pulse amplitude response of an arbitrary n-layered structure for use in modeling the wave propagations in multilayered structures and identifying the critical structural interfaces. The time and echographic amplitude responses are calculated by computer using routines programmed for a given specimen. A comparison of the results of laboratory measurements of various glass and aluminum specimens with the results from computer-simulated experiments have verified the validity of the formulas.
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  • 94
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 2838-2858 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Acceleration instability occurs when a body is accelerated by surface tractions. This situation resembles classic Rayleigh–Taylor instability, but differs due to the temporal and spatial variation of the stress field in the accelerated body caused by wave propagation and the time dependence of the accelerating forces. These factors produce phenomena in acceleration instability which are without precedent in classical Rayleigh–Taylor analyses. An extensive numerical study of acceleration instability using a Lagrangian finite-difference wavecode has determined the influence of various parameters including amplitude and wavelength of initial surface perturbations, material yield strength, and time dependence of the driving force. The nature of the criteria determining stability or instability is established, and the fundamental physical quantity controlling perturbation growth at an interface is shown to be the local stress gradient.
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  • 95
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3798-3813 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We present a new model (including both temperature and electron-hole effects) of two-beam coupling in photorefractive semiconductors under an external dc field E0. This model predicts that the exponential gain Γ can exhibit an intensity-dependent resonant behavior, yielding a π/2 phase shift of the space-charge field with respect to the incident fringe pattern. This optimum intensity strongly depends on crystal temperature but it is practically independent of the grating period. As an illustration this model is applied to InP:Fe. In this case the resonance occurs when the hole photoionization rate and the electron thermal emission rate are equal. Values of Γ as high as 20 cm−1 at 1.06 μm, for a fringe spacing of 15 μm and E0 =10 kV/cm, are predicted. The comparison between theory and experimental data requires taking into account the variation of the pump intensity throughout the sample (due to optical absorption), which reduces the volume where the resonance condition is fulfilled; in this way a satisfactory fit of the experimental gain versus intensity curve has been obtained. The characteristics of this new resonance mechanism suggest several gain enhancement techniques which are briefly discussed. In particular, an increase of Γ by using an additional incoherent backward propagating beam is predicted and experimentally demonstrated.
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  • 96
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3820-3823 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Despite their increased safety, alkylarsine compounds have not generally replaced arsine (AsH3) in the metalorganic vapor phase epitaxy (MOVPE) of GaAs because of carbon incorporation and high background doping levels. We have studied the thermal decomposition of AsH3 and its alkyl derivatives (methyl, ethyl, and butyl compounds) to determine the impact of the thermochemistry on growth processes. The thermal stability of the As-precursor compounds was found to decrease in the order AsH3〉MenAsH3−n 〉Et3As〉t-BuAsH2. We report the first evidence for production of diarsine (As2H4) from t-BuAsH2 and for formation of lower substituted methylarsine homologs from Me3As and Me2AsH. The presence of these species is strong evidence that decomposition of the alkylarsines occurs via a free-radical mechanism. Formation of carbon-free arsenic products appears to be the key difference between t-BuAsH2 and the more highly substituted alkylarsines in attaining high quality films by MOVPE.
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  • 97
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3814-3819 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A new type of application of porous silicon formation is proposed, which does not deal with the material properties, but with the characteristics of the involved electrochemical silicon dissolution reaction. The anodization potential of p-type silicon in concentrated hydrofluoric acid under galvanostatic conditions has been shown to be characteristic of the silicon doping concentration at the interface and independent of the porous silicon-layer thickness. This close correlation between potential and doping level is used to determine concentration profiles of p-type implanted dopants. During anodization of silicon presenting dopant concentration variations, the anodization potential varies according to silicon doping concentration. The potential values can be converted to dopant concentration, and the electrolysis time scale to a depth scale, leading then to the doping impurity profile. This method, which is used as well for deep and shallow diffused impurities, exhibits a very good agreement with spreading resistance measurement and secondary-ion mass spectrometry analysis. Simultaneous anodization of regions of different doping concentration has also been investigated. It allows the characterization of the porous silicon formation selectivity by a selectivity coefficient, which is measured on a large range of silicon doping concentration. The selectivity is found to be strongly dependent on the doping level: it is nearly infinite for samples presenting highly doped regions (greater than 3×1018 cm−3), but decreases sharply when the doping concentration is below 1018 cm−3.
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  • 98
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3824-3830 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The complete reduction of oxides on the chemically polished surface of (100)InP has been obtained by exposure at 300 °C to low-pressure ammonia. The whole process was monitored by various surface techniques. In a first step, exposure to ammonia removes the weakly bonded oxygen atoms and stabilizes the one-monolayer oxide, i.e., turns the initial wet oxide to a thinner, well-defined, and more stable oxide, which should prove to be a better base for further processing. Excitation of the ammonia gas by an ion gauge, i.e., use of highly active radicals, is necessary for the second step, where the oxygen atoms strongly bonded to InP are finally completely removed. The final surface is free of all contaminants and of nitrogen, its crystal structure displays a 4×1 reconstruction, and its Fermi level is pinned at 0.8 eV above the top of the valence band, i.e., 0.2 eV lower than on the clean InP surface. It is mostly InP covered by adsorbed hydrogen, with a small coverage of indium atoms liberated by the reduction of the native oxides and grouped as metallic clusters.
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  • 99
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: GaAs layers grown by organometallic chemical vapor deposition (OMCVD) on Si substrates oriented 2° off (100) toward [011] have been studied by 10-K filtered cathodoluminescence, deep-level transient spectroscopy (DLTS), electron-beam-induced current (EBIC), and secondary ion mass spectrometry (SIMS) measurements. The mapping of the near-band-edge emission intensity shows the existence of zones of lower defect density, whose relative volume increases with the layer thickness. Four deep-level energy peaks have been characterized at 1.33, 1.20, 1.15, and 1.02 eV. The 1.33 and 1.20 eV energy peaks are attributed to Si in GaAs. Strong inhomogeneities in the intensity of these two emissions have been observed with depth of the layers, and this behavior has been related to the silicon distribution. From measurements on structures grown with different buffer layers, we show that a GaAs/AlAs supperlattice located at 1 μm from the Si substrate is efficient in decreasing the width of a highly Si-doped interface region. DLTS measurements confirm the decrease in the deep-level concentration with increasing thickness. Furthermore, by EBIC characterization, we measure a minority-carrier diffusion length of 2.7–3 μm on a 5-μm-thick layer. This corresponds to a dislocation density of 8×106 cm−2.
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  • 100
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    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 66 (1989), S. 3850-3856 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Polycrystalline barium titanate that has been doped to give a positive temperature coefficient of resistance (PTCR) effect is an inhomogeneous material electrically. Analysis of ac impedance data using the complex impedance plane representation gives the dc resistance of PTCR ceramics. By additional use of the complex electric modulus formalism to analyze the same data, the inhomogeneous nature of the ceramics may be probed. This reveals the presence of two, sometimes three elements in the equivalent circuit. Grain-boundary and bulk effects may be distinguished from capacitance data: grain-boundary effects have temperature-independent capacitances, whereas bulk effects show a capacitance maximum at the Curie point and Curie–Weiss behavior above the Curie point. Both grain-boundary and bulk effects appear to contribute to the PTCR effect. These results reveal limitations in current theories of the PTCR effect.
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